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  • Top All36 Cgenff

    Hochgeladen von

    Gonzalo Muñoz Rojas
    700 Ansichten430 Seiten
    This document provides information about atom types and parameters for the CHARMM General Force Field (CGenFF) version 2a5. It includes mass values and descriptions for atom types covering hydrogens, carbons, nitrogens, oxygens, sulphurs, and halogens. Comments indicate that small changes to existing parameters or charges may occur as more functional groups are introduced. All comments and questions about the parameter set should be directed to the maintainer via the CHARMM website.

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    This document provides information about atom types and parameters for the CHARMM General Force Field (CGenFF) version 2a5. It includes mass values and descriptions for atom types covering hydrogens, carbons, nitrogens, oxygens, sulphurs, and halogens. Comments indicate that small changes to existing parameters or charges may occur as more functional groups are introduced. All comments and questions about the parameter set should be directed to the maintainer via the CHARMM website.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Als TXT, PDF, TXT herunterladen oder online auf Scribd lesen
    Markieren Sie unangemessene Inhalte
    700 Ansichten430 Seiten

    Top All36 Cgenff

    Hochgeladen von

    Gonzalo Muñoz Rojas
    This document provides information about atom types and parameters for the CHARMM General Force Field (CGenFF) version 2a5. It includes mass values and descriptions for atom types covering hydrogens, carbons, nitrogens, oxygens, sulphurs, and halogens. Comments indicate that small changes to existing parameters or charges may occur as more functional groups are introduced. All comments and questions about the parameter set should be directed to the maintainer via the CHARMM website.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Als TXT, PDF, TXT herunterladen oder online auf Scribd lesen
    Markieren Sie unangemessene Inhalte
    von 430

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    36

    -------------------------------------------------------------------------- *
    CGenFF: Topology for the Charmm General Force Field v. 2a5
    for Small Molecule Drug Design
    -------------------------------------------------------------------------- As more functional groups will be introduced, small changes in
    existing parameters and/or charges may occur.
    - Comments in this file may be misleading.
    -------------------------------------------------------------------------All comments to ADM jr. via the CHARMM web site: www.charmm.org
    parameter set discussion forum
    --------------------------------------------------------------------------

    *
    *
    *
    *
    *
    *
    *
    *
    *

    ! -------------------------------------------------------------------------- !
    !
    ATOM NAME
    SERIAL NO. SLOTS
    !
    !
    RESERVED FOR THE ATOMS
    !
    !
    Hydrogens
    1 -- 39
    !
    !
    Carbons
    40 -- 99
    !
    !
    Nitrogens
    100 -- 149
    !
    !
    Oxygens
    150 -- 189
    !
    !
    Sulphurs
    190 -- 209
    !
    !
    Halogens
    210 -- 249
    !
    !
    Miscellaneous 250 -- --!
    ! -------------------------------------------------------------------------- !
    !hydrogens
    MASS
    1 HGA1
    1.00800 ! alphatic proton, CH
    MASS
    2 HGA2
    1.00800 ! alphatic proton, CH2
    MASS
    3 HGA3
    1.00800 ! alphatic proton, CH3
    MASS
    4 HGA4
    1.00800 ! alkene proton; RHC=
    MASS
    5 HGA5
    1.00800 ! alkene proton; H2C=CR
    MASS
    6 HGA6
    1.00800 ! aliphatic H on fluorinated C, monofluoro
    MASS
    7 HGA7
    1.00800 ! aliphatic H on fluorinated C, difluoro
    MASS
    8 HGAAM0 1.00800 ! aliphatic H, NEUTRAL trimethylamine (#)
    MASS
    9 HGAAM1 1.00800 ! aliphatic H, NEUTRAL dimethylamine (#)
    MASS
    10 HGAAM2 1.00800 ! aliphatic H, NEUTRAL methylamine (#)
    !(#) EXTREME care is required when doing atom typing on compounds that look like
    this. Use ONLY
    !on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guani
    dine nitrogens
    MASS
    11 HGP1
    1.00800 ! polar H
    MASS
    12 HGP2
    1.00800 ! polar H, +ve charge
    MASS
    13 HGP3
    1.00800 ! polar H, thiol
    MASS
    14 HGP4
    1.00800 ! polar H, neutral conjugated -NH2 group (NA bases)
    MASS
    15 HGP5
    1.00800 ! polar H on quarternary ammonium salt (choline)
    MASS
    16 HGPAM1 1.00800 ! polar H, NEUTRAL dimethylamine (#)
    MASS
    17 HGPAM2 1.00800 ! polar H, NEUTRAL methylamine (#)
    MASS
    18 HGPAM3 1.00800 ! polar H, NEUTRAL ammonia (#)
    !(#) EXTREME care is required when doing atom typing on compounds that look like
    this. Use ONLY
    !on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guani
    dine nitrogens
    MASS
    19 HGR51
    1.00800 ! nonpolar H, neutral 5-mem planar ring C, LJ based
    on benzene
    MASS
    20 HGR52
    1.00800 ! Aldehyde H, formamide H (RCOH); nonpolar H, neutr
    al 5-mem planar ring C adjacent to heteroatom or + charge
    MASS
    21 HGR53
    1.00800 ! nonpolar H, +ve charge HIS he1(+1)
    MASS
    23 HGR61
    1.00800 ! aromatic H

    MASS
    24 HGR62
    1.00800 ! nonpolar H, neutral 6-mem planar ring C adjacent
    to heteroatom
    MASS
    25 HGR63
    1.00800 ! nonpolar H, NAD+ nicotineamide all ring CH hydrog
    ens
    MASS
    26 HGR71
    1.00800 ! nonpolar H, neutral 7-mem arom ring, AZUL, azulen
    e
    !MASS
    27 HGTIP3 1.00800 ! polar H, TIPS3P WATER HYDROGEN
    !carbons
    MASS
    40 CG1T1 12.01100 ! alkyn C
    MASS
    41 CG1N1 12.01100 ! C for cyano group
    MASS
    42 CG2D1 12.01100 ! alkene; RHC= ; imine C
    MASS
    43 CG2D2 12.01100 ! alkene; H2C=
    MASS
    44 CG2D1O 12.01100 ! double bond carbon adjacent to heteroatom. In con
    jugated systems, the atom to which it is double bonded must be CG2DC1.
    MASS
    45 CG2D2O 12.01100 ! double bond carbon adjacent to heteroatom. In con
    jugated systems, the atom to which it is double bonded must be CG2DC2.
    MASS
    46 CG2DC1 12.01100 ! conjugated alkenes, R2C=CR2
    MASS
    47 CG2DC2 12.01100 ! conjugated alkenes, R2C=CR2
    MASS
    48 CG2DC3 12.01100 ! conjugated alkenes, H2C=
    MASS
    49 CG2N1 12.01100 ! conjugated C in guanidine/guanidinium
    MASS
    50 CG2N2 12.01100 ! conjugated C in amidinium cation
    MASS
    51 CG2O1 12.01100 ! carbonyl C: amides
    MASS
    52 CG2O2 12.01100 ! carbonyl C: esters, [neutral] carboxylic acids
    MASS
    53 CG2O3 12.01100 ! carbonyl C: [negative] carboxylates
    MASS
    54 CG2O4 12.01100 ! carbonyl C: aldehydes
    MASS
    55 CG2O5 12.01100 ! carbonyl C: ketones
    MASS
    56 CG2O6 12.01100 ! carbonyl C: urea, carbonate
    MASS
    57 CG2O7 12.01100 ! CO2 carbon
    MASS
    58 CG2R51 12.01100 ! 5-mem ring, his CG, CD2(0), trp
    MASS
    59 CG2R52 12.01100 ! 5-mem ring, double bound to N, PYRZ, pyrazole
    MASS
    60 CG2R53 12.01100 ! 5-mem ring, double bound to N and adjacent to ano
    ther heteroatom, purine C8, his CE1 (0,+1), 2PDO
    MASS
    61 CG2R61 12.01100 ! 6-mem aromatic C
    MASS
    62 CG2R62 12.01100 ! 6-mem aromatic C for protonated pyridine (NIC) an
    d rings containing carbonyls (see CG2R63) (NA)
    MASS
    63 CG2R63 12.01100 ! 6-mem aromatic amide carbon (NA) (and other 6-mem
    aromatic carbonyls?)
    MASS
    64 CG2R64 12.01100 ! 6-mem aromatic amidine and guanidine carbon (betw
    een 2 or 3 Ns and double-bound to one of them), NA, PYRM
    MASS
    65 CG2R66 12.01100 ! 6-mem aromatic carbon bound to F
    MASS
    66 CG2R67 12.01100 ! 6-mem aromatic carbon of biphenyl
    MASS
    67 CG2RC0 12.01100 ! 6/5-mem ring bridging C, guanine C4,C5, trp
    MASS
    68 CG2R71 12.01100 ! 7-mem ring arom C, AZUL, azulene
    MASS
    69 CG2RC7 12.01100 ! sp2 ring connection with single bond(!), AZUL, az
    ulene
    MASS
    70 CG301 12.01100 ! aliphatic C, no hydrogens, neopentane
    MASS
    71 CG302 12.01100 ! aliphatic C, no hydrogens, trifluoromethyl
    MASS
    72 CG311 12.01100 ! aliphatic C with 1 H, CH
    MASS
    73 CG312 12.01100 ! aliphatic C with 1 H, difluoromethyl
    MASS
    74 CG314 12.01100 ! aliphatic C with 1 H, adjacent to positive N (PRO
    T NTER) (+)
    MASS
    75 CG321 12.01100 ! aliphatic C for CH2
    MASS
    76 CG322 12.01100 ! aliphatic C for CH2, monofluoromethyl
    MASS
    77 CG323 12.01100 ! aliphatic C for CH2, thiolate carbon
    MASS
    78 CG324 12.01100 ! aliphatic C for CH2, adjacent to positive N (pipe
    ridine) (+)
    MASS
    79 CG331 12.01100 ! aliphatic C for methyl group (-CH3)
    MASS
    80 CG334 12.01100 ! aliphatic C for methyl group (-CH3), adjacent to
    positive N (PROT NTER) (+)
    MASS
    81 CG3AM0 12.01100 ! aliphatic C for CH3, NEUTRAL trimethylamine methy

    l carbon (#)
    MASS
    82 CG3AM1 12.01100 ! aliphatic C for CH3, NEUTRAL dimethylamine methyl
    carbon (#)
    MASS
    83 CG3AM2 12.01100 ! aliphatic C for CH3, NEUTRAL methylamine methyl c
    arbon (#)
    !(#) EXTREME care is required when doing atom typing on compounds that look like
    this. Use ONLY
    !on NEUTRAL METHYLAMINE groups, NOT ETHYL, NOT Schiff Bases, but DO use on 2 out
    of 3 guanidine nitrogens
    MASS
    84 CG3C31 12.01100 ! cyclopropyl carbon
    !MASS
    85 CG3C41 12.01100 ! cyclobutyl carbon RESERVED!
    MASS
    86 CG3C50 12.01100 ! 5-mem ring aliphatic quaternary C (cholesterol, b
    ile acids)
    MASS
    87 CG3C51 12.01100 ! 5-mem ring aliphatic CH (proline CA, furanoses)
    MASS
    88 CG3C52 12.01100 ! 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF,
    deoxyribose)
    MASS
    89 CG3C53 12.01100 ! 5-mem ring aliphatic CH adjacent to positive N (
    proline.H+ CA) (+)
    MASS
    90 CG3C54 12.01100 ! 5-mem ring aliphatic CH2 adjacent to positive N (
    proline.H+ CD) (+)
    MASS
    91 CG3RC1 12.01100 ! bridgehead in bicyclic systems containing at leas
    t one 5-membered or smaller ring
    !(+) Includes protonated Shiff base (NG3D5, NG2R52 in 2HPP) but NOT amidinium (N
    G2R52 in IMIM), guanidinium
    !nitrogens
    MASS 100 NG1T1 14.00700 ! N for cyano group
    MASS 101 NG2D1 14.00700 ! N for neutral imine/Schiff's base (C=N-R, acyclic
    amidine, gunaidine)
    MASS 102 NG2S0 14.00700 ! N,N-disubstituted amide, proline N (CO=NRR')
    MASS 103 NG2S1 14.00700 ! peptide nitrogen (CO=NHR)
    MASS 104 NG2S2 14.00700 ! terminal amide nitrogen (CO=NH2)
    MASS 105 NG2S3 14.00700 ! external amine ring nitrogen (planar/aniline), ph
    osphoramidate
    MASS 106 NG2O1 14.00700 ! NITB, nitrobenzene
    MASS 107 NG2P1 14.00700 ! N for protonated imine/Schiff's base (C=N(+)H-R,
    acyclic amidinium, guanidinium)
    MASS 108 NG2R50 14.00700 ! unprotonated neutral 5-mem planar ring, purine N7
    MASS 109 NG2R51 14.00700 ! protonated neutral 5-mem planar (all atom types s
    p2) ring, his, trp pyrrole (fused)
    MASS 110 NG2R52 14.00700 ! protonated schiff base, amidinium, guanidinium in
    5-membered ring, HIS, 2HPP
    MASS 111 NG2R53 14.00700 ! amide in 5-memebered ring (slightly pyramidized),
    2PDO
    MASS 112 NG2R60 14.00700 ! unprotonated neutral 6-mem planar ring, pyr1, pyz
    n
    MASS 113 NG2R61 14.00700 ! protonated neutral 6-mem planar ring imino nitrog
    en; glycosyl linkage
    MASS 114 NG2R62 14.00700 ! unprotonated 6-mem planar ring with heteroatoms i
    n o or m, pyrd, pyrm
    MASS 115 NG2RC0 14.00700 ! 6/5-mem ring bridging N, indolizine, INDZ
    MASS 116 NG301 14.00700 ! neutral trimethylamine nitrogen
    MASS 117 NG311 14.00700 ! neutral dimethylamine nitrogen
    MASS 118 NG321 14.00700 ! neutral methylamine nitrogen
    MASS 119 NG331 14.00700 ! neutral ammonia nitrogen
    MASS 120 NG3C51 14.00700 ! secondary sp3 amine in 5-membered ring
    MASS 121 NG3N1 14.00700 ! N in hydrazine, HDZN
    MASS 122 NG3P0 14.00700 ! quarternary N+, choline
    MASS 123 NG3P1 14.00700 ! tertiary NH+ (PIP)
    MASS 124 NG3P2 14.00700 ! secondary NH2+ (proline)
    MASS 125 NG3P3 14.00700 ! primary NH3+, phosphatidylethanolamine

    !oxygens
    MASS 150 OG2D1 15.99940
    acids, aldehydes, uera
    MASS 151 OG2D2 15.99940
    ate
    MASS 152 OG2D3 15.99940
    MASS 153 OG2D4 15.99940
    MASS 154 OG2D5 15.99940
    MASS 155 OG2N1 15.99940
    MASS 156 OG2P1 15.99940
    MASS 157 OG2R50 15.99940
    MASS 158 OG3R60 15.99940
    r
    MASS 159 OG301 15.99940
    ? IF YES, SHOULD WE MERGE IT
    MASS 160 OG302 15.99940
    MASS 161 OG303 15.99940
    MASS 163 OG311 15.99940
    MASS 164 OG312 15.99940
    MASS 165 OG3C51 15.99940
    MASS 166 OG3C61 15.99940
    !MASS 167 OGTIP3 15.99940
    !sulphurs
    MASS 190 SG2R50 32.06000
    MASS 191 SG3O1 32.06000
    MASS 192 SG301 32.06000
    MASS 193 SG302 32.06000
    MASS 194 SG311 32.06000
    !halogens
    MASS 210 CLGA1 35.45300
    MASS 211 CLGA3 35.45300
    MASS 212 CLGR1 35.45300
    MASS 213 BRGA1 79.90400
    MASS 214 BRGA2 79.90400
    MASS 215 BRGA3 79.90400
    MASS 216 BRGR1 79.90400
    MASS 217 IGR1 126.90447
    MASS 218 FGA1
    18.99800
    MASS 219 FGA2
    18.99800
    MASS 220 FGA3
    18.99800
    MASS 221 FGP1
    18.99800
    MASS 222 FGR1
    18.99800
    !miscellaneous
    !MASS 250 DUM
    0.00000
    !MASS 251 HE
    4.00260
    !MASS 252 NE
    20.17970
    MASS 253 PG1
    30.97400
    MASS 254 PG2
    30.97400
    MASS 255 PG3
    30.97400
    MASS 256 ALG1
    26.98154

    ! carbonyl O: amides, esters, [neutral] carboxylic


    ! carbonyl O: negative groups: carboxylates, carbon
    !
    !
    !
    !
    !
    !
    !

    carbonyl O: ketones
    6-mem aromatic carbonyl oxygen (nucleic bases)
    CO2 oxygen
    NITB, nitrobenzene
    =O in phosphate or sulfate
    FURA, furan
    O in 6-mem cyclic enol ether (PY01, PY02) or este

    ! ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??


    WITH OG3R60???
    ! ester -O! phosphate/sulfate ester oxygen
    ! hydroxyl oxygen
    ! ionized alcohol oxygen
    ! 5-mem furanose ring oxygen (ether)
    ! DIOX, dioxane, ether in 6-membered ring
    ! TIPS3P WATER OXYGEN
    !
    !
    !
    !
    !

    THIP, thiophene
    sulfate sulfur
    sulfur C-S-S-C type
    thiolate sulfur (-1)
    sulphur, SH, -S-

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CLET, DCLE, chloroethane, 1,1-dichloroethane


    TCLE, 1,1,1-trichloroethane
    CHLB, chlorobenzene
    BRET, bromoethane
    DBRE, 1,1-dibromoethane
    TBRE, 1,1,1-dibromoethane
    BROB, bromobenzene
    IODB, iodobenzene
    aliphatic fluorine, monofluoro
    aliphatic fluorine, difluoro
    aliphatic fluorine, trifluoro
    anionic F, for ALF4 AlF4aromatic flourine

    ! dummy atom
    ! helium
    ! neon
    ! phosphorus
    ! pyrophosphate
    ! protonated pyrophosphate
    ! Aluminum, for ALF4, AlF4-

    DEFA FIRS NONE LAST NONE


    AUTO ANGLES DIHE
    !RESI TIP3
    0.00 ! tip3p water model, generate using noangle nodihedral
    !GROUP
    !ATOM OH2 OGTIP3 -0.834
    !ATOM H1 HGTIP3 0.417
    !ATOM H2 HGTIP3 0.417
    !BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake

    !ANGLE H1 OH2 H2
    ! required
    !ACCEPTOR OH2
    !PATCHING FIRS NONE LAST NONE
    !protein model compounds
    !toppar_all22_model_aliphatic.str
    RESI ACET
    -1.00 ! C2H3O2 acetate, K. Kuczera
    GROUP
    ATOM C1 CG331 -0.37 !
    ATOM C2 CG2O3
    0.62 !
    H1
    O1 (-)
    ATOM H1 HGA3
    0.09 !
    |
    /
    ATOM H2 HGA3
    0.09 ! H2--C1--C2
    ATOM H3 HGA3
    0.09 !
    |
    \\
    ATOM O1 OG2D2 -0.76 !
    H3
    O2
    ATOM O2 OG2D2 -0.76 !
    BOND C1 H1 C1 H2 C1 H3
    BOND C1 C2 C2 O1
    DOUBLE C2 O2
    IMPR C2 C1 O2 O1
    IC O1 C2 C1 H1 0.00 0.00
    0.0 0.00 0.00
    IC C2 H1 *C1 H2 0.00 0.00 120.0 0.00 0.00
    IC C2 H1 *C1 H3 0.00 0.00 -120.0 0.00 0.00
    IC C1 O1 *C2 O2 0.00 0.00 180.0 0.00 0.00
    PATC FIRS NONE LAST NONE
    RESI PROA
    GROUP
    ATOM C2
    ATOM C1
    ATOM H21
    ATOM H22

    -1.00 ! C3H5O2 propionic acid


    CG321
    CG2O3
    HGA2
    HGA2

    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM

    CG331
    HGA3
    HGA3
    HGA3

    !
    !
    H21 O1 (-)
    !
    |
    /
    ! H22-C2--C1
    !
    |
    \\
    -0.76 !
    |
    O2
    -0.76 !H31--C3
    !
    | \
    -0.27 ! H32 H33
    0.09
    0.09
    0.09

    O1 OG2D2
    O2 OG2D2

    -0.28
    0.62
    0.09
    0.09

    C3
    H31
    H32
    H33

    BOND C1
    BOND C2
    BOND C3
    DOUBLE
    IMPR C1

    C2 C2 C3 C1 O1
    H21 C2 H22
    H31 C3 H32 C3 H33
    C1 O2
    C2 O2 O1

    IC O1
    C1
    IC C3
    C2
    IC C3
    C1
    IC C3
    C1
    IC C3
    C2
    IC O1
    C2
    IC C1
    C2
    IC H31 C2
    IC H31 C2
    PATC FIRS NONE
    RESI GUAN
    GROUP
    ATOM C CG2N1

    C2
    C1
    *C2
    *C2
    C1
    *C1
    C3
    *C3
    *C3
    LAST

    C3
    O2
    H21
    H22
    O1
    O2
    H31
    H32
    H33
    NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    0.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    120.00
    -120.00

    1.00 ! CH6N3 guandinium, K. Kuczera


    0.64 !

    H11 H12

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM N1 NG2P1 -0.80 !


    ATOM H11 HGP2
    0.46 !
    ATOM H12 HGP2
    0.46 !
    ATOM N2 NG2P1 -0.80 !
    ATOM H21 HGP2
    0.46 !
    ATOM H22 HGP2
    0.46 !
    ATOM N3 NG2P1 -0.80 !
    ATOM H31 HGP2
    0.46 !
    ATOM H32 HGP2
    0.46 !
    BOND
    C N2 C N3
    DOUBLE C N1
    BOND N1 H11 N1 H12 N2
    IMPR C N2 N1 N3
    IC H11 N1 C N2
    0.00
    IC H11 N1 C N3
    0.00
    IC H12 N1 C N3
    0.00
    IC H21 N2 C N1
    0.00
    IC H22 N2 C N3
    0.00
    IC H31 N3 C N1
    0.00
    IC H32 N3 C N2
    0.00
    PATC FIRS NONE LAST NONE

    \ /
    N1 (+)
    ||
    C
    / \
    H21-N2 N3-H31
    | |
    H22 H32

    H21

    N2 H22 N3 H31 N3 H32

    0.00 0.0
    0.00 180.0
    0.00 0.0
    0.00 0.0
    0.00 0.0
    0.00 0.0
    0.00 0.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI MGUA
    1.00 ! C2H8N3 methyl-guanidinium
    GROUP
    ATOM C CG2N1
    0.64 !
    H11 H12
    ATOM N1 NG2P1 -0.80 !
    \ /
    ATOM H11 HGP2
    0.46 !
    N1 (+)
    ATOM H12 HGP2
    0.46 !
    ||
    ATOM N2 NG2P1 -0.80 !
    C
    HC1
    ATOM H21 HGP2
    0.46 !
    / \
    /
    ATOM H22 HGP2
    0.46 ! H21-N2 N3--C2-HC2
    ATOM N3 NG2P1 -0.70 !
    | |
    \
    ATOM H31 HGP2
    0.44 !
    H22 H31 HC3
    ATOM C2 CG334
    0.11 !
    ATOM HC1 HGA3
    0.09
    ATOM HC2 HGA3
    0.09
    ATOM HC3 HGA3
    0.09
    BOND C N2 C N3
    DOUBLE C N1
    BOND N1 H11 N1 H12 N2 H21 N2 H22 N3 H31 N3 C2
    BOND C2 HC1 C2 HC2 C2 HC3
    IMPR C N2 N1 N3
    IC H11 N1 C N2
    0.00 0.00 0.0 0.00 0.00
    IC H11 N1 C N3
    0.00 0.00 180.0 0.00 0.00
    IC H12 N1 C N3
    0.00 0.00 0.0 0.00 0.00
    IC H21 N2 C N1
    0.00 0.00 0.0 0.00 0.00
    IC H22 N2 C N3
    0.00 0.00 0.0 0.00 0.00
    IC H31 N3 C N1
    0.00 0.00 0.0 0.00 0.00
    IC C2 N3 C N1
    0.00 0.00 180.0 0.00 0.00
    IC C N3 C2 HC1 0.00 0.00 0.0 0.00 0.00
    IC C N3 C2 HC2 0.00 0.00 120.0 0.00 0.00
    IC C N3 C2 HC3 0.00 0.00 240.0 0.00 0.00
    PATC FIRS NONE LAST NONE
    RESI GLYN
    GROUP
    ATOM N
    ATOM HT1
    ATOM HT2
    ATOM CA

    0.00 ! C2H5NO2 neutral glycine


    !
    NG321 -0.96 !
    HGPAM2 0.34 ! HT1 HT2
    HGPAM2 0.34 !
    \ /
    CG321
    0.18 !
    N

    ATOM HA1
    ATOM HA2
    GROUP
    ATOM C
    ATOM OT1
    ATOM OT2
    ATOM HO2

    HGA2
    HGA2

    0.05 !
    |
    0.05 ! HA1-CA-HA2
    !
    |
    CG2O2
    0.75 !
    C
    OG2D1 -0.55 ! // \
    OG311 -0.63 ! OT1 OT2
    HGP1
    0.43 !
    |
    !
    HO2
    !
    BOND N CA CA C C OT2 OT2 HO2
    BOND N HT1 N HT2 CA HA1 CA HA2
    DOUBLE OT1 C
    DONO HT1 N
    DONO HT2 N
    DONO HO2 OT2
    IC N
    CA C
    OT1 1.5010 119.00 88.76
    IC N
    CA C
    OT2 1.5010 119.00 -111.57
    IC OT1 OT2 *C CA
    1.2218 117.44 -161.57
    IC CA C
    OT2 HO2 1.5780 113.44 -168.97
    IC C
    CA N
    HT1 1.5780 119.00 164.86
    IC C
    CA N
    HT2 1.5780 119.00 -77.98
    IC N
    C
    *CA HA1 1.5010 119.00 120.0
    IC N
    C
    *CA HA2 1.5010 119.00 -120.0
    PATCHING FIRS NONE LAST NONE

    126.10
    113.44
    113.44
    107.16
    110.99
    111.22
    110.0
    110.0

    RESI MAMM
    1.00 ! CH6N methylammonium, K. Kuczera
    GROUP
    ATOM CE CG334
    0.16 !
    ATOM NZ NG3P3
    -0.30 ! HE1
    HZ1
    ATOM HE1 HGA3
    0.05 !
    \ (+) |
    ATOM HE2 HGA3
    0.05 !HE2-CE---NZ--HZ2
    ATOM HE3 HGA3
    0.05 !
    /
    |
    ATOM HZ1 HGP2
    0.33 ! HE3
    HZ3
    ATOM HZ2 HGP2
    0.33 !
    ATOM HZ3 HGP2
    0.33 !
    BOND CE HE1 CE HE2 CE HE3
    BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3
    IC HE1 CE NZ HZ1 0.00 0.00
    0.0 0.0 0.0
    IC HE1 CE NZ HZ2 0.00 0.00 120.0 0.0 0.0
    IC HE1 CE NZ HZ3 0.00 0.00 240.0 0.0 0.0
    IC HE2 CE NZ HZ1 0.00 0.00 120.0 0.0 0.0
    IC HE2 CE NZ HZ2 0.00 0.00
    0.0 0.0 0.0
    IC HE2 CE NZ HZ3 0.00 0.00 240.0 0.0 0.0
    IC HE3 CE NZ HZ1 0.00 0.00 240.0 0.0 0.0
    IC HE3 CE NZ HZ2 0.00 0.00 120.0 0.0 0.0
    IC HE3 CE NZ HZ3 0.00 0.00
    0.0 0.0 0.0
    IC CE NZ HZ1 HZ3 0.00 0.00
    0.0 0.0 0.0
    PATC FIRS NONE LAST NONE

    1.2218
    1.3958
    1.5780
    0.9565
    1.0023
    1.0030
    1.1
    1.1

    RESI EAMM
    GROUP
    ATOM CE CG324
    ATOM NZ NG3P3
    ATOM HE1 HGA2
    ATOM HE2 HGA2
    ATOM HZ1 HGP2
    ATOM HZ2 HGP2
    ATOM HZ3 HGP2
    GROUP

    1.00 ! C2H8N ethylammonium, adm jr.


    0.21
    -0.30
    0.05
    0.05

    !
    ! HE1
    HZ1
    !
    \ (+) |
    !HE2-CE---NZ--HZ2
    !
    /
    |
    0.33 ! /
    HZ3
    0.33 ! C1-H13
    0.33 ! / \
    !H11 H12

    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND

    C1 CG331
    -0.27 !
    H11 HGA3
    0.09 !
    H12 HGA3
    0.09 !
    H13 HGA3
    0.09 !
    CE HE1 CE HE2 CE C1
    CE NZ NZ HZ1 NZ HZ2 NZ HZ3
    C1 H11 C1 H12 C1 H13

    IC H11 C1
    CE
    IC C1 NZ
    *CE
    IC HE1 NZ
    *CE
    IC HE1 CE
    NZ
    IC HZ1 CE
    *NZ
    IC HZ1 CE
    *NZ
    IC HE1 CE
    C1
    IC H11 CE
    *C1
    IC H11 CE
    *C1
    PATC FIRS NONE LAST

    NZ
    HE1
    HE2
    HZ1
    HZ2
    HZ3
    H11
    H12
    H13
    NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI ACEH
    0.00 ! C2H4O2 acetic acid, ADM jr.
    GROUP
    ATOM C2 CG331 -0.30 !
    ATOM C1 CG2O2
    0.75 ! H21
    O2
    ATOM H21 HGA3
    0.09 !
    \
    //
    ATOM H22 HGA3
    0.09 ! H22-C2--C1
    ATOM H23 HGA3
    0.09 !
    /
    \
    ATOM O2 OG2D1 -0.55 ! H23
    O1-HO1
    ATOM O1 OG311 -0.60 !
    ATOM HO1 HGP1
    0.43 !
    BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23
    DOUBLE C1 O2
    IMPR C1 C2 O1 O2
    DONO BLNK HO1 ! O1
    ACCE O1
    ACCE O2
    IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000
    IC HO1 O1 C1 O2
    0.0000 0.0000 0.0000 0.0000
    IC HO1 O1 C1 C2
    0.0000 0.0000 180.0000 0.0000
    IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000
    IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000
    IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000
    RESI MEOH
    0.00
    GROUP
    ATOM CB CG331 -0.04
    ATOM OG OG311 -0.65
    ATOM HG1 HGP1
    0.42
    ATOM HB1 HGA3
    0.09
    ATOM HB2 HGA3
    0.09
    ATOM HB3 HGA3
    0.09
    BOND CB OG OG HG1
    BOND CB HB1 CB HB2 CB
    DONO HG1 OG
    ACCE OG
    ! only for analysis
    IC HG1 OG CB HB1
    IC OG HB1 *CB HB2
    IC OG HB1 *CB HB3
    RESI METO

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! CH4O methanol, adm jr.


    ! H11
    !
    \
    ! H12--C1--O1
    !
    /
    \
    ! H13
    HO1
    !
    HB3

    0.0000 0.0000 180.0000 0.0000 0.0000


    0.0000 0.0000 120.0000 0.0000 0.0000
    0.0000 0.0000 -120.0000 0.0000 0.0000

    -1.00 ! CH3O methoxide, adm jr.

    GROUP
    ! order of atoms to match that used in
    ATOM CB CG331 -0.41 ! HB1
    ATOM OG OG312 -0.92 !
    \
    ! HB2--CB--OG (-)
    ATOM HB1 HGA3
    0.11 !
    /
    ATOM HB2 HGA3
    0.11 ! HB3
    ATOM HB3 HGA3
    0.11 !
    BOND CB OG
    BOND CB HB1 CB HB2 CB HB3
    ACCE OG
    ! only for analysis
    IC HB2 OG CB HB1 0.0000 0.0000 180.0000
    IC OG HB2 *CB HB1 0.0000 0.0000 180.0000
    IC OG CB HB1 HB2 0.0000 0.0000 180.0000
    RESI ETOH
    GROUP
    ATOM C1 CG321
    ATOM O1 OG311
    ATOM HO1 HGP1
    ATOM H11 HGA2
    ATOM H12 HGA2
    GROUP
    ATOM C2 CG331
    ATOM H21 HGA3
    ATOM H22 HGA3
    ATOM H23 HGA3
    BOND C1 C2 C1
    BOND C2 H21 C2
    DONO HO1 O1
    ACCE O1
    ! for ic build
    IC O1 C1 C2
    IC C1 H21 *C2
    IC C1 H21 *C2
    IC O1 C2 *C1
    IC O1 C2 *C1
    IC C2 C1 O1
    RESI ETO
    GROUP
    ATOM OG OG312
    ATOM CB CG321
    ATOM CA CG331
    ATOM HB1 HGA2
    ATOM HB2 HGA2
    ATOM HA1 HGA3
    ATOM HA2 HGA3
    ATOM HA3 HGA3
    BOND CA CB CB
    BOND CA HA1 CA
    ACCE OG
    ! for ic build
    IC CB CA HA1
    IC CA OG CB
    IC CA OG CB
    IC CA OG CB
    IC OG CB CA
    IC OG CB CA
    IC OG CB CA

    ab initio

    0.0000 0.0000
    0.0000 0.0000
    0.0000 0.0000

    0.00 ! C2H6O Ethanol, adm jr.


    0.05
    -0.65
    0.42
    0.09
    0.09

    ! H21 H11 H12


    !
    \ \ /
    ! H22--C2--C1
    !
    /
    \
    ! H23
    O1--HO1

    -0.27
    0.09
    0.09
    0.09
    O1 C1 H11 C1 H12 O1 HO1
    H22 C2 H23

    H21
    H22
    H23
    H11
    H12
    HO1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    180.0000
    120.0000
    240.0000
    240.0000
    120.0000
    180.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -1.00 ! C2H5O Ethoxide, adm jr.


    -0.92 !
    -0.30 !
    -0.27 !
    0.11 !
    0.11 !
    0.09
    0.09
    0.09
    OG CB
    HA2 CA
    HA2
    HB1
    HB2
    HB3
    HA1
    HA2
    HA3

    HA1 HB1 HB2


    \ \ /
    HA2--CA--CB
    /
    \
    HA3
    OG (-)

    HB1 CB HB2
    HA3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    60.0000
    300.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC HA1 CA
    IC HA1 CA

    CB
    CB

    HB1
    HB2

    RESI PRO2
    GROUP
    ATOM C2 CG311
    ATOM O2 OG311
    ATOM HO2 HGP1
    ATOM H21 HGA1
    GROUP
    ATOM C1 CG331
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    GROUP
    ATOM C3 CG331
    ATOM H31 HGA3
    ATOM H32 HGA3
    ATOM H33 HGA3
    BOND C1 C2 C2
    BOND C1 H11 C1
    DONO HO2 O2
    ACCE O2
    IC C1 C2 C3
    IC C2 H31 *C3
    IC C2 H31 *C3
    IC C3 C2 C1
    IC C2 H11 *C1
    IC C2 H11 *C1
    IC C1 C3 *C2
    IC C1 C3 *C2
    IC C3 C2 O2
    RESI FORM
    GROUP
    ATOM HA
    ATOM C
    ATOM N
    ATOM HC
    ATOM HT
    ATOM O

    0.0000 0.0000 120.0000 0.0000 0.0000


    0.0000 0.0000 240.0000 0.0000 0.0000

    0.00 ! C3H8O 2-propanol, adm jr.


    0.14
    -0.65
    0.42
    0.09
    -0.27
    0.09
    0.09
    0.09

    ! H12 H13 H33 H32


    !
    \ /
    \ /
    ! H11--C1
    C3--H31
    !
    \
    /
    !
    C2
    !
    /
    \
    !
    O2
    H21
    !
    |
    !
    HO2
    !
    !

    -0.27
    0.09
    0.09
    0.09
    C3 C2 O2 C2 H21 O2 HO2
    H12 C1 H13 C3 H31 C3 H32 C3 H33
    H31
    H32
    H33
    H11
    H12
    H13
    O2
    H21
    HO2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000

    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000
    120.0000
    -120.0000
    180.0000

    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! CH3NO formamide, adm jr.


    HGR52
    CG2O1
    NG2S2
    HGP1
    HGP1
    OG2D1

    0.08 !
    0.42 !
    -0.69 !
    0.35 !
    0.35 !
    -0.51 !
    !
    C N N

    BOND C HA
    DOUBLE C O
    !BOND O DUM
    IMPR C HA N O C
    ! GAS PHASE GEOMETRY
    !IC DUM O C N
    !Gives strange error:
    !IC O C N HC
    !IC HC N C HA
    !IC O C N HT
    !Works with IC param:
    IC O C N HT
    IC O N *C HA
    IC C HT *N HC

    O
    Hc
    \\ /
    C--N
    /
    \
    HA
    Ht
    HC

    HT

    N HA O
    1.00

    90.0

    0. 124.70 1.352

    1.2190 124.70
    0. 118.50 1.0016 ! variable 1
    1.0016 118.50 180. 112.70 1.0980 ! variable 2
    1.2190 124.70 180. 120.00 1.0015 ! variable 3
    0.0000 0.0000 180.0000 0.0000 0.0000
    0.0000 0.0000 180.0000 0.0000 0.0000
    0.0000 0.0000 180.0000 0.0000 0.0000

    RESI ACEM
    0.00 ! C2H5NO acetamide, adm jr.
    ! the amide charges listed below are used in asparagine and glutamine
    ! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32

    GROUP
    ATOM CC CG331 -0.27 !
    ATOM C
    CG2O1
    0.55 ! HC1
    Ht
    ATOM N
    NG2S2 -0.62 !
    \
    /
    ATOM HC HGP1
    0.32 ! HC2--CC--C---N
    ATOM HT HGP1
    0.30 !
    /
    || \
    ATOM O
    OG2D1 -0.55 ! HC3
    O
    Hc
    ATOM HC1 HGA3
    0.09 !
    ATOM HC2 HGA3
    0.09 !
    ATOM HC3 HGA3
    0.09 !
    !atom dum dum
    0.0 ! dummy for ic build
    BOND C N N HC N HT
    DOUBLE C O
    BOND C CC CC HC1 CC HC2 CC HC3
    !BOND O DUM
    IMPR C CC N O C N CC O
    IMPR N C HC HT N C HT HC
    ! GAS PHASE GEOMETRY
    IC HC1 CC C N
    1.0832 113.80 180. 124.70
    IC O C N HC
    1.2012 124.70
    0. 118.63
    IC O C N HT
    1.2012 124.70 180. 120.92
    IC HC N C CC
    1.0016 118.63 180. 115.65
    IC O C CC HC1
    1.2012 123.27
    0. 113.80
    IC O C CC HC2
    1.2012 123.27 120. 108.52
    IC O C CC HC3
    1.2012 123.27 300. 108.52

    1.3523
    0.9929 ! variable 1
    0.9960 ! variable 3
    1.5150 ! variable 2
    1.0832
    1.0836
    1.0836

    RESI PRAM
    0.00 ! C3H7NO propionamide, adm jr.
    ! the amide charges listed below are used in asparagine and glutamine
    ! if Hc and HT are made equivalent use N = -0.64, Hc = HT = 0.32
    GROUP
    ATOM CC CG321 -0.18 !
    ATOM C
    CG2O1
    0.55 ! HC1
    Ht
    ATOM N
    NG2S2 -0.62 !
    \
    /
    ATOM HC HGP1
    0.32 ! HC2--CC--C---N
    ATOM HT HGP1
    0.30 !
    /
    || \
    ATOM O
    OG2D1 -0.55 !
    /
    O
    Hc
    ATOM HC1 HGA2
    0.09 ! C1-H13
    ATOM HC2 HGA2
    0.09 ! / \
    GROUP
    !H11 H12
    ATOM C1 CG331 -0.27
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    !atom dum dum
    0.0 ! dummy for ic build
    BOND C N N HC N HT
    DOUBLE C O
    BOND C CC CC HC1 CC HC2 CC C1
    BOND C1 H11 C1 H12 C1 H13
    !BOND O DUM
    IMPR C CC N O C N CC O
    IMPR N C HC HT N C HT HC
    ! GAS PHASE GEOMETRY
    IC HC1 CC C N
    1.0832 113.80 180. 124.70 1.3523
    IC O C N HC
    1.2012 124.70
    0. 118.63 0.9929 ! variable 1
    IC O C N HT
    1.2012 124.70 180. 120.92 0.9960 ! variable 3
    IC HC N C CC
    1.0016 118.63 180. 115.65 1.5150 ! variable 2
    IC O C CC HC1
    1.2012 123.27 60. 113.80 1.0832
    IC O C CC HC2
    1.2012 123.27 300. 108.52 1.0836
    IC O C CC C1
    1.2012 123.27 180. 108.52 1.5000
    IC C CC C1 H11
    0.0
    0.0 180. 0.0 0.0

    IC C
    IC C

    CC C1 H12
    CC C1 H13

    0.0
    0.0

    RESI NMA
    0.00
    GROUP
    ATOM CL CG331 -0.27
    ATOM HL1 HGA3
    0.09
    ATOM HL2 HGA3
    0.09
    ATOM HL3 HGA3
    0.09
    ATOM C
    CG2O1
    0.51
    ATOM O
    OG2D1 -0.51
    ATOM N
    NG2S1 -0.47
    ATOM H
    HGP1
    0.31
    ATOM CR CG331 -0.11
    ATOM HR1 HGA3
    0.09
    ATOM HR2 HGA3
    0.09
    ATOM HR3 HGA3
    0.09
    BOND HL1 CL HL2 CL
    BOND CL C
    C N
    BOND N H
    BOND HR1 CR HR2 CR
    DOUBLE C O
    IMPR N C CR H
    IMPR C CL N O
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O
    H
    O
    N
    N
    N
    C
    C
    C

    C
    N
    C
    C
    C
    C
    N
    N
    N

    RESI ALAD
    GROUP
    ATOM CL
    ATOM HL1
    ATOM HL2
    ATOM HL3
    GROUP
    ATOM CLP
    ATOM OL
    GROUP
    ATOM NL
    ATOM HL
    ATOM CA
    ATOM HA
    GROUP
    ATOM CB
    ATOM HB1
    ATOM HB2
    ATOM HB3
    GROUP
    ATOM CRP
    ATOM OR
    GROUP
    ATOM NR

    N
    C
    N
    CL
    CL
    CL
    CR
    CR
    CR

    0.0
    0.0

    60.
    300.

    0.0 0.0
    0.0 0.0

    ! C3H7NO N-methylacetamide, Louis Kuchnir

    H
    CL
    CR
    HL1
    HL2
    HL3
    HR1
    HR2
    HR3

    HL3 CL !
    N CR !
    !
    HR3 CR !

    1.2233
    0.9933
    1.2233
    1.3418
    1.3418
    1.3418
    1.3418
    1.3418
    1.3418

    122.84
    119.23
    122.84
    116.25
    116.25
    116.25
    122.57
    122.57
    122.57

    N-Methylacetamide:
    HL1\
    O
    /HR1
    HL2-- CL -- C -- N -- CR --HR2
    HL3/
    H
    \HR3

    180.
    0.
    0.
    180.
    60.
    300.
    180.
    60.
    300.

    119.23
    116.25
    122.57
    109.3
    109.3
    109.3
    110.7
    110.7
    110.7

    0.9933
    1.5118
    1.4488
    1.109
    1.109
    1.109
    1.113
    1.113
    1.113

    !
    !
    !
    !
    !
    !
    !
    !
    !

    variable
    variable
    variable
    variable
    variable
    variable
    variable
    variable
    variable

    1
    8
    8
    2
    3
    4
    5
    6
    7

    0.00 ! C6H12N2O2 Alanine dipeptide


    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG2O1
    OG2D1

    0.51
    -0.51

    NG2S1
    HGP1
    CG311
    HGA1

    -0.47
    0.31
    0.07
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG2O1
    OG2D1
    NG2S1

    !
    !
    !
    !
    !
    0.51 !
    -0.51 !
    !
    -0.47

    HL1
    \

    OL
    OR
    HR1
    || HL HA || HR
    /
    \
    || | | || |
    /
    HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2
    /
    |
    \
    /
    HB1--CB--HB3
    \
    HL3
    |
    HR3
    HB2

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HR
    CR
    HR1
    HR2
    HR3

    HGP1
    CG331
    HGA3
    HGA3
    HGA3

    BOND CL CLP
    BOND CA CRP
    DOUBLE CLP OL
    BOND NL HL
    BOND CA HA
    BOND CL HL1
    BOND CB HB1
    BOND CR HR1
    IMPR CLP CL NL
    IMPR CRP CA NR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CLP
    CA
    HL
    NL
    CA
    NL
    CL
    NL
    OL
    CA
    CRP
    CA
    NL
    NL
    HL1
    HL2
    HL3
    HA
    NL
    CRP
    CRP
    CRP
    HR
    CA
    CA
    HB1
    HL1
    HR1
    HA

    NL
    CLP
    NL
    CA
    NR
    CA
    CLP
    CL
    CLP
    CRP
    CR
    CRP
    CRP
    CRP
    CL
    CL
    CL
    CA
    CA
    CA
    NR
    NR
    NR
    CLP
    NR
    HB2
    HL2
    HR2
    CA

    0.31
    -0.11
    0.09
    0.09
    0.09
    CLP NL
    NL
    CRP NR
    NR
    CRP OR
    NR HR
    CA CB
    CL HL2 CL
    CB HB2 CB
    CR HR2 CR
    OL
    NL CLP
    OR
    NR CRP

    CA CRP
    *NL HL
    CA CRP
    CRP NR
    *CRP OR
    CRP OR
    NL CA
    *CLP OL
    NL CA
    NR CR
    *NR HR
    NR HR
    *CA HA
    *CA CB
    CLP NL
    CLP NL
    CLP OL
    CB HB1
    CB HB2
    CB HB3
    CR HR1
    CR HR2
    CR HR3
    *NL HL
    *CRP OR
    *CB HB3
    *CL HL3
    *CR HR3
    NL HL

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    CA
    CR

    HL3
    HB3
    HR3
    CA HL
    CR HR
    180.0
    180.0
    0.0
    180.0
    180.0
    0.0
    180.0
    180.0
    0.0
    180.0
    180.0
    180.0
    240.0
    120.0
    180.0
    60.0
    120.0
    180.0
    180.0
    180.0
    180.0
    60.0
    120.0
    180.0
    180.0
    120.0
    240.0
    240.0
    240.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    ! Phi
    ! Psi
    ! Omega Left
    ! Omega Right

    RESI MESH
    0.00 ! CH4S methanethiol, DZUNG NGUYEN
    GROUP
    ATOM H1 HGA3
    0.09 ! H1
    ATOM H2 HGA3
    0.09 !
    \
    ATOM H3 HGA3
    0.09 ! H2--CM--S
    ATOM CM CG331
    -0.20 !
    /
    \
    ATOM S SG311
    -0.23 ! H3
    H4
    ATOM H4 HGP3
    0.16 !
    BOND CM H1 CM H2 CM H3
    BOND CM S S H4
    IC H1 CM S H4 0.00 0.00
    0.0 0.00 0.00
    IC H2 CM S H4 0.00 0.00 120.0 0.00 0.00
    IC H3 CM S H4 0.00 0.00 240.0 0.00 0.00

    IC CM S H4 H1 0.00 0.00
    PATC FIRS NONE LAST NONE
    RESI MES1
    GROUP
    ATOM S
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13

    0.0 0.00 0.00

    -1.00 ! CH3S methylthiolate, adm jr.


    SG302
    CG323
    HGA3
    HGA3
    HGA3

    BOND S C1
    IC BLNK H11
    IC S
    H11
    IC S
    H11
    IC H12 H13
    PATCH FIRST

    -0.80
    -0.47
    0.09
    0.09
    0.09

    ! H11
    !
    \
    ! H12--C1--S (-)
    !
    /
    ! H13
    !
    C1 H11 C1 H12 C1 H13
    C1 S
    0.0000 0.0000 60.0000
    *C1 H12 0.0000 0.0000 120.0000
    *C1 H13 0.0000 0.0000 -120.0000
    *C1 H11 0.0000 0.0000 120.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000

    RESI ETSH
    0.00 ! C2H6S ethanethiol, Dzung Nguyen
    GROUP
    ATOM H1 HGA3
    0.09 ! H1 H4 H5
    ATOM H2 HGA3
    0.09 !
    \ \ /
    ATOM H3 HGA3
    0.09 ! H2-CM1--CM2
    ATOM CM1 CG331 -0.27 !
    /
    \
    GROUP
    ! H3
    S3--H6
    ATOM H4 HGA2
    0.09
    ATOM H5 HGA2
    0.09
    ATOM CM2 CG321 -0.11
    ATOM S3 SG311 -0.23
    ATOM H6 HGP3
    0.16
    BOND CM1 H1 CM1 H2 CM1 H3
    BOND CM1 CM2 CM2 H4 CM2 H5
    BOND CM2 S3 S3 H6
    IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0
    IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0
    IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0
    IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0
    IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0
    IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0
    IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0
    IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0
    IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0
    IC CM1 CM2 S3 H6 0.00 0.00 60.0 0.0 0.0
    IC H4 CM2 S3 H6 0.00 0.00 180.0 0.0 0.0
    IC H5 CM2 S3 H6 0.00 0.00 300.0 0.0 0.0
    PATCH FIRST NONE LAST NONE
    RESI ES1
    -1.00 ! C2H5S ethylthiolate, adm jr.
    GROUP
    ATOM S
    SG302 -0.80 ! H21 H11 H12
    ATOM C1 CG323 -0.38 !
    \ \ /
    ATOM C2 CG331 -0.27 ! H22--C2--C1
    ATOM H21 HGA3
    0.09 !
    /
    \
    ATOM H22 HGA3
    0.09 ! H23
    S (-)
    ATOM H23 HGA3
    0.09
    ATOM H11 HGA2
    0.09
    ATOM H12 HGA2
    0.09
    BOND S C1 C1 H11 C1 H12 C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC BLNK H11 C1 S
    0.0000
    0.00
    0.00 109.72

    1.8281

    IC S
    H11
    IC S
    H11
    IC H12 C2
    IC S
    C1
    IC S
    C1
    IC S
    C1
    PATCH FIRST

    *C1
    *C1
    *C1
    C2
    C2
    C2
    NONE

    H12 1.8281
    C2
    1.8281
    H11 1.1131
    H21 1.8281
    H22 1.8281
    H23 1.8281
    LAST NONE

    109.72
    109.72
    108.57
    114.02
    114.02
    114.02

    118.35
    -125.21
    -114.71
    -180.00
    59.57
    -59.57

    105.91
    108.57
    108.57
    110.65
    109.98
    109.98

    1.1131
    1.5315
    1.1131
    1.1089
    1.1111
    1.1111

    RESI DMDS
    0.00 ! C2H6S2 dimethyldisulfide, Dzung Nguyen
    GROUP
    ATOM H1 HGA3
    0.09 !
    ATOM H2 HGA3
    0.09 ! H1
    ATOM H3 HGA3
    0.09 !
    \
    ATOM CM1 CG331 -0.19 ! H2-CM1
    ATOM S2 SG301 -0.08 !
    / \
    GROUP
    ! H3 S2--S3
    H4
    ATOM S3 SG301 -0.08 !
    \ /
    ATOM CM4 CG331 -0.19 !
    CM4-H5
    ATOM H4 HGA3
    0.09 !
    \
    ATOM H5 HGA3
    0.09 !
    H6
    ATOM H6 HGA3
    0.09 !
    BOND H1 CM1
    H2 CM1
    H3 CM1
    CM1 S2
    BOND S2 S3
    S3 CM4
    CM4 H4
    CM4 H5
    BOND CM4 H6
    IC H1 CM1 S2 S3 0.00 0.00
    60.0 0.0 0.0
    IC H2 CM1 S2 S3 0.00 0.00 180.0 0.0 0.0
    IC H3 CM1 S2 S3 0.00 0.00 300.0 0.0 0.0
    IC CM1 S2 S3 CM4 0.00 0.00
    90.0 0.0 0.0
    IC S2 S3 CM4 H4 0.00 0.00
    60.0 0.0 0.0
    IC S2 S3 CM4 H5 0.00 0.00 180.0 0.0 0.0
    IC S2 S3 CM4 H6 0.00 0.00 300.0 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI DEDS
    GROUP
    ATOM H1 HGA2
    ATOM H2 HGA2
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    BOND

    CM1 CG321
    S2 SG301

    0.00 ! C4H10S2 diethyldisulfide, adm jr.


    0.09 !
    0.09 ! H1
    !
    \
    -0.10 ! H2-CM1
    -0.08 !
    / \
    ! CM0 S2--S3
    H4
    -0.08 ! / | \
    \ /
    -0.10 !H01| H03
    CM4-H5
    0.09 ! H02
    \
    0.09 !
    CM5-H53
    !
    / \
    -0.27 !
    H51 H52
    0.09 !
    0.09
    0.09

    S3
    CM4
    H4
    H5

    SG301
    CG321
    HGA2
    HGA2

    CM0
    H01
    H02
    H03

    CG331
    HGA3
    HGA3
    HGA3

    CM5
    H51
    H52
    H53

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09

    H1
    S2
    CM4
    CM0

    CM1
    S3
    CM5
    H01

    H2
    S3

    CM1
    CM4

    CM1 CM0
    CM4 H4

    CM0 H02

    CM0 H03

    CM1 S2
    CM4 H5

    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    CM5 H51

    CM5 H52

    CM0 CM1 S2 S3 0.00


    H1 CM1 S2 S3 0.00
    H2 CM1 S2 S3 0.00
    CM0 CM1 S2 S3 0.00
    S2 CM1 CM0 H01 0.00
    S2 CM1 CM0 H02 0.00
    S2 CM1 CM0 H03 0.00
    CM1 S2 S3 CM4 0.00
    S2 S3 CM4 H4 0.00
    S2 S3 CM4 H5 0.00
    S2 S3 CM4 CM5 0.00
    S3 CM4 CM5 H51 0.00
    S3 CM4 CM5 H52 0.00
    S3 CM4 CM5 H53 0.00
    FIRS NONE LAST NONE

    CM5 H53
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    60.0
    60.0
    300.0
    180.0
    180.0
    60.0
    300.0
    90.0
    60.0
    300.0
    180.0
    180.0
    60.0
    300.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    RESI EMS
    0.00 ! C3H8S ethylmethylsulfide, Dzung Nguyen
    GROUP
    ATOM H1 HGA3
    0.09 !
    ATOM H2 HGA3
    0.09 ! H1 H4 H5
    ATOM H3 HGA3
    0.09 !
    \
    \ /
    ATOM CM1 CG331 -0.27 ! H2-CM1--CM2
    H6
    GROUP
    !
    \
    /
    ATOM H4 HGA2
    0.09 !
    S3--CM4-H7
    ATOM H5 HGA2
    0.09 !
    \
    ATOM CM2 CG321 -0.13 ! kevo: symmetrized H8
    ATOM S3 SG311 -0.10 ! kevo: symmetrized
    ATOM CM4 CG331 -0.22 !
    ATOM H6 HGA3
    0.09 !
    ATOM H7 HGA3
    0.09 !
    ATOM H8 HGA3
    0.09 !
    BOND CM1 H1 CM1 H2 CM1 H3
    BOND CM1 CM2 CM2 H4 CM2 H5
    BOND CM2 S3 S3 CM4
    BOND CM4 H6 CM4 H7 CM4 H8
    IC H1 CM1 CM2 S3 0.00 0.00 60.0 0.0 0.0
    IC H2 CM1 CM2 S3 0.00 0.00 180.0 0.0 0.0
    IC H3 CM1 CM2 S3 0.00 0.00 300.0 0.0 0.0
    IC H1 CM1 CM2 H4 0.00 0.00 180.0 0.0 0.0
    IC H2 CM1 CM2 H4 0.00 0.00 300.0 0.0 0.0
    IC H3 CM1 CM2 H4 0.00 0.00 60.0 0.0 0.0
    IC H1 CM1 CM2 H5 0.00 0.00 300.0 0.0 0.0
    IC H2 CM1 CM2 H5 0.00 0.00 60.0 0.0 0.0
    IC H3 CM1 CM2 H5 0.00 0.00 180.0 0.0 0.0
    IC CM1 CM2 S3 CM4 0.00 0.00 60.0 0.0 0.0
    IC H4 CM2 S3 CM4 0.00 0.00 180.0 0.0 0.0
    IC H5 CM2 S3 CM4 0.00 0.00 300.0 0.0 0.0
    IC CM2 S3 CM4 H6 0.00 0.00 60.0 0.0 0.0
    IC CM2 S3 CM4 H7 0.00 0.00 180.0 0.0 0.0
    IC CM2 S3 CM4 H8 0.00 0.00 300.0 0.0 0.0
    PATCH FIRST NONE LAST NONE
    RESI IMIA
    GROUP
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2

    0.00 ! C3H4N2 Imidazole, adm jr.


    CG2R51 -0.05 !
    HGR52
    0.09 !
    CG2R51 0.22 !
    HGR52
    0.10 !

    HD1
    HE1
    |
    /
    ND1--CE1
    /
    ||

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    ND1
    HD1
    CE1
    HE1
    NE2

    NG2R51 -0.36 ! HG-CG


    ||
    HGP1
    0.32 !
    \\
    ||
    CG2R53 0.25 !
    CD2--NE2
    HGR52
    0.13 !
    |
    NG2R50 -0.70 !
    HD2
    !
    BOND NE2 CD2
    ND1 CG
    CE1 ND1
    BOND CG HG
    DOUBLE NE2 CE1
    CD2 CG
    BOND ND1 HD1
    CD2 HD2
    CE1 HE1
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 HD1
    ND1 CE1 CG
    IMPR CD2 CG NE2 HD2
    CD2 NE2 CG
    IMPR CE1 ND1 NE2 HE1
    CE1 NE2 ND1
    IMPR CG CD2 ND1 HG
    CG ND1 CD2
    DONO HD1 ND1
    ACCE NE2
    ! for analysis
    DONO HE1 CE1
    DONO HG CG
    ACCE CE1
    ACCE ND1
    ACCE CD2
    IC HG
    CG
    ND1 CE1
    1.5421 122.67
    IC CG
    ND1 CE1 NE2
    1.2854 109.79
    IC ND1 CE1 NE2 CD2
    1.2987 110.31
    IC CE1 NE2 CD2 CG
    1.3071 105.82
    IC NE2 CD2 CG
    ND1
    1.3165 108.68
    IC NE2 CD2 CG
    HG
    1.3165 108.68
    IC CD2 CG
    ND1 CE1
    1.3758 105.39
    IC CD2 NE2 CE1 HE1
    1.3165 105.82
    IC NE2 CE1 ND1 HD1
    1.3071 110.31
    IC HG
    CG
    CD2 HD2
    1.5421 131.52

    HD1
    HD2
    HE1
    HG

    -173.67
    0.21
    0.03
    -0.23
    0.35
    172.86
    -0.34
    149.51
    157.04
    -48.16

    109.79
    110.31
    105.82
    108.68
    105.39
    131.52
    109.79
    119.57
    123.39
    118.30

    1.2987
    1.3071
    1.3165
    1.3758
    1.2854
    1.5421
    1.2987
    1.0879
    0.9770
    1.0902

    RESI MIMI
    0.00 ! C4H6N2 4-methylimidazole, adm jr.
    GROUP
    ATOM ND1 NG2R51 -0.36 !
    HD1
    HE1
    ATOM HD1 HGP1
    0.32 !
    |
    /
    ATOM CG CG2R51 -0.05 !
    HB1
    ND1--CE1
    ATOM CB CG331 -0.18 !
    |
    /
    ||
    ATOM HB1 HGA3
    0.09 ! HB2-CB-CG
    ||
    ATOM HB2 HGA3
    0.09 !
    |
    \\
    ||
    ATOM HB3 HGA3
    0.09 !
    HB3
    CD2--NE2
    GROUP
    !
    |
    ATOM NE2 NG2R50 -0.70 !
    HD2
    ATOM CD2 CG2R51 0.22 !
    ATOM HD2 HGR52
    0.10 !
    ATOM CE1 CG2R53 0.25 !
    ATOM HE1 HGR52
    0.13 !
    BOND NE2 CD2
    ND1 CG
    CE1 ND1
    BOND CG CB
    DOUBLE NE2 CE1
    CD2 CG
    BOND ND1 HD1
    CD2 HD2
    CE1 HE1
    BOND CB HB1
    CB HB2
    CB HB3
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 HD1
    CD2 CG NE2 HD2
    CE1 ND1 NE2 HE1
    DONO HD1 ND1
    ACCE NE2
    IC CB
    CG
    ND1 CE1
    1.5421 122.67 180.0 109.79 1.2987
    IC CG
    ND1 CE1 NE2
    1.2854 109.79
    0.21 110.31 1.3071

    IC ND1
    IC CD2
    IC NE2
    IC CB
    IC CD2
    IC CD2
    IC CD2
    !IC CD2
    !IC CE1
    !IC NE2
    !IC NE2
    !Multiple

    CE1
    NE2
    CE1
    CG
    CG
    CG
    CG
    CG
    NE2
    CD2
    CD2
    errors

    NE2 CD2
    CE1 HE1
    ND1 HD1
    CD2 HD2
    CB
    HB1
    CB
    HB2
    CB
    HB3
    ND1 CE1
    CD2 CG
    CG
    ND1
    CG
    HG
    corrected.

    1.2987
    1.3165
    1.3071
    1.5421
    0.0
    0.0
    0.0
    1.3758
    1.3071
    1.3165
    1.3165

    110.31
    105.82
    110.31
    131.52
    0.0
    0.0
    0.0
    105.39
    105.82
    108.68
    108.68

    0.03
    180.0
    180.0
    0.0
    0.0
    120.0
    240.0
    -0.34
    -0.23
    0.35
    172.86

    105.82
    119.57
    123.39
    118.30
    0.0
    0.0
    0.0
    109.79
    108.68
    105.39
    131.52

    1.3165
    1.0879
    0.9770
    1.0902
    0.0
    0.0
    0.0
    1.2987
    1.3758
    1.2854
    1.5421

    RESI EIMI
    0.00 ! C5H8N2 4-ethylimidazole, adm jr.
    GROUP
    ATOM CA CG331 -0.27 ! Optimized charges to minimize group size
    ATOM HA1 HGA3
    0.09
    ATOM HA2 HGA3
    0.09
    ATOM HA3 HGA3
    0.09
    GROUP
    ATOM ND1 NG2R51 -0.36 !
    HD1
    HE1
    ATOM HD1 HGP1
    0.32 !
    |
    /
    ATOM CG CG2R51 -0.05 ! HA1 HB1
    ND1--CE1
    ATOM CB CG321 -0.09 !
    \
    |
    /
    ||
    ATOM HB1 HGA2
    0.09 ! HA2-CA--CB-CG
    ||
    ATOM HB2 HGA2
    0.09 !
    /
    | \\
    ||
    GROUP
    ! HA3 HB2
    CD2--NE2
    ATOM NE2 NG2R50 -0.70 !
    |
    ATOM CD2 CG2R51 0.22 !
    HD2
    ATOM HD2 HGR52
    0.10 !
    ATOM CE1 CG2R53 0.25 !
    ATOM HE1 HGR52
    0.13 !
    BOND NE2 CD2
    ND1 CG
    CE1 ND1
    BOND CG CB
    DOUBLE NE2 CE1
    CD2 CG
    BOND ND1 HD1
    CD2 HD2
    CE1 HE1
    BOND CB HB1
    CB HB2
    CB CA
    BOND CA HA1
    CA HA2
    CA HA3
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 HD1
    CD2 CG NE2 HD2
    CE1 ND1 NE2 HE1
    DONO HD1 ND1
    ACCE NE2
    IC CB
    CG
    ND1 CE1
    1.5421 122.67 -173.67 109.79 1.2987
    IC CG
    ND1 CE1 NE2
    1.2854 109.79
    0.21 110.31 1.3071
    IC ND1 CE1 NE2 CD2
    1.2987 110.31
    0.03 105.82 1.3165
    IC CE1 NE2 CD2 CG
    1.3071 105.82 -0.23 108.68 1.3758
    IC NE2 CD2 CG
    ND1
    1.3165 108.68
    0.35 105.39 1.2854
    IC NE2 CD2 CG
    HG
    1.3165 108.68 172.86 131.52 1.5421
    IC CD2 CG
    ND1 CE1
    1.3758 105.39 -0.34 109.79 1.2987
    IC CD2 NE2 CE1 HE1
    1.3165 105.82 149.51 119.57 1.0879
    IC NE2 CE1 ND1 HD1
    1.3071 110.31 157.04 123.39 0.9770
    IC CG
    NE2 *CD2 HD2
    0.0
    0.0 180.0
    0.0
    0.0
    IC ND1 CD2 *CG CB
    0.0
    0.0 180.0
    0.0
    0.0
    IC CD2 CG
    CB
    CA
    0.0
    0.0 240.0
    0.0
    0.0
    IC CA
    CG
    *CB HB1
    0.0
    0.0 120.0
    0.0
    0.0
    IC CA
    CG
    *CB HB2
    0.0
    0.0 -120.0
    0.0
    0.0
    IC CG
    CB
    CA
    HA1
    0.0
    0.0 180.0
    0.0
    0.0
    IC HA1 CB
    *CA HA2
    0.0
    0.0 120.0
    0.0
    0.0
    IC HA1 CB
    *CA HA3
    0.0
    0.0 -120.0
    0.0
    0.0

    RESI IMIM
    1.00 ! C3H5N2 Imidazolium, adm jr.
    GROUP
    ATOM CG CG2R51 0.19 !
    HD1
    HE1
    ATOM HG HGR52
    0.13 !
    |
    /
    ATOM CD2 CG2R51 0.19 !
    ND1--CE1
    ATOM HD2 HGR52
    0.13 !
    /
    ||
    GROUP
    ! HG-CG
    ||
    ATOM ND1 NG2R52 -0.51 !
    \\
    ||
    ATOM HD1 HGP2
    0.44 !
    CD2--NE2 (+)
    ATOM NE2 NG2R52 -0.51 !
    |
    \
    ATOM HE2 HGP2
    0.44 !
    HD2
    HE2
    ATOM CE1 CG2R53 0.32
    ATOM HE1 HGR53
    0.18
    BOND NE2 CD2
    ND1 CG
    CE1 ND1
    BOND CG HG
    DOUBLE NE2 CE1
    CD2 CG
    BOND ND1 HD1
    CD2 HD2
    CE1 HE1
    NE2
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 HD1
    NE2 CD2 CE1 HE2
    IMPR ND1 CE1 CG HD1
    NE2 CE1 CD2 HE2
    DONO HD1 ND1
    DONO HE2 NE2
    IC HG
    CG
    ND1 CE1
    1.5421 122.67 -173.67
    IC CG
    ND1 CE1 NE2
    1.2854 109.79
    0.21
    IC ND1 CE1 NE2 CD2
    1.2987 110.31
    0.03
    IC CE1 NE2 CD2 CG
    1.3071 105.82 -0.23
    IC NE2 CD2 CG
    ND1
    1.3165 108.68
    0.35
    IC NE2 CD2 CG
    HG
    1.3165 108.68 172.86
    IC CD2 CG
    ND1 CE1
    1.3758 105.39 -0.34
    IC CD2 NE2 CE1 HE1
    1.3165 105.82 149.51
    IC NE2 CE1 ND1 HD1
    1.3071 110.31 157.04
    IC HG
    CG
    CD2 HD2
    1.5421 131.52 -48.16
    IC HE1 CE1 NE2 HE2
    1.0879 125.00
    0.00
    RESI EIMM
    GROUP
    ATOM CA CG331
    ATOM HA1 HGA3
    ATOM HA2 HGA3
    ATOM HA3 HGA3
    GROUP
    ATOM CB CG321
    ATOM HB1 HGA2
    ATOM HB2 HGA2
    ATOM CG CG2R51
    ATOM CD2 CG2R51
    ATOM HD2 HGR52
    GROUP
    ATOM ND1 NG2R52
    ATOM HD1 HGP2
    ATOM NE2 NG2R52
    ATOM HE2 HGP2
    ATOM CE1 CG2R53
    ATOM HE1 HGR53
    BOND NE2 CD2
    BOND CG CB
    DOUBLE CD2 CG
    BOND ND1 HD1
    BOND CB HB1
    BOND CA HA1

    HE2

    109.79
    110.31
    105.82
    108.68
    105.39
    131.52
    109.79
    119.57
    123.39
    118.30
    125.00

    1.00 ! C5H9N2 Ethyl-Imidazolium, adm jr.


    -0.27
    0.09
    0.09
    0.09
    !
    !
    HD1
    HE1
    !
    |
    /
    ! HA1 HB1
    ND1--CE1
    !
    \
    |
    /
    ||
    ! HA2-CA--CB-CG
    ||
    !
    /
    | \\
    ||
    ! HA3 HB2
    CD2--NE2(+)
    -0.51 !
    |
    \
    0.44 !
    HD2
    HE2
    -0.51 !
    0.44
    0.32
    0.18
    ND1 CG
    CE1 ND1
    NE2 HE2
    NE2 CE1
    CD2 HD2
    CE1 HE1
    CB HB2
    CB CA
    CA HA2
    CA HA3
    -0.05
    0.09
    0.09
    0.19
    0.19
    0.13

    1.2987
    1.3071
    1.3165
    1.3758
    1.2854
    1.5421
    1.2987
    1.0879
    0.9770
    1.0902
    1.0000

    ! KEEPS HYDROGENS IN RING PLANE


    IMPR ND1 CG CE1 HD1
    NE2 CD2 CE1 HE2
    IMPR ND1 CE1 CG HD1
    NE2 CE1 CD2 HE2
    DONO HD1 ND1
    ACCE NE2
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CA
    HA1
    HA1
    HA1
    CG
    CG
    CA
    ND1
    CB
    NE2
    CB
    CE1
    CE1
    NE2

    CB
    CB
    CB
    CA
    CA
    CA
    CB
    CB
    CG
    CG
    CG
    CG
    CD2
    ND1

    CG
    *CA
    *CA
    CB
    *CB
    *CB
    CG
    *CG
    CD2
    *CD2
    ND1
    *ND1
    *NE2
    *CE1

    ND1
    HA2
    HA3
    CG
    HB1
    HB2
    ND1
    CD2
    NE2
    HD2
    CE1
    HD1
    HE2
    HE1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    RESI BENZ
    0.00 ! C6H6 benzene, adm jr.
    GROUP
    ATOM CG CG2R61 -0.115 !
    ATOM HG HGR61
    0.115 !
    HD1 HE1
    GROUP
    !
    |
    |
    ATOM CD1 CG2R61 -0.115 !
    CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    /
    \
    GROUP
    ! HG--CG
    CZ--HZ
    ATOM CD2 CG2R61 -0.115 !
    \
    /
    ATOM HD2 HGR61
    0.115 !
    CD2--CE2
    GROUP
    !
    |
    |
    ATOM CE1 CG2R61 -0.115 !
    HD2 HE2
    ATOM HE1 HGR61
    0.115 !
    GROUP
    ATOM CE2 CG2R61 -0.115
    ATOM HE2 HGR61
    0.115
    GROUP
    ATOM CZ CG2R61 -0.115
    ATOM HZ HGR61
    0.115
    BOND CD1 CG CD2 CG CE1 CD1
    BOND CE2 CD2 CZ CE1 CZ CE2
    BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1
    BOND CE2 HE2 CZ HZ
    IC CG CD1 CE1 CZ
    0.0000 0.0000 0.0000
    IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000
    IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000
    IC CD1 CD2 *CG HG
    0.0000 0.0000 180.0000
    IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000
    IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000
    IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000
    IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000
    IC CE1 CE2 *CZ HZ
    0.0000 0.0000 180.0000
    RESI EBEN
    GROUP
    ATOM CG CG2R61

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H10 ethylbenzene, adm jr.

    0.000 !
    !
    GROUP
    !
    ATOM CD1 CG2R61 -0.115 !HA1

    HB1

    HD1 HE1
    |
    |
    CD1--CE1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CZ
    ATOM HZ
    GROUP
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CA
    ATOM HA1
    ATOM HA2
    ATOM HA3
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HGR61

    0.115 ! \
    |
    /
    \
    !HA2-CA--CB--CG
    CZ--HZ
    CG2R61 -0.115 ! /
    |
    \
    /
    HGR61
    0.115 !HA3
    HB2 CD2--CE2
    !
    |
    |
    CG2R61 -0.115 !
    HD2 HE2
    HGR61
    0.115 !
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    CD1
    CE2
    CG
    CE2
    CB
    CA

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CD2
    CD2
    CD2
    CG
    CG
    CG

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG
    CD2
    CB
    HE2
    HB1
    HA1
    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CG
    CG
    CG
    CB
    CB
    CB

    RESI PHEN
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP

    CD2
    CZ
    CD1
    CZ
    CB
    CA
    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    CB
    CB
    CB
    CA
    CA
    CA

    CG
    CE1
    HD1
    HZ
    HB2
    HA2

    CE1 CD1
    CZ CE2
    CD2 HD2 CE1 HE1

    CZ
    CE2
    CD2
    CB
    HD1
    HD2
    HE1
    HE2
    HZ
    HB1
    HB2
    CA
    HA1
    HA2
    HA3

    CB CA
    CA HA3
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    120.0000
    240.0000
    0.0000
    180.0000
    60.0000
    300.0000

    0.00 ! C6H6O phenol, adm jr.


    CG2R61 -0.115 !
    HGR61
    0.115 !
    HD1 HE1
    !
    |
    |
    CG2R61 -0.115 !
    CD1--CE1
    HGR61
    0.115 !
    //
    \\
    ! HG--CG
    CZ--OH
    CG2R61 -0.115 !
    \
    /
    \
    HGR61
    0.115 !
    CD2==CE2
    HH
    !
    |
    |
    CG2R61 -0.115 !
    HD2 HE2
    HGR61
    0.115

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM CE2 CG2R61 -0.115


    ATOM HE2 HGR61
    0.115
    GROUP
    ATOM CZ CG2R61 0.11
    ATOM OH OG311 -0.53
    ATOM HH HGP1
    0.42
    BOND CD2 CG CE1 CD1
    BOND CZ CE2
    BOND CG HG CD1 HD1 CD2 HD2 CE1
    BOND CE2 HE2 CZ OH OH HH
    DOUBLE CD1 CG CE2 CD2 CZ CE1
    IC CG CD1 CE1 CZ
    0.0000
    IC CD1 CE1 CZ CE2 0.0000
    IC CE1 CZ CE2 CD2 0.0000
    IC CD1 CD2 *CG HG
    0.0000
    IC CE1 CG *CD1 HD1 0.0000
    IC CE2 CG *CD2 HD2 0.0000
    IC CZ CD1 *CE1 HE1 0.0000
    IC CZ CD2 *CE2 HE2 0.0000
    IC CE1 CE2 *CZ OH
    0.0000
    IC CE1 CZ OH HH
    0.0000
    RESI EPHE
    GROUP
    ATOM CG CG2R61
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CZ
    ATOM OH
    ATOM HH
    GROUP
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CA
    ATOM HA1
    ATOM HA2
    ATOM HA3

    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    HE1
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H10O p-ethylphenol, adm jr.


    0.00 !
    !
    HD1 HE1
    !
    |
    |
    -0.115 !HA1
    HB1 CD1--CE1
    0.115 ! \
    |
    /
    \
    !HA2-CA--CB--CG
    CZ--OH
    -0.115 ! /
    |
    \
    /
    \
    0.115 !HA3
    HB2 CD2--CE2
    HH
    !
    |
    |
    -0.115 !
    HD2 HE2
    0.115 !
    !
    -0.115 !
    0.115 !

    CG2R61 0.11
    OG311 -0.53
    HGP1
    0.42
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    BOND CD2 CG CE1 CD1


    BOND CZ CE2
    BOND CG CB CD1 HD1 CD2 HD2 CE1 HE1
    BOND CE2 HE2 CZ OH OH HH
    BOND CB HB1 CB HB2 CB CA
    BOND CA HA1 CA HA2 CA HA3
    DOUBLE CD1 CG CE2 CD2 CZ CE1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CE1
    CD2
    CD2
    CD2
    CG
    CG
    CG

    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CZ
    CG
    CG
    CG
    CB
    CB
    CB

    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    OH
    CB
    CB
    CB
    CA
    CA
    CA

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI PHEO
    -1.00 ! C6H5O phenoxide, adm jr.
    GROUP
    ATOM CG CG2R61 -0.115 !
    ATOM HG HGR61
    0.115 !
    HD1 HE1
    GROUP
    !
    |
    |
    ATOM CD1 CG2R61 -0.115 !
    CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    /
    \
    GROUP
    ! HG--CG
    CZ--OH (-)
    ATOM CD2 CG2R61 -0.115 !
    \
    /
    ATOM HD2 HGR61
    0.115 !
    CD2--CE2
    GROUP
    !
    |
    |
    ATOM CE1 CG2R61 -0.60 !
    HD2 HE2
    ATOM HE1 HGR61
    0.28
    ATOM CE2 CG2R61 -0.60
    ATOM HE2 HGR61
    0.28
    ATOM CZ CG2R61 0.40
    ATOM OH OG312 -0.76
    BOND CD1 CG CD2 CG CE1 CD1
    BOND CE2 CD2 CZ CE1 CZ CE2
    BOND CG HG CD1 HD1 CD2 HD2 CE1 HE1
    BOND CE2 HE2 CZ OH
    IC CG CD1 CE1 CZ
    0.0000 0.0000 0.0000 0.0000
    IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000
    IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000
    IC CD1 CD2 *CG HG
    0.0000 0.0000 180.0000 0.0000
    IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000
    IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000
    IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000
    IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000
    IC CE1 CE2 *CZ OH
    0.0000 0.0000 180.0000 0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI AP2
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N
    CA
    CB
    CG
    CD
    CY
    OY
    C
    HA

    NG2S0
    CG3C51
    CG3C52
    CG3C52
    CG3C52
    CG2O1
    OG2D1
    CG2O1
    HGA1

    CZ
    CE2
    CD2
    CB
    HD1
    HD2
    HE1
    HE2
    OH
    HH
    HB1
    HB2
    CA
    HA1
    HA2
    HA3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    120.0000
    240.0000
    0.0000
    180.0000
    60.0000
    300.0000

    0.00 ! C7H12N2O2 acetyl-prolineamide, R. Dunbrack


    !
    !HY1 HY2 HY3
    -0.29 ! \ | /
    0.02 !
    CAY
    -0.18 !
    |
    -0.18 ! OY=CY HD1 HD2
    0.00 !
    \
    \ /
    0.51 !
    N---CD HG1
    -0.51 !
    |
    \ /
    0.51 !
    |
    CG
    0.09 !
    |
    / \

    ATOM HB1 HGA2


    0.09 !
    HA-CA--CB HG2
    ATOM HB2 HGA2
    0.09 !
    | / \
    ATOM HG1 HGA2
    0.09 !
    | HB1 HB2
    ATOM HG2 HGA2
    0.09 !
    O=C
    ATOM HD1 HGA2
    0.09 !
    |
    ATOM HD2 HGA2
    0.09 !
    NT
    ATOM CAY CG331 -0.27 !
    / \
    ATOM HY1 HGA3
    0.09 ! HT1 HT2
    ATOM HY2 HGA3
    0.09
    ATOM HY3 HGA3
    0.09
    ATOM O
    OG2D1 -0.51
    ATOM NT NG2S2 -0.62
    ATOM HT1 HGP1
    0.31
    ATOM HT2 HGP1
    0.31
    BOND CY N CAY HY1 CAY HY2 CAY HY3
    BOND CY CAY N CA CA CB CB CG CG CD CD N
    BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB
    BOND C CA C NT NT HT1 NT HT2
    DOUBLE C O CY OY
    IMPR CY CAY N OY
    IMPR C CA NT O
    IMPR C NT CA O
    IMPR N CY CA CD
    IMPR NT C HT2 HT1
    DONOR HT1 NT
    DONOR HT2 NT
    ACCEPTOR OY CY
    ACCEPTOR O C
    ! Improper ICs
    IC CY CA *N CD
    0.00 0.00 180.00 0.00
    IC N C *CA CB
    0.00 0.00 120.00 0.00
    IC N C *CA HA
    0.00 0.00 -120.00 0.00
    IC N CAY *CY OY
    0.00 0.00 180.00 0.00
    ! Backbone + Peptide bond IC's
    IC OY CY N CA
    0.00 0.00
    0.00 0.00
    IC CAY CY N CA
    0.00 0.00 180.00 0.00
    IC CY N CA C
    0.00 120.64 -60.00 0.00
    IC N CA C NT
    0.00 0.00 180.0
    0.00
    IC CAY CY N CD
    0.00 0.00
    0.00 120.64
    IC CY N CD CG
    0.00 0.00 168.60 103.28
    IC CY N CA CB
    0.00 0.00 168.64 103.34
    ! Ring IC's
    IC N CA CB CG
    0.00 103.34 29.25 103.67
    IC CA CB CG CD
    0.00 103.67 -36.72 103.63
    IC CB CG CD N
    0.00 103.63 29.50 103.28
    IC CG CD N CA
    0.00 103.28 -11.61 112.90
    IC CD N CA CB
    0.00 112.90 -11.17 103.34
    ! Carbonyl IC's
    IC CD N CA C
    0.00 112.90 120.00 108.00
    ! Hydrogen IC's
    IC CD N CA HA
    0.00 0.00 -120.00 108.00
    IC N CA CB HB1
    0.00 0.00 120.00 108.00
    IC N CA CB HB2
    0.00 0.00 -120.00 108.00
    IC CA CB CG HG1
    0.00 0.00 120.00 108.00
    IC CA CB CG HG2
    0.00 0.00 -120.00 108.00
    IC CB CG CD HD1
    0.00 0.00 120.00 108.00
    IC CB CG CD HD2
    0.00 0.00 -120.00 108.00
    IC NT CA *C O
    0.00 0.00 180.00 0.00
    IC CA C NT HT2
    0.00 0.00 180.00 0.00
    IC C HT2 *NT HT1
    0.00 0.00 180.00 0.00

    HB2 CB

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    !Omega
    !Omega
    !Psi
    !Phi

    IC OY CY CAY HY1 0.00


    IC CY HY1 *CAY HY2 0.00
    IC CY HY1 *CAY HY3 0.00
    RESI PDIP
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N
    CA
    CB
    CG
    CD
    CY
    OY
    C
    HA
    HB1
    HB2
    HG1
    HG2
    HD1
    HD2
    CAY
    HY1
    HY2
    HY3
    O
    NT
    HT1
    CR
    HR1
    HR2
    HR3

    CAY
    CY
    N
    CY
    N
    N
    N
    OY
    CAY
    CY
    N
    CAY

    NG2S0
    CG3C51
    CG3C52
    CG3C52
    CG3C52
    CG2O1
    OG2D1
    CG2O1
    HGA1
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3
    OG2D1
    NG2S1
    HGP1
    CG331
    HGA3
    HGA3
    HGA3

    CY
    N
    CA
    CA
    C
    C
    CAY
    CY
    CY
    N
    CA
    CY

    0.00 0.00
    0.00 0.00
    0.00 0.00

    0.00 ! C8H14N2O2 proline dipeptide


    !
    !HY1 HY2 HY3
    -0.29 ! \ | /
    0.02 !
    CAY
    -0.18 !
    |
    -0.18 ! OY=CY HD1 HD2
    0.00 !
    \
    \ /
    0.51 !
    N---CD HG1
    -0.51 !
    |
    \ /
    0.51 !
    |
    CG
    0.09 !
    |
    / \
    0.09 !
    HA-CA--CB HG2
    0.09 !
    | / \
    0.09 !
    | HB1 HB2
    0.09 !
    O=C
    0.09 !
    |
    0.09 !
    NT
    -0.27 !
    / \
    0.09 ! HT1 CR-HR3
    0.09 !
    / \
    0.09 !
    HR1 HR2
    -0.51
    -0.47
    0.31
    -0.11
    0.09
    0.09
    0.09

    BOND CY N CAY HY1


    BOND CY CAY N CA
    BOND HA CA HG1 CG
    BOND C CA C NT
    BOND CR HR1 CR HR2
    DOUBLE C O CY OY
    IMPR CY CAY N OY
    IMPR C CA NT O
    IMPR C NT CA O
    IMPR N CY CA CD
    DONOR HT1 NT
    ACCEPTOR OY CY
    ACCEPTOR O C
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.00 90.00
    0.00 120.00
    0.00 -120.00

    N
    CA
    C
    *N
    *CA
    *CA
    *CY
    N
    N
    CA
    C
    N

    CAY
    CA
    HG2
    NT
    CR

    CA
    C
    NT
    CD
    CB
    HA
    OY
    CA
    CA
    C
    NT
    CD

    HY2
    CB
    CG
    HT1
    HR3

    CAY
    CB
    HD1
    NT

    HY3
    CG CG CD CD N
    CD HD2 CD HB1 CB HB2 CB
    CR

    1.4871
    1.3234
    1.4590
    1.3234
    1.4590
    1.4590
    1.3234
    1.2260
    1.4871
    1.3234
    1.4590
    1.4871

    118.91
    123.38
    111.46
    123.38
    111.46
    111.46
    118.91
    121.95
    118.91
    123.38
    111.46
    118.91

    174.70
    -72.54
    117.46
    176.71
    114.78
    -122.11
    -179.24
    -6.08
    174.70
    -72.54
    117.46
    -1.63

    123.38
    111.46
    121.78
    112.56
    112.03
    109.86
    119.14
    123.38
    123.38
    111.46
    121.78
    123.97

    1.4590
    1.5357
    1.3479
    1.4667
    1.5409
    1.0785
    1.2260
    1.4590
    1.4590
    1.5357
    1.3479
    1.4667

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CY
    CY
    N
    CA
    CB
    CG
    CD
    CD
    CD
    N
    N
    CA
    CA
    CB
    CB
    NT
    CA
    N
    HY1
    HY1
    C
    C
    C
    C

    N
    N
    CA
    CB
    CG
    CD
    N
    N
    N
    CA
    CA
    CB
    CB
    CG
    CG
    CA
    C
    CY
    CY
    CY
    HT1
    NT
    NT
    NT

    CD
    CA
    CB
    CG
    CD
    N
    CA
    CA
    CA
    CB
    CB
    CG
    CG
    CD
    CD
    *C
    NT
    CAY
    *CAY
    *CAY
    *NT
    CR
    CR
    CR

    CG
    CB
    CG
    CD
    N
    CA
    CB
    C
    HA
    HB1
    HB2
    HG1
    HG2
    HD1
    HD2
    O
    HT1
    HY1
    HY2
    HY3
    CR
    HR1
    HR2
    HR3

    RESI TP2
    1.00 !
    ATOM N
    NG3P2 -0.07 !
    ATOM HN1 HGP2
    0.24 !
    ATOM HN2 HGP2
    0.24 !
    ATOM CD CG3C54 0.16 !
    ATOM CB CG3C52 -0.18 !
    ATOM CG CG3C52 -0.18 !
    ATOM CA CG3C53 0.16 !
    ATOM C
    CG2O1
    0.51 !
    ATOM O
    OG2D1 -0.51 !
    ATOM HA HGA1
    0.09 !
    ATOM HB1 HGA2
    0.09 !
    ATOM HB2 HGA2
    0.09 !
    ATOM HG1 HGA2
    0.09 !
    ATOM HG2 HGA2
    0.09 !
    ATOM HD1 HGA2
    0.09 !
    ATOM HD2 HGA2
    0.09 !
    ATOM NT NG2S2 -0.62 !
    ATOM HT1 HGP1
    0.31 !
    ATOM HT2 HGP1
    0.31 !
    BOND HN1 N HN2 N N CA CA
    BOND HA CA HG1 CG HG2 CG
    BOND C CA C NT NT HT1 NT
    DOUBLE C O
    IMPR C CA NT O
    IMPR C NT CA O
    IMPR NT C HT2 HT1
    DONOR HT1 NT
    DONOR HT2 NT
    DONOR HN1 N
    DONOR HN2 N
    ACCEPTOR O C
    ! Improper ICs
    IC HN1 CA *N CD
    0.00
    IC HN2 CA *N HN1
    0.00

    1.3234
    1.3234
    1.4590
    1.5409
    1.5340
    1.5319
    1.4667
    1.4667
    1.4667
    1.4590
    1.4590
    1.5409
    1.5409
    1.5340
    1.5340
    1.3479
    1.5357
    1.3234
    1.1118
    1.1118
    1.3479
    1.3479
    1.3479
    1.3479

    123.97
    123.38
    102.97
    104.52
    103.37
    105.08
    112.56
    112.56
    112.56
    102.97
    102.97
    104.52
    104.52
    103.37
    103.37
    121.78
    121.78
    118.91
    108.99
    108.99
    114.38
    127.54
    127.54
    127.54

    171.81
    167.19
    30.57
    -33.72
    23.86
    -4.88
    -16.10
    104.17
    -133.77
    153.44
    -85.51
    82.51
    -155.89
    144.10
    -93.57
    179.58
    -178.24
    177.72
    119.00
    -119.34
    -176.13
    -178.11
    62.09
    -58.81

    105.08
    102.97
    104.52
    103.37
    105.08
    112.56
    102.97
    111.46
    109.94
    113.27
    108.72
    109.30
    112.80
    110.20
    110.40
    119.57
    114.38
    108.99
    110.21
    110.53
    117.94
    110.27
    110.97
    110.79

    C5H11N2O prolineamide, R. Dunbrack

    HN1 HD1 HD2


    \
    \ /
    HN2--N---CD HG1
    |(+) \ /
    |
    CG
    |
    / \
    HA-CA--CB HG2
    | / \
    | HB1 HB2
    O=C
    |
    NT
    / \
    HT1 HT2
    CB CB CG CG CD CD N
    HD1 CD HD2 CD HB1 CB HB2 CB
    HT2

    0.00 120.00
    0.00 120.00

    0.00 0.00
    0.00 0.00

    1.5319
    1.5409
    1.5340
    1.5319
    1.4667
    1.4590
    1.5409
    1.5357
    1.0785
    1.1091
    1.1129
    1.1137
    1.1079
    1.1134
    1.1126
    1.2276
    0.9952
    1.1118
    1.1099
    1.1094
    1.4463
    1.1125
    1.1130
    1.1141

    IC N C *CA CB
    0.00 0.00
    IC N C *CA HA
    0.00 0.00
    ! Backbone + Peptide bond IC's
    IC N CA C NT
    0.00 0.00
    ! Ring IC's
    IC N CA CB CG
    0.00 103.34
    IC CA CB CG CD
    0.00 103.67
    IC CB CG CD N
    0.00 103.63
    IC CG CD N CA
    0.00 103.28
    IC CD N CA CB
    0.00 112.90
    ! Carbonyl IC's
    IC CD N CA C
    0.00 112.90
    ! Hydrogen IC's
    IC CD N CA HA
    0.00 0.00
    IC N CA CB HB1
    0.00 0.00
    IC N CA CB HB2
    0.00 0.00
    IC CA CB CG HG1
    0.00 0.00
    IC CA CB CG HG2
    0.00 0.00
    IC CB CG CD HD1
    0.00 0.00
    IC CB CG CD HD2
    0.00 0.00
    IC NT CA *C O
    0.00 0.00
    IC CA C NT HT2
    0.00 0.00
    IC C HT2 *NT HT1
    0.00 0.00
    RESI ETHA
    GROUP
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    ATOM C1 CG331
    GROUP
    ATOM H21 HGA3
    ATOM H22 HGA3
    ATOM H23 HGA3
    ATOM C2 CG331
    BOND C1 H11 C1
    BOND C1 C2 C2
    IC C2 H11 *C1
    IC C2 H11 *C1
    IC H11 C1 C2
    IC C1 H21 *C2
    IC C1 H21 *C2

    120.00
    -120.00

    0.00 0.00
    0.00 0.00

    180.0

    0.00 0.00

    29.25
    -36.72
    29.50
    -11.61
    -11.17

    103.67
    103.63
    103.28
    112.90
    103.34

    0.00
    0.00
    0.00
    0.00
    0.00

    120.00 108.00 0.00


    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    180.00
    180.00

    108.00
    108.00
    108.00
    108.00
    108.00
    108.00
    108.00
    0.00
    0.00
    0.00

    0.00 ! C2H6 ethane

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.09
    0.09
    0.09
    -0.27

    ! H11
    H21
    !
    \
    /
    ! H12-C1--C2-H22
    !
    /
    \
    ! H13
    H23

    0.09
    0.09
    0.09
    -0.27
    H12 C1 H13
    H21 C2 H22 C2 H23
    H12 0.00 0.00 120.0
    H13 0.00 0.00 -120.0
    H21 0.00 0.00 180.0
    H22 0.00 0.00 120.0
    H23 0.00 0.00 -120.0

    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0

    RESI PRPA
    0.00 ! C3H8 propane, adm jr.
    GROUP
    !
    ATOM H11 HGA3
    0.09 ! H11 H21
    H31
    ATOM H12 HGA3
    0.09 !
    \
    |
    /
    ATOM H13 HGA3
    0.09 ! H12-C1--C2--C3-H32
    ATOM C1 CG331 -0.27 !
    /
    |
    \
    GROUP
    ! H13 H22
    H33
    ATOM C2 CG321 -0.18 !
    ATOM H21 HGA2
    0.09 !
    ATOM H22 HGA2
    0.09
    GROUP
    ATOM H31 HGA3
    0.09
    ATOM H32 HGA3
    0.09
    ATOM H33 HGA3
    0.09
    ATOM C3 CG331 -0.27
    BOND C1 H11 C1 H12 C1 H13
    BOND C1 C2 C2 H21 C2 H22

    !Phi

    BOND C2
    IC C1
    IC C2
    IC C2
    IC C3
    IC C2
    IC C2
    IC C1
    IC C1

    C3
    C2
    H31
    H31
    C2
    H11
    H11
    C3
    C3

    C3 H31
    C3 H31
    *C3 H32
    *C3 H33
    C1 H11
    *C1 H12
    *C1 H13
    *C2 H21
    *C2 H22

    C3 H32 C3
    0.00 0.00
    0.00 0.00
    0.00 0.00
    0.00 0.00
    0.00 0.00
    0.00 0.00
    0.00 0.00
    0.00 0.00

    H33
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    120.0
    -120.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    RESI BUTA
    0.00 ! C4H10 butane
    GROUP
    ATOM H11 HGA3
    0.09 ! H11 H21 H31
    H41
    ATOM H12 HGA3
    0.09 !
    \
    | |
    /
    ATOM H13 HGA3
    0.09 ! H12-C1--C2--C3--C4-H42
    ATOM C1 CG331 -0.27 !
    /
    | |
    \
    GROUP
    ! H13 H22 H33
    H43
    ATOM H21 HGA2
    0.09
    ATOM H22 HGA2
    0.09
    ATOM C2 CG321 -0.18
    GROUP
    ATOM H31 HGA2
    0.09
    ATOM H32 HGA2
    0.09
    ATOM C3 CG321 -0.18
    GROUP
    ATOM H41 HGA3
    0.09
    ATOM H42 HGA3
    0.09
    ATOM H43 HGA3
    0.09
    ATOM C4 CG331 -0.27
    BOND H11 C1 H12 C1 H13 C1 C1 C2
    BOND H21 C2 H22 C2 C2 C3
    BOND H31 C3 H32 C3 C3 C4
    BOND H41 C4 H42 C4 H43 C4
    IC C1 C2 C3 C4 0.00 0.00 180.0 0.0 0.0
    IC C3 C2 C1 H11 0.00 0.00 180.0 0.0 0.0
    IC C2 H11 *C1 H12 0.00 0.00 120.0 0.0 0.0
    IC C2 H11 *C1 H13 0.00 0.00 -120.0 0.0 0.0
    IC C1 C3 *C2 H21 0.00 0.00 120.0 0.0 0.0
    IC C1 C3 *C2 H22 0.00 0.00 -120.0 0.0 0.0
    IC C2 C4 *C3 H31 0.00 0.00 120.0 0.0 0.0
    IC C2 C4 *C3 H32 0.00 0.00 -120.0 0.0 0.0
    IC C2 C3 C4 H41 0.00 0.00 180.0 0.0 0.0
    IC C3 H41 *C4 H42 0.00 0.00 120.0 0.0 0.0
    IC C3 H41 *C4 H43 0.00 0.00 -120.0 0.0 0.0
    RESI IBUT
    GROUP
    ATOM CT
    ATOM HT
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23
    GROUP

    0.00 ! C4H10 Iso-butane, S. Fischer


    CG311
    HGA1
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    -0.09 !
    0.09 !
    !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !
    !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !

    H12
    |
    H11-C1-H13
    |
    CT-HT
    / \
    / \
    H21-C2
    C3-H31
    / |
    | \
    H22 H23 H33 H32

    ATOM C3 CG331 -0.27


    ATOM H31 HGA3
    0.09
    ATOM H32 HGA3
    0.09
    ATOM H33 HGA3
    0.09
    BOND CT C1 CT C2 CT C3 CT
    BOND C1 H11 C1 H12 C1 H13
    BOND C2 H21 C2 H22 C2 H23
    BOND C3 H31 C3 H32 C3 H33
    IC C1 C2 *CT C3 0.00 0.00
    IC C1 C2 *CT HT 0.00 0.00
    IC C2 CT C1 H11 0.00 0.00
    IC CT H11 *C1 H12 0.00 0.00
    IC CT H11 *C1 H13 0.00 0.00
    IC C1 CT C2 H21 0.00 0.00
    IC CT H21 *C2 H22 0.00 0.00
    IC CT H21 *C2 H23 0.00 0.00
    IC C1 CT C3 H31 0.00 0.00
    IC CT H31 *C3 H32 0.00 0.00
    IC CT H31 *C3 H33 0.00 0.00
    RESI PENT
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C3
    C5
    H11
    C1
    C2
    C3
    H11
    H11
    C1
    C1
    C2
    C2
    C3
    C3

    HT

    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.00 ! C5H12 pentane, adm jr.


    CG331 -0.27 ! H11 H21 H31 H41
    H51
    HGA3
    0.09 !
    \
    | | |
    /
    HGA3
    0.09 ! H12-C1--C2--C3--C4--C5-H52
    HGA3
    0.09 !
    /
    | | |
    \
    ! H13 H22 H33 H42
    H53
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    C2
    H11
    H31
    H52
    C1 C2
    C2 C3
    C3 C4
    C4 C5
    C2 *C1
    C2 *C1
    C3 *C2
    C3 *C2
    C4 *C3
    C4 *C3
    C5 *C4
    C5 *C4

    C2
    C1
    C3
    C5

    C3
    C3
    H12
    C1
    H32
    C4
    H53
    C3 0.0000
    C4 0.0000
    C5 0.0000
    H51 0.0000
    H12 0.0000
    H13 0.0000
    H21 0.0000
    H22 0.0000
    H31 0.0000
    H32 0.0000
    H41 0.0000
    H42 0.0000

    C4
    H13
    H41

    C4
    C2
    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    C5
    H21
    H42

    C2
    C5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H22
    H51
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC C4 H51 *C5 H52 0.0000


    IC C4 H51 *C5 H53 0.0000
    PATC FIRS NONE LAST NONE
    RESI OCOH
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM O1
    ATOM HO1
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C7
    ATOM H71
    ATOM H72
    GROUP
    ATOM C8
    ATOM H81
    ATOM H82
    ATOM H83
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C5
    C1
    C3
    C5
    C8
    H11
    C1
    C2
    C3
    C4
    C5
    C6
    H11
    H11
    C2
    C1
    C1
    C2

    0.00 120.00
    0.00 -120.00

    0.00
    0.00

    0.0000
    0.0000

    0.00 ! C8H18O OCTANOL


    CG321 0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311 -0.65
    HGP1
    0.42
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    C2
    C6
    H11
    H31
    H52
    H81
    C1 C2
    C2 C3
    C3 C4
    C4 C5
    C5 C6
    C6 C7
    C7 C8
    C2 *C1
    C2 *C1
    C1 O1
    C3 *C2
    C3 *C2
    C4 *C3

    C2
    C6
    C1
    C3
    C6
    C8

    C3
    C3
    C7
    C7
    H12
    C2
    H32
    C4
    H61
    C6
    H82
    C8
    C3 0.0000
    C4 0.0000
    C5 0.0000
    C6 0.0000
    C7 0.0000
    C8 0.0000
    H83 0.0000
    H12 0.0000
    O1 0.0000
    HO1 0.0000
    H21 0.0000
    H22 0.0000
    H31 0.0000

    C4
    C8
    H21
    H41
    H62
    H83
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4
    C1
    C2
    C4
    C7
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    120.00

    C5
    O1
    H22
    H42
    H71

    O1

    HO1

    C5
    C7

    H51
    H72

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    C2
    C3
    C3
    C4
    C4
    C5
    C5
    C6
    C6
    C7
    C7
    FIRS

    RESI CO2
    GROUP
    ATOM C
    ATOM OC1
    ATOM OC2
    BOND OC1

    C4 *C3
    C5 *C4
    C5 *C4
    C6 *C5
    C6 *C5
    C7 *C6
    C7 *C6
    C8 *C7
    C8 *C7
    H83 *C8
    H83 *C8
    NONE LAST

    H32
    H41
    H42
    H51
    H52
    H61
    H62
    H71
    H72
    H81
    H82
    NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! CO2 Carbon Dioxide, John Straub


    CG2O7
    0.60
    OG2D5 -0.30
    OG2D5 -0.30
    C OC2 C

    RESI CO3
    -2.00 ! CO3 ionized carbonate, adm jr., aug 2001
    !As organic carbonates and carbamates are uncharged, we definitely want to use
    !other (ester respectively amide?) atom typing for those. This leaves the atom
    !typing for their (-1) counterparts undefined, but these are unstable anyway...
    GROUP
    ATOM C1 CG2O6
    1.42
    ATOM O1 OG2D2 -1.14
    ATOM O2 OG2D2 -1.14
    ATOM O3 OG2D2 -1.14
    BOND C1 O1 C1 O2 C1 O3
    ! required for out-of-plane vibrations
    IMPR C1 O1 O2 O3
    IC O2 O1 *C1 O3
    0.0000
    0.00 180.00
    IC O3 O2 *C1 O1
    0.0000
    0.00 180.00
    nition needed to enable seeding.
    RESI C3
    0.00 !
    GROUP
    ATOM C1 CG3C31 -0.18
    ATOM H11 HGA2
    0.09
    ATOM H12 HGA2
    0.09
    GROUP
    ATOM C2 CG3C31 -0.18
    ATOM H21 HGA2
    0.09
    ATOM H22 HGA2
    0.09
    GROUP
    ATOM C3 CG3C31 -0.18
    ATOM H31 HGA2
    0.09
    ATOM H32 HGA2
    0.09
    BOND C1 C2 C2 C3 C3 C1
    BOND C1 H11 C1 H12
    BOND C2 H21 C2 H22
    BOND C3 H31 C3 H32
    IC
    IC
    IC
    IC
    IC

    C1
    C3
    C3
    C3
    C3

    C2
    C2
    C2
    C1
    C1

    C3
    *C1
    *C1
    *C2
    *C2

    H31
    H11
    H12
    H21
    H22

    0.00
    0.00

    0.0000
    0.0000 !redundant defi

    C3H6 Cyclopropane Model Compound


    ! JMW and CBP 16 April 2004
    !
    !
    H11 H12
    !
    \ /
    !
    C1
    !
    / \
    ! H21--C2----C3--H31
    !
    |
    |
    !
    H22 H32
    !
    !
    !

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    120.00
    -120.00
    -120.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC C2
    IC C2

    C1 *C3 H31
    C1 *C3 H32

    0.0000
    0.0000

    0.00 120.00
    0.00 -120.00

    0.00
    0.00

    0.0000
    0.0000

    PATCHING FIRST NONE LAST NONE


    !toppar_all22_prot_aldehydes.str
    !acetaldehyde additions, ssc & adm, jr., 2/01
    RESI AALD
    0.00 ! C2H4O Acetaldehyde, adm, Oct 2008
    GROUP
    !
    ATOM HA HGR52
    0.09 ! HB3
    ATOM C CG2O4
    0.20 !
    |
    ATOM O OG2D1
    -0.40 !HB1-CB-HB2
    ATOM CB CG331
    -0.16 !
    |
    ATOM HB1 HGA3
    0.09 ! O=C
    ATOM HB2 HGA3
    0.09 !
    |
    ATOM HB3 HGA3
    0.09 !
    HA
    BOND HA C C CB CB HB1 CB HB2 CB HB3
    DOUB C O
    IMPH C CB O HA
    ACCE O
    IC O C CB HB1
    1.2074 123.73 -0.46 108.58
    IC HB2 CB C
    O
    1.0625 110.65 118.23 123.73
    IC HB3 CB C
    O
    1.0898 105.98 -126.83 123.73
    IC HA O *C CB
    1.1347 126.86 -176.51 123.73
    PATCHING FIRST NONE LAST NONE
    RESI PALD
    0.00 ! C3H6O Propionaldehyde
    GROUP
    !
    ATOM O OG2D1
    -0.40 ! HG3
    ATOM C CG2O4
    0.20 !
    |
    ATOM CB CG321
    -0.07 !HG1-CG-HG2
    ATOM HB1 HGA2
    0.09 !
    |
    ATOM HB2 HGA2
    0.09 !HB1-CB-HB2
    ATOM HA HGR52
    0.09 !
    |
    GROUP
    ! O=C
    ATOM CG CG331
    -0.27 !
    |
    ATOM HG1 HGA3
    0.09 !
    HA
    ATOM HG2 HGA3
    0.09 !
    ATOM HG3 HGA3
    0.09
    BOND HA C C CB CB HB1 CB HB2
    BOND CB CG CG HG1 CG HG3 CG HG2
    DOUBLE C O
    IMPR C CB O HA
    ACCE O
    IC O C CB CG
    0.0
    0.0
    0.0
    0.0
    IC CG CB C HA
    0.0
    0.0 180.0
    0.0
    IC HB1 CB C O
    0.0
    0.0 120.0
    0.0
    IC HB2 CB C O
    0.0
    0.0 -120.0
    0.0
    IC C CB CG HG1
    0.0
    0.0 180.0
    0.0
    IC C CB CG HG2
    0.0
    0.0
    60.0
    0.0
    IC C CB CG HG3
    0.0
    0.0 -60.0
    0.0
    PATCHING FIRST NONE LAST NONE
    RESI CALD
    0.00
    !KEVO: charges adjusted
    !==> RE-OPTIMIZE!!!
    GROUP
    ATOM O OG2D1
    -0.40
    ATOM C CG2O4
    0.20

    1.1053
    1.2074
    1.2074
    1.5462

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    ! C2H3ClO Chloroacetaldehyde
    to reflect updated aldehyde AND aliphatic chlorine L-J.
    !
    CL
    !
    |
    !HB1-CB-HB2

    ATOM CB CG321
    -0.03 !
    |
    ATOM HB1 HGA2
    0.09 ! O=C
    ATOM HB2 HGA2
    0.09 !
    |
    ATOM CL CLGA1
    -0.04 !
    HA
    ATOM HA HGR52
    0.09
    BOND HA C C CB CB HB1 CB HB2
    BOND CB CL
    DOUBLE C O
    IMPR C CB O HA
    ACCE O
    IC O C CB CL
    0.0
    0.0
    IC CL CB C HA
    0.0
    0.0
    IC HA O *C CB
    0.0
    0.0
    IC CL C *CB HB1
    0.0
    0.0
    IC HB1 C *CB HB2
    0.0
    0.0
    PATCHING FIRST NONE LAST NONE

    180.0
    0.0
    0.0
    120.0
    120.0

    0.0
    0.0
    0.0
    0.0
    0.0

    !benzaldehyde additions, ssc & adm, jr., 2/01


    RESI BALD
    0.00 ! C7H6O Benzaldehyde
    GROUP
    !
    ATOM HA HGR52
    0.08 !
    HZ
    ATOM C CG2O4
    0.24 !
    |
    ATOM O OG2D1
    -0.41 !
    CZ
    ATOM CG CG2R61
    0.09 !
    // \
    GROUP
    !HE1-CE1 CE2-HE2
    ATOM CD1 CG2R61 -0.115 !
    |
    ||
    ATOM HD1 HGR61
    0.115 !HD1-CD1 CD2-HD2
    GROUP
    !
    \\ /
    ATOM CE1 CG2R61 -0.115 !
    CG
    ATOM HE1 HGR61
    0.115 !
    |
    GROUP
    !
    O=C
    ATOM CZ CG2R61 -0.115 !
    |
    ATOM HZ HGR61
    0.115 !
    HA
    GROUP
    ATOM CD2 CG2R61 -0.115
    ATOM HD2 HGR61
    0.115
    GROUP
    ATOM CE2 CG2R61 -0.115
    ATOM HE2 HGR61
    0.115
    BOND HA C C CG CG CD1 CG CD2
    BOND CD1 HD1 CD2 HD2 CD1 CE1 CD2 CE2
    BOND CE1 HE1 CE2 HE2 CE1 CZ CE2 CZ
    BOND CZ HZ
    DOUBLE C O
    IMPR C CG O HA
    ACCE O
    IC O
    C
    CG CD1 0.0
    0.0
    0.0
    IC HA O
    *C CG
    0.0
    0.0
    180.0
    IC CD1 C
    *CG CD2 0.0
    0.0
    -177.9600
    IC C
    CG CD1 CE1 0.0
    0.0
    -177.3700
    IC CE1 CG *CD1 HD1 0.0
    0.0
    179.7000
    IC C
    CG CD2 CE2 0.0
    0.0
    177.2000
    IC CE2 CG *CD2 HD2 0.0
    0.0
    -178.6900
    IC CG CD1 CE1 CZ
    0.0
    0.0
    -0.1200
    IC CZ CD1 *CE1 HE1 0.0
    0.0
    -179.6900
    IC CZ CD2 *CE2 HE2 0.0
    0.0
    -179.9300
    IC CE1 CE2 *CZ HZ
    0.0
    0.0
    179.5100
    PATCHING FIRST NONE LAST NONE
    !toppar_all22_prot_fluoro_alkanes.str

    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    RESI FETH
    0.00 ! C2H5F fluoroethane, adm jr., 4/99
    GROUP
    ATOM H13 HGA3
    0.09
    ATOM C1 CG331 -0.21
    ATOM C2 CG322 -0.06
    ATOM F21 FGA1
    -0.22
    ATOM H22 HGA6
    0.11
    ATOM H23 HGA6
    0.11
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    BOND C1 H11 C1 H12 C1 H13
    BOND C1 C2
    BOND C2 F21 C2 H22 C2 H23
    IC H13 C1 C2 F21 1.1111 110.55 180.00 109.78 1.3721
    IC H13 C1 C2 H22 1.1111 110.55 60.02 111.56 1.0839
    IC H13 C1 C2 H23 1.1111 110.55 -60.02 111.56 1.0839
    IC C1 C2 H22 H23 1.5188 111.56 -122.50 36.33 1.7464
    IC H13 C2 *C1 H11 1.1111 110.55 -120.29 110.55 1.1111
    IC H13 C2 *C1 H12 1.1111 110.55 120.29 110.55 1.1111
    PATC FIRS NONE LAST NONE
    RESI DFET
    0.00 ! C2H4F2 difluoroethane, adm jr., 4/99
    GROUP
    ATOM H13 HGA3
    0.09
    ATOM C1 CG331 -0.23
    ATOM C2 CG312
    0.24
    ATOM H21 HGA7
    0.10
    ATOM F22 FGA2
    -0.19
    ATOM F23 FGA2
    -0.19
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    BOND C1 H11 C1 H12 C1 H13
    BOND C1 C2
    BOND C2 F23 C2 F22 C2 H21
    IC H13 C1 C2 H21 0.00 0.00 180.0 0.0 0.0
    IC C1 C2 F23 F22 0.00 0.00
    0.0 0.0 0.0
    IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0
    IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0
    IC H12 C1 C2 H21 0.00 0.00 -60.0 0.0 0.0
    IC H11 C1 C2 H21 0.00 0.00 60.0 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI TFET
    0.00 ! C2H3F3 trifluoroethane
    GROUP
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    ATOM C1 CG331 -0.20
    ATOM F21 FGA3
    -0.15
    ATOM F22 FGA3
    -0.15
    ATOM F23 FGA3
    -0.15
    ATOM C2 CG302
    0.38
    BOND C1 H11 C1 H12 C1 H13
    BOND C1 C2 C2 F21 C2 F22 C2 F23
    IC H13 C1 C2 F21 0.00 0.00 180.0 0.0 0.0
    IC C1 C2 F22 F23 0.00 0.00
    0.0 0.0 0.0
    IC H13 C1 C2 F22 0.00 0.00 60.0 0.0 0.0
    IC H13 C1 C2 F23 0.00 0.00 -60.0 0.0 0.0
    IC H11 C1 C2 F21 0.00 0.00 60.0 0.0 0.0
    IC H12 C1 C2 F21 0.00 0.00 -60.0 0.0 0.0

    PATC FIRS NONE LAST NONE


    RESI TFE
    0.00 ! C2H3F3O trifluoroethanol
    GROUP
    !
    ATOM O1 OG311 -0.59
    ATOM HO1 HGP1
    0.41
    ATOM H11 HGA2
    0.09
    ATOM H12 HGA2
    0.09
    ATOM C1 CG321
    0.08
    ATOM F21 FGA3
    -0.14
    ATOM F22 FGA3
    -0.14
    ATOM F23 FGA3
    -0.14
    ATOM C2 CG302
    0.34
    BOND C1 H11 C1 H12 C1 O1 O1 HO1
    BOND C1 C2 C2 F21 C2 F22 C2 F23
    IC HO1 O1 C1 C2
    0.0000
    0.00 180.00
    0.00
    IC C2
    O1 *C1 H11
    0.0000
    0.00 120.00
    0.00
    IC H11 O1 *C1 H12
    0.0000
    0.00 -120.00
    0.00
    IC O1
    C1 C2 F21
    0.0000
    0.00 180.00
    0.00
    IC F21 C1 *C2 F22
    0.0000
    0.00 120.00
    0.00
    IC F21 C1 *C2 F23
    0.0000
    0.00 -120.00
    0.00
    PATC FIRS NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !toppar_all22_prot_pyridines.str
    RESI PYR1
    0.00 ! C5H5N pyridine
    GROUP
    ATOM N1 NG2R60 -0.600
    ATOM C2 CG2R61 0.180
    ATOM C3 CG2R61 -0.115
    ATOM C4 CG2R61 -0.115
    ATOM C5 CG2R61 -0.115
    ATOM C6 CG2R61 0.180
    ATOM H2 HGR62
    0.120
    ATOM H3 HGR61
    0.115
    ATOM H4 HGR61
    0.115
    ATOM H5 HGR61
    0.115
    ATOM H6 HGR62
    0.120
    BOND N1 C2
    BOND C2 H2
    IC N1 C2
    IC C2 C3
    IC C6 N1
    IC C3 N1
    IC C4 C2
    IC C5 C3
    IC C6 C4
    IC C5 N1
    PATCH FIRST
    RESI 4AP2
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CE2
    ATOM CD2
    ATOM NG

    C2 C3
    C3 H3
    C3
    C4
    C2
    *C2
    *C3
    *C4
    *C5
    *C6
    NONE

    C3 C4 C4 C5 C5 C6 C6 N1
    C4 H4 C5 H5 C6 H6

    C4
    0.0000
    C5
    0.0000
    C3
    0.0000
    H2
    0.0000
    H3
    0.0000
    H4
    0.0000
    H5
    0.0000
    H6
    0.0000
    LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00 ! C5H6N2 4-aminopyridine


    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    NG2S3

    -0.600
    0.180
    -0.115
    0.050
    0.180
    -0.115
    -0.850

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HE1
    HD1
    HD2
    HE2
    HG11
    HG12

    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CD1
    CE2
    CG

    HGR62
    HGR61
    HGR61
    HGR62
    HGP4
    HGP4
    CG
    CD2
    HD1
    HE2
    NG

    0.120
    0.115
    0.115
    0.120
    0.400
    0.400

    CD2 CG CE1 CD1


    NZ CE1 NZ CE2
    CD2 HD2 CE1 HE1
    NG HG11 NG HG12

    IMPR NG CG HG11 HG12


    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC CD1 CG
    IC HG11 CG
    IC NZ CE1
    IC CE2 NZ
    PATCH FIRST

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG NG
    0.0000
    *CD1 HD1 0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    NG HG11 0.0000
    *NG HG12 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    120.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 3APY

    0.00 ! C5H6N2 3-aminopyridine


    !
    GROUP
    ! HD11 HD12
    ATOM CG CG2R61 -0.115 !
    \ /
    ATOM HG HGR61
    0.115 !
    ND1
    HE1
    GROUP
    !
    \
    |
    ATOM CD1 CG2R61 0.090 !
    CD1--CE1
    ATOM ND1 NG2S3 -0.840 !
    /
    \
    ATOM HD11 HGP4
    0.370 ! HG--CG
    NZ
    ATOM HD12 HGP4
    0.380 !
    \
    /
    GROUP
    !
    CD2--CE2
    ATOM CD2 CG2R61 -0.115 !
    |
    |
    ATOM HD2 HGR61
    0.115 !
    HD2 HE2
    GROUP
    ATOM CE1 CG2R61 0.180
    ATOM HE1 HGR62
    0.120
    ATOM CE2 CG2R61 0.180
    ATOM HE2 HGR62
    0.120
    ATOM NZ NG2R60 -0.600
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE2
    CD1

    CG
    CD2
    HG
    HE2
    ND1

    CD2 CG CE1 CD1


    NZ CE1 NZ CE2
    CD2 HD2 CE1 HE1
    ND1 HD11 ND1 HD12

    !delete this line IMPR HD11 CD1 HD12 ND1


    IMPR ND1 CD1 HD11 HD12
    IC CG CD1 CE1 NZ
    IC CD1 CE1 NZ CE2

    0.0000 0.0000
    0.0000 0.0000

    0.0000 0.0000 0.0000


    0.0000 0.0000 0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CE1
    HD11
    NZ
    CE2

    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CD1
    CD1
    CE1
    NZ

    RESI 34AP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CE2
    ATOM CD2
    ATOM ND1
    ATOM NG
    ATOM HE1
    ATOM HD2
    ATOM HE2
    ATOM HD11
    ATOM HD12
    ATOM HG11
    ATOM HG12
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    ND1
    *ND1
    CD1
    CE1

    CD1
    CE2
    CD2
    CE2
    CD1
    CG

    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    NG2S3
    NG2S3
    HGR62
    HGR61
    HGR62
    HGP4
    HGP4
    HGP4
    HGP4
    CG
    CD2
    HD2
    HE2
    ND1
    NG

    CD2
    HG
    ND1
    HD2
    HE1
    HE2
    HD11
    HD12
    CG
    CD1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    180.0000
    0.0000
    0.0000

    CD2 CG CE1 CD1


    NZ CE1 NZ CE2
    CE1 HE1
    ND1 HD11 ND1 HD12
    NG HG11 NG HG12
    line
    line
    HD11
    HG11

    IMPR HD11 CD1 HD12 ND1


    IMPR HG11 CG HG12 NG
    HD12
    HG12

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    NG
    *NG
    ND1
    *ND1
    CD1
    CE1

    NZ
    CE2
    CD2
    NG
    ND1
    HD2
    HE1
    HE2
    HG11
    HG12
    HD11
    HD12
    CG
    CD1

    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CG
    CG
    CD1
    CD1
    CE1
    NZ

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H7N3 3,4-diaminopyridine, adm jr.


    !
    -0.600
    0.180
    0.120
    0.070
    0.180
    -0.115
    -0.850
    -0.850
    0.120
    0.115
    0.120
    0.350
    0.380
    0.390
    0.390

    !delete this
    !delete this
    IMPR ND1 CD1
    IMPR NG CG
    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CD1
    HG11
    CE1
    HD11
    NZ
    CE2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    120.0000
    0.0000
    120.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI 3CPY
    GROUP

    -1.00 ! C6H4NO2 pyridine-3-carboxylate (niacinate)

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    NZ
    CE1
    CD1
    CG
    CE2
    CD2
    HE1
    HG
    HD2
    HE2
    CD3
    O1
    O2

    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB
    IMPR

    CD1
    CE2
    CG
    CE2
    CD1
    CD3
    CD3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG2O3
    OG2D2
    OG2D2

    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CD1
    CD1
    CE1
    NZ

    RESI 3CB
    GROUP
    ATOM CZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CE2
    ATOM CD2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM HZ
    ATOM CD3
    ATOM O1
    ATOM O2

    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    CD3
    *CD3
    CD1
    CE1

    NZ
    CE2
    CD2
    HG
    CD3
    HD2
    HE1
    HE2
    O1
    O2
    CG
    CD1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    180.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -1.00 ! C7H5O2 benzoate


    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    HGR61
    HGR61
    HGR61
    HGR61
    CG2O3
    OG2D2
    OG2D2

    CD1
    CE2
    CG
    CD2
    CE2
    CD3

    IC CG

    !
    O1
    HG
    !
    \
    |
    ! (-) ) CD3 CG
    !
    / \ / \\
    !
    O2
    CD1 CD2--HD2
    !
    ||
    |
    !
    HE1--CE1 CE2--HE2
    !
    \ //
    !
    NZ

    CG CD2 CG CE1 CD1


    CD2 NZ CE1 NZ CE2
    HG CD2 HD2 CE1 HE1
    HE2
    CD3 CD3 O1
    O2
    CD1 O1 O2

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CE1
    O1
    NZ
    CE2

    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB

    -0.600
    0.180
    -0.10
    -0.155
    0.180
    -0.115
    0.120
    0.155
    0.115
    0.120
    0.62
    -0.76
    -0.76

    CG
    CD2
    HG
    HD2
    HE2
    O2

    CD2
    CZ
    CD1
    CE1
    CZ

    -0.115
    -0.115
    -0.100
    -0.115
    -0.115
    -0.115
    0.115
    0.115
    0.115
    0.115
    0.115
    0.620
    -0.760
    -0.760

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CG CE1 CD1
    CE1 CZ CE2
    CD3 CD3 O1
    HE1
    HZ

    CD1 CE1 CZ

    0.0000 0.0000

    0.0000 0.0000 0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CE1
    O1
    NZ
    CE2

    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CD1
    CD1
    CE1
    NZ

    RESI 3FLP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CE2
    ATOM CD2
    ATOM HE1
    ATOM F1
    ATOM HG
    ATOM HD2
    ATOM HE2
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE2

    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    CD3
    *CD3
    CD1
    CE1

    CE2
    CD2
    HG
    CD3
    HD2
    HE1
    HE2
    HZ
    O1
    O2
    CG
    CD1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    180.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H4FN 3-fluoropyridine


    NG2R60
    CG2R61
    CG2R66
    CG2R61
    CG2R61
    CG2R61
    HGR62
    FGR1
    HGR62
    HGR61
    HGR62

    -0.600
    0.220
    0.175
    -0.115
    0.180
    -0.115
    0.120
    -0.215 !charge similar to difluorotoluene
    0.115
    0.115
    0.120

    CG CD2 CG CE1 CD1


    CD2 NZ CE1 NZ CE2
    HG CD1 F1 CD2 HD2 CE1 HE1
    HE2

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    PATCH FIRST

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 F1
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    NONE LAST NONE

    RESI 3ALP
    cotinaldehyde
    GROUP
    ATOM NZ NG2R60
    ATOM CE1 CG2R61
    ATOM CD1 CG2R61
    ATOM CG CG2R61
    ATOM CD2 CG2R61
    ATOM CE2 CG2R61
    ATOM HE1 HGR62
    ATOM HG HGR61
    ATOM HD2 HGR61
    ATOM HE2 HGR62
    ATOM CD3 CG2O4
    ATOM O1 OG2D1
    ATOM H3 HGR52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H5NO 3-pyridinecarboxaldehyde, 3-formylpyridine, ni


    -0.600
    0.180
    0.09
    -0.115
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    0.24
    -0.41
    0.08

    ! H3
    HG
    ! \
    |
    !
    CD3 CG
    ! // \ / \\
    ! O1 CD1 CD2--HD2
    !
    ||
    |
    ! HE1--CE1 CE2--HE2
    !
    \ //
    !
    NZ
    !benzaldehyde
    !benzaldehyde
    !benzaldehyde

    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB

    CD1
    CE2
    CG
    CE2
    CD1
    CD3

    CG
    CD2
    HG
    HE2
    CD3
    O1

    CD2 CG CE1 CD1


    NZ CE1 NZ CE2
    CD2 HD2 CE1 HE1
    CD3 H3

    IMPR CD3 CD1 O1 H3


    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CE1
    O1
    NZ
    CE2

    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CD1
    CD1
    CE1
    NZ

    RESI 3HOP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM CD1
    ATOM OH
    ATOM HO1
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1

    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    CD3
    *CD3
    CD1
    CE1

    NZ
    CE2
    CD2
    HG
    CD3
    HD2
    HE1
    HE2
    O1
    H3
    CG
    CD1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    180.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C5H5NO 3-hydroxypyridine


    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG2R61
    OG311
    HGP1
    CG
    CD2
    HG
    HE1

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC HO1 OH
    PATCH FIRST

    CD2
    NZ
    CD1
    CE2

    -0.600
    0.180
    -0.115
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    0.11 !phenol
    -0.53 !phenol
    0.42 !phenol
    CG
    CE1
    OH
    HE2

    CE1
    NZ
    CD2
    OH

    CD1
    CE2
    HD2
    HO1

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 OH
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD2 CE1 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    0.0000

    RESI 3MEP
    0.00 ! C6H7N 3-methylpyridine
    GROUP
    ATOM NZ NG2R60 -0.600
    ATOM CE1 CG2R61 0.180

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CD1
    CG
    CD2
    CE2
    HE1
    HG
    HD2
    HE2
    CD3
    H31
    H32
    H33

    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1
    CD3

    CG2R61 0.000 !
    H32 H33
    CG2R61 -0.115 !
    \ /
    CG2R61 -0.115 ! H31--CD3
    HE1
    CG2R61 0.180 !
    \
    |
    HGR62
    0.120 !
    CD1--CE1
    HGR61
    0.115 !
    /
    \
    HGR61
    0.115 !
    HG--CG
    NZ
    HGR62
    0.120 !
    \
    /
    CG331 -0.27 !
    CD2--CE2
    HGA3
    0.09 !
    |
    |
    HGA3
    0.09 !
    HD2 HE2
    HGA3
    0.09
    CG
    CD2
    HG
    HE1
    H31

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC CE1 CD1
    IC CE1 CD1
    IC CE1 CD1
    PATCH FIRST

    CD2
    NZ
    CD1
    CE2
    CD3

    RESI 3ETP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM CD3
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1
    CD3
    H21

    CG
    CE1
    CD3
    HE2
    H32

    CE1 CD1
    NZ CE2
    CD2 HD2
    CD3 H33

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 CD3 0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD3 H31 0.0000
    CD3 H32 0.0000
    CD3 H33 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    60.0000
    180.0000
    300.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C7H9N ethylpyridine


    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3
    CG
    CD2
    HG
    HE1
    H11
    C2

    CD2
    NZ
    CD1
    CE2
    CD3
    H22

    -0.600
    0.180
    0.000
    -0.115
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    CG
    CE1
    CD3
    HE2
    H12
    C2

    !aliphatic, corresponds to new CT2, HA2


    !
    !
    !aliphatic, corresponds to new CT3, HA3
    !
    !
    !

    CE1 CD1
    NZ CE2
    CD2 HD2
    CD3 C2
    H23 C2

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC CE1 CG
    IC CE1 CD1
    IC CD1 C2
    IC CD1 C2
    IC CD1 CD3
    IC CD3 H21
    IC CD3 H21
    PATCH FIRST
    RESI 3BPY
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CE2
    ATOM CD2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM CD3
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CE2
    CG
    CD1
    CD3
    C2
    C3
    C4

    CG
    CD1
    CE1
    CD1
    CE2
    NZ
    NZ
    NZ

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    *CD1 CD3 0.0000
    CD3 C2
    0.0000
    *CD3 H11 0.0000
    *CD3 H12 0.0000
    C2 H21 0.0000
    *C2 H22 0.0000
    *C2 H23 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    90.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C9H13N butylpyridine


    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3
    CG
    CD2
    HG
    CD3
    C2
    H21
    H31
    H41

    CD1
    CE1
    NZ
    CD2
    CG
    CD1
    CD2
    CE1

    -0.600
    0.180
    0.000
    -0.115
    0.180
    -0.115
    0.120
    0.115
    0.115
    0.120
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    CD2
    NZ
    CD2
    CD3
    C2
    C2
    C3
    C4

    CG
    CE1
    HD2
    H11
    C3
    H22
    H32
    H42

    CE1
    NZ
    CE2
    *CG
    *CD2
    *CE1
    *CE2
    CD1

    NZ
    CE2
    CD2
    HG
    HD2
    HE1
    HE2
    CG

    CE1
    NZ
    CE1
    CD3
    C3

    CD1
    CE2
    HE1 CE2 HE2
    H12
    C4

    C4 H43
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000

    IC CE2 NZ
    IC CE1 CG
    IC CE1 CD1
    IC CD1 C2
    IC CD1 C2
    IC CD1 CD3
    IC CD3 C3
    IC CD3 C3
    IC CD3 C2
    IC C2 C4
    IC C2 C4
    IC C2 C3
    IC C3 H41
    IC C3 H41
    PATCH FIRST

    CE1 CD1 0.0000


    *CD1 CD3 0.0000
    CD3 C2
    0.0000
    *CD3 H11 0.0000
    *CD3 H12 0.0000
    C2 C3
    0.0000
    *C2 H21 0.0000
    *C2 H22 0.0000
    C3 C4
    0.0000
    *C3 H31 0.0000
    *C3 H32 0.0000
    C4 H41 0.0000
    *C4 H42 0.0000
    *C4 H43 0.0000
    NONE LAST NONE

    RESI 3CYP
    0.00
    GROUP
    ATOM NZ NG2R60 -0.600
    ATOM CE1 CG2R61 0.180
    ATOM CD1 CG2R61 0.100
    ATOM CG CG2R61 -0.115
    ATOM CD2 CG2R61 -0.115
    ATOM CE2 CG2R61 0.180
    ATOM HE1 HGR62
    0.120
    ATOM HG HGR61
    0.115
    ATOM HD2 HGR61
    0.115
    ATOM HE2 HGR62
    0.120
    ATOM C3N CG1N1
    0.360
    ATOM N3C NG1T1 -0.460
    ! Original charges after

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    180.0000
    90.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! C6H4N2 3-Cyanopyridine
    !
    N3C
    !
    \\\
    !
    C3N
    HE1
    !
    \
    |
    !
    CD1--CE1
    !
    /
    \
    !
    HG--CG
    NZ
    !
    \
    /
    !
    CD2--CE2
    !
    |
    |
    !
    HD2 HE2
    bringing HE1 and HE2 in line with the other pyridines.

    !ATOM NZ NG2R60 -0.600


    !ATOM CE1 CG2R61 0.180 !
    N3C
    !ATOM CD1 CG2R61 0.080 !
    \\\
    !ATOM CG CG2R61 -0.120 !
    C3N
    HE1
    !ATOM CD2 CG2R61 -0.115 !
    \
    |
    !ATOM CE2 CG2R61 0.180 !
    CD1--CE1
    !ATOM HE1 HGR62
    0.120 !
    /
    \
    !ATOM HG HGR61
    0.140 !
    HG--CG
    NZ
    !ATOM HD2 HGR61
    0.115 !
    \
    /
    !ATOM HE2 HGR62
    0.120 !
    CD2--CE2
    !ATOM C3N CG1N1
    0.360 !
    |
    |
    !ATOM N3C NG1T1 -0.460 !
    HD2 HE2
    !! Partially optimized charges with
    !! - Dipoles and H2O interactions substantially better
    !! - DHvap slightly worse (but not really significant)
    !! - Not transferable
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC

    CD1
    CE2
    CG
    CE1
    CD1
    C3N

    CG
    CD1
    CE1
    CD1

    CG
    CD2
    HG
    HE1
    C3N
    N3C
    CD1
    CE1
    NZ
    CD2

    CD2
    NZ
    CD2
    CE2

    CE1
    NZ
    CE2
    *CG

    CG CE1 CD1
    CE1 NZ CE2
    HD2
    HE2

    NZ
    CE2
    CD2
    HG

    0.0000
    0.0000
    0.0000
    0.0000

    0.0000 0.000
    0.0000 0.0000
    0.0000 0.0000
    0.0000 180.0000

    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000

    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC CE1 CG
    IC NZ CE1
    IC CE2 NZ
    IC N3C C3N
    PATCH FIRST

    *CD2 HD2 0.0000


    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    *CD1 C3N 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD1 CE1 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 3ACP
    0.00 ! C7H7NO 3-acetylpyridine
    !KEVO: charges adjusted to reflect updated acetone L-J.
    !Resulting charge on CD1 is unlikely ==> re-optimize?
    GROUP
    ATOM NZ NG2R60 -0.600 ! HC2
    HC3
    ATOM CE1 CG2R61 0.180 !
    \ /
    ATOM CD1 CG2R61 0.040 ! HC1--CH3
    HG
    ATOM CG CG2R61 -0.115 !
    \
    |
    ATOM CD2 CG2R61 -0.115 !
    C
    CG
    ATOM CE2 CG2R61 0.180 !
    //\ / \\
    ATOM HE1 HGR62
    0.120 !
    O CD1 CD2--HD2
    ATOM HG HGR61
    0.115 !
    ||
    |
    ATOM HD2 HGR61
    0.115 !
    HE1--CE1 CE2--HE2
    ATOM HE2 HGR62
    0.120 !
    \ //
    ATOM C
    CG2O5
    0.400 !
    NZ
    ATOM O
    OG2D3 -0.480
    ATOM CH3 CG331 -0.230 !aliphatic, corresponds to new CT3, HA3
    ATOM HC1 HGA3
    0.090 !
    ATOM HC2 HGA3
    0.090 !
    ATOM HC3 HGA3
    0.090 !
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB

    CD1
    CE2
    CG
    CE1
    CD1
    HC1
    C

    IMPR C

    CG
    CD2
    HG
    HE1
    C
    CH3
    O

    CG CE1 CD1
    CE1 NZ CE2
    HD2
    HE2
    CH3
    CH3 HC3 CH3

    CD1 CH3 O

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC CH3 C
    IC CH3 CD1
    IC O
    C
    IC O
    C
    IC O
    C
    PATCH FIRST
    RESI 3NAP
    e,
    GROUP

    CD2
    NZ
    CD2
    CE2
    C
    HC2

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 C
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD1 CE1 0.0000
    *C O
    0.0000
    CH3 HC1 0.0000
    CH3 HC2 0.0000
    CH3 HC3 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    60.0000
    -60.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H6N2O Really just unprotonated oxidized nicotinamid


    ! aka. "nicotinamide". Other correct names include:

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    NZ
    CE1
    CD1
    CG
    CD2
    CE2
    HE1
    HG
    HD2
    HE2
    C
    O
    N
    HC
    HT

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB

    CD1
    CE2
    CG
    CE1
    CD1
    HC
    C

    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    IMPR C

    CG
    CD2
    HG
    HE1
    C
    N
    O

    CD1 N

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC N
    C
    IC N
    CD1
    IC HC N
    IC HT N
    PATCH FIRST
    RESI 3CAP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    GROUP
    ATOM CD3
    ATOM H11
    ATOM H12
    ATOM OH
    ATOM HO

    CD2
    NZ
    CD2
    CE2
    C
    HT

    -0.600
    0.180
    -0.020
    -0.115
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    0.630
    -0.460
    -0.900
    0.390
    0.360

    ! 3-pyridinecarboxamide, 3-amidopyridine,
    ! 3-(aminocarbonyl)pyridine.
    !
    HT
    !
    /
    ! Hc--N
    HG
    !
    \
    |
    !
    C
    CG
    !
    //\ / \\
    !
    O CD1 CD2--HD2
    !
    ||
    |
    !
    HE1--CE1 CE2--HE2
    !
    \ //
    !
    NZ

    CG CE1 CD1
    CE1 NZ CE2
    HD2
    HE2
    N
    N
    O

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 C
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD1 CE1 0.0000
    *C O
    0.0000
    C
    O
    0.0000
    C
    O
    0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    0.0000
    180.0000
    0.0000
    180.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H7NO carbinol-pyridine, by daxu


    NG2R60 -0.600
    CG2R61 0.180
    CG2R61 0.000
    CG2R61 -0.115
    CG2R61 -0.115
    CG2R61 0.180
    HGR62
    0.120
    HGR61
    0.115
    HGR61
    0.115
    HGR62
    0.120
    CG321
    HGA2
    HGA2
    OG311
    HGP1

    0.05 !aliphatic, corresponds to new CT2, HA2


    0.09
    0.09
    -0.65
    0.42

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CE2
    CG
    CE1
    CD1
    CD3

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    NZ
    CE2
    NZ
    CE1
    CD1
    OH
    OH

    CG
    CD2
    HG
    HE1
    CD3
    H11
    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CE1
    NZ
    CE1
    CD1
    CD3
    CD1
    CD1

    CD2
    NZ
    CD2
    CE2
    CD3
    CD3
    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    CD1
    CE1
    CD1
    CD3
    OH
    *CD3
    *CD3

    CG CE1 CD1
    CE1 NZ CE2
    HD2
    HE2
    OH OH HO
    H12
    NZ
    CE2
    CD2
    HG
    C
    HD2
    HE1
    HE2
    CG
    CD1
    CD3
    OH
    HO
    H11
    H12

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    120.0000
    -120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI 3PHP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM CA1
    ATOM CA2
    ATOM CA3
    ATOM CA4
    ATOM CA5
    ATOM CA6
    ATOM HA2
    ATOM HA3
    ATOM HA4
    ATOM HA5
    ATOM HA6
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1
    CD1
    CA3
    CA6
    CA2
    CA5

    0.00 ! C11H9N 3-phenyl-pyridine


    NG2R60
    CG2R61
    CG2R67
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG2R67
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    HGR61
    HGR61
    HGR61
    HGR61
    CG
    CD2
    HG
    HE1
    CA1
    CA4
    CA1
    HA2
    HA5

    CD2
    NZ
    CD2
    CE2
    CA1
    CA4

    -0.600
    0.180
    0.000
    -0.115
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    0.000
    -0.115
    -0.115
    -0.115
    -0.115
    -0.115
    0.115
    0.115
    0.115
    0.115
    0.115
    CG
    CE1
    HD2
    HE2
    CA2
    CA5

    CE1 CD1
    NZ CE2
    CA2 CA3
    CA6 CA5

    CA3 HA3 CA4 HA4


    CA6 HA6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC CA2 CA1
    IC CA3 CA2
    IC CA4 CA3
    IC CA5 CA4
    IC CA6 CA5
    IC CA1 CA3
    IC CA2 CA4
    IC CA3 CA5
    IC CA4 CA6
    IC CA5 CA1
    PATCH FIRST
    RESI 3BNP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HG
    ATOM HD2
    ATOM HE2
    ATOM C
    ATOM HC1
    ATOM HC2
    ATOM CA1
    ATOM CA2
    ATOM CA3
    ATOM CA4
    ATOM CA5
    ATOM CA6
    ATOM HA2
    ATOM HA3
    ATOM HA4
    ATOM HA5
    ATOM HA6
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1
    CD1
    C
    CA1
    CA3
    CA6
    CA2
    CA5

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 CA1 0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    CD1 CG
    0.0000
    CA1 CD1 0.0000
    CA2 CA1 0.0000
    CA3 CA2 0.0000
    CA4 CA3 0.0000
    *CA2 HA2 0.0000
    *CA3 HA3 0.0000
    *CA4 HA4 0.0000
    *CA5 HA5 0.0000
    *CA6 HA6 0.0000
    NONE LAST NONE

    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG321
    HGA2
    HGA2
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    HGR61
    HGR61
    HGR61
    HGR61
    CG
    CD2
    HG
    HE1
    C
    HC1
    CA2
    CA4
    CA1
    HA2
    HA5

    CD2
    NZ
    CD2
    CE2
    C
    C
    CA2
    CA4

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    0.0000
    180.0000
    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C12H11N 3-benzyl-pyridine


    !methylene between rings
    -0.600 !1
    0.180 !2
    0.000 !3
    -0.115 !4
    -0.115 !5
    0.180 !6
    0.120 !7
    0.115 !8
    0.115 !9
    0.120 !10
    -0.180 !11
    0.090 !12
    0.090 !13
    0.000 !14
    -0.115 !15
    -0.115 !16
    -0.115 !17
    -0.115 !18
    -0.115 !19
    0.115 !20
    0.115 !21
    0.115 !22
    0.115 !23
    0.115 !24
    CG CE1 CD1
    CE1 NZ CE2
    HD2
    HE2
    CA1
    HC2
    CA3
    CA5 CA6 CA5

    CA3 HA3 CA4 HA4


    CA6 HA6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC CG CD1
    IC CD1 CE1
    IC CE1 NZ
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC NZ CD1
    IC NZ CD2
    IC NZ CE1
    IC CE2 NZ
    IC CE1 CD1
    IC CD1 C
    IC CA1 CD1
    IC CA1 CD1
    IC C
    CA1
    IC CA1 CA2
    IC CA2 CA3
    IC CA3 CA4
    IC CA1 CA3
    IC CA2 CA4
    IC CA3 CA5
    IC CA4 CA6
    IC CA5 CA1
    PATCH FIRST

    CE1 NZ
    0.0000
    NZ CE2 0.0000
    CE2 CD2 0.0000
    *CG HG
    0.0000
    *CD1 C
    0.0000
    *CD2 HD2 0.0000
    *CE1 HE1 0.0000
    *CE2 HE2 0.0000
    CD1 CG
    0.0000
    CE1 CD1 0.0000
    C
    CA1 0.0000
    CA1 CA2 0.0000
    *C HC1 0.0000
    *C HC2 0.0000
    CA2 CA3 0.0000
    CA3 CA4 0.0000
    CA4 CA5 0.0000
    CA5 CA6 0.0000
    *CA2 HA2 0.0000
    *CA3 HA3 0.0000
    *CA4 HA4 0.0000
    *CA5 HA5 0.0000
    *CA6 HA6 0.0000
    NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000
    0.0000
    0.0000
    90.0000
    90.0000
    120.0000
    -120.0000
    180.0000
    0.0000
    0.0000
    0.0000
    180.0000
    180.0000
    180.0000
    180.0000
    180.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !toppar_all27_lipid_cholesterol.str
    RESI CHL1
    0.00 ! C27H46O cholesterol (name to avoid conflict with chol
    ine)
    ! atoms names correspond to the correct cholesterol nomenclature
    GROUP
    ATOM C3 CG311
    0.14
    ATOM O3 OG311 -0.65
    ATOM H3' HGP1
    0.42
    ATOM H3 HGA1
    0.09
    GROUP
    ATOM C4 CG321 -0.18
    ATOM H4A HGA2
    0.09
    ATOM H4B HGA2
    0.09
    GROUP
    ATOM C5 CG2D1
    0.00
    ATOM C6 CG2D1 -0.15
    ATOM H6 HGA4
    0.15
    GROUP
    ATOM C7 CG321 -0.18
    ATOM H7A HGA2
    0.09
    ATOM H7B HGA2
    0.09
    GROUP
    ATOM C8 CG311 -0.09
    ATOM H8 HGA1
    0.09
    GROUP
    ATOM C14 CG311 -0.09
    ATOM H14 HGA1
    0.09
    GROUP
    ATOM C15 CG321 -0.18
    ATOM H15A HGA2
    0.09
    ATOM H15B HGA2
    0.09
    GROUP
    ATOM C16 CG321 -0.18
    ATOM H16A HGA2
    0.09

    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM C24
    ATOM H24A
    ATOM H24B
    GROUP
    ATOM C25
    ATOM H25

    HGA2

    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG311

    0.00

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG311

    0.00

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18 !beyond this nomenclature may not be correct


    0.09
    0.09

    CG311
    HGA1

    -0.09 !c25
    0.09

    GROUP
    ATOM C26
    ATOM H26A
    ATOM H26B
    ATOM H26C
    GROUP
    ATOM C27
    ATOM H27A
    ATOM H27B
    ATOM H27C

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !terminal methyl, c26


    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !terminal methyl, c27


    0.09
    0.09
    0.09

    BOND C3 O3 C3 H3 O3 H3'
    BOND C3 C2 C2 H2A C2 H2B
    BOND C2 C1 C1 H1A C1 H1B
    BOND C3 C4 C4 H4A C4 H4B
    BOND C4 C5
    BOND C5 C10
    BOND C10 C1
    BOND C10 C19 C19 H19A C19 H19B C19 H19C
    DOUBLE C5 C6
    BOND C6 H6
    BOND C6 C7 C7 H7A C7 H7B
    BOND C7 C8 C8 H8
    BOND C8 C9 C9 H9
    BOND C9 C10
    BOND C8 C14 C14 H14
    BOND C14 C13
    BOND C13 C12 C12 H12A C12 H12B
    BOND C12 C11 C11 H11A C11 H11B
    BOND C11 C9
    BOND C13 C18 C18 H18A C18 H18B C18 H18C
    BOND C14 C15 C15 H15A C15 H15B
    BOND C15 C16 C16 H16A C16 H16B
    BOND C16 C17 C17 H17
    BOND C17 C13
    BOND C17 C20 C20 H20
    BOND C20 C21 C21 H21A C21 H21B C21 H21C
    BOND C20 C22 C22 H22A C22 H22B
    BOND C22 C23 C23 H23A C23 H23B
    BOND C23 C24 C24 H24A C24 H24B
    BOND C24 C25 C25 H25
    BOND C25 C26 C26 H26A C26 H26B C26 H26C
    BOND C25 C27 C27 H27A C27 H27B C27 H27C
    !ICs based on CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5383 110.44 55.92
    IC C4 C2 *C3 O3
    1.5367 110.66 120.28
    IC O3 C2 *C3 H3
    1.4158 109.14 118.92
    IC C2 C3 O3 H3' 1.5311 109.14 -58.51
    IC C2 C3 C4 C5
    1.5311 110.66 -55.96
    IC C5 C3 *C4 H4A 1.5156 111.70 121.99
    IC H4A C3 *C4 H4B 1.1099 109.16 115.03
    IC C3 C4 C5 C10 1.5367 111.70 54.04
    IC C10 C4 *C5 C6
    1.5304 115.09 -177.32
    IC C4 C5 C6 C7
    1.5156 121.28 -178.39
    IC C7 C5 *C6 H6
    1.5018 123.88 177.19
    IC C5 C6 C7 C8
    1.3432 123.88 14.50
    IC C8 C6 *C7 H7A 1.5506 112.36 122.18
    IC H7A C6 *C7 H7B 1.1114 110.84 118.17
    IC C6 C7 C8 C14 1.5018 112.36 -165.89
    IC C14 C7 *C8 C9
    1.5202 110.02 121.07

    110.66
    109.14
    109.40
    105.39
    111.70
    109.16
    107.34
    115.09
    121.28
    123.88
    119.54
    112.36
    110.84
    109.17
    110.02
    110.84

    1.5367
    1.4158
    1.1155
    0.9593
    1.5156
    1.1099
    1.1142
    1.5304
    1.3432
    1.5018
    1.1001
    1.5506
    1.1114
    1.1124
    1.5202
    1.5327

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C9
    C7
    C13
    C13
    C8
    C16
    H15A
    C14
    C17
    H16A
    C13
    C13
    C17
    C12
    C14
    H18A
    H18A
    C14
    C11
    H12A
    C9
    H11A
    C10
    C9
    C19
    C5
    H19A
    H19A
    C2
    C2
    C1
    H2A
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    C23
    H22A
    C20
    C24
    H23A
    C22
    C25
    H24A
    C23
    C26
    C26
    C24
    H26A
    H26A
    C24
    H27A
    H27A

    C7
    C8
    C8
    C8
    C14
    C14
    C14
    C15
    C15
    C15
    C16
    C16
    C14
    C14
    C13
    C13
    C13
    C13
    C13
    C13
    C12
    C12
    C8
    C5
    C5
    C10
    C10
    C10
    C10
    C10
    C3
    C3
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23
    C23
    C24
    C24
    C24
    C25
    C25
    C25
    C25
    C25
    C25

    *C8
    C14
    *C14
    *C14
    C15
    *C15
    *C15
    C16
    *C16
    *C16
    *C17
    *C17
    *C13
    *C13
    C18
    *C18
    *C18
    C12
    *C12
    *C12
    *C11
    *C11
    *C9
    *C10
    *C10
    C19
    *C19
    *C19
    *C1
    *C1
    *C2
    *C2
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    C24
    *C24
    *C24
    C25
    *C25
    *C25
    C26
    *C26
    *C26
    C27
    *C27
    *C27

    H8
    C13
    C15
    H14
    C16
    H15A
    H15B
    C17
    H16A
    H16B
    C20
    H17
    C12
    C18
    H18A
    H18B
    H18C
    C11
    H12A
    H12B
    H11A
    H11B
    H9
    C19
    C1
    H19A
    H19B
    H19C
    H1A
    H1B
    H2A
    H2B
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    C24
    H23A
    H23B
    C25
    H24A
    H24B
    C26
    C27
    H25
    H26A
    H26B
    H26C
    H27A
    H27B
    H27C

    1.5327
    1.5506
    1.5247
    1.5247
    1.5202
    1.5360
    1.1113
    1.5382
    1.5620
    1.1107
    1.5401
    1.5401
    1.5401
    1.5408
    1.5247
    1.1077
    1.1077
    1.5247
    1.5422
    1.1067
    1.5593
    1.1093
    1.5531
    1.5531
    1.5524
    1.5304
    1.1082
    1.1082
    1.5383
    1.5383
    1.5383
    1.1119
    1.5620
    1.5476
    1.5349
    1.5633
    1.1077
    1.1077
    1.5633
    1.5394
    1.1116
    1.5476
    1.5377
    1.1108
    1.5394
    1.5418
    1.1132
    1.5377
    1.5378
    1.5378
    1.5418
    1.1105
    1.1105
    1.5418
    1.1105
    1.1105

    110.84
    110.02
    115.21
    115.21
    117.86
    103.40
    109.62
    103.40
    106.79
    109.25
    104.94
    104.94
    100.27
    106.98
    110.83
    111.48
    111.48
    106.98
    111.10
    111.21
    113.54
    107.06
    112.73
    111.91
    108.03
    108.03
    110.67
    110.67
    114.55
    114.55
    110.44
    109.41
    112.36
    110.55
    113.32
    113.32
    110.93
    110.93
    110.55
    115.12
    109.35
    115.12
    112.25
    109.69
    112.25
    114.06
    108.44
    114.06
    111.24
    111.24
    111.24
    110.52
    110.52
    112.86
    110.40
    110.40

    119.34
    179.73
    126.69
    -116.05
    -163.10
    117.45
    121.32
    7.85
    118.96
    120.76
    132.02
    -111.76
    122.68
    122.91
    60.33
    119.80
    -121.00
    56.78
    121.37
    118.82
    121.67
    115.98
    -114.54
    -120.04
    -119.87
    -172.88
    118.48
    -120.66
    122.42
    -120.71
    121.16
    118.30
    55.21
    125.88
    118.87
    64.90
    -121.00
    118.40
    -174.59
    120.23
    117.13
    172.50
    121.13
    118.14
    -176.23
    120.56
    117.11
    174.26
    119.63
    -119.50
    -178.53
    120.00
    -120.09
    -178.28
    119.95
    -119.82

    108.18
    115.21
    117.86
    105.83
    103.40
    109.62
    111.94
    106.79
    109.25
    111.65
    112.36
    106.42
    106.98
    110.83
    111.48
    110.01
    111.71
    111.10
    111.21
    108.68
    107.06
    108.75
    104.68
    108.03
    109.26
    110.67
    111.77
    110.97
    109.26
    108.29
    109.41
    109.70
    110.55
    113.32
    107.27
    110.93
    110.41
    111.29
    115.12
    109.35
    108.75
    112.25
    109.69
    108.99
    114.06
    108.44
    109.39
    111.24
    112.86
    108.47
    110.52
    110.36
    110.33
    110.40
    110.31
    110.77

    1.1123
    1.5247
    1.5382
    1.1205
    1.5360
    1.1113
    1.1082
    1.5620
    1.1107
    1.1090
    1.5633
    1.1153
    1.5408
    1.5518
    1.1077
    1.1086
    1.1067
    1.5422
    1.1067
    1.1119
    1.1093
    1.1100
    1.1185
    1.5524
    1.5579
    1.1082
    1.1080
    1.1095
    1.1104
    1.1134
    1.1119
    1.1112
    1.5476
    1.5349
    1.1157
    1.1077
    1.1104
    1.1085
    1.5394
    1.1116
    1.1121
    1.5377
    1.1108
    1.1129
    1.5418
    1.1132
    1.1121
    1.5378
    1.5381
    1.1151
    1.1105
    1.1105
    1.1106
    1.1105
    1.1105
    1.1097

    RESI CHNS
    0.00 ! C20H32O cholesterol with sidechain beyond c18(c20) omi
    tted
    ! atoms names after the comments correspond to the

    ! correct
    GROUP
    ATOM C1
    ATOM O1
    ATOM HO1
    ATOM H1

    cholesterol nomenclature
    CG311
    OG311
    HGP1
    HGA1

    0.14 !c3
    -0.65
    0.42
    0.09

    ATOM C2 CG321
    ATOM H2 HGA2
    ATOM H2' HGA2

    -0.18 !c4
    0.09
    0.09

    ATOM C3
    ATOM C4
    ATOM H4

    CG2D1
    CG2D1
    HGA4

    0.00 !c5
    -0.15 !c6
    0.15

    ATOM C5 CG321
    ATOM H5 HGA2
    ATOM H5' HGA2

    -0.18 !c7
    0.09
    0.09

    ATOM C6
    ATOM H6
    GROUP
    ATOM C7
    ATOM H7

    CG311
    HGA1

    -0.09 !c8
    0.09

    CG311
    HGA1

    -0.09 !c14
    0.09

    ATOM C8 CG321
    ATOM H8 HGA2
    ATOM H8' HGA2

    -0.18 !c15
    0.09
    0.09

    ATOM C9 CG321
    ATOM H9 HGA2
    ATOM H9' HGA2

    -0.18 !c16
    0.09
    0.09

    ATOM C10 CG311


    ATOM H10 HGA1

    -0.09 !c17
    0.09

    ATOM C11
    GROUP
    ATOM CC11
    ATOM H111
    ATOM H112
    ATOM H113

    CG311
    CG331
    HGA3
    HGA3
    HGA3

    0.00 !c13
    -0.27 !c18, methyl at c13
    0.09
    0.09
    0.09

    ATOM C12 CG321


    ATOM H12 HGA2
    ATOM H12' HGA2

    -0.18 !c12
    0.09
    0.09

    ATOM C13 CG321


    ATOM H13 HGA2
    ATOM H13' HGA2

    -0.18 !c11
    0.09
    0.09

    ATOM C14 CG311


    ATOM H14 HGA1

    -0.09 !c9
    0.09

    ATOM C15
    GROUP
    ATOM CC15
    ATOM H151
    ATOM H152
    ATOM H153

    CG311
    CG331
    HGA3
    HGA3
    HGA3

    0.00 !c10
    -0.27 !c19, methyl at c10
    0.09
    0.09
    0.09

    ATOM C16 CG321


    ATOM H16 HGA2
    ATOM H16' HGA2

    -0.18 !c1
    0.09
    0.09

    ATOM C17 CG321


    ATOM H17 HGA2
    ATOM H17' HGA2

    -0.18 !c2
    0.09
    0.09

    ATOM
    ATOM
    ATOM
    ATOM

    -0.27 !c20
    0.09
    0.09
    0.09

    C18
    H181
    H182
    H183

    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 O1 C1 H1 C1 C2
    BOND O1 HO1
    BOND C2 C3 C2 H2 C2 H2'
    DOUBLE C3 C4
    BOND C4 C5 C4 H4
    BOND C5 C6 C5 H5 C5 H5'
    BOND C6 C7 C6 H6
    BOND C7 C8 C7 H7
    BOND C8 C9 C8 H8 C8 H8'
    BOND C9 C10 C9 H9 C9 H9'
    BOND C10 C18 C10 C11 C10 H10
    BOND C11 CC11 C11 C7 C11 C12
    BOND CC11 H111 CC11 H112 CC11 H113
    BOND C12 C13 C12 H12 C12 H12'
    BOND C13 C14 C13 H13 C13 H13'
    BOND C14 C15 C14 C6 C14 H14
    BOND C15 C16 C15 C3 C15 CC15
    BOND CC15 H151 CC15 H152 CC15 H153
    BOND C16 C17 C16 H16 C16 H16'
    BOND C17 C1 C17 H17 C17 H17'
    BOND C18 H181 C18 H182 C18 H183
    !DONO HO1 O1
    !ACCE O1
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O1
    C1
    C2
    C3
    C4
    C5
    C6
    C7
    C8
    C9
    C7
    C10
    C10
    C11
    CC11
    CC11
    C12
    C13
    C13
    C13
    CC15

    C1
    C2
    C3
    C4
    C5
    C6
    C7
    C8
    C9
    C10
    C12
    C11
    C11
    C12
    C11
    C11
    C13
    C14
    C14
    C14
    C15

    C2
    C3
    C4
    C5
    C6
    C7
    C8
    C9
    C10
    C11
    *C11
    C12
    C7
    C13
    C12
    C7
    C14
    C15
    C15
    C6
    C16

    C3
    C4
    C5
    C6
    C7
    C8
    C9
    C10
    C11
    C12
    CC11
    C13
    C8
    C14
    C13
    C8
    C15
    CC15
    C16
    C7
    C17

    1.4158
    1.5368
    1.5153
    1.3430
    1.5019
    1.5504
    1.5192
    1.5447
    1.5418
    1.5530
    1.5194
    1.5300
    1.5300
    1.5351
    1.5530
    1.5530
    1.5414
    1.5626
    1.5626
    1.5626
    1.5522

    109.24
    111.80
    121.41
    123.84
    112.44
    109.90
    118.74
    103.72
    105.45
    105.85
    108.58
    116.00
    99.46
    110.42
    111.88
    111.12
    113.50
    114.52
    114.52
    113.16
    110.15

    -176.17
    -123.48
    -178.76
    14.64
    -166.16
    -54.73
    -161.90
    5.69
    21.50
    -155.90
    -123.00
    167.75
    43.93
    -52.28
    -66.16
    -70.96
    179.43
    -50.80
    69.29
    -48.42
    -68.75

    111.80
    121.41
    123.84
    112.44
    109.90
    118.74
    103.72
    105.45
    105.85
    116.00
    111.88
    110.42
    105.86
    113.50
    110.42
    105.86
    114.52
    109.07
    108.64
    109.31
    114.54

    1.5153
    1.3430
    1.5019
    1.5504
    1.5192
    1.5447
    1.5418
    1.5530
    1.5300
    1.5351
    1.5530
    1.5414
    1.5447
    1.5626
    1.5414
    1.5447
    1.5524
    1.5522
    1.5574
    1.5192
    1.5383

    IC C14 C15
    IC C14 C15
    IC C15 C16
    IC C11 C9
    IC O1 C2
    IC C2 C1
    IC C3 C1
    IC C3 C1
    IC C5 C3
    IC C6 C4
    IC C6 C4
    IC C7 C5
    IC C8 C6
    IC C9 C7
    IC C9 C7
    IC C10 C8
    IC C10 C8
    IC C18 C9
    IC C7 C11
    IC H111 C11
    IC H111 C11
    IC C13 C11
    IC C13 C11
    IC C14 C12
    IC C14 C12
    IC C13 C6
    IC C3 C15
    IC H151 C15
    IC H151 C15
    IC C17 C15
    IC C17 C15
    IC C16 C1
    IC C16 C1
    !use hbuild

    C16 C17
    1.5524
    C3 C4
    1.5524
    C17 C1
    1.5574
    *C10 C18
    1.5300
    *C1 H1
    1.4158
    O1 HO1
    1.5368
    *C2 H2
    1.5153
    *C2 H2'
    1.5153
    *C4 H4
    1.5019
    *C5 H5
    1.5504
    *C5 H5'
    1.5504
    *C6 H6
    1.5192
    *C7 H7
    1.5447
    *C8 H8
    1.5418
    *C8 H8'
    1.5418
    *C9 H9
    1.5530
    *C9 H9'
    1.5530
    *C10 H10
    1.5413
    CC11 H111 1.5194
    *CC1 H112 1.1092
    *CC1 H113 1.1092
    *C12 H12
    1.5414
    *C12 H12' 1.5414
    *C13 H13
    1.5626
    *C13 H13' 1.5626
    *C14 H14
    1.5626
    CC15 H151 1.5435
    *CC1 H152 1.1082
    *CC1 H153 1.1082
    *C16 H16
    1.5383
    *C16 H16' 1.5383
    *C17 H17
    1.5383
    *C17 H17' 1.5383
    for c18 hydrogens

    RESI CHM1

    108.64
    111.86
    114.54
    105.85
    109.24
    109.24
    111.80
    111.80
    123.84
    112.44
    112.44
    109.90
    118.74
    103.72
    103.72
    105.45
    105.45
    114.22
    111.12
    110.01
    110.01
    110.42
    110.42
    113.50
    113.50
    113.16
    107.81
    110.68
    110.68
    114.54
    114.54
    110.51
    110.51

    171.83
    7.71
    -54.68
    126.88
    -119.02
    62.69
    121.88
    -123.05
    177.13
    122.17
    -119.69
    -119.58
    117.73
    117.51
    -121.25
    118.45
    -120.18
    119.69
    -178.60
    118.82
    -120.26
    122.09
    -119.49
    121.59
    -122.38
    113.80
    -172.81
    118.52
    -120.68
    122.43
    -120.70
    121.12
    -120.62

    114.54
    123.46
    110.51
    114.22
    109.53
    105.39
    109.11
    107.36
    119.55
    110.88
    109.16
    108.19
    105.77
    109.61
    111.67
    109.64
    112.16
    107.07
    110.01
    111.63
    111.66
    109.96
    108.88
    107.14
    108.79
    104.59
    110.68
    111.71
    110.98
    109.27
    108.26
    109.37
    109.70

    1.5383
    1.3430
    1.5312
    1.5413
    1.1156
    0.9593
    1.1100
    1.1142
    1.1001
    1.1114
    1.1124
    1.1122
    1.1205
    1.1108
    1.1078
    1.1105
    1.1085
    1.1162
    1.1092
    1.1068
    1.1075
    1.1102
    1.1120
    1.1091
    1.1098
    1.1184
    1.1082
    1.1081
    1.1094
    1.1104
    1.1134
    1.1120
    1.1111

    0.00 ! C11H18O cholesterol analog with only rings 1 and 2


    !and the position 19 methyl
    ! atoms names after the comments correspond to the
    ! correct cholesterol nomenclature
    !
    ! ring 1
    !
    GROUP
    ATOM C1 CG311
    0.14 !c3
    ATOM O1 OG311 -0.65
    ATOM HO1 HGP1
    0.42
    ATOM H1 HGA1
    0.09
    ATOM C2 CG321
    ATOM H2 HGA2
    ATOM H2' HGA2
    ATOM C3 CG2D1
    ATOM C15 CG311

    -0.18 !c4
    0.09
    0.09
    0.00 !c5
    0.00 !c10

    ATOM C16 CG321


    ATOM H16 HGA2
    ATOM H16' HGA2

    -0.18 !c1
    0.09
    0.09

    ATOM C17 CG321

    -0.18 !c2

    ATOM H17 HGA2


    ATOM H17' HGA2
    ATOM CC15
    ATOM H151
    ATOM H152
    ATOM H153
    ! ring 2
    GROUP
    ATOM C4
    ATOM H4

    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !c19, methyl at c10


    0.09
    0.09
    0.09

    CG2D1
    HGA4

    -0.15 !c6
    0.15

    ATOM C5 CG321
    ATOM H5 HGA2
    ATOM H5' HGA2

    -0.18 !c7
    0.09
    0.09

    ATOM C6 CG321
    ATOM H6 HGA2
    ATOM H6' HGA2

    -0.18 !c8
    0.09
    0.09

    ATOM C14 CG321


    ATOM H14 HGA2
    ATOM H14' HGA2

    -0.18 !c9
    0.09
    0.09

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C2
    C15
    C16
    C17
    C3
    C4
    C4
    C5
    C6
    C14

    C1
    C2
    C17
    C2
    C2
    C17
    C3
    C3
    C1
    C2
    C3
    C4
    C14
    C17
    C17
    C16
    C16
    C3
    H151
    H151
    C5
    C6
    C6

    C2
    O1
    H2
    CC15
    H16
    H17
    C4
    C5
    H4
    H5
    H6
    H14
    C2
    C3
    C1
    C17
    C17
    C1
    C1
    C1
    C2
    C3
    C4
    C5
    C3
    C15
    C15
    C1
    C1
    C15
    C15
    C15
    C3
    C4
    C4

    C2
    O1
    C2
    CC15
    C16
    C17

    C3 C3 C15 C15 C16 C16 C17 C17 C1


    HO1 C1 H1
    H2'
    H151 CC15 H152 CC15 H153
    H16'
    H17'

    C5

    C6

    C6 C14 C14 C15

    C5 H5'
    C6 H6'
    C14 H14'
    C3
    C15
    C2
    *C1
    *C1
    O1
    *C2
    *C2
    C3
    C4
    C5
    C6
    *C15
    *C16
    *C16
    *C17
    *C17
    CC15
    *CC15
    *CC15
    *C4
    *C5
    *C5

    C15
    C16
    C3
    O1
    H1
    HO1
    H2
    H2'
    C4
    C5
    C6
    C14
    CC15
    H16
    H16'
    H17
    H17'
    H151
    H152
    H153
    H4
    H5
    H5'

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 180.00
    0.00 15.00
    0.00 -45.00
    0.00 -120.00
    0.00 120.00
    0.00 -120.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC

    C14
    C14
    C6
    C6

    C5
    C5
    C15
    C15

    *C6
    *C6
    *C14
    *C14

    H6
    H6'
    H14
    H14'

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    !toppar_all27_lipid_model.str
    RESI MAS
    0.00 ! C3H6O2 methylacetate
    GROUP
    !
    ATOM C1 CG331
    -0.31 !
    H22
    ATOM C
    CG2O2
    0.90 !
    |
    ATOM OM OG302
    -0.49 !
    H21-C2-H23
    ATOM C2 CG331
    -0.01 !
    \
    ATOM O
    OG2D1
    -0.63 !
    OM
    ATOM H11 HGA3
    0.09 !
    /
    ATOM H12 HGA3
    0.09 !
    O=C
    ATOM H13 HGA3
    0.09 !
    |
    ATOM H21 HGA3
    0.09 !
    H11-C1-H13
    ATOM H22 HGA3
    0.09 !
    |
    ATOM H23 HGA3
    0.09 !
    H12
    BOND C1 C
    C
    DOUBLE C
    O
    BOND C1 H11
    C1
    BOND C2 H21
    C2
    IMPR C OM C1 O
    ! internal coordinates
    IC C1 C
    OM C2
    IC O
    C
    OM C2
    IC H11 C1 C
    OM
    IC H12 C1 C
    OM
    IC H13 C1 C
    OM
    IC H21 C2 OM C
    IC H22 C2 OM C
    IC H23 C2 OM C

    OM

    OM

    C2

    H12
    H22

    C1
    C2

    H13
    H23

    from experiment for


    1.520
    109.0
    1.200
    125.9
    1.1
    108.9
    1.1
    109.75
    1.1
    109.75
    1.0788
    109.94
    1.0802
    110.50
    1.0802
    110.50

    heavy atoms
    180.0
    114.8
    0.0
    114.8
    180.0
    109.0
    60.4
    109.0
    -60.4
    109.0
    180.0
    114.8
    60.5
    114.8
    -60.5
    114.8

    RESI ETAC
    0.00 ! C4H8O2 Ethylacetate
    !
    !
    H213
    GROUP
    !
    |
    ATOM C1 CG331
    -0.31 !
    H211-C21-H212
    ATOM C
    CG2O2
    0.90 !
    /
    ATOM OM OG302
    -0.49 !
    H22-C2-H23
    ATOM C2 CG321
    0.08 !
    \
    ATOM O
    OG2D1
    -0.63 !
    OM
    ATOM H11 HGA3
    0.09 !
    /
    ATOM H12 HGA3
    0.09 !
    O=C
    ATOM H13 HGA3
    0.09 !
    \
    ATOM H22 HGA2
    0.09 !
    H11-C1-H13
    ATOM H23 HGA2
    0.09 !
    |
    GROUP
    !
    H12
    ATOM C21 CG331
    -0.27
    ATOM H211 HGA3
    0.09
    ATOM H212 HGA3
    0.09
    ATOM H213 HGA3
    0.09
    BOND C1 C
    C
    OM
    OM
    C2
    BOND C1 H11
    C1 H12
    C1 H13
    BOND C2 C21
    C2 H22
    C2 H23
    BOND C21 H211
    C21 H212
    C21 H213
    DOUBLE C
    O
    IMPR C OM C1 O
    ! internal coordinates from experiment for heavy atoms

    1.437
    1.437
    1.334
    1.334
    1.334
    1.334
    1.334
    1.334

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    O
    H11
    H12
    H13
    C21
    H22
    H23
    H211
    H212
    H213

    C
    C
    C1
    C1
    C1
    C2
    C2
    C2
    C21
    C21
    C21

    114.8
    114.8
    109.0
    109.0
    109.0
    114.8
    114.8
    114.8
    116.7
    116.7
    116.7

    1.437
    1.437
    1.334
    1.334
    1.334
    1.334
    1.334
    1.334
    1.437
    1.437
    1.437

    RESI MPRO
    0.00 ! C4H8O2 Methylpropionate
    GROUP
    !
    ATOM C1 CG321
    -0.22 !
    H22
    ATOM C
    CG2O2
    0.90 !
    |
    ATOM OM OG302
    -0.49 !
    H21-C2-H23
    ATOM C2 CG331
    -0.01 !
    \
    ATOM O
    OG2D1
    -0.63 !
    OM
    ATOM H12 HGA2
    0.09 !
    /
    ATOM H13 HGA2
    0.09 !
    O=C
    ATOM H21 HGA3
    0.09 !
    \
    ATOM H22 HGA3
    0.09 !
    H12-C1-H13
    ATOM H23 HGA3
    0.09 !
    /
    GROUP
    !
    H112-C11-H111
    ATOM C11 CG331
    -0.27 !
    |
    ATOM H111 HGA3
    0.09 !
    H113
    ATOM H112 HGA3
    0.09 !
    ATOM H113 HGA3
    0.09 !
    BOND C1 C
    C
    OM
    C
    O
    OM
    C2
    BOND C1 C11
    C1 H12
    C1 H13
    BOND C11 H111
    C11 H112
    C11 H113
    BOND C2 H21
    C2 H22
    C2 H23
    IMPR C OM C1 O
    ! internal coordinates from experiment for heavy atoms
    IC C1 C
    OM C2 1.520
    109.0
    180.0
    114.8
    IC O
    C
    OM C2 1.200
    125.9
    0.0
    114.8
    IC C11 C1 C
    OM 1.520
    108.9
    180.0
    109.0
    IC H12 C1 C
    OM 1.1
    109.75
    60.4
    109.0
    IC H13 C1 C
    OM 1.1
    109.75
    -60.4
    109.0
    IC H21 C2 OM C
    1.0788
    109.94
    180.0
    114.8
    IC H22 C2 OM C
    1.0802
    110.50
    60.5
    114.8
    IC H23 C2 OM C
    1.0802
    110.50
    -60.5
    114.8
    IC H111 C11 C1 C
    1.1
    109.75
    180.0
    109.0
    IC H112 C11 C1 C
    1.1
    109.75
    60.4
    109.0
    IC H113 C11 C1 C
    1.1
    109.75
    -60.4
    109.0

    1.437
    1.437
    1.334
    1.334
    1.334
    1.334
    1.334
    1.334
    1.520
    1.520
    1.520

    RESI MSO4
    GROUP
    ATOM S
    ATOM OS1
    ATOM OS2
    ATOM OS3
    ATOM OS4
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13

    OM
    OM
    C
    C
    C
    OM
    OM
    OM
    C2
    C2
    C2

    SG3O1
    OG303
    OG2P1
    OG2P1
    OG2P1
    CG331
    HGA3
    HGA3
    HGA3

    C2
    C2
    OM
    OM
    OM
    C
    C
    C
    OM
    OM
    OM

    1.520
    1.200
    1.1
    1.1
    1.1
    1.520
    1.0802
    1.0802
    1.1
    1.1
    1.1

    109.0
    125.9
    108.9
    109.75
    109.75
    109.94
    110.50
    110.50
    108.90
    108.90
    108.90

    180.0
    0.0
    180.0
    60.4
    -60.4
    180.0
    60.5
    -60.5
    180.0
    60.0
    -60.0

    -1.00 ! CH3O4S Methylsulfate


    !
    1.33 !
    OS2(-1)
    -0.28 !
    |
    -0.65 ! (-1) OS2--S(+2)--OS4 (-1)
    -0.65 !
    |
    -0.65 !
    OS1
    -0.37 !
    \
    0.09 !
    H11-C1-H13
    0.09 !
    |
    0.09 !
    H12

    BOND S OS1 S OS2 S OS3 S OS4 OS1 C1

    BOND
    ACCE
    ACCE
    ACCE
    ACCE
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OS4
    OS2
    OS3
    OS1
    C1
    S
    OS1
    OS1
    OS1
    OS4
    OS4
    OS3
    OS4
    OS2
    OS3

    C1 H11 C1 H12 C1 H13


    OS1
    OS2
    OS3
    OS4
    S
    S
    S
    S
    OS1
    OS1
    S
    S
    S
    S
    S
    S
    S
    S
    S

    OS2
    OS2
    OS1
    OS3
    S
    C1
    OS4
    OS2
    OS3
    OS2
    OS3
    OS2
    OS1
    OS1
    OS1

    OS1
    OS3
    OS4
    OS2
    OS2
    OS3
    OS2
    OS3
    OS2
    OS1
    OS1
    OS1
    C1
    C1
    C1

    RESI HEXA
    0.00
    GROUP
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    ATOM C1 CG331
    -0.27
    GROUP
    ATOM H21 HGA2
    0.09
    ATOM H22 HGA2
    0.09
    ATOM C2 CG321
    -0.18
    GROUP
    ATOM H31 HGA2
    0.09
    ATOM H32 HGA2
    0.09
    ATOM C3 CG321
    -0.18
    GROUP
    ATOM H41 HGA2
    0.09
    ATOM H42 HGA2
    0.09
    ATOM C4 CG321
    -0.18
    GROUP
    ATOM H51 HGA2
    0.09
    ATOM H52 HGA2
    0.09
    ATOM C5 CG321
    -0.18
    GROUP
    ATOM H61 HGA3
    0.09
    ATOM H62 HGA3
    0.09
    ATOM H63 HGA3
    0.09
    ATOM C6 CG331
    -0.27
    BOND H11 C1 H12 C1 H13
    BOND H21 C2 H22 C2 C2
    BOND H31 C3 H32 C3 C3
    BOND H41 C4 H42 C4 C4
    BOND H51 C5 H52 C5 C5
    BOND H61 C6 H62 C6 C6
    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 C6 0.00
    IC C3 C2 C1 H11 0.00
    IC H11 C2 *C1 H12 0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    60.0000
    -60.0000
    60.0000
    60.0000
    60.0000
    60.0000
    180.0000
    180.0000
    180.0000
    60.0000
    60.0000
    60.0000
    60.0000
    60.0000
    60.0000

    ! C6H14 hexane
    !
    H2
    !
    |
    ! H1-C1-H3
    !
    |
    !
    |
    ! H4-C2-H5
    !
    |
    !
    |
    !
    |
    ! H6-C3-H7
    !
    |
    !
    |
    !
    |
    ! H8-C4-H10
    !
    |
    !
    |
    !
    |
    ! H51-C5-H152
    !
    |
    !
    |
    !
    |
    ! H61-C4-H62
    !
    |
    !
    H63
    !
    C1 C1 C2
    C3
    C4
    C5
    C6
    H63
    0.00 180.0
    0.00 180.0
    0.00 180.0
    0.00 180.0
    0.00 120.0

    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H11
    C1
    C1
    C2
    C2
    C3
    C3
    C4
    C4
    C4
    H61
    H61

    C2
    C3
    C3
    C4
    C4
    C5
    C5
    C6
    C6
    C5
    C5
    C5

    *C1
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    C6
    *C6
    *C6

    H13
    H21
    H22
    H31
    H32
    H41
    H42
    H51
    H52
    H61
    H62
    H63

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI ETHE
    0.00 !
    GROUP
    ATOM C1 CG2D2 -0.42 !
    ATOM H11 HGA5
    0.21 !
    ATOM H12 HGA5
    0.21 !
    GROUP
    !
    ATOM C2 CG2D2 -0.42 !
    ATOM H21 HGA5
    0.21 !
    ATOM H22 HGA5
    0.21 !
    BOND C1 H11 C1 H12
    DOUBLE C1 C2
    BOND C2 H21 C2 H22
    IMPR C1 C2 H12 H11
    IMPR C1 C2 H11 H12
    IMPR C2 C1 H22 H21
    IMPR C2 C1 H21 H22
    IC H11 C1 C2 H21 1.1036
    IC H12 C2 *C1 H11 1.1036
    IC H22 C1 *C2 H21 1.1036
    IC C1 C2 H21 H22 1.3370
    PATC FIRS NONE LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    240.0
    120.0
    240.0
    120.0
    240.0
    120.0
    240.0
    120.0
    240.0
    180.0
    120.0
    240.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C2H4 ethylene, yin/adm jr.


    H11
    \

    H21
    /
    C1=C2

    /
    H12

    121.37
    121.37
    121.37
    121.37

    \
    H22

    180.00 121.37
    180.00 121.37
    180.00 121.37
    -180.00 31.37

    RESI PRPE
    0.00 ! C3H6 propene, yin/adm jr.
    GROUP
    ATOM C1 CG2D2 -0.42 !
    ATOM H11 HGA5
    0.21 ! H11
    H21
    ATOM H12 HGA5
    0.21 ! \
    /
    GROUP
    !
    C1=C2 H31
    ATOM C2 CG2D1 -0.15 ! /
    \ /
    ATOM H21 HGA4
    0.15 ! H12
    C3
    GROUP
    !
    / \
    ATOM C3 CG331 -0.27 !
    H33 H32
    ATOM H31 HGA3
    0.09 !
    ATOM H32 HGA3
    0.09 !
    ATOM H33 HGA3
    0.09 !
    BOND C1 H11 C1 H12
    DOUBLE C1 C2
    BOND C2 H21
    BOND C2 C3
    BOND C3 H31 C3 H32 C3 H33
    IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0
    IC H12 C2 *C1 H11 0.00 0.00 180.0 0.0 0.0
    IC C3 C1 *C2 H21 0.00 0.00 180.0 0.0 0.0
    IC H31 C3 C2 C1 0.00 0.00
    0.0 0.0 0.0
    IC H32 C3 C2 C1 0.00 0.00 120.0 0.0 0.0
    IC H33 C3 C2 C1 0.00 0.00 -120.0 0.0 0.0
    PATC FIRS NONE LAST NONE

    1.1036
    1.1036
    1.1036
    1.8845

    RESI BTE1
    0.00 ! C4H8 1-Butene, yin/adm jr.
    GROUP
    ATOM C1 CG2D2 -0.42 !
    ATOM H11 HGA5
    0.21 ! H11
    H21 H41
    ATOM H12 HGA5
    0.21 ! \
    /
    |
    GROUP
    !
    C1=C2
    C4-H42
    ATOM C2 CG2D1 -0.15 ! /
    \ / \
    ATOM H21 HGA4
    0.15 ! H12
    C3
    H43
    GROUP
    !
    / \
    ATOM C3 CG321 -0.18 !
    H31 H32
    ATOM H31 HGA2
    0.09 !
    ATOM H32 HGA2
    0.09 !
    GROUP
    ATOM C4 CG331 -0.27
    ATOM H41 HGA3
    0.09
    ATOM H42 HGA3
    0.09
    ATOM H43 HGA3
    0.09
    BOND C1 H11 C1 H12
    DOUBLE C1 C2
    BOND C2 H21
    BOND C2 C3
    BOND C3 H31 C3 H32
    BOND C3 C4
    BOND C4 H41 C4 H42 C4 H43
    IC C1 C2 C3 C4 0.00 0.00 180.0 0.00 0.00
    IC H11 C1 C2 C3 0.00 0.00 180.0 0.00 0.00
    IC H12 C1 C2 C3 0.00 0.00
    0.0 0.00 0.00
    IC H21 C1 *C2 C3 0.00 0.00 180.0 0.00 0.00
    IC H31 C2 *C3 C4 0.00 0.00 120.0 0.00 0.00
    IC H32 C2 *C3 C4 0.00 0.00 -120.0 0.00 0.00
    IC H41 C4 C3 C2 0.00 0.00 180.0 0.00 0.00
    IC H42 C4 C3 C2 0.00 0.00 60.0 0.00 0.00
    IC H43 C4 C3 C2 0.00 0.00 -60.0 0.00 0.00
    PATC FIRS NONE LAST NONE
    RESI BTE2
    0.00
    GROUP
    ATOM C1 CG331 -0.27
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    GROUP
    ATOM C2 CG2D1 -0.15
    ATOM H21 HGA4
    0.15
    GROUP
    ATOM C3 CG2D1 -0.15
    ATOM H31 HGA4
    0.15
    GROUP
    ATOM C4 CG331 -0.27
    ATOM H41 HGA3
    0.09
    ATOM H42 HGA3
    0.09
    ATOM H43 HGA3
    0.09
    BOND C1 H11 C1 H12 C1
    BOND C1 C2
    BOND C2 H21
    DOUBLE C2 C3
    BOND C3 H31
    BOND C3 C4
    BOND C4 H41 C4 H42 C4

    ! C4H8 2-Butene, yin/adm jr.


    ! H12 H13
    !
    \ |
    ! H13-C1
    H31
    !
    \
    /
    !
    C2=C3
    !
    /
    \
    !
    H21
    C4-H41
    !
    | \
    !
    H43 H42
    !

    H13

    H43

    IC C1 C2 C3 C4
    IC H11 C1 C2 C3
    IC H12 C1 C2 C3
    IC H13 C1 C2 C3
    IC H21 C1 *C2 C3
    IC H31 C4 *C3 C2
    IC H41 C4 C3 C2
    IC H42 C4 C3 C2
    IC H43 C4 C3 C2
    PATC FIRS NONE LAST

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    0.0
    120.0
    -120.0
    180.0
    180.0
    0.0
    120.0
    -120.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI DIPE
    0.00 ! C5H8 1,4-dipentene, adm
    GROUP
    ATOM C1 CG2D2 -0.42 !
    ATOM H11 HGA5
    0.21 ! H11
    H21 H41 H51
    ATOM H12 HGA5
    0.21 ! \
    /
    | /
    GROUP
    !
    C1=C2
    C4=C5
    ATOM C2 CG2D1 -0.15 ! /
    \ /
    \
    ATOM H21 HGA4
    0.15 ! H12
    C3
    H52
    GROUP
    !
    / \
    ATOM C3 CG321 -0.18 !
    H31 H32
    ATOM H31 HGA2
    0.09 !
    ATOM H32 HGA2
    0.09 !
    GROUP
    ATOM C4 CG2D1 -0.15
    ATOM H41 HGA4
    0.15
    GROUP
    ATOM C5 CG2D2 -0.42
    ATOM H51 HGA5
    0.21
    ATOM H52 HGA5
    0.21
    BOND C1 H11 C1 H12
    DOUBLE C1 C2
    BOND C2 H21
    BOND C2 C3
    BOND C3 H31 C3 H32
    BOND C3 C4
    BOND C4 H41
    DOUBLE C4 C5
    BOND C5 H51 C5 H52
    IC H11 C1 C2 H21
    0.0000
    0.00
    0.00
    IC H11 C2 *C1 H12
    0.0000
    0.00 180.00
    IC H11 C1 C2 C3
    0.0000
    0.00 180.00
    IC C1 C2 C3 C4
    0.0000
    0.00 180.00
    IC C4 C2 *C3 H31
    0.0000
    0.00 120.00
    IC C4 C2 *C3 H32
    0.0000
    0.00 -120.00
    IC C2 C3 C4 C5
    0.0000
    0.00 180.00
    IC C5 C3 *C4 H41
    0.0000
    0.00 180.00
    IC C3 C4 C5 H51
    0.0000
    0.00 180.00
    IC H51 C4 *C5 H52
    0.0000
    0.00 180.00
    PATC FIRS NONE LAST NONE
    RESI DIHE
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM

    C1
    H11
    H12
    H13

    jr.

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C7H12 2,5-diheptene, adm jr.


    CG331
    HGA3
    HGA3
    HGA3

    C2 CG2D1

    -0.27
    0.09
    0.09
    0.09

    !
    !
    !
    !

    -0.15 !

    H21

    H31 H51 H61

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    GROUP
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM

    H21 HGA4

    C4 CG321
    H41 HGA2
    H42 HGA2

    0.15 !
    \
    /
    | /
    !
    C2=C3
    C5=C6
    -0.15 !
    /
    \ /
    \
    0.15 ! H11-C1
    C4
    C7-H71
    !
    / \
    / \
    / \
    -0.18 ! H12 H13 H41 H42 H73 H72
    0.09 !
    0.09 !

    C5 CG2D1
    H51 HGA4

    -0.15
    0.15

    C6 CG2D1
    H61 HGA4

    -0.15
    0.15

    C7
    H71
    H72
    H73

    -0.27
    0.09
    0.09
    0.09

    C3 CG2D1
    H31 HGA4

    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 H11 C1 H12 C1 H13


    BOND C1 C2 C2 H21
    DOUBLE C2 C3
    BOND C3 H31
    BOND C3 C4 C4 H41 C4 H42
    BOND C4 C5 C5 H51
    DOUBLE C5 C6
    BOND C6 H61
    BOND C6 C7 C7 H71 C7 H72 C7 H73
    IC H11 C1 C2 H21
    0.0000
    0.00
    0.00
    IC H11 C2 *C1 H12
    0.0000
    0.00 120.00
    IC H11 C2 *C1 H13
    0.0000
    0.00 -120.00
    IC H11 C1 C2 C3
    0.0000
    0.00 180.00
    IC C3 C1 *C2 H21
    0.0000
    0.00 180.00
    IC C1 C2 C3 C4
    0.0000
    0.00
    0.00
    IC C4 C2 *C3 H31
    0.0000
    0.00 180.00
    IC C2 C3 C4 C5
    0.0000
    0.00 180.00
    IC C5 C3 *C4 H41
    0.0000
    0.00 120.00
    IC C5 C3 *C4 H42
    0.0000
    0.00 -120.00
    IC C3 C4 C5 C6
    0.0000
    0.00 180.00
    IC C6 C4 *C5 H51
    0.0000
    0.00 180.00
    IC C4 C5 C6 C7
    0.0000
    0.00
    0.00
    IC C7 C5 *C6 H61
    0.0000
    0.00 180.00
    IC C5 C6 C7 H71
    0.0000
    0.00 180.00
    IC H71 C6 *C7 H72
    0.0000
    0.00 120.00
    IC H71 C6 *C7 H73
    0.0000
    0.00 -120.00
    PATC FIRS NONE LAST NONE
    RESI HXE2
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    GROUP
    ATOM C3
    ATOM H31

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C6H12 2-hexene, yin/adm jr.


    CG331 -0.27 ! H12 H13
    HGA3
    0.09 !
    \ |
    HGA3
    0.09 ! H13-C1
    H31 H51 H52
    HGA3
    0.09 !
    \
    /
    \ /
    !
    C2=C3
    C5
    H61
    CG2D1 -0.15 !
    /
    \ / \ /
    HGA4
    0.15 !
    H21
    C4
    C6-H62
    !
    / \
    \
    CG2D1 -0.15 !
    H41 H42
    H63
    HGA4
    0.15 !

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    GROUP
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM

    C4 CG321 -0.18
    H41 HGA2
    0.09
    H42 HGA2
    0.09
    C5 CG321 -0.18
    H51 HGA2
    0.09
    H52 HGA2
    0.09
    C6
    H61
    H62
    H63

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09

    BOND C1 H11 C1 H12


    BOND C1 C2
    BOND C2 H21
    DOUBLE C2 C3
    BOND C3 H31
    BOND C3 C4
    BOND C4 H41 C4 H42
    BOND C4 C5 C5 H51
    BOND C5 C6 C6 H61
    ! all trans
    IC C1 C2 C3 C4
    IC H11 C1 C2 C3
    IC H12 C1 C2 C3
    IC H13 C1 C2 C3
    IC H21 C1 *C2 C3
    IC H31 C4 *C3 C2
    IC C2 C3 C4 C5
    IC C3 C5 *C4 H41
    IC C3 C5 *C4 H42
    IC C3 C4 C5 C6
    IC C4 C6 *C5 H51
    IC C4 C6 *C5 H52
    IC H61 C6 C5 C4
    IC H62 C6 C5 C4
    IC H63 C6 C5 C4
    PATC FIRS NONE LAST
    RESI NC4
    GROUP
    ATOM N
    ATOM C1
    ATOM C2
    ATOM C3
    ATOM C4
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM H21
    ATOM H22
    ATOM H23
    ATOM H31
    ATOM H32
    ATOM H33
    ATOM H41
    ATOM H42
    ATOM H43

    NG3P0
    CG334
    CG334
    CG334
    CG334
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5
    HGP5

    C1 H13

    C5 H52
    C6 H62 C6 H63
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    0.0
    120.0
    -120.0
    180.0
    180.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    60.0
    300.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    1.00 ! C4H12N tetramethylammonium


    !
    -0.60 !
    H32
    -0.35 !
    |
    -0.35 !
    H31-C3-H33
    -0.35 !
    H23
    |
    H41
    -0.35 !
    |
    |
    |
    0.25 !
    H22-C2------N------C4-H42
    0.25 !
    |
    |
    |
    0.25 !
    H21
    |
    H43
    0.25 !
    H11-C1-H13
    0.25 !
    |
    0.25 !
    H12
    0.25
    0.25
    0.25
    0.25
    0.25
    0.25

    (+)

    BOND N C1 N
    BOND C1 H11
    BOND C2 H21
    BOND C3 H31
    BOND C4 H41
    IC C2 N
    IC N
    H11
    IC N
    H11
    IC C2 C1
    IC C2 C1
    IC C3 N
    IC N
    H21
    IC N
    H21
    IC C4 N
    IC N
    H31
    IC N
    H31
    IC C1 N
    IC N
    H41
    IC N
    H41

    C2 N C3 N
    C1 H12 C1
    C2 H22 C2
    C3 H32 C3
    C4 H42 C4
    C1 H11
    *C1 H12
    *C1 H13
    *N C3
    *N C4
    C2 H21
    *C2 H22
    *C2 H23
    C3 H31
    *C3 H32
    *C3 H33
    C4 H41
    *C4 H42
    *C4 H43

    C4
    H13
    H23
    H33
    H43
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    180.0000
    120.0000
    -120.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI NC5
    1.00 ! C5H14N tetramethylammonium ethyl
    GROUP
    ATOM N
    NG3P0
    -0.60 !
    ATOM C1 CG324
    -0.10 !
    |
    ATOM C2 CG334
    -0.35 !
    -C3ATOM C3 CG334
    -0.35 !
    |
    ATOM C4 CG334
    -0.35 !
    |
    | |
    ATOM H11 HGP5
    0.25 !
    -C2---N---C4(+)
    ATOM H12 HGP5
    0.25 !
    |
    | |
    ATOM H21 HGP5
    0.25 !
    |
    ATOM H22 HGP5
    0.25 !
    -C1ATOM H23 HGP5
    0.25 !
    |
    ATOM H31 HGP5
    0.25 !
    |
    ATOM H32 HGP5
    0.25 !
    -C5ATOM H33 HGP5
    0.25 !
    |
    ATOM H41 HGP5
    0.25
    ATOM H42 HGP5
    0.25
    ATOM H43 HGP5
    0.25
    GROUP
    ATOM C5 CG331
    -0.27
    ATOM H51 HGA3
    0.09
    ATOM H52 HGA3
    0.09
    ATOM H53 HGA3
    0.09
    BOND N C1 N C2 N C3 N C4
    BOND C1 H11 C1 H12 C1 C5
    BOND C2 H21 C2 H22 C2 H23
    BOND C3 H31 C3 H32 C3 H33
    BOND C4 H41 C4 H42 C4 H43
    BOND C5 H51 C5 H52 C5 H53
    ! ab-initio HF/6-31G* structure
    IC C4
    N
    C1
    C5
    1.4967 107.80 180.00 115.98
    IC C5
    C1
    N
    C2
    1.5217 115.98 -61.05 111.12
    IC C5
    C1
    N
    C3
    1.5217 115.98 61.05 111.12
    IC C4
    N
    C1
    H11
    1.4967 107.80 57.27 105.76
    IC C4
    N
    C1
    H12
    1.4967 107.80 -57.27 105.76
    IC C1
    N
    C2
    H21
    1.5176 111.12 -174.50 108.75
    IC C1
    N
    C2
    H22
    1.5176 111.12 65.81 109.69
    IC C1
    N
    C2
    H23
    1.5176 111.12 -54.79 109.07
    IC C1
    N
    C3
    H31
    1.5176 111.12 174.50 108.75
    IC C1
    N
    C3
    H32
    1.5176 111.12 -65.81 109.69

    analog

    1.5217
    1.4950
    1.4950
    1.0809
    1.0809
    1.0795
    1.0773
    1.0797
    1.0795
    1.0773

    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C1
    C1
    N
    N
    N

    1.5176
    1.5176
    1.5176
    1.5176
    1.5176
    1.5176
    1.5176

    111.12
    107.80
    107.80
    107.80
    115.98
    115.98
    115.98

    RESI CHOL
    1.00 ! C5H14NO
    GROUP
    !
    ATOM N
    NG3P0
    -0.60 !
    ATOM C1 CG324
    -0.10 !
    ATOM C2 CG334
    -0.35 !
    ATOM C3 CG334
    -0.35 !
    ATOM C4 CG334
    -0.35 !
    ATOM H11 HGP5
    0.25 !
    ATOM H12 HGP5
    0.25 !
    ATOM H21 HGP5
    0.25 !
    ATOM H22 HGP5
    0.25 !
    ATOM H23 HGP5
    0.25 !
    ATOM H31 HGP5
    0.25 !
    ATOM H32 HGP5
    0.25 !
    ATOM H33 HGP5
    0.25 !
    ATOM H41 HGP5
    0.25 !
    ATOM H42 HGP5
    0.25 !
    ATOM H43 HGP5
    0.25 !
    GROUP
    !
    ATOM C5 CG321
    0.05 !
    ATOM H51 HGA2
    0.09 !
    ATOM H52 HGA2
    0.09 !
    ATOM OH1 OG311
    -0.65 !
    ATOM HO1 HGP1
    0.42 !
    BOND N C1 N C2 N C3 N C4
    BOND C1 H11 C1 H12 C1 C5
    BOND C2 H21 C2 H22 C2 H23
    BOND C3 H31 C3 H32 C3 H33
    BOND C4 H41 C4 H42 C4 H43
    BOND C5 H51 C5 H52
    BOND C5 OH1 OH1 HO1
    ! ab-initio HF/6-31G* geometry of
    IC C4
    N
    C1
    C5
    1.4964
    IC C5
    C1
    N
    C2
    1.5208
    IC C5
    C1
    N
    C3
    1.5208
    IC N
    C1
    C5
    OH1
    1.5158
    IC C1
    C5
    OH1 HO1
    1.5208
    IC C2
    N
    C1
    H11
    1.5031
    IC C3
    N
    C1
    H12
    1.4945
    IC C1
    N
    C2
    H21
    1.5158
    IC C3
    N
    C2
    H22
    1.4945
    IC C4
    N
    C2
    H23
    1.4964
    IC C1
    N
    C3
    H31
    1.5158
    IC C2
    N
    C3
    H32
    1.5031
    IC C4
    N
    C3
    H33
    1.4964
    IC C1
    N
    C4
    H41
    1.5158
    IC C2
    N
    C4
    H42
    1.5031
    IC C3
    N
    C4
    H43
    1.4945
    IC N
    C1
    C5
    H51
    1.5158
    IC N
    C1
    C5
    H52
    1.5158

    choline

    RESI ACHO

    N
    N
    N
    N
    C1
    C1
    C1

    C3
    C4
    C4
    C4
    C5
    C5
    C5

    H33
    H41
    H42
    H43
    H51
    H52
    H53

    54.79
    180.00
    60.03
    -60.03
    180.00
    62.29
    -62.29

    |
    -C3|
    |
    | |
    -C2---N---C4|
    | |
    |
    -C1|
    |
    |
    |
    |
    |
    |
    |
    |
    -C5|
    OH1---HO1

    109.07
    109.11
    109.12
    109.12
    107.05
    112.91
    112.91

    gauche conformer
    107.76 161.60
    116.58 -80.13
    116.58 42.05
    116.58 56.02
    109.57 169.05
    111.04 158.76
    111.71 165.25
    111.04 -179.38
    109.20 -63.85
    108.15 57.69
    111.71 173.42
    109.20 177.22
    108.88 174.14
    107.76 175.04
    108.15 -64.86
    108.88 56.40
    116.58 176.61
    116.58 -67.32

    1.00 ! C7H16NO2 acetylcholine

    1.0797
    1.0793
    1.0793
    1.0793
    1.0836
    1.0820
    1.0820

    (+)

    116.58
    111.04
    111.71
    109.57
    110.84
    106.72
    106.14
    108.21
    109.22
    108.56
    108.53
    109.23
    109.12
    109.01
    109.05
    109.30
    105.66
    110.89

    1.5208
    1.5031
    1.4945
    1.3947
    0.9491
    1.0813
    1.0802
    1.0796
    1.0746
    1.0794
    1.0794
    1.0800
    1.0773
    1.0793
    1.0796
    1.0794
    1.0855
    1.0847

    GROUP
    !
    ATOM N
    NG3P0
    -0.60 !
    ATOM C1 CG324
    -0.10 !
    ATOM C2 CG334
    -0.35 !
    ATOM C3 CG334
    -0.35 !
    ATOM C4 CG334
    -0.35 !
    ATOM H11 HGP5
    0.25 !
    ATOM H12 HGP5
    0.25 !
    ATOM H21 HGP5
    0.25 !
    ATOM H22 HGP5
    0.25 !
    ATOM H23 HGP5
    0.25 !
    ATOM H31 HGP5
    0.25 !
    ATOM H32 HGP5
    0.25 !
    ATOM H33 HGP5
    0.25 !
    ATOM H41 HGP5
    0.25 !
    ATOM H42 HGP5
    0.25 !
    ATOM H43 HGP5
    0.25 !
    GROUP
    !
    ATOM C5 CG321
    0.08 !
    ATOM OM OG302
    -0.49 !
    ATOM C
    CG2O2
    0.90 !
    ATOM C7 CG331
    -0.31 !
    ATOM O
    OG2D1
    -0.63 !
    ATOM H51 HGA2
    0.09 !
    ATOM H52 HGA2
    0.09 !
    ATOM H71 HGA3
    0.09 !
    ATOM H72 HGA3
    0.09 !
    ATOM H73 HGA3
    0.09 !
    BOND N C1 N C2 N C3 N
    BOND C1 H11 C1 H12 C1 C5
    BOND C2 H21 C2 H22 C2 H23
    BOND C3 H31 C3 H32 C3 H33
    BOND C4 H41 C4 H42 C4 H43
    BOND C5 H51 C5 H52
    BOND C7 C
    C
    OM
    DOUBLE C O
    BOND C7 H71
    C7 H72
    IMPR C OM C7 O
    IC C4
    N
    C1
    C5
    IC C5
    C1
    N
    C2
    IC C5
    C1
    N
    C3
    IC C2
    N
    C1
    H11
    IC C3
    N
    C1
    H12
    IC C1
    N
    C2
    H21
    IC C3
    N
    C2
    H22
    IC C4
    N
    C2
    H23
    IC C1
    N
    C3
    H31
    IC C2
    N
    C3
    H32
    IC C4
    N
    C3
    H33
    IC C1
    N
    C4
    H41
    IC C2
    N
    C4
    H42
    IC C3
    N
    C4
    H43
    IC N
    C1
    C5
    H51
    IC N
    C1
    C5
    H52
    IC N
    C1
    C5
    OM
    IC C1
    C5
    OM
    C
    IC C7
    C
    OM
    C5
    IC O
    C
    OM
    C5
    IC H71 C7
    C
    OM
    IC H72 C7
    C
    OM

    |
    -C3|
    |
    | |
    -C2---N---C4|
    | |
    |
    -C1|
    |
    |
    |
    |
    |
    |
    |
    -C5|
    OM
    /
    O==C
    |
    --C7-|

    (+)

    C4

    OM

    C5

    C7

    H73

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    161.60
    -80.13
    42.05
    158.76
    165.25
    -179.38
    -63.85
    57.69
    173.42
    177.22
    174.14
    175.04
    -64.86
    56.40
    180.00
    -60.0
    72.0
    166.9
    20.0
    -160.0
    180.0
    60.4

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC H73

    C7

    OM

    0.0000 000.00 -60.4

    000.00

    RESI PC
    GROUP
    ATOM N
    ATOM C1
    ATOM C2
    ATOM C3
    ATOM C4
    ATOM H11
    ATOM H12
    ATOM H21
    ATOM H22
    ATOM H23
    ATOM H31
    ATOM H32
    ATOM H33
    ATOM H41
    ATOM H42
    ATOM H43
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    GROUP
    ATOM P1
    ATOM O3
    ATOM O4
    ATOM O1
    ATOM O2
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM H63
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    0.00 ! C6H16NO4P phosphatidylcholine


    !
    NG3P0
    -0.60 !
    CG324
    -0.10 !
    |
    CG334
    -0.35 !
    -C3CG334
    -0.35 !
    |
    CG334
    -0.35 !
    |
    | |
    HGP5
    0.25 !
    -C2---N---C4(+)
    HGP5
    0.25 !
    |
    | |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    -C1HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    HGP5
    0.25 !
    |
    !
    |
    CG321
    -0.08 !
    |
    HGA2
    0.09 !
    H52---C5---H51
    HGA2
    0.09 !
    |
    !
    |
    PG1
    1.50 !
    (-) O3 O1
    OG2P1
    -0.78 !
    \ /
    OG2P1
    -0.78 !
    P1 (+)
    OG303
    -0.57 !
    / \
    OG303
    -0.57 !
    (-) O4 O2
    !
    |
    CG331
    -0.17 !
    |
    HGA3
    0.09 !
    H63-C6-H62
    HGA3
    0.09 !
    |
    HGA3
    0.09 !
    H61
    !
    N C1 N C2 N C3 N C4
    C1 H11 C1 H12 C1 C5
    C2 H21 C2 H22 C2 H23
    C3 H31 C3 H32 C3 H33
    C4 H41 C4 H42 C4 H43
    C5 H51 C5 H52
    P1 O1
    P1 O2
    P1 O3
    P1 O4
    O1 C5
    C6 H61
    C6 H62 C6 H63

    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C4
    C5
    C5
    C2
    C3
    C1
    C3
    C4
    C1
    C2
    C4
    C1
    C2
    C3
    N

    N
    C1
    C1
    N
    N
    N
    N
    N
    N
    N
    N
    N
    N
    N
    C1

    C1
    N
    N
    C1
    C1
    C2
    C2
    C2
    C3
    C3
    C3
    C4
    C4
    C4
    C5

    C5
    C2
    C3
    H11
    H12
    H21
    H22
    H23
    H31
    H32
    H33
    H41
    H42
    H43
    H51

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    112.00
    -121.00
    0.00
    120.00
    120.00
    180.00
    -60.00
    60.00
    180.00
    180.00
    180.00
    180.00
    -60.00
    60.00
    -150.00

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    O2

    C6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N
    N
    C1
    C5
    O3
    O4
    O1
    H61
    H62
    H63

    C1
    C1
    C5
    O1
    P1
    P1
    P1
    C6
    C6
    C6

    C5
    C5
    O1
    P1
    O1
    O1
    O2
    O2
    O2
    O2

    H52
    O1
    P1
    O2
    C5
    C5
    C6
    P1
    P1
    P1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    100.00
    -30.00
    130.00
    -160.0
    80.00
    -60.00
    180.00
    0.00
    120.00
    -120.00

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI GPC
    0.00 ! C8H20NO6P glycerolphosphorylcholine
    GROUP
    !
    ATOM N
    NG3P0
    -0.60 !
    ATOM C1 CG324
    -0.10 !
    |
    ATOM C2 CG334
    -0.35 !
    -C3ATOM C3 CG334
    -0.35 !
    |
    ATOM C4 CG334
    -0.35 !
    |
    | |
    ATOM H11 HGP5
    0.25 !
    -C2---N---C4(+)
    ATOM H12 HGP5
    0.25 !
    |
    | |
    ATOM H21 HGP5
    0.25 !
    |
    ATOM H22 HGP5
    0.25 !
    -C1ATOM H23 HGP5
    0.25 !
    |
    ATOM H31 HGP5
    0.25 !
    |
    ATOM H32 HGP5
    0.25 !
    |
    ATOM H33 HGP5
    0.25 !
    |
    ATOM H41 HGP5
    0.25 !
    |
    ATOM H42 HGP5
    0.25 !
    |
    ATOM H43 HGP5
    0.25 !
    |
    GROUP
    !
    |
    ATOM C5 CG321
    -0.08 !
    |
    ATOM H51 HGA2
    0.09 !
    H51---C5---H52
    ATOM H52 HGA2
    0.09 !
    |
    ATOM P
    PG1
    1.50 !
    (-) O3 O1
    ATOM O3 OG2P1
    -0.78 !
    \ /
    ATOM O4 OG2P1
    -0.78 !
    P (+)
    ATOM O1 OG303
    -0.57 !
    / \
    ATOM O2 OG303
    -0.57 !
    (-) O4 O2
    ATOM CG1 CG321
    -0.08 !
    |
    ATOM HG11 HGA2
    0.09 !
    HG11-CG1-HG12
    ATOM HG12 HGA2
    0.09 !
    |
    GROUP
    !
    |
    ATOM CG2 CG311
    0.14 !
    |
    ATOM HG21 HGA1
    0.09 !
    HG21-CG2-OG2-HO2
    ATOM OG2 OG311
    -0.65 !
    |
    ATOM HO2 HGP1
    0.42 !
    |
    GROUP
    !
    |
    ATOM CG3 CG321
    0.05 !
    |
    ATOM HG31 HGA2
    0.09 !
    HG31-CG3-OG3-HO3
    ATOM HG32 HGA2
    0.09 !
    |
    ATOM OG3 OG311
    -0.65 !
    HG32
    ATOM HO3 HGP1
    0.42 !
    BOND CG1 O2 CG1 HG11 CG1 HG12
    BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2
    BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3
    BOND N C1 N C2
    N C3
    N C4
    BOND C1 H11 C1 H12 C1 C5
    BOND C2 H21 C2 H22 C2 H23
    BOND C3 H31 C3 H32 C3 H33
    BOND C4 H41 C4 H42 C4 H43

    BOND C5 H51 C5 H52


    BOND P O1 P O2

    O3

    O4

    O1

    C5

    ! internal coordinates for analysis


    ! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650,
    ! glycerol backbone
    IC O2 CG1 CG2 CG3 0.
    0.
    0.
    0.
    IC O2 CG1 CG2 OG2 0.
    0.
    0.
    0.
    IC CG1 CG2 CG3 OG3 0.
    0.
    0.
    0.
    IC OG2 CG2 CG3 OG3 0.
    0.
    0.
    0.
    !
    ! zwitterionic headgroup
    IC P
    O2 CG1 CG2 0.
    0.
    0.
    0.
    IC O1 P
    O2 CG1 0.
    0.
    0.
    0.
    IC O2 P
    O1 C5
    0.
    0.
    0.
    0.
    IC C1 C5 O1 P
    0.
    0.
    0.
    0.
    IC N
    C1 C5 O1
    0.
    0.
    0.
    0.
    IC C2 N
    C1 C5
    0.
    0.
    0.
    0.
    IC C3 N
    C1 C5
    0.
    0.
    0.
    0.
    IC C4 N
    C1 C5
    0.
    0.
    0.
    0.
    IC O1 O2 *P O3
    0.
    0.
    120.
    0.
    IC O1 O2 *P O4
    0.
    0.
    -120.
    0.
    PATCH FIRST NONE LAST NONE
    RESI TEA

    GROUP
    ATOM N
    NG3P0
    ATOM C1 CG324
    ATOM C2 CG324
    ATOM C3 CG324
    ATOM C4 CG324
    ATOM H11 HGP5
    ATOM H12 HGP5
    ATOM H21 HGP5
    ATOM H22 HGP5
    ATOM H31 HGP5
    ATOM H32 HGP5
    ATOM H41 HGP5
    ATOM H42 HGP5
    !
    ! in the following
    ! has been changed
    !
    GROUP
    ATOM C5 CG331
    ATOM H51 HGA3
    ATOM H52 HGA3
    ATOM H53 HGA3
    GROUP
    ATOM C6 CG331
    ATOM H61 HGA3
    ATOM H62 HGA3
    ATOM H63 HGA3
    GROUP
    ATOM C7 CG331

    1.00 !
    !
    !
    !
    !
    !
    !
    -0.60 !
    -0.10 !
    -0.10 !
    -0.10 !
    -0.10 !
    0.25 !
    0.25 !
    0.25 !
    0.25 !
    0.25 !
    0.25 !
    0.25 !
    0.25 !

    -0.27
    0.09
    0.09
    0.09
    -0.27

    0.
    0.
    0.
    0.

    !
    !
    !
    !

    t1
    t2
    t3
    t3

    0.
    0.
    0.
    0.
    0.
    0.
    0.
    0.
    0.
    0.

    !
    !
    !
    !
    !
    !
    !
    !

    a1
    a2
    a3
    a4
    a5
    a6
    a6
    a6

    C8H20N tetra ethylammonium (TEA)


    S. Crouzy, S. Berneche and B. Roux
    calc F.E. solvation = -51 kcal/mol
    versus experiment = -49 kcal/mol
    |
    -C7|
    |
    -C3|
    | |
    | | |
    -C6--C2---N---C4--C8| |
    | | |
    |
    -C1|
    -C5|

    methyl groups, the atom type HAL


    to HGA3 . adm jr.
    -0.27
    0.09
    0.09
    0.09

    21-51 (1981)

    (+)

    ATOM H71 HGA3


    0.09
    ATOM H72 HGA3
    0.09
    ATOM H73 HGA3
    0.09
    GROUP
    ATOM C8 CG331
    -0.27
    ATOM H81 HGA3
    0.09
    ATOM H82 HGA3
    0.09
    ATOM H83 HGA3
    0.09
    BOND N C1 N C2 N C3 N C4
    BOND C1 H11 C1 H12 C1 C5
    BOND C2 H21 C2 H22 C2 C6
    BOND C3 H31 C3 H32 C3 C7
    BOND C4 H41 C4 H42 C4 C8
    BOND C5 H51 C5 H52 C5 H53
    BOND C6 H61 C6 H62 C6 H63
    BOND C7 H71 C7 H72 C7 H73
    BOND C8 H81 C8 H82 C8 H83
    ! ab-initio HF/6-31G* structure
    IC C4
    N
    C1
    C5
    1.4967
    IC C5
    C1
    N
    C2
    1.5217
    IC C5
    C1
    N
    C3
    1.5217
    IC C4
    N
    C1
    H11
    1.4967
    IC C4
    N
    C1
    H12
    1.4967
    IC C1
    N
    C2
    H21
    1.5176
    IC C1
    N
    C2
    H22
    1.5176
    IC C1
    N
    C3
    H31
    1.5176
    IC C1
    N
    C3
    H32
    1.5176
    IC C1
    N
    C4
    H41
    1.5176
    IC C1
    N
    C4
    H42
    1.5176
    IC N
    C1
    C5
    H51
    1.5176
    IC N
    C1
    C5
    H52
    1.5176
    IC N
    C1
    C5
    H53
    1.5176
    IC C3
    N
    C2
    C6
    1.4967
    IC N
    C1
    C6
    H61
    1.5176
    IC N
    C1
    C6
    H62
    1.5176
    IC N
    C1
    C6
    H63
    1.5176
    IC C2
    N
    C3
    C7
    1.4967
    IC N
    C1
    C7
    H71
    1.5176
    IC N
    C1
    C7
    H72
    1.5176
    IC N
    C1
    C7
    H73
    1.5176
    IC C1
    N
    C4
    C8
    1.4967
    IC N
    C1
    C8
    H81
    1.5176
    IC N
    C1
    C8
    H82
    1.5176
    IC N
    C1
    C8
    H83
    1.5176
    RESI ETAM
    GROUP
    ATOM N
    ATOM HN1
    ATOM HN2
    ATOM HN3
    ATOM C1
    ATOM H11
    ATOM H12
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM OH1

    NG3P3
    HGP2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    OG311

    107.80
    115.98
    115.98
    107.80
    107.80
    111.12
    111.12
    111.12
    111.12
    107.80
    107.80
    115.98
    115.98
    115.98
    107.80
    115.98
    115.98
    115.98
    107.80
    115.98
    115.98
    115.98
    107.80
    115.98
    115.98
    115.98

    180.00
    -61.05
    61.05
    57.27
    -57.27
    -174.50
    65.81
    174.50
    -65.81
    180.00
    60.03
    180.00
    62.29
    -62.29
    180.00
    180.00
    62.29
    -62.29
    180.00
    180.00
    62.29
    -62.29
    180.00
    180.00
    62.29
    -62.29

    1.00 ! C2H8NO ethanolamine


    !
    -0.30 !
    HN2
    0.33 !
    |
    0.33 ! (+) HN1---N---HN3
    0.33 !
    |
    0.13 !
    |
    0.09 !
    H12---C1---H11
    0.09 !
    |
    !
    |
    0.05 !
    |
    0.09 !
    H52---C5---H51
    0.09 !
    |
    -0.65 !
    OH1---HO1

    115.98
    111.12
    111.12
    105.76
    105.76
    108.75
    109.69
    108.75
    109.69
    109.11
    109.12
    107.05
    112.91
    112.91
    115.98
    107.05
    112.91
    112.91
    115.98
    107.05
    112.91
    112.91
    115.98
    107.05
    112.91
    112.91

    1.5217
    1.4950
    1.4950
    1.0809
    1.0809
    1.0795
    1.0773
    1.0795
    1.0773
    1.0793
    1.0793
    1.0836
    1.0820
    1.0820
    1.5217
    1.0836
    1.0820
    1.0820
    1.5217
    1.0836
    1.0820
    1.0820
    1.5217
    1.0836
    1.0820
    1.0820

    ATOM HO1 HGP1


    0.42 !
    BOND N HN1 N HN2 N HN3 N C1
    BOND C1 H11 C1 H12 C1 C5
    BOND C5 H51 C5 H52
    BOND C5 OH1 OH1 HO1
    ! HF/6-31G* OPTIMIZED STRUCTURE:
    IC N
    C1
    C5
    OH1
    1.5084
    IC C1 C5
    OH1 HO1
    1.5191
    IC HN1 N
    C1
    C5
    1.0145
    IC HN2 N
    C1
    C5
    1.0107
    IC HN3 N
    C1
    C5
    1.0102
    IC N
    C5
    *C1 H11
    0.0000
    IC N
    C5
    *C1 H12
    0.0000
    IC OH1 C1
    *C5 H51
    0.0000
    IC OH1 C1
    *C5 H52
    0.0000
    RESI GLYC

    107.86
    104.92
    108.35
    112.05
    112.39
    000.00
    000.00
    000.00
    000.00

    48.44
    173.19
    -49.03
    69.23
    -169.37
    120.00
    -120.00
    120.00
    -120.00

    104.92
    111.99
    107.86
    107.86
    107.86
    000.00
    000.00
    000.00
    000.00

    1.3987
    0.9495
    1.5191
    1.5191
    1.5191
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C7H12O4 Model compound for glycerol headgroup the


    ! aliphatic tail linker region
    !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !
    !
    0.08 !
    H12 H21 H31
    0.09 !
    |
    | |
    0.09 !
    H11--C1--C2--C3--H32
    -0.49 !
    /
    | |
    0.90 !
    O4 O8 H33
    -0.63 !
    /
    \
    -0.31 !
    O6=C5
    C9=O10
    0.09 !
    /
    \
    0.09 ! H71-C7-H73 H113-C11-H111
    0.09 !
    |
    |
    !
    H72
    H112
    0.17 !
    0.09 !
    -0.49 !
    0.90 !
    -0.63 !
    -0.31 !
    0.09 !
    0.09 !
    0.09 !

    GROUP
    ATOM C3 CG331
    ATOM H31 HGA3
    ATOM H32 HGA3
    ATOM H33 HGA3
    GROUP
    ATOM C1 CG321
    ATOM H11 HGA2
    ATOM H12 HGA2
    ATOM O4 OG302
    ATOM C5 CG2O2
    ATOM O6 OG2D1
    ATOM C7 CG331
    ATOM H71 HGA3
    ATOM H72 HGA3
    ATOM H73 HGA3
    GROUP
    ATOM C2 CG311
    ATOM H21 HGA1
    ATOM O8 OG302
    ATOM C9 CG2O2
    ATOM O10 OG2D1
    ATOM C11 CG331
    ATOM H111 HGA3
    ATOM H112 HGA3
    ATOM H113 HGA3
    BOND C1 C2 C2 C3
    BOND C1 O4 O4 C5 C5 C7 C5 O6
    BOND C2 O8 O8 C9 C9 C11 C9 O10
    BOND C1 H11 C1 H12
    BOND C2 H21
    BOND C3 H31
    C3 H32 C3 H33
    BOND C7 H71 C7 H72 C7 H73
    BOND C11 H111 C11 H112 C11 H113
    ! internal coordinates
    IC C1
    C2
    C3 H31
    0.0000
    IC C3
    C2
    C1 H11
    0.0000
    IC H31 C2 *C3 H32
    0.0000
    IC H31 C2 *C3 H33
    0.0000
    IC H31 C3
    C2 C1
    0.0000
    IC C1
    C3 *C2 O8
    0.0000
    IC C1
    C3 *C2 H21
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C3
    O4
    O4
    C2
    C1
    O6
    O4
    H71
    H71
    C3
    C2
    O10
    O8
    H111
    H111

    C2
    C2
    C2
    C1
    O4
    O4
    C5
    C5
    C5
    C2
    O8
    O8
    C9
    C9
    C9

    C1
    *C1
    *C1
    O4
    C5
    *C5
    C7
    *C7
    *C7
    O8
    C9
    *C9
    C11
    *C11
    *C11

    O4
    H11
    H12
    C5
    O6
    C7
    H71
    H72
    H73
    C9
    O10
    C11
    H111
    H112
    H113

    !was giving an error


    RESI GLYP
    -1.00 !
    !
    GROUP
    !
    ATOM P1 PG1
    1.50 !
    ATOM OP3 OG2P1
    -0.78 !
    ATOM OP4 OG2P1
    -0.78 !
    ATOM OP1 OG303
    -0.57 !
    ATOM OP2 OG303
    -0.57 !
    !
    ATOM CP1 CG331
    -0.17 !
    ATOM HP11 HGA3
    0.09 !
    ATOM HP12 HGA3
    0.09 !
    ATOM HP13 HGA3
    0.09 !
    !
    !
    ATOM C3 CG321
    -0.08 !
    ssion
    ATOM H31 HGA2
    0.09 !
    ATOM H32 HGA2
    0.09 !
    GROUP
    !
    ATOM C1 CG321
    0.08 !
    ATOM H11 HGA2
    0.09 !
    ATOM H12 HGA2
    0.09 !
    ATOM O4 OG302
    -0.49 !
    ATOM C5 CG2O2
    0.90 !
    ATOM O6 OG2D1
    -0.63 !
    ATOM C7 CG331
    -0.31 !
    ATOM H71 HGA3
    0.09 !
    ATOM H72 HGA3
    0.09 !
    ATOM H73 HGA3
    0.09 !
    GROUP
    !
    ATOM C2 CG311
    0.17 !
    ATOM H21 HGA1
    0.09 !
    ATOM O8 OG302
    -0.49 !
    ATOM C9 CG2O2
    0.90 !
    ATOM O10 OG2D1
    -0.63 !
    ATOM C11 CG331
    -0.31 !
    ATOM H111 HGA3
    0.09 !
    ATOM H112 HGA3
    0.09 !
    ATOM H113 HGA3
    0.09 !
    BOND P1 OP1
    P1 OP2
    BOND CP1 HP11 CP1 HP12
    BOND C1 C2
    C2 C3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    0.00
    180.00
    180.00
    120.00
    -120.00
    90.00
    0.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C8H14O8P Model compound for glycerol headgroup the


    aliphatic tail linker region, phosphorylated

    HP11
    |
    HP13-CP1-HP12
    \
    (-)OP3 OP1
    \ /
    P1 (+)
    / \
    (-)OP4 OP2
    \
    \ Combining DMPA and GLYC lead to omi
    \ of the C2 methylene group
    \
    |
    H12 H21 |
    |
    | |
    H11--C1--C2--C3--H31
    /
    | |
    O4 O8 H32
    /
    \
    O6=C5
    C9=O10
    /
    \
    H71-C7-H73 H113-C11-H111
    |
    |
    H72
    H112

    P1 OP3 P1 OP4
    CP1 HP13 OP2 C3

    OP1 CP1

    BOND C1 O4
    O4 C5
    C5 C7
    C5 O6
    BOND C2 O8
    O8 C9
    C9 C11 C9 O10
    BOND C1 H11
    C1 H12 C2 H21 C3 H31
    C3 H32
    BOND C7 H71
    C7 H72 C7 H73
    BOND C11 H111 C11 H112 C11 H113
    ! internal coordinates from ic generate, dihedrals corrected
    IC CP1 OP1 P1 OP2
    0.0000
    0.00 60.00
    0.00 0.0000
    IC OP1 OP2 *P1 OP3
    0.0000
    0.00 120.00
    0.00 0.0000
    IC OP1 OP2 *P1 OP4
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC OP2 P1
    OP1 CP1
    0.0000
    0.00 60.00
    0.00 0.0000
    IC P1
    OP1 CP1 HP11 0.0000
    0.00 180.00
    0.00 0.0000
    IC HP11 OP1 *CP1 HP12 0.0000
    0.00 120.00
    0.00 0.0000
    IC HP11 OP1 *CP1 HP13 0.0000
    0.00 -120.00
    0.00 0.0000
    IC OP1 P1
    OP2 C3
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC P1
    OP2 C3 C2
    0.0000
    0.00 180.00
    0.00 0.0000
    IC C2
    OP2 *C3 H31
    0.0000
    0.00 120.00
    0.00 0.0000
    IC C2
    OP2 *C3 H32
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC OP2 C3
    C2 C1
    0.0000
    0.00 120.00
    0.00 0.0000
    IC C1
    C3
    *C2 O8
    0.0000
    0.00 120.00
    0.00 0.0000
    IC C1
    C3
    *C2 H21
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC C3
    C2
    C1 O4
    0.0000
    0.00 180.00
    0.00 0.0000
    IC O4
    C2
    *C1 H11
    0.0000
    0.00 120.00
    0.00 0.0000
    IC O4
    C2
    *C1 H12
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC C2
    C1
    O4 C5
    0.0000
    0.00 180.00
    0.00 0.0000
    IC C1
    O4
    C5 O6
    0.0000
    0.00 180.00
    0.00 0.0000
    IC O6
    O4
    *C5 C7
    0.0000
    0.00 180.00
    0.00 0.0000
    IC O4
    C5
    C7 H71
    0.0000
    0.00 180.00
    0.00 0.0000
    IC H71 C5
    *C7 H72
    0.0000
    0.00 120.00
    0.00 0.0000
    IC H71 C5
    *C7 H73
    0.0000
    0.00 -120.00
    0.00 0.0000
    IC C3
    C2
    O8 C9
    0.0000
    0.00 60.00
    0.00 0.0000
    IC C2
    O8
    C9 O10
    0.0000
    0.00 180.00
    0.00 0.0000
    IC O10 O8
    *C9 C11
    0.0000
    0.00 180.00
    0.00 0.0000
    IC O8
    C9
    C11 H111 0.0000
    0.00 180.00
    0.00 0.0000
    IC H111 C9
    *C11 H112 0.0000
    0.00 120.00
    0.00 0.0000
    IC H111 C9
    *C11 H113 0.0000
    0.00 -120.00
    0.00 0.0000
    !Small corrections
    RESI MBUT
    GROUP
    ATOM C4 CG331
    ATOM H41 HGA3
    ATOM H42 HGA3
    ATOM H43 HGA3
    GROUP
    ATOM C3 CG321
    ATOM H31 HGA2
    ATOM H32 HGA2
    GROUP
    ATOM C2 CG321
    ATOM H21 HGA2
    ATOM H22 HGA2
    ATOM C1 CG2O2
    ATOM O1 OG2D1
    ATOM OM OG302
    ATOM CM CG331
    ATOM HM1 HGA3
    ATOM HM2 HGA3
    ATOM HM3 HGA3
    BOND C1 OM OM CM
    BOND C1 C2 C2 H21

    0.00 ! C5H10O2 methyl-butyrate


    -0.27
    0.09
    0.09
    0.09
    -0.18
    0.09
    0.09

    !
    H42
    !
    |
    ! H41-C4-H43
    !
    |
    !
    |
    ! H31-C3-H32
    !
    |
    !
    |
    ! H21-C2-H22
    !
    |
    !
    |
    !
    C1
    HM1
    !
    // \
    /
    ! O1
    OM-CM-HM2
    !
    \
    !
    HM3
    !

    0.08
    0.09
    0.09
    0.90
    -0.63
    -0.49
    -0.31
    0.09
    0.09
    0.09
    CM HM1 CM HM2 CM HM3
    C2 H22

    BOND C2 C3 C3 H31 C3 H32


    BOND C3 C4 C4 H41 C4 H42 C4 H43
    DOUBLE C1 O1
    IMPR C1 OM C2 O1
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C3
    H41
    H41
    H41
    C2
    C2
    C4
    C1
    C1
    C3
    OM
    C2
    C1
    HM1
    HM1

    C2
    C2
    C3
    C3
    C4
    C4
    C4
    C3
    C3
    C3
    C2
    C2
    C1
    OM
    OM
    OM

    C3
    C1
    *C4
    *C4
    C3
    *C3
    *C3
    C2
    *C2
    *C2
    C1
    *C1
    OM
    CM
    *CM
    *CM

    C4
    OM
    H42
    H43
    C2
    H31
    H32
    C1
    H21
    H22
    OM
    O1
    CM
    HM1
    HM2
    HM3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    60.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !toppar_all27_na_base_modifications.str
    RESI DFT
    GROUP
    ATOM C1
    ATOM C2
    ATOM C3
    ATOM C4
    ATOM C5
    ATOM C6
    ATOM H1
    ATOM F2
    ATOM H3
    ATOM F4
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53
    ATOM H6
    BOND
    BOND
    BOND
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD

    C1
    C1
    C5M
    C1
    C2
    C3
    C4
    C5
    C6
    C3
    C4
    C5
    C6
    C3
    C4
    C4
    H51
    H51

    0.00
    CG2R61
    CG2R66
    CG2R61
    CG2R66
    CG2R61
    CG2R61
    HGR62
    FGR1
    HGR62
    FGR1
    CG331
    HGA3
    HGA3
    HGA3
    HGR61

    -0.24
    0.28
    -0.24
    0.22
    0.10
    -0.28
    0.21
    -0.21
    0.19
    -0.21
    -0.24
    0.07
    0.07
    0.07
    0.21

    ! C7H6F2 2,4-difluorotoluene
    ! adm jr. w/Daniel Barsky
    !
    F4
    !
    |
    !
    H51
    C4
    H3
    !
    \
    / \\ /
    ! H52--C5M-C5
    C3
    !
    / ||
    |
    !
    H52 C6
    C2
    !
    / \ // \
    !
    H6
    C1
    F2
    !
    |
    !
    H1

    C2 C2 C3 C3
    H1 C2 F2 C3
    H51 C5M H52 C5M
    C2 C3 C4
    C3 C4 C5
    C4 C5 C6
    C5 C6 C1
    C6 C1 C2
    C1 C2 C3
    C2 C1 H1
    C3 C2 F2
    C4 C3 H3
    C5 C4 F4
    C4 C5 C5M
    C5 C6 H6
    C5 C5M H51
    C5 *C5M H52
    C5 *C5M H53

    C4 C4 C5 C5 C6 C6 C1
    H3 C4 F4 C5 C5M C6 H6
    H53
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00 60.00
    0.00
    0.00
    0.00 240.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI DFB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM F2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM F4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6

    0.00
    CG2R61
    HGR62
    CG2R66
    FGR1
    CG2R61
    HGR62
    CG2R66
    FGR1
    CG2R61
    HGR62
    CG2R61
    HGR61

    BOND C1 C2
    BOND C1 H1
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD

    C1
    C2
    C3
    C4
    C5
    C6
    C3
    C4
    C5
    C6
    C3
    C4

    C2
    C3
    C4
    C5
    C6
    C1
    C2
    C3
    C4
    C5
    C4
    C5

    -0.26
    0.23
    0.27
    -0.19
    -0.23
    0.19
    0.27
    -0.19
    -0.26
    0.23
    -0.32
    0.26

    C2 C3
    C2 F2
    C3
    C4
    C5
    C6
    C1
    C2
    C1
    C2
    C3
    C4
    C5
    C6

    ! C6H4F2 1,3-difluorobenzene aka m-difluorobenzene


    ! adm jr. w/Daniel Barsky
    ! atom numbering based in difluorotoluene
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5

    H3
    \ / \\ /
    C5
    C3
    ||
    |
    C6
    C2
    / \ // \
    H6
    C1
    F2
    |
    H1

    C3 C4
    C3 H3
    C4
    C5
    C6
    C1
    C2
    C3
    H1
    F2
    H3
    F4
    H5
    H6

    F4
    |
    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4 C5
    C4 F4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5 C6
    C5 H5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    C6 C1
    C6 H6
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    !toppar_all27_na_bkb_modifications.str
    RESI BPET
    -2.00 ! C4H10O8P2 Bis-methylphosphate-ethane
    ! adm jr., w/Daniel Barsky
    GROUP
    !
    ATOM C1 CG331
    -0.17 !
    H11
    ATOM H11 HGA3
    0.09 !
    |
    ATOM H12 HGA3
    0.09 !
    H13-C1-H12
    ATOM H13 HGA3
    0.09 !
    \
    ATOM O2 OG303
    -0.57 !
    O31 O2
    ATOM P3 PG1
    1.50 !
    \\ /
    ATOM O31 OG2P1
    -0.78 !
    (-) P3
    ATOM O32 OG2P1
    -0.78 !
    // \
    ATOM O4 OG303
    -0.57 !
    O32 O4
    ATOM C5 CG321
    -0.08 !
    /
    ATOM H51 HGA2
    0.09 !
    H51-C5-H52
    ATOM H52 HGA2
    0.09 !
    |
    ATOM C6 CG321
    -0.08 !
    H51-C6-H52
    ATOM H61 HGA2
    0.09 !
    \
    ATOM H62 HGA2
    0.09 !
    O81 O7
    ATOM O7 OG303
    -0.57 !
    \\ /
    ATOM P8 PG1
    1.50 !
    (-) P8
    ATOM O81 OG2P1
    -0.78 !
    // \
    ATOM O82 OG2P1
    -0.78 !
    O82 O9
    ATOM O9 OG303
    -0.57 !
    /
    ATOM C10 CG331
    -0.17 !
    H101-C10-H102
    ATOM H101 HGA3
    0.09 !
    |
    ATOM H102 HGA3
    0.09 !
    H103

    ATOM H103 HGA3


    BOND C1
    BOND O7
    BOND P8
    BOND C1
    BOND C6
    !from IC
    IC H11
    IC C1
    IC H11
    IC H11
    IC O4
    IC O4
    IC O2
    IC P3
    IC C6
    IC C6
    IC O4
    IC O7
    IC O7
    IC C5
    IC C6
    IC O9
    IC O9
    IC O7
    IC P8
    IC H101
    IC H101

    O2
    O2
    P8
    P8
    O81
    P8
    H11
    C1
    H61
    C6
    generate
    C1
    O2
    O2
    P3
    O2
    *C1
    O2
    *C1
    O2
    *P3
    O2
    *P3
    P3
    O4
    O4
    C5
    O4
    *C5
    O4
    *C5
    C5
    C6
    C5
    *C6
    C5
    *C6
    C6
    O7
    O7
    P8
    O7
    *P8
    O7
    *P8
    P8
    O9
    O9
    C10
    O9
    *C10
    O9
    *C10

    RESI ABNS
    GROUP
    ATOM H5T
    ATOM O5'
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM C4'
    ATOM H42'
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C2'
    ATOM H21'
    ATOM H22'
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM H32'

    HGP1
    OG311
    CG321
    HGA2
    HGA2
    CG3C51
    HGA1
    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1
    OG311
    HGP1

    BOND
    BOND
    BOND
    BOND

    C4'
    H11'
    H31'
    H52'

    O4'
    C1'
    C3'
    C5'

    0.09 !
    P3
    O9
    O82
    H12
    H62

    P3
    O9

    O4
    C10

    O4
    P3

    C5
    O31

    C5
    P3

    C6
    O32

    C6

    O7

    P3
    O4
    H12
    H13
    O31
    O32
    C5
    C6
    H51
    H52
    O7
    H61
    H62
    P8
    O9
    O81
    O82
    C10
    H101
    H102
    H103

    C1 H13 C5 H51 C5 H52


    C10 H101 C10 H102 C10 H103
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00
    0.00 180.00
    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H10O3 abasic deoxyribose nucleoside (susil)


    ! adm jr., w/Daniel Barsky
    !
    0.42 !
    -0.65 !
    0.05 !
    H5T
    0.09 !
    \
    0.09 ! H51' O5'
    0.11 !
    \ /
    0.09 ! H52'--C5' O4' H11'
    -0.40 !
    \ / \ /
    0.02 !
    H42'-C4' C1'-H12'
    0.09 !
    |
    |
    0.09 !
    C3'---C2'-H21'
    -0.18 !
    / |
    \
    0.09 !
    O3' H31' H22'
    0.09 !
    |
    0.14 !
    H32'
    0.09
    -0.65
    0.42
    O4'
    C1'
    C3'
    O5'

    BILD O4' C1' C2' C3'


    BILD C1' C2' C3' C4'
    BILD C2' C3' C4' C5'

    C1'
    H12'
    O3'
    H5T
    1.433
    1.521
    1.525

    C4'
    C1'
    O3'
    C2'
    104.1
    100.9
    102.6

    C5'
    C2'
    H32'
    C3'
    41.2
    325.1
    257.8

    C4' H42'
    C2' H21'
    C5' O5'
    100.9
    102.6
    113.7

    C4' C3'
    C2' H22'
    C5' H51'
    1.525
    1.533
    1.513

    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD

    C3'
    C4'
    C3'
    C3'
    C2'
    C1'
    C1'
    C2'
    O4'
    O4'
    O4'
    O4'

    C4'
    C5'
    C4'
    C4'
    C3'
    C2'
    C2'
    C3'
    C1'
    C1'
    C1'
    C1'

    RESI PHA
    GROUP
    ATOM P1
    ATOM O3
    ATOM O4
    ATOM O2
    ATOM N1
    ATOM H1

    PG1
    OG2P1
    OG2P1
    OG303
    NG2S3
    HGP1

    ATOM
    ATOM
    ATOM
    ATOM

    C1
    H11
    H12
    H13

    CG331
    HGA3
    HGA3
    HGA3

    ATOM
    ATOM
    ATOM
    ATOM

    C2
    H21
    H22
    H23

    CG331
    HGA3
    HGA3
    HGA3

    C5'
    O5'
    C5'
    C5'
    C4'
    C3'
    C3'
    O3'
    C2'
    C2'
    C2'
    C2'

    O5'
    H5T
    H52'
    H51'
    H42'
    H31'
    O3'
    H32'
    H22'
    H21'
    H11'
    H12'

    1.534
    1.513
    1.534
    1.534
    1.525
    1.521
    1.521
    1.525
    1.433
    1.433
    1.433
    1.433

    113.7
    108.2
    113.7
    113.7
    102.6
    100.9
    100.9
    111.7
    104.1
    104.1
    104.1
    104.1

    46.5
    170.4
    167.5
    285.5
    135.9
    204.2
    78.3
    65.4
    162.1
    285.5
    243.2
    119.0

    108.2
    107.7
    108.4
    109.1
    108.6
    113.0
    111.7
    107.1
    113.9
    110.1
    26.8
    28.2

    1.428
    0.971
    1.098
    1.101
    1.099
    1.097
    1.434
    0.973
    1.096
    1.093
    2.209
    2.173

    -1.00 ! C2H7NO3P Phosphoramidate (backbone for DNA)


    !
    1.57 !
    -0.82 !
    -0.82 !
    -0.56 !
    H11
    -0.86 !
    |
    0.33 !
    H13- C1-H12
    !
    \
    -0.19 !
    (-)O3 N1-H1
    0.09 !
    \ /
    0.09 !
    P1(+1)
    0.09 !
    / \
    !
    (-)O4 O2
    -0.19 !
    /
    0.09 !
    H23-C2-H22
    0.09 !
    |
    0.09 !
    H21

    BOND P1 N1
    P1 O2
    P1 O3
    BOND C1 H11
    C1 H12 C1 H13
    ! IC FOR THE g,g crystal conformation
    IC O3 P1 N1 C2 1.4816 107.70
    IC O3 P1 N1 H1 1.4816 107.70
    IC O4 P1 O2 C1 1.4812 105.80
    IC N1 P1 O2 C1 1.6728 99.90
    IC O2 P1 N1 C2 1.6480 99.90
    IC H11 C1 O2 P1 1.0913 113.30
    IC H12 C1 O2 P1 1.0790 106.20
    IC H13 C1 O2 P1 1.0898 111.90
    IC H21 C2 N1 P1 1.0841 108.20
    IC H22 C2 N1 P1 1.0805 109.90
    IC H23 C2 N1 P1 1.0862 111.20
    PATC FIRS NONE LAST NONE

    P1 O4
    N1 C2 N1
    C2 H21 C2 H22 C2
    (6-31G* opt. structure)
    342.80 123.13 1.4559
    171.10 119.02 0.9986
    43.90 118.08 1.4331
    158.10 118.08 1.4331
    96.20 123.13 1.4559
    253.00 123.13 1.6728
    12.40 123.13 1.6728
    131.00 123.13 1.6728
    196.00 118.08 1.6480
    316.40 118.08 1.6480
    76.70 118.08 1.6480

    H1 O2
    H23

    C1

    RESI TPHC
    -1.00 ! C5H11NO4P monoanionic 3'phosphoramidate-tetrahydrofur
    an
    ! used to fit epsilon
    ! Charges and atom types for the monoanionic phosphate groups were
    ! transfered from residue PHA
    ! Atom types for aliphatic hydrogens are a mess
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'

    OG3C51
    CG3C52
    HGA2
    HGA2

    -0.40 ! Note: has 1 asymmetric carbon.


    0.02 ! Abs. config is arbitrary.
    0.09
    0.09 !
    H41' O4' H11'

    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM N1
    ATOM H1
    ATOM P1
    ATOM O3
    ATOM O4
    ATOM O2
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'

    CG3C52
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O4' C1'
    H1 C1'
    H41' C4'
    C5' C5'
    O4'
    C1'
    C2'
    C3'
    C4'
    C2'
    C2'
    C3'
    C3'
    C4'
    O4'
    O4'
    C1'
    C1'
    C2'
    C2'
    C3'
    C4'
    C4'
    C3'
    P1
    N1
    P1
    P1
    P1
    O2
    C5'
    C5'
    C5'

    C1'
    N1
    C4'
    O2
    C4'
    O4'
    C1'
    C2'
    C3'
    O4'
    O4'
    C1'
    C1'
    C2'
    C3'
    C3'
    H11'
    H12'
    H21'
    H22'
    H31'
    H41'
    H42'
    N1
    O3
    P1
    O3
    O4
    O2
    C5'
    H51'
    H52'
    H53'

    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1
    NG2S3
    HGP1
    PG1
    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3

    0.02 !
    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.01 !
    0.09 !
    -0.86 !
    0.33 !
    1.57 !
    -0.82 !
    -0.82
    -0.56
    -0.19
    0.09
    0.09
    0.09
    C2'
    H11'
    H42'
    H51'
    C1'
    C2'
    C3'
    C4'
    O4'
    *C1'
    *C1'
    *C2'
    *C2'
    *C3'
    *C4'
    *C4'
    C2'
    C2'
    C3'
    C3'
    C4'
    O4'
    O4'
    C4'
    N1
    C3'
    N1
    N1
    N1
    P1
    O2
    O2
    O2

    C2'
    C1'
    N1
    C5'

    \ / \ /
    H42'-C4' C1'-H12'
    |
    |
    H31'-C3'-C2'-H21'
    /
    \
    H1-N1 O3 H22'
    \ /
    P1
    / \
    O2 O4
    |
    H51'-C5-H52'
    |
    H53'

    C3'
    H12'
    P1
    H52'
    C2'
    C3'
    C4'
    O4'
    C1'
    H11'
    H12'
    H21'
    H22'
    H31'
    H41'
    H42'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    C1'
    O4'
    H1
    C4'
    C3'
    C3'
    C3'
    N1
    P1
    P1
    P1

    C3' C4' C4' O4' C3'


    C2' H21' C2' H22' C3'
    P1 O3 P1 O4 P1
    C5' H53'
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    0.0000
    0.00 120.00
    0.0000
    0.00 -120.00
    0.0000
    0.00 120.00
    0.0000
    0.00 -120.00
    0.0000
    0.00 120.00
    0.0000
    0.00 120.00
    0.0000
    0.00 -120.00
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    1.0891 110.89 77.76
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    1.4816 107.70 171.10
    1.7190 119.98 185.77
    1.4771 109.35 14.75
    1.4818 105.19 150.42
    1.6379 101.65 263.47
    1.3955 119.61 286.08
    1.0859 107.43 179.85
    1.0835 111.18 299.56
    1.0868 111.29 60.84

    N1
    H31'
    O2
    106.18
    103.11
    100.86
    103.15
    108.09
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    119.02
    110.95
    120.00
    120.00
    120.00
    101.65
    119.61
    119.61
    119.61

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.9986
    1.5332
    1.4525
    1.4525
    1.4525
    1.7190
    1.6379
    1.6379
    1.6379

    PATC FIRS NONE LAST NONE


    RESI THNI
    imidazole
    GROUP

    0.00 ! C8H13N3O2 tetrahydrofuran with 3'-NH2, 5'-CH2OH, 1'-

    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2
    GROUP !
    ATOM H31'
    ATOM C3'
    ATOM N1
    ATOM H1
    ATOM H2
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5'

    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    -0.40 ! Note: has 3 asymmetric carbons.


    0.11 ! Abs. config is arbitrary.
    0.09
    0.11
    0.09

    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    ! Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    HE1
    HGR52
    0.09 !
    /
    CG2R51
    0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    |
    NG2R51 -0.04 ! HG-CG
    |
    CG2R53
    0.25 !
    \
    |
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2
    Hydroxyl group on C3'
    HGA1
    0.09
    CG3C51
    0.14
    NG321
    -0.91
    HGPAM2
    0.34
    HGPAM2
    0.34
    Methyl group on C4'
    CG321
    -0.17
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.09
    HGP1
    0.08

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' N1 N1 H1 N1 H2 C1' H12' C2' H21' C2' H22'
    BOND C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5'
    BOND C1' ND1 ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    N1
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    IC
    H1
    N1
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H2
    N1
    C3'
    C2'
    0.0 0.0 60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC
    C4'
    O4'
    C1'
    ND1
    0.0 0.0 256.98 0.0 0.0
    IC
    O4'
    C1'
    ND1
    CE1
    0.0 0.0 180.00 0.0 0.0
    IC
    C1'
    ND1
    CE1
    NE2
    0.0 0.0 181.56 0.0 0.0
    IC
    ND1
    CE1
    NE2
    CD2
    0.0 0.0 0.34 0.0 0.0
    IC
    CE1
    NE2
    CD2
    CG
    0.0 0.0 0.00 0.0 0.0
    IC
    HE1
    CE1
    NE2
    CD2
    0.0 0.0 180.40 0.0 0.0
    IC
    CE1
    NE2
    CD2
    HD2
    0.0 0.0 179.83 0.0 0.0
    IC
    NE2
    CD2
    CG
    HG
    0.0 0.0 178.45 0.0 0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0

    IC
    H52'
    IC
    O5'
    IC
    H5'
    PATC FIRS NONE

    C5'
    C4'
    C5'
    C4'
    O5'
    C5'
    LAST NONE

    O4'
    O4'
    C4'

    0.0 0.0 -59.66 0.0 0.0


    0.0 0.0 59.68 0.0 0.0
    0.0 0.0 59.68 0.0 0.0

    RESI THNP
    -1.00 ! C9H15N3O5P Tetrahydrofuran with 3'-NH-PO2-OCH3, 5'-C
    H2OH, 1'-imidazole
    GROUP
    ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons.
    ATOM C4' CG3C51
    0.11 ! Abs. config is arbitrary.
    ATOM H42' HGA1
    0.09
    ATOM C1' CG3C51
    0.11
    ATOM H12' HGA1
    0.09
    GROUP
    ATOM C2' CG3C52 -0.18
    ATOM H21' HGA2
    0.09
    ATOM H22' HGA2
    0.09
    GROUP
    ! Imidazole: transferred from isolated imidazole (IMIA)
    ATOM CG CG2R51 -0.05 !
    HE1
    ATOM HG HGR52
    0.09 !
    /
    ATOM CD2 CG2R51
    0.22 !
    ND1---CE1
    ATOM HD2 HGR52
    0.10 !
    /
    |
    ATOM ND1 NG2R51 -0.04 ! HG-CG
    |
    ATOM CE1 CG2R53
    0.25 !
    \
    |
    ATOM HE1 HGR52
    0.13 !
    CD2---NE2
    ATOM NE2 NG2R50 -0.70 !
    |
    !
    HD2
    GROUP ! phosphoramidate group on C3'
    ATOM H31' HGA1
    0.09
    ATOM C3' CG3C51
    0.14
    ATOM N1 NG2S3
    -0.86
    ATOM P1 PG1
    1.57
    ATOM H1 HGP1
    0.33
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5'

    Methyl group on C4'


    CG321
    -0.17
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.58
    HGP1
    0.42

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3

    -0.820
    -0.820
    -0.560
    -0.190
    0.090
    0.090
    0.090

    O4' C1'
    N1 N1
    H31' C4'
    H51' C5'
    ND1 ND1
    HE1 CD2
    N1 P1
    H51 C5
    table is
    O4'
    C1'

    C2' C2' C3'


    H1 C1' H12'
    H42'
    H52' C5' O5'
    CE1 CE1 NE2
    HD2 CG HG
    O5 P1 O3
    H52 C5 H53
    only an initial
    C1'
    C2'
    C2'
    C3'

    O3
    O4
    O5
    C5
    H51
    H52
    H53

    BOND C1'
    BOND C3'
    BOND C3'
    BOND C5'
    BOND C1'
    BOND CE1
    BOND P1
    BOND C5
    ! This IC
    IC C4'
    IC O4'

    !
    !
    !
    !
    !
    !
    !
    C3' C4' C4' O4' C4' C5'
    C2' H21' C2' H22'
    O5' H5'
    NE2 CD2 CD2 CG CG ND1
    P1

    O4

    O5

    guess:
    1.4055 108.09
    1.4127 106.18

    C5
    23.45 106.18
    3.96 103.11

    1.5457
    1.5346

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    C1'
    C2'
    C2'
    C3'
    C3'
    C4'
    ND1
    C1'
    H12'
    C1'
    H21'
    C2'
    H22'
    C2'
    H31'
    C3'
    C5'
    C4'
    H42'
    C4'
    N1
    C3'
    P1
    N1
    C3'
    N1
    O5
    N1
    O5
    N1
    O3
    P1
    C5
    O5
    H51
    C5
    H52
    C5
    H53
    C5
    O4'
    C1'
    C1'
    ND1
    ND1
    CE1
    CE1
    NE2
    HE1
    CE1
    CE1
    NE2
    NE2
    CD2
    H51'
    C5'
    H52'
    C5'
    O5'
    C5'
    H5'
    O5'
    FIRS NONE LAST

    C3'
    C4'
    O4'
    C2'
    C2'
    C3'
    C3'
    C4'
    O4'
    O4'
    C4'
    C3'
    P1
    *P1
    *P1
    N1
    P1
    O5
    O5
    O5
    ND1
    CE1
    NE2
    CD2
    NE2
    CD2
    CG
    C4'
    C4'
    C4'
    C5'
    NONE

    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    C1'
    O4'
    C4'
    O5
    O3
    O4
    H1
    N1
    P1
    P1
    P1
    CE1
    NE2
    CD2
    CG
    CD2
    HD2
    HG
    O4'
    O4'
    O4'
    C4'

    1.5457
    1.5346
    1.5211
    1.0856
    1.0818
    1.0846
    1.0822
    1.0806
    1.0891
    1.0808
    1.4028
    0.0000
    0.0000
    0.0000
    0.0000
    1.4816
    0.0000
    0.0000
    0.0000
    0.0000
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    103.11 -26.93 100.86


    100.86 41.73 103.15
    103.15 -41.62 108.09
    111.62 123.53 103.11
    113.32 -114.11 103.11
    110.65 91.68 100.86
    110.88 -148.45 100.86
    113.53 162.89 103.15
    110.89 77.76 108.09
    108.72 -162.12 108.09
    110.98 -77.39 103.15
    000.00 180.00 000.00
    000.00 -95.22 000.00
    000.00 -115.82 000.00
    000.00 115.90 000.00
    107.70 171.10 119.02
    000.00 -46.90 000.00
    000.00 180.00 000.00
    000.00 60.00 000.00
    000.00 -60.00 000.00
    0.0 180.00 0.0 0.0
    0.0 181.56 0.0 0.0
    0.0 0.34 0.0 0.0
    0.0 0.00 0.0 0.0
    0.0 180.40 0.0 0.0
    0.0 179.83 0.0 0.0
    0.0 178.45 0.0 0.0
    0.0 -179.98 0.0 0.0
    0.0 -59.66 0.0 0.0
    0.0 59.68 0.0 0.0
    0.0 59.68 0.0 0.0

    !toppar_all27_na_carbocyclic.str
    RESI CPEN
    0.00 ! C5H10 cyclopentane, adm jr.
    ! with north atom types
    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C1 CG3C52 -0.18 !
    H51 H52
    ATOM H11 HGA2
    0.09 !
    \ /
    ATOM H12 HGA2
    0.09 !
    C5
    GROUP
    !
    H41 / \ H11
    ATOM C2 CG3C52 -0.18 !
    \ /
    \ /
    ATOM H21 HGA2
    0.09 !
    H42-C4
    C1-H12
    ATOM H22 HGA2
    0.09 !
    |
    |
    GROUP
    !
    H31-C3------C2-H21
    ATOM C3 CG3C52 -0.18 !
    |
    |
    ATOM H31 HGA2
    0.09 !
    H32
    H22
    ATOM H32 HGA2
    0.09
    GROUP
    ATOM C4 CG3C52 -0.18
    ATOM H41 HGA2
    0.09
    ATOM H42 HGA2
    0.09
    GROUP
    ATOM C5 CG3C52 -0.18
    ATOM H51 HGA2
    0.09
    ATOM H52 HGA2
    0.09

    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0000
    0.0000
    0.0000
    0.0000
    0.9986
    0.0000
    0.0000
    0.0000
    0.0000

    BOND C1 C2
    C2 C3
    C3
    BOND C1 H11
    C1 H12
    C2
    BOND C3 H31
    C3 H32
    C4
    BOND C5 H51
    C5 H52
    ! internal coordinates from parameter
    IC C1 C2 C3
    C4
    0.0000
    IC C2 C3 C4
    C5
    0.0000
    IC C3 C4 C5
    C1
    0.0000
    IC C5 C2 *C1 H11
    0.0000
    IC C5 C2 *C1 H12
    0.0000
    IC C1 C3 *C2 H21
    0.0000
    IC C1 C3 *C2 H22
    0.0000
    IC C2 C4 *C3 H31
    0.0000
    IC C2 C4 *C3 H32
    0.0000
    IC C3 C5 *C4 H41
    0.0000
    IC C3 C5 *C4 H42
    0.0000
    IC C4 C1 *C5 H51
    0.0000
    IC C4 C1 *C5 H52
    0.0000
    PATC FIRS NONE LAST NONE
    RESI CPES

    C4
    H21
    H41
    file,
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4
    C2
    C4

    C5
    H22
    H42

    C5

    C1

    note initial planar geometry


    0.0
    0.00 0.0000
    0.0
    0.00 0.0000
    0.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000

    0.00 ! C5H10 cyclopentane, adm jr.


    ! with south atom types

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C1 CG3C52 -0.18 !
    H51 H52
    ATOM H11 HGA2
    0.09 !
    \ /
    ATOM H12 HGA2
    0.09 !
    C5
    GROUP
    !
    H41 / \ H11
    ATOM C2 CG3C52 -0.18 !
    \ /
    \ /
    ATOM H21 HGA2
    0.09 !
    H42-C4
    C1-H12
    ATOM H22 HGA2
    0.09 !
    |
    |
    GROUP
    !
    H31-C3------C2-H21
    ATOM C3 CG3C52 -0.18 !
    |
    |
    ATOM H31 HGA2
    0.09 !
    H32
    H22
    ATOM H32 HGA2
    0.09
    GROUP
    ATOM C4 CG3C52 -0.18
    ATOM H41 HGA2
    0.09
    ATOM H42 HGA2
    0.09
    GROUP
    ATOM C5 CG3C52 -0.18
    ATOM H51 HGA2
    0.09
    ATOM H52 HGA2
    0.09
    BOND C1 C2
    C2 C3
    C3
    BOND C1 H11
    C1 H12
    C2
    BOND C3 H31
    C3 H32
    C4
    BOND C5 H51
    C5 H52
    ! internal coordinates from parameter
    IC C1 C2 C3
    C4
    0.0000
    IC C2 C3 C4
    C5
    0.0000
    IC C3 C4 C5
    C1
    0.0000
    IC C5 C2 *C1 H11
    0.0000
    IC C5 C2 *C1 H12
    0.0000
    IC C1 C3 *C2 H21
    0.0000
    IC C1 C3 *C2 H22
    0.0000

    C4
    H21
    H41
    file,
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4
    C2
    C4

    C5
    H22
    H42

    C5

    C1

    note initial planar geometry


    0.0
    0.00 0.0000
    0.0
    0.00 0.0000
    0.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000
    120.0
    0.00 0.0000
    240.0
    0.00 0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    C2 C4 *C3 H31
    C2 C4 *C3 H32
    C3 C5 *C4 H41
    C3 C5 *C4 H42
    C4 C1 *C5 H51
    C4 C1 *C5 H52
    FIRS NONE LAST NONE

    RESI BPNP

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.0
    240.0
    120.0
    240.0
    120.0
    240.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -1.00 ! C7H12O4P North carbocyclic sugar with 3'-OPOCH3


    ! used to parameterize epsilon

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C2 CG3C51
    0.01 ! This charge changed from -0.09 to make it
    ATOM H21 HGA1
    0.09 ! compatible with -OPOCH3
    ATOM O3' OG303
    -0.57 !
    ATOM P
    PG1
    1.50 !
    ATOM O1P OG2P1
    -0.78 !
    ATOM O2P OG2P1
    -0.78 !
    ATOM O5' OG303
    -0.57 !
    ATOM C5' CG331
    -0.17 !
    ATOM H51' HGA3
    0.09 !
    ATOM H52' HGA3
    0.09 !
    ATOM H53' HGA3
    0.09 !
    !
    H61 H62
    !
    \ /
    !
    C6
    GROUP
    !
    / \ H11
    ATOM C4 CG3C52 -0.18 !
    /
    \ /
    ATOM H41 HGA2
    0.09 !
    H51-C5-----C1
    H51'
    ATOM H42 HGA2
    0.09 !
    |
    |
    /
    GROUP
    !
    H41-C4
    C2--O3'--P--O5'-C5'-H52'
    ATOM C3 CG3C52 -0.18 !
    / \
    / \
    // \ _ \
    ATOM H31 HGA2
    0.09 !
    H42 \ / H21 O1P O2P
    H53'
    ATOM H32 HGA2
    0.09 !
    C3
    GROUP
    !
    / \
    ATOM C1 CG3RC1 -0.09 !
    H31 H32
    ATOM H11 HGA1
    0.09
    GROUP
    ATOM C5 CG3RC1 -0.09 !
    ATOM H51 HGA1
    0.09 !
    GROUP
    ATOM C6 CG3C31 -0.18 !
    ATOM H61 HGA2
    0.09 !
    ATOM H62 HGA2
    0.09 !
    BOND C1 C2
    C2 C3
    C3 C4
    C4 C5
    BOND C5 C1
    C5 C6
    C6 C1
    C5 H51
    BOND C2 H21
    C4 H42
    C3 H31
    C3 H32
    BOND C4 H41
    C6 H61
    C1 H11
    BOND C6 H62
    C2 O3'
    O3' P
    P
    O1P
    BOND P
    O2P
    P
    O5'
    O5' C5'
    C5' H51'
    BOND C5' H52'
    C5' H53'
    ! internal coordinates from parameter file, note initial planar geometry
    IC C1 C2 C3
    C4
    0.0000
    0.00
    0.0
    0.00 0.0000
    IC C2 C3 C4
    C5
    0.0000
    0.00
    0.0
    0.00 0.0000
    IC C3 C4 C5
    C1
    0.0000
    0.00
    0.0
    0.00 0.0000
    IC C2 C5 *C1 H11
    0.0000
    0.00 120.0
    0.00 0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C2
    C2
    C3
    C3
    C1
    C4
    C1
    C1
    O3'
    P
    O1P
    O2P
    O5'
    C5'
    H51'
    H52'
    H53'

    C3
    C3
    C4
    C4
    C5
    C5
    C4
    C1
    C5
    C5
    C2
    O3'
    P
    P
    P
    O5'
    C5'
    C5'
    C5'

    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    *C6
    *C6
    C1
    C2
    O3'
    O3'
    O3'
    P
    O5'
    O5'
    O5'

    H21
    O3'
    H31
    H32
    H41
    H42
    H51
    C6
    H61
    H62
    C5
    C1
    C2
    C2
    C2
    O3'
    P
    P
    P

    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    1.4028 110.98 -77.39 103.15
    0.0
    0.0 180.00
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0 180.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI BPSP
    -1.00 ! C7H12O4P south carbcyclic sugar with 3'-OPOCH3
    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C1 CG3RC1 -0.09 !
    H31 H32
    ATOM H11 HGA1
    0.09 !
    \ /
    !
    C6
    GROUP
    !
    / \
    ATOM C2 CG3C52 -0.18 !
    /
    \
    ATOM H21 HGA2
    0.09 !
    H51-C5------C1-H11
    ATOM H22 HGA2
    0.09 !
    |
    |
    GROUP
    !
    H41-C4
    C2-H22
    ATOM C6 CG3C31 -0.18 !
    / \
    / \
    ATOM H61 HGA2
    0.09 !
    H42 \ / H21
    ATOM H62 HGA2
    0.09 !
    C3-H31
    GROUP
    !
    |
    ATOM C4 CG3C52 -0.18 !
    O3'
    H51'
    ATOM H41 HGA2
    0.09 !
    \
    /
    ATOM H42 HGA2
    0.09 !
    P--O5'-C5'-H52'
    !
    // \ _ \
    GROUP
    !
    O1P O2P
    H53'
    ATOM C5 CG3RC1 -0.09
    ATOM H51 HGA1
    0.09
    GROUP
    ATOM C3 CG3C51
    0.01 ! This charge changed from -0.09 to make it
    ATOM H31 HGA1
    0.09 ! compatible with -OPOCH3
    ATOM O3' OG303
    -0.57 !
    ATOM P
    PG1
    1.50 !
    ATOM O1P OG2P1
    -0.78 !
    ATOM O2P OG2P1
    -0.78 !
    ATOM O5' OG303
    -0.57 !
    ATOM C5' CG331
    -0.17 !
    ATOM H51' HGA3
    0.09 !
    ATOM H52' HGA3
    0.09 !
    ATOM H53' HGA3
    0.09 !

    BOND C1 C2
    C2
    BOND C5 C1
    C5
    BOND C1 H11
    C2
    BOND C6 H61
    C6
    BOND C5 H51
    C3
    BOND P
    O1P
    P
    BOND C5' H51'
    C5'
    ! internal coordinates
    IC C1 C2 C3
    C4
    IC C2 C3 C4
    C5
    IC C3 C4 C5
    C1
    IC C5 C2 *C1 H11
    IC C2 C5 *C1 C6
    IC C1 C3 *C2 H21
    IC C1 C3 *C2 H22
    IC C2 C4 *C3 H31
    IC C2 C4 *C3 O3'
    IC C3 C5 *C4 H41
    IC C3 C5 *C4 H42
    IC C4 C1 *C5 H51
    IC C4 C1 *C5 H52
    IC C1 C5 *C6 H61
    IC C1 C5 *C6 H62
    IC O3' C3 C4
    C5
    IC P
    O3' C3
    C4
    IC O1P P O3' C3
    IC O2P P O3' C3
    IC O5' P O3' C3
    IC C5' O5' P
    O3'
    IC H51' C5' O5' P
    IC H52' C5' O5' P
    IC H53' C5' O5' P

    C3
    C6
    H21
    H62
    H31
    O2P
    H52'

    C3
    C6
    C2
    C4
    C3
    P
    C5'

    C4
    C1
    H22
    H41
    O3'
    O5'
    H53'

    C4
    C4

    C5
    H42

    O3' P
    O5' C5'

    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    1.4028 110.98 -77.39 103.15
    0.0
    0.0 180.00
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0 180.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI CSAD

    0.00 ! C11H13N5 carbocyclic sugar with adenine base, south


    ! base attached to C1 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C52 -0.18 !
    /
    \
    ATOM H21S HGA2
    0.09 ! H51S-C5S----C1S-----------*
    ATOM H22S HGA2
    0.09 !
    |
    |
    GROUP
    ! H41S-C4S
    C2S-H22S
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !

    ATOM H61S
    ATOM H62S
    GROUP
    ATOM C1S
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9

    HGA2
    HGA2
    CG3RC1
    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.00
    0.28
    -0.71
    0.34
    0.12
    -0.05

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N1
    C2
    H2
    N3
    C4
    C6
    N6
    H61
    H62

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64
    NG2S3
    HGP4
    HGP4

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46
    -0.77
    0.38
    0.38

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    DOUB

    C1S
    C5S
    C2S
    C4S
    C6S
    N9
    C6
    C5
    N1

    C2S
    C1S
    H21S
    H41S
    H62S
    C4
    N6
    N7
    C6

    IMPR H62 C6

    0.09 !
    0.09 !

    C2S
    C5S
    C2S
    C4S
    C1S
    N9
    N6
    C8
    C2
    H61 N6

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S N9
    IC C1S C3S *C2S H21S
    IC C1S C3S *C2S H22S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C3S C2S C1S N9
    ady defined
    IC C5S C1S N9 C4
    IC C1S C4 *N9 C8
    IC C4 N9 C8 N7
    IC C8 N9 C4 C5
    IC C8 N7 C5 C6
    IC N7 C5 C6 N1
    IC C5 C6 N1 C2
    IC N9 C5 *C4 N3
    IC C5 N1 *C6 N6
    IC N1 C6 N6 H61
    IC H61 C6 *N6 H62

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H61 H62
    \ /
    N6
    |
    C6
    // \
    N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H2 N3
    \
    \
    \
    \
    *

    C3S
    C6S
    H22S
    H42S
    N9
    C8
    H61
    H8
    N3
    N6

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C4
    N6
    C2
    C4

    N3
    H62
    H2
    C5

    C2
    C6

    N1
    C5

    N7

    C8

    N1

    C5

    C3S H32S
    C6S H61S

    C6

    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 300.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000 108.00 140.0 120.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    1.5284 101.97 147.80 120.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre

    1.5251
    1.4896
    1.376
    1.367
    0.0
    0.0
    0.0
    1.376
    1.409
    1.337
    1.01

    1.3783 !chi
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01

    120.00
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0

    -150.0
    -180.00
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0

    125.59
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00

    IC
    IC
    IC
    IC
    IC
    PATC

    C5 N1 *C6 N6
    N1 C6 N6 H61
    H61 C6 *N6 H62
    N9 N7 *C8 H8
    N1 N3 *C2 H2
    FIRS NONE LAST NONE

    RESI CSGU

    1.409
    1.337
    1.01
    0.0
    0.0

    117.6 -180.0
    119.0
    0.0
    119.0 180.0
    0.0 180.0
    0.0 180.0

    119.0
    119.0
    121.00
    0.0
    0.0

    0.00 ! C11H13N5O carbocyclic sugar with guanine base, south


    ! base attached to C1 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C52 -0.18 !
    /
    \
    ATOM H21S HGA2
    0.09 ! H51S-C5S----C1S-----------*
    ATOM H22S HGA2
    0.09 !
    |
    |
    GROUP
    ! H41S-C4S
    C2S-H22S
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1
    0.00 !
    ATOM N9 NG2R51 -0.14 !
    O6
    ATOM C4 CG2RC0
    0.14 !
    ||
    GROUP
    !
    C6
    ATOM N3 NG2R62 -0.66 !
    / \
    ATOM C2 CG2R64
    0.76 !
    H1-N1 C5--N7\\
    ATOM N1 NG2R61 -0.38 !
    |
    ||
    C8-H8
    ATOM H1 HGP1
    0.28 !
    C2 C4--N9/
    GROUP
    !
    / \\ /
    \
    ATOM N2 NG2S3
    -0.64 !
    H21-N2 N3
    \
    ATOM H21 HGP4
    0.31 !
    |
    \
    ATOM H22 HGP4
    0.33 !
    H22
    \
    GROUP
    !
    *
    ATOM C6 CG2R63
    0.55 !
    ATOM O6 OG2D4
    -0.47 !
    ATOM C5 CG2RC0 -0.08
    GROUP
    ATOM N7 NG2R50 -0.69
    ATOM C8 CG2R53
    0.41
    ATOM H8 HGR52
    0.28
    BOND
    BOND
    BOND
    BOND

    C1S
    C5S
    C2S
    C4S

    1.337
    1.01
    1.01
    0.0
    0.0

    C2S
    C1S
    H21S
    H41S

    C2S
    C5S
    C2S
    C4S

    C3S
    C6S
    H22S
    H42S

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S
    C3S H32S
    C6S H61S

    BOND
    BOND
    BOND
    BOND
    BOND

    C6S
    N9
    C4
    N2
    C5

    H62S
    C4
    C5
    H22
    N7

    IMPR N2

    N3

    DONO
    DONO
    DONO
    ACCE
    ACCE
    ACCE

    N2
    N2
    N1
    C6

    H21
    H22
    H1
    O6
    N3
    N7

    C1S
    N9
    N3
    N1
    N7
    N1

    C2

    N9
    C8
    C2
    H1
    C8

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S N9
    IC C1S C3S *C2S H21S
    IC C1S C3S *C2S H22S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C3S C2S C1S N9
    ady defined
    IC C5S C1S N9 C4
    IC C1S C4 *N9 C8
    IC C4 N9 C8 N7
    IC C8 N9 C4 C5
    IC N9 C5 *C4 N3
    IC C5 C4 N3 C2
    IC C4 N3 C2 N1
    IC N1 N3 *C2 N2
    IC N3 C2 N2 H21
    IC H21 C2 *N2 H22
    IC N3 C2 N1 C6
    IC C6 C2 *N1 H1
    IC C5 N1 *C6 O6
    IC N9 N7 *C8 H8

    O6

    C4
    C2
    N1

    N3
    N2
    C6

    N1

    C5

    C8
    C2
    C6
    C6

    H8
    N1
    O6

    N2
    C6

    H22 H21 C2

    H21
    C5
    N2

    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 300.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000 108.00 140.0 120.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    1.5284 101.97 147.80 113.71

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre

    1.5251
    1.4896
    1.377
    1.374
    1.377
    1.377
    1.355
    1.375
    1.327
    1.01
    1.327
    1.393
    1.415
    0.0

    1.3783 !chi
    1.367
    1.304
    1.377
    1.355
    1.327
    1.375
    1.341
    1.01
    1.01
    1.393
    1.03
    1.239
    0.0

    120.00
    125.97
    106.0
    106.0
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    124.0
    124.9
    111.7
    0.0

    -150.0
    -180.00
    0.0
    0.0
    180.0
    0.0
    0.0
    180.0
    180.0
    -180.0
    0.0
    180.00
    180.0
    180.0

    125.59
    106.0
    113.5
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    116.5
    124.9
    117.4
    120.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI CSTH

    0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, south


    ! base attached to C1 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S

    GROUP
    ATOM C2S
    ATOM H21S
    ATOM H22S
    GROUP
    ATOM C3S
    ATOM H31S
    ATOM H32S
    GROUP
    ATOM C5S
    ATOM H51S
    GROUP
    ATOM C6S
    ATOM H61S
    ATOM H62S
    GROUP
    ATOM C1S
    ATOM N1
    ATOM C6
    ATOM H6
    GROUP
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    GROUP
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C1S
    C5S
    C2S
    C4S
    C6S
    N1
    C2
    C5
    C5M

    CG3RC1
    HGA1

    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    !
    -0.09 !
    0.09

    CG3C31
    HGA2
    HGA2

    -0.18 !
    0.09 !
    0.09 !

    CG3RC1
    NG2R61
    CG2R62
    HGR62

    0.00
    -0.30
    0.17
    0.13

    CG2R63
    OG2D4
    NG2R61
    HGP1

    0.57
    -0.47
    -0.46
    0.36

    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3
    HGA3

    0.54
    -0.49
    -0.15
    -0.11
    0.07
    0.07
    0.07

    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    C2S
    C1S
    H21S
    H41S
    H62S
    C2
    N3
    C5M
    H52

    IMPR O2

    N1

    DONO H3
    ACCE O2
    ACCE O4

    N3
    C2
    C4

    C2S
    C5S
    C2S
    C4S
    C1S
    N1
    N3
    C5
    C5M
    N3

    C2

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S N1
    IC C1S C3S *C2S H21S

    / \
    /
    \
    H51S-C5S----C1S-----------*
    |
    |
    H41S-C4S
    C2S-H22S
    / \
    / \
    H42S \ / H21S
    C3S
    / \
    H31S H32S

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H51
    O4
    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    *

    C3S
    C6S
    H22S
    H42S
    N1
    C6
    H3
    C6
    H53
    O4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C2
    N3
    C6

    O2
    C4
    H6

    C4 C5
    C4 O4
    C5M H51

    N3

    C5

    C3S H32S
    C6S H61S

    C4

    0.0000
    0.00
    0.0
    0.0000
    0.00
    0.0
    0.0000
    0.00
    0.0
    0.0000
    0.00 300.0
    0.0000
    0.00 120.0
    0.0000
    0.00 240.0
    0.0000 108.00 140.0
    0.0000
    0.00 120.0

    C5M C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    120.00
    0.00

    C6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5

    IC
    IC
    IC
    IC
    IC
    IC
    !IC
    ady
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1S C3S *C2S


    C2S C4S *C3S
    C2S C4S *C3S
    C3S C5S *C4S
    C3S C5S *C4S
    C4S C1S *C5S
    C3S C2S C1S
    defined
    C5S C1S N1
    C1S C2 *N1
    C2 N1 C6
    C6 N1 C2
    N1 N3 *C2
    N1 C2 N3
    C5 N3 *C4
    C2 C4 *N3
    C4 C6 *C5
    N1 C5 *C6
    C6 C5 C5M
    C5 H51 *C5M
    H51 H52 *C5M

    H22S
    H31S
    H32S
    H41S
    H42S
    H51S
    N1

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97

    240.0
    120.0
    240.0
    120.0
    240.0
    120.0
    147.80

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    120.00

    C2
    C6
    C5
    N3
    O2
    C4
    O4
    H3
    C5M
    H6
    H51
    H52
    H53

    0.0000 120.00 -130.0 125.59


    0.0000
    0.0 -180.00
    0.0
    0.0000
    0.0
    -0.02
    0.0
    0.0000
    0.0
    0.06
    0.0
    0.0000
    0.0 -179.95
    0.0
    0.0000
    0.0
    -0.07
    0.0
    0.0000
    0.0 179.98
    0.0
    0.0000
    0.0 180.00
    0.0
    0.0000
    0.0 -179.94
    0.0
    0.0
    0.0
    180.0
    0.0
    0.0
    0.0
    90.0
    0.0
    0.0
    0.0
    115.0
    0.0
    0.0
    0.0 -115.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    1.3783 !chi
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI CSCY

    0.00 ! C10H13N3O carbocyclic sugar with cytosine base, south


    ! base attached to C1 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C52 -0.18 !
    /
    \
    ATOM H21S HGA2
    0.09 ! H51S-C5S----C1S-----------*
    ATOM H22S HGA2
    0.09 !
    |
    |
    GROUP
    ! H41S-C4S
    C2S-H22S
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1
    0.00 !
    GROUP
    !
    H42 H41
    ATOM N1 NG2R61 -0.16 !
    \ /
    ATOM C6 CG2R62
    0.11 !
    N4
    ATOM H6 HGR62
    0.05 !
    |
    GROUP
    !
    C4
    ATOM C2 CG2R63
    0.53 !
    / \\
    ATOM O2 OG2D4
    -0.48 !
    H5-C5 N3

    ATOM N3
    ATOM C4
    GROUP
    ATOM N4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H5

    NG2R62
    CG2R64

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2S
    C1S
    H21S
    H41S
    H62S
    C2
    N3
    C5

    C1S
    C5S
    C2S
    C4S
    C6S
    N1
    C2
    C4

    NG2S3
    HGP4
    HGP4
    CG2R62
    HGR62

    IMPR O2 N1
    IMPR H42 C4
    DONO
    DONO
    ACCE
    ACCE

    -0.67 !
    0.62 !
    !
    -0.58 !
    0.31 !
    0.27 !
    !
    -0.10 !
    0.10 !
    C2S
    C5S
    C2S
    C4S
    C1S
    N1
    N3
    C5

    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    *

    N3 C2
    H41 N4

    C3S
    C6S
    H22S
    H42S
    N1
    C6
    C4
    C6
    N4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C2
    C4
    C5

    O2
    N4
    H5

    N3

    C5

    C4S C5S
    C3S H32S
    C6S H61S
    N4
    C6

    H41
    H6

    N4

    H42

    C4

    H42 N4
    H41 N4
    O2 C2
    N3

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S N1
    IC C1S C3S *C2S H21S
    IC C1S C3S *C2S H22S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C3S C2S C1S N1
    ady defined
    IC C5S C1S N1 C2
    IC C1S C2 *N1 C6
    IC C2 N1 C6 C5
    IC C6 N1 C2 N3
    IC N1 N3 *C2 O2
    IC N1 C2 N3 C4
    IC C5 N3 *C4 N4
    IC N3 C4 N4 H41
    IC H41 C4 *N4 H42
    IC C6 C4 *C5 H5
    IC N1 C5 *C6 H6

    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 300.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000 108.00 140.0 120.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    0.0000
    0.00 240.0
    0.00
    0.0000
    0.00 120.0
    0.00
    1.5284 101.97 147.80 113.71

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre

    0.0000 120.00 -130.0 125.59


    0.0000
    0.00 -180.00
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 180.0
    0.00
    0.0000
    0.00
    0.0
    0.00
    0.0000
    0.00 180.00
    0.00
    0.0000
    0.00
    0.00
    0.00
    0.0000
    0.00 180.00
    0.00
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.0
    0.0

    1.3783 !chi
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI CNAD

    0.00 ! C11H13N5 carbocyclic sugar with adenine base, north


    ! base attached to C2 of carbocyclic sugar

    ! used to parameterize chi


    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1 -0.09 !
    ATOM H11S HGA1
    0.09 !
    GROUP
    ATOM C5 CG2RC0
    0.28 !
    H61 H62
    ATOM N7 NG2R50 -0.71 !
    \ /
    ATOM C8 CG2R53
    0.34 !
    N6
    ATOM H8 HGR52
    0.12 !
    |
    ATOM N9 NG2R51 -0.05 !
    C6
    !
    // \
    ATOM N1 NG2R62 -0.74 !
    N1 C5--N7\\
    ATOM C2 CG2R64
    0.50 !
    |
    ||
    C8-H8
    ATOM H2 HGR62
    0.13 !
    C2 C4--N9/
    ATOM N3 NG2R62 -0.75 !
    / \\ /
    \
    ATOM C4 CG2RC0
    0.43 !
    H2 N3
    \
    ATOM C6 CG2R64
    0.46 !
    \
    ATOM N6 NG2S3
    -0.77 !
    \
    ATOM H61 HGP4
    0.38 !
    \
    ATOM H62 HGP4
    0.38 !
    *
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    H2
    DOUB

    C1S
    C5S
    C1S
    C4S
    C6S
    N9
    N6

    C2S
    C1S
    H11S
    H41S
    H62S
    C4
    H61

    C2S
    C5S
    C2S
    C4S
    C2S
    N9
    N6

    C3S
    C6S
    H21S
    H42S
    N9
    C8
    H62

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C4
    C6

    N3
    C5

    C2
    C5

    N1
    N7

    N1

    C6

    C2

    N3

    C4

    C5

    N7

    C8

    IMPR H62 C6

    H61 N6

    N1

    C5

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S

    N6
    0.0000
    0.0000

    0.00
    0.00

    C3S H32S
    C6S H61S
    C6
    C8

    C6
    0.0
    0.0

    0.00
    0.00

    0.0000
    0.0000

    N6
    H8

    C2

    IC C3S C4S C5S C1S


    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N9
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N9
    ady defined
    IC C1S C2S N9 C4
    IC C2S C4 *N9 C8
    IC C4 N9 C8 N7
    IC C8 N9 C4 C5
    IC C8 N7 C5 C6
    IC N7 C5 C6 N1
    IC C5 C6 N1 C2
    IC N9 C5 *C4 N3
    IC C5 N1 *C6 N6
    IC N1 C6 N6 H61
    IC H61 C6 *N6 H62
    IC C5 N1 *C6 N6
    IC N1 C6 N6 H61
    IC H61 C6 *N6 H62
    IC N9 N7 *C8 H8
    IC N1 N3 *C2 H2
    PATCH FIRST NONE LAST NONE
    RESI CNGU

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97
    1.5251
    1.4896
    1.376
    1.367
    0.0
    0.0
    0.0
    1.376
    1.409
    1.337
    1.01
    1.409
    1.337
    1.01
    0.0
    0.0

    113.71
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0
    0.0
    0.0

    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71
    -120.0
    -180.00
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0

    125.59
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    1.3783 !chi
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0

    0.00 ! C11H13N5O carbocyclic sugar with guanine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP

    ATOM C1S
    ATOM H11S
    GROUP
    ATOM N9
    ATOM C4
    GROUP
    ATOM N3
    ATOM C2
    ATOM N1
    ATOM H1
    GROUP
    ATOM N2
    ATOM H21
    ATOM H22
    GROUP
    ATOM C6
    ATOM O6
    ATOM C5
    GROUP
    ATOM N7
    ATOM C8
    ATOM H8

    CG3RC1
    HGA1

    -0.09 !
    0.09 !

    NG2R51
    CG2RC0

    CG2R63
    OG2D4
    CG2RC0

    -0.14 !
    0.14 !
    !
    -0.66 !
    0.76 !
    -0.38 !
    0.28 !
    !
    -0.64 !
    0.31 !
    0.33 !
    !
    0.55 !
    -0.47 !
    -0.08

    NG2R50
    CG2R53
    HGR52

    -0.69
    0.41
    0.28

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2S
    C1S
    H11S
    H41S
    H62S
    C4
    C5
    H22
    N7

    C1S
    C5S
    C1S
    C4S
    C6S
    N9
    C4
    N2
    C5

    NG2R62
    CG2R64
    NG2R61
    HGP1
    NG2S3
    HGP4
    HGP4

    IMPR N2

    N3

    DONO
    DONO
    DONO
    ACCE
    ACCE
    ACCE

    N2
    N2
    N1
    C6

    H21
    H22
    H1
    O6
    N3
    N7

    C2S
    C5S
    C2S
    C4S
    C2S
    N9
    N3
    N1
    N7
    N1

    C2

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N9
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N9
    ady defined
    IC C1S C2S N9 C4

    O6
    ||
    C6
    / \
    H1-N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H21-N2 N3
    \
    |
    \
    H22
    \
    *

    C3S
    C6S
    H21S
    H42S
    N9
    C8
    C2
    H1
    C8
    O6

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C4
    C2
    N1

    N3
    N2
    C6

    C8
    C2
    C6

    N1

    C5

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97

    C3S H32S
    C6S H61S

    C6

    H8
    N1
    O6

    N2
    C6

    H22 H21 C2

    0.0
    0.00
    0.0
    0.00
    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71

    1.5251 113.71 -120.00 125.59

    H21
    C5
    N2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    1.3783 !chi

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2S
    C4
    C8
    N9
    C5
    C4
    N1
    N3
    H21
    N3
    C6
    C5
    N9

    C4
    N9
    N9
    C5
    C4
    N3
    N3
    C2
    C2
    C2
    C2
    N1
    N7

    *N9
    C8
    C4
    *C4
    N3
    C2
    *C2
    N2
    *N2
    N1
    *N1
    *C6
    *C8

    C8
    N7
    C5
    N3
    C2
    N1
    N2
    H21
    H22
    C6
    H1
    O6
    H8

    1.4896
    1.377
    1.374
    1.377
    1.377
    1.355
    1.375
    1.327
    1.01
    1.327
    1.393
    1.415
    0.0

    125.97
    106.0
    106.0
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    124.0
    124.9
    111.7
    0.0

    -180.00
    0.0
    0.0
    180.0
    0.0
    0.0
    180.0
    180.0
    -180.0
    0.0
    180.00
    180.0
    180.0

    106.0
    113.5
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    116.5
    124.9
    117.4
    120.0
    0.0

    1.367
    1.304
    1.377
    1.355
    1.327
    1.375
    1.341
    1.01
    1.01
    1.393
    1.03
    1.239
    0.0

    PATCH FIRST NONE LAST NONE


    RESI CNTH

    0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1 -0.09 !
    ATOM H11S HGA1
    0.09 !
    GROUP
    !
    ATOM N1 NG2R61 -0.30 !
    H51
    O4
    ATOM C6
    ATOM H6

    CG2R62
    HGR62

    ATOM
    ATOM
    ATOM
    ATOM

    C2
    O2
    N3
    H3

    CG2R63
    OG2D4
    NG2R61
    HGP1

    ATOM C4
    ATOM O4
    ATOM C5

    CG2R63
    OG2D4
    CG2R62

    0.17 !
    0.13 !
    !
    0.57 !
    -0.47 !
    -0.46 !
    0.36 !
    !
    0.54 !
    -0.49 !
    -0.15 !

    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \

    ATOM
    ATOM
    ATOM
    ATOM

    C5M
    H51
    H52
    H53

    CG331
    HGA3
    HGA3
    HGA3

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C1S
    C5S
    C1S
    C4S
    C6S
    N1
    C2
    C5
    C5M

    C2S
    C1S
    H11S
    H41S
    H62S
    C2
    N3
    C5M
    H52

    IMPR O2

    N1

    DONO H3
    ACCE O2
    ACCE O4

    N3
    C2
    C4

    -0.11 !
    0.07 !
    0.07 !
    0.07
    C2S
    C5S
    C2S
    C4S
    C2S
    N1
    N3
    C5
    C5M
    N3

    C3S
    C6S
    H21S
    H42S
    N1
    C6
    H3
    C6
    H53

    C2

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N1
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N1
    ady defined
    IC C1S C2S N1 C2
    IC C2S C2 *N1 C6
    IC C2 N1 C6 C5
    IC C6 N1 C2 N3
    IC N1 N3 *C2 O2
    IC N1 C2 N3 C4
    IC C5 N3 *C4 O4
    IC C2 C4 *N3 H3
    IC C4 C6 *C5 C5M
    IC N1 C5 *C6 H6
    IC C6 C5 C5M H51
    IC C5 H51 *C5M H52
    IC H51 H52 *C5M H53

    O4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C2
    N3
    C6

    O2
    C4
    H6

    C4 C5
    C4 O4
    C5M H51

    N3

    C5

    C4

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C3S H32S
    C6S H61S

    C5M C4

    0.0
    0.00
    0.0
    0.00
    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71

    -160.0
    -180.00
    -0.02
    0.06
    -179.95
    -0.07
    179.98
    180.00
    -179.94
    180.0
    -90.0
    115.0
    -115.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C6

    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    0.0 !chi
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATCH FIRST NONE LAST NONE


    RESI CNT1

    0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA

    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1 -0.09 !
    ATOM H11S HGA1
    0.09 !
    GROUP
    !
    ATOM N1 NG2R61 -0.30 !
    H51
    O4
    ATOM C6
    ATOM H6
    GROUP
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    GROUP
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53

    CG2R62
    HGR62

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2S
    C1S
    H11S
    H41S
    H62S
    C2
    N3
    C5M
    H52

    C1S
    C5S
    C1S
    C4S
    C6S
    N1
    C2
    C5
    C5M

    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3
    HGA3

    IMPR O2

    N1

    DONO H3
    ACCE O2
    ACCE O4

    N3
    C2
    C4

    0.17 !
    0.13 !
    !
    0.57 !
    -0.47 !
    -0.46 !
    0.36 !
    !
    0.54 !
    -0.49 !
    -0.15 !
    -0.11 !
    0.07 !
    0.07 !
    0.07
    C2S
    C5S
    C2S
    C4S
    C2S
    N1
    N3
    C5
    C5M

    N3

    C2

    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    *

    C3S
    C6S
    H21S
    H42S
    N1
    C6
    H3
    C6
    H53
    O4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C2
    N3
    C6

    O2
    C4
    H6

    C4 C5
    C4 O4
    C5M H51

    N3

    C5

    C3S H32S
    C6S H61S

    C4

    C5M C4

    C6

    C5

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N1
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N1
    ady defined
    IC C1S C2S N1 C2
    IC C2S C2 *N1 C6
    IC C2 N1 C6 C5
    IC C6 N1 C2 N3
    IC N1 N3 *C2 O2
    IC N1 C2 N3 C4
    IC C5 N3 *C4 O4
    IC C2 C4 *N3 H3
    IC C4 C6 *C5 C5M
    IC N1 C5 *C6 H6
    IC C6 C5 C5M H51
    IC C5 H51 *C5M H52
    IC H51 H52 *C5M H53

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.00
    0.0
    0.00
    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71
    -160.00
    -180.00
    -0.02
    0.06
    -179.95
    -0.07
    179.98
    180.00
    -179.94
    180.0
    -90.0
    115.0
    -115.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    0.0 !chi
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATCH FIRST NONE LAST NONE


    RESI CNT2

    0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !

    ATOM H62S
    GROUP
    ATOM C1S
    ATOM H11S
    GROUP
    ATOM N1

    HGA2

    ATOM C6
    ATOM H6
    GROUP
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    GROUP
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53

    CG2R62
    HGR62

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2S
    C1S
    H11S
    H41S
    H62S
    C2
    N3
    C5M
    H52

    C1S
    C5S
    C1S
    C4S
    C6S
    N1
    C2
    C5
    C5M

    0.09 !

    CG3RC1
    HGA1
    NG2R61

    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3
    HGA3

    IMPR O2

    N1

    DONO H3
    ACCE O2
    ACCE O4

    N3
    C2
    C4

    -0.09 !
    0.09 !
    !
    -0.30 !
    0.17 !
    0.13 !
    !
    0.57 !
    -0.47 !
    -0.46 !
    0.36 !
    !
    0.54 !
    -0.49 !
    -0.15 !
    -0.11 !
    0.07 !
    0.07 !
    0.07
    C2S
    C5S
    C2S
    C4S
    C2S
    N1
    N3
    C5
    C5M

    N3

    H51

    C2

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N1
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N1
    ady defined
    IC C1S C2S N1 C2
    IC C2S C2 *N1 C6
    IC C2 N1 C6 C5

    O4

    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    *

    C3S
    C6S
    H21S
    H42S
    N1
    C6
    H3
    C6
    H53
    O4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C2
    N3
    C6

    O2
    C4
    H6

    C4 C5
    C4 O4
    C5M H51

    N3

    C5

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97
    0.0
    0.0
    0.0

    C3S H32S
    C6S H61S

    C4

    C5M C4

    0.0
    0.00
    0.0
    0.00
    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71

    0.0 -160.00
    0.0 -180.00
    0.0
    -0.02

    0.0
    0.0
    0.0

    C6

    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    0.0 !chi
    0.0
    0.0

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C6
    N1
    N1
    C5
    C2
    C4
    N1
    C6
    C5
    H51

    N1
    N3
    C2
    N3
    C4
    C6
    C5
    C5
    H51
    H52

    C2
    *C2
    N3
    *C4
    *N3
    *C5
    *C6
    C5M
    *C5M
    *C5M

    N3
    O2
    C4
    O4
    H3
    C5M
    H6
    H51
    H52
    H53

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.06
    0.0 -179.95
    0.0
    -0.07
    0.0 179.98
    0.0 180.00
    0.0 -179.94
    0.0 180.0
    0.0 -90.0
    0.0 115.0
    0.0 -115.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATCH FIRST NONE LAST NONE


    RESI CNT3

    0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !
    GROUP
    !
    ATOM C4S CG3C52 -0.18 !
    H61S H62S
    ATOM H41S HGA2
    0.09 !
    \ /
    ATOM H42S HGA2
    0.09 !
    C6S
    GROUP
    !
    / \
    ATOM C2S CG3C51 -0.09 !
    /
    \
    ATOM H21S HGA1
    0.09 ! H51S-C5S----C1S-H11S
    !
    |
    |
    GROUP
    ! H41S-C4S
    C2S---------*
    ATOM C3S CG3C52 -0.18 !
    / \
    / \
    ATOM H31S HGA2
    0.09 !
    H42S \ / H21S
    ATOM H32S HGA2
    0.09 !
    C3S
    !
    / \
    GROUP
    !
    H31S H32S
    ATOM C5S CG3RC1 -0.09 !
    ATOM H51S HGA1
    0.09
    GROUP
    ATOM C6S CG3C31 -0.18 !
    ATOM H61S HGA2
    0.09 !
    ATOM H62S HGA2
    0.09 !
    GROUP
    ATOM C1S CG3RC1 -0.09 !
    ATOM H11S HGA1
    0.09 !
    GROUP
    !
    ATOM N1 NG2R61 -0.30 !
    H51
    O4
    ATOM C6
    ATOM H6
    GROUP
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    GROUP
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52

    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3

    0.17 !
    0.13 !
    !
    0.57 !
    -0.47 !
    -0.46 !
    0.36 !
    !
    0.54 !
    -0.49 !
    -0.15 !
    -0.11 !
    0.07 !
    0.07 !

    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    *

    ATOM H53 HGA3

    0.07

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2S
    C5S
    C2S
    C4S
    C2S
    N1
    N3
    C5
    C5M

    C1S
    C5S
    C1S
    C4S
    C6S
    N1
    C2
    C5
    C5M

    C2S
    C1S
    H11S
    H41S
    H62S
    C2
    N3
    C5M
    H52

    IMPR O2

    N1

    DONO H3
    ACCE O2
    ACCE O4

    N3
    C2
    C4

    N3

    C3S
    C6S
    H21S
    H42S
    N1
    C6
    H3
    C6
    H53

    C2

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S
    IC C3S C4S C5S C1S
    IC C5S C2S *C1S C6S
    IC C1S C5S *C6S H61S
    IC C1S C5S *C6S H62S
    IC C5S C2S *C1S H11S
    IC C1S C3S *C2S N1
    IC C1S C3S *C2S H21S
    IC C2S C4S *C3S H31S
    IC C2S C4S *C3S H32S
    IC C3S C5S *C4S H41S
    IC C3S C5S *C4S H42S
    IC C4S C1S *C5S H51S
    !IC C4S C3S C2S N1
    ady defined
    IC C1S C2S N1 C2
    IC C2S C2 *N1 C6
    IC C2 N1 C6 C5
    IC C6 N1 C2 N3
    IC N1 N3 *C2 O2
    IC N1 C2 N3 C4
    IC C5 N3 *C4 O4
    IC C2 C4 *N3 H3
    IC C4 C6 *C5 C5M
    IC N1 C5 *C6 H6
    IC C6 C5 C5M H51
    IC C5 H51 *C5M H52
    IC H51 H52 *C5M H53

    O4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C4S C5S

    C2
    N3
    C6

    O2
    C4
    H6

    C4 C5
    C4 O4
    C5M H51

    N3

    C5

    C4

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C3S H32S
    C6S H61S

    C5M C4

    0.0
    0.00
    0.0
    0.00
    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71
    -160.00
    -180.00
    -0.02
    0.06
    -179.95
    -0.07
    179.98
    180.00
    -179.94
    180.0
    -90.0
    115.0
    -115.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C6

    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    0.0 !chi
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATCH FIRST NONE LAST NONE


    RESI CNCY

    0.00 ! C10H13N3O carbocyclic sugar with cytosine base, north


    ! base attached to C2 of carbocyclic sugar
    ! used to parameterize chi

    !
    ! the atom types used correspond to those used in the NA
    ! ribose/deoxyribose moieties
    !

    GROUP
    ATOM C4S
    ATOM H41S
    ATOM H42S
    GROUP
    ATOM C2S
    ATOM H21S

    CG3RC1
    HGA1

    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.09 !
    0.09 !
    !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    !
    -0.09 !
    0.09

    CG3C31
    HGA2
    HGA2

    -0.18 !
    0.09 !
    0.09 !

    CG3RC1
    HGA1

    -0.09 !
    0.09 !
    !
    -0.16 !
    0.11 !
    0.05 !
    !
    0.53 !
    -0.48 !
    -0.67 !
    0.62 !
    !
    -0.58 !
    0.31 !
    0.27 !
    !
    -0.10 !
    0.10 !

    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    GROUP
    ATOM C3S CG3C52
    ATOM H31S HGA2
    ATOM H32S HGA2
    GROUP
    ATOM C5S
    ATOM H51S
    GROUP
    ATOM C6S
    ATOM H61S
    ATOM H62S
    GROUP
    ATOM C1S
    ATOM H11S
    GROUP
    ATOM N1
    ATOM C6
    ATOM H6
    GROUP
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM C4
    GROUP
    ATOM N4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H5
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C1S
    C5S
    C1S
    C4S
    C6S
    N1
    C2
    C4

    NG2R61
    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R62
    CG2R64
    NG2S3
    HGP4
    HGP4
    CG2R62
    HGR62
    C2S
    C1S
    H11S
    H41S
    H62S
    C2
    N3
    C5

    IMPR O2 N1
    IMPR H42 C4
    DONO
    DONO
    ACCE
    ACCE

    C2S
    C5S
    C2S
    C4S
    C2S
    N1
    N3
    C5
    N3 C2
    H41 N4

    H61S H62S
    \ /
    C6S
    / \
    /
    \
    H51S-C5S----C1S-H11S
    |
    |
    H41S-C4S
    C2S---------*
    / \
    / \
    H42S \ / H21S
    C3S
    / \
    H31S H32S

    H42 H41
    \ /
    N4
    |
    C4
    / \\
    H5-C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    *

    C3S
    C6S
    H21S
    H42S
    N1
    C6
    C4
    C6
    N4

    C3S
    C6S
    C3S
    C5S

    C4S
    C1S
    H31S
    H51S

    C2
    C4
    C5

    O2
    N4
    H5

    N3

    C5

    C4S C5S
    C3S H32S
    C6S H61S
    N4
    C6

    H41
    H6

    N4

    0.00
    0.00

    0.0000
    0.0000

    C4

    H42 N4
    H41 N4
    O2 C2
    N3

    ! internal coordinates
    IC C1S C2S C3S C4S
    IC C2S C3S C4S C5S

    0.0000
    0.0000

    0.00
    0.00

    0.0
    0.0

    H42

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    !IC
    ady
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C3S C4S C5S


    C5S C2S *C1S
    C1S C5S *C6S
    C1S C5S *C6S
    C5S C2S *C1S
    C1S C3S *C2S
    C1S C3S *C2S
    C2S C4S *C3S
    C2S C4S *C3S
    C3S C5S *C4S
    C3S C5S *C4S
    C4S C1S *C5S
    C4S C3S C2S
    defined
    C1S C2S N1
    C2S C2 *N1
    C2 N1 C6
    C6 N1 C2
    N1 N3 *C2
    N1 C2 N3
    C5 N3 *C4
    N3 C4 N4
    H41 C4 *N4
    C6 C4 *C5
    N1 C5 *C6

    C1S
    C6S
    H61S
    H62S
    H11S
    N1
    H21S
    H31S
    H32S
    H41S
    H42S
    H51S
    N1

    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    1.5284 101.97

    C2
    C6
    C5
    N3
    O2
    C4
    N4
    H41
    H42
    H5
    H6

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.00
    300.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    240.0
    0.00
    120.0
    0.00
    147.80 113.71

    0.0 -160.00
    0.0 -180.00
    0.0
    0.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.00
    0.0
    0.00
    0.0 180.00
    0.0 180.0
    0.0 180.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.4896 !N9 is alre
    0.0 !chi
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    PATCH FIRST NONE LAST NONE


    RESI B5NP
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3'
    ATOM C3'
    ATOM H31'
    ATOM H32'
    ATOM H33'
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C1
    GROUP
    ATOM C2
    ATOM H21
    ATOM O3T
    ATOM H3T

    CG3RC1

    -1.00 !
    !
    !
    !
    -0.08 !
    0.09 !
    0.09 !
    -0.57 !
    1.50 !
    -0.78 !
    -0.78 !
    -0.57 !
    -0.17 !
    0.09 !
    0.09 !
    0.09 !
    !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    0.00 !

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2
    OG303
    PG1
    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    C8H14O5P carbocyclic sugar with 5' OPOCH3


    north conformation
    used to parameterize gamma
    Note : C1 charge changed from -0.09 to 0.00 to
    accomodate the CH2-OPOCH3

    H31'
    H61 H62
    /
    \ / H51'
    O1P C3'-H32'
    C6
    |
    | / \
    / \ C5'-O5'-P-O3' H33'
    /
    \ / \
    |
    H51-C5-----C1 H52' O2P
    |
    |
    H41-C4
    C2--H21
    / \
    / \
    H42 \ / O3T-H3T
    C3
    / \
    H31 H32

    ! changed from -0.18 to accomodate O3'-H


    !
    !
    !

    GROUP
    ATOM C5
    ATOM H51
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C1
    C5
    C2
    C4
    C6
    P
    C3'
    O3T

    CG3RC1
    HGA1

    -0.09 !
    0.09 !

    CG3C31
    HGA2
    HGA2

    -0.18 !
    0.09 !
    0.09 !

    C2
    C1
    H21
    H41
    H62
    O2P
    H32'
    H3T

    C2
    C5
    C4
    C6
    C5'
    P
    C3'

    C3
    C6
    H42
    H61
    O5'
    O3'
    H33'

    ! internal coordinates from


    IC C1 C2 C3
    C4
    IC C2 C3 C4
    C5
    IC C3 C4 C5
    C1
    IC C5 C2 *C1 C5'
    IC C1 O5' *C5' H51'
    IC C1 O5' *C5' H52'
    IC C3 C5 *C2 H21
    IC C3 C5 *C2 O3T
    IC C1 C2 O3T H3T
    IC C2 C4 *C3 H31
    IC C2 C4 *C3 H32
    IC C3 C5 *C4 H41
    IC C3 C5 *C4 H42
    IC C1 C4 *C5 H51
    IC C4 C1 *C5 C6
    IC C1 C5 *C6 H61
    IC C1 C5 *C6 H62
    IC C5' C1 C2
    O3T
    IC O5' C5' C1
    C2
    IC P
    O5' C5' C1
    IC C5' O5' P
    O3'
    IC O5' O3' *P
    O1P
    IC O5' O3' *P
    O2P
    IC O5' P O3' C3'
    IC H31' C3' O3' P
    IC H32' C3' O3' P
    IC H33' C3' O3' P

    C3
    C6
    C3
    C1
    O5'
    O3'
    C5'

    parameter
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C4
    C1
    H31
    C5'
    P
    C3'
    H51'

    C4
    C5
    C3
    C2
    P
    C3'
    C5'

    C5
    H51
    H32
    O3T
    O1P
    H31'
    H52'

    file, note initial planar geometry


    0.00
    0.0
    0.00 0.0000
    0.00
    0.0
    0.00 0.0000
    0.00
    0.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 -60.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 120.0
    0.00 0.0000
    0.00 240.0
    0.00 0.0000
    0.00 70.0
    0.00 0.0000
    0.00 50.0
    0.00 0.0000
    0.0 -105.0
    0.0
    0.0
    0.0 140.0
    0.0
    0.0
    0.0 120.0
    0.0
    0.0
    0.0 240.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI B5SP
    GROUP
    ATOM C1
    ATOM H11
    GROUP
    ATOM C3
    ATOM H31
    ATOM O3T
    ATOM H3T
    GROUP
    ATOM C6

    -1.00 ! C8H14O5P south carbcyclic sugar with C5'-OPOCH3


    CG3RC1
    HGA1
    CG3C51
    HGA1
    OG311
    HGP1
    CG3C31

    !
    -0.09 !
    0.09 !
    !
    0.14 !
    0.09 !
    -0.65 !
    0.42 !
    !
    -0.18 !

    H61 H62
    \ /
    C6
    / \
    H51-C5------C1-H11 H51' O1P
    H31'
    |
    |
    /
    |
    /
    H41-C4
    C2-----C5'-O5'-P-O3'-C3'-H32'
    / \
    / \
    \
    |
    \

    ATOM H61
    ATOM H62
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51
    GROUP
    ATOM C2
    ATOM H21
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3'
    ATOM C3'
    ATOM H31'
    ATOM H32'
    ATOM H33'

    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C1
    H41
    H52'
    H51
    P
    O1P
    H31'

    C1
    C5
    C4
    C5'
    C5
    O5'
    P
    C3'

    CG3RC1
    HGA1

    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.09 !
    0.09 !

    CG3C51
    HGA1
    CG321
    HGA2
    HGA2
    OG303
    PG1
    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3

    -0.09
    0.09
    -0.08
    0.09
    0.09
    -0.57
    1.50
    -0.78
    -0.78
    -0.57
    -0.17
    0.09
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    C2
    C5
    C4
    C6
    C3
    O3T
    P
    C3'

    ! internal coordinates
    IC C1 C2 C3
    C4
    IC C2 C3 C4
    C5
    IC C3 C4 C5
    C1
    IC C4 C5 C1
    C6
    IC C5 C2 *C1 H11
    IC C5 C3 *C4 H41
    IC C3 C5 *C4 H42
    IC C4 C3 O3T H3T
    IC C2 C4 *C3 H31
    IC C2 C4 *C3 O3T
    IC C3 C1 *C2 C5'
    IC C2 O5' *C5' H51'
    IC C2 O5' *C5' H52'
    IC C5 C3 *C2 H21
    IC C4 C1 *C5 H51
    IC C1 C4 *C5 C6
    IC C1 C5 *C6 H61
    IC C1 C5 *C6 H62
    IC C5' C2 C3
    O3T
    IC O5' C5' C2
    C3
    IC P
    O5' C5' C2
    IC O1P P O5' C5'
    IC O2P P O5' C5'
    IC C5' O5' P
    O3'
    IC O5' P O3' C3'

    H42 \ / H21
    C3-H31
    |
    O3T
    \
    H3T

    H52' O2P

    H33'

    ! This charge changed from -0.18 to make it


    ! compatible with C5'-OPOCH3
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    C3
    C6
    H42
    H61
    H31
    H3T
    O2P
    H32'
    0.0000
    0.0000
    0.0000
    1.5000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.5000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0
    0.0
    0.0
    0.0
    0.0

    C3
    C6
    C5'
    C6
    C3

    C4
    C1
    H51'
    H62
    O3T

    C4
    C2
    C1
    C2
    C5'

    P
    O3'
    C3' H33'
    0.00
    0.00
    0.00
    60.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    60.00
    60.00
    0.00
    0.00
    0.0
    0.0
    0.0
    0.0
    0.0

    C5
    C5'
    H11
    H21
    O5'

    O3' C3'

    0.0
    0.0
    0.0
    120.0
    120.0
    120.0
    120.0
    270.0
    240.0
    120.0
    120.0
    120.0
    240.0
    120.0
    120.0
    120.0
    120.0
    240.0
    150.0
    60.0
    180.00
    -60.0
    60.0
    180.0
    180.0

    0.00
    0.00
    0.00
    60.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    60.00
    0.00
    0.00
    0.00
    0.00
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0000
    0.0000
    0.0000
    1.5000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.5000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0
    0.0
    0.0
    0.0
    0.0

    IC
    IC
    IC
    PATC

    H31' C3' O3' P


    H32' C3' O3' P
    H33' C3' O3' P
    FIRS NONE LAST NONE

    0.0
    0.0
    0.0

    0.0
    0.0
    0.0

    60.0
    -60.0
    180.0

    0.0
    0.0
    0.0

    0.0
    0.0
    0.0

    !toppar_all27_na_model.str
    RESI DMPA
    GROUP
    ATOM P1
    ATOM O3
    ATOM O4
    ATOM O1
    ATOM O2
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23

    PG1
    OG2P1
    OG2P1
    OG303
    OG303
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    -1.00 ! C2H6O4P Dimethylphosphate


    !
    1.50 !
    H11!
    -0.78 !
    |
    -0.78 !
    H13- C1-H12
    -0.57 !
    \
    -0.57 !
    O3 O1
    -0.17 !
    \\ /
    0.09 !
    (-) P1
    0.09 !
    // \
    0.09 !
    O4 O2
    -0.17 !
    /
    0.09 !
    H23-C2-H22
    0.09 !
    |
    0.09 !
    H21
    !
    P1 O2
    P1 O3
    P1 O4
    O1 C1
    O2 C2
    C1 H12 C1 H13 C2 H21 C2 H22 C2 H23
    conformation (3-21G* opt. structure)
    C1 1.4723
    107.31
    000.0
    117.79
    1.4356
    C2 1.4722
    000.0
    000.0
    117.79
    1.4357
    C2 1.6343
    000.0
    73.8
    117.79
    1.4357
    C1 1.6344
    000.0
    73.7
    117.79
    1.4356
    P1 1.0827
    107.8
    174.8
    117.79
    1.6343
    P1 1.0800
    110.4
    54.1
    117.79
    1.6343
    P1 1.0848
    110.7
    294.3
    117.79
    1.6343
    P1 1.0827
    107.9
    174.7
    117.79
    1.6344
    P1 1.0800
    110.4
    54.1
    117.79
    1.6344
    P1 1.0848
    110.7
    294.2
    117.79
    1.6344

    BOND P1 O1
    BOND C1 H11
    ! IC FOR THE g,g
    IC O3 P1 O1
    IC O4 P1 O2
    IC O1 P1 O2
    IC O2 P1 O1
    IC H11 C1 O1
    IC H12 C1 O1
    IC H13 C1 O1
    IC H21 C2 O2
    IC H22 C2 O2
    IC H23 C2 O2

    RESI MP_0
    0.00
    GROUP
    ! atom order for molvib
    ATOM C1 CG331
    -0.17
    ATOM O1 OG303
    -0.56
    ATOM P1 PG1
    1.50
    ATOM O2 OG311
    -0.62
    ATOM O3 OG311
    -0.62
    ATOM O4 OG2P1
    -0.64
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    ATOM H2 HGP1
    0.42
    ATOM H3 HGP1
    0.42
    BOND P1
    BOND C1
    IC
    IC
    IC
    IC

    H11
    C1
    H11
    H11

    O1
    H11
    C1
    O1
    O1
    O1

    P1
    C1
    O1
    P1
    *C1
    *C1

    O2
    H12
    P1
    O2
    H12
    H13

    ! CH5O4P Methylphosphate, neutral


    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H11
    |
    H13--C1--H12
    |
    O1
    |
    O4==P1--O3
    |
    \
    O2
    H3
    \
    H2
    P1
    C1

    0.0000
    0.0000
    0.0000
    0.0000

    O3
    H13

    P1
    O2
    0.00
    0.00
    0.00
    0.00

    O4
    H2
    180.00
    180.00
    120.00
    -120.00

    O1
    O3

    C1
    H3
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC

    O2
    O2
    O1
    O1

    O1
    O1
    P1
    P1

    *P1
    *P1
    O2
    O3

    O3
    O4
    H2
    H3

    RESI MP_1
    -1.00
    GROUP
    ! atom order for molvib
    ATOM C1 CG331
    -0.170
    ATOM O1 OG303
    -0.620
    ATOM P1 PG1
    1.500
    ATOM O2 OG311
    -0.670
    ATOM O3 OG2P1
    -0.820
    ATOM O4 OG2P1
    -0.820
    ATOM H11 HGA3
    0.090
    ATOM H12 HGA3
    0.090
    ATOM H13 HGA3
    0.090
    ATOM H2 HGP1
    0.330

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    -2.00
    PG1
    OG303
    OG2P1
    OG2P1
    OG2P1

    1.100
    -0.400
    -0.900
    -0.900
    -0.900

    CG331
    HGA3
    HGA3
    HGA3

    -0.270
    0.090
    0.090
    0.090

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    ! CH4O4P Methylphosphate, anionic


    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H11
    |
    H13--C1--H12
    |
    O1
    |
    O4==P1==O3 (-)
    |
    O2
    \
    H2

    BOND P1 O1
    P1 O2
    P1 O3
    P1
    BOND C1 H11
    C1 H12 C1 H13 O2
    ! IC
    IC O3 P1 O1 C1 0.0000
    000.00
    IC O4 P1 O1 C1 0.0000
    000.00
    IC O2 P1 O1 C1 0.0000
    000.00
    IC H11 C1 O1 P1 0.0000
    000.00
    IC H12 C1 O1 P1 0.0000
    000.00
    IC H13 C1 O1 P1 0.0000
    000.00
    IC H2 O2 P1 O1 0.0000
    000.00
    ! dummies to analyze cetain angles
    IC O3 P1 O4 O1 0.0
    0.0
    RESI MP_2
    GROUP
    ATOM P1
    ATOM O1
    ATOM O2
    ATOM O3
    ATOM O4
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13

    120.00
    -120.00
    180.00
    180.00

    O4
    H2

    O1

    000.0
    000.0
    000.0
    000.0
    000.0
    000.0
    000.0

    C1
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0

    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0

    ! CH3O4P Methylphosphate, dianionic


    !
    !
    !
    H11
    !
    |
    !
    H13--C1--H12
    !
    |
    !
    O1
    !
    |
    !
    (-) O4==P1==O3 (-)
    !
    ||
    !
    O2

    !
    BOND P1 O1
    P1 O2
    P1 O3
    P1
    BOND C1 H11
    C1 H12 C1 H13
    ! IC
    IC O3 P1 O1 C1 0.0000
    000.00
    IC O4 P1 O1 C1 0.0000
    000.00
    IC O2 P1 O1 C1 0.0000
    000.00
    IC H11 C1 O1 P1 0.0000
    000.00
    IC H12 C1 O1 P1 0.0000
    000.00
    IC H13 C1 O1 P1 0.0000
    000.00
    ! dummies to analyze cetain angles
    IC O3 P1 O4 O1 0.0
    0.0

    O4
    000.0
    000.0
    000.0
    000.0
    000.0
    000.0
    0.0

    O1

    C1
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    0.0

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0

    ! below are residues and patches added for the 97/98 optimization

    ! and extension of the na all-atom parameters


    RESI THF
    !
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM C3'
    ATOM C2'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM H21'
    ATOM H22'
    ATOM H31'
    ATOM H32'
    ATOM H41'
    ATOM H42'

    0.00 ! C4H8O tetrahydrofuran, for MOLVIB


    OG3C51
    CG3C52
    CG3C52
    CG3C52
    CG3C52
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2

    -0.40
    0.02
    -0.18
    -0.18
    0.02
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H41' O4' H11'


    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    H32'
    H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
    BOND C4' H41' C4' H42'
    IC C1' O4' C4' C3'
    IC C3' O4' *C4' H41'
    IC C3' O4' *C4' H42'
    IC C4' O4' C1' C2'
    IC C2' O4' *C1' H11'
    IC C2' O4' *C1' H12'
    IC C3' C1' *C2' H21'
    IC C3' C1' *C2' H22'
    IC C2' C4' *C3' H31'
    IC C2' C4' *C3' H32'
    PATC FIRS NONE LAST NONE
    RESI THFM
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C2'
    ATOM C3'
    ATOM C4'
    ATOM H11'
    ATOM H12'
    ATOM H21'
    ATOM H22'
    ATOM H31'
    ATOM H32'
    ATOM H42'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    45.00
    120.00
    -120.00
    -45.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H10O Methyl-tetrahydrofuran


    OG3C51
    CG3C52
    CG3C52
    CG3C52
    CG3C51
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA1

    -0.40
    0.02
    -0.18
    -0.18
    0.11
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    !
    H52' H53'
    !
    \ /
    ! H51'-C5' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    H32'
    H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
    BOND C4' H42' C5' H51' C5' H52' C5' H53'
    IC C4' O4'

    C1'

    C2'

    0.0000

    0.00

    45.00

    0.00

    0.0000

    IC C2' O4' *C1' H11'


    IC C2' O4' *C1' H12'
    IC O4' C1' C2' C3'
    IC C3' C1' *C2' H21'
    IC C3' C1' *C2' H22'
    IC C4' C2' *C3' H31'
    IC C4' C2' *C3' H32'
    IC C3' O4' *C4' C5'
    IC C3' O4' *C4' H42'
    IC O4' C4' C5' H51'
    IC H51' C4' *C5' H52'
    IC H51' C4' *C5' H53'
    PATC FIRS NONE LAST NONE
    RESI THFO
    e
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C2'
    ATOM C4'
    ATOM H11'
    ATOM H12'
    ATOM H21'
    ATOM H22'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM H32'

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    -25.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C4H8O2 3'-hydroxyl-tetrahydrofuran


    ! Atom types for aliphatic hydrogens based on nucleotid
    OG3C51
    CG3C52
    CG3C52
    CG3C52
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    HGA2
    CG3C51
    HGA1
    OG311
    HGP1

    -0.40
    0.02
    -0.18
    0.02
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    0.14 !
    0.09
    -0.65
    0.42

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    H41' O4' H11'
    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    O3'
    H22'
    |
    H32'

    BOND C1' O4' C1' C2' C2' C3'


    BOND C1' H11' C1' H12' C2' H21'
    BOND C4' H42' O3' H32'
    !Nicolas: the following IC are for
    s
    IC C4'
    O4'
    C1'
    C2'
    IC O4'
    C1'
    C2'
    C3'
    IC C1'
    C2'
    C3'
    C4'
    IC C2'
    C3'
    C4'
    O4'
    IC C3'
    C4'
    O4'
    C1'
    IC H11'
    C1'
    C2'
    C3'
    IC H12'
    C1'
    C2'
    C3'
    IC H21'
    C2'
    C3'
    C4'
    IC H22'
    C2'
    C3'
    C4'
    IC H31'
    C3'
    C4'
    O4'
    IC H41'
    C4'
    O4'
    C1'
    IC H42'
    C4'
    O4'
    C1'
    IC O3'
    C3'
    C4'
    O4'
    IC H32'
    O3'
    C3'
    C4'
    PATC FIRS NONE LAST NONE

    C3' C4' C4' O4' C3' O3'


    C2' H22' C3' H31' C4' H41'
    thf-oh as optimized via ab initio calculation
    1.4055
    1.4127
    1.5457
    1.5346
    1.5211
    1.0856
    1.0818
    1.0846
    1.0822
    1.0806
    1.0891
    1.0808
    1.4028
    0.9492

    108.09
    106.18
    103.11
    100.86
    103.15
    111.62
    113.32
    110.65
    110.88
    113.53
    110.89
    108.72
    110.98
    108.72

    23.45
    3.96
    -26.93
    41.73
    -41.62
    123.53
    -114.11
    91.68
    -148.45
    162.89
    77.76
    -162.12
    -77.39
    44.80

    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    110.98

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    1.5211

    RESI THFI
    0.00 ! C7H10N2O imidazole analog with THF ring
    ! Sugar: transferred from thf; used for optimization of chi, therefore
    ! the sugar carbon atom types are not rigorously correct
    ! Atom types for aliphatic hydrogens based on nucleotide

    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'
    GROUP !
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2

    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    !
    !
    !
    !
    -0.18 !
    0.09 !
    0.09 !

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    H41' O4' Imidazole
    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    H32'
    H22'

    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    C1'
    HE1
    HGR52
    0.09 !
    \
    /
    CG2R51 0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    |
    NG2R51 -0.04 ! HG-CG
    |
    CG2R53 0.25 !
    \
    |
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2

    BOND C1' O4' C1' C2' C2' C3' C3'


    BOND C1' H12' C2' H21' C2' H22' C3'
    BOND C4' H41' C4' H42'
    BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2
    BOND CE1 HE1 CD2 HD2 CG HG
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 C1'
    ND1 CE1
    IMPR CD2 CG NE2 HD2
    CD2 NE2
    IMPR CE1 ND1 NE2 HE1
    CE1 NE2
    IMPR CG CD2 ND1 HG
    CG ND1
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    IC
    C2'
    C3'
    C4'
    O4'
    IC
    H12'
    C1'
    C2'
    C3'
    IC
    H21'
    C2'
    C3'
    C4'
    IC
    H22'
    C2'
    C3'
    C4'
    IC
    H31'
    C3'
    C4'
    O4'
    IC
    H32'
    C3'
    C4'
    O4'
    IC
    H41'
    C4'
    O4'
    C1'
    IC
    H42'
    C4'
    O4'
    C1'
    IC
    C4'
    O4'
    C1'
    ND1
    IC
    O4'
    C1'
    ND1
    CE1
    IC
    C1'
    ND1
    CE1
    NE2
    IC
    ND1
    CE1
    NE2
    CD2
    IC
    CE1
    NE2
    CD2
    CG
    IC
    HE1
    CE1
    NE2
    CD2
    IC
    CE1
    NE2
    CD2
    HD2
    IC
    NE2
    CD2
    CG
    HG
    PATC FIRS NONE LAST NONE

    C4' C4' O4' C1' ND1


    H31' C3' H32'
    CG CG ND1
    CG
    CG
    ND1
    CD2
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C1'
    HD2
    HE1
    HG
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    324.92
    33.390
    268.35
    82.530
    204.06
    155.99
    276.70
    132.30
    220.70
    256.98
    180.00
    181.56
    0.34
    0.00
    180.40
    179.83
    178.45

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    RESI THMI
    0.00 ! C8H12N2O thf-ch3-imidazole
    ! C5' has been declared as CN8, and C3' as CN7, for compatibility
    ! with DNA, but these carbons are rigorously CG331 and CG321 respectively

    ! Atom types for aliphatic hydrogens based on nucleotide


    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    GROUP !
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2

    ! Sugar:
    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    BOND C1'
    BOND C1'
    BOND C4'
    BOND ND1
    BOND CE1
    DOUBLE CG

    O4'
    H12'
    H42'
    CE1
    HE1
    CD2

    IMPR
    IMPR
    IMPR
    IMPR
    ! ic
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    transferred from thf


    -0.40 ! Note: has 2 asymmetric carbons.
    0.11 ! Abs. config is arbitrary.
    0.09
    0.11 !
    H52' H53'
    0.09 !
    \ /
    ! H51'-C5' O4' Imidazole
    -0.18 !
    \ / \ /
    0.09 ! H42'--C4' C1'--H12'
    0.09 !
    |
    |
    ! H31'--C3'--C2'--H21'
    -0.18 !
    /
    \
    0.09 !
    H32'
    H22'
    0.09

    CG331
    -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    C1'
    HE1
    HGR52
    0.09 !
    \
    /
    CG2R51
    0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    ||
    NG2R51 -0.04 ! HG-CG
    ||
    CG2R53
    0.25 !
    \\
    ||
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2
    C1' C2' C2'
    C2' H21' C2'
    C4' C5' C5'
    NE2 CD2 CG
    CD2 HD2 CG
    CE1 NE2

    C3' C3' C4' C4' O4' C1' ND1


    H22' C3' H31' C3' H32'
    H51' C5' H52' C5' H53'
    ND1
    HG

    ND1 CG CE1 C1'


    ND1 CE1
    CD2 CG NE2 HD2
    CD2 NE2
    CE1 ND1 NE2 HE1
    CE1 NE2
    CG CD2 ND1 HG
    CG ND1
    table for thfim, from Nicolas:
    C1'
    C2'
    C3'
    C4'
    C2'
    C3'
    C4'
    O4'
    H12'
    C1'
    C2'
    C3'
    H21'
    C2'
    C3'
    C4'
    H22'
    C2'
    C3'
    C4'
    H31'
    C3'
    C4'
    O4'
    H32'
    C3'
    C4'
    O4'
    C5'
    C4'
    O4'
    C1'
    H51'
    C5'
    C4'
    O4'
    H52'
    C5'
    C4'
    O4'
    H53'
    C5'
    C4'
    O4'
    H42'
    C4'
    O4'
    C1'
    C4'
    O4'
    C1'
    ND1
    O4'
    C1'
    ND1
    CE1
    C1'
    ND1
    CE1
    NE2
    ND1
    CE1
    NE2
    CD2

    CG
    CG
    ND1
    CD2
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    C1'
    HD2
    HE1
    HG
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    324.92 0.0 0.0


    33.390 0.0 0.0
    268.35 0.0 0.0
    82.530 0.0 0.0
    204.06 0.0 0.0
    155.99 0.0 0.0
    276.70 0.0 0.0
    132.30 0.0 0.0
    -179.98 0.0 0.0
    -59.66 0.0 0.0
    59.68 0.0 0.0
    220.70 0.0 0.0
    256.98 0.0 0.0
    180.00 0.0 0.0
    181.56 0.0 0.0
    0.34 0.0 0.0

    IC
    CE1
    IC
    HE1
    IC
    CE1
    IC
    NE2
    PATC FIRS NONE

    NE2
    CD2
    CE1
    NE2
    NE2
    CD2
    CD2
    CG
    LAST NONE

    RESI THFC

    CG
    CD2
    HD2
    HG

    0.0
    0.0
    0.0
    0.0

    0.0 0.00 0.0 0.0


    0.0 180.40 0.0 0.0
    0.0 179.83 0.0 0.0
    0.0 178.45 0.0 0.0

    0.00 ! C5H10O2 THF-3'-OH-4'-CH3

    ! Atom types for aliphatic hydrogens based on nucleotide


    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    BOND C1'
    BOND C3'
    BOND C1'
    BOND C2'
    BOND C3'
    BOND C4'
    BOND C5'
    BOND O3'

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.40
    0.02
    0.09
    0.09
    0.11
    0.09

    ! Note: has 2 asymmetric carbons.


    ! Abs. config is arbitrary.

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    HGA1
    CG3C51
    OG311
    HGP1

    0.09
    0.14
    -0.65
    0.42

    CG331
    HGA3
    HGA3
    HGA3
    O4' C1'
    O3'
    H11'
    H21'
    H31'
    H42'
    H51'
    H32'

    -0.27
    0.09
    0.09
    0.09
    C2' C2' C3' C3' C4' C4' O4' C4' C5'

    !
    H52' H53'
    !
    \ /
    ! H51'-C5' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    !
    H32'

    C1' H12'
    C2' H22'
    C5' H52'

    IC C4' O4' C1' C2'


    IC C2' O4' *C1' H11'
    IC C2' O4' *C1' H12'
    IC C1' O4' C4' C3'
    IC C3' O4' *C4' C5'
    IC C3' O4' *C4' H42'
    IC C3' C1' *C2' H21'
    IC C3' C1' *C2' H22'
    IC C2' C4' *C3' O3'
    IC C2' C4' *C3' H31'
    IC C4' C3' O3' H32'
    IC O4' C4' C5' H51'
    IC H51' C4' *C5' H52'
    IC H51' C4' *C5' H53'
    PATC FIRS NONE LAST NONE
    RESI TH5P
    e -2)

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5' H53'
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -2.00 ! C5H9O5P 5'-phosphate-methyl-tetrahydrofuran (phosphat


    ! Atom types for aliphatic hydrogens based on nucleotid

    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H1'
    ATOM H1''
    ATOM C4'
    ATOM H4''
    GROUP
    ATOM C2'
    ATOM H2'
    ATOM H2''
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM H3''
    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    GROUP
    ATOM O5'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.40
    0.02
    0.09
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    !
    O1P (-2)
    !
    ||
    ! O2P==P==O2P
    !
    |
    ! H5'' O5'
    !
    \ |
    ! H5'--C5' O4' H1'
    !
    \ / \ /
    !
    H4'--C4' C1'--H1''
    !
    |
    |
    !
    H3'--C3'--C2'--H2'
    !
    /
    \
    !
    H3''
    H2''

    C1' O4' C1' C2' C2'


    C1' H1' C1' H1'' C2'
    C4' H4'' C5' H5' C5'
    P
    O2P P
    O3P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H1'
    C1'
    C2'
    H1''
    C1'
    C2'
    H2'
    C2'
    C3'
    H2''
    C2'
    C3'
    H3'
    C3'
    C4'
    H3''
    C3'
    C4'
    H4''
    C4'
    O4'
    C5'
    C4'
    O4'
    H51'
    C5'
    C4'
    H52'
    C5'
    C4'
    O4'
    C4'
    C5'
    C4'
    C5'
    O5'
    C5'
    O5'
    P
    C5'
    O5'
    P
    C5'
    O5'
    P
    FIRS NONE LAST NONE

    RESI TH5H
    -2)

    C3' C3' C4' C4' O4' C4' C5'


    H2' C2' H2'' C3' H3' C3' H3''
    H5'' C5' O5' O5' P
    P
    O1P
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    O4'
    C1'
    C1'
    O4'
    O4'
    O5'
    P
    O1P
    O2P
    O3P

    1.4416
    1.4471
    1.5328
    1.5200
    1.5321
    1.1099
    1.1111
    1.1135
    1.1076
    1.1127
    1.1069
    1.1127
    1.5325
    1.1092
    1.1104
    0.0
    0.0
    0.0
    0.0
    0.0

    109.61
    106.74
    103.38
    102.18
    105.43
    113.03
    111.16
    109.13
    113.49
    108.68
    112.41
    106.71
    108.43
    110.48
    110.01
    0.0
    0.0
    0.0
    0.0
    0.0

    0.45
    -21.92
    33.49
    -34.11
    21.23
    -141.96
    93.50
    -81.76
    155.97
    81.68
    -156.66
    -95.75
    144.82
    180.00
    -60.00
    60.00
    180.0
    -60.0
    180.0
    60.0

    106.74
    103.38
    102.18
    105.43
    109.61
    103.38
    103.38
    102.18
    102.18
    105.43
    105.43
    109.61
    109.61
    108.43
    108.43
    0.0
    0.0
    0.0
    0.0
    0.0

    1.5328
    1.5200
    1.5321
    1.4416
    1.4471
    1.5200
    1.5200
    1.5321
    1.5321
    1.4416
    1.4416
    1.4471
    1.4471
    1.4416
    1.4416
    0.0
    0.0
    0.0
    0.0
    0.0

    0.00 ! C5H10O2 5'-hydroxy-methyl-tetrahydrofuran (phosphate


    ! Atom types for aliphatic hydrogens based on nucleotid

    e
    GROUP
    ATOM O4' OG3C51
    ATOM C1' CG3C52

    -0.40 ! Note: has 1 asymmetric carbon.


    0.02 ! Abs. config is arbitrary.

    ATOM H1'
    ATOM H1''
    ATOM C4'
    ATOM H4''
    GROUP
    ATOM C2'
    ATOM H2'
    ATOM H2''
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM H3''
    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    ATOM O5'
    ATOM H5T

    HGA2
    HGA2
    CG3C51
    HGA1

    CG3C52
    HGA2
    HGA2

    0.09
    0.09 !
    H5T
    0.11 !
    /
    0.09 ! H5'' O5'
    !
    \ |
    -0.18 ! H5'--C5' O4' H1'
    0.09 !
    \ / \ /
    0.09 !
    H4'--C4' C1'--H1''
    !
    |
    |
    -0.18 !
    H3'--C3'--C2'--H2'
    0.09 !
    /
    \
    0.09 !
    H3''
    H2''

    CG321
    HGA2
    HGA2
    OG311
    HGP1

    0.05
    0.09
    0.09
    -0.65
    0.42

    CG3C52
    HGA2
    HGA2

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3''
    BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    C4'
    O4'
    O4'
    C1'
    C1'
    C2'
    C2'
    C3'
    C3'
    C4'
    H1'
    C1'
    H1''
    C1'
    H2'
    C2'
    H2''
    C2'
    H3'
    C3'
    H3''
    C3'
    H4''
    C4'
    C5'
    C4'
    H5'
    C5'
    H5''
    C5'
    O4'
    C4'
    C4'
    C5'
    FIRS NONE LAST

    RESI T5PH
    te -1)

    C1'
    C2'
    C3'
    C4'
    O4'
    C2'
    C2'
    C3'
    C3'
    C4'
    C4'
    O4'
    O4'
    C4'
    C4'
    C5'
    O5'
    NONE

    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    O4'
    C1'
    C1'
    O4'
    O4'
    O5'
    H5T

    1.4416
    1.4471
    1.5328
    1.5200
    1.5321
    1.1099
    1.1111
    1.1135
    1.1076
    1.1127
    1.1069
    1.1127
    1.5325
    1.1092
    1.1104
    0.0
    0.0

    109.61
    106.74
    103.38
    102.18
    105.43
    113.03
    111.16
    109.13
    113.49
    108.68
    112.41
    106.71
    108.43
    110.48
    110.01
    0.0
    0.0

    0.45
    -21.92
    33.49
    -34.11
    21.23
    -141.96
    93.50
    -81.76
    155.97
    81.68
    -156.66
    -95.75
    144.82
    180.00
    -60.00
    60.00
    180.0

    1.5328
    1.5200
    1.5321
    1.4416
    1.4471
    1.5200
    1.5200
    1.5321
    1.5321
    1.4416
    1.4416
    1.4471
    1.4471
    1.4416
    1.4416
    0.0
    0.0

    -1.00 ! C5H10O5P 5'-phosphate-methyl-tetrahydrofuran (phospha

    ! Atom types for aliphatic hydrogens based on nucleotide


    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    ATOM O5'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    ATOM H5T
    GROUP
    ATOM O4'
    ATOM C1'

    106.74
    103.38
    102.18
    105.43
    109.61
    103.38
    103.38
    102.18
    102.18
    105.43
    105.43
    109.61
    109.61
    108.43
    108.43
    0.0
    0.0

    CG321
    HGA2
    HGA2
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1
    OG3C51
    CG3C52

    -0.08
    0.09
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.

    !
    O1P
    H5T
    !
    ||
    /
    ! O2P==P==O3P
    !
    |
    !
    O5'
    !
    |
    ! H5'' |
    -0.40 !
    \ |
    0.02 ! H5'--C5' O4' H1'

    ATOM H1'
    ATOM H1''
    ATOM C4'
    ATOM H4''
    GROUP
    ATOM C2'
    ATOM H2'
    ATOM H2''
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM H3''
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    HGA2
    HGA2
    CG3C51
    HGA1

    0.09
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    !
    !
    !
    !
    !
    -0.18 !
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    \ / \ /
    H4'--C4' C1'--H1''
    |
    |
    H3'--C3'--C2'--H2'
    /
    \
    H3''
    H2''

    C1' O4' C1' C2' C2'


    C1' H1' C1' H1'' C2'
    C4' H4'' C5' H5' C5'
    P
    O2P P
    O3P O3P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H1'
    C1'
    C2'
    H1''
    C1'
    C2'
    H2'
    C2'
    C3'
    H2''
    C2'
    C3'
    H3'
    C3'
    C4'
    H3''
    C3'
    C4'
    H4''
    C4'
    O4'
    C5'
    C4'
    O4'
    H51'
    C5'
    C4'
    H52'
    C5'
    C4'
    O4'
    C4'
    C5'
    O4'
    C4'
    C5'
    O4'
    C4'
    C5'
    C4'
    C5'
    O5'
    C5'
    O5'
    P
    C5'
    O5'
    P
    C5'
    O5'
    P
    O5'
    P
    O3P
    FIRS NONE LAST NONE

    RESI TH3P
    ate -2)

    C3'
    H2'
    H5''
    H5T
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    O4'
    C1'
    C1'
    O4'
    O4'
    O5'
    H5'
    H5''
    P
    O1P
    O2P
    O3P
    H5T

    C3' C4' C4' O4' C4' C5'


    C2' H2'' C3' H3' C3' H3''
    C5' O5' O5' P
    P
    O1P
    1.4416
    1.4471
    1.5328
    1.5200
    1.5321
    1.1099
    1.1111
    1.1135
    1.1076
    1.1127
    1.1069
    1.1127
    1.5325
    1.1092
    1.1104
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    109.61
    106.74
    103.38
    102.18
    105.43
    113.03
    111.16
    109.13
    113.49
    108.68
    112.41
    106.71
    108.43
    110.48
    110.01
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.45
    -21.92
    33.49
    -34.11
    21.23
    -141.96
    93.50
    -81.76
    155.97
    81.68
    -156.66
    -95.75
    144.82
    180.00
    -60.00
    60.0
    180.0
    -60.0
    180.0
    -60.0
    180.0
    60.0
    180.0

    1.5328
    1.5200
    1.5321
    1.4416
    1.4471
    1.5200
    1.5200
    1.5321
    1.5321
    1.4416
    1.4416
    1.4471
    1.4471
    1.4416
    1.4416
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    -2.00 ! C4H7O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosph


    ! used to fit epsilon

    ! Atom types for aliphatic hydrogens based on nucleotide


    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'

    106.74
    103.38
    102.18
    105.43
    109.61
    103.38
    103.38
    102.18
    102.18
    105.43
    105.43
    109.61
    109.61
    108.43
    108.43
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    !
    !
    !
    !
    !
    -0.18 !
    0.09 !
    0.09 !

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    H41' O4' H11'
    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    O3'
    H22'
    |

    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    CG3C51
    HGA1

    ! O1P==P==O2P
    -0.09 !
    ||
    0.09 !
    O3P (-2)

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    C1' O4' C1' C2' C2'


    C1' H11' C1' H12' C2'
    C4' H42' O3' P
    P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    H21'
    C2'
    C3'
    H22'
    C2'
    C3'
    H31'
    C3'
    C4'
    H41'
    C4'
    O4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3P
    P
    O3'
    FIRS NONE LAST NONE

    RESI T3PH

    C3'
    H21'
    O1P
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    C1'
    O4'
    C4'
    C3'
    C3'
    C3'

    C3' C4' C4' O4' C3'


    C2' H22' C3' H31' C4'
    P
    O2P P
    O3P
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    1.0891 110.89 77.76
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    0.0
    0.0 180.00
    0.0
    0.0 -60.0
    0.0
    0.0 180.0
    0.0
    0.0
    60.0

    O3'
    H41'
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0

    -1.00 ! C4H8O5P monoanionic 3'phosphate-tetrahydrofuran


    ! used to fit epsilon

    ! Atom types for aliphatic hydrogens based on nucleotide


    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3T
    ATOM H3T

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1

    0.01
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    ! O1P==P==O2P
    !
    |
    !
    O3T (-1)
    !
    \
    !
    H3T

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'

    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1' H11' C1' H12' C2'


    C4' H42' O3' P
    P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    H21'
    C2'
    C3'
    H22'
    C2'
    C3'
    H31'
    C3'
    C4'
    H41'
    C4'
    O4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3T
    P
    O3'
    H3T
    O3T
    P

    H21'
    O1P
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    C1'
    O4'
    C4'
    C3'
    C3'
    C3'
    O3'

    C2' H22' C3' H31' C4'


    P
    O2P P
    O3T O3T
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    1.0891 110.89 77.76
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    0.0
    0.0 180.00
    0.0
    0.0 -60.0
    0.0
    0.0
    60.0
    0.0
    0.0 180.0
    0.0
    0.0 180.0

    H41'
    H3T
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI R3PH

    -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran


    ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA

    ! Atom types for aliphatic hydrogens based on RNA nucleotide


    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM O2'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3T
    ATOM H3T
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1

    0.01
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    ! O1P==P==O2P H22'
    !
    |
    !
    O3T (-1)
    !
    \
    !
    H3T

    C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
    C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4'
    C4' H42' O3' P
    P
    O1P P
    O2P P
    O3T O3T H3T
    C4'
    O4'
    C1'
    C2'
    1.4055 108.09 23.45 106.18
    O4'
    C1'
    C2'
    C3'
    1.4127 106.18
    3.96 103.11
    C1'
    C2'
    C3'
    C4'
    1.5457 103.11 -26.93 100.86
    C2'
    C3'
    C4'
    O4'
    1.5346 100.86 41.73 103.15
    C3'
    C4'
    O4'
    C1'
    1.5211 103.15 -41.62 108.09
    H11'
    C1'
    C2'
    C3'
    1.0856 111.62 123.53 103.11

    H41'
    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H12'
    H21'
    O2'
    H22'
    H31'
    H41'
    H42'
    O3'
    P
    O1P
    O2P
    O3T
    H3T

    C1'
    C2'
    C2'
    O2'
    C3'
    C4'
    C4'
    C3'
    O3'
    P
    P
    P
    O3T

    C2'
    C3'
    C3'
    C2'
    C4'
    O4'
    O4'
    C4'
    C3'
    O3'
    O3'
    O3'
    P

    C3'
    C4'
    C4'
    C3'
    O4'
    C1'
    C1'
    O4'
    C4'
    C3'
    C3'
    C3'
    O3'

    1.0818
    1.0846
    1.0822
    1.0822
    1.0806
    1.0891
    1.0808
    1.4028
    0.0
    0.0
    0.0
    0.0
    0.0

    113.32
    110.65
    110.88
    110.88
    113.53
    110.89
    108.72
    110.98
    0.0
    0.0
    0.0
    0.0
    0.0

    -114.11
    91.68
    283.41
    0.00
    162.89
    77.76
    -162.12
    -77.39
    180.00
    -60.0
    60.0
    180.0
    180.0

    103.11
    100.86
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0
    0.0

    1.5346
    1.5211
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0

    PATC FIRS NONE LAST NONE


    RESI A3PH

    -1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran


    ! with O2' hydroxyl in an arabinose (beta) conformation

    .
    ! The furanose ring contains atom type CG311 , specific of arabinose
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM O2'
    ATOM H21'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3T
    ATOM H3T
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1

    0.01
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    !
    !
    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2' O2' is beta
    !
    |
    |
    ! O1P==P==O2P H22'
    !
    |
    !
    O3T (-1)
    !
    \
    !
    H3T

    C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
    C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4'
    C4' H42' O3' P
    P
    O1P P
    O2P P
    O3T O3T H3T
    C4'
    O4'
    C1'
    C2'
    1.4055 108.09 23.45 106.18
    O4'
    C1'
    C2'
    C3'
    1.4127 106.18
    3.96 103.11
    C1'
    C2'
    C3'
    C4'
    1.5457 103.11 -26.93 100.86
    C2'
    C3'
    C4'
    O4'
    1.5346 100.86 41.73 103.15
    C3'
    C4'
    O4'
    C1'
    1.5211 103.15 -41.62 108.09
    H11'
    C1'
    C2'
    C3'
    1.0856 111.62 123.53 103.11
    H12'
    C1'
    C2'
    C3'
    1.0818 113.32 -114.11 103.11
    H22'
    C2'
    C3'
    C4'
    1.0822 110.88 283.41 100.86
    O2'
    C2'
    C3'
    C4'
    1.0846 110.65 120.00 100.86
    H21'
    O2'
    C2'
    C3'
    1.0822 110.88 120.00 100.86
    H31'
    C3'
    C4'
    O4'
    1.0806 113.53 162.89 103.15
    H41'
    C4'
    O4'
    C1'
    1.0891 110.89 77.76 108.09

    H41'
    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.5211
    1.4055
    1.4127

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    H42'
    C4'
    O3'
    C3'
    P
    O3'
    O1P
    P
    O2P
    P
    O3T
    P
    H3T
    O3T
    FIRS NONE LAST

    RESI T3PM
    ate -1)

    O4'
    C4'
    C3'
    O3'
    O3'
    O3'
    P
    NONE

    C1'
    O4'
    C4'
    C3'
    C3'
    C3'
    O3'

    1.0808 108.72 -162.12 108.09


    1.4028 110.98 -77.39 103.15
    0.0
    0.0 180.00
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.0
    0.0

    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0

    -1.00 ! C5H10O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosph


    ! capped with a methyl group. This is to investigate th

    e differences
    ! between BI and BII forms of DNA
    ! C3T is defined as CG321 to miminck DNA
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3T
    ATOM C3T
    ATOM H3T1
    ATOM H3T2
    ATOM H3T3
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1'
    C1'
    C4'
    C3T
    C4'
    O4'
    C1'
    C2'
    C3'
    H11'
    H12'
    H21'
    H22'
    H31'
    H41'
    H42'
    O3'
    P
    C3'

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1

    0.01
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3

    -0.57
    1.50
    -0.78
    -0.78
    -0.57
    -0.17
    0.09
    0.09
    0.09

    ! Note: has 1 asymmetric carbon.


    ! Abs. config is arbitrary.
    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    ! O1P==P==O2P
    !
    |
    !
    O3T (-1)
    !
    \
    !
    C3T--H3T3
    !
    / \
    !
    H3T1 H3T2

    O4' C1' C2' C2' C3' C3' C4' C4' O4' C3'
    H11' C1' H12' C2' H21' C2' H22' C3' H31' C4'
    H42' O3' P
    P
    O1P P
    O2P P
    O3T O3T
    H3T1 C3T H3T2 C3T H3T3
    O4'
    C1'
    C2'
    1.4055 108.09 23.45
    C1'
    C2'
    C3'
    1.4127 106.18
    3.96
    C2'
    C3'
    C4'
    1.5457 103.11 -26.93
    C3'
    C4'
    O4'
    1.5346 100.86 41.73
    C4'
    O4'
    C1'
    1.5211 103.15 -41.62
    C1'
    C2'
    C3'
    1.0856 111.62 123.53
    C1'
    C2'
    C3'
    1.0818 113.32 -114.11
    C2'
    C3'
    C4'
    1.0846 110.65 91.68
    C2'
    C3'
    C4'
    1.0822 110.88 -148.45
    C3'
    C4'
    O4'
    1.0806 113.53 162.89
    C4'
    O4'
    C1'
    1.0891 110.89 77.76
    C4'
    O4'
    C1'
    1.0808 108.72 -162.12
    C3'
    C4'
    O4'
    1.4028 110.98 -77.39
    O3'
    C3'
    C4'
    0.0000 000.00 180.00
    O3'
    P
    O3T
    0.0000 000.00 -95.22

    O3'
    H41'
    C3T
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    000.00
    000.00

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    O3T
    O3'
    O3T
    O3'
    C3T
    O3T
    H3T1
    C3T
    H3T2
    C3T
    H3T3
    C3T
    FIRS NONE LAST

    RESI TM3P
    hate -2)

    *P
    *P
    P
    O3T
    O3T
    O3T
    NONE

    O1P
    O2P
    O3'
    P
    P
    P

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    -115.82
    115.90
    -46.90
    180.00
    60.00
    -60.00

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosp

    ! This is the DNA version (the RNA version is RM3P, see below)
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1'
    C1'
    O3'
    C4'
    C4'
    O4'
    C1'
    C2'
    C3'
    H11'
    H12'
    H21'
    H22'
    H31'
    C5'
    H51'
    H52'
    H53'
    H42'
    O3'
    P

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.40
    0.02
    0.09
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1

    -0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    O4' C1'
    H11' C1'
    P
    P
    C5' C5'
    O4'
    C1'
    C2'
    C3'
    C4'
    C1'
    C1'
    C2'
    C2'
    C3'
    C4'
    C5'
    C5'
    C5'
    C4'
    C3'
    O3'

    C2'
    H12'
    O1P
    H51'
    C1'
    C2'
    C3'
    C4'
    O4'
    C2'
    C2'
    C3'
    C3'
    C4'
    O4'
    C4'
    C4'
    C4'
    O4'
    C4'
    C3'

    ! Note: has 2 asymmetric carbons.


    ! Abs. config is arbitrary.
    !
    H52' H53'
    !
    \ /
    ! H51'-C5' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    ! O1P==P==O2P
    !
    ||
    !
    O3P (-2)

    C2'
    C2'
    P
    C5'

    C3'
    H21'
    O2P
    H52'
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    O4'
    O4'
    O4'
    C1'
    O4'
    C4'

    C3' C4' C4' O4' C3'


    C2' H22' C3' H31' C4'
    P
    O3P
    C5' H53'
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    0.0000 000.00 77.76
    0.0
    0.0 180.0
    0.0
    0.0 -60.0
    0.0
    0.0
    60.0
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    0.0
    0.0 180.00

    O3'
    H42'
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    0.0
    0.0
    0.0
    108.09
    103.15
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    0.0
    0.0
    0.0
    1.4127
    1.4055
    0.0

    IC
    IC
    IC
    PATC

    O1P
    P
    O2P
    P
    O3P
    P
    FIRS NONE LAST

    RESI RM3P
    hate -2)

    O3'
    O3'
    O3'
    NONE

    C3'
    C3'
    C3'

    0.0
    0.0
    0.0

    0.0
    0.0
    0.0

    -60.0
    180.0
    60.0

    0.0
    0.0
    0.0

    0.0
    0.0
    0.0

    -2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosp

    ! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to
    ! allow for the determination of the influence of the ring dihedrals on the
    ! sugar puckering energetics in the absence of the 2' hydroxyl
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1'
    C1'
    O3'
    C4'
    C4'
    O4'
    C1'
    C2'
    C3'
    H11'
    H12'
    H21'
    H22'
    H31'
    C5'
    H51'
    H52'
    H53'
    H42'
    O3'
    P
    O1P

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.40 ! Note: has 2 asymmetric carbons.


    0.02 ! Abs. config is arbitrary.
    0.09
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1

    -0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    O4' C1'
    H11' C1'
    P
    P
    C5' C5'
    O4'
    C1'
    C2'
    C3'
    C4'
    C1'
    C1'
    C2'
    C2'
    C3'
    C4'
    C5'
    C5'
    C5'
    C4'
    C3'
    O3'
    P

    C2'
    H12'
    O1P
    H51'
    C1'
    C2'
    C3'
    C4'
    O4'
    C2'
    C2'
    C3'
    C3'
    C4'
    O4'
    C4'
    C4'
    C4'
    O4'
    C4'
    C3'
    O3'

    C2'
    C2'
    P
    C5'

    C3'
    H21'
    O2P
    H52'
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    O4'
    O4'
    O4'
    C1'
    O4'
    C4'
    C3'

    C3' C4' C4' O4' C3'


    C2' H22' C3' H31' C4'
    P
    O3P
    C5' H53'
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    0.0000 000.00 77.76
    0.0
    0.0
    180.0
    0.0
    0.0
    -60.0
    0.0
    0.0
    60.0
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    0.0
    0.0 180.00
    0.0
    0.0 -60.0

    O3'
    H42'
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    0.0
    0.0
    0.0
    108.09
    103.15
    0.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    0.0
    0.0
    0.0
    1.4127
    1.4055
    0.0
    0.0

    IC O2P
    P
    O3'
    IC O3P
    P
    O3'
    PATC FIRS NONE LAST NONE
    RESI T2FU
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C4'
    ATOM H11'
    ATOM H12'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM F2'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    C3'
    C3'

    0.0
    0.0

    0.0
    0.0

    180.0
    60.0

    0.0
    0.0

    0.0
    0.0

    -2.00 ! C4H6FO5P THF with PO3 on c3, F (beta, up) on c2


    ! Charge distribution is preliminary
    OG3C51
    CG3C52
    CG3C52
    HGA2
    HGA2
    HGA2
    HGA2

    -0.40
    0.02
    0.02
    0.09
    0.09
    0.09
    0.09

    CG3C51
    HGA1
    FGA1

    0.14
    0.09
    -0.23

    CG3C51
    HGA1

    -0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    ! Note: has 2 asymmetric carbons.


    ! Abs. config is arbitrary.
    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--F2' (beta)
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    ! O1P==P==O2P
    !
    ||
    !
    O3P (-2)

    C1' O4' C1' C2' C2'


    C1' H11' C1' H12' C2'
    C4' H42' O3' P
    P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    F2'
    C2'
    C3'
    H22'
    C2'
    C3'
    H31'
    C3'
    C4'
    H41'
    C4'
    O4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3P
    P
    O3'
    FIRS NONE LAST NONE

    RESI TMFU
    p) on c2'

    C3' C3' C4' C4' O4' C3'


    F2' C2' H22' C3' H31' C4'
    O1P P
    O2P P
    O3P
    C2'
    1.4055 108.09 23.45
    C3'
    1.4127 106.18
    3.96
    C4'
    1.5457 103.11 -26.93
    O4'
    1.5346 100.86 41.73
    C1'
    1.5211 103.15 -41.62
    C3'
    1.0856 111.62 123.53
    C3'
    1.0818 113.32 -114.11
    C4'
    1.0846 110.65 91.68
    C4'
    1.0822 110.88 -148.45
    O4'
    1.0806 113.53 162.89
    C1'
    1.0891 110.89 77.76
    C1'
    1.0808 108.72 -162.12
    O4'
    1.4028 110.98 -77.39
    C4'
    0.0
    0.0 180.00
    C3'
    0.0
    0.0 -60.0
    C3'
    0.0
    0.0 180.0
    C3'
    0.0
    0.0
    60.0

    O3'
    H41'
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0

    -2.00 ! C5H8FO5P THF with ch3 on c4', opo3 on c3', F (beta, u


    ! Caution: Charges are preliminary. Charge on fluorine wa

    s
    ! taken from Daxu Yin's thesis (monofluoroethane).
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'

    OG3C51
    CG3C52
    HGA2
    HGA2

    -0.40 ! Note: has 3 asymmetric carbons.


    0.02 ! Abs. config is arbitrary.
    0.09
    0.09 !
    H52' H53'

    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM F2'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'

    CG3C51
    HGA1

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    0.11 !
    \ /
    0.09 ! H51'-C5' O4' H11'
    !
    \ / \ /
    0.19 ! H42'--C4' C1'--H12'
    0.09 !
    |
    |
    -0.28 ! H31'--C3'--C2'--F2' (beta)
    !
    /
    \
    -0.09 !
    O3'
    H22'
    0.09 !
    |
    ! O1P==P==O2P
    -0.40 !
    ||
    1.10 !
    O3P (-2)
    -0.90
    -0.90
    -0.90

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG3C51
    HGA1
    FGA1
    CG3C51
    HGA1

    BOND C1' O4' C1' C2' C2'


    BOND C1' H11' C1' H12'
    BOND C2' H22' C2' F2'
    BOND C3' O3' C3' H31'
    BOND O3' P
    P
    O1P P
    BOND C4' C5' C5' H51' C5'
    ! The following IC table is a
    IC
    C1'
    C2'
    C3'
    IC
    C2'
    C3'
    C4'
    IC
    H11'
    C1'
    C2'
    IC
    H12'
    C1'
    C2'
    IC
    F2'
    C2'
    C3'
    IC
    H22'
    C2'
    C3'
    IC
    H31'
    C3'
    C4'
    IC
    O3'
    C3'
    C4'
    IC
    P
    O3'
    C3'
    IC
    O1P
    P
    O3'
    IC
    O2P
    P
    O3'
    IC
    O3P
    P
    O3'
    IC
    C5'
    C4'
    O4'
    IC
    H51'
    C5'
    C4'
    IC
    H52'
    C5'
    C4'
    IC
    H53'
    C5'
    C4'
    IC
    H42'
    C4'
    O4'

    C3' C3' C4' C4' O4'

    O2P P O3P
    H52' C5' H53' C4' H42'
    guess from thfohch3 (Nicolas):
    C4'
    0.0 0.0 330.81 0.0 0.0
    O4'
    0.0 0.0 39.77 0.0 0.0
    C3'
    0.0 0.0 129.38 0.0 0.0
    C3'
    0.0 0.0 251.29 0.0 0.0
    C4'
    0.0 0.0 89.74 0.0 0.0
    C4'
    0.0 0.0 209.60 0.0 0.0
    O4'
    0.0 0.0 161.48 0.0 0.0
    O4'
    0.0 0.0 280.72 0.0 0.0
    C4'
    0.0 0.0 180.00 0.0 0.0
    C3'
    0.0 0.0 180.00 0.0 0.0
    C3'
    0.0 0.0 60.00 0.0 0.0
    C3'
    0.0 0.0 -60.00 0.0 0.0
    C1'
    0.0 0.0 87.60 0.0 0.0
    O4'
    0.0 0.0 176.37 0.0 0.0
    O4'
    0.0 0.0 56.84 0.0 0.0
    O4'
    0.0 0.0 297.06 0.0 0.0
    C1'
    0.0 0.0 207.55 0.0 0.0

    PATC FIRS NONE LAST NONE


    RESI T2FD
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C4'
    ATOM H11'
    ATOM H12'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'

    -2.00 ! C4H6FO5P THF with PO3 on c3, F (alpha, down) on c2


    ! Charge distribution is preliminary
    OG3C51
    CG3C52
    CG3C52
    HGA2
    HGA2
    HGA2
    HGA2
    CG3C51

    -0.40
    0.02
    0.02
    0.09
    0.09
    0.09
    0.09

    !
    !
    !
    !
    !
    0.14 !

    ! Note: has 2 asymmetric carbons.


    ! Abs. config is arbitrary.
    H41' O4' H11'
    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--F2' (alpha)
    /
    \

    ATOM H21'
    ATOM F2'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    HGA1
    FGA1
    CG3C51
    HGA1

    0.09 !
    O3'
    H22'
    -0.23 !
    |
    ! O1P==P==O2P
    -0.09 !
    ||
    0.09 !
    O3P (-2)

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    C1' O4' C1' C2' C2'


    C1' H11' C1' H12' C2'
    C4' H42' O3' P
    P
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    F2'
    C2'
    C3'
    H21'
    C2'
    C3'
    H31'
    C3'
    C4'
    H41'
    C4'
    O4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3P
    P
    O3'
    FIRS NONE LAST NONE

    C3' C3' C4' C4' O4' C3'


    F2' C2' H21' C3' H31' C4'
    O1P P
    O2P P
    O3P
    C2'
    1.4055 108.09 23.45
    C3'
    1.4127 106.18
    3.96
    C4'
    1.5457 103.11 -26.93
    O4'
    1.5346 100.86 41.73
    C1'
    1.5211 103.15 -41.62
    C3'
    1.0856 111.62 123.53
    C3'
    1.0818 113.32 -114.11
    C4'
    1.0846 110.65 -148.45
    C4'
    1.0822 110.88 91.68
    O4'
    1.0806 113.53 162.89
    C1'
    1.0891 110.89 77.76
    C1'
    1.0808 108.72 -162.12
    O4'
    1.4028 110.98 -77.39
    C4'
    0.0
    0.0 180.00
    C3'
    0.0
    0.0 -60.0
    C3'
    0.0
    0.0 180.0
    C3'
    0.0
    0.0
    60.0

    O3'
    H41'
    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0

    RESI TMFD
    -2.00 ! C5H8FO5P Flourine on C2' (alpha, down) with ch3 on c4
    ', opo3 on c3', oh on c2'
    ! Charge distribution is preliminary
    GROUP
    ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons.
    ATOM C1' CG3C52
    0.02 ! Abs. config is arbitrary.
    ATOM H11' HGA2
    0.09
    ATOM H12' HGA2
    0.09 !
    H52' H53'
    ATOM C4' CG3C51
    0.11 !
    \ /
    ATOM H42' HGA1
    0.09 ! H51'-C5' O4' H11'
    GROUP
    !
    \ / \ /
    ATOM C2' CG3C51
    0.19 ! H42'--C4' C1'--H12'
    ATOM H21' HGA1
    0.09 !
    |
    |
    ATOM F2' FGA1
    -0.28 ! H31'--C3'--C2'--F2' (alpha)
    GROUP
    !
    /
    \
    ATOM C3' CG3C51 -0.09 !
    O3'
    H22'
    ATOM H31' HGA1
    0.09 !
    |
    GROUP
    ! O1P==P==O2P
    ATOM O3' OG303
    -0.40 !
    ||
    ATOM P
    PG1
    1.10 !
    O3P (-2)
    ATOM O1P OG2P1
    -0.90
    ATOM O2P OG2P1
    -0.90
    ATOM O3P OG2P1
    -0.90
    GROUP
    ATOM C5' CG331
    -0.27
    ATOM H51' HGA3
    0.09

    ATOM H52' HGA3


    ATOM H53' HGA3

    0.09
    0.09

    BOND C1' O4' C1' C2' C2'


    BOND C1' H11' C1' H12'
    BOND C2' F2' C2' H21'
    BOND C3' O3' C3' H31'
    BOND O3' P
    P
    O1P P
    BOND C4' C5' C5' H51' C5'
    ! The following IC table is a
    IC
    C1'
    C2'
    C3'
    IC
    C2'
    C3'
    C4'
    IC
    H11'
    C1'
    C2'
    IC
    H12'
    C1'
    C2'
    IC
    H21'
    C2'
    C3'
    IC
    F2'
    C2'
    C3'
    IC
    H31'
    C3'
    C4'
    IC
    O3'
    C3'
    C4'
    IC
    P
    O3'
    C3'
    IC
    O1P
    P
    O3'
    IC
    O2P
    P
    O3'
    IC
    O3P
    P
    O3'
    IC
    C5'
    C4'
    O4'
    IC
    H51'
    C5'
    C4'
    IC
    H52'
    C5'
    C4'
    IC
    H53'
    C5'
    C4'
    IC
    H42'
    C4'
    O4'
    PATC FIRS NONE LAST NONE

    C3' C3' C4' C4' O4'

    O2P P O3P
    H52' C5' H53' C4' H42'
    guess from thfohch3 (Nicolas):
    C4'
    0.0 0.0 330.81 0.0 0.0
    O4'
    0.0 0.0 39.77 0.0 0.0
    C3'
    0.0 0.0 129.38 0.0 0.0
    C3'
    0.0 0.0 251.29 0.0 0.0
    C4'
    0.0 0.0 89.74 0.0 0.0
    C4'
    0.0 0.0 209.60 0.0 0.0
    O4'
    0.0 0.0 161.48 0.0 0.0
    O4'
    0.0 0.0 280.72 0.0 0.0
    C4'
    0.0 0.0 180.00 0.0 0.0
    C3'
    0.0 0.0 180.00 0.0 0.0
    C3'
    0.0 0.0 60.00 0.0 0.0
    C3'
    0.0 0.0 -60.00 0.0 0.0
    C1'
    0.0 0.0 87.60 0.0 0.0
    O4'
    0.0 0.0 176.37 0.0 0.0
    O4'
    0.0 0.0 56.84 0.0 0.0
    O4'
    0.0 0.0 297.06 0.0 0.0
    C1'
    0.0 0.0 207.55 0.0 0.0

    RESI ARMO
    0.00
    the beta configuration
    GROUP
    ATOM O4' OG3C51 -0.40
    ATOM C1' CG3C52
    0.02
    ATOM H11' HGA2
    0.09
    ATOM H12' HGA2
    0.09
    ATOM C4' CG3C51
    0.11
    ATOM H42' HGA1
    0.09
    GROUP
    ATOM C2' CG3C51
    0.14
    ATOM H22' HGA1
    0.09
    ATOM O2' OG311
    -0.65
    ATOM H21' HGP1
    0.42
    GROUP
    ATOM C3' CG3C51
    0.14
    ATOM H31' HGA1
    0.09
    ATOM O3' OG311
    -0.65
    ATOM H32' HGP1
    0.42
    GROUP
    ATOM C5' CG331
    -0.27
    ATOM H51' HGA3
    0.09
    ATOM H52' HGA3
    0.09
    ATOM H53' HGA3
    0.09

    ! C5H10O3 ribose, thfch3ohoh, with the c2' hydroxyl in

    BOND
    BOND
    BOND
    BOND
    BOND

    C2' C3' C3' C4' C4' O4'

    C1'
    C1'
    C2'
    C3'
    C4'

    O4'
    H11'
    O2'
    O3'
    C5'

    C1'
    C1'
    C2'
    O3'
    C5'

    C2'
    H12'
    H22'
    H32'
    H51'

    !
    H52' H53'
    !
    \ /
    ! H51'-C5' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    (beta)
    !
    H32'
    H22'
    !

    O2' H21'
    C3' H31'
    C5' H52' C5' H53' C4' H42'

    ! The following IC table is a guess from thfohch3 (Nicolas):


    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 330.81 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 39.77 0.0 0.0
    IC
    H11'
    C1'
    C2'
    C3'
    0.0 0.0 129.38 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 251.29 0.0 0.0
    IC
    O2'
    C2'
    C3'
    C4'
    0.0 0.0 89.74 0.0 0.0
    IC
    H21'
    O2'
    C2'
    C3'
    0.0 0.0 90.00 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 209.60 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 161.48 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 280.72 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C4'
    0.0 0.0 44.72 0.0 0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 87.60 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 176.37 0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 56.84 0.0 0.0
    IC
    H53'
    C5'
    C4'
    O4'
    0.0 0.0 297.06 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 207.55 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI THFA
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    GROUP !
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2

    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2
    HGA1
    CG3C51
    OG311
    HGP1

    0.00 !
    !
    -0.40 !
    0.11
    0.09 !
    0.11 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    0.09 !
    0.14 !
    -0.65 !
    0.42

    C8H12N2O2 THF-OH-CH3-IM
    Note: has 3 asymmetric carbons.
    Abs. config is arbitrary.
    H52' H53'
    \ /
    H51'-C5' O4' Imidazole
    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    O3'
    H22'
    |
    H32'

    CG331
    -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    C1'
    HE1
    HGR52
    0.09 !
    \
    /
    CG2R51
    0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    ||
    NG2R51 -0.04 ! HG-CG
    ||
    CG2R53
    0.25 !
    \\
    ||
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31'
    BOND C5' H51' C5' H52' C5' H53'
    BOND O3' H32'
    BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    DOUBLE CG CD2 CE1 NE2
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390

    C4' C5'
    C4' H42'

    0.0 0.0
    0.0 0.0

    IC
    H12'
    IC
    H21'
    IC
    H22'
    IC
    O3'
    IC
    H32'
    IC
    H31'
    IC
    H41'
    IC
    H42'
    IC
    C4'
    IC
    O4'
    IC
    C1'
    IC
    ND1
    IC
    CE1
    IC
    HE1
    IC
    CE1
    IC
    NE2
    IC
    C5'
    IC
    H51'
    IC
    H52'
    IC
    H53'
    PATC FIRS NONE
    RESI ARAO
    2'
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM O2'
    ATOM H21'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM H32'
    BOND C1'
    BOND C1'
    BOND C4'
    !Nicolas:
    s
    IC C4'
    IC O4'
    IC C1'
    IC C2'
    IC C3'
    IC H11'
    IC H12'
    IC O2'
    IC H21'
    IC H22'
    IC H31'
    IC H41'

    C1'
    C2'
    C2'
    C3'
    C2'
    C3'
    C3'
    C4'
    O3'
    C3'
    C3'
    C4'
    C4'
    O4'
    C4'
    O4'
    O4'
    C1'
    C1'
    ND1
    ND1
    CE1
    CE1
    NE2
    NE2
    CD2
    CE1
    NE2
    NE2
    CD2
    CD2
    CG
    C4'
    O4'
    C5'
    C4'
    C5'
    C4'
    C5'
    C4'
    LAST NONE

    C3'
    C4'
    C4'
    O4'
    C2'
    O4'
    C1'
    C1'
    ND1
    CE1
    NE2
    CD2
    CG
    CD2
    HD2
    HG
    C1'
    O4'
    O4'
    O4'

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    268.35 0.0 0.0


    82.530 0.0 0.0
    204.06 0.0 0.0
    -93.14 0.0 0.0
    -60.00 0.0 0.0
    147.80 0.0 0.0
    132.30 0.0 0.0
    220.70 0.0 0.0
    256.98 0.0 0.0
    180.00 0.0 0.0
    181.56 0.0 0.0
    0.34 0.0 0.0
    0.00 0.0 0.0
    180.40 0.0 0.0
    179.83 0.0 0.0
    178.45 0.0 0.0
    144.82 0.0 0.0
    -179.98 0.0 0.0
    -59.66 0.0 0.0
    59.68 0.0 0.0

    0.00 ! C4H8O3 arabinose sugar, oh alpha on c3', oh beta on c


    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.02
    0.09
    0.09
    0.02
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H41' O4' H11'


    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    O3'
    O2'
    |
    |
    (beta)
    H32'
    H22'

    O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
    H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41'
    H42' O2' H21' O3' H32'
    the following IC are for thf-oh as optimized via ab initio calculation
    O4'
    C1'
    C2'
    C3'
    C4'
    C1'
    C1'
    C2'
    O2'
    C2'
    C3'
    C4'

    C1'
    C2'
    C3'
    C4'
    O4'
    C2'
    C2'
    C3'
    C2'
    C3'
    C4'
    O4'

    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C3'
    C4'
    O4'
    C1'

    1.4055
    1.4127
    1.5457
    1.5346
    1.5211
    1.0856
    1.0818
    0.0000
    0.0
    1.0822
    1.0806
    1.0891

    108.09
    106.18
    103.11
    100.86
    103.15
    111.62
    113.32
    0.00
    0.0
    110.88
    113.53
    110.89

    23.45
    3.96
    -26.93
    41.73
    -41.62
    123.53
    -114.11
    91.68
    -60.0
    -148.45
    162.89
    77.76

    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    0.0000
    0.0
    100.86
    103.15
    108.09

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    0.0000
    0.0
    1.5211
    1.4055
    1.4127

    IC
    IC
    IC
    PATC

    H42'
    C4'
    O3'
    C3'
    H32'
    O3'
    FIRS NONE LAST

    RESI ARIM
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM O2'
    ATOM H21'
    GROUP !
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2

    O4'
    C4'
    C3'
    NONE

    C1'
    O4'
    C4'

    1.0808 108.72 -162.12 108.09


    1.4028 110.98 -77.39 103.15
    0.9492 108.72 44.80 110.98

    0.00 ! C7H10N2O2 arabinose sugar with imidazole


    ! transferred from thf
    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    -0.18 !
    0.09 !
    0.09 !

    H41' O4' Imidazole


    \ / \ /
    H42'--C4' C1'--H12'
    |
    |
    H31'--C3'--C2'--H21'
    /
    \
    H32'
    O2'
    |
    (beta)
    H22'

    CG3C51
    0.14
    HGA1
    0.09
    OG311
    -0.65
    HGP1
    0.42
    Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    C1'
    HE1
    HGR52
    0.09 !
    \
    /
    CG2R51
    0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    ||
    NG2R51 -0.04 ! HG-CG
    ||
    CG2R53
    0.25 !
    \\
    ||
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2

    BOND C1' O4' C1' C2' C2' C3' C3'


    BOND C2' O2' C1' H12' C2' H22' C3'
    BOND C4' H41' C4' H42'
    BOND ND1 CE1 NE2 CD2 CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    DOUBLE CG CD2 CE1 NE2
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 C1'
    ND1 CE1
    IMPR CD2 CG NE2 HD2
    CD2 NE2
    IMPR CE1 ND1 NE2 HE1
    CE1 NE2
    IMPR CG CD2 ND1 HG
    CG ND1
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    IC
    C2'
    C3'
    C4'
    O4'
    IC
    H12'
    C1'
    C2'
    C3'
    IC
    O2'
    C2'
    C3'
    C4'
    IC
    H21'
    O2'
    C2'
    C3'
    IC
    H22'
    C2'
    C3'
    C4'
    IC
    H31'
    C3'
    C4'
    O4'
    IC
    H32'
    C3'
    C4'
    O4'
    IC
    H41'
    C4'
    O4'
    C1'
    IC
    H42'
    C4'
    O4'
    C1'
    IC
    C4'
    O4'
    C1'
    ND1
    IC
    O4'
    C1'
    ND1
    CE1
    IC
    C1'
    ND1
    CE1
    NE2
    IC
    ND1
    CE1
    NE2
    CD2

    C4' C4' O4' C1' ND1


    H31' C3' H32' O2' H21'

    CG
    CG
    ND1
    CD2

    C1'
    HD2
    HE1
    HG

    1.532 101.886 324.92 0.0 0.0


    0.0 0.0 33.390 0.0 0.0
    0.0 0.0 268.35 0.0 0.0
    0.0 0.0 82.530 0.0 0.0
    0.0 0.0 -60.0 0.0 0.0
    0.0 0.0 204.06 0.0 0.0
    0.0 0.0 155.99 0.0 0.0
    0.0 0.0 276.70 0.0 0.0
    0.0 0.0 132.30 0.0 0.0
    0.0 0.0 220.70 0.0 0.0
    0.0 0.0 256.98 0.0 0.0
    0.0 0.0 180.00 0.0 0.0
    0.0 0.0 181.56 0.0 0.0
    0.0 0.0 0.34 0.0 0.0

    1.4127
    1.4055
    1.5211

    IC
    CE1
    IC
    HE1
    IC
    CE1
    IC
    NE2
    PATC FIRS NONE
    RESI AR3P
    te -2)
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C4'
    ATOM H11'
    ATOM H12'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H22'
    ATOM O2'
    ATOM H21'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    NE2
    CD2
    CE1
    NE2
    NE2
    CD2
    CD2
    CG
    LAST NONE

    0.0
    0.0
    0.0
    0.0

    0.0 0.00 0.0 0.0


    0.0 180.40 0.0 0.0
    0.0 179.83 0.0 0.0
    0.0 178.45 0.0 0.0

    -2.00 ! C4H7O6P arabinose sugar with phosphate on 3' (phospha


    OG3C51
    CG3C52
    CG3C52
    HGA2
    HGA2
    HGA2
    HGA2

    -0.40
    0.02
    0.02
    0.09
    0.09
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    !
    H41' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H22' (alpha)
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    0.14 ! O1P==P==O2P H21'
    0.09 !
    ||
    -0.65 !
    O3P (-2)
    0.42

    CG3C51
    HGA1

    -0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    C1' O4' C1' C2' C2'


    C1' H11' C1' H12' C2'
    C4' H42' O2' H21' O3'
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    O2'
    C2'
    C3'
    H21'
    O2'
    C2'
    H22'
    C2'
    C3'
    H31'
    C3'
    C4'
    H41'
    C4'
    O4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3P
    P
    O3'
    FIRS NONE LAST NONE

    RESI RIBO
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C4'
    ATOM H11'

    CG
    CD2
    HD2
    HG

    C3' C3' C4' C4' O4' C3' O3'


    O2' C2' H22' C3' H31' C4' H41'
    P
    P
    O1P P
    O2P P
    O3P
    C2'
    1.4055 108.09
    6.07 106.18
    C3'
    1.4127 106.18 -25.13 103.11
    C4'
    1.5457 103.11 33.40 100.86
    O4'
    1.5346 100.86 -30.20 103.15
    C1'
    1.5211 103.15 14.98 108.09
    C3'
    1.0856 111.62 91.77 103.11
    C3'
    1.0818 113.32 -144.31 103.11
    C4'
    1.0846 110.65 152.51 100.86
    C3'
    0.0
    0.0
    60.0
    0.0
    C4'
    1.0822 110.88 -84.13 100.86
    O4'
    1.0806 113.53 87.99 103.15
    C1'
    1.0891 110.89 136.35 108.09
    C1'
    1.0808 108.72 -102.74 108.09
    O4'
    1.4028 110.98 -151.73 103.15
    C4'
    0.0
    0.0 180.00
    0.0
    C3'
    0.0
    0.0 -60.0
    0.0
    C3'
    0.0
    0.0 180.0
    0.0
    C3'
    0.0
    0.0
    60.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    0.0
    1.5211
    1.4055
    1.4127
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0

    0.00 ! C4H8O3 ribose, both c2' and c3' hydroxyls are alpha
    OG3C51
    CG3C52
    CG3C52
    HGA2

    -0.40
    0.02
    0.02
    0.09

    !
    !
    !
    !

    H41' O4' H11'


    \ / \ /
    H42'--C4' C1'--H12'
    |
    |

    ATOM H12'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM O2'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM H32'

    HGA2
    HGA2
    HGA2
    CG3C51
    HGA1
    OG311
    HGP1

    0.09 !
    0.09 !
    0.09 !
    !
    0.14 !
    0.09 !
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    H31'--C3'--C2'--H22'
    /
    \
    O3'
    O2'
    |
    |
    H32'
    H21'

    BOND C1' O4' C1' C2' C2' C3'


    BOND C1' H11' C1' H12' C2' O2'
    BOND C4' H42' O2' H22' O3' H32'
    !Nicolas: the following IC are for
    s
    IC C4'
    O4'
    C1'
    C2'
    IC O4'
    C1'
    C2'
    C3'
    IC C1'
    C2'
    C3'
    C4'
    IC C2'
    C3'
    C4'
    O4'
    IC C3'
    C4'
    O4'
    C1'
    IC H11'
    C1'
    C2'
    C3'
    IC H12'
    C1'
    C2'
    C3'
    IC H21'
    C2'
    C3'
    C4'
    IC O2'
    C2'
    C3'
    C4'
    IC H22'
    O2'
    C2'
    C3'
    IC H31'
    C3'
    C4'
    O4'
    IC H41'
    C4'
    O4'
    C1'
    IC H42'
    C4'
    O4'
    C1'
    IC O3'
    C3'
    C4'
    O4'
    IC H32'
    O3'
    C3'
    C4'
    PATC FIRS NONE LAST NONE
    RESI TMPM
    (phosphate -1)

    C3' C4' C4' O4' C3' O3'


    C2' H21' C3' H31' C4' H41'
    thf-oh as optimized via ab initio calculation
    1.4055
    1.4127
    1.5457
    1.5346
    1.5211
    1.0856
    1.0818
    1.0846
    1.0822
    0.0
    1.0806
    1.0891
    1.0808
    1.4028
    0.9492

    108.09
    106.18
    103.11
    100.86
    103.15
    111.62
    113.32
    110.65
    110.88
    0.0
    113.53
    110.89
    108.72
    110.98
    108.72

    23.45
    3.96
    -26.93
    41.73
    -41.62
    123.53
    -114.11
    91.68
    -148.45
    -60.0
    162.89
    77.76
    -162.12
    -77.39
    44.80

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    0.0
    1.4055
    1.4127
    1.4127
    1.4055
    1.5211

    -1.00 ! C6H12O5P 4'-methyl,3'-methylphosphate tetrahydrofuran


    !charges corrected by adm jr. 9/98

    GROUP
    ATOM O4'
    ATOM C1'
    ATOM H11'
    ATOM H12'
    ATOM C4'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    GROUP
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    ATOM C3T

    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    0.0
    103.15
    108.09
    108.09
    103.15
    110.98

    OG3C51
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.40
    0.02
    0.09
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1

    0.01
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG303
    CG331

    -0.57
    1.50
    -0.78
    -0.78
    -0.57
    -0.17

    !
    H52' H53'
    !
    \ /
    ! H51'-C5' O4' H11'
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    ! O1P==P==O2P
    !
    |
    !
    O3P (-1)
    !
    \
    !
    C3T--H3T3
    !
    / \
    !
    H3T1 H3T2
    !

    ATOM H3T1
    ATOM H3T2
    ATOM H3T3
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H53'
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    HGA3
    HGA3
    HGA3

    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    C1' O4' C1' C2' C2'


    C1' H11' C1' H12' C2'
    O3' P
    P
    O1P P
    O3P C3T C3T H3T1 C3T
    C4' C5' C5' H51' C5'
    C4'
    O4'
    C1'
    O4'
    C1'
    C2'
    C1'
    C2'
    C3'
    C2'
    C3'
    C4'
    C3'
    C4'
    O4'
    H11'
    C1'
    C2'
    H12'
    C1'
    C2'
    H21'
    C2'
    C3'
    H22'
    C2'
    C3'
    H31'
    C3'
    C4'
    C5'
    C4'
    O4'
    H51'
    C5'
    C4'
    H52'
    C5'
    C4'
    H53'
    C5'
    C4'
    H42'
    C4'
    O4'
    O3'
    C3'
    C4'
    P
    O3'
    C3'
    O1P
    P
    O3'
    O2P
    P
    O3'
    O3P
    P
    O3'
    C3T
    O3P
    P
    H3T1
    C3T
    O3P
    H3T2
    C3T
    O3P
    H3T3
    C3T
    O3P
    FIRS NONE LAST NONE

    RESI TADE
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C6
    ATOM N6
    ATOM H61
    ATOM H62
    ATOM O4'
    ATOM C1'

    C3'
    H21'
    O2P
    H3T2
    H52'
    C2'
    C3'
    C4'
    O4'
    C1'
    C3'
    C3'
    C4'
    C4'
    O4'
    C1'
    O4'
    O4'
    O4'
    C1'
    O4'
    C4'
    C3'
    C3'
    C3'
    O3'
    P
    P
    P

    C3' C4' C4' O4' C3'


    C2' H22' C3' H31' C4'
    P
    O3P
    C3T H3T3
    C5' H53'
    1.4055 108.09 23.45
    1.4127 106.18
    3.96
    1.5457 103.11 -26.93
    1.5346 100.86 41.73
    1.5211 103.15 -41.62
    1.0856 111.62 123.53
    1.0818 113.32 -114.11
    1.0846 110.65 91.68
    1.0822 110.88 -148.45
    1.0806 113.53 162.89
    0.0000 000.00 77.76
    0.0
    0.0
    180.0
    0.0
    0.0
    -60.0
    0.0
    0.0
    60.0
    1.0808 108.72 -162.12
    1.4028 110.98 -77.39
    0.0
    0.0 180.00
    0.0
    0.0 -60.0
    0.0
    0.0
    60.0
    0.0
    0.0 180.0
    0.0
    0.0 180.0
    0.0
    0.0
    60.0
    0.0
    0.0 -60.0
    0.0
    0.0 180.0

    O3'
    H42'

    106.18
    103.11
    100.86
    103.15
    108.09
    103.11
    103.11
    100.86
    100.86
    103.15
    108.09
    0.0
    0.0
    0.0
    108.09
    103.15
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127
    1.5346
    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    0.0
    0.0
    0.0
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.00 ! C9H11N5O thf with adenine


    ! Atom types for aliphatic atoms based on nucleotide
    ! atom order consistent with 9-m-ade
    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51
    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64
    NG2S3
    HGP4
    HGP4
    OG3C51
    CG3C51

    0.28
    -0.71
    0.34
    0.12
    -0.05
    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46
    -0.77
    0.38
    0.38
    -0.40
    0.11

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H61 H62!
    \ /
    N6
    |
    C6
    // \
    N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H2 N3
    \
    \
    \
    \
    H42' O4' \
    \ / \ \

    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'

    HGA1
    CG3C52
    HGA2
    HGA2

    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    !
    !
    !
    !
    !
    -0.18 !
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    H41'-C4'
    C1'
    \
    / \
    H31'--C3'--C2' H12'
    /
    / \
    H32' H21' H22'

    BOND C1' O4' C1' C2' C2' C3' C3'


    BOND C1' H12' C2' H21' C2' H22' C3'
    BOND C4' H41' C4' H42'
    BOND C1' N9
    BOND N9 C4
    N9 C8 C4 N3
    C2
    BOND N6 H61 N6 H62 C6 C5
    C5
    DOUBLE N1 C6
    C2 N3
    C4 C5
    IMPR N6 C6 H61 H62
    C6 N1
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    IC
    C2'
    C3'
    C4'
    O4'
    IC
    H12'
    C1'
    C2'
    C3'
    IC
    H21'
    C2'
    C3'
    C4'
    IC
    H22'
    C2'
    C3'
    C4'
    IC
    H31'
    C3'
    C4'
    O4'
    IC
    H32'
    C3'
    C4'
    O4'
    IC
    H41'
    C4'
    O4'
    C1'
    IC
    H42'
    C4'
    O4'
    C1'
    IC C3' C2' C1' N9
    1.5284 101.97
    IC O4' C1' N9 C4
    1.5251 113.71
    IC C1' C4 *N9 C8
    1.4896 125.97
    IC C4 N9 C8 N7
    1.376 106.0
    IC C8 N9 C4 C5
    1.367 106.0
    IC C8 N7 C5 C6
    0.0
    0.0
    IC N7 C5 C6 N1
    0.0
    0.0
    IC C5 C6 N1 C2
    0.0
    0.0
    IC N9 C5 *C4 N3
    1.376 105.6
    IC C5 N1 *C6 N6
    1.409 117.6
    IC N1 C6 N6 H61
    1.337 121.2
    IC H61 C6 *N6 H62
    1.01
    119.0
    IC C5 N1 *C6 N6
    1.409 117.6
    IC N1 C6 N6 H61
    1.337 119.0
    IC H61 C6 *N6 H62
    1.01
    119.0
    IC N9 N7 *C8 H8
    0.0
    0.0
    IC N1 N3 *C2 H2
    0.0
    0.0
    PATC FIRS NONE LAST NONE
    RESI TCYT
    GROUP
    ATOM N1
    ATOM C6
    ATOM H6
    ATOM C2
    ATOM O2
    ATOM N3

    C4' C4' O4'


    H31' C3' H32'
    N1
    N7
    N7
    C5

    C6
    C8
    C8

    N6
    H8

    C2

    H2

    N6

    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    147.80
    180.2
    -180.00
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0

    324.92 0.0 0.0


    33.390 0.0 0.0
    268.35 0.0 0.0
    82.530 0.0 0.0
    204.06 0.0 0.0
    155.99 0.0 0.0
    276.70 0.0 0.0
    132.30 0.0 0.0
    220.70 0.0 0.0
    113.71 1.4896
    125.59 1.3783 !chi
    106.0
    1.367
    113.6
    1.312
    105.6
    1.382
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    126.9
    1.342
    121.2
    1.337
    119.0
    1.01
    119.00 1.01
    119.0
    1.337
    119.0
    1.01
    121.00 1.01
    0.0
    0.0
    0.0
    0.0

    0.00 ! C8H11N3O2 THF with cytosine


    ! Atom types for aliphatic atoms based on nucleotide
    !atom order to be consistent with 1-m-cyt
    NG2R61
    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R62

    -0.13
    0.05
    0.17
    0.52
    -0.49
    -0.66

    !
    !
    !
    !
    !

    H42 H41
    \ /
    N4
    |
    C4

    ATOM C4
    ATOM N4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H5
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'

    CG2R64
    NG2S3
    HGP4
    HGP4
    CG2R62
    HGR62
    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2

    0.65
    -0.75
    0.37
    0.33
    -0.13
    0.07
    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    / \\
    H5-C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    H42' O4' \
    \ / \ \
    H41'-C4'
    C1'
    \
    / \
    H31'--C3'--C2' H12'
    /
    / \
    H32' H21' H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
    BOND C4' H41' C4' H42'
    BOND C1' N1
    BOND N1 C2
    N1 C6
    C4 N4
    N4 H41 N4 H42
    BOND C2 N3
    C4 C5
    C5 H5
    C6 H6
    DOUBLE C2 O2
    C5 C6
    N3 C4
    IMPR C2 N1 N3 O2
    C4 N3 C5 N4
    IMPR N4 C4 H41 H42
    BILD C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    BILD O4' C1' N1 C2
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    BILD C1' C2 *N1 C6
    1.4896 117.79 -180.00 120.6
    1.364
    BILD C2 N1 C6 C5
    1.399 120.6
    0.0 121.0
    1.337
    BILD C6 N1 C2 N3
    1.364 120.6
    0.0 118.9
    1.356
    BILD N1 N3 *C2 O2
    1.399 118.9 180.0 121.9
    1.237
    BILD N1 C2 N3 C4
    1.399 118.9
    0.0 120.0
    1.334
    BILD C5 N3 *C4 N4
    1.426 121.8 180.00 118.9
    1.337
    BILD N3 C4 N4 H41
    1.337 117.9
    0.00 118.9
    1.01
    BILD H41 C4 *N4 H42
    1.01
    118.9 180.00 120.7
    1.01
    BILD C6 C4 *C5 H5
    0.0
    0.0 180.0
    0.0
    0.0
    BILD N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 155.99 0.0 0.0
    IC
    H32'
    C3'
    C4'
    O4'
    0.0 0.0 276.70 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.79 -180.00 120.6
    1.364
    IC C2 N1 C6 C5
    1.399 120.6
    0.0 121.0
    1.337
    IC C6 N1 C2 N3
    1.364 120.6
    0.0 118.9
    1.356
    IC N1 N3 *C2 O2
    1.399 118.9 180.0 121.9
    1.237
    IC N1 C2 N3 C4
    1.399 118.9
    0.0 120.0
    1.334
    IC C5 N3 *C4 N4
    1.426 121.8 180.00 118.9
    1.337

    IC N3 C4 N4 H41
    1.337
    IC H41 C4 *N4 H42
    1.01
    IC C6 C4 *C5 H5
    0.0
    IC N1 C5 *C6 H6
    0.0
    PATC FIRS NONE LAST NONE
    RESI TGUA
    GROUP
    ATOM N9
    ATOM C4
    ATOM N3
    ATOM C2
    ATOM N1
    ATOM H1
    ATOM N2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM O6
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'

    117.9
    118.9
    0.0
    0.0

    0.00 118.9
    180.00 120.7
    180.0
    0.0
    180.0
    0.0

    1.01
    1.01
    0.0
    0.0

    0.00 ! C9H11N5O2 thf with guanine


    ! Atom types for aliphatic atoms based on nucleotide
    ! atom order consistent with 9-m-gua
    NG2R51
    CG2RC0
    NG2R62
    CG2R64
    NG2R61
    HGP1
    NG2S3
    HGP4
    HGP4
    CG2R63
    OG2D4
    CG2RC0
    NG2R50
    CG2R53
    HGR52
    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2

    -0.02
    0.26
    -0.74
    0.75
    -0.34
    0.26
    -0.68
    0.32
    0.35
    0.54
    -0.51
    0.00
    -0.60
    0.25
    0.16
    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    O6
    ||
    C6
    / \
    H1-N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H21-N2 N3
    \
    |
    \
    H22
    \
    \
    H42' O4' \
    \ / \ \
    H41'-C4'
    C1'
    \
    / \
    H31'--C3'--C2' H12'
    /
    / \
    H32' H21' H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
    BOND C4' H41' C4' H42'
    BOND C1' N9
    BOND N9 C4
    N9 C8
    C4 N3
    C2 N2 C2 N1
    N2
    BOND N2 H22
    N1 H1
    N1 C6
    C6 C5 C5 N7
    C8
    DOUBLE C2 N3
    C4 C5
    N7 C8 C6 O6
    IMPR C2 N3 N1 N2
    C6 N1 C5 O6
    N2 H21
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 155.99 0.0 0.0
    IC
    H32'
    C3'
    C4'
    O4'
    0.0 0.0 276.70 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N9
    1.5284 101.97 147.80 113.71 1.4896
    IC O4' C1' N9 C4
    1.5251 113.71 -97.2 125.59 1.3783

    H21
    H8
    C2

    !chi

    H22

    IC C1' C4 *N9 C8
    1.4896
    IC C4 N9 C8 N7
    1.377
    IC C8 N9 C4 C5
    1.374
    IC N9 C5 *C4 N3
    1.377
    IC C5 C4 N3 C2
    1.377
    IC C4 N3 C2 N1
    1.355
    IC N1 N3 *C2 N2
    1.375
    IC N3 C2 N2 H21
    1.327
    IC H21 C2 *N2 H22
    1.01
    IC N3 C2 N1 C6
    1.327
    IC C6 C2 *N1 H1
    1.393
    IC C5 N1 *C6 O6
    1.415
    IC N9 N7 *C8 H8
    0.0
    PATC FIRS NONE LAST NONE
    RESI TTHY

    GROUP
    ATOM N1
    ATOM C6
    ATOM H6
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'

    125.59
    106.0
    106.0
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    124.0
    124.9
    111.7
    0.0

    -179.99
    0.0
    0.0
    180.0
    0.0
    0.0
    180.0
    180.0
    -180.0
    0.0
    180.00
    180.0
    180.0

    106.0
    113.5
    105.6
    128.4
    111.8
    124.0
    119.7
    127.0
    116.5
    124.9
    117.4
    120.0
    0.0

    1.374
    1.304
    1.377
    1.355
    1.327
    1.375
    1.341
    1.01
    1.01
    1.393
    1.03
    1.239
    0.0

    0.00 ! C9H12N2O3 THF with thymine on C1'


    ! Atom type for N1 changed from NN2 to NN2B, to adjust
    ! chi in thymine independantly of cytosine.
    ! Atom types for aliphatic atoms based on nucleotide
    ! atom order consistent with 1-m-thy
    NG2R61

    -0.34 !

    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3
    HGA3
    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2

    0.17
    0.17
    0.51
    -0.41
    -0.46
    0.36
    0.50
    -0.45
    -0.15
    -0.11
    0.07
    0.07
    0.07
    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    H51

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    BOND C1' O4' C1' C2' C2' C3' C3'


    BOND C1' H12' C2' H21' C2' H22' C3'
    BOND C4' H41' C4' H42'
    BOND C1' N1
    BOND N1 C2 N1 C6 C2 N3 N3
    BOND C5 C5M C6 H6 C5M H51 C5M
    DOUBLE C2 O2
    C4 O4
    C5 C6
    IMPR C2 N1 N3 O2
    C4 N3
    ! ic table for thfim, from Nicolas:

    O4

    |
    ||
    H52-C5M C4
    H3
    | \ / \ /
    H53 C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    H42' O4' \
    \ / \ \
    H41'-C4'
    C1'
    \
    / \
    H31'--C3'--C2' H12'
    /
    / \
    H32' H21' H22'

    C4' C4' O4'


    H31' C3' H32'
    H3 N3 C4 C4
    H52 C5M H53

    C5

    C5

    C4

    O4

    C5

    C6

    C5M

    IC
    C1'
    C2'
    C3'
    IC
    C2'
    C3'
    C4'
    IC
    H12'
    C1'
    C2'
    IC
    H21'
    C2'
    C3'
    IC
    H22'
    C2'
    C3'
    IC
    H31'
    C3'
    C4'
    IC
    H32'
    C3'
    C4'
    IC
    H41'
    C4'
    O4'
    IC
    H42'
    C4'
    O4'
    IC C3' C2' C1' N1
    1.5284
    IC C3' C2' C1' N1
    1.5284
    IC O4' C1' N1 C2
    1.5251
    IC C1' C2 *N1 C6
    1.4896
    IC C2 N1 C6 C5
    1.3746
    IC C6 N1 C2 N3
    1.3704
    IC N1 N3 *C2 O2
    1.3746
    IC N1 C2 N3 C4
    1.3746
    IC C5 N3 *C4 O4
    1.4439
    IC C2 C4 *N3 H3
    1.3813
    IC C4 C6 *C5 C5M
    1.4439
    IC N1 C5 *C6 H6
    0.0
    IC C6 C5 C5M H51
    0.0
    IC C5 H51 *C5M H52
    0.0
    IC H51 H52 *C5M H53
    0.0
    PATC FIRS NONE LAST NONE
    RESI TURA

    C4'
    O4'
    C3'
    C4'
    C4'
    O4'
    O4'
    C1'
    C1'
    101.97
    101.97
    113.71
    117.06
    122.08
    122.08
    115.38
    115.38
    114.07
    126.46
    120.78
    0.0
    0.0
    0.0
    0.0

    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    147.89
    147.89
    180.0
    -179.96
    -0.02
    0.06
    -179.95
    -0.07
    179.98
    180.00
    -179.94
    180.0
    0.0
    115.0
    -115.0

    324.92 0.0 0.0


    33.390 0.0 0.0
    268.35 0.0 0.0
    82.530 0.0 0.0
    204.06 0.0 0.0
    155.99 0.0 0.0
    276.70 0.0 0.0
    132.30 0.0 0.0
    220.70 0.0 0.0
    113.71 1.4896
    113.71 1.4896
    125.59 1.3783 !chi
    122.08 1.3704
    121.23 1.3432
    115.38 1.3813
    121.70 1.2191
    126.46 1.3795
    120.59 1.2327
    116.77 1.0900
    121.63 1.5000
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.00 ! C8H10N2O3 THF with uracil on C1'


    ! Atom type for N1 changed from NN2 to NN2B, in order

    to adjust
    ! chi in uracil/thymine independantly of cytosine.
    ! Atom types for aliphatic atoms based on nucleotide
    ! atom order consistent with 1-m-thy
    GROUP
    ATOM N1
    ATOM C6
    ATOM H6
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM H5
    ATOM O4'
    ATOM C1'
    ATOM H12'
    ATOM C4'
    ATOM H41'
    ATOM H42'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM H32'

    NG2R61

    -0.34 !

    O4

    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    HGR62
    OG3C51
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2

    0.20
    0.14
    0.55
    -0.45
    -0.46
    0.36
    0.53
    -0.48
    -0.15
    0.10
    -0.40
    0.11
    0.09
    0.02
    0.09
    0.09

    ||
    C4

    CG3C52
    HGA2
    HGA2

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    -0.18 !
    0.09
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    H3
    / \ /
    H5-C5 N3
    || |
    H6-C6 C2
    \ / \\
    N1 O2
    \
    \
    \
    H42' O4' \
    \ / \ \
    H41'-C4'
    C1'
    \
    / \
    H31'--C3'--C2' H12'
    /
    / \
    H32' H21' H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
    BOND C4' H41' C4' H42'
    BOND C1' N1
    BOND N1 C2 N1 C6
    BOND C2 N3 N3 H3 N3 C4
    C4 C5
    BOND C5 H5 C6 H6
    DOUBLE C2 O2
    C4 O4
    C5 C6
    IMPR C2 N1 N3 O2
    C4 N3 C5 O4
    ! ic table for thfim, from Nicolas:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 155.99 0.0 0.0
    IC
    H32'
    C3'
    C4'
    O4'
    0.0 0.0 276.70 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 180.0 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.06 -179.96 122.08 1.3704
    IC C2 N1 C6 C5
    1.3746 122.08 -0.02 121.23 1.3432
    IC C6 N1 C2 N3
    1.3704 122.08
    0.06 115.38 1.3813
    IC N1 N3 *C2 O2
    1.3746 115.38 -179.95 121.70 1.2191
    IC N1 C2 N3 C4
    1.3746 115.38 -0.07 126.46 1.3795
    IC C5 N3 *C4 O4
    1.4439 114.07 179.98 120.59 1.2327
    IC C2 C4 *N3 H3
    1.3813 126.46 180.00 116.77 1.0900
    IC C4 C6 *C5 C5M
    1.4439 120.78 -179.94 121.63 1.5000
    IC C4 C6 *C5 H5
    0.0
    0.0 180.0
    0.0
    0.0
    IC N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0
    IC C6 C5 C5M H51
    0.0
    0.0
    0.0
    0.0
    0.0
    IC C5 H51 *C5M H52
    0.0
    0.0 115.0
    0.0
    0.0
    IC H51 H52 *C5M H53
    0.0
    0.0 -115.0
    0.0
    0.0
    PATC FIRS NONE LAST NONE
    RESI THAO
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T
    GROUP !

    0.00 ! C8H12N2O3 Nucleoside analogue with imidazole


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    -0.40
    0.11
    0.09
    0.11
    0.09

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    HGA1
    CG3C51
    OG311
    HGP1

    0.09
    0.14
    -0.65
    0.42

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Imidazole
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    !
    H32'
    !

    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42
    Imidazole: transferred from isolated imidazole (IMIA)

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CG
    HG
    CD2
    HD2
    ND1
    CE1
    HE1
    NE2

    CG2R51
    HGR52
    CG2R51
    HGR52
    NG2R51
    CG2R53
    HGR52
    NG2R50

    -0.05
    0.09
    0.22
    0.10
    -0.04
    0.25
    0.13
    -0.70

    !
    C1'
    HE1
    !
    \
    /
    !
    ND1---CE1
    !
    /
    ||
    ! HG-CG
    ||
    !
    \\
    ||
    !
    CD2---NE2
    !
    |
    !
    HD2

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O3' H32'
    BOND C1' ND1
    BOND ND1 CE1 NE2 CD2 CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    DOUBLE CG CD2 CE1 NE2
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 C1'
    ND1 CE1 CG C1'
    IMPR CD2 CG NE2 HD2
    CD2 NE2 CG HD2
    IMPR CE1 ND1 NE2 HE1
    CE1 NE2 ND1 HE1
    IMPR CG CD2 ND1 HG
    CG ND1 CD2 HG
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC
    C4'
    O4'
    C1'
    ND1
    0.0 0.0 256.98 0.0 0.0
    IC
    O4'
    C1'
    ND1
    CG
    0.0 0.0 90.00 0.0 0.0
    IC
    C1'
    ND1
    CE1
    NE2
    0.0 0.0 181.56 0.0 0.0
    IC
    ND1
    CE1
    NE2
    CD2
    0.0 0.0 0.34 0.0 0.0
    IC
    CE1
    NE2
    CD2
    CG
    0.0 0.0 0.00 0.0 0.0
    IC
    HE1
    CE1
    NE2
    CD2
    0.0 0.0 180.40 0.0 0.0
    IC
    CE1
    NE2
    CD2
    HD2
    0.0 0.0 179.83 0.0 0.0
    IC
    NE2
    CD2
    CG
    HG
    0.0 0.0 178.45 0.0 0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI NUSA
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'

    0.00 ! C10H13N5O3 deoxy-nucleoside with adenine


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1
    CG3C52
    HGA2
    HGA2

    -0.40
    0.11
    0.09
    0.11
    0.09

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Adenine
    !
    \ / \ /
    -0.18 ! H42'--C4' C1'--H12'
    0.09 !
    |
    |
    0.09 ! H31'--C3'--C2'--H21'

    ! Adenine
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C6
    ATOM N6
    ATOM H61
    ATOM H62
    GROUP !
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T

    atoms

    !
    /
    !
    O3'
    CG2RC0
    0.28 !
    |
    NG2R50 -0.71 !
    H32'
    CG2R53
    0.34
    HGR52
    0.12
    NG2R51 -0.05
    NG2R62 -0.74
    CG2R64
    0.50
    HGR62
    0.13
    NG2R62 -0.75
    CG2RC0
    0.43
    CG2R64
    0.46
    NG2S3
    -0.77
    HGP4
    0.38
    HGP4
    0.38
    Hydroxyl group on C3'
    HGA1
    0.09
    CG3C51
    0.14
    OG311
    -0.65
    HGP1
    0.42
    Methyl group on C4'
    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42

    \
    H22'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O3' H32'
    BOND C1' N9
    BOND N9 C4
    N9 C8 C4 N3
    C2 N1
    C6 N6
    BOND N6 H61 N6 H62 C6 C5
    C5 N7
    C8 H8
    C2 H2
    DOUBLE N1 C6
    C2 N3
    C4 C5
    N7 C8
    IMPR N6 C6 H61 H62
    C6 N1 C5 N6
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N9
    1.5284 101.97 147.80 113.71 1.4896
    IC O4' C1' N9 C4
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    IC C1' C4 *N9 C8
    1.4896 125.97 -179.94 106.0
    1.367
    IC C4 N9 C8 N7
    1.376 106.0
    0.0 113.6
    1.312
    IC C8 N9 C4 C5
    1.367 106.0
    0.0 105.6
    1.382
    IC C8 N7 C5 C6
    0.0
    0.0 180.0
    0.0
    0.0
    IC N7 C5 C6 N1
    0.0
    0.0 180.0
    0.0
    0.0
    IC C5 C6 N1 C2
    0.0
    0.0
    0.0
    0.0
    0.0
    IC N9 C5 *C4 N3
    1.376 105.6 -180.0 126.9
    1.342
    IC C5 N1 *C6 N6
    1.409 117.6 -180.0 121.2
    1.337
    IC N1 C6 N6 H61
    1.337 121.2
    0.0 119.0
    1.01
    IC H61 C6 *N6 H62
    1.01
    119.0 180.0 119.00 1.01

    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC N9 N7 *C8 H8
    0.0
    IC N1 N3 *C2 H2
    0.0
    IC
    C5'
    C4'
    O4'
    IC
    H51'
    C5'
    C4'
    IC
    H52'
    C5'
    C4'
    IC
    O5'
    C5'
    C4'
    IC
    H5T
    O5'
    C5'
    PATC FIRS NONE LAST NONE
    RESI NUSG
    0.00
    GROUP
    ATOM O4' OG3C51 -0.40
    ATOM C4' CG3C51
    0.11
    ATOM H42' HGA1
    0.09
    ATOM C1' CG3C51
    0.11
    ATOM H12' HGA1
    0.09
    GROUP
    ATOM C2' CG3C52 -0.18
    ATOM H21' HGA2
    0.09
    ATOM H22' HGA2
    0.09
    !Guanine atoms
    GROUP
    ATOM N9 NG2R51 -0.02
    ATOM C4 CG2RC0
    0.26
    ATOM N3 NG2R62 -0.74
    ATOM C2 CG2R64
    0.75
    ATOM N1 NG2R61 -0.34
    ATOM H1 HGP1
    0.26
    ATOM N2 NG2S3
    -0.68
    ATOM H21 HGP4
    0.32
    ATOM H22 HGP4
    0.35
    ATOM C6 CG2R63
    0.54
    ATOM O6 OG2D4
    -0.51
    ATOM C5 CG2RC0
    0.00
    ATOM N7 NG2R50 -0.60
    ATOM C8 CG2R53
    0.25
    ATOM H8 HGR52
    0.16
    GROUP ! Hydroxyl group
    ATOM H31' HGA1
    0.09
    ATOM C3' CG3C51
    0.14
    ATOM O3' OG311
    -0.65
    ATOM H32' HGP1
    0.42
    GROUP ! C5' hydroxyl
    ATOM C5' CG321
    0.05
    ATOM H51' HGA2
    0.09
    ATOM H52' HGA2
    0.09
    ATOM O5' OG311
    -0.65
    ATOM H5T HGP1
    0.42

    117.6
    119.0
    119.0
    0.0
    0.0
    C1'
    O4'
    O4'
    O4'
    C4'

    -180.0
    0.0
    180.0
    180.0
    180.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0
    0.0 0.0

    119.0
    1.337
    119.0
    1.01
    121.00 1.01
    0.0
    0.0
    0.0
    0.0
    144.82 0.0 0.0
    -179.98 0.0 0.0
    59.66 0.0 0.0
    -59.68 0.0 0.0
    180.0 0.0 0.0

    ! C10H13N5O4 nucleoside with guanine


    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Guanine
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    !
    H32'

    on C3'

    BOND C1' O4' C1' C2' C2' C3' C3'


    BOND C3' O3' C1' H12' C2' H21' C2'
    BOND C5' H51' C5' H52' C5' O5' O5'
    BOND O3' H32'
    BOND C1' N9
    BOND N9 C4
    N9 C8
    C4 N3
    BOND N2 H22
    N1 H1
    N1 C6
    DOUBLE C2 N3
    C4 C5
    N7 C8

    C4' C4' O4' C4' C5'


    H22' C3' H31' C4' H42'
    H5T
    C2 N2 C2
    C6 C5 C5
    C6 O6

    N1
    N7

    N2
    C8

    H21
    H8

    IMPR C2 N3 N1 N2
    C6 N1 C5 O6
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0
    IC C3' C2' C1' N9
    1.5284 101.97 147.80
    IC O4' C1' N9 C4
    1.5251 113.71 -97.2
    IC C1' C4 *N9 C8
    1.4896 125.59 -179.99
    IC C4 N9 C8 N7
    1.377 106.0
    0.0
    IC C8 N9 C4 C5
    1.374 106.0
    0.0
    IC N9 C5 *C4 N3
    1.377 105.6 180.0
    IC C5 C4 N3 C2
    1.377 128.4
    0.0
    IC C4 N3 C2 N1
    1.355 111.8
    0.0
    IC N1 N3 *C2 N2
    1.375 124.0 180.0
    IC N3 C2 N2 H21
    1.327 119.7 180.0
    IC H21 C2 *N2 H22
    1.01
    127.0 -180.0
    IC N3 C2 N1 C6
    1.327 124.0
    0.0
    IC C6 C2 *N1 H1
    1.393 124.9 180.00
    IC C5 N1 *C6 O6
    1.415 111.7 180.0
    IC N9 N7 *C8 H8
    0.0
    0.0 180.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI NUSC
    GROUP
    ATOM O4' OG3C51
    ATOM C4' CG3C51
    ATOM H42' HGA1
    ATOM C1' CG3C51
    ATOM H12' HGA1
    GROUP
    ATOM C2' CG3C52
    ATOM H21' HGA2
    ATOM H22' HGA2
    ! Cytosine atoms
    GROUP
    ATOM N1 NG2R61
    ATOM C6 CG2R62
    ATOM H6 HGR62
    ATOM C2 CG2R63
    ATOM O2 OG2D4
    ATOM N3 NG2R62
    ATOM C4 CG2R64
    ATOM N4 NG2S3
    ATOM H41 HGP4
    ATOM H42 HGP4
    ATOM C5 CG2R62
    ATOM H5 HGR62
    GROUP ! Hydroxyl

    N2 H21 C2
    324.92 0.0 0.0
    33.390 0.0 0.0
    268.35 0.0 0.0
    82.530 0.0 0.0
    204.06 0.0 0.0
    -93.14 0.0 0.0
    -60.00 0.0 0.0
    147.80 0.0 0.0
    132.30 0.0 0.0
    220.70 0.0 0.0
    113.71 1.4896
    125.59 1.3783 !chi
    106.0
    1.374
    113.5
    1.304
    105.6
    1.377
    128.4
    1.355
    111.8
    1.327
    124.0
    1.375
    119.7
    1.341
    127.0
    1.01
    116.5
    1.01
    124.9
    1.393
    117.4
    1.03
    120.0
    1.239
    0.0
    0.0
    144.82 0.0 0.0
    -179.98 0.0 0.0
    59.66 0.0 0.0
    -59.68 0.0 0.0
    180.0 0.0 0.0

    0.00 ! C9H13N3O4 nucleoside with cytosine


    -0.40
    0.11
    0.09
    0.11
    0.09
    -0.18
    0.09
    0.09

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Cytosine
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    !
    H32'

    -0.13
    0.05
    0.17
    0.52
    -0.49
    -0.66
    0.65
    -0.75
    0.37
    0.33
    -0.13
    0.07
    group on C3'

    H22

    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T

    HGA1
    0.09
    CG3C51
    0.14
    OG311
    -0.65
    HGP1
    0.42
    C5' hydroxyl
    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O3' H32'
    BOND C1' N1
    BOND N1 C2
    N1 C6
    C4 N4
    N4 H41 N4 H42
    BOND C2 N3
    C4 C5
    C5 H5
    C6 H6
    DOUBLE C2 O2
    C5 C6
    N3 C4
    IMPR N4 C4 H41 H42
    C2 N1 N3 O2
    C4 N3 C5 N4
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.79 -180.00 120.6
    1.364
    IC C2 N1 C6 C5
    1.399 120.6
    0.0 121.0
    1.337
    IC C6 N1 C2 N3
    1.364 120.6
    0.0 118.9
    1.356
    IC N1 N3 *C2 O2
    1.399 118.9 180.0 121.9
    1.237
    IC N1 C2 N3 C4
    1.399 118.9
    0.0 120.0
    1.334
    IC C5 N3 *C4 N4
    1.426 121.8 180.00 118.9
    1.337
    IC N3 C4 N4 H41
    1.337 117.9
    0.00 118.9
    1.01
    IC H41 C4 *N4 H42
    1.01
    118.9 180.00 120.7
    1.01
    IC C6 C4 *C5 H5
    0.0
    0.0 180.0
    0.0
    0.0
    IC N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI NUST
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'

    0.00 ! C10H14N2O5 nucleoside with thymine


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1
    CG3C52
    HGA2

    -0.40
    0.11
    0.09
    0.11
    0.09

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Thymine
    !
    \ / \ /
    -0.18 ! H42'--C4' C1'--H12'
    0.09 !
    |
    |

    ATOM H22' HGA2


    0.09 ! H31'--C3'--C2'--H21'
    ! Atoms for thymine
    !
    /
    \
    GROUP
    !
    O3'
    H22'
    ATOM N1 NG2R61 -0.34 !
    |
    ATOM C6 CG2R62
    0.17 !
    H32'
    ATOM H6 HGR62
    0.17
    ATOM C2 CG2R63
    0.51
    ATOM O2 OG2D4
    -0.41
    ATOM N3 NG2R61 -0.46
    ATOM H3 HGP1
    0.36
    ATOM C4 CG2R63
    0.50
    ATOM O4 OG2D4
    -0.45
    ATOM C5 CG2R62 -0.15
    ATOM C5M CG331
    -0.11
    ATOM H51 HGA3
    0.07
    ATOM H52 HGA3
    0.07
    ATOM H53 HGA3
    0.07
    GROUP ! Hydroxyl group on C3'
    ATOM H31' HGA1
    0.09
    ATOM C3' CG3C51
    0.14
    ATOM O3' OG311
    -0.65
    ATOM H32' HGP1
    0.42
    GROUP ! C5' hydroxyl
    ATOM C5' CG321
    0.05
    ATOM H51' HGA2
    0.09
    ATOM H52' HGA2
    0.09
    ATOM O5' OG311
    -0.65
    ATOM H5T HGP1
    0.42
    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O3' H32'
    BOND C1' N1
    BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5
    BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53
    DOUBLE C2 O2
    C4 O4
    C5 C6
    IMPR C2 N1 N3 O2
    C4 N3 C5 O4
    C5 C4 C6 C5M
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.06 -179.96 122.08 1.3704
    IC C2 N1 C6 C5
    1.3746 122.08 -0.02 121.23 1.3432
    IC C6 N1 C2 N3
    1.3704 122.08
    0.06 115.38 1.3813
    IC N1 N3 *C2 O2
    1.3746 115.38 -179.95 121.70 1.2191
    IC N1 C2 N3 C4
    1.3746 115.38 -0.07 126.46 1.3795
    IC C5 N3 *C4 O4
    1.4439 114.07 179.98 120.59 1.2327
    IC C2 C4 *N3 H3
    1.3813 126.46 180.00 116.77 1.0900
    IC C4 C6 *C5 C5M
    1.4439 120.78 -179.94 121.63 1.5000
    IC N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0

    IC C6 C5 C5M H51
    0.0
    IC C5 H51 *C5M H52
    0.0
    IC H51 H52 *C5M H53
    0.0
    IC
    C5'
    C4'
    O4'
    IC
    H51'
    C5'
    C4'
    IC
    H52'
    C5'
    C4'
    IC
    O5'
    C5'
    C4'
    IC
    H5T
    O5'
    C5'
    PATC FIRS NONE LAST NONE
    RESI NUSU
    0.00
    GROUP
    ATOM O4' OG3C51 -0.40
    ATOM C4' CG3C51
    0.11
    ATOM H42' HGA1
    0.09
    ATOM C1' CG3C51
    0.11
    ATOM H12' HGA1
    0.09
    GROUP
    ATOM C2' CG3C52 -0.18
    ATOM H21' HGA2
    0.09
    ATOM H22' HGA2
    0.09
    ! Atoms for uracil
    GROUP
    ATOM N1 NG2R61 -0.34
    ATOM C6 CG2R62
    0.20
    ATOM H6 HGR62
    0.14
    ATOM C2 CG2R63
    0.55
    ATOM O2 OG2D4
    -0.45
    ATOM N3 NG2R61 -0.46
    ATOM H3 HGP1
    0.36
    ATOM C4 CG2R63
    0.53
    ATOM O4 OG2D4
    -0.48
    ATOM C5 CG2R62 -0.15
    ATOM H5 HGR62
    0.10
    GROUP ! Hydroxyl group
    ATOM H31' HGA1
    0.09
    ATOM C3' CG3C51
    0.14
    ATOM O3' OG311
    -0.65
    ATOM H32' HGP1
    0.42
    GROUP ! C5' hydroxyl
    ATOM C5' CG321
    0.05
    ATOM H51' HGA2
    0.09
    ATOM H52' HGA2
    0.09
    ATOM O5' OG311
    -0.65
    ATOM H5T HGP1
    0.42

    0.0
    0.0
    0.0 115.0
    0.0 -115.0
    C1'
    0.0 0.0
    O4'
    0.0 0.0
    O4'
    0.0 0.0
    O4'
    0.0 0.0
    C4'
    0.0 0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    144.82 0.0 0.0
    -179.98 0.0 0.0
    59.66 0.0 0.0
    -59.68 0.0 0.0
    180.0 0.0 0.0

    ! C9H12N2O5 nucleoside with uracil


    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Uracil
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    H22'
    !
    |
    !
    H32'

    on C3'

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
    BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O3' H32'
    BOND C1' N1
    N1 C2
    N1 C6
    C2
    BOND C2 N3
    N3 H3
    N3 C4
    C4
    BOND C5 C6
    C5 H5
    C6 H6
    IMPR C2 N1 N3 O2
    C4 N3 C5 O4
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530
    IC
    H22'
    C2'
    C3'
    C4'
    0.0 0.0 204.06

    C4' C5'
    C4' H42'
    O2
    O4

    0.0
    0.0
    0.0
    0.0
    0.0

    C4

    0.0
    0.0
    0.0
    0.0
    0.0

    C5

    IC
    IC
    IC
    IC
    IC
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    IC
    IC
    IC
    IC
    IC
    PATC

    O3'
    C3'
    C4'
    O4'
    0.0 0.0 -93.14 0.0 0.0
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    C3' C2' C1' N1
    1.5284 101.97 144.39 113.71 1.4896
    O4' C1' N1 C2
    1.5251 113.71 -96.0 117.06 1.3746
    C1' C2 *N1 C6
    1.4896 117.06 -180.0 121.3
    1.379
    C2 N1 C6 C5
    1.379 121.3
    0.0 122.8
    1.338
    C6 N1 C2 N3
    1.380 121.3
    0.0 114.8
    1.373
    N1 N3 *C2 O2
    1.379 114.8 -180.0 122.0
    1.218
    N1 C2 N3 C4
    1.379 114.8
    0.0 127.0
    1.383
    C5 N3 *C4 O4
    1.440 114.7 180.0 119.8
    1.227
    C2 C4 *N3 H3
    1.373 127.0 180.0 116.5
    1.03
    C6 C4 *C5 H5
    0.0
    0.0 180.0
    0.0
    0.0
    N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0
    FIRS NONE LAST NONE

    RESI RNUS
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM O2'
    ATOM H22'
    GROUP
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T
    GROUP !
    ATOM CG
    ATOM HG
    ATOM CD2
    ATOM HD2
    ATOM ND1
    ATOM CE1
    ATOM HE1
    ATOM NE2

    0.00 ! C8H12N2O4 Ribonucleoside analogue with imidazole


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    -0.40
    0.11
    0.09
    0.11
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    HGA1
    CG3C51
    OG311
    HGP1

    0.09
    0.14
    -0.65
    0.42

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Imidazole
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    !
    H32'
    H22'

    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42
    Imidazole: transferred from isolated imidazole (IMIA)
    CG2R51 -0.05 !
    C1'
    HE1
    HGR52
    0.09 !
    \
    /
    CG2R51
    0.22 !
    ND1---CE1
    HGR52
    0.10 !
    /
    ||
    NG2R51 -0.04 ! HG-CG
    ||
    CG2R53
    0.25 !
    \\
    ||
    HGR52
    0.13 !
    CD2---NE2
    NG2R50 -0.70 !
    |
    !
    HD2

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31'
    BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T

    BOND O3' H32'


    BOND C1' ND1
    BOND ND1 CE1 NE2 CD2 CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    DOUBLE CG CD2 CE1 NE2
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 C1'
    ND1 CE1 CG
    IMPR CD2 CG NE2 HD2
    CD2 NE2 CG
    IMPR CE1 ND1 NE2 HE1
    CE1 NE2 ND1
    IMPR CG CD2 ND1 HG
    CG ND1 CD2
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0
    IC
    O2'
    C2'
    C3'
    C4'
    0.0
    IC
    H22'
    O2'
    C2'
    C3'
    0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0
    IC
    C4'
    O4'
    C1'
    ND1
    0.0
    IC
    O4'
    C1'
    ND1
    CE1
    0.0
    IC
    C1'
    ND1
    CE1
    NE2
    0.0
    IC
    ND1
    CE1
    NE2
    CD2
    0.0
    IC
    CE1
    NE2
    CD2
    CG
    0.0
    IC
    HE1
    CE1
    NE2
    CD2
    0.0
    IC
    CE1
    NE2
    CD2
    HD2
    0.0
    IC
    NE2
    CD2
    CG
    HG
    0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0
    PATC FIRS NONE LAST NONE
    RESI RNUA
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM H21'
    ATOM C2'
    ATOM O2'
    ATOM H22'
    ! Adenine
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3

    C1'
    HD2
    HE1
    HG
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    324.92 0.0 0.0


    33.390 0.0 0.0
    268.35 0.0 0.0
    82.530 0.0 0.0
    204.06 0.0 0.0
    -60.00 0.0 0.0
    -93.14 0.0 0.0
    -60.00 0.0 0.0
    147.80 0.0 0.0
    132.30 0.0 0.0
    220.70 0.0 0.0
    256.98 0.0 0.0
    180.00 0.0 0.0
    181.56 0.0 0.0
    0.34 0.0 0.0
    0.00 0.0 0.0
    180.40 0.0 0.0
    179.83 0.0 0.0
    178.45 0.0 0.0
    144.82 0.0 0.0
    -179.98 0.0 0.0
    59.66 0.0 0.0
    -59.68 0.0 0.0
    180.0 0.0 0.0

    0.00 ! C10H13N5O4 ribo-nucleoside with adenine


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    -0.40
    0.11
    0.09
    0.11
    0.09

    HGA1
    CG3C51
    OG311
    HGP1
    atoms

    0.09
    0.14
    -0.65
    0.42

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51
    NG2R62
    CG2R64
    HGR62
    NG2R62

    0.28
    -0.71
    0.34
    0.12
    -0.05
    -0.74
    0.50
    0.13
    -0.75

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Adenine
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    !
    H32'
    H22'

    ATOM C4
    ATOM C6
    ATOM N6
    ATOM H61
    ATOM H62
    GROUP !
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T

    CG2RC0
    0.43
    CG2R64
    0.46
    NG2S3
    -0.77
    HGP4
    0.38
    HGP4
    0.38
    Hydroxyl group on C3'
    HGA1
    0.09
    CG3C51
    0.14
    OG311
    -0.65
    HGP1
    0.42
    C5' hydroxyl
    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O2' H22' O3' H32'
    BOND C1' N9
    BOND N9 C4
    N9 C8 C4 N3
    C2 N1
    C6 N6
    BOND N6 H61 N6 H62 C6 C5
    C5 N7
    C8 H8
    C2 H2
    DOUBLE N1 C6
    C2 N3
    C4 C5
    N7 C8
    IMPR N6 C6 H61 H62
    C6 N1 C5 N6
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    O2'
    C2'
    C3'
    C4'
    1.42 109.06 283.42 0.0 0.0
    IC
    H22'
    O2'
    C2'
    C3'
    0.98 109.05 283.42 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 324.95 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N9
    1.5284 101.97 150.8 113.71 1.4896
    IC O4' C1' N9 C4
    1.5251 108.6 229.5 125.5
    1.3783 !chi
    IC C1' C4 *N9 C8
    1.4896 125.97 -179.94 106.0
    1.367
    IC C4 N9 C8 N7
    1.376 106.0
    0.0 113.6
    1.312
    IC C8 N9 C4 C5
    1.367 106.0
    0.0 105.6
    1.382
    IC C8 N7 C5 C6
    0.0
    0.0 180.0
    0.0
    0.0
    IC N7 C5 C6 N1
    0.0
    0.0 180.0
    0.0
    0.0
    IC C5 C6 N1 C2
    0.0
    0.0
    0.0
    0.0
    0.0
    IC N9 C5 *C4 N3
    1.376 105.6 -180.0 126.9
    1.342
    IC C5 N1 *C6 N6
    1.409 117.6 -180.0 121.2
    1.337
    IC N1 C6 N6 H61
    1.337 121.2
    0.0 119.0
    1.01
    IC H61 C6 *N6 H62
    1.01
    119.0 180.0 119.00 1.01
    IC C5 N1 *C6 N6
    1.409 117.6 -180.0 119.0
    1.337
    IC N1 C6 N6 H61
    1.337 119.0
    0.0 119.0
    1.01
    IC H61 C6 *N6 H62
    1.01
    119.0 180.0 121.00 1.01
    IC N9 N7 *C8 H8
    0.0
    0.0 180.0
    0.0
    0.0
    IC N1 N3 *C2 H2
    0.0
    0.0 180.0
    0.0
    0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0

    PATC FIRS NONE LAST NONE


    RESI RNUG
    GROUP
    ATOM O4'
    ATOM C4'
    ATOM H42'
    ATOM C1'
    ATOM H12'
    GROUP
    ATOM H21'
    ATOM C2'
    ATOM O2'
    ATOM H22'
    ! Guanine
    GROUP
    ATOM N9
    ATOM C4
    ATOM N3
    ATOM C2
    ATOM N1
    ATOM H1
    ATOM N2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM O6
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    GROUP !
    ATOM H31'
    ATOM C3'
    ATOM O3'
    ATOM H32'
    GROUP !
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM O5'
    ATOM H5T

    0.00 ! C10H13N5O5 ribo-nucleoside with guanine


    OG3C51
    CG3C51
    HGA1
    CG3C51
    HGA1

    -0.40
    0.11
    0.09
    0.11
    0.09

    HGA1
    CG3C51
    OG311
    HGP1
    atoms

    0.09
    0.14
    -0.65
    0.42

    !
    H5T
    !
    /
    ! H51' O5'
    !
    \ |
    !H52'--C5' O4' Guanine
    !
    \ / \ /
    ! H42'--C4' C1'--H12'
    !
    |
    |
    ! H31'--C3'--C2'--H21'
    !
    /
    \
    !
    O3'
    O2'
    !
    |
    |
    !
    H32'
    H22'

    NG2R51 -0.02
    CG2RC0
    0.26
    NG2R62 -0.74
    CG2R64
    0.75
    NG2R61 -0.34
    HGP1
    0.26
    NG2S3
    -0.68
    HGP4
    0.32
    HGP4
    0.35
    CG2R63
    0.54
    OG2D4
    -0.51
    CG2RC0
    0.00
    NG2R50 -0.60
    CG2R53
    0.25
    HGR52
    0.16
    Hydroxyl group on C3'
    HGA1
    0.09
    CG3C51
    0.14
    OG311
    -0.65
    HGP1
    0.42
    C5' hydroxyl
    CG321
    0.05
    HGA2
    0.09
    HGA2
    0.09
    OG311
    -0.65
    HGP1
    0.42

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4'
    BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O2' H22' O3' H32'
    BOND C1' N9
    BOND N9 C4
    N9 C8
    C4 N3
    C2 N2 C2 N1
    BOND N2 H22
    N1 H1
    N1 C6
    C6 C5 C5 N7
    DOUBLE C2 N3
    C4 C5
    N7 C8 C6 O6
    IMPR C2 N3 N1 N2
    C6 N1 C5 O6
    N2
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0
    IC
    O2'
    C2'
    C3'
    C4'
    1.42 109.06 283.42
    IC
    H22'
    O2'
    C2'
    C3'
    0.98 109.05 283.42
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 324.95 0.0

    C5'
    H42'

    N2
    C8

    H21
    H8

    H21 C2
    0.0
    0.0
    0.0
    0.0
    0.0 0.0
    0.0 0.0
    0.0

    H22

    IC
    IC
    IC
    IC
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    BILD
    IC
    IC
    IC
    IC
    IC
    PATC

    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    C3' C2' C1' N9
    1.5284 101.97 147.80 113.71 1.4896
    O4' C1' N9 C4
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    C1' C4 *N9 C8
    1.4896 125.59 -179.99 106.0
    1.374
    C4 N9 C8 N7
    1.377 106.0
    0.0 113.5
    1.304
    C8 N9 C4 C5
    1.374 106.0
    0.0 105.6
    1.377
    N9 C5 *C4 N3
    1.377 105.6 180.0 128.4
    1.355
    C5 C4 N3 C2
    1.377 128.4
    0.0 111.8
    1.327
    C4 N3 C2 N1
    1.355 111.8
    0.0 124.0
    1.375
    N1 N3 *C2 N2
    1.375 124.0 180.0 119.7
    1.341
    N3 C2 N2 H21
    1.327 119.7 180.0 127.0
    1.01
    H21 C2 *N2 H22
    1.01
    127.0 -180.0 116.5
    1.01
    N3 C2 N1 C6
    1.327 124.0
    0.0 124.9
    1.393
    C6 C2 *N1 H1
    1.393 124.9 180.0 117.4
    1.03
    C5 N1 *C6 O6
    1.415 111.7 180.0 120.0
    1.239
    N9 N7 *C8 H8
    0.0
    0.0 180.0
    0.0
    0.0
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0
    FIRS NONE LAST NONE

    RESI RNUC
    0.00 ! C9H13N3O5 ribo-nucleoside with cytosine
    GROUP
    ATOM O4' OG3C51 -0.40 !
    H5T
    ATOM C4' CG3C51
    0.11 !
    /
    ATOM H42' HGA1
    0.09 ! H51' O5'
    ATOM C1' CG3C51
    0.11 !
    \ |
    ATOM H12' HGA1
    0.09 !H52'--C5' O4' Cytosine
    GROUP
    !
    \ / \ /
    ATOM H21' HGA1
    0.09 ! H42'--C4' C1'--H12'
    ATOM C2' CG3C51
    0.14 !
    |
    |
    ATOM O2' OG311
    -0.65 ! H31'--C3'--C2'--H21'
    ATOM H22' HGP1
    0.42 !
    /
    \
    ! Cytosine atoms
    !
    O3'
    O2'
    GROUP
    !
    |
    |
    ATOM N1 NG2R61 -0.13 !
    H32'
    H22'
    ATOM C6 CG2R62
    0.05
    ATOM H6 HGR62
    0.17
    ATOM C2 CG2R63
    0.52
    ATOM O2 OG2D4
    -0.49
    ATOM N3 NG2R62 -0.66
    ATOM C4 CG2R64
    0.65
    ATOM N4 NG2S3
    -0.75
    ATOM H41 HGP4
    0.37
    ATOM H42 HGP4
    0.33
    ATOM C5 CG2R62 -0.13
    ATOM H5 HGR62
    0.07
    GROUP ! Hydroxyl group on C3'
    ATOM H31' HGA1
    0.09
    ATOM C3' CG3C51
    0.14
    ATOM O3' OG311
    -0.65
    ATOM H32' HGP1
    0.42
    GROUP ! Methyl group on C4'
    ATOM C5' CG321
    0.05
    ATOM H51' HGA2
    0.09

    ATOM H52' HGA2


    ATOM O5' OG311
    ATOM H5T HGP1

    0.09
    -0.65
    0.42

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
    BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42'
    BOND C5' H51' C5' H52' C5' O5' O5' H5T
    BOND O2' H22' O3' H32'
    BOND C1' N1
    BOND N1 C2
    N1 C6
    BOND C2 N3
    C4 N4
    N4 H41
    N4 H42
    BOND C4 C5
    C5 H5
    C6 H6
    DOUBLE C2 O2
    C5 C6
    N3 C4
    IMPR N4 C4 H41 H42
    C2 N1 N3 O2
    C4 N3 C5 N4
    ! This IC table is only an initial guess:
    IC
    C1'
    C2'
    C3'
    C4'
    0.0 0.0 324.92 0.0 0.0
    IC
    C2'
    C3'
    C4'
    O4'
    0.0 0.0 33.390 0.0 0.0
    IC
    H12'
    C1'
    C2'
    C3'
    0.0 0.0 268.35 0.0 0.0
    IC
    H21'
    C2'
    C3'
    C4'
    0.0 0.0 82.530 0.0 0.0
    IC
    O2'
    C2'
    C3'
    C4'
    1.42 109.06 283.42 0.0 0.0
    IC
    H22'
    O2'
    C2'
    C3'
    0.98 109.05 283.42 0.0 0.0
    IC
    O3'
    C3'
    C4'
    O4'
    0.0 0.0 324.95 0.0 0.0
    IC
    H32'
    O3'
    C3'
    C2'
    0.0 0.0 -60.00 0.0 0.0
    IC
    H31'
    C3'
    C4'
    O4'
    0.0 0.0 147.80 0.0 0.0
    IC
    H41'
    C4'
    O4'
    C1'
    0.0 0.0 132.30 0.0 0.0
    IC
    H42'
    C4'
    O4'
    C1'
    0.0 0.0 220.70 0.0 0.0
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 -97.2 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.79 -180.00 120.6
    1.364
    IC C2 N1 C6 C5
    1.399 120.6
    0.0 121.0
    1.337
    IC C6 N1 C2 N3
    1.364 120.6
    0.0 118.9
    1.356
    IC N1 N3 *C2 O2
    1.399 118.9 180.0 121.9
    1.237
    IC N1 C2 N3 C4
    1.399 118.9
    0.0 120.0
    1.334
    IC C5 N3 *C4 N4
    1.426 121.8 180.00 118.9
    1.337
    IC N3 C4 N4 H41
    1.337 117.9
    0.00 118.9
    1.01
    IC H41 C4 *N4 H42
    1.01
    118.9 180.00 120.7
    1.01
    IC C6 C4 *C5 H5
    0.0
    0.0 180.0
    0.0
    0.0
    IC N1 C5 *C6 H6
    0.0
    0.0 180.0
    0.0
    0.0
    IC
    C5'
    C4'
    O4'
    C1'
    0.0 0.0 144.82 0.0 0.0
    IC
    H51'
    C5'
    C4'
    O4'
    0.0 0.0 -179.98 0.0 0.0
    IC
    H52'
    C5'
    C4'
    O4'
    0.0 0.0 59.66 0.0 0.0
    IC
    O5'
    C5'
    C4'
    O4'
    0.0 0.0 -59.68 0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4'
    0.0 0.0 180.0 0.0 0.0
    PATC FIRS NONE LAST NONE
    RESI NUCL
    -1.00 ! C9H14N2O6P
    !WARNING: - The charge distribution on the imidazole is identical
    ! to the charge distribution on the imidazole in THFI, which is
    ! different from the charge distribution on the equivalent moiety
    ! in adenine.
    !
    - The charge distribution on the sugar is identical to what
    ! it is in the DNA.
    !
    - The charge' on the 3' end of the "backbone" is identical to
    ! what it is in the DNA, except for the terminal methyl group for which
    ! there is no DNA equivalent.
    !
    - The charges on the 5' extremity of the backbone is as in the
    ! 5TER patch used for the DNA. An alternative to that would be to use
    ! charges more similar to what is in non-terminal residues in DNA.
    GROUP
    ATOM O4' OG3C51 -0.40

    ATOM C1' CG3C51


    0.11
    ATOM H12' HGA1
    0.09
    ATOM C4' CG3C51
    0.11
    ATOM H42' HGA1
    0.09
    GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
    ! The following atom types use the parameters specifically developed
    ! for the imidazole
    ! Atom types for aliphatic atoms based on nucleotide
    ATOM CG CG2R51 -0.05 !
    C1'
    HE1
    ATOM HG HGR52
    0.09 !
    \
    /
    ATOM CD2 CG2R51
    0.22 !
    ND1---CE1
    ATOM HD2 HGR52
    0.10 !
    /
    ||
    ATOM ND1 NG2R51 -0.04 ! HG-CG
    ||
    ATOM CE1 CG2R53
    0.25 !
    \\
    ||
    ATOM HE1 HGR52
    0.13 !
    CD2---NE2
    ATOM NE2 NG2R50 -0.70 !
    |
    !
    HD2
    GROUP
    !
    ATOM C2' CG3C52 -0.18 !
    ATOM H21' HGA2
    0.09 !
    H5T
    ATOM H22' HGA2
    0.09 !
    |
    GROUP
    !
    H52' O5'
    ATOM C3' CG3C51
    0.01 !
    \ /
    ATOM H31' HGA1
    0.09 ! H51'-C5' O4' Imidazole
    ATOM O3' OG303
    -0.57 !
    \ / \ /
    ATOM P
    PG1
    1.50 ! H42'--C4' C1'--H12'
    ATOM O1P OG2P1
    -0.78 !
    |
    |
    ATOM O2P OG2P1
    -0.78 ! H31'--C3'--C2'--H21'
    ATOM O3P OG303
    -0.57 !
    /
    \
    ATOM C3T CG331
    -0.17 !
    O3'
    H22'
    ATOM H3T1 HGA3
    0.09 !
    |
    ATOM H3T2 HGA3
    0.09 ! O1P==P==O2P
    ATOM H3T3 HGA3
    0.09 !
    |
    GROUP
    !
    O3P (-1)
    ATOM C5' CG321
    0.05 !
    \
    ATOM H51' HGA2
    0.09 !
    C3T--H3T3
    ATOM H52' HGA2
    0.09 !
    / \
    ATOM H5T HGP1
    0.42 !
    H3T1 H3T2
    ATOM O5' OG311
    -0.65
    BOND C1' O4' C1' C2' C2' C3'
    BOND C1' H12' C2' H21' C2' H22'
    BOND O3' P
    P
    O1P P
    O2P
    BOND O3P C3T C3T H3T1 C3T H3T2
    BOND C4' C5' C5' H51' C5' H52'
    BOND C5' O5' O5' H5T
    BOND C1' ND1
    BOND ND1 CE1 NE2 CD2 CG ND1
    BOND CE1 HE1 CD2 HD2 CG HG
    DOUBLE CG CD2 CE1 NE2
    ! KEEPS HYDROGENS IN RING PLANE
    IMPR ND1 CG CE1 C1'
    ND1
    IMPR CD2 CG NE2 HD2
    CD2
    IMPR CE1 ND1 NE2 HE1
    CE1
    IMPR CG CD2 ND1 HG
    CG
    IC C4'
    O4'
    C1'
    C2'
    IC O4'
    C1'
    C2'
    C3'
    IC C1'
    C2'
    C3'
    C4'
    IC C2'
    C3'
    C4'
    O4'
    IC C3'
    C4'
    O4'
    C1'

    C3'
    C3'
    P
    C3T

    C4' C4' O4' C3' O3'


    H31' C4' H42'
    O3P
    H3T3

    CE1 CG
    NE2 CG
    NE2 ND1
    ND1 CD2
    1.4055
    1.4127
    1.5457
    1.5346
    1.5211

    C1'
    HD2
    HE1
    HG
    108.09 23.45 106.18
    106.18
    3.96 103.11
    103.11 -26.93 100.86
    100.86 41.73 103.15
    103.15 -41.62 108.09

    1.5457
    1.5346
    1.5211
    1.4055
    1.4127

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    PATC

    H12'
    C1'
    H21'
    C2'
    H22'
    C2'
    H31'
    C3'
    C5'
    C4'
    H51'
    C5'
    H52'
    C5'
    H42'
    C4'
    O3'
    C3'
    P
    O3'
    O1P
    P
    O2P
    P
    O3P
    P
    C3T
    O3P
    H3T1
    C3T
    H3T2
    C3T
    H3T3
    C3T
    C4'
    O4'
    O4'
    C1'
    C1'
    ND1
    ND1
    CE1
    CE1
    NE2
    HE1
    CE1
    CE1
    NE2
    NE2
    CD2
    C3'
    C4'
    H5T
    O5'
    FIRS NONE LAST

    C2'
    C3'
    C3'
    C4'
    O4'
    C4'
    C4'
    O4'
    C4'
    C3'
    O3'
    O3'
    O3'
    P
    O3P
    O3P
    O3P
    C1'
    ND1
    CE1
    NE2
    CD2
    NE2
    CD2
    CG
    C5'
    C5'
    NONE

    C3'
    C4'
    C4'
    O4'
    C1'
    O4'
    O4'
    C1'
    O4'
    C4'
    C3'
    C3'
    C3'
    O3'
    P
    P
    P
    ND1
    CE1
    NE2
    CD2
    CG
    CD2
    HD2
    HG
    O5'
    C4'

    1.0818 113.32 -114.11 103.11


    1.0846 110.65 91.68 100.86
    1.0822 110.88 -148.45 100.86
    1.0806 113.53 162.89 103.15
    0.0000 000.00 77.76 108.09
    0.0
    0.0
    180.0
    0.0
    0.0
    0.0
    -60.0
    0.0
    1.0808 108.72 -162.12 108.09
    1.4028 110.98 -77.39 103.15
    0.0
    0.0 180.00
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0
    0.0
    60.0
    0.0
    0.0
    0.0 -60.0
    0.0
    0.0
    0.0 180.0
    0.0
    0.0 0.0 256.98 0.0 0.0
    0.0 0.0 90.00 0.0 0.0
    0.0 0.0 181.56 0.0 0.0
    0.0 0.0 0.34 0.0 0.0
    0.0 0.0 0.00 0.0 0.0
    0.0 0.0 180.40 0.0 0.0
    0.0 0.0 179.83 0.0 0.0
    0.0 0.0 178.45 0.0 0.0
    0.0 0.0 60.0 0.0 0.0
    0.0000
    0.00 180.00
    0.00

    1.5346
    1.5211
    1.5211
    1.4055
    1.4127
    0.0
    0.0
    1.4127
    1.4055
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0000

    RESI NADE
    -1.00 ! C11H15N5O6P
    ! NADE is a nucleotide analogue similar to NUCL, except that the imidazole
    ! has been replaced by an adenine
    !
    - The charge distribution on the sugar is identical to what
    ! it is in the DNA.
    !
    - The charge' on the 3' end of the "backbone" is identical to
    ! what it is in the DNA, except for the terminal methyl group for which
    ! there is no DNA equivalent.
    !
    - The charges on the 5' extremity of the backbone is as in the
    ! 5TER patch used for the DNA. An alternative to that would be to use
    ! charges more similar to what is actuallly in non-terminal residues in the
    ! DNA.
    GROUP
    ATOM O4' OG3C51 -0.40 !
    H5T
    ATOM C1' CG3C51
    0.11 !
    |
    ATOM H12' HGA1
    0.09 !
    H52' O5'
    ATOM C4' CG3C51
    0.11 !
    \ /
    ATOM H42' HGA1
    0.09 ! H51'-C5' O4' Adenine
    GROUP
    !
    \ / \ /
    ATOM C5 CG2RC0
    0.30 ! H42'--C4' C1'--H12'
    ATOM N7 NG2R50 -0.69 !
    |
    |
    ATOM C8 CG2R53
    0.34 ! H31'--C3'--C2'--H21'
    ATOM H8 HGR52
    0.10 !
    /
    \
    ATOM N9 NG2R51 -0.06 !
    O3'
    H22'
    ATOM N1 NG2R62 -0.74 !
    |
    ATOM C2 CG2R64
    0.50 ! O1P==P==O2P
    ATOM H2 HGR62
    0.13 !
    |
    ATOM N3 NG2R62 -0.75 !
    O3P (-1)
    ATOM C4 CG2RC0
    0.43 !
    \
    ATOM C6 CG2R64
    0.44 !
    C3T--H3T3
    ATOM N6 NG2S3
    -0.75 !
    / \

    ATOM H61
    ATOM H62
    GROUP
    ATOM C2'
    ATOM H21'
    ATOM H22'
    GROUP
    ATOM C3'
    ATOM H31'
    ATOM O3'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O3P
    ATOM C3T
    ATOM H3T1
    ATOM H3T2
    ATOM H3T3
    GROUP
    ATOM C5'
    ATOM H51'
    ATOM H52'
    ATOM H5T
    ATOM O5'

    HGP4
    HGP4

    0.38 !
    0.37

    CG3C52
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG303
    CG331
    HGA3
    HGA3
    HGA3

    0.01
    0.09
    -0.57
    1.50
    -0.78
    -0.78
    -0.57
    -0.17
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2
    HGP1
    OG311

    0.05
    0.09
    0.09
    0.42
    -0.65

    H3T1 H3T2

    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
    BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND O3' P
    P
    O1P P
    O2P P
    O3P
    BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3
    BOND C4' C5' C5' H51' C5' H52'
    BOND C5' O5' O5' H5T
    BOND C1' N9
    BOND N9 C4
    N9 C8 C4 N3
    C2 N1
    C6 N6
    BOND N6 H61 N6 H62 C6 C5
    C5 N7
    C8 H8
    C2 H2
    DOUBLE N1 C6
    C2 N3
    C4 C5
    N7 C8
    IMPR N6 C6 H61 H62
    C6 N1 C5 N6
    IC C4'
    O4'
    C1'
    C2'
    1.4055 108.09 23.45 106.18 1.5457
    IC O4'
    C1'
    C2'
    C3'
    1.4127 106.18
    3.96 103.11 1.5346
    IC C1'
    C2'
    C3'
    C4'
    1.5457 103.11 -26.93 100.86 1.5211
    IC C2'
    C3'
    C4'
    O4'
    1.5346 100.86 41.73 103.15 1.4055
    IC C3'
    C4'
    O4'
    C1'
    1.5211 103.15 -41.62 108.09 1.4127
    IC H12'
    C1'
    C2'
    C3'
    1.0818 113.32 -114.11 103.11 1.5346
    IC H21'
    C2'
    C3'
    C4'
    1.0846 110.65 91.68 100.86 1.5211
    IC H22'
    C2'
    C3'
    C4'
    1.0822 110.88 -148.45 100.86 1.5211
    IC H31'
    C3'
    C4'
    O4'
    1.0806 113.53 162.89 103.15 1.4055
    IC C5'
    C4'
    O4'
    C1'
    0.0000 000.00 77.76 108.09 1.4127
    IC H51'
    C5'
    C4'
    O4'
    0.0
    0.0
    180.0
    0.0
    0.0
    IC H52'
    C5'
    C4'
    O4'
    0.0
    0.0
    -60.0
    0.0
    0.0
    IC H42'
    C4'
    O4'
    C1'
    1.0808 108.72 -162.12 108.09 1.4127
    IC O3'
    C3'
    C4'
    O4'
    1.4028 110.98 -77.39 103.15 1.4055
    IC P
    O3'
    C3'
    C4'
    0.0
    0.0 180.00
    0.0
    0.0
    IC O1P
    P
    O3'
    C3'
    0.0
    0.0 -60.0
    0.0
    0.0
    IC O2P
    P
    O3'
    C3'
    0.0
    0.0
    60.0
    0.0
    0.0
    IC O3P
    P
    O3'
    C3'
    0.0
    0.0 180.0
    0.0
    0.0
    IC C3T
    O3P
    P
    O3'
    0.0
    0.0 180.0
    0.0
    0.0
    IC H3T1
    C3T
    O3P
    P
    0.0
    0.0
    60.0
    0.0
    0.0
    IC H3T2
    C3T
    O3P
    P
    0.0
    0.0 -60.0
    0.0
    0.0
    IC H3T3
    C3T
    O3P
    P
    0.0
    0.0 180.0
    0.0
    0.0
    IC C3' C2' C1' N9
    1.5284 101.97 147.80 113.71 1.4896
    IC O4' C1' N9 C4
    1.5251 113.71 180.2 125.59 1.3783 !chi

    IC C1' C4 *N9 C8
    1.4896
    IC C4 N9 C8 N7
    1.376
    IC C8 N9 C4 C5
    1.367
    IC C8 N7 C5 C6
    0.0
    IC N7 C5 C6 N1
    0.0
    IC C5 C6 N1 C2
    0.0
    IC N9 C5 *C4 N3
    1.376
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC N9 N7 *C8 H8
    0.0
    IC N1 N3 *C2 H2
    0.0
    IC C3' C4' C5' O5'
    0.0
    IC H5T O5' C5' C4'
    0.0
    PATC FIRS NONE LAST NONE

    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0
    0.0
    0.0
    0.0
    0.0

    -180.00
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0
    60.0
    180.0

    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0
    0.0
    0.0

    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0
    0.0
    0.0

    RESI NTHY
    -1.00 ! C11H16N2O8P
    ! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole
    ! has been replaced by a thymine
    !
    - The charge distribution on the sugar is identical to what
    ! it is in the DNA.
    !
    - The charge' on the 3' end of the "backbone" is identical to
    ! what it is in the DNA, except for the terminal methyl group for which
    ! there is no DNA equivalent.
    !
    - The charges on the 5' extremity of the backbone is as in the
    ! 5TER patch used for the DNA. An alternative to that would be to use
    ! charges more similar to what is actuallly in non-terminal residues in the
    ! DNA.
    GROUP
    ATOM O4' OG3C51 -0.40 !
    H5T
    ATOM C1' CG3C51
    0.11 !
    |
    ATOM H12' HGA1
    0.09 !
    H52' O5'
    ATOM C4' CG3C51
    0.11 !
    \ /
    ATOM H42' HGA1
    0.09 ! H51'-C5' O4' Thymine
    GROUP
    !
    \ / \ /
    ATOM N1 NG2R61 -0.34 ! H42'--C4' C1'--H12'
    ATOM C6 CG2R62
    0.17 !
    |
    |
    ATOM H6 HGR62
    0.17 ! H31'--C3'--C2'--H21'
    ATOM C2 CG2R63
    0.51 !
    /
    \
    ATOM O2 OG2D4
    -0.41 !
    O3'
    H22'
    ATOM N3 NG2R61 -0.46 !
    |
    ATOM H3 HGP1
    0.36 ! O1P==P==O2P
    ATOM C4 CG2R63
    0.50 !
    |
    ATOM O4 OG2D4
    -0.45 !
    O3P (-1)
    ATOM C5 CG2R62 -0.15 !
    \
    ATOM C5M CG331
    -0.11 !
    C3T--H3T3
    ATOM H51 HGA3
    0.07 !
    / \
    ATOM H52 HGA3
    0.07 !
    H3T1 H3T2
    ATOM H53 HGA3
    0.07
    GROUP
    ATOM C2' CG3C52 -0.18
    ATOM H21' HGA2
    0.09
    ATOM H22' HGA2
    0.09
    GROUP
    ATOM C3' CG3C51
    0.01
    ATOM H31' HGA1
    0.09
    ATOM O3' OG303
    -0.57

    ATOM P
    PG1
    1.50
    ATOM O1P OG2P1
    -0.78
    ATOM O2P OG2P1
    -0.78
    ATOM O3P OG303
    -0.57
    ATOM C3T CG331
    -0.17
    ATOM H3T1 HGA3
    0.09
    ATOM H3T2 HGA3
    0.09
    ATOM H3T3 HGA3
    0.09
    GROUP
    ATOM C5' CG321
    0.05
    ATOM H51' HGA2
    0.09
    ATOM H52' HGA2
    0.09
    ATOM H5T HGP1
    0.42
    ATOM O5' OG311
    -0.65
    BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
    BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
    BOND O3' P
    P
    O1P P
    O2P P
    O3P
    BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3
    BOND C4' C5' C5' H51' C5' H52'
    BOND C5' O5' O5' H5T
    BOND C1' N1
    BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5
    BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53
    DOUBLE C2 O2
    C4 O4
    C5 C6
    IMPR C2 N1 N3 O2
    C4 N3 C5 O4
    C5 C4 C6 C5M
    IC C4'
    O4'
    C1'
    C2'
    1.4055 108.09 23.45 106.18 1.5457
    IC O4'
    C1'
    C2'
    C3'
    1.4127 106.18
    3.96 103.11 1.5346
    IC C1'
    C2'
    C3'
    C4'
    1.5457 103.11 -26.93 100.86 1.5211
    IC C2'
    C3'
    C4'
    O4'
    1.5346 100.86 41.73 103.15 1.4055
    IC C3'
    C4'
    O4'
    C1'
    1.5211 103.15 -41.62 108.09 1.4127
    IC H12'
    C1'
    C2'
    C3'
    1.0818 113.32 -114.11 103.11 1.5346
    IC H21'
    C2'
    C3'
    C4'
    1.0846 110.65 91.68 100.86 1.5211
    IC H22'
    C2'
    C3'
    C4'
    1.0822 110.88 -148.45 100.86 1.5211
    IC H31'
    C3'
    C4'
    O4'
    1.0806 113.53 162.89 103.15 1.4055
    IC C5'
    C4'
    O4'
    C1'
    0.0000 000.00 77.76 108.09 1.4127
    IC H51'
    C5'
    C4'
    O4'
    0.0
    0.0
    180.0
    0.0
    0.0
    IC H52'
    C5'
    C4'
    O4'
    0.0
    0.0
    -60.0
    0.0
    0.0
    IC H42'
    C4'
    O4'
    C1'
    1.0808 108.72 -162.12 108.09 1.4127
    IC O3'
    C3'
    C4'
    O4'
    1.4028 110.98 -77.39 103.15 1.4055
    IC P
    O3'
    C3'
    C4'
    0.0
    0.0 180.00
    0.0
    0.0
    IC O1P
    P
    O3'
    C3'
    0.0
    0.0 -60.0
    0.0
    0.0
    IC O2P
    P
    O3'
    C3'
    0.0
    0.0
    60.0
    0.0
    0.0
    IC O3P
    P
    O3'
    C3'
    0.0
    0.0 180.0
    0.0
    0.0
    IC C3T
    O3P
    P
    O3'
    0.0
    0.0 180.0
    0.0
    0.0
    IC H3T1
    C3T
    O3P
    P
    0.0
    0.0
    60.0
    0.0
    0.0
    IC H3T2
    C3T
    O3P
    P
    0.0
    0.0 -60.0
    0.0
    0.0
    IC H3T3
    C3T
    O3P
    P
    0.0
    0.0 180.0
    0.0
    0.0
    IC
    C3'
    C4'
    C5'
    O5'
    0.0 0.0 60.0 0.0 0.0
    IC
    H5T
    O5'
    C5'
    C4' 0.0000
    0.00 180.00
    0.00 0.0000
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC C3' C2' C1' N1
    1.5284 101.97 147.89 113.71 1.4896
    IC O4' C1' N1 C2
    1.5251 113.71 180.0 125.59 1.3783 !chi
    IC C1' C2 *N1 C6
    1.4896 117.06 -179.96 122.08 1.3704
    IC C2 N1 C6 C5
    1.3746 122.08 -0.02 121.23 1.3432
    IC C6 N1 C2 N3
    1.3704 122.08
    0.06 115.38 1.3813
    IC N1 N3 *C2 O2
    1.3746 115.38 -179.95 121.70 1.2191
    IC N1 C2 N3 C4
    1.3746 115.38 -0.07 126.46 1.3795
    IC C5 N3 *C4 O4
    1.4439 114.07 179.98 120.59 1.2327
    IC C2 C4 *N3 H3
    1.3813 126.46 180.00 116.77 1.0900
    IC C4 C6 *C5 C5M
    1.4439 120.78 -179.94 121.63 1.5000

    IC N1 C5 *C6 H6
    0.0
    IC C6 C5 C5M H51
    0.0
    IC C5 H51 *C5M H52
    0.0
    IC H51 H52 *C5M H53
    0.0
    PATC FIRS NONE LAST NONE

    0.0 180.0
    0.0
    0.0
    0.0 115.0
    0.0 -115.0

    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0

    !toppar_all27_na_nad_ppi.str
    RESI NIC
    1.00 ! C6H7N2O oxidized nicotinamide (protonated), jjp1/adm
    jr.
    ! checked for consistency with new NA params, adm jr.,
    9/98
    ! note that differences with respect to published resul
    ts exist
    ! due to new NA params
    !
    !
    H15
    GROUP
    !
    \
    ATOM H1 HGP2
    0.45 !
    H16-N14
    H8
    ATOM N2 NG2R61 -0.52 !
    \
    |
    ATOM C3 CG2R62
    0.16 !
    C12 C7
    ATOM H4 HGR63
    0.19 !
    // \ / \\
    ATOM C5 CG2R62 -0.10 !
    O13 C9 C5-H6
    ATOM H6 HGR63
    0.16 !
    || |
    ATOM C7 CG2R62 -0.05 !
    H11-C10 C3-H4
    ATOM H8 HGR63
    0.16 !
    \+ //
    ATOM C9 CG2R62
    0.05 !
    N2
    ATOM C10 CG2R62
    0.18 !
    |
    ATOM H11 HGR63
    0.16 !
    H1
    ATOM C12 CG2O1
    0.68 !
    ATOM O13 OG2D1
    -0.40 !
    ATOM N14 NG2S2
    -0.82 !
    ATOM H15 HGP1
    0.34 ! trans to O13
    ATOM H16 HGP1
    0.36 ! cis to O13
    BOND N2 H1 C3 H4 C3 C5 C5 H6
    BOND C7 H8 C7 C9 N2 C10
    BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16
    DOUBLE C12 O13 C9 C10 C5 C7 N2 C3
    ! amide impropers
    IMPR C12 N14 C9 O13 C12 C9 N14 O13
    IMPR N14 C12 H16 H15 N14 C12 H15 H16
    ! ring hydrogen impropers
    IMPR N2 C10 C3 H1
    C3 N2 C5 H4
    C5 C3 C7 H6
    IMPR C7 C5 C9 H8
    C10 C9 N2 H11
    ! ic table for analysis
    IC N2 C3 C5 C7
    0.0000 000.00 000.00 000.00 0.000
    IC C3 C5 C7 C9
    0.0000 000.00 000.00 000.00 0.000
    IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000
    IC C7 C9 C10 N2
    0.0000 000.00 000.00 000.00 0.000
    IC C9 C10 N2 C3
    0.0000 000.00 000.00 000.00 0.000
    IC C10 N2 C3 C5
    0.0000 000.00 000.00 000.00 0.000
    IC C9 C10 N2 H1
    0.0000 000.00 000.00 000.00 0.000
    IC C10 N2 C3 H4
    0.0000 000.00 000.00 000.00 0.000
    IC N2 C3 C5 H6
    0.0000 000.00 000.00 000.00 0.000
    IC C3 C5 C7 H8
    0.0000 000.00 000.00 000.00 0.000
    IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000
    IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000
    IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000
    IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000
    IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000
    IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000

    PATCH FIRST NONE LAST NONE


    RESI NICH

    0.00 ! C6H8N2O reduced nicotinamide, jjp1/adm jr.


    ! checked for consistency with new NA params, adm jr.,

    9/98
    ! note that differences with respect to published resul
    ts exist
    ! due to new NA params
    ! HN3 to HN6 atom type switch to maintain proper vdw pa
    rams, 9/98
    GROUP
    ATOM H1
    ATOM N2
    ATOM C3
    ATOM H4
    ATOM C5
    ATOM H6
    ATOM C7
    ATOM H8
    ATOM H17
    ATOM C10
    ATOM H11
    ATOM C9
    ATOM C12
    ATOM O13
    ATOM N14
    ATOM H15
    ATOM H16

    HGPAM1
    NG311
    CG2D1O
    HGA4
    CG2D1
    HGA4
    CG321
    HGA2
    HGA2
    CG2D1O
    HGA4
    CG2DC1
    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    0.42
    -0.69
    -0.06
    0.17
    -0.18
    0.14
    -0.28
    0.09
    0.09
    -0.10
    0.14
    0.36
    0.55
    -0.51
    -0.72
    0.26
    0.32

    !
    !
    H15
    !
    \
    !
    H16-N14 H8 H17
    !
    \
    \ /
    !
    C12 C7
    !
    / \ / \
    !
    O13 C9 C5-H6
    !
    || ||
    !
    H11-C10 C3-H4
    !
    \ /
    !
    N2
    !
    |
    !
    H1
    !
    !
    !
    !
    ! trans to O13
    ! cis to O13

    BOND N2 H1 N2 C3 C3 H4 C5 H6
    BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10
    BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16
    DOUBLE C12 O13 C9 C10 C3 C5
    ! amide impropers
    IMPR C12 N14 C9 O13 C12 C9 N14 O13
    IMPR N14 C12 H16 H15 N14 C12 H15 H16
    ! ring hydrogen impropers
    ! IMPR N2 C10 C3 H1 ! Unlikely; removed by kevo
    IMPR C3 N2 C5 H4 C5 C3 C7 H6
    IMPR C10 C9 N2 H11
    ! new IC table by kevo. Deliberately slightly distorted.
    IC C10 C9
    C7
    C5
    0.0000
    0.00 10.00
    IC C7
    C9
    C10 N2
    0.0000
    0.00
    0.00
    IC C10 C7
    *C9 C12
    0.0000
    0.00 180.00
    IC C9
    C7
    C5
    C3
    0.0000
    0.00 -10.00
    IC C10 C9
    C12 N14
    0.0000
    0.00 180.00
    IC C9
    N14 *C12 O13
    0.0000
    0.00 180.00
    IC C9
    C12 N14 H15
    0.0000
    0.00
    0.00
    IC C12 H15 *N14 H16
    0.0000
    0.00 180.00
    IC C9
    N2
    *C10 H11
    0.0000
    0.00 180.00
    IC C10 C3
    *N2 H1
    0.0000
    0.00 175.00
    IC N2
    C5
    *C3 H4
    0.0000
    0.00 180.00
    IC C3
    C7
    *C5 H6
    0.0000
    0.00 180.00
    IC C5
    C9
    *C7 H8
    0.0000
    0.00 120.00
    IC C5
    C9
    *C7 H17
    0.0000
    0.00 -120.00
    PATCH FIRST NONE LAST NONE
    RESI PPI1

    -3.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! CH3O7P2 Inorganic phosphate, jjp1/adm jr.

    GROUP
    ATOM C1
    ATOM O11
    ATOM P1
    ATOM O12
    ATOM O13
    ATOM O14

    CG331
    OG303
    PG2
    OG303
    OG2P1
    OG2P1

    -0.17
    -0.62
    1.50
    -0.74
    -0.82
    -0.82

    ATOM
    ATOM
    ATOM
    ATOM

    PG2
    OG2P1
    OG2P1
    OG2P1

    1.10
    -0.90
    -0.90
    -0.90

    P2
    O22
    O23
    O24

    ATOM H11 HGA3


    ATOM H12 HGA3
    ATOM H13 HGA3

    0.09
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    BOND P1 O11 P1 O12 P1 O13


    BOND C1 H11 C1 H12 C1 H13
    BOND O12 P2
    P2 O22 P2 O23
    ! IC Table
    IC C1 O11 P1 O12 0.0000
    IC O11 P1 O12 P2 0.0000
    IC P1 O12 P2 O22 0.0000
    IC C1 O11 P1 O13 0.0000
    IC C1 O11 P1 O14 0.0000
    IC P1 O12 P2 O23 0.0000
    IC P1 O12 P2 O24 0.0000
    IC P1 O11 C1 H11 0.0000
    IC P1 O11 C1 H12 0.0000
    IC P1 O11 C1 H13 0.0000
    PATC FIRS NONE LAST NONE
    RESI PPI2

    -2.00

    GROUP
    ATOM C1
    ATOM O11
    ATOM P1
    ATOM O12
    ATOM O13
    ATOM O14

    CG331
    OG303
    PG2
    OG303
    OG2P1
    OG2P1

    -0.17
    -0.62
    1.46
    -0.63
    -0.83
    -0.83

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    PG3
    OG311
    HGP1
    OG2P1
    OG2P1

    1.34
    -0.71
    0.44
    -0.86
    -0.86

    P2
    O22
    H22
    O23
    O24

    ATOM H11 HGA3


    ATOM H12 HGA3
    ATOM H13 HGA3

    BOND P1 O11 P1
    BOND C1 H11 C1
    BOND O12 P2
    P2
    ! IC Table
    IC C1 O11 P1

    0.09
    0.09
    0.09

    O12
    H12
    O22

    H11
    |
    H13--C1--H12
    |
    O11
    |
    O14==P1==O13 (-)
    |
    O12
    |
    (-) O24==P2==O23 (-)
    ||
    O22
    P1 O14

    O11 C1

    P2 O24
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    180.0
    180.0
    180.0
    60.0
    -60.0
    60.0
    -60.0
    180.0
    60.0
    -60.0

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! CH4O7P2 Inorganic phosphate, protonated, adm jr.


    ! terminal P charges based on neutral
    ! methylphosphate
    !
    !
    !
    H11
    !
    |
    !
    H13--C1--H12
    !
    |
    !
    O11
    !
    |
    !
    O14==P1==O13 (-)
    !
    |
    !
    |
    !
    O12
    !
    |
    !
    (-) O24==P2==O23 (-)
    !
    |
    !
    O22
    !
    \
    !
    H22
    P1 O13
    C1 H13
    P2 O23

    O12 0.0000

    P1 O14

    O11 C1

    P2 O24

    O22 H22

    000.00

    180.0

    000.00

    0.0000

    IC O11 P1 O12 P2 0.0000


    IC P1 O12 P2 O22 0.0000
    IC C1 O11 P1 O13 0.0000
    IC C1 O11 P1 O14 0.0000
    IC P1 O12 P2 O23 0.0000
    IC P1 O12 P2 O24 0.0000
    IC P1 O11 C1 H11 0.0000
    IC P1 O11 C1 H12 0.0000
    IC P1 O11 C1 H13 0.0000
    IC O12 P2 O22 H22 0.0000
    PATC FIRS NONE LAST NONE
    RESI AMP
    GROUP
    ATOM C4'
    ATOM H4'
    ATOM O4'
    ATOM C1'
    ATOM H1'
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N1
    C2
    H2
    N3
    C4
    C6

    ATOM N6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C2'
    ATOM H2''
    ATOM O2'
    ATOM H2'
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM O3'
    ATOM H3T
    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    GROUP
    ATOM O5'
    ATOM PA
    ATOM O1A
    ATOM O2A
    ATOM O3A

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    180.0
    180.0
    60.0
    -60.0
    60.0
    -60.0
    180.0
    60.0
    -60.0
    180.0

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -2.00 ! C10H12N5O7P adenosine monophosphate, jjp1/adm jr.


    ! atom names correspond to pdb nomenclature
    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    0.11
    0.09
    -0.40
    0.11
    0.09

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.28
    -0.71
    0.34
    0.12
    -0.05

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    OG303
    PG1
    OG2P1
    OG2P1
    OG2P1

    -0.40
    1.10
    -0.90
    -0.90
    -0.90

    BOND PA O1A
    BOND O5' C5'

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    PA O2A
    C5' C4'

    H61 H62
    \ /
    N6
    |
    C6
    // \
    N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H2 N3
    \
    \
    \
    \
    O1A
    H5' H4' O4' \
    |
    |
    \ / \ \
    O3A=PA-O5'-C5'---C4'
    C1'
    |
    |
    \
    / \
    O2A
    H5'' C3'--C2' H1'
    / \ / \
    O3' H3' O2' H2''
    |
    |
    H3T
    H2'

    PA O3A
    C4' O4'

    PA
    O5'
    C4' C3'

    O3' H3T
    O4' C1'

    BOND C1' N9
    C1' C2'
    BOND C2 N1
    C6 N6
    BOND N6 H61
    N6 H62
    BOND C2' C3'
    C2' O2'
    BOND C1' H1'
    C2' H2''
    BOND C5' H5''
    C8 H8
    DOUBLE N1 C6
    N3 C2
    C4
    IMPR N6 C6 H61 H62
    C6
    DONO H61 N6
    DONO H62 N6
    DONO H2' O2'
    ACCE N3
    ACCE N7
    ACCE N1
    ACCE O1A PA
    ACCE O2A PA
    ACCE O3A PA
    ACCE O2'
    ACCE O3'
    ACCE O4'
    ACCE O5'
    IC O5' O3A *PA O1A
    0.0000
    IC O5' O3A *PA O2A
    0.0000
    IC O3A PA O5' C5'
    0.0000
    !IC PA O5' C5' C4'
    1.5996
    minimum
    IC PA O5' C5' C4'
    0.0000
    !IC O5' C5' C4' C3'
    1.4401
    minimum
    IC O5' C5' C4' C3'
    0.0000
    IC C5' C4' C3' O3'
    1.5160
    IC H3T O3' C3' C4'
    0.9650
    IC O4' C3' *C4' C5'
    1.4572
    IC C2' C4' *C3' O3'
    1.5284
    IC C4' C3' C2' C1'
    1.5284
    !IC C3' C2' C1' N9
    1.5284
    be right
    IC O4' C2' *C1' N9
    0.0
    !IC O4' C1' N9 C4
    1.5251
    ixing N9
    IC O4' C1' N9 C4
    0.0
    IC C1' C4 *N9 C8
    1.4896
    IC C4 N9 C8 N7
    1.376
    IC C8 N9 C4 C5
    1.367
    IC C8 N7 C5 C6
    0.0
    IC N7 C5 C6 N1
    0.0
    IC C5 C6 N1 C2
    0.0
    IC N9 C5 *C4 N3
    1.376
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC N9 N7 *C8 H8
    0.0
    IC N1 N3 *C2 H2
    0.0
    IC C1' C3' *C2' O2'
    1.5284
    IC H2' O2' C2' C3'
    0.9600
    IC O4' C2' *C1' H1'
    0.0
    IC C1' C3' *C2' H2'' 0.0

    N9

    C4

    N9

    C6
    O2'
    C3'
    C2
    C5
    N1

    C5
    H2'
    H3'
    H2

    C5 N7
    C3' O3'
    C4' H4'

    C5

    C8

    C4

    N3

    C5' H5'

    N7 C8
    N6

    000.00 120.0
    000.00 -120.0
    000.00 -30.0
    119.00 -151.39

    000.00 0.0000
    000.00 0.0000
    000.00 0.0000
    110.04 1.5160 !Not-so-stable

    000.00 -110.0 000.00 0.0000


    108.83 -179.85 116.10 1.5284 !Not-so-stable
    000.00 70.0
    116.10 76.70
    105.47 38.18
    104.06 -120.04
    100.16 -124.08
    100.16 39.58
    101.97 144.39

    000.00
    115.12
    111.98
    116.10
    115.12
    102.04
    113.71

    0.0000
    1.4212
    1.5386
    1.5160
    1.4212
    1.5251
    1.4896 !144.39 can't

    0.0 120.0
    0.0
    0.0
    113.71 -96.00 125.97 1.3703 !clash after f
    0.0
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0
    0.0
    0.0
    102.04
    114.97
    0.0
    0.0

    -150.0
    -179.94
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0
    -114.67
    148.63
    -115.0
    115.0

    0.0
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0
    110.81
    111.92
    0.0
    0.0

    0.0
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0
    1.4212
    1.5284
    0.0
    0.0

    IC C2' C4' *C3' H3'


    0.0
    IC C3' O4' *C4' H4'
    0.0
    IC C4' O5' *C5' H5'
    0.0
    IC C4' O5' *C5' H5'' 0.0
    PATC FIRS NONE LAST NONE
    RESI ADP
    GROUP
    ATOM C4'
    ATOM H4'
    ATOM O4'
    ATOM C1'
    ATOM H1'
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9

    0.11
    0.09
    -0.40
    0.11
    0.09

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.28
    -0.71
    0.34
    0.12
    -0.05

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    ATOM N6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C2'
    ATOM H2''
    ATOM O2'
    ATOM H2'
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM O3'
    ATOM H3T
    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    ATOM O5'
    ATOM PA
    ATOM O1A
    ATOM O2A
    ATOM O3A
    ATOM PB
    ATOM O1B
    ATOM O2B
    ATOM O3B

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2
    OG303
    PG2
    OG2P1
    OG2P1
    OG303
    PG2
    OG2P1
    OG2P1
    OG2P1

    -0.08
    0.09
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.74
    1.10
    -0.90
    -0.90
    -0.90

    BOND
    BOND
    BOND
    BOND

    O3A
    O1A
    C5'
    N9

    N1
    C2
    H2
    N3
    C4
    C6

    PB
    PA
    O5'
    C1'

    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0

    -3.00 ! C10H12N5O10P2 adenosine diphosphate, jjp1/adm jr.


    ! atom names correspond to pdb nomenclature
    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    0.0 115.0
    0.0 -115.0
    0.0 -115.0
    0.0 115.0

    PB
    PA
    C5'
    C1'

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    O1B
    O2A
    C4'
    C2'

    H61 H62
    \ /
    N6
    |
    C6
    // \
    N1 C5--N7\\
    |
    ||
    C8-H8
    C2 C4--N9/
    / \\ /
    \
    H2 N3
    \
    \
    \
    \
    O3B
    O1A
    H5' H4' O4' \
    |
    |
    |
    \ / \ \
    O1B=PB-O3A--PA-O5'-C5'---C4'
    C1'
    |
    |
    |
    \
    / \
    O2B
    O2A
    H5'' C3'--C2' H1'
    / \ / \
    O3' H3' O2' H2''
    |
    |
    H3T
    H2'

    PB
    O2B
    PA
    O5'
    C4' O4'
    N9 C4

    PB
    O3'
    C4'
    N9

    O3B
    H3T
    C3'
    C8

    O3A PA
    O4' C1'
    C4 N3

    BOND C2 N1
    C6 N6
    BOND N6 H61
    N6 H62
    BOND C2' C3'
    C2' O2'
    BOND C1' H1'
    C2' H2''
    BOND C5' H5''
    C8 H8
    DOUBLE N1 C6
    N3 C2
    C4
    IMPR N6 C6 H61 H62
    C6
    DONO H61 N6
    DONO H62 N6
    DONO H2' O2'
    ACCE N3
    ACCE N7
    ACCE N1
    ACCE O1A PA
    ACCE O2A PA
    ACCE O2'
    ACCE O3'
    ACCE O4'
    ACCE O5'
    ACCE O3A
    ACCE O3B
    ACCE O2B
    ACCE O1B
    IC PA O3A PB O3B
    0.0000
    IC PB O3A PA O5'
    0.0000
    IC O5' O3A *PA O1A
    0.0000
    IC O5' O3A *PA O2A
    0.0000
    IC O3A O3B *PB O1B
    0.0000
    IC O3A O3B *PB O2B
    0.0000
    IC O3A PA O5' C5'
    0.0000
    !IC PA O5' C5' C4'
    1.5996
    minimum
    IC PA O5' C5' C4'
    0.0000
    !IC O5' C5' C4' C3'
    1.4401
    minimum
    IC O5' C5' C4' C3'
    0.0000
    IC C5' C4' C3' O3'
    1.5160
    IC H3T O3' C3' C4'
    0.9650
    IC O4' C3' *C4' C5'
    1.4572
    IC C2' C4' *C3' O3'
    1.5284
    IC C4' C3' C2' C1'
    1.5284
    !IC C3' C2' C1' N9
    1.5284
    be right
    IC O4' C2' *C1' N9
    0.0
    !IC O4' C1' N9 C4
    1.5251
    ixing N9
    IC O4' C1' N9 C4
    0.0
    IC C1' C4 *N9 C8
    1.4896
    IC C4 N9 C8 N7
    1.376
    IC C8 N9 C4 C5
    1.367
    IC C8 N7 C5 C6
    0.0
    IC N7 C5 C6 N1
    0.0
    IC C5 C6 N1 C2
    0.0
    IC N9 C5 *C4 N3
    1.376
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01

    C6
    O2'
    C3'
    C2
    C5
    N1

    C5
    H2'
    H3'
    H2
    C5

    C5 N7
    C3' O3'
    C4' H4'

    C5' H5'

    N7 C8
    N6

    000.00 180.0
    000.00 120.0
    000.00 120.0
    000.00 -120.0
    000.00 120.0
    000.00 -120.0
    000.00 -30.0
    119.00 -151.39

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    110.04

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.5160 !Not-so-stable

    000.00 -110.0 000.00 0.0000


    108.83 -179.85 116.10 1.5284 !Not-so-stable
    000.00 70.0
    116.10 76.70
    105.47 38.18
    104.06 -120.04
    100.16 -124.08
    100.16 39.58
    101.97 144.39

    000.00
    115.12
    111.98
    116.10
    115.12
    102.04
    113.71

    0.0000
    1.4212
    1.5386
    1.5160
    1.4212
    1.5251
    1.4896 !144.39 can't

    0.0 120.0
    0.0
    0.0
    113.71 -96.00 125.97 1.3703 !clash after f
    0.0
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0

    -150.0
    -179.94
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0

    0.0
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00

    0.0
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01

    IC N9 N7 *C8 H8
    0.0
    0.0 180.0
    0.0
    IC N1 N3 *C2 H2
    0.0
    0.0 180.0
    0.0
    IC C1' C3' *C2' O2'
    1.5284 102.04 -114.67 110.81
    IC H2' O2' C2' C3'
    0.9600 114.97 148.63 111.92
    IC O4' C2' *C1' H1'
    0.0
    0.0 -115.0
    0.0
    IC C1' C3' *C2' H2'' 0.0
    0.0 115.0
    0.0
    IC C2' C4' *C3' H3'
    0.0
    0.0 115.0
    0.0
    IC C3' O4' *C4' H4'
    0.0
    0.0 -115.0
    0.0
    IC C4' O5' *C5' H5'
    0.0
    0.0 -115.0
    0.0
    IC C4' O5' *C5' H5'' 0.0
    0.0 115.0
    0.0
    PATC FIRS NONE LAST NONE
    RESI ATP
    GROUP
    ATOM C4'
    ATOM H4'
    ATOM O4'
    ATOM C1'
    ATOM H1'
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N1
    C2
    H2
    N3
    C4
    C6

    ATOM N6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C2'
    ATOM H2''
    ATOM O2'
    ATOM H2'
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM O3'
    ATOM H3T
    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    ATOM O5'
    ATOM PA
    ATOM O1A
    ATOM O2A
    ATOM O3A
    ATOM PB
    ATOM O1B
    ATOM O2B

    0.0
    0.0
    1.4212
    1.5284
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    -4.00 ! C10H12N5O13P3 adenosine triphosphate , jjp1/adm jr.


    !atom names correspond to pdb nomenclature
    !
    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    0.11
    0.09
    -0.40
    0.11
    0.09

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.28
    -0.71
    0.34
    0.12
    -0.05

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2
    OG303
    PG2
    OG2P1
    OG2P1
    OG303
    PG2
    OG2P1
    OG2P1

    -0.08
    0.09
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.74
    1.50
    -0.82
    -0.82

    !
    H61 H62
    !
    \ /
    !
    N6
    !
    |
    !
    C6
    !
    // \
    !
    N1 C5--N7\\
    !
    |
    ||
    C8-H8
    !
    C2 C4--N9/
    !
    / \\ /
    \
    !
    H2 N3
    \
    !
    \
    !
    \
    !
    \
    ! (-)O3G O2B
    O1A
    H5' H4' O4' \
    !
    |
    |
    |
    |
    \ / \ \
    !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4'
    C1'
    !
    |
    |
    |
    |
    \
    / \
    ! (-)O2G (-)O1B (-)O2A
    H5'' C3'--C2' H1'
    !
    / \ / \
    !
    O3' H3' O2' H2''
    !
    |
    |
    !
    H3T
    H2'
    !

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    O3B
    PG
    O1G
    O2G
    O3G

    OG303
    PG2
    OG2P1
    OG2P1
    OG2P1

    -0.86 ! charge adjusted to yield total triP of -4.0


    1.10
    -0.90
    -0.90
    -0.90

    BOND O5' C5'


    O5' PA
    BOND O3A PB
    PB O1B
    BOND PG O1G
    PG O2G
    BOND C5' C4'
    C4' O4'
    BOND C1' N9
    C1' C2'
    BOND C2 N1
    C6 N6
    BOND N6 H61
    N6 H62
    BOND C2' C3'
    C2' O2'
    BOND C1' H1'
    C2' H2''
    BOND C5' H5''
    C8 H8
    DOUBLE N1 C6
    N3 C2
    C4
    IMPR N6 C6 H61 H62
    C6
    DONO H61 N6
    DONO H62 N6
    DONO H2' O2'
    ACCE N3
    ACCE N7
    ACCE N1
    ACCE O1A PA
    ACCE O2A PA
    ACCE O2'
    ACCE O3'
    ACCE O4'
    ACCE O5'
    ACCE O3A
    ACCE O2B
    ACCE O1B
    ACCE O3B
    ACCE O3G
    ACCE O2G
    ACCE O2G
    IC PA O3A PB O3B
    0.0000
    IC PB O3A PA O5'
    0.0000
    IC O5' O3A *PA O1A
    0.0000
    IC O5' O3A *PA O2A
    0.0000
    IC O3A O3B *PB O1B
    0.0000
    IC O3A O3B *PB O2B
    0.0000
    IC O3A PB O3B PG
    0.0000
    IC PB O3B PG O1G
    0.0000
    IC O3B O1G *PG O2G
    0.0000
    IC O3B O1G *PG O3G
    0.0000
    IC O3A PA O5' C5'
    0.0000
    !IC PA O5' C5' C4'
    1.5996
    minimum
    IC PA O5' C5' C4'
    0.0000
    !IC O5' C5' C4' C3'
    1.4401
    minimum
    IC O5' C5' C4' C3'
    0.0000
    IC C5' C4' C3' O3'
    1.5160
    IC H3T O3' C3' C4'
    0.9650
    IC O4' C3' *C4' C5'
    1.4572
    IC C2' C4' *C3' O3'
    1.5284
    IC C4' C3' C2' C1'
    1.5284
    !IC C3' C2' C1' N9
    1.5284

    PA
    PB
    PG
    C4'
    N9

    O1A
    O2B
    O3G
    C3'
    C4

    PA
    PB

    O4' C1'
    N9 C8

    C4

    C6
    O2'
    C3'
    C2
    C5
    N1

    C5
    H2'
    H3'
    H2

    C5 N7
    C3' O3'
    C4' H4'

    O3' H3T
    C5' H5'

    C5

    O2A
    O3B

    PA O3A
    O3B PG
    N3

    N7 C8
    N6

    000.00 180.0
    000.00 120.0
    000.00 120.0
    000.00 -120.0
    000.00 120.0
    000.00 -120.0
    000.00 150.0
    000.00 150.0
    000.00 120.0
    000.00 -120.0
    000.00 -30.0
    119.00 -151.39

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    110.04

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    1.5160 !Not-so-stable

    000.00 -110.0 000.00 0.0000


    108.83 -179.85 116.10 1.5284 !Not-so-stable
    000.00 70.0
    116.10 76.70
    105.47 38.18
    104.06 -120.04
    100.16 -124.08
    100.16 39.58
    101.97 144.39

    000.00
    115.12
    111.98
    116.10
    115.12
    102.04
    113.71

    0.0000
    1.4212
    1.5386
    1.5160
    1.4212
    1.5251
    1.4896 !144.39 can't

    be right
    IC O4' C2' *C1' N9
    0.0
    !IC O4' C1' N9 C4
    1.5251
    ixing N9
    IC O4' C1' N9 C4
    0.0
    IC C1' C4 *N9 C8
    1.4896
    IC C4 N9 C8 N7
    1.376
    IC C8 N9 C4 C5
    1.367
    IC C8 N7 C5 C6
    0.0
    IC N7 C5 C6 N1
    0.0
    IC C5 C6 N1 C2
    0.0
    IC N9 C5 *C4 N3
    1.376
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC C5 N1 *C6 N6
    1.409
    IC N1 C6 N6 H61
    1.337
    IC H61 C6 *N6 H62
    1.01
    IC N9 N7 *C8 H8
    0.0
    IC N1 N3 *C2 H2
    0.0
    IC C1' C3' *C2' O2'
    1.5284
    IC H2' O2' C2' C3'
    0.9600
    IC O4' C2' *C1' H1'
    0.0
    IC C1' C3' *C2' H2'' 0.0
    IC C2' C4' *C3' H3'
    0.0
    IC C3' O4' *C4' H4'
    0.0
    IC C4' O5' *C5' H5'
    0.0
    IC C4' O5' *C5' H5'' 0.0
    PATC FIRS NONE LAST NONE
    PRES 5DP
    jjp1/adm jr.

    0.0 120.0
    0.0
    0.0
    113.71 -96.00 125.97 1.3703 !clash after f
    0.0
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0
    0.0
    0.0
    102.04
    114.97
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    -150.0
    -179.94
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0
    -114.67
    148.63
    -115.0
    115.0
    115.0
    -115.0
    -115.0
    115.0

    0.0
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0
    110.81
    111.92
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0
    1.4212
    1.5284
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    -3.00 ! CH2O7P2 patch to create 5' diphosphate on nucleotides,


    ! as in ADP, use in generate statement

    GROUP
    ATOM C5'
    ATOM H5'
    ATOM H5''
    ATOM O5'
    ATOM P
    ATOM O1P
    ATOM O2P
    ATOM O13
    ATOM P2
    ATOM O21
    ATOM O22
    ATOM O23

    CG321
    HGA2
    HGA2
    OG303
    PG2
    OG2P1
    OG2P1
    OG303
    PG2
    OG2P1
    OG2P1
    OG2P1

    -0.08
    0.09
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.74
    1.10
    -0.90
    -0.90
    -0.90

    BOND P
    O13
    O13 P2
    BOND P2
    O21
    P2
    O22
    ACCE O13
    ACCE O21
    ACCE O22
    ACCE O23
    IC C5' O5' P
    O13
    0.0000
    IC O5' P
    O13 P2
    0.0000
    IC P
    O13 P2
    O21
    0.0000
    IC P
    O13 P2
    O22
    0.0000
    IC P
    O13 P2
    O23
    0.0000
    PATC FIRS NONE LAST NONE

    P2

    000.00
    000.00
    000.00
    000.00
    000.00

    O23

    180.0 000.00 0.0000


    180.0 000.00 0.0000
    180.0 000.00 0.0000
    60.0 000.00 0.0000
    -60.0 000.00 0.0000

    RESI NAD
    -1.00 !
    tide, jjp1/adm jr.
    !
    !
    9/98
    !
    lts exist
    !
    GROUP
    !
    ATOM AC4' CG3C51
    0.11 !
    ATOM AH4' HGA1
    0.09 !
    ATOM AO4' OG3C51 -0.40 !
    ATOM AC1' CG3C51
    0.11 !
    ATOM AH1' HGA1
    0.09 !
    GROUP
    !
    ATOM AC5 CG2RC0
    0.28 !
    ATOM AN7 NG2R50 -0.71 !
    ATOM AC8 CG2R53
    0.34 !
    ATOM AH8 HGR52
    0.12 !
    ATOM AN9 NG2R51 -0.05 !
    !
    ATOM AN1 NG2R62 -0.74 !
    ATOM AC2 CG2R64
    0.50 !
    ATOM AH2 HGR62
    0.13 !
    ATOM AN3 NG2R62 -0.75 !
    ATOM AC4 CG2RC0
    0.43 !
    ATOM AC6 CG2R64
    0.46 !
    !
    ATOM AN6 NG2S3
    -0.77 !
    ATOM AH61 HGP4
    0.38 !
    ATOM AH62 HGP4
    0.38 !
    GROUP
    !
    ATOM AC2' CG3C51
    0.14 !
    ATOM AH2' HGA1
    0.09 !
    ATOM AO2' OG311
    -0.65 !
    ATOM AH2T HGP1
    0.42 !
    GROUP
    !
    ATOM AC3' CG3C51
    0.14 !
    ATOM AH3' HGA1
    0.09 !
    ATOM AO3' OG311
    -0.65 !
    ATOM AH3T HGP1
    0.42 !
    GROUP
    !
    ATOM AC5' CG321
    -0.08 !
    ATOM AH5' HGA2
    0.09 !
    ATOM AH5S HGA2
    0.09 !
    ATOM AP PG2
    1.50 !
    ATOM AO1 OG2P1
    -0.82 !
    ATOM AO2 OG2P1
    -0.82 !
    ATOM AO5' OG303
    -0.62 !
    ATOM O3 OG303
    -0.68
    ATOM NP PG2
    1.50
    ATOM NO1 OG2P1
    -0.82
    ATOM NO2 OG2P1
    -0.82
    ATOM NO5' OG303
    -0.62
    ATOM NC5' CG321
    -0.08
    ATOM NH5S HGA2
    0.09
    ATOM NH5' HGA2
    0.09
    GROUP
    ATOM NC2' CG3C51
    0.14
    ATOM NH2' HGA1
    0.09

    C21H26N7O14P2 oxidized nicotinamide adenine dinucleo


    atom names correspond to pdb nomenclature
    checked for consistency with new NA params, adm jr.,
    note that differences with respect to published resu
    due to new NA params
    AH61 AH62
    \ /
    AN6
    |
    AC6
    // \
    AN1 AC5--AN7\\
    |
    ||
    AC8-AH8
    AC2 AC4--AN9/
    / \\ /
    \
    AH2 AN3
    \
    \
    \
    \
    NO1
    AO1
    AH5sAH4' AO4' \
    |
    |
    |
    \ / \ \
    NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
    \ |
    |
    |
    \
    / \
    \ NO2
    AO2
    AH5' AC3'-AC2' AH1'
    \
    / \ / \
    \
    AO3' AH3'AO2'AH2'
    \
    |
    |
    \
    AH3T
    AH2T
    \
    NH71
    \
    \
    \
    NH72-NN7
    NH4
    \
    \
    |
    \
    NC7 NC4
    \
    // \ / \\
    \
    NO7 NC3 NC5-NH5
    \
    ||
    |
    \ NH5s NH4'NO4'
    NH2-NC2 NC6-NH6
    \ |
    \ / \
    \+//
    NC5'--NC4' NC1'---------NN1
    |
    \
    / \
    NH5' NC3'-NC2'NH1'
    / \ / \
    NO3' NH3'NO2'NH2'
    |
    |
    NH3T
    NH2T

    ATOM NO2'
    ATOM NH2T
    GROUP
    ATOM NC3'
    ATOM NH3'
    ATOM NO3'
    ATOM NH3T
    GROUP
    ATOM NC1'
    ATOM NH1'
    ATOM NC4'
    ATOM NH4'
    ATOM NO4'
    GROUP
    ATOM NN1
    ATOM NC6
    ATOM NH6
    ATOM NC5
    ATOM NH5
    ATOM NC4
    ATOM NH4
    ATOM NC3
    ATOM NC2
    ATOM NH2
    ATOM NC7
    ATOM NO7
    ATOM NN7
    ATOM NH71
    ATOM NH72

    OG311
    HGP1

    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C53
    HGA1
    CG3C51
    HGA1
    OG3C51

    0.11
    0.09
    0.11
    0.09
    -0.40

    NG2R61
    CG2R62
    HGR63
    CG2R62
    HGR63
    CG2R62
    HGR63
    CG2R62
    CG2R62
    HGR63
    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    -0.07
    0.16
    0.19
    -0.10
    0.16
    -0.05
    0.16
    0.05
    0.18
    0.16
    0.68
    -0.40
    -0.82
    0.34 ! trans to amide O
    0.36 ! cis to amide O

    BOND AN1 AC2


    AN3 AC4
    BOND AC6 AN6
    AC5 AN7
    BOND AN9 AC4
    AC2 AH2
    DOUBLE AC6 AN1
    AC2 AN3
    BOND AN9 AC1'
    AC1' AC2'
    BOND AO4' AC1'
    AC1' AH1'
    BOND AC3' AH3'
    AC3' AO3'
    BOND AC5' AH5S
    AC5' AH5'
    BOND AP AO2
    AP O3
    BOND NP NO5'
    NO5' NC5'
    BOND NC4' NO4'
    NO4' NC1'
    BOND NC1' NH1'
    NC2' NH2'
    BOND NC3' NO3'
    NO3' NH3T
    BOND NC3 NC4
    NC5 NC6
    BOND NC2 NH2
    NC3 NC7
    BOND NN7 NH72
    NC4 NH4
    DOUBLE NC2 NC3
    NC4 NC5
    ! adenine impropers
    IMPR AN6 AC6 AH61 AH62
    AC6
    ! amide impropers
    IMPR NC7 NN7 NC3 NO7
    NC7
    IMPR NN7 NC7 NH71 NH72 NN7
    ! ring hydrogen impropers
    IMPR NC6 NN1 NC5 NH6
    NC5
    IMPR NC4 NC5 NC3 NH4
    NC2
    DONO AH61 AN6
    DONO AH62 AN6
    DONO AH2T AO2'
    DONO AH3T AO3'
    ACCE AN1

    AC5 AC6
    AC8 AN9
    AN6 AH61
    AC4 AC5
    AC2' AC3'
    AC2' AO2'
    AO3' AH3T
    AC5' AO5'
    O3 NP
    NC5' NH5S
    NC1' NC2'
    NC2' NO2'
    NC4' NH4'

    AN6
    AN7
    AC3'
    AO2'
    AC4'
    AO5'
    NP
    NC5'
    NC2'
    NO2'
    NC1'

    NC7 NO7
    NC5 NH5
    NC6 NN1

    AH62
    AC8
    AC4'
    AH2T
    AH4'
    AP
    NO1
    NH5'
    NC3'
    NH2T
    NN1

    NC7 NN7
    NC6 NH6

    AN1

    AC5 AN6

    NC3
    NC7

    NN7 NO7
    NH72 NH71

    NC6
    NC3

    NC4
    NN1

    NH5
    NH2

    AC8 AH8
    AC4'
    AC2'
    AC4'
    AP
    NP
    NC5'
    NC3'
    NC3'
    NN1

    AO4'
    AH2'
    AC5'
    AO1
    NO2
    NC4'
    NC4'
    NH3'
    NC2

    NN7 NH71

    ACCE AN3
    ACCE AN7
    ACCE AO4'
    ACCE AO2'
    ACCE AO3'
    ACCE AO5'
    ACCE AO1
    ACCE AO2
    ACCE O3
    ACCE NO1
    ACCE NO2
    ACCE NO5'
    ACCE NO4'
    ACCE NO3'
    ACCE NO2'
    ACCE NO7
    DONO NH2T
    DONO NH3T
    DONO NH71
    DONO NH72
    IC AP
    IC AC5'
    IC AC5'
    IC AH5S
    IC AP
    IC AP
    IC AP
    IC AO1
    IC AO5'
    IC AC5'
    IC AH3T
    IC AO4'
    IC AC2'
    IC AC4'
    IC AC3'
    IC AO4'
    IC AC1'
    IC AC4
    IC AC8
    IC AC8
    IC AN7
    IC AC5
    IC AN9
    IC AC5
    IC AN1
    IC AH61
    IC AC5
    IC AN1
    IC AH61
    IC AN9
    IC AN1
    IC AC1'
    IC AH2'
    IC AH2T
    IC AO4'
    IC AC1'
    IC AC2'
    IC AC3'
    IC AC4'
    IC AC4'

    AP
    AP
    NP
    NP

    NO2'
    NO3'
    NN7
    NN7
    O3
    AO5'
    AO5'
    AC5'
    O3
    O3
    AO5'
    AP
    AC5'
    AC4'
    AO3'
    AC3'
    AC4'
    AC3'
    AC2'
    AC1'
    AC4
    AN9
    AN9
    AN7
    AC5
    AC6
    AC5
    AN1
    AC6
    AC6
    AN1
    AC6
    AC6
    AN7
    AN3
    AC3'
    AO2'
    AO2'
    AC2'
    AC3'
    AC4'
    AO4'
    AO5'
    AO5'

    NP
    AP
    AP
    AC4'
    NP
    NP
    AC5'
    AO5'
    AC4'
    AC3'
    AC3'
    *AC4
    *AC3'
    AC2'
    AC1'
    AN9
    *AN9
    AC8
    AC4
    AC5
    AC6
    AN1
    *AC4
    *AC6
    AN6
    *AN6
    *AC6
    AN6
    *AN6
    *AC8
    *AC2
    *AC2
    AC2'
    AC2'
    *AC1'
    *AC2
    *AC3'
    *AC4
    *AC5
    *AC5

    NO5'
    O3
    AO2
    AC3'
    NO1
    NO2
    AC4'
    AC5'
    AC3'
    AO3'
    AC4'
    AC5'
    AO3'
    AC1'
    AN9
    AC4
    AC8
    AN7
    AC5
    AC6
    AN1
    AC2
    AN3
    AN6
    AH61
    AH62
    AN6
    AH61
    AH62
    AH8
    AH2
    AO2'
    AC3'
    AC3'
    AH1'
    AH2'
    AH3'
    AH4'
    AH5'
    AH5'

    1.4863
    1.4232
    1.4232
    0.9935
    1.4863
    1.4863
    1.5901
    1.5901
    1.4232
    1.5491
    0.9671
    1.8868
    1.5097
    1.6942
    1.5097
    1.3646
    1.4847
    1.4013
    1.3777
    1.3282
    1.3814
    1.4146
    1.4013
    1.4146
    1.3482
    0.9912
    1.4146
    1.3482
    0.9912
    1.3777
    1.3300
    1.5415
    2.0386
    0.9953
    1.3646
    1.5415
    1.5097
    1.6942
    1.5491
    1.5491

    65.28
    127.31
    127.31
    120.00
    65.28
    65.28
    127.31
    127.31
    111.63
    111.58
    98.77
    112.95
    93.22
    93.22
    117.82
    95.44
    125.96
    105.34
    105.34
    103.21
    130.78
    117.85
    105.06
    117.85
    119.69
    116.60
    117.85
    119.69
    116.60
    114.01
    129.42
    117.82
    31.12
    99.36
    120.77
    117.82
    93.22
    112.95
    111.63
    111.63

    -169.00
    -165.10
    73.33
    -58.20
    78.51
    -54.29
    121.29
    121.29
    -58.20
    128.42
    147.40
    -118.10
    -117.72
    -12.93
    135.56
    -90.72
    -176.52
    -0.07
    0.11
    -179.92
    -179.94
    -0.14
    -179.67
    179.89
    -0.39
    -179.02
    179.89
    -0.39
    -179.02
    -179.37
    179.97
    -145.06
    -93.63
    -93.63
    -114.99
    108.23
    117.28
    -140.26
    -123.75
    -123.75

    98.59
    103.27
    111.48
    111.58
    108.97
    112.88
    111.63
    127.31
    111.58
    114.19
    114.19
    111.58
    114.19
    117.82
    115.01
    125.96
    105.34
    114.01
    105.06
    130.78
    117.85
    118.87
    126.14
    119.69
    116.60
    116.94
    119.69
    116.60
    116.94
    126.34
    114.82
    114.13
    114.13
    114.13
    109.65
    86.44
    111.94
    57.99
    111.23
    111.23

    1.5977
    1.4863
    1.4836
    1.6942
    1.4756
    1.4636
    1.5491
    1.4232
    1.6942
    1.4337
    1.6942
    1.5491
    1.4337
    1.5415
    1.4847
    1.4013
    1.3777
    1.3282
    1.3782
    1.4146
    1.3482
    1.3300
    1.3648
    1.3419
    0.9912
    0.9978
    1.3419
    0.9912
    0.9978
    1.0962
    1.0928
    1.4294
    1.5097
    1.5097
    1.1105
    1.0999
    1.1110
    1.0000
    1.1111
    1.1111

    IC NC5' NO5'
    IC NH5S NC5'
    IC NH5' NC5'
    IC NP
    NO5'
    IC NO5' NC5'
    IC NC5' NC4'
    IC NC4' NC3'
    IC NC3' NC2'
    IC NC2' NC1'
    IC NO2' NC2'
    IC NH2T NO2'
    IC NO4' NC2'
    IC NC1' NC3'
    IC NC2' NC4'
    IC NC3' NO4'
    IC NC4' NO5'
    IC NC4' NO5'
    IC NC3' NC2'
    IC NO3' NC3'
    IC NH3T NO3'
    IC NC2' NC1'
    IC NC1' NN1
    IC NN1
    NC2
    IC NC2
    NC3
    IC NC3
    NC4
    IC NC4
    NC5
    IC NC5
    NC6
    IC NN1
    NC2
    IC NC2
    NC3
    IC NC2
    NC3
    IC NO7
    NC7
    IC NO7
    NC7
    IC NC2
    NC3
    IC NC3
    NC4
    IC NC4
    NC5
    IC NC6
    NN1
    PATCH FIRST NONE

    NP
    NO2
    NO5' NP
    NO5' NP
    NC5' NC4'
    NC4' NC3'
    NC3' NC2'
    NC2' NC1'
    NC1' NO4'
    NO4' NC4'
    NC1' NO4'
    NC2' NC1'
    *NC1' NH1'
    *NC2 NH2'
    *NC3 NH3'
    *NC4 NH4'
    *NC5 NH5'
    *NC5 NH5S
    NC1' NN1
    NC2' NC1'
    NC3' NC2'
    NN1
    NC2
    NC2
    NC3
    NC3
    NC4
    NC4
    NC5
    NC5
    NC6
    NC6
    NN1
    NN1
    NC2
    NC3
    NC7
    NC7
    NO7
    NC7
    NN7
    NN7
    NH71
    NN7
    NH72
    NC4
    NH4
    NC5
    NH5
    NC6
    NH6
    NC2
    NH2
    LAST NONE

    RESI NADH
    -2.00 !
    ide, jjp1/adm jr.
    !
    !
    9/98
    !
    lts exist
    !
    !
    GROUP
    !
    ATOM AC4' CG3C51
    0.11 !
    ATOM AH4' HGA1
    0.09 !
    ATOM AO4' OG3C51 -0.40 !
    ATOM AC1' CG3C51
    0.11 !
    ATOM AH1' HGA1
    0.09 !
    GROUP
    !
    ATOM AC5 CG2RC0
    0.28 !
    ATOM AN7 NG2R50 -0.71 !
    ATOM AC8 CG2R53
    0.34 !
    ATOM AH8 HGR52
    0.12 !
    ATOM AN9 NG2R51 -0.05 !
    !

    1.4451
    1.1110
    1.1110
    1.5977
    1.4451
    1.5160
    1.5160
    1.5160
    1.5270
    1.4200
    0.9600
    1.4100
    1.5270
    1.5160
    1.5160
    1.5160
    1.5160
    1.5160
    1.4200
    0.9600
    1.5270
    1.4800
    1.3150
    1.3500
    1.3600
    1.3600
    1.3500
    1.3150
    1.3500
    1.3500
    1.2300
    1.2300
    1.3500
    1.3600
    1.3600
    1.2199

    128.40
    109.50
    109.50
    128.40
    110.10
    108.50
    111.00
    105.50
    105.00
    110.10
    106.00
    105.00
    105.50
    111.00
    100.64
    110.10
    110.10
    105.50
    110.10
    106.00
    113.70
    121.70
    122.00
    118.00
    118.00
    118.00
    124.51
    122.00
    131.80
    131.80
    120.00
    120.00
    118.00
    118.00
    118.00
    119.49

    -49.72
    115.00
    -115.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    180.00
    -115.00
    115.00
    115.00
    -115.00
    -115.00
    115.00
    0.00
    180.00
    180.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    0.00
    0.00

    108.83
    128.40
    128.40
    110.10
    108.50
    111.00
    105.50
    105.00
    117.86
    105.00
    110.10
    110.10
    110.10
    110.10
    107.24
    109.50
    109.50
    113.70
    105.50
    110.10
    121.70
    122.00
    118.00
    118.00
    118.00
    124.51
    119.49
    131.80
    118.50
    113.00
    120.00
    120.00
    121.00
    119.00
    120.50
    117.50

    1.4636
    1.5977
    1.5977
    1.5160
    1.5160
    1.5160
    1.5270
    1.4100
    1.4712
    1.4100
    1.5270
    1.1110
    1.1110
    1.1110
    1.1110
    1.1110
    1.1110
    1.4800
    1.5270
    1.5160
    1.3150
    1.3500
    1.3600
    1.3600
    1.3500
    1.2199
    1.3150
    1.4800
    1.2300
    1.3600
    1.0000
    1.0000
    1.0900
    1.0900
    1.0900
    1.0900

    C21H27N7O14P2 reduced nicotinamide adenine dinucleot


    atom names correspond to pdb nomenclature
    checked for consistency with new NA params, adm jr.,
    note that differences with respect to published resu
    due to new NA params
    AH61 AH62
    \ /
    AN6
    |
    AC6
    // \
    AN1 AC5--AN7\\
    |
    ||
    AC8-AH8
    AC2 AC4--AN9/
    / \\ /
    \
    AH2 AN3
    \
    \

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    AN1
    AC2
    AH2
    AN3
    AC4
    AC6

    ATOM AN6
    ATOM AH61
    ATOM AH62
    GROUP
    ATOM AC2'
    ATOM AH2'
    ATOM AO2'
    ATOM AH2T
    GROUP
    ATOM AC3'
    ATOM AH3'
    ATOM AO3'
    ATOM AH3T
    GROUP
    ATOM AC5'
    ATOM AH5'
    ATOM AH5S
    ATOM AP
    ATOM AO1
    ATOM AO2
    ATOM AO5'
    ATOM O3
    ATOM NP
    ATOM NO1
    ATOM NO2
    ATOM NO5'
    ATOM NC5'
    ATOM NH5S
    ATOM NH5'
    GROUP
    ATOM NC2'
    ATOM NH2'
    ATOM NO2'
    ATOM NH2T
    GROUP
    ATOM NC3'
    ATOM NH3'
    ATOM NO3'
    ATOM NH3T
    GROUP
    ATOM NC1'
    ATOM NH1'
    ATOM NC4'
    ATOM NH4'
    ATOM NO4'
    GROUP
    ATOM NN1
    ATOM NC6
    ATOM NH6
    ATOM NC5
    ATOM NH5
    ATOM NC4
    ATOM NH4

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2
    PG2
    OG2P1
    OG2P1
    OG303
    OG303
    PG2
    OG2P1
    OG2P1
    OG303
    CG321
    HGA2
    HGA2

    -0.08
    0.09
    0.09
    1.50
    -0.82
    -0.82
    -0.62
    -0.68
    1.50
    -0.82
    -0.82
    -0.62
    -0.08
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    CG3C51
    HGA1
    OG3C51

    0.11
    0.09
    0.11
    0.09
    -0.40

    NG301
    CG2D1O
    HGA4
    CG2D1
    HGA4
    CG321
    HGA2

    -0.27
    -0.06
    0.17
    -0.18
    0.14
    -0.28
    0.09

    !
    \
    !
    \
    !
    NO1
    AO1
    AH5sAH4' AO4' \
    !
    |
    |
    |
    \ / \ \
    ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
    ! \ |
    |
    |
    \
    / \
    ! \ NO2
    AO2
    AH5' AC3'-AC2' AH1'
    ! \
    / \ / \
    !
    \
    AO3' AH3'AO2'AH2'
    !
    \
    |
    |
    !
    \
    AH3T
    AH2T
    !
    \
    NH71
    !
    \
    \
    !
    \
    NH72-NN7 NH4 NH42
    !
    \
    \
    \ /
    !
    \
    NC7 NC4
    !
    \
    / \ / \
    !
    \
    NO7 NC3 NC5-NH5
    !
    \
    || ||
    !
    \ NH5s NH4'NO4'
    NH2-NC2 NC6-NH6
    !
    \ |
    \ / \
    \ /
    !
    NC5'--NC4' NC1'---------NN1
    !
    |
    \
    / \
    !
    NH5' NC3'-NC2'NH1'
    !
    / \ / \
    !
    NO3' NH3'NO2'NH2'
    !
    |
    |
    !
    NH3T
    NH2T

    !N2
    !C3
    !H4
    !C5
    !H6
    !C7
    !H8

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    NH42
    NC3
    NC2
    NH2
    NC7
    NO7
    NN7
    NH71
    NH72

    HGA2
    CG2DC1
    CG2D1O
    HGA4
    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    0.09
    0.36
    -0.10
    0.14
    0.55
    -0.51
    -0.72
    0.26
    0.32

    !H17
    !C9
    !C10
    !H11
    !C12
    !O13
    !N14
    !H15 ! trans to amide O
    !H16 ! cis to amide O

    BOND AN1 AC2


    AN3 AC4
    AC5 AC6
    BOND AC6 AN6
    AC5 AN7
    AC8 AN9
    BOND AN9 AC4
    AC2 AH2
    AN6 AH61
    AN6
    DOUBLE AC6 AN1
    AC2 AN3
    AC4 AC5
    AN7
    BOND AN9 AC1'
    AC1' AC2'
    AC2' AC3'
    AC3'
    BOND AO4' AC1'
    AC1' AH1'
    AC2' AO2'
    AO2'
    BOND AC3' AH3'
    AC3' AO3'
    AO3' AH3T
    AC4'
    BOND AC5' AH5S
    AC5' AH5'
    AC5' AO5'
    AO5'
    BOND AP AO2
    AP O3
    O3 NP
    NP
    BOND NP NO5'
    NO5' NC5'
    NC5' NH5S
    NC5'
    BOND NC4' NO4'
    NO4' NC1'
    NC1' NC2'
    NC2'
    BOND NC1' NH1'
    NC2' NH2'
    NC2' NO2'
    NO2'
    BOND NC3' NO3'
    NO3' NH3T
    NC4' NH4'
    NC1'
    BOND NC3 NC4
    NC4 NC5
    NC6 NN1
    BOND NC2 NH2
    NC3 NC7
    NC7 NO7
    NC7
    BOND NN7 NH72
    NC4 NH4
    NC4 NH42
    NC5
    DOUBLE NC2 NC3
    NC5 NC6
    ! adenine impropers
    IMPR AN6 AC6 AH61 AH62
    AC6 AN1 AC5 AN6
    ! amide impropers
    IMPR NC7 NN7 NC3 NO7
    NC7 NC3 NN7 NO7
    IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71
    ! ring hydrogen impropers
    IMPR NC6 NN1 NC5 NH6
    NC5 NC6 NC4 NH5
    IMPR NC2 NC3 NN1 NH2
    DONO AH61 AN6
    DONO AH62 AN6
    DONO AH2T AO2'
    DONO AH3T AO3'
    ACCE AN1
    ACCE AN3
    ACCE AN7
    ACCE AO4'
    ACCE AO2'
    ACCE AO3'
    ACCE AO5'
    ACCE AO1 AP
    ACCE AO2 AP
    ACCE O3
    ACCE NO1 NP
    ACCE NO2 NP
    ACCE NO5'
    ACCE NO4'
    ACCE NO3'
    ACCE NO2'
    ACCE NO7
    DONO NH2T NO2'
    DONO NH3T NO3'
    DONO NH71 NN7
    DONO NH72 NN7

    AH62
    AC8
    AC4'
    AH2T
    AH4'
    AP
    NO1
    NH5'
    NC3'
    NH2T
    NN1

    AC8 AH8

    NN7
    NH5

    NN7 NH71
    NC6 NH6

    AC4'
    AC2'
    AC4'
    AP
    NP
    NC5'
    NC3'
    NC3'
    NN1

    AO4'
    AH2'
    AC5'
    AO1
    NO2
    NC4'
    NC4'
    NH3'
    NC2

    ! IC table was beyond repair ==> replaced (kevo)


    IC AP
    O3
    NP
    NO5' 1.6011 92.88 167.64
    IC AP
    O3
    NP
    NO1
    1.6011 92.88 62.12
    IC AP
    O3
    NP
    NO2
    1.6011 92.88 -85.34
    IC NP
    O3
    AP
    AO5' 1.6074 92.88 169.27
    IC O3
    AO5' *AP
    AO1
    1.6011 93.16 -115.15
    IC O3
    AO5' *AP
    AO2
    1.6011 93.16 120.82
    IC O3
    AP
    AO5' AC5' 1.6011 93.16 -65.25
    IC AP
    AO5' AC5' AC4' 1.6636 117.89 -111.08
    IC AC4' AO5' *AC5' AH5' 1.5437 111.72 121.91
    IC AC4' AO5' *AC5' AH5S 1.5437 111.72 -120.24
    IC AO5' AC5' AC4' AC3' 1.4434 111.72 32.23
    IC AC5' AC4' AC3' AO3' 1.5437 115.30 82.44
    IC AH3T AO3' AC3' AC4' 0.9956 102.19 -78.33
    IC AO4' AC3' *AC4' AC5' 1.4436 105.34 -122.02
    IC AC2' AC4' *AC3' AO3' 1.5312 103.02 -124.10
    IC AC4' AC3' AC2' AC1' 1.5403 103.02 34.98
    IC AC3' AC2' AC1' AN9
    1.5312 101.18 88.32
    IC AO4' AC1' AN9
    AC4
    1.4336 105.95 -149.10
    IC AC1' AC4
    *AN9 AC8
    1.4609 127.35 179.89
    IC AC4
    AN9
    AC8
    AN7
    1.3682 106.85
    0.34
    IC AC8
    AN9
    AC4
    AC5
    1.3818 106.85 -0.12
    IC AC8
    AN7
    AC5
    AC6
    1.3338 103.64 -179.39
    IC AN7
    AC5
    AC6
    AN1
    1.3924 132.41 179.90
    IC AC5
    AC6
    AN1
    AC2
    1.4083 118.87 -0.29
    IC AN9
    AC5
    *AC4 AN3
    1.3682 105.55 -179.81
    IC AC5
    AN1
    *AC6 AN6
    1.4083 118.87 179.60
    IC AN1
    AC6
    AN6
    AH61 1.3616 117.11 -176.96
    IC AH61 AC6
    *AN6 AH62 0.9980 119.87 174.83
    IC AN9
    AN7
    *AC8 AH8
    1.3818 112.92 -179.84
    IC AN1
    AN3
    *AC2 AH2
    1.3626 125.37 -179.78
    IC AO4' AC2' *AC1' AH1' 1.4336 107.49 -118.51
    IC AC1' AC3' *AC2' AH2' 1.5414 101.18 120.60
    IC AC2' AC4' *AC3' AH3' 1.5312 103.02 114.75
    IC AC3' AO4' *AC4' AH4' 1.5403 105.34 -116.63
    IC NC5' NO5' NP
    NO2
    1.4353 125.45 -110.33
    IC NP
    NO5' NC5' NC4' 1.6600 125.45 -100.01
    IC NO5' NC5' NC4' NC3' 1.4353 114.36 42.03
    IC NC5' NC4' NC3' NC2' 1.5573 115.36 -91.03
    IC NC4' NC3' NC2' NC1' 1.5403 101.62 -39.21
    IC NC3' NC2' NC1' NO4' 1.5376 100.72 35.40
    IC NO2' NC2' NC1' NO4' 1.4392 115.62 158.69
    IC NH2T NO2' NC2' NC1' 0.9686 102.30 157.15
    IC NO4' NC2' *NC1' NH1' 1.4395 105.65 -114.11
    IC NC1' NC3' *NC2 NH2' 2.4605
    9.08 131.65
    IC NC2' NC4' *NC3 NH3' 4.7247 22.53 -7.48
    IC NC3' NO4' *NC4 NH4' 6.4634 19.31 -56.73
    IC NC4' NO5' *NC5 NH5' 5.1412 29.29 35.30
    IC NC4' NO5' *NC5 NH5S 5.1412 29.29 55.33
    IC NC3' NC2' NC1' NN1
    1.5376 100.72 153.61
    IC NO3' NC3' NC2' NC1' 1.4390 111.69 79.56
    IC NH3T NO3' NC3' NC2' 0.9633 102.31 55.04
    IC NC2' NC1' NN1
    NC2
    1.5399 113.06 115.33
    IC NC1' NN1
    NC2
    NC3
    1.4871 119.55 179.60
    IC NN1
    NC2
    NC3
    NC4
    1.3595 123.83
    5.03
    IC NC2
    NC3
    NC4
    NC5
    1.3763 118.94 -6.70
    IC NC3
    NC4
    NC5
    NC6
    1.5428 111.53
    5.08
    IC NN1
    NC2
    NC3
    NC7
    1.3595 123.83 -158.70
    IC NC2
    NC3
    NC7
    NO7
    1.3763 118.33 -160.59
    IC NC2
    NC3
    NC7
    NN7
    1.3763 118.33 20.47

    96.12
    118.93
    112.47
    93.16
    102.32
    100.53
    117.89
    111.72
    113.03
    108.95
    115.30
    113.07
    113.07
    115.30
    113.07
    101.18
    111.78
    127.35
    106.85
    112.92
    105.55
    132.41
    118.87
    119.53
    125.91
    117.11
    119.87
    117.95
    125.33
    117.21
    111.70
    111.56
    109.97
    105.95
    103.18
    114.36
    115.36
    101.62
    100.72
    105.65
    105.65
    115.62
    109.56
    26.20
    17.99
    2.93
    14.10
    24.87
    113.06
    100.72
    111.69
    119.55
    123.83
    118.94
    111.53
    122.32
    118.33
    120.47
    119.04

    1.6600
    1.5360
    1.5263
    1.6636
    1.5255
    1.5378
    1.4434
    1.5437
    1.1186
    1.1118
    1.5403
    1.4340
    1.5403
    1.5437
    1.4340
    1.5414
    1.4609
    1.3682
    1.3818
    1.3338
    1.3970
    1.4083
    1.3616
    1.3626
    1.3450
    1.3448
    0.9980
    0.9930
    1.0978
    1.0932
    1.1012
    1.0994
    1.1020
    1.1009
    1.5263
    1.5573
    1.5403
    1.5376
    1.5399
    1.4395
    1.4395
    1.5399
    1.1015
    3.7695
    6.8615
    7.0769
    6.2151
    4.9161
    1.4871
    1.5399
    1.5376
    1.3595
    1.3763
    1.5428
    1.5189
    1.3550
    1.5212
    1.2354
    1.3683

    IC NO7
    NC7
    IC NO7
    NC7
    IC NC2
    NC3
    IC NC2
    NC3
    IC NC3
    NC4
    IC NC4
    NC5
    IC NC6
    NN1
    IC AC1' AC3'
    IC AC3' AC2'
    PATCH FIRST NONE
    RESI NADP
    tide,

    NN7
    NH71
    NN7
    NH72
    NC4
    NH4
    NC4
    NH42
    NC5
    NH5
    NC6
    NH6
    NC2
    NH2
    *AC2' AO2'
    AO2' AH2T
    LAST NONE

    1.2354
    1.2354
    1.3763
    1.3763
    1.5428
    1.5189
    1.3589
    1.5414
    1.5312

    120.48
    120.48
    118.94
    118.94
    111.53
    122.32
    121.05
    101.18
    110.89

    -176.29
    0.52
    -136.51
    108.33
    -149.76
    179.97
    177.95
    -118.90
    -28.83

    120.56
    116.91
    113.66
    105.96
    116.93
    119.29
    116.69
    110.89
    100.98

    0.9982
    0.9963
    1.1068
    1.1115
    1.0907
    1.0969
    1.0900
    1.4319
    0.9715

    -2.00 ! C21H26N7O17P3 oxidized nicotinamide adenine dinucleo


    ! NADP+, adm jr.
    ! atom names correspond to pdb nomenclature
    ! checked for consistency with new NA params, adm jr.,

    9/98
    ! note that differences with respect to published resu
    lts exist
    GROUP
    ATOM AC4'
    ATOM AH4'
    ATOM AO4'
    ATOM AC1'
    ATOM AH1'
    GROUP
    ATOM AC5
    ATOM AN7
    ATOM AC8
    ATOM AH8
    ATOM AN9
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    AN1
    AC2
    AH2
    AN3
    AC4
    AC6

    ATOM AN6
    ATOM AH61
    ATOM AH62
    GROUP
    ATOM AC2'
    ATOM AH2'
    ATOM AO2'
    ATOM AP2
    ATOM AO1P
    ATOM AO2P
    ATOM AO2T
    ATOM AH2T
    GROUP
    ATOM AC3'
    ATOM AH3'
    ATOM AO3'
    ATOM AH3T
    GROUP
    ATOM AC5'

    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    0.11
    0.09
    -0.40
    0.11
    0.09

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.28
    -0.71
    0.34
    0.12
    -0.05

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1

    0.01
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321

    -0.08

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    due to new NA params


    AH61 AH62
    \ /
    AN6
    |
    AC6
    // \
    AN1 AC5--AN7\\
    |
    ||
    AC8-AH8
    AC2 AC4--AN9/
    / \\ /
    \
    AH2 AN3
    \
    \
    \
    \
    NO1
    AO1
    AH5sAH4' AO4' \
    |
    |
    |
    \ / \ \
    NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
    \ |
    |
    |
    \
    / \
    \ NO2
    AO2
    AH5' AC3'-AC2' AH1'
    \
    / \ / \
    \
    AO3' AH3'AO2'AH2'
    \
    |
    |
    \
    AH3T AO1P=AP2==AO2P (-)
    \
    |
    NH71
    \
    AH2T-AO2T /
    \
    NH72-NN7
    NH4
    \
    \
    |
    \
    NC7 NC4
    \
    / \ / \\
    \
    NO7 NC3 NC5-NH5
    \
    || |
    \ NH5s NH4'NO4'
    NH2-NC2 NC6-NH6
    \ |
    \ / \
    \+ //
    NC5'--NC4' NC1'---------NN1
    |
    \
    / \
    NH5' NC3'-NC2'NH1'
    / \ / \
    NO3' NH3'NO2'NH2'

    ATOM AH5'
    ATOM AH5S
    ATOM AP
    ATOM AO1
    ATOM AO2
    ATOM AO5'
    ATOM O3
    ATOM NP
    ATOM NO1
    ATOM NO2
    ATOM NO5'
    ATOM NC5'
    ATOM NH5S
    ATOM NH5'
    GROUP
    ATOM NC2'
    ATOM NH2'
    ATOM NO2'
    ATOM NH2T
    GROUP
    ATOM NC3'
    ATOM NH3'
    ATOM NO3'
    ATOM NH3T
    GROUP
    ATOM NC1'
    ATOM NH1'
    ATOM NC4'
    ATOM NH4'
    ATOM NO4'
    GROUP
    ATOM NN1
    ATOM NC6
    ATOM NH6
    ATOM NC5
    ATOM NH5
    ATOM NC4
    ATOM NH4
    ATOM NC3
    ATOM NC2
    ATOM NH2
    ATOM NC7
    ATOM NO7
    ATOM NN7
    ATOM NH71
    ATOM NH72

    HGA2
    HGA2
    PG2
    OG2P1
    OG2P1
    OG303
    OG303
    PG2
    OG2P1
    OG2P1
    OG303
    CG321
    HGA2
    HGA2

    0.09 !
    0.09 !
    1.50
    -0.82
    -0.82
    -0.62
    -0.68
    1.50
    -0.82
    -0.82
    -0.62
    -0.08
    0.09
    0.09

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C53
    HGA1
    CG3C51
    HGA1
    OG3C51

    0.11
    0.09
    0.11
    0.09
    -0.40

    NG2R61
    CG2R62
    HGR63
    CG2R62
    HGR63
    CG2R62
    HGR63
    CG2R62
    CG2R62
    HGR63
    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    -0.07
    0.16
    0.19
    -0.10
    0.16
    -0.05
    0.16
    0.05
    0.18
    0.16
    0.68
    -0.40
    -0.82
    0.34 ! trans to amide O
    0.36 ! cis to amide O

    BOND AN1 AC2


    BOND AC6 AN6
    BOND AN9 AC4
    DOUBLE AC6 AN1
    BOND AN9 AC1'
    BOND AO4' AC1'
    BOND AC3' AH3'
    BOND AC5' AH5S
    BOND AP AO2
    BOND NP NO5'
    BOND NC4' NO4'
    BOND NC1' NH1'
    BOND NC3' NO3'

    AN3 AC4
    AC5 AN7
    AC2 AH2
    AC2 AN3
    AC1' AC2'
    AC1' AH1'
    AC3' AO3'
    AC5' AH5'
    AP O3
    NO5' NC5'
    NO4' NC1'
    NC2' NH2'
    NO3' NH3T

    |
    NH3T

    AC5 AC6
    AC8 AN9
    AN6 AH61
    AC4 AC5
    AC2' AC3'
    AC2' AO2'
    AO3' AH3T
    AC5' AO5'
    O3 NP
    NC5' NH5S
    NC1' NC2'
    NC2' NO2'
    NC4' NH4'

    |
    NH2T

    AN6
    AN7
    AC3'
    AO2'
    AC4'
    AO5'
    NP
    NC5'
    NC2'
    NO2'
    NC1'

    AH62
    AC8
    AC4'
    AP2
    AH4'
    AP
    NO1
    NH5'
    NC3'
    NH2T
    NN1

    AC8 AH8
    AC4' AO4'
    AC2' AH2'
    AC4' AC5'
    AP AO1
    NP NO2
    NC5' NC4'
    NC3' NC4'
    NC3' NH3'
    NN1 NC2

    BOND NC3 NC4


    NC5 NC6
    BOND NC2 NH2
    NC3 NC7
    NC7 NO7
    NC7
    BOND NN7 NH72
    NC4 NH4
    NC5 NH5
    NC6
    BOND AP2 AO1P
    AP2 AO2P
    AP2 AO2T
    AO2T
    DOUBLE NC2 NC3
    NC4 NC5
    NC6 NN1
    ! adenine impropers
    IMPR AN6 AC6 AH61 AH62
    AC6 AN1 AC5 AN6
    ! amide impropers
    IMPR NC7 NN7 NC3 NO7
    NC7 NC3 NN7 NO7
    IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71
    ! ring hydrogen impropers
    IMPR NC6 NN1 NC5 NH6
    NC5 NC6 NC4 NH5
    IMPR NC4 NC5 NC3 NH4
    NC2 NC3 NN1 NH2
    DONO AH61 AN6
    DONO AH62 AN6
    DONO AH3T AO3'
    ACCE AN1
    ACCE AN3
    ACCE AN7
    ACCE AO4'
    ACCE AO2'
    ACCE AO3'
    ACCE AO5'
    ACCE AO1 AP
    ACCE AO2 AP
    ACCE O3
    ACCE NO1 NP
    ACCE NO2 NP
    ACCE NO5'
    ACCE NO4'
    ACCE NO3'
    ACCE NO2'
    ACCE NO7
    DONO NH2T NO2'
    DONO NH3T NO3'
    DONO NH71 NN7
    DONO NH72 NN7
    DONO AH2T AO2T
    ACCE AO2T
    ACCE AO1P
    ACCE AO2P
    ACCE AO2'
    IC AP
    O3
    NP
    NO5' 1.4863 65.28 -169.00
    IC AC5' AO5' AP
    O3
    1.4232 127.31 -165.10
    IC AC5' AO5' AP
    AO2
    1.4232 127.31 73.33
    IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20
    IC AP
    O3
    NP
    NO1
    1.4863 65.28 78.51
    IC AP
    O3
    NP
    NO2
    1.4863 65.28 -54.29
    IC AP
    AO5' AC5' AC4' 1.5901 127.31 121.29
    IC AO1
    AP
    AO5' AC5' 1.5901 127.31 121.29
    IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20
    IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42
    IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40
    IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10
    IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72
    IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93
    IC AC3' AC2' AC1' AN9
    1.5097 117.82 135.56
    IC AO4' AC1' AN9
    AC4
    1.3646 95.44 -90.72
    IC AC1' AC4
    *AN9 AC8
    1.4847 125.96 -176.52
    IC AC4
    AN9
    AC8
    AN7
    1.4013 105.34 -0.07

    NN7
    NH6
    AH2T

    98.59
    103.27
    111.48
    111.58
    108.97
    112.88
    111.63
    127.31
    111.58
    114.19
    114.19
    111.58
    114.19
    117.82
    115.01
    125.96
    105.34
    114.01

    NN7 NH71

    1.5977
    1.4863
    1.4836
    1.6942
    1.4756
    1.4636
    1.5491
    1.4232
    1.6942
    1.4337
    1.6942
    1.5491
    1.4337
    1.5415
    1.4847
    1.4013
    1.3777
    1.3282

    IC AC8
    IC AC8
    IC AN7
    IC AC5
    IC AN9
    IC AC5
    IC AN1
    IC AH61
    IC AC5
    IC AN1
    IC AH61
    IC AN9
    IC AN1
    IC AC1'
    IC AH2'
    !IC AH2T
    IC AO4'
    IC AC1'
    IC AC2'
    IC AC3'
    IC AC4'
    IC AC4'
    IC NC5'
    IC NH5S
    IC NH5'
    IC NP
    IC NO5'
    IC NC5'
    IC NC4'
    IC NC3'
    IC NC2'
    IC NO2'
    IC NH2T
    IC NO4'
    IC NC1'
    IC NC2'
    IC NC3'
    IC NC4'
    IC NC4'
    IC NC3'
    IC NO3'
    IC NH3T
    IC NC2'
    IC NC1'
    IC NN1
    IC NC2
    IC NC3
    IC NC4
    IC NC5
    IC NN1
    IC NC2
    IC NC2
    IC NO7
    IC NO7
    IC NC2
    IC NC3
    IC NC4
    IC NC6
    IC AC3'
    IC AC2'

    AN9
    AN7
    AC5
    AC6
    AC5
    AN1
    AC6
    AC6
    AN1
    AC6
    AC6
    AN7
    AN3
    AC3'
    AO2'
    AO2'
    AC2'
    AC3'
    AC4'
    AO4'
    AO5'
    AO5'
    NO5'
    NC5'
    NC5'
    NO5'
    NC5'
    NC4'
    NC3'
    NC2'
    NC1'
    NC2'
    NO2'
    NC2'
    NC3'
    NC4'
    NO4'
    NO5'
    NO5'
    NC2'
    NC3'
    NO3'
    NC1'
    NN1
    NC2
    NC3
    NC4
    NC5
    NC6
    NC2
    NC3
    NC3
    NC7
    NC7
    NC3
    NC4
    NC5
    NN1
    AC2'
    AO2'

    AC4
    AC5
    AC6
    AN1
    *AC4
    *AC6
    AN6
    *AN6
    *AC6
    AN6
    *AN6
    *AC8
    *AC2
    *AC2
    AC2'
    AC2'
    *AC1'
    *AC2
    *AC3'
    *AC4
    *AC5
    *AC5
    NP
    NO5'
    NO5'
    NC5'
    NC4'
    NC3'
    NC2'
    NC1'
    NO4'
    NC1'
    NC2'
    *NC1'
    *NC2
    *NC3
    *NC4
    *NC5
    *NC5
    NC1'
    NC2'
    NC3'
    NN1
    NC2
    NC3
    NC4
    NC5
    NC6
    NN1
    NC3
    NC7
    NC7
    NN7
    NN7
    NC4
    NC5
    NC6
    NC2
    AO2'
    AP2

    AC5
    AC6
    AN1
    AC2
    AN3
    AN6
    AH61
    AH62
    AN6
    AH61
    AH62
    AH8
    AH2
    AO2'
    AC3'
    AC3'
    AH1'
    AH2'
    AH3'
    AH4'
    AH5'
    AH5'
    NO2
    NP
    NP
    NC4'
    NC3'
    NC2'
    NC1'
    NO4'
    NC4'
    NO4'
    NC1'
    NH1'
    NH2'
    NH3'
    NH4'
    NH5'
    NH5S
    NN1
    NC1'
    NC2'
    NC2
    NC3
    NC4
    NC5
    NC6
    NN1
    NC2
    NC7
    NO7
    NN7
    NH71
    NH72
    NH4
    NH5
    NH6
    NH2
    AP2
    AO2T

    1.3777
    1.3282
    1.3814
    1.4146
    1.4013
    1.4146
    1.3482
    0.9912
    1.4146
    1.3482
    0.9912
    1.3777
    1.3300
    1.5415
    2.0386
    0.9953
    1.3646
    1.5415
    1.5097
    1.6942
    1.5491
    1.5491
    1.4451
    1.1110
    1.1110
    1.5977
    1.4451
    1.5160
    1.5160
    1.5160
    1.5270
    1.4200
    0.9600
    1.4100
    1.5270
    1.5160
    1.5160
    1.5160
    1.5160
    1.5160
    1.4200
    0.9600
    1.5270
    1.4800
    1.3150
    1.3500
    1.3600
    1.3600
    1.3500
    1.3150
    1.3500
    1.3500
    1.2300
    1.2300
    1.3500
    1.3600
    1.3600
    1.2199
    0.0000
    0.0000

    105.34
    0.11
    103.21 -179.92
    130.78 -179.94
    117.85 -0.14
    105.06 -179.67
    117.85 179.89
    119.69 -0.39
    116.60 -179.02
    117.85 179.89
    119.69 -0.39
    116.60 -179.02
    114.01 -179.37
    129.42 179.97
    117.82 -145.06
    31.12 -93.63
    99.36 -93.63
    120.77 -114.99
    117.82 108.23
    93.22 117.28
    112.95 -140.26
    111.63 -123.75
    111.63 -123.75
    128.40 -49.72
    109.50 115.00
    109.50 -115.00
    128.40
    0.00
    110.10
    0.00
    108.50
    0.00
    111.00
    0.00
    105.50
    0.00
    105.00
    0.00
    110.10 180.00
    106.00 180.00
    105.00 -115.00
    105.50 115.00
    111.00 115.00
    100.64 -115.00
    110.10 -115.00
    110.10 115.00
    105.50
    0.00
    110.10 180.00
    106.00 180.00
    113.70
    0.00
    121.70
    0.00
    122.00
    0.00
    118.00
    0.00
    118.00
    0.00
    118.00
    0.00
    124.51
    0.00
    122.00
    0.00
    131.80
    0.00
    131.80
    0.00
    0.00 180.00
    0.00
    0.00
    118.00
    0.00
    118.00
    0.00
    118.00
    0.00
    119.49
    0.00
    000.00 180.00
    000.00 -39.52

    105.06
    130.78
    117.85
    118.87
    126.14
    119.69
    116.60
    116.94
    119.69
    116.60
    116.94
    126.34
    114.82
    114.13
    114.13
    114.13
    109.65
    86.44
    111.94
    57.99
    111.23
    111.23
    108.83
    128.40
    128.40
    110.10
    108.50
    111.00
    105.50
    105.00
    117.86
    105.00
    110.10
    110.10
    110.10
    110.10
    107.24
    109.50
    109.50
    113.70
    105.50
    110.10
    121.70
    122.00
    118.00
    118.00
    118.00
    124.51
    119.49
    131.80
    118.50
    113.00
    120.00
    120.00
    121.00
    119.00
    120.50
    117.50
    000.00
    000.00

    1.3782
    1.4146
    1.3482
    1.3300
    1.3648
    1.3419
    0.9912
    0.9978
    1.3419
    0.9912
    0.9978
    1.0962
    1.0928
    1.4294
    1.5097
    1.5097
    1.1105
    1.0999
    1.1110
    1.0000
    1.1111
    1.1111
    1.4636
    1.5977
    1.5977
    1.5160
    1.5160
    1.5160
    1.5270
    1.4100
    1.4712
    1.4100
    1.5270
    1.1110
    1.1110
    1.1110
    1.1110
    1.1110
    1.1110
    1.4800
    1.5270
    1.5160
    1.3150
    1.3500
    1.3600
    1.3600
    1.3500
    1.2199
    1.3150
    1.4800
    1.2300
    1.3600
    1.0000
    1.0000
    1.0900
    1.0900
    1.0900
    1.0900
    0.0000
    0.0000

    IC AO2T AO2'
    IC AO2T AO2'
    IC AH2T AO2T
    PATCH FIRST NONE
    RESI NDPH
    ide

    *AP2 AO1P
    *AP2 AO2P
    AP2
    AO2'
    LAST NONE

    0.0000 000.00 -115.82 000.00


    0.0000 000.00 115.90 000.00
    0.0000 000.00 180.00 000.00

    0.0000
    0.0000
    0.0000

    -3.00 ! C21H27N7O17P3 reduced nicotinamide adenine dinucleot


    ! NADPH, VARNAI/adm jr.
    ! from RESI NADH and 3PHO
    ! checked for consistency with new NA params, adm jr.,

    9/98
    ! note that differences with respect to published resu
    lts exist
    GROUP
    ATOM AC4'
    ATOM AH4'
    ATOM AO4'
    ATOM AC1'
    ATOM AH1'
    GROUP
    ATOM AC5
    ATOM AN7
    ATOM AC8
    ATOM AH8
    ATOM AN9
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    AN1
    AC2
    AH2
    AN3
    AC4
    AC6

    ATOM AN6
    ATOM AH61
    ATOM AH62
    GROUP
    ATOM AC2'
    ATOM AH2'
    ATOM AO2'
    ATOM AP2
    ATOM AO1P
    ATOM AO2P
    ATOM AO2T
    ATOM AH2T
    GROUP
    ATOM AC3'
    ATOM AH3'
    ATOM AO3'
    ATOM AH3T
    GROUP
    ATOM AC5'
    ATOM AH5'
    ATOM AH5S
    ATOM AP
    ATOM AO1
    ATOM AO2
    ATOM AO5'

    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    0.11
    0.09
    -0.40
    0.11
    0.09

    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51

    0.28
    -0.71
    0.34
    0.12
    -0.05

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64

    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46

    NG2S3
    HGP4
    HGP4

    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG303
    PG1
    OG2P1
    OG2P1
    OG311
    HGP1

    0.01
    0.09
    -0.62
    1.50
    -0.82
    -0.82
    -0.67
    0.33

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2
    PG2
    OG2P1
    OG2P1
    OG303

    -0.08
    0.09
    0.09
    1.50
    -0.82
    -0.82
    -0.62

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    due to new NA params


    AH61 AH62
    \ /
    AN6
    |
    AC6
    // \
    AN1 AC5--AN7\\
    |
    ||
    AC8-AH8
    AC2 AC4--AN9/
    / \\ /
    \
    AH2 AN3
    \
    \
    \
    \
    NO1
    AO1
    AH5sAH4' AO4' \
    |
    |
    |
    \ / \ \
    NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
    \ |
    |
    |
    \
    / \
    \ NO2
    AO2
    AH5' AC3'-AC2' AH1'
    \
    / \ / \
    \
    AO3' AH3'AO2'AH2'
    \
    |
    |
    \
    AH3T AO1P=AP2==AO2P (-)
    \
    |
    NH71
    \
    AH2T-AO2T /
    \
    NH72-NN7 NH4 NH42
    \
    \
    \ /
    \
    NC7 NC4
    \
    / \ / \
    \
    NO7 NC3 NC5-NH5
    \
    ||
    ||
    \ NH5s NH4'NO4'
    NH2-NC2 NC6-NH6
    \ |
    \ / \
    \ /
    NC5'--NC4' NC1'---------NN1
    |
    \
    / \
    NH5' NC3'-NC2'NH1'
    / \ / \
    NO3' NH3'NO2'NH2'
    |
    |
    NH3T
    NH2T

    ATOM O3 OG303
    -0.68
    ATOM NP PG2
    1.50
    ATOM NO1 OG2P1
    -0.82
    ATOM NO2 OG2P1
    -0.82
    ATOM NO5' OG303
    -0.62
    ATOM NC5' CG321
    -0.08
    ATOM NH5S HGA2
    0.09
    ATOM NH5' HGA2
    0.09
    GROUP
    ATOM NC2' CG3C51
    0.14
    ATOM NH2' HGA1
    0.09
    ATOM NO2' OG311
    -0.65
    ATOM NH2T HGP1
    0.42
    GROUP
    ATOM NC3' CG3C51
    0.14
    ATOM NH3' HGA1
    0.09
    ATOM NO3' OG311
    -0.65
    ATOM NH3T HGP1
    0.42
    GROUP
    ATOM NC1' CG3C51
    0.11
    ATOM NH1' HGA1
    0.09
    ATOM NC4' CG3C51
    0.11
    ATOM NH4' HGA1
    0.09
    ATOM NO4' OG3C51 -0.40
    GROUP
    ATOM NN1 NG301
    -0.27 !N2
    ATOM NC6 CG2D1O -0.06 !C3
    ATOM NH6 HGA4
    0.17 !H4
    ATOM NC5 CG2D1
    -0.18 !C5
    ATOM NH5 HGA4
    0.14 !H6
    ATOM NC4 CG321
    -0.28 !C7
    ATOM NH4 HGA2
    0.09 !H8
    ATOM NH42 HGA2
    0.09 !H17
    ATOM NC3 CG2DC1
    0.36 !C9
    ATOM NC2 CG2D1O -0.10 !C10
    ATOM NH2 HGA4
    0.14 !H11
    ATOM NC7 CG2O1
    0.55 !C12
    ATOM NO7 OG2D1
    -0.51 !O13
    ATOM NN7 NG2S2
    -0.72 !N14
    ATOM NH71 HGP1
    0.26 !H15 ! trans to amide O
    ATOM NH72 HGP1
    0.32 !H16 ! cis to amide O
    BOND AN1 AC2
    AN3 AC4
    AC5 AC6
    BOND AC6 AN6
    AC5 AN7
    AC8 AN9
    BOND AN9 AC4
    AC2 AH2
    AN6 AH61
    AN6 AH62
    DOUBLE AC6 AN1
    AC2 AN3
    AC4 AC5
    AN7 AC8
    BOND AN9 AC1'
    AC1' AC2'
    AC2' AC3'
    AC3' AC4'
    BOND AO4' AC1'
    AC1' AH1'
    AC2' AO2'
    AO2' AP2
    BOND AC3' AH3'
    AC3' AO3'
    AO3' AH3T
    AC4' AH4'
    BOND AC5' AH5S
    AC5' AH5'
    AC5' AO5'
    AO5' AP
    BOND AP AO2
    AP O3
    O3 NP
    NP NO1
    BOND NP NO5'
    NO5' NC5'
    NC5' NH5S
    NC5' NH5'
    BOND NC4' NO4'
    NO4' NC1'
    NC1' NC2'
    NC2' NC3'
    BOND NC1' NH1'
    NC2' NH2'
    NC2' NO2'
    NO2' NH2T
    BOND NC3' NO3'
    NO3' NH3T
    NC4' NH4'
    NC1' NN1
    BOND NC3 NC4
    NC5 NC6
    BOND NC2 NH2
    NC3 NC7
    NC7 NO7
    NC7 NN7
    BOND NN7 NH72
    NC4 NH4
    NC4 NH42
    NC5 NH5
    BOND AP2 AO1P
    AP2 AO2P
    AP2 AO2T
    AO2T AH2T
    DOUBLE NC2 NC3
    NC4 NC5
    NC6 NN1
    ! adenine impropers

    AC8 AH8
    AC4'
    AC2'
    AC4'
    AP
    NP
    NC5'
    NC3'
    NC3'
    NN1

    AO4'
    AH2'
    AC5'
    AO1
    NO2
    NC4'
    NC4'
    NH3'
    NC2

    NN7 NH71
    NC6 NH6

    IMPR AN6 AC6


    AH61 AH62
    ! amide impropers
    IMPR NC7 NN7 NC3 NO7
    IMPR NN7 NC7 NH71 NH72
    ! ring hydrogen impropers
    IMPR NC6 NN1 NC5 NH6
    IMPR NC2 NC3 NN1 NH2
    DONO AH61 AN6
    DONO AH62 AN6
    DONO AH3T AO3'
    ACCE AN1
    ACCE AN3
    ACCE AN7
    ACCE AO4'
    ACCE AO3'
    ACCE AO5'
    ACCE AO1 AP
    ACCE AO2 AP
    ACCE O3
    ACCE NO1 NP
    ACCE NO2 NP
    ACCE NO5'
    ACCE NO4'
    ACCE NO3'
    ACCE NO2'
    ACCE NO7
    DONO NH2T NO2'
    DONO NH3T NO3'
    DONO NH71 NN7
    DONO NH72 NN7
    DONO AH2T AO2T
    ACCE AO2T
    ACCE AO1P
    ACCE AO2P
    ACCE AO2'
    ! IC table was beyond repair
    IC AP
    O3
    NP
    NO5'
    IC AP
    O3
    NP
    NO1
    IC AP
    O3
    NP
    NO2
    IC NP
    O3
    AP
    AO5'
    IC O3
    AO5' *AP
    AO1
    IC O3
    AO5' *AP
    AO2
    IC O3
    AP
    AO5' AC5'
    IC AP
    AO5' AC5' AC4'
    IC AC4' AO5' *AC5' AH5'
    IC AC4' AO5' *AC5' AH5S
    IC AO5' AC5' AC4' AC3'
    IC AC5' AC4' AC3' AO3'
    IC AH3T AO3' AC3' AC4'
    IC AO4' AC3' *AC4' AC5'
    IC AC2' AC4' *AC3' AO3'
    IC AC4' AC3' AC2' AC1'
    IC AC3' AC2' AC1' AN9
    IC AO4' AC1' AN9
    AC4
    IC AC1' AC4
    *AN9 AC8
    IC AC4
    AN9
    AC8
    AN7
    IC AC8
    AN9
    AC4
    AC5
    IC AC8
    AN7
    AC5
    AC6
    IC AN7
    AC5
    AC6
    AN1
    IC AC5
    AC6
    AN1
    AC2

    AC6

    AN1

    AC5

    AN6

    NC7
    NN7

    NC3
    NC7

    NN7 NO7
    NH72 NH71

    NC5

    NC6

    NC4

    NH5

    ==> replaced (kevo)


    1.5954 101.60 146.76
    1.5954 101.60 37.78
    1.5954 101.60 -103.74
    1.6061 101.60 164.74
    1.5954 96.46 -112.08
    1.5954 96.46 120.37
    1.5954 96.46 -55.54
    1.6655 115.61 -176.43
    1.5479 112.56 120.22
    1.5479 112.56 -120.20
    1.4409 112.56 51.86
    1.5479 114.73 138.72
    0.9769 98.08 131.19
    1.4383 107.54 -123.87
    1.5457 105.32 -117.01
    1.5409 105.32 -20.11
    1.5457 102.83 133.28
    1.4312 106.95 -116.73
    1.4587 127.46 -179.84
    1.3677 106.79
    0.68
    1.3782 106.79 -0.37
    1.3348 103.19 179.17
    1.3939 132.19 -179.58
    1.4074 119.12 -0.76

    97.71
    120.83
    108.35
    96.46
    103.67
    104.32
    115.61
    112.56
    110.27
    110.70
    114.73
    111.81
    111.81
    114.73
    111.81
    102.83
    112.16
    127.46
    106.79
    113.34
    105.46
    132.19
    119.12
    119.15

    1.6612
    1.5331
    1.5264
    1.6655
    1.5327
    1.5300
    1.4409
    1.5479
    1.1161
    1.1158
    1.5409
    1.4297
    1.5409
    1.5479
    1.4297
    1.5465
    1.4587
    1.3677
    1.3782
    1.3348
    1.3976
    1.4074
    1.3630
    1.3635

    IC AN9
    AC5
    IC AC5
    AN1
    IC AN1
    AC6
    IC AH61 AC6
    IC AN9
    AN7
    IC AN1
    AN3
    IC AO4' AC2'
    IC AC1' AC3'
    IC AC2' AC4'
    IC AC3' AO4'
    IC NC5' NO5'
    IC NP
    NO5'
    IC NO5' NC5'
    IC NC5' NC4'
    IC NC4' NC3'
    IC NC3' NC2'
    IC NO2' NC2'
    IC NH2T NO2'
    IC NO4' NC2'
    IC NC1' NC3'
    IC NC2' NC4'
    IC NC3' NO4'
    IC NC4' NO5'
    IC NC4' NO5'
    IC NC3' NC2'
    IC NO3' NC3'
    IC NH3T NO3'
    IC NC2' NC1'
    IC NC1' NN1
    IC NN1
    NC2
    IC NC2
    NC3
    IC NC3
    NC4
    IC NN1
    NC2
    IC NC2
    NC3
    IC NC2
    NC3
    IC NO7
    NC7
    IC NO7
    NC7
    IC NC2
    NC3
    IC NC2
    NC3
    IC NC3
    NC4
    IC NC4
    NC5
    IC NC6
    NN1
    IC AC1' AC3'
    IC AC3' AC2'
    IC AC2' AO2'
    IC AO2T AO2'
    IC AO2T AO2'
    IC AO2' AP2
    PATCH FIRST NONE

    *AC4 AN3
    *AC6 AN6
    AN6
    AH61
    *AN6 AH62
    *AC8 AH8
    *AC2 AH2
    *AC1' AH1'
    *AC2' AH2'
    *AC3' AH3'
    *AC4' AH4'
    NP
    NO2
    NC5' NC4'
    NC4' NC3'
    NC3' NC2'
    NC2' NC1'
    NC1' NO4'
    NC1' NO4'
    NC2' NC1'
    *NC1' NH1'
    *NC2 NH2'
    *NC3 NH3'
    *NC4 NH4'
    *NC5 NH5'
    *NC5 NH5S
    NC1' NN1
    NC2' NC1'
    NC3' NC2'
    NN1
    NC2
    NC2
    NC3
    NC3
    NC4
    NC4
    NC5
    NC5
    NC6
    NC3
    NC7
    NC7
    NO7
    NC7
    NN7
    NN7
    NH71
    NN7
    NH72
    NC4
    NH4
    NC4
    NH42
    NC5
    NH5
    NC6
    NH6
    NC2
    NH2
    *AC2' AO2'
    AO2' AP2
    AP2
    AO2T
    *AP2 AO1P
    *AP2 AO2P
    AO2T AH2T
    LAST NONE

    1.3677
    1.4074
    1.3630
    0.9983
    1.3782
    1.3635
    1.4312
    1.5465
    1.5457
    1.5409
    1.4347
    1.6612
    1.4347
    1.5645
    1.5406
    1.5383
    1.4360
    0.9842
    1.4444
    2.4561
    4.7358
    6.4975
    5.2257
    5.2257
    1.5383
    1.4402
    0.9765
    1.5383
    1.4868
    1.3589
    1.3767
    1.5415
    1.3589
    1.3767
    1.3767
    1.2364
    1.2364
    1.3767
    1.3767
    1.5415
    1.5185
    1.3587
    1.5465
    1.5457
    1.4465
    1.5606
    1.5606
    1.5853

    105.46
    119.12
    117.19
    119.41
    113.34
    125.66
    109.65
    102.83
    105.32
    107.54
    124.65
    124.65
    115.34
    114.08
    100.78
    100.30
    117.19
    100.86
    104.62
    9.02
    22.19
    19.19
    29.02
    29.02
    100.30
    112.92
    102.62
    113.54
    119.27
    123.90
    118.97
    111.44
    123.90
    117.98
    117.98
    120.30
    120.30
    118.97
    118.97
    111.44
    122.41
    120.94
    102.83
    111.15
    121.36
    103.37
    103.37
    103.37

    179.47
    -178.70
    175.38
    -173.82
    -179.89
    -177.12
    -115.54
    118.17
    120.87
    -117.93
    -95.76
    -102.77
    72.35
    -96.03
    -41.51
    39.58
    163.91
    159.27
    -113.82
    118.36
    -3.45
    -28.86
    -4.03
    51.20
    157.86
    77.43
    77.94
    116.11
    179.46
    5.63
    -6.62
    4.92
    -157.15
    -162.23
    18.92
    -176.87
    1.04
    -136.44
    108.13
    -151.27
    178.77
    176.28
    -119.62
    -174.33
    -92.28
    -113.56
    109.47
    81.16

    !toppar_amines.str
    RESI AMM1
    0.00 ! NH3 Ammonia
    GROUP
    ATOM N1 NG331 -1.125
    ATOM H11 HGPAM3 0.375
    ATOM H12 HGPAM3 0.375
    ATOM H13 HGPAM3 0.375
    BOND N1 H11 N1 H12 N1 H13
    IC H11 H12 *N1 H13
    0.0 0.0 120.

    0.0 0.0

    125.74
    117.19
    119.41
    118.04
    124.72
    116.89
    110.14
    107.40
    111.10
    106.34
    105.77
    115.34
    114.08
    100.78
    100.30
    104.62
    104.62
    117.19
    109.33
    26.48
    17.84
    1.80
    10.68
    19.04
    113.54
    100.30
    112.92
    119.27
    123.90
    118.97
    111.44
    122.41
    117.98
    120.57
    119.12
    120.26
    117.08
    113.82
    105.93
    117.50
    119.10
    116.55
    111.15
    121.36
    103.37
    111.24
    111.16
    108.83

    1.3491
    1.3459
    0.9983
    0.9911
    1.0924
    1.0924
    1.1011
    1.1056
    1.0996
    1.1019
    1.5264
    1.5645
    1.5406
    1.5383
    1.5383
    1.4444
    1.4444
    1.5383
    1.1012
    3.8155
    6.8914
    7.1052
    6.4109
    5.7156
    1.4868
    1.5383
    1.5383
    1.3589
    1.3767
    1.5415
    1.5185
    1.3553
    1.5220
    1.2364
    1.3682
    0.9992
    0.9956
    1.1070
    1.1113
    1.0907
    1.0963
    1.0900
    1.4465
    1.5853
    1.5606
    1.4737
    1.4708
    0.9674

    IC H13 H11 *N1 H12


    to enable seeding.

    0.0

    0.0

    120.

    0.0 0.0 !redundant definition needed

    RESI MAM1
    0.00 !
    GROUP
    ATOM N1 NG321 -0.99 !
    ATOM C1 CG3AM2 -0.06 !
    ATOM HN1 HGPAM2 0.39 !
    ATOM HN2 HGPAM2 0.39 !
    ATOM HC1 HGAAM2 0.09 !
    ATOM HC2 HGAAM2 0.09 !
    ATOM HC3 HGAAM2 0.09 !
    BOND N1 C1 N1 HN1 N1
    BOND C1 HC1 C1 HC2 C1
    IC N1 HC1 *C1 HC2 0.00
    IC N1 HC1 *C1 HC3 0.00
    IC HC1 C1 N1 HN1 0.00
    IC C1 HN1 *N1 HN2 0.00

    CH5N methylamine

    RESI DMAM
    0.00 !
    GROUP
    ATOM N1 NG311 -0.82 !
    ATOM HN1 HGPAM1 0.40 !
    ATOM C1 CG3AM1 -0.06 !
    ATOM C2 CG3AM1 -0.06 !
    ATOM H11 HGAAM1 0.09 !
    ATOM H12 HGAAM1 0.09 !
    ATOM H13 HGAAM1 0.09 !
    ATOM H21 HGAAM1 0.09 !
    ATOM H22 HGAAM1 0.09 !
    ATOM H23 HGAAM1 0.09 !
    BOND N1 HN1 N1 C1 N1
    BOND C1 H11 C1 H12 C1
    BOND C2 H21 C2 H22 C2
    IC C1 N1 C2 H21 0.00
    IC N1 H21 *C2 H22 0.00
    IC N1 H21 *C2 H23 0.00
    IC C1 C2 *N1 HN1 0.00
    IC C2 N1 C1 H11 0.00
    IC N1 H11 *C1 H12 0.00
    IC N1 H11 *C1 H13 0.00

    C2H7N dimethylamine

    RESI TMAM
    GROUP
    ATOM N1 NG301
    ATOM C1 CG3AM0
    ATOM C2 CG3AM0
    ATOM C3 CG3AM0
    ATOM H11 HGAAM0
    ATOM H12 HGAAM0
    ATOM H13 HGAAM0
    ATOM H21 HGAAM0
    ATOM H22 HGAAM0
    ATOM H23 HGAAM0
    ATOM H31 HGAAM0
    ATOM H32 HGAAM0
    ATOM H33 HGAAM0
    BOND N1 C1 N1
    BOND C1 H11 C1
    BOND C2 H21 C2

    C3H9N trimethylamine, adm jr.


    H31 H32
    \ /
    H11
    C3-H33
    \
    /
    H12-C1---N1
    /
    \
    H13
    C2-H23
    / \
    H21 H22

    0.00 !
    !
    -0.63 !
    -0.06 !
    -0.06 !
    -0.06 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    0.09 !
    C2 N1
    H12 C1
    H22 C2

    HC1

    HN1
    \
    /
    HC2-C1---N1
    /
    \
    HC3
    HN2
    HN2
    HC3
    0.00
    0.00
    0.00
    0.00

    120.0
    -120.0
    180.0
    120.0

    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0

    H11

    HN1
    \
    /
    H12-C1---N1
    /
    \
    H13
    C2-H23
    / \
    H21 H22
    C2
    H13
    H23
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C3
    H13
    H23

    180.0
    120.0
    -120.0
    120.0
    180.0
    120.0
    -120.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    BOND C3
    IC C1
    IC C2
    IC N1
    IC N1
    IC C1
    IC N1
    IC N1
    IC C1
    IC N1
    IC N1

    H31
    C2
    N1
    H11
    H11
    N1
    H21
    H21
    N1
    H31
    H31

    C3
    *N1
    C1
    *C1
    *C1
    C2
    *C2
    *C2
    C3
    *C3
    *C3

    H32
    C3
    H11
    H12
    H13
    H21
    H22
    H23
    H31
    H32
    H33

    C3
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H33
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0

    !toppar_prot_na_all.str
    RESI PPH1
    -1.00 ! C6H6O4P phenol-phosphate residue
    GROUP
    ATOM CG CG2R61 -0.115 !
    ATOM HG HGR61
    0.115 !
    HD1 HE1
    GROUP
    !
    |
    |
    ATOM CD1 CG2R61 -0.115 !
    CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    //
    \\
    GROUP
    !
    HG--CG
    CZ--OH
    O2-H2
    ATOM CD2 CG2R61 -0.115 !
    \ __ /
    \ /
    ATOM HD2 HGR61
    0.115 !
    CD2--CE2
    P1 (-)
    GROUP
    !
    |
    |
    // \\
    ATOM CE1 CG2R61 -0.21 !
    HD2 HE2 O4
    O3
    ATOM HE1 HGR61
    0.21 !
    GROUP
    ATOM CE2 CG2R61 -0.21
    ATOM HE2 HGR61
    0.21
    GROUP
    ATOM CZ CG2R61 -0.16
    ATOM OH OG303 -0.36
    ATOM P1 PG1
    1.40
    ATOM O2 OG311 -0.75
    ATOM H2 HGP1
    0.39
    ATOM O3 OG2P1 -0.76
    ATOM O4 OG2P1 -0.76
    BOND
    BOND
    BOND
    BOND
    BOND

    CG
    CE1
    CG
    P1
    O2

    CD1
    CZ
    HG
    OH
    H2

    ! IC table
    IC CD2 CG
    IC CD1 CG
    IC CG CD1
    IC CD1 CD2
    IC CE1 CG
    IC CE2 CG
    IC CZ CD1
    IC CZ CD2
    IC CE2 CE1
    IC CE1 CZ
    IC CZ OH
    IC O2 OH
    IC O2 OH
    IC OH P1

    CG
    CE2
    CD1
    P1

    CD1
    CD2
    CE1
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    OH
    P1
    *P1
    *P1
    O2

    CE1
    CE2
    CZ
    HG
    HD1
    HD2
    HE1
    HE2
    OH
    P1
    O2
    O3
    O4
    H2

    CD2
    CZ
    HD1
    O2

    CD1
    CZ
    CD2
    P1

    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3800
    1.5800
    1.5800
    1.6100

    CE1
    OH
    HD2
    O3

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    108.00
    108.00
    108.00

    CD2 CE2
    CE1 HE1 CE2 HE2
    P1 O4

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    300.00
    120.00
    -120.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    108.00
    103.00
    103.00
    115.00

    1.3750
    1.3750
    1.3750
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.3800
    1.6100
    1.5800
    1.4800
    1.4800
    0.9600

    RESI BMPH
    -1.00 ! C7H8O3P Benz.methylene phosphate
    GROUP
    ATOM CG CG2R61 -0.115 !
    HD1 HE1
    ATOM HG HGR61
    0.115 !
    |
    |
    GROUP
    !
    CD1--CE1 HH1
    O2-H2
    ATOM CD1 CG2R61 -0.115 !
    //
    \\
    \
    /
    ATOM HD1 HGR61
    0.115 ! HG--CG
    CZ---CH---P1 (-)
    GROUP
    !
    \ __ /
    / //\\
    ATOM CD2 CG2R61 -0.115 !
    CD2--CE2 HH2 O4 O3
    ATOM HD2 HGR61
    0.115 !
    |
    |
    GROUP
    !
    HD2 HE2
    ATOM CE1 CG2R61 -0.21
    ATOM HE1 HGR61
    0.24
    ATOM CE2 CG2R61 -0.21
    ATOM HE2 HGR61
    0.24
    ATOM CZ CG2R61 -0.44
    ATOM CH CG321 -0.18
    ATOM HH1 HGA2
    0.09
    ATOM HH2 HGA2
    0.09
    ATOM P1 PG1
    1.53
    ATOM O2 OG311 -0.79
    ATOM H2 HGP1
    0.36
    ATOM O3 OG2P1 -0.86
    ATOM O4 OG2P1 -0.86
    ! NA ATOM TYPE
    BOND CG CD1
    CG CD2 CD1 CE1 CD2 CE2
    BOND CE1 CZ
    CE2 CZ
    CZ CH
    BOND CG HG
    CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2
    BOND CH HH1
    CH HH2 CH P1
    P1 O2 P1 O3
    BOND P1 O4
    O2 H2
    ! IC table
    IC CD2 CG CD1 CE1
    1.3750 120.00
    0.00 120.00 1.3750
    IC CD1 CG CD2 CE2
    1.3750 120.00
    0.00 120.00 1.3750
    IC CG CD1 CE1 CZ
    1.3750 120.00
    0.00 120.00 1.3750
    IC CE2 CE1 *CZ CH
    1.3750 120.00 180.00 122.30 1.4900
    IC CD1 CD2 *CG HG
    1.3750 120.00 180.00 120.00 1.0800
    IC CE1 CG *CD1 HD1
    1.3750 120.00 180.00 120.00 1.0800
    IC CE2 CG *CD2 HD2
    1.3750 120.00 180.00 120.00 1.0800
    IC CZ CD1 *CE1 HE1
    1.3750 120.00 180.00 120.00 1.0800
    IC CZ CD2 *CE2 HE2
    1.3750 120.00 180.00 120.00 1.0800
    IC CE1 CZ CH P1
    1.3750 122.30 270.00 111.00 1.8800
    IC P1 CZ *CH HH1
    1.8800 111.00 120.00 107.50 1.1110
    IC HH1 CZ *CH HH2
    1.1110 107.50 -120.00 107.50 1.1110
    IC CZ CH P1 O2
    1.4900 111.00 180.00 93.00 1.5800
    IC O2 CH *P1 O3
    1.5800 93.00 120.00 103.00 1.4800
    IC O2 CH *P1 O4
    1.5800 93.00 -120.00 103.00 1.4800
    IC CH P1 O2 H2
    1.8800 93.00 120.00 115.00 0.9600
    RESI BMPD
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1

    -2.00 ! C7H7O3P Benz.methyl phosphate dianionic


    CG2R61 -0.115 !
    HD1 HE1
    HGR61
    0.115 !
    |
    |
    !
    CD1--CE1 HH1
    O2
    CG2R61 -0.115 !
    //
    \\
    \
    /
    HGR61
    0.115 ! HG--CG
    CZ---CH---P1 (-2)
    !
    \ __ /
    / //\\
    CG2R61 -0.115 !
    CD2--CE2 HH2 O4 O3
    HGR61
    0.115 !
    |
    |
    HD2 HE2
    CG2R61 -0.24

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    BOND
    BOND
    ! IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HE1 HGR61
    CE2 CG2R61
    HE2 HGR61
    CZ CG2R61
    CH CG321
    HH1 HGA2
    HH2 HGA2
    P1 PG1
    O2 OG2P1
    O3 OG2P1
    O4 OG2P1
    CG CD1
    CE1 CZ
    CG HG
    CH HH1
    P1 O4
    table

    CE1
    CZ
    O2
    O2
    O2
    CD1
    HD1
    CG
    HG
    CD2
    HD2
    CE2
    HH1
    HH2
    HE1
    HE2

    RESI BDFP
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM CF
    ATOM F1
    ATOM F2
    ATOM P1
    ATOM O2
    ATOM H2
    ATOM O3
    ATOM O4

    CZ
    CH
    CH
    CH
    CH
    CE1
    CD1
    CD1
    CG
    CG
    CD2
    CD2
    CH
    CH
    CE1
    CE2

    CH
    P1
    *P1
    *P1
    *P1
    CZ
    CG
    CE1
    CD1
    CD1
    CG
    CG
    P1
    P1
    CD1
    CD2

    0.26
    -0.24
    0.26
    -0.45
    -0.28
    0.09
    0.09
    1.90
    -1.13
    -1.13
    -1.13
    CG CD2
    CE2 CZ
    CD1 HD1
    CH HH2

    P1
    O2
    O3
    O3
    O4
    CH
    CD2
    CZ
    CE1
    CE1
    HG
    CD1
    O3
    O3
    HD1
    HD2

    CD1
    CZ
    CD2
    CH

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    CE1
    CH
    HD2
    P1

    CD2 CE2

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    CE1 HE1 CE2 HE2


    P1 O2 P1 O3

    90.00
    180.00
    -115.82
    -115.82
    115.90
    180.00
    180.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00

    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00
    000.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -1.00 ! C7H6F2O3P Benz.difluor.phosphate


    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG312
    FGA2
    FGA2
    PG1
    OG311
    HGP1
    OG2P1
    OG2P1

    -0.21
    0.24
    -0.21
    0.24
    -0.40
    0.21
    -0.17
    -0.17
    1.43
    -0.72
    0.36
    -0.80
    -0.80

    HD1 HE1
    |
    |
    CD1--CE1
    F1
    O2-H2
    //
    \\
    \
    /
    HG--CG
    CZ---CF---P1 (-)
    \ __ /
    / //\\
    CD2--CE2
    F2 O4 O3
    |
    |
    HD2 HE2

    BOND CG CD1 CG CD2


    BOND CE1 CZ
    CE2 CZ
    BOND CG HG
    CD1 HD1
    BOND CF F1
    CF F2
    BOND P1 O4
    O2 H2
    ! IC table
    IC CD2 CG CD1 CE1
    IC CD1 CG CD2 CE2
    IC CG CD1 CE1 CZ
    IC CE2 CE1 *CZ CF
    IC CD1 CD2 *CG HG
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 HD2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 HE2
    IC CE1 CZ CF P1
    IC P1 CZ *CF F1
    IC F1 CZ *CF F2
    IC CZ CF P1 O2
    IC O2 CF *P1 O3
    IC O2 CF *P1 O4
    IC CF P1 O2 H2
    RESI BDFD
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM CF
    ATOM F1
    ATOM F2
    ATOM P1
    ATOM O2
    ATOM O3
    ATOM O4
    BOND
    BOND
    BOND
    BOND
    BOND

    CG
    CE1
    CG
    CF
    P1

    CD1
    CZ
    CD2
    CF
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.8800
    1.3530
    1.4500
    1.5800
    1.5800
    1.8800

    CE1 CD2 CE2


    CF
    HD2 CE1 HE1 CE2 HE2
    P1 P1 O2 P1 O3
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    115.00
    118.00
    115.00
    86.00
    86.00
    86.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    270.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    115.00
    118.00
    118.00
    86.00
    95.00
    95.00
    115.00

    1.3750
    1.3750
    1.3750
    1.4500
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.8800
    1.3530
    1.3530
    1.5800
    1.4800
    1.4800
    0.9600

    -2.00 ! C7H5F2O3P Benz.difluor.phosphate dianionic, chris


    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !

    HD1 HE1
    |
    |
    CD1--CE1
    F1
    O2
    //
    \\
    \
    /
    HG--CG
    CZ---CF---P1
    (-2)
    \ __ /
    / //\\
    CD2--CE2
    F2 O4 O3
    |
    |
    HD2 HE2

    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG312
    FGA2
    FGA2
    PG1
    OG2P1
    OG2P1
    OG2P1
    CD1
    CZ
    HG
    F1
    O4

    ! IC table
    IC CD2 CG
    IC CD1 CG
    IC CG CD1
    IC CE2 CE1
    IC CD1 CD2
    IC CE1 CG

    -0.24
    0.26
    -0.24
    0.26
    -0.36
    0.24
    -0.28
    -0.28
    2.00
    -1.12
    -1.12
    -1.12
    CG
    CE2
    CD1
    CF

    CD1
    CD2
    CE1
    *CZ
    *CG
    *CD1

    CE1
    CE2
    CZ
    CF
    HG
    HD1

    CD2
    CZ
    HD1
    F2

    CD1
    CZ
    CD2
    CF

    CE1 CD2 CE2


    CF
    HD2 CE1 HE1 CE2 HE2
    P1 P1 O2 P1 O3

    1.3750
    1.3750
    1.3750
    1.3750
    1.3750
    1.3750

    120.00
    0.00 120.00
    120.00
    0.00 120.00
    120.00
    0.00 120.00
    120.00 180.00 120.00
    120.00 180.00 120.00
    120.00 180.00 120.00

    1.3750
    1.3750
    1.3750
    1.4500
    1.0800
    1.0800

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CE2
    CZ
    CZ
    CE1
    P1
    F1
    CZ
    O2
    O2

    CG
    CD1
    CD2
    CZ
    CZ
    CZ
    CF
    CF
    CF

    *CD2
    *CE1
    *CE2
    CF
    *CF
    *CF
    P1
    *P1
    *P1

    HD2
    HE1
    HE2
    P1
    F1
    F2
    O2
    O3
    O4

    1.3750
    1.3750
    1.3750
    1.3750
    1.8800
    1.3530
    1.4500
    1.4800
    1.4800

    120.00
    120.00
    120.00
    120.00
    115.00
    118.00
    115.00
    95.00
    95.00

    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    115.00
    118.00
    118.00
    95.00
    95.00
    95.00

    1.0800
    1.0800
    1.0800
    1.8800
    1.3530
    1.3530
    1.4800
    1.4800
    1.4800

    RESI EP_2
    -2.00 ! C2H5O4P Ethylphosphate, dianionic
    !test CT3-CT2-ON2-P dihedral without complications from phosphate proton
    GROUP
    !
    H21
    ATOM P1 PG1
    1.10 !
    |
    ATOM O1 OG303 -0.40 !
    H23--C2--H22
    ATOM O2 OG2P1 -0.90 !
    |
    ATOM O3 OG2P1 -0.90 !
    H11--C1--H12
    ATOM O4 OG2P1 -0.90 !
    |
    GROUP
    !
    O1
    ATOM C1 CG321 -0.18 !
    |
    ATOM H11 HGA2
    0.09 !
    (-) O4==P1==O3 (-)
    ATOM H12 HGA2
    0.09 !
    ||
    GROUP
    !
    O2
    ATOM C2 CG331 -0.27 !
    ATOM H21 HGA3
    0.09 !
    ATOM H22 HGA3
    0.09 !
    ATOM H23 HGA3
    0.09 !
    BOND P1
    BOND C1
    BOND C2
    !
    IC C1 O1
    IC O2 O1
    IC O2 O1
    IC O2 P1
    IC P1 O1
    IC C2 O1
    IC H11 O1
    IC O1 C1
    IC H21 C1
    IC H21 C1

    O1
    H11
    H21
    P1
    *P1
    *P1
    O1
    C1
    *C1
    *C1
    C2
    *C2
    *C2

    P1
    C1
    C2
    O2
    O3
    O4
    C1
    C2
    H11
    H12
    H21
    H22
    H23

    O2
    H12
    H22

    P1
    C1
    C2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    O3
    C2
    H23
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    P1

    O4

    180.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    O1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI IP_2
    -2.00 ! C3H7O4P isopropylphosphate, dianionic
    !test CT3-CT1-ON2-P dihedral without complications from phosphate proton
    GROUP
    !
    H21
    ATOM P1 PG1
    1.10 !
    |
    ATOM O1 OG303 -0.40 !
    H23--C2--H22 H31
    ATOM O2 OG2P1 -0.90 !
    |
    /
    ATOM O3 OG2P1 -0.90 !
    H11--C1----C3--H32
    ATOM O4 OG2P1 -0.90 !
    |
    \
    GROUP
    !
    O1
    H33
    ATOM C1 CG311 -0.09 !
    |
    ATOM H11 HGA1
    0.09 !
    (-) O4==P1==O3 (-)
    !
    ||
    GROUP
    !
    O2
    ATOM C2 CG331 -0.27 !
    ATOM H21 HGA3
    0.09 !
    ATOM H22 HGA3
    0.09 !
    ATOM H23 HGA3
    0.09 !

    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM H33
    BOND P1
    BOND C1
    BOND C2
    BOND C3
    !
    IC C1 O1
    IC O2 O1
    IC O2 O1
    IC O2 P1
    IC P1 O1
    IC C2 O1
    IC C3 O1
    IC O1 C1
    IC H21 C1
    IC H21 C1
    IC O1 C1
    IC H31 C1
    IC H31 C1
    RESI SAHC
    GROUP
    ATOM N
    ATOM HT1
    ATOM HT2
    ATOM HT3
    ATOM CA
    ATOM HA
    GROUP
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CG
    ATOM HG1
    ATOM HG2
    ATOM SD
    ATOM C5'
    ATOM H5'
    ATOM H5''
    GROUP
    ATOM C
    ATOM OT1
    ATOM OT2
    GROUP
    ATOM C4'
    ATOM H4'
    ATOM O4'
    ATOM C1'
    ATOM H1'
    GROUP
    ATOM N9
    ATOM C5
    ATOM N7
    ATOM C8

    CG331
    HGA3
    HGA3
    HGA3
    O1
    H11
    H21
    H31
    P1
    *P1
    *P1
    O1
    C1
    *C1
    *C1
    C2
    *C2
    *C2
    C3
    *C3
    *C3

    !
    !
    !
    !
    !

    -0.27
    0.09
    0.09
    0.09
    P1
    C1
    C2
    C3

    O2
    C2
    H22
    H32

    O2
    O3
    O4
    C1
    C2
    C3
    H11
    H21
    H22
    H23
    H31
    H32
    H33

    P1
    C1
    C2
    C3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    O3
    C3
    H23
    H33
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    P1

    O4

    60.00
    120.00
    -120.00
    60.00
    220.00
    -120.00
    -120.00
    -60.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    O1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C14H20N6O5S S-adenosyl-homocysteine


    NG3P3
    HGP2
    HGP2
    HGP2
    CG314
    HGA1

    -0.30
    0.33
    0.33
    0.33
    0.21
    0.10

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2
    SG311
    CG321
    HGA2
    HGA2

    -0.13
    0.09
    0.09
    -0.10
    -0.13
    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.34
    -0.67
    -0.67

    CG3C51
    HGA1
    OG3C51
    CG3C51
    HGA1

    0.16
    0.09
    -0.50
    0.16
    0.09

    NG2R51
    CG2RC0
    NG2R50
    CG2R53

    -0.05
    0.28
    -0.71
    0.34

    !
    !
    (2)
    HT1
    !
    |
    /
    !(1)--CA--N--HT2 (+)
    !
    |
    \
    !
    HA
    HT3
    !
    !
    !
    !
    HB1 HG1
    H5' H4' O4' Adenine
    !
    | |
    |
    \ / \ /
    !
    (1)--CB--CG--SD--C5'----C4' C1'-H1'
    !
    | |
    |
    |
    |
    !
    HB2 HG2
    H5'' H3'-C3'--C2'-H21'
    ! kevo: symmetrized
    |
    |
    !
    H3T--O3' O2'-H2'
    !
    !
    OT2(-)
    !
    /
    !(2)-C
    !
    \\
    !
    OT1

    ATOM H8
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C6
    ATOM N6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C2'
    ATOM H2''
    ATOM O2'
    ATOM H2'
    GROUP
    ATOM C3'
    ATOM H3'
    ATOM O3'
    ATOM H3T

    HGR52
    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R64
    NG2S3
    HGP4
    HGP4

    0.12
    -0.74
    0.50
    0.13
    -0.75
    0.43
    0.46
    -0.77
    0.38
    0.38

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG3C51
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    BOND C5' C4'


    C4' O4'
    BOND C1' N9
    C1' C2'
    BOND C2 N1
    C6 N6
    BOND N6 H61
    N6 H62
    BOND C2' C3'
    C2' O2'
    BOND C1' H1'
    C2' H2''
    BOND C5' H5''
    C8 H8
    BOND N CA O3' H3T
    BOND CB CA CG CB SD CG
    BOND CA HA CB HB1 CB HB2
    BOND HT1 N
    HT2 N
    HT3 N
    DOUBLE N1 C6
    C2 N3
    DOUBLE C OT1
    IMPR N6 C6 H61 H62
    IMPR OT1 CA OT2 C
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C5'
    O4'
    C2'
    C4'
    C3'
    O4'
    C1'
    C4
    C8
    C8
    N7
    C5
    N9
    C5
    N1
    H61
    C5
    N1
    H61
    N9
    N1
    C1'
    H2'

    C4'
    C3'
    C4'
    C3'
    C2'
    C1'
    C4
    N9
    N9
    N7
    C5
    C6
    C5
    N1
    C6
    C6
    N1
    C6
    C6
    N7
    N3
    C3'
    O2'

    C3'
    *C4'
    *C3'
    C2'
    C1'
    N9
    *N9
    C8
    C4
    C5
    C6
    N1
    *C4
    *C6
    N6
    *N6
    *C6
    N6
    *N6
    *C8
    *C2
    *C2'
    C2'

    O3'
    C5'
    O3'
    C1'
    N9
    C4
    C8
    N7
    C5
    C6
    N1
    C2
    N3
    N6
    H61
    H62
    N6
    H61
    H62
    H8
    H2
    O2'
    C3'

    C4' C3'
    N9 C4

    O4' C1'
    N9 C8

    C4

    C6
    O2'
    C3'
    C2

    C5 N7
    C3' O3'
    C4' H4'

    C5' H5'

    C5
    H2'
    H3'
    H2

    C5' SD C CA
    CG HG1 CG HG2
    OT2 C
    C4 C5

    1.5160
    1.4572
    1.5284
    1.5284
    1.5284
    1.5251
    1.4896
    1.376
    1.367
    0.0
    0.0
    0.0
    1.376
    1.409
    1.337
    1.01
    1.409
    1.337
    1.01
    0.0
    0.0
    1.5284
    0.9600

    C6

    N1
    116.10
    104.06
    100.16
    100.16
    101.97
    113.71
    125.97
    106.0
    106.0
    0.0
    0.0
    0.0
    105.6
    117.6
    121.2
    119.0
    117.6
    119.0
    119.0
    0.0
    0.0
    102.04
    114.97

    C5

    N7

    N3

    C8

    N6

    140.00
    -120.04
    -124.08
    -30.00
    147.80
    -97.2
    -179.94
    0.0
    0.0
    180.0
    180.0
    0.0
    -180.0
    -180.0
    0.0
    180.0
    -180.0
    0.0
    180.0
    180.0
    180.0
    -114.67
    148.63

    115.12
    116.10
    115.12
    102.04
    113.71
    125.59
    106.0
    113.6
    105.6
    0.0
    0.0
    0.0
    126.9
    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0
    110.81
    111.92

    1.4212 !delta
    1.5160
    1.4212
    1.5251 !puck
    1.4896
    1.3783 !chi
    1.367
    1.312
    1.382
    0.0
    0.0
    0.0
    1.342
    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0
    1.4212
    1.5284

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O4'
    C1'
    C2'
    C3'
    N
    CA
    HT1
    HT1
    HT1
    CB
    CB
    CG
    CG
    SD
    SD
    CB
    CG
    C4'
    C4'
    N
    OT1
    SD
    O4'
    O4'
    C5'
    C4'
    N9
    N9
    C4
    C1'
    C5
    N9
    C6
    N7
    C4
    N1
    N3
    C5
    C3'
    C3'
    C1'
    C4'

    C2'
    C3'
    C4'
    O4'
    CA
    CB
    CA
    CA
    N
    N
    N
    CA
    CA
    CB
    CB
    CG
    SD
    SD
    SD
    CA
    CA
    C5'
    C5'
    C5'
    C4'
    O4'
    O4'
    O4'
    C1'
    N9
    N9
    C4
    C4
    N9
    C5
    C5
    N1
    C6
    C1'
    C1'
    C2'
    C3'

    RESI INDO
    GROUP
    ATOM HG
    ATOM CG
    ATOM CD2
    ATOM CD1
    ATOM HD1
    ATOM NE1
    ATOM HE1
    ATOM CE2
    ATOM CE3
    ATOM HE3
    ATOM CZ2
    ATOM HZ2
    ATOM CZ3
    ATOM HZ3
    ATOM CH2

    *C1' H1'
    0.0
    *C2' H2'' 0.0
    *C3' H3'
    0.0
    *C4' H4'
    0.0
    CB
    CG
    1.4863
    CG
    SD
    1.5495
    *N
    HT2
    1.0633
    *N
    HT3
    1.0633
    CA
    CB
    1.0633
    *CA C
    1.5495
    *CA HA
    1.5495
    *CB HB1
    1.5438
    *CB HB2
    1.5438
    *CG HG1
    1.8249
    *CG HG2
    1.8249
    SD
    C5'
    1.5438
    C5' C4'
    1.8249
    *C5' H5'
    1.5403
    *C5' H5'' 1.5403
    C
    OT1
    1.4863
    *C
    OT2
    1.2492
    C4' O4'
    1.8303
    *C4' C3'
    1.4591
    *C4' H4'
    1.4591
    O4' C1'
    1.5403
    C1' N9
    1.4591
    *C1' C2'
    1.4614
    *C1' H1'
    1.4614
    *N9 C8
    1.3837
    C4
    C5
    1.4614
    *C4 N3
    1.3831
    C5
    C6
    1.3837
    *C5 N7
    1.4115
    *C8 H8
    1.3073
    C6
    N1
    1.3831
    *C6 N6
    1.3524
    *C2 H2
    1.3403
    N6
    H61
    1.4115
    *C2' O2'
    1.5132
    *C2' H2'' 1.5132
    O2' H2'
    1.5135
    O3' H3T
    1.5499

    0.0 -115.0
    0.0 115.0
    0.0 115.0
    0.0 -115.0
    111.52 -68.05
    114.80 -169.85
    98.00 113.14
    98.00 -117.28
    98.00 -136.27
    111.52 123.39
    111.52 -122.64
    114.80 125.78
    114.80 -119.31
    111.97 120.25
    111.97 -122.78
    111.97 149.65
    104.32 -59.34
    117.91 122.31
    117.91 -122.71
    106.34 -166.34
    117.88 -178.37
    117.91 169.12
    108.69 118.83
    108.69 -116.07
    108.69 133.30
    108.22 -159.13
    111.15 124.24
    111.15 -119.53
    126.86 175.00
    126.86 176.84
    105.37 179.25
    105.37 179.94
    116.97 179.52
    113.91 -179.74
    116.97 -0.21
    118.01 -179.35
    129.44 -179.97
    123.62 179.97
    95.49 115.41
    95.49 -116.10
    113.17 177.31
    116.35 167.44

    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    0.0
    114.80 1.5438
    111.97 1.8249
    109.99 1.0338
    113.48 1.0305
    111.52 1.5495
    106.34 1.5395
    109.49 1.0806
    110.22 1.1112
    106.97 1.1179
    107.22 1.1112
    110.68 1.1101
    104.32 1.8303
    117.91 1.5403
    108.22 1.1127
    108.62 1.1118
    117.88 1.2492
    117.42 1.2654
    108.69 1.4591
    122.55 1.5499
    109.38 1.1099
    108.22 1.4240
    111.15 1.4614
    102.39 1.5135
    107.46 1.1156
    127.05 1.3697
    105.37 1.3831
    128.02 1.3472
    116.97 1.4115
    110.80 1.3914
    121.60 1.0918
    118.01 1.3524
    123.62 1.3438
    115.20 1.0945
    117.15 0.9949
    113.17 1.4151
    112.79 1.1120
    109.89 0.9633
    110.25 0.9629

    0.00 ! C8H7N indole, adm jr., atm


    HGR51
    CG2R51
    CG2RC0
    CG2R51
    HGR52
    NG2R51
    HGP1
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    0.14
    -0.17
    0.11
    -0.15
    0.22
    -0.51
    0.37
    0.24
    -0.25
    0.17
    -0.27
    0.16
    -0.20
    0.14
    -0.14

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    HE3
    |
    HG
    CE3
    \
    / \\
    CG-----CD2 CZ3-HZ3
    ||
    ||
    |
    CD1
    CE2 CH2-HH2
    / \ / \ //
    HD1
    NE1 CZ2
    |
    |
    HE1 HZ2

    ATOM HH2 HGR61


    0.14
    BOND CG HG CD2 CG NE1 CD1
    BOND CZ2 CE2
    BOND CZ3 CH2 CD2 CE3 NE1 CE2
    BOND CD1 HD1 NE1 HE1 CE3 HE3
    BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
    DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
    DONOR HE1 NE1
    IC CG CD1 NE1 CE2 1.3650 110.50
    IC CD1 CG CD2 CE2 1.3650 106.40
    IC CD2 CG CD1 NE1 1.4300 106.40
    IC CE2 CG *CD2 CE3 1.3850 108.00
    IC CE2 CD2 CE3 CZ3 1.3850 110.00
    IC CD2 CE3 CZ3 CH2 1.3600 113.20
    IC CE3 CZ3 CH2 CZ2 1.3750 120.00
    IC CZ3 CD2 *CE3 HE3 1.3750 113.20
    IC CH2 CE3 *CZ3 HZ3 1.3750 120.00
    IC CZ2 CZ3 *CH2 HH2 1.3750 120.00
    IC CE2 CH2 *CZ2 HZ2 1.3600 113.20
    IC CD1 CE2 *NE1 HE1 1.3700 112.00
    IC CG NE1 *CD1 HD1 1.3650 110.50
    IC CD1 CD2 *CG HG
    1.3650 106.40
    PATCH FIRST NONE LAST NONE

    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    RESI MIND
    0.00 ! C9H9N 3-methylindole,
    GROUP
    ATOM CB CG331 -0.27
    ATOM HB1 HGA3
    0.09
    ATOM HB2 HGA3
    0.09
    ATOM HB3 HGA3
    0.09
    GROUP
    ATOM CG CG2R51 -0.03
    ATOM CD2 CG2RC0 0.11
    ATOM CD1 CG2R51 -0.15
    ATOM HD1 HGR52
    0.22
    ATOM NE1 NG2R51 -0.51
    ATOM HE1 HGP1
    0.37
    ATOM CE2 CG2RC0 0.24
    ATOM CE3 CG2R61 -0.25
    ATOM HE3 HGR61
    0.17
    ATOM CZ2 CG2R61 -0.27
    ATOM HZ2 HGR61
    0.16
    ATOM CZ3 CG2R61 -0.20
    ATOM HZ3 HGR61
    0.14
    ATOM CH2 CG2R61 -0.14
    ATOM HH2 HGR61
    0.14
    BOND CB HB1 CB HB2 CB HB3
    BOND CG CB CD2 CG NE1 CD1
    BOND CZ2 CE2
    BOND CZ3 CH2 CD2 CE3 NE1 CE2
    BOND CD1 HD1 NE1 HE1 CE3 HE3
    BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
    DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
    DONOR HE1 NE1
    IC CB CG CD1 NE1
    1.4920 127.00 180.00
    IC CG CD1 NE1 CE2
    1.3650 110.50
    0.00
    IC CD1 CG CD2 CE2
    1.3650 106.40
    0.00
    IC CD2 CB *CG CD1
    1.4300 126.70 180.00
    IC HB1 CB CG CD1
    1.1110 109.50
    0.00
    IC HB2 CB CG CD1
    1.1110 109.50 120.00

    112.00
    108.00
    110.50
    133.50
    113.20
    120.00
    120.00
    122.00
    120.00
    120.00
    120.00
    126.00
    125.00
    126.40

    1.3700
    1.3850
    1.3700
    1.3600
    1.3750
    1.3750
    1.3750
    1.0800
    1.0800
    1.0800
    1.0800
    0.9760
    1.0800
    1.0800

    adm jr., atm

    110.50
    112.00
    108.00
    127.00
    127.00
    127.00

    1.3700
    1.3700
    1.3850
    1.3650
    1.3650
    1.3650

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HB3
    CD2
    CE2
    CE2
    CD2
    CE3
    CZ3
    CH2
    CZ2
    CE2
    CD1
    CG

    CB
    CG
    CG
    CD2
    CE3
    CZ3
    CD2
    CE3
    CZ3
    CH2
    CE2
    NE1

    CG
    CD1
    *CD2
    CE3
    CZ3
    CH2
    *CE3
    *CZ3
    *CH2
    *CZ2
    *NE1
    *CD1

    CD1
    NE1
    CE3
    CZ3
    CH2
    CZ2
    HE3
    HZ3
    HH2
    HZ2
    HE1
    HD1

    1.1110
    1.4300
    1.3850
    1.3850
    1.3600
    1.3750
    1.3750
    1.3750
    1.3750
    1.3600
    1.3700
    1.3650

    109.50
    106.40
    108.00
    110.00
    113.20
    120.00
    113.20
    120.00
    120.00
    113.20
    112.00
    110.50

    240.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    127.00
    110.50
    133.50
    113.20
    120.00
    120.00
    122.00
    120.00
    120.00
    120.00
    126.00
    125.00

    RESI EIND
    0.00 ! C10H11N ethylindole, adm jr.,
    GROUP
    ATOM CA CG331 -0.27 !
    HA2
    ATOM HA1 HGA3
    0.09 !
    |
    ATOM HA2 HGA3
    0.09 ! HA1-CA-HA3
    HE3
    ATOM HA3 HGA3
    0.09 !
    |
    |
    GROUP
    ! HB1-CB-HB2
    CE3
    ATOM CB CG321 -0.18 !
    \
    / \\
    ATOM HB1 HGA2
    0.09 !
    CG-----CD2 CZ3-HZ3
    ATOM HB2 HGA2
    0.09 !
    ||
    ||
    |
    GROUP
    !
    CD1
    CE2 CH2-HH2
    ATOM CG CG2R51 -0.03 !
    / \ / \ //
    ATOM CD2 CG2RC0 0.11 !
    HD1
    NE1 CZ2
    ATOM CD1 CG2R51 -0.15 !
    |
    |
    ATOM HD1 HGR52
    0.22 !
    HE1 HZ2
    ATOM NE1 NG2R51 -0.51
    ATOM HE1 HGP1
    0.37
    ATOM CE2 CG2RC0 0.24
    ATOM CE3 CG2R61 -0.25
    ATOM HE3 HGR61
    0.17
    ATOM CZ2 CG2R61 -0.27
    ATOM HZ2 HGR61
    0.16
    ATOM CZ3 CG2R61 -0.20
    ATOM HZ3 HGR61
    0.14
    ATOM CH2 CG2R61 -0.14
    ATOM HH2 HGR61
    0.14
    BOND CA HA1 CA HA2 CA HA3
    BOND CA CB CB HB1 CB HB2
    BOND CG CB CD2 CG NE1 CD1
    BOND CZ2 CE2
    BOND CZ3 CH2 CD2 CE3 NE1 CE2
    BOND CD1 HD1 NE1 HE1 CE3 HE3
    BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
    DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
    DONOR HE1 NE1
    IC CA CB CG CD1 0.0000 0.0000 180.0000 0.0000
    IC CB CG CD1 NE1 0.0000 0.0000 180.0000 0.0000
    IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000
    IC HA1 CB *CA HA2 0.0000 0.0000 120.0000 0.0000
    IC HA1 CB *CA HA3 0.0000 0.0000 240.0000 0.0000
    IC CA CG *CB HB1 0.0000 0.0000 120.0000 0.0000
    IC CA CG *CB HB2 0.0000 0.0000 240.0000 0.0000
    IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000
    IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000
    IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000
    IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000

    1.3650
    1.3700
    1.3600
    1.3750
    1.3750
    1.3750
    1.0800
    1.0800
    1.0800
    1.0800
    0.9760
    1.0800
    atm

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC CE2 CG *CD2 CE3 0.0000


    IC CE2 CD2 CE3 CZ3 0.0000
    IC CD2 CE3 CZ3 CH2 0.0000
    IC CE3 CZ3 CH2 CZ2 0.0000
    IC CZ3 CD2 *CE3 HE3 0.0000
    IC CH2 CE3 *CZ3 HZ3 0.0000
    IC CZ2 CZ3 *CH2 HH2 0.0000
    IC CE2 CH2 *CZ2 HZ2 0.0000
    IC CD1 CE2 *NE1 HE1 0.0000
    IC CG NE1 *CD1 HD1 0.0000
    !IC CD1 CD2 *CG HG
    0.0000
    !reset default patches
    DEFA FIRS NONE LAST NONE
    RESI BFL
    GROUP
    ATOM CG1
    ATOM CG2
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ1
    ATOM HZ1
    ATOM CD3
    ATOM HD3
    ATOM CD4
    ATOM HD4
    ATOM CE3
    ATOM HE3
    ATOM CE4
    ATOM HE4
    ATOM CZ2
    ATOM HZ2
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.00 ! C12H10 biphenyl, peml.


    CG2R67
    CG2R67
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4
    CZ1

    CG2
    CD1
    CG2
    CE1
    CG2
    CE2
    CG1
    CZ1
    CZ1
    CE2
    CD1

    0.0000 180.0000 0.0000 0.0000


    0.0000 0.0000 0.0000 0.0000
    0.0000 0.0000 0.0000 0.0000
    0.0000 0.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000
    0.0000 180.0000 0.0000 0.0000

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4
    HZ1
    CG1
    CG2
    CG1
    CG1
    CG1
    CG1
    CD1
    CD1
    CD2
    CE1
    CG1

    CG1
    CE2
    CG2
    CZ2

    0.000
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    CD2
    CZ1
    CD3
    CE4

    CG1
    CZ1
    CD3
    CE4

    !
    HE1
    HD1 HD3
    HE3
    !
    \
    /
    \
    /
    !
    CE1--CD1
    CD3--CE3
    !
    /
    \
    /
    \
    ! HZ1--CZ1
    CG1---CG2
    CZ2--HZ2
    !
    \
    /
    \
    /
    !
    CE2--CD2
    CD4--CE4
    !
    /
    \
    /
    \
    !
    HE2
    HD2 HD4
    HE4

    CG2
    CE1
    CE3
    CD4

    CD2 HD2 CE1 HE1


    CD3 HD3
    CE3 HE3 CE4 HE4
    CZ2 HZ2
    CD1
    *CG1
    CD1
    *CD1
    CD2
    *CD2
    CE1
    *CE1
    *CE2
    *CZ1
    CG2

    CE1
    CD2
    CE1
    HD1
    CE2
    HD2
    CZ1
    HE1
    HE2
    HZ1
    CD4

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD4
    CG1
    CE3
    CG1
    CE4
    CG2
    CZ2
    CZ2
    CE4

    CG1
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE3

    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ2

    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    HZ2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI BF6
    -2.00 ! C16H12O6 biphenyl analog, peml.
    !KEVO: charges adjusted to reflect updated acetone L-J.
    !Resulting charges are unlikey to be good ==> re-optimize?
    GROUP
    ATOM CG1 CG2R67 0.000
    ATOM CG2 CG2R67 0.000
    ATOM CD1 CG2R61 -0.115
    ATOM HD1 HGR61
    0.115
    ATOM CD2 CG2R61 -0.115
    ATOM HD2 HGR61
    0.115
    ATOM CE1 CG2R61 -0.115
    !
    HE1
    HD1 HD3
    HE3
    ATOM HE1 HGR61
    0.115
    !
    \
    /
    \
    /
    ATOM CE2 CG2R61 -0.115
    !
    CE1--CD1
    CD3--CE3
    ATOM HE2 HGR61
    0.115
    !
    /
    \
    /
    \
    ATOM CZ1 CG2R61 0.000
    !
    SUBS--CZ1
    CG1---CG2
    CZ2--SUBS
    ATOM CD3 CG2R61 -0.115
    !
    \
    /
    \
    /
    ATOM HD3 HGR61
    0.115
    !
    CE2--CD2
    CD4--CE4
    ATOM CD4 CG2R61 -0.115
    !
    /
    \
    /
    \
    ATOM HD4 HGR61
    0.115
    !
    HE2
    HD2 HD4
    HE4
    ATOM CE3 CG2R61 -0.115
    ATOM HE3 HGR61
    0.115
    ATOM CE4 CG2R61 -0.115
    ATOM HE4 HGR61
    0.115
    ATOM CZ2 CG2R61 0.000
    GROUP
    ATOM C1
    ATOM O1
    ATOM C2
    ATOM H2
    ATOM O2A
    ATOM H2A
    ATOM O2B

    CG2O5
    OG2D3
    CG311
    HGA1
    OG311
    HGP1
    OG312

    0.38
    -0.48
    0.17
    0.09
    -0.60
    0.32
    -0.88

    GROUP
    ATOM C3
    ATOM O3
    ATOM C4
    ATOM H4
    ATOM O4A
    ATOM H4A
    ATOM O4B

    CG2O5
    OG2D3
    CG311
    HGA1
    OG311
    HGP1
    OG312

    0.38
    -0.48
    0.17
    0.09
    -0.60
    0.32
    -0.88

    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CD2
    CE1
    CE3
    CD4

    CG1
    CE2
    CD1
    CZ2
    CG2

    CG1
    CE2
    CG2
    CZ2

    CD2
    CZ1
    CD3
    CE4

    CG1
    CZ1
    CD3
    CE4

    !
    O1
    !
    //
    !Ring--C1 H2
    !
    \ /
    !
    C2--O2A--H2A
    !
    \
    !
    O2B (-)

    CG2
    CE1
    CE3
    CD4

    BOND CD1 HD1 CD2 HD2 CE1 HE1

    BOND CE2 HE2


    CD3 HD3
    BOND CD4 HD4 CE3 HE3 CE4 HE4
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CZ1
    C2
    C2
    CZ2
    C4
    C4

    C1
    H2
    O2B
    C3
    H4
    O4B

    C1 O1 C1 C2
    C2 O2A O2A H2A
    C3 O3 C3 C4
    C4 O4A O4A H4A

    IMPR C1 CZ1 C2 O1
    IMPR C3 CZ2 C4 O3
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CG2
    CE1
    CG2
    CE2
    CG1
    CZ1
    CZ1
    CD1
    CD4
    CG1
    CE3
    CG1
    CE4
    CG2
    CZ2
    CZ2
    CE2
    CE1
    C2
    CZ1
    O2A
    O2A
    C1
    CE4
    CE3
    C4
    CZ2
    O4A
    O4A
    C3

    CG2
    CG1
    CG1
    CG1
    CG1
    CD1
    CD1
    CD2
    CG1
    CG1
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE1
    CZ1
    CZ1
    C1
    C1
    C1
    C2
    CE3
    CZ2
    CZ2
    C3
    C3
    C3
    C4

    *CG1
    CD1
    *CD1
    CD2
    *CD2
    CE1
    *CE1
    *CE2
    CG2
    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ1
    C1
    *C1
    C2
    *C2
    *C2
    O2A
    *CZ2
    C3
    *C3
    C4
    *C4
    *C4
    O4A

    CD2
    CE1
    HD1
    CE2
    HD2
    CZ1
    HE1
    HE2
    CD4
    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    C1
    C2
    O1
    O2A
    O2B
    H2
    H2A
    C3
    C4
    O3
    O4A
    O4B
    H4
    H4A

    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00
    120.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00

    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    -60.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    -60.00
    120.00
    -120.00
    180.00

    RESI BF7
    -2.00 ! C16H8O6 biphenyl analog, peml.
    !KEVO: charges adjusted to reflect updated acetone L-J.
    !Resulting charges are probably not that bad.
    GROUP
    ATOM CG1 CG2R67 0.00 !
    ATOM CG2 CG2R67 0.00 !
    GROUP
    !
    ATOM CD1 CG2R61 -0.115 !
    ATOM HD1 HGR61
    0.115 !
    GROUP
    !
    ATOM CD2 CG2R61 -0.115 !
    ATOM HD2 HGR61
    0.115 !
    GROUP
    !
    ATOM CE1 CG2R61 -0.115 !
    ATOM HE1 HGR61
    0.115 !

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00
    110.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00
    110.00

    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.2000
    1.4000
    1.4000
    1.1000
    0.9000
    1.0900
    1.4000
    1.2000
    1.4000
    1.4000
    1.1000
    0.9000

    GROUP
    ATOM CE2 CG2R61 -0.115
    ATOM HE2 HGR61
    0.115

    HE1

    GROUP

    0.000 !

    CE1--CD1

    CD3--CE3

    ATOM CD3 CG2R61 -0.115 !

    SUBS--CZ1

    ATOM HD3 HGR61

    0.115 !

    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !

    !
    !
    !

    ATOM CZ1 CG2R61


    GROUP

    GROUP
    ATOM CD4
    ATOM HD4
    GROUP
    ATOM CE3
    ATOM HE3
    GROUP
    ATOM CE4
    ATOM HE4
    GROUP
    ATOM CZ2
    GROUP
    ATOM C1
    ATOM O1
    ATOM C2
    ATOM O2A
    ATOM O2B
    GROUP
    ATOM C3
    ATOM O3
    ATOM C4
    ATOM O4A
    ATOM O4B
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR
    IMPR
    IC
    IC
    IC
    IC

    HD1 HD3

    HE3

    CG1---CG2
    /

    CZ2--SUBS
    /

    CE2--CD2
    CD4--CE4
    /
    \
    /
    \
    HE2
    HD2 HD4
    HE4

    CG2R61 -0.115
    HGR61
    0.115

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4
    CZ1
    C1
    C2
    C3
    C4
    C1
    C2
    C3
    C4

    CG2R61
    CG2O5
    OG2D3
    CG2O3
    OG2D2
    OG2D2

    0.38
    -0.48
    0.62
    -0.76
    -0.76

    CG2O5
    OG2D3
    CG2O3
    OG2D2
    OG2D2

    0.38
    -0.48
    0.62
    -0.76
    -0.76

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4
    C1
    O1
    O2B
    O3
    O4B
    CZ1
    C1
    CZ2
    C3

    CD1
    CG2
    CE1
    CG2

    0.000

    CG1
    CE2
    CG2
    CZ2

    CD2
    CZ1
    CD3
    CE4

    !
    O
    !
    //
    ! Ring-C
    !
    \
    !
    C==O
    !
    |
    !
    O (-)
    !
    !
    !
    !

    CG1
    CZ1
    CD3
    CE4

    CG2
    CE1
    CE3
    CD4

    CD2 HD2 CE1


    CD3
    CE3 HE3 CE4
    CZ2 C3
    C1 C2 C2

    HE1
    HD3
    HE4
    O2A

    C3 C4 C4 O4A
    C2
    O2A
    C4
    O4A
    CG2
    CG1
    CG1
    CG1

    O1
    O2B
    O3
    O4B
    *CG1
    CD1
    *CD1
    CD2

    CD2
    CE1
    HD1
    CE2

    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00

    180.00
    180.00
    180.00
    180.00

    120.00
    120.00
    120.00
    120.00

    1.4000
    1.4000
    1.0900
    1.4000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CE2
    CG1
    CZ1
    CZ1
    CD1
    CD4
    CG1
    CE3
    CG1
    CE4
    CG2
    CZ2
    CZ2
    CE2
    CE1
    C2
    CZ1
    O2A
    CE4
    CE3
    C4
    CZ2
    O4A

    RESI BCA
    GROUP
    ATOM CG1
    ATOM CG2
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD3
    ATOM HD3
    GROUP
    ATOM CD4
    ATOM HD4
    GROUP
    ATOM CE3
    ATOM HE3
    GROUP
    ATOM CE4
    ATOM HE4
    GROUP
    ATOM CZ1
    ATOM C1
    ATOM O1A
    ATOM O1B
    GROUP
    ATOM CZ2
    ATOM C2

    CG1
    CD1
    CD1
    CD2
    CG1
    CG1
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE1
    CZ1
    CZ1
    C1
    C1
    CE3
    CZ2
    CZ2
    C3
    C3

    *CD2
    CE1
    *CE1
    *CE2
    CG2
    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ1
    C1
    *C1
    C2
    *C2
    *CZ2
    C3
    *C3
    C4
    *C4

    HD2
    CZ1
    HE1
    HE2
    CD4
    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    C1
    C2
    O1
    O2A
    O2B
    C3
    C4
    O3
    O4A
    O4B

    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    110.00
    120.00
    120.00
    120.00
    120.00
    110.00

    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    -60.00
    120.00
    180.00
    180.00
    180.00
    -60.00
    120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    110.00
    110.00
    120.00
    120.00
    120.00
    110.00
    110.00

    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.2000
    1.4000
    1.4000
    1.0900
    1.4000
    1.2000
    1.4000
    1.4000

    -2.00 ! C14H8O4 biphenyl analog, peml., acid analog


    CG2R67
    CG2R67

    0.000
    0.000

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    !
    !
    !
    !
    !
    !
    !
    !
    !

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.10 !
    O
    CG2O3
    0.62 !
    //
    OG2D2 -0.76 ! Ring-C (-)
    OG2D2 -0.76 !
    \
    !
    O
    CG2R61 -0.10 !
    CG2O3
    0.62

    HE1
    HD1 HD3
    HE3
    \
    /
    \
    /
    CE1--CD1
    CD3--CE3
    /
    \
    /
    \
    SUBS--CZ1
    CG1---CG2
    CZ2--SUBS
    \
    /
    \
    /
    CE2--CD2
    CD4--CE4
    /
    \
    /
    \
    HE2
    HD2 HD4
    HE4

    ATOM O2A OG2D2


    ATOM O2B OG2D2
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4
    CZ1
    CZ2

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4
    C1
    C2
    CD1
    CG2
    CE1
    CG2
    CE2
    CG1
    CZ1
    CZ1
    CD1
    CD4
    CG1
    CE3
    CG1
    CE4
    CG2
    CZ2
    CZ2
    CE2
    CE1
    O1A
    CE4
    CE3
    O2A

    -0.76
    -0.76

    CG1
    CE2
    CG2
    CZ2

    CD2
    CZ1
    CD3
    CE4

    CG1
    CZ1
    CD3
    CE4

    CG2
    CE1
    CE3
    CD4

    CD2 HD2 CE1


    CD3
    CE3 HE3 CE4
    C1 O1A C1
    C2 O2A C2

    HE1
    HD3
    HE4
    O1B
    O2B

    CG2
    CG1
    CG1
    CG1
    CG1
    CD1
    CD1
    CD2
    CG1
    CG1
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE1
    CZ1
    CZ1
    CE3
    CZ2
    CZ2

    *CG1
    CD1
    *CD1
    CD2
    *CD2
    CE1
    *CE1
    *CE2
    CG2
    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ1
    C1
    *C1
    *CZ2
    C2
    *C2

    CD2
    CE1
    HD1
    CE2
    HD2
    CZ1
    HE1
    HE2
    CD4
    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    C1
    O1A
    O1B
    C2
    O2A
    O2B

    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    RESI C36
    -2.00 ! C16H12O7 biphenyl with bridging O analog, peml.
    !KEVO: charges adjusted to reflect updated acetone L-J.
    !Resulting charges are unlikey to be good ==> re-optimize?
    GROUP
    ! hydrated aldehyde analog (ionized)
    ATOM CG1 CG2R61 0.215
    ATOM O
    OG301 -0.430
    ATOM CD1 CG2R61 -0.115
    ATOM HD1 HGR61
    0.115
    !
    HE3
    ATOM CD2 CG2R61 -0.115
    !
    \
    /
    ATOM HD2 HGR61
    0.115
    !
    CD3--CE3
    ATOM CE1 CG2R61 -0.115
    !
    /
    \
    ATOM HE1 HGR61
    0.115
    !
    HD1
    O ---CG2
    CZ2--SUBS
    ATOM CE2 CG2R61 -0.115
    !
    \
    /
    \
    /
    ATOM HE2 HGR61
    0.115
    !
    CD1--CG1
    CD4--CE4
    ATOM CZ1 CG2R61 0.000
    !
    /
    \
    /
    \
    ATOM CG2 CG2R61 0.215
    ! HE1--CE1
    CD2--HD2 HD4
    HE4
    ATOM CD3 CG2R61 -0.115
    !
    \
    /
    ATOM HD3 HGR61
    0.115
    !
    CZ1--CE2
    ATOM CD4 CG2R61 -0.115
    !
    /
    \
    ATOM HD4 HGR61
    0.115
    !
    SUBS
    HE2
    ATOM CE3 CG2R61 -0.115

    ATOM HE3
    ATOM CE4
    ATOM HE4
    ATOM CZ2
    GROUP
    ATOM C1
    ATOM O1
    ATOM C2
    ATOM H2
    ATOM O2A
    ATOM H2A
    ATOM O2B
    GROUP
    ATOM C3
    ATOM O3
    ATOM C4
    ATOM H4
    ATOM O4A
    ATOM H4A
    ATOM O4B
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4
    CZ1
    C2
    C2
    CZ2
    C4
    C4

    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 0.000
    CG2O5
    OG2D3
    CG311
    HGA1
    OG311
    HGP1
    OG312

    0.38
    -0.48
    0.17
    0.09
    -0.60
    0.32
    -0.88

    CG2O5
    OG2D3
    CG311
    HGA1
    OG311
    HGP1
    OG312

    0.38
    -0.48
    0.17
    0.09
    -0.60
    0.32
    -0.88

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4
    C1
    H2
    O2B
    C3
    H4
    O4B

    CG1
    CE2
    CG2
    CZ2
    CG2
    CD2

    CD2
    CZ1
    CD3
    CE4
    O
    HD2

    !
    O1
    !
    //
    !Ring--C1 H2
    !
    \ /
    !
    C2--OH
    !
    \
    !
    O (-)

    CG1
    CZ1
    CD3
    CE4

    O
    CE1
    CE3
    CD4

    CE1
    CD3
    CE3 HE3 CE4
    C1 O1 C1
    C2 O2A O2A

    HE1
    HD3
    HE4
    C2
    H2A

    C3 O3 C3 C4
    C4 O4A O4A H4A

    IMPR C1 CZ1 C2 O1
    IMPR C3 CZ2 C4 O3
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    O
    CE1
    O
    CE2
    CG1
    CZ1
    CZ1
    CD1
    CG1
    CD4
    O
    CE3
    O
    CE4
    CG2
    CZ2
    CZ2
    CE2
    CE1
    C2

    O
    CG1
    CG1
    CG1
    CG1
    CD1
    CD1
    CD2
    CG1
    O
    O
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE1
    CZ1
    CZ1

    *CG1
    CD1
    *CD1
    CD2
    *CD2
    CE1
    *CE1
    *CE2
    O
    CG2
    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ1
    C1
    *C1

    CD2
    CE1
    HD1
    CE2
    HD2
    CZ1
    HE1
    HE2
    CG2
    CD4
    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    C1
    C2
    O1

    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    -144.00
    40.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.3820
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.2000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CZ1
    O2A
    O2A
    C1
    CE4
    CE3
    C4
    CZ2
    O4A
    O4A
    C3

    C1
    C1
    C1
    C2
    CE3
    CZ2
    CZ2
    C3
    C3
    C3
    C4

    C2
    *C2
    *C2
    O2A
    *CZ2
    C3
    *C3
    C4
    *C4
    *C4
    O4A

    O2A
    O2B
    H2
    H2A
    C3
    C4
    O3
    O4A
    O4B
    H4
    H4A

    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    110.00
    110.00
    110.00
    120.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00

    -60.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    -60.00
    120.00
    -120.00
    180.00

    110.00
    110.00
    110.00
    110.00
    120.00
    120.00
    120.00
    110.00
    110.00
    110.00
    110.00

    RESI C37
    -2.00 ! C16H8O7 biphenyl analog, peml.
    !KEVO: charges adjusted to reflect updated acetone L-J.
    !Resulting charges are probably not that bad.
    GROUP
    ATOM CG1 CG2R61 0.215
    ATOM O
    OG301 -0.430
    ATOM CD1 CG2R61 -0.115
    ATOM HD1 HGR61
    0.115
    !
    ATOM
    ATOM
    ATOM
    ATOM
    S
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    1.4000
    1.4000
    1.1000
    0.9000
    1.0900
    1.4000
    1.2000
    1.4000
    1.4000
    1.1000
    0.9000

    HE3

    CD2
    HD2
    CE1
    HE1

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    !
    !
    !
    !

    CE2
    HE2
    CZ1
    CG2
    CD3
    HD3
    CD4
    HD4
    CE3
    HE3
    CE4
    HE4
    CZ2

    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    !
    \
    /
    \
    /
    !
    CD1--CG1
    CD4--CE4
    !
    /
    \
    /
    \
    ! HE1--CE1
    CD2--HD2 HD4
    HE4
    !
    \
    /
    !
    CZ1--CE2
    !
    /
    \
    !
    SUBS
    HE2

    -0.115
    0.115
    0.000
    0.215
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000

    C1
    O1
    C2
    O2A
    O2B

    CG2O5
    OG2D3
    CG2O3
    OG2D2
    OG2D2

    0.38
    -0.48
    0.62
    -0.76
    -0.76

    C3
    O3
    C4
    O4A
    O4B

    CG2O5
    OG2D3
    CG2O3
    OG2D2
    OG2D2

    0.38
    -0.48
    0.62
    -0.76
    -0.76

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4

    CG1
    CE2
    CG2
    CZ2
    CG2
    CD2

    CD2
    CZ1
    CD3
    CE4
    O
    HD2

    CG1
    CZ1
    CD3
    CE4

    O
    CE1
    CE3
    CD4

    CE1 HE1
    CD3 HD3
    CE3 HE3 CE4 HE4

    \
    /
    CD3--CE3
    /
    \
    O ---CG2
    CZ2--SUB

    HD1

    !
    !
    !
    !
    !
    !
    !

    O
    //
    Ring--C
    \
    C--O (-)
    //
    O

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CZ1 C1 C1
    C2
    C2 O2B
    CZ2 C3 C3
    C4
    C4 O4B
    C1 CZ1 C2
    C2 C1 O2A
    C3 CZ2 C4
    C4 C3 O4A
    CD1
    O
    CE1
    O
    CE2
    CG1
    CZ1
    CZ1
    CD1
    CG1
    CD4
    O
    CE3
    O
    CE4
    CG2
    CZ2
    CZ2
    CE2
    CE1
    C2
    CZ1
    O2A
    CE4
    CE3
    C4
    CZ2
    O4A

    RESI C3C
    GROUP
    ATOM CG1
    ATOM O
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM
    ATOM
    ATOM
    ATOM
    S
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    O1 C1 C2
    O2A
    O3 C3 C4
    O4A
    O1
    O2B
    O3
    O4B

    O
    CG1
    CG1
    CG1
    CG1
    CD1
    CD1
    CD2
    CG1
    O
    O
    CG2
    CG2
    CG2
    CG2
    CD3
    CD3
    CD4
    CE1
    CZ1
    CZ1
    C1
    C1
    CE3
    CZ2
    CZ2
    C3
    C3

    *CG1
    CD1
    *CD1
    CD2
    *CD2
    CE1
    *CE1
    *CE2
    O
    CG2
    *CG2
    CD3
    *CD3
    CD4
    *CD4
    CE3
    *CE3
    *CE4
    *CZ1
    C1
    *C1
    C2
    *C2
    *CZ2
    C3
    *C3
    C4
    *C4

    CD2
    CE1
    HD1
    CE2
    HD2
    CZ1
    HE1
    HE2
    CG2
    CD4
    CD3
    CE3
    HD3
    CE4
    HD4
    CZ2
    HE3
    HE4
    C1
    C2
    O1
    O2A
    O2B
    C3
    C4
    O3
    O4A
    O4B

    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    -144.00
    40.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.3820
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.2000
    1.4000
    1.4000
    1.0900
    1.4000
    1.2000
    1.4000
    1.4000

    -2.00 ! C14H8O5
    CG2R61 0.215
    OG301 -0.430
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115

    HD2
    CE1
    HE1
    CE2

    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115

    !
    !
    !
    !

    HE2
    CZ1
    CG2
    CD3
    HD3
    CD4
    HD4

    HGR61
    0.115
    CG2R61 -0.100
    CG2R61 0.215
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    !
    \
    /
    \
    /
    !
    CD1--CG1
    CD4--CE4
    !
    /
    \
    /
    \
    ! HE1--CE1
    CD2--HD2 HD4
    HE4
    !
    \
    /
    !
    CZ1--CE2
    !
    /
    \

    HE3

    HD1

    \
    /
    CD3--CE3
    /
    \
    O ---CG2
    CZ2--SUB

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    GROUP
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CE3
    HE3
    CE4
    HE4
    CZ2

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.100

    C1
    O1A
    O1B

    CG2O3
    OG2D2
    OG2D2

    0.62
    -0.76
    -0.76

    C2
    O2A
    O2B

    CG2O3
    OG2D2
    OG2D2

    0.62
    -0.76
    -0.76

    CD1
    CD2
    CE1
    CE3
    CD4
    CD1
    CE2
    CD4
    CZ1
    CZ2

    CG1
    CE2
    CD1
    CZ2
    CG2
    HD1
    HE2
    HD4
    C1
    C2

    CG1
    CE2
    CG2
    CZ2
    CG2
    CD2

    CG1
    CZ1
    CD3
    CE4

    O
    CE1
    CE3
    CD4

    CE1
    CD3
    CE3 HE3 CE4
    C1 O1A C1
    C2 O2A C2

    HE1
    HD3
    HE4
    O1B
    O2B

    IC CD1
    IC O
    IC CE1
    IC O
    IC CE2
    IC CG1
    IC CZ1
    IC CZ1
    IC CD1
    IC CG1
    IC CD3
    IC O
    IC CE3
    IC O
    IC CE4
    IC CG2
    IC CZ2
    IC CZ2
    IC CE2
    IC CE1
    IC O1A
    IC CE4
    IC CE3
    IC O2A
    PATCHING FIRST

    CD2
    CZ1
    CD3
    CE4
    O
    HD2

    HE2

    !
    O
    !
    //
    ! Ring-C (-)
    !
    \
    !
    O
    !

    O
    *CG1 CD2
    CG1
    CD1
    CE1
    CG1
    *CD1 HD1
    CG1
    CD2
    CE2
    CG1
    *CD2 HD2
    CD1
    CE1
    CZ1
    CD1
    *CE1 HE1
    CD2
    *CE2 HE2
    CG1
    O
    CG2
    O
    CG2
    CD3
    O
    *CG2 CD4
    CG2
    CD3
    CE3
    CG2
    *CD3 HD3
    CG2
    CD4
    CE4
    CG2
    *CD4 HD4
    CD3
    CE3
    CZ2
    CD3
    *CE3 HE3
    CD4
    *CE4 HE4
    CE1
    *CZ1 C1
    CZ1
    C1
    O1A
    CZ1
    *C1
    O1B
    CE3
    *CZ2 C2
    CZ2
    C2
    O2A
    CZ2
    *C2
    O2B
    NONE LAST NONE

    !toppar_retinol_2.str
    RESI HEX3
    0.00
    !
    GROUP
    ATOM C1 CG2DC3 -0.42
    ATOM H11 HGA5
    0.21
    ATOM H12 HGA5
    0.21
    ATOM C2 CG2DC2 -0.15

    SUBS

    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.3820
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    ! C6H8 1,3,5-hexatriene
    !
    ! H11
    H21
    !
    \
    /
    !
    C1=C2

    H41

    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    -144.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.3820
    1.4000
    1.4000
    1.4000
    1.0900
    1.4000
    1.0900
    1.4000
    1.0900
    1.0900
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    ATOM H21
    GROUP
    ATOM C3
    ATOM H31
    ATOM C4
    ATOM H41
    GROUP
    ATOM C5
    ATOM H51
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62

    HGA4

    BOND C1
    BOND C1
    BOND C4

    C2 C2
    H11 C1
    H41 C5

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.15 !
    /
    ! H12
    CG2DC1 -0.15 !
    HGA4
    0.15 !
    CG2DC1 -0.15 !
    HGA4
    0.15 !
    !
    CG2DC2 -0.15
    HGA4
    0.15

    /
    C3=C4
    H61
    /
    \
    /
    H31
    C5=C6
    /
    \
    H51
    H62

    C1
    C2
    C3
    H11
    H11
    C3
    C4
    C5
    C6
    C4
    H61

    CG2DC3 -0.42
    HGA5
    0.21
    HGA5
    0.21

    C2
    C3
    C4
    C2
    C1
    C1
    C2
    C3
    C4
    C5
    C5

    C3
    C4
    C5
    *C1
    C2
    *C2
    *C3
    *C4
    *C5
    C6
    *C6

    C3 C3
    H12 C2
    H51 C6
    C4
    C5
    C6
    H12
    C3
    H21
    H31
    H41
    H51
    H61
    H62

    C4
    H21
    H61

    C4
    C3
    C6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    H31
    H62
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    PATCH FIRST NONE LAST NONE


    RESI 13DB
    !
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    GROUP
    ATOM C2
    ATOM H21
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42

    0.00 ! C4H6 1,3-dibutene


    CG2DC3 -0.42 ! H11
    H21
    HGA5
    0.21 ! \
    /
    HGA5
    0.21 !
    C1=C2
    H41
    ! /
    \
    /
    CG2DC2 -0.15 ! H12
    C3=C4
    HGA4
    0.15 !
    /
    \
    CG2DC1 -0.15 !
    H31
    H42
    HGA4
    0.15 !
    !
    CG2DC3 -0.42 !
    HGA5
    0.21 !
    HGA5
    0.21 !

    BOND C1
    BOND C1
    BOND C4

    C2 C2
    H11 C1
    H41 C4

    C3 C3
    H12 C2
    H42

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 H41 0.00
    IC C3 C2 C1 H11 0.00
    IC C2 H11 *C1 H12 0.00
    IC C3 H41 *C4 H42 0.00
    IC C1 C3 *C2 H21 0.00
    IC C2 C4 *C3 H31 0.00
    PATCH FIRST NONE LAST NONE

    C4
    H21

    C3

    H31

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 13DP
    !
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    GROUP
    ATOM C3
    ATOM H31
    ATOM C4
    ATOM H41
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53
    BOND C1
    BOND C1
    BOND C4

    0.00 ! C5H8 1,3-dipentene


    CG2DC3
    HGA5
    HGA5
    CG2DC2
    HGA4

    -0.42
    0.21
    0.21
    -0.15
    0.15

    CG2DC1
    HGA4
    CG2DC1
    HGA4

    -0.15
    0.15
    -0.15
    0.15

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    C2 C2
    H11 C1
    H41 C5

    !
    ! H11
    H21
    !
    \
    /
    !
    C1=C2
    H41
    !
    /
    \
    /
    ! H12
    C3=C4 H51
    !
    /
    \ /
    !
    H31
    C5-H52
    !
    \
    !
    H53
    !
    !
    !
    !
    !

    C3 C3
    H12 C2
    H51 C5

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 H51 0.00
    IC C3 C2 C1 H11 0.00
    IC C2 H11 *C1 H12 0.00
    IC C1 C3 *C2 H21 0.00
    IC C2 C4 *C3 H31 0.00
    IC C3 C5 *C4 H41 0.00
    IC C4 H51 *C5 H52 0.00
    IC C4 H51 *C5 H53 0.00
    PATCH FIRST NONE LAST NONE
    RESI DMB1
    !
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    GROUP
    ATOM C2
    ATOM C2M
    ATOM H2M1
    ATOM H2M2
    ATOM H2M3
    GROUP
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42

    C4
    H21
    H52

    C4
    C3
    C5

    C5
    H31
    H53

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    180.0
    0.0
    180.0
    180.0
    180.0
    180.0
    180.0
    120.0
    -120.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C5H8 2-methyl-1,3-butadiene


    CG2DC3 -0.42 !
    HGA5
    0.21 !
    H2M1 H2M2
    HGA5
    0.21 !
    \ /
    ! H11
    C2M-H2M3
    CG2DC2 0.00 !
    \
    /
    CG331 -0.27 !
    C1=C2
    H41
    HGA3
    0.09 !
    /
    \
    /
    HGA3
    0.09 ! H12
    C3=C4
    HGA3
    0.09 !
    /
    \
    !
    H31
    H42
    CG2DC1 -0.15 !
    HGA4
    0.15 !
    !
    CG2DC3 -0.42 !
    HGA5
    0.21 !
    HGA5
    0.21 !

    BOND C1 C2 C2 C3 C3 C4
    C2
    BOND C1 H11 C1 H12 C3 H31 C4
    BOND C2M H2M1 C2M H2M2 C2M H2M3

    C2M
    H41 C4

    H42

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 H41 0.00
    IC C3 C2 C1 H11 0.00
    IC C2 H11 *C1 H12 0.00
    IC C1 C3 *C2 C2M 0.00
    IC C2 C4 *C3 H31 0.00
    IC C3 H41 *C4 H42 0.00
    IC C1 C2 C2M H2M1 0.00
    IC C2 H2M1 *C2M H2M2 0.00
    IC C2 H2M1 *C2M H2M3 0.00
    PATCH FIRST NONE LAST NONE
    RESI DMP1
    !
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    GROUP
    ATOM C2
    ATOM H21
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM C4M
    ATOM H4M1
    ATOM H4M2
    ATOM H4M3
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53
    BOND
    BOND
    BOND
    BOND

    C1
    C1
    C4M
    C5

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    120.0
    -120.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C6H10 4-methyl-1,3-pentadiene


    CG2DC3 -0.42 !
    HGA5
    0.21 ! H11
    H21 H4M1 H4M2
    HGA5
    0.21 !
    \
    /
    \ /
    !
    C1=C2
    C4M-H4M3
    CG2DC2 -0.15 !
    /
    \
    /
    HGA4
    0.15 ! H12
    C3=C4 H51
    CG2DC1 -0.15 !
    /
    \ /
    HGA4
    0.15 !
    H31
    C5-H52
    !
    \
    CG2DC1 0.00 !
    H53
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    C2
    H11
    H4M1
    H51

    C2
    C1
    C4M
    C5

    C3
    H12
    H4M2
    H52

    C3
    C2
    C4M
    C5

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 H51 0.00
    IC C3 C2 C1 H11 0.00
    IC C2 H11 *C1 H12 0.00
    IC C1 C3 *C2 H21 0.00
    IC C2 C4 *C3 H31 0.00
    IC C3 C5 *C4 C4M 0.00
    IC C3 C4 C4M H4M1 0.00
    IC C4 H4M1 *C4M H4M2 0.00
    IC C4 H4M1 *C4M H4M3 0.00
    IC C4 H51 *C5 H52 0.00
    IC C4 H51 *C5 H53 0.00
    PATCH FIRST NONE LAST NONE

    C4
    C4
    H21 C3
    H4M3
    H53
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    120.0
    -120.0
    120.0
    -120.0

    C5 C4
    H31

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4M

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI DMP2
    0.00 ! C6H10 2-methyl-1,3-pentadiene
    !
    GROUP
    !
    H2M1 H2M2
    ATOM C1 CG2DC3 -0.42 !
    \ /

    ATOM H11
    ATOM H12
    GROUP
    ATOM C2
    ATOM C2M
    ATOM H2M1
    ATOM H2M2
    ATOM H2M3
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM H41
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53

    HGA5
    HGA5

    BOND
    BOND
    BOND
    BOND

    C2
    H11
    H2M1
    H51

    C1
    C1
    C2M
    C5

    CG2DC2
    CG331
    HGA3
    HGA3
    HGA3
    CG2DC1
    HGA4
    CG2DC1
    HGA4
    CG331
    HGA3
    HGA3
    HGA3

    0.21 ! H11
    C2M-H2M3
    0.21 !
    \
    /
    !
    C1=C2
    H41
    0.00 !
    /
    \
    /
    -0.27 ! H12
    C3=C4 H51
    0.09 !
    /
    \ /
    0.09 !
    H31
    C5-H52
    0.09 !
    \
    -0.15 !
    H53
    0.15 !
    !
    -0.15 !
    0.15 !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !

    C2
    C1
    C2M
    C5

    C3
    H12
    H2M2
    H52

    C3
    C3
    C2M
    C5

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 H51 0.00
    IC C3 C2 C1 H11 0.00
    IC C2 H11 *C1 H12 0.00
    IC C1 C3 *C2 C2M 0.00
    IC C2 C4 *C3 H31 0.00
    IC C3 C5 *C4 H41 0.00
    IC C1 C2 C2M H2M1 0.00
    IC C2 H2M1 *C2M H2M2 0.00
    IC C2 H2M1 *C2M H2M3 0.00
    IC C4 H51 *C5 H52 0.00
    IC C4 H51 *C5 H53 0.00
    PATCH FIRST NONE LAST NONE
    RESI CROT

    C4
    C4
    H31 C4
    H2M3
    H53
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    180.0
    120.0
    -120.0
    120.0
    -120.0

    C5 C2 C2M
    H41

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C6H11NO 2-buteneamide,N,3-dimethyl (crotonamide)


    ! numbering as in fennretinide
    ! note different atom types for N21 and C15: this is consistent
    ! with differences in NMA and acetamide
    GROUP
    ATOM C12 CG331 -0.27 !
    ATOM H121 HGA3
    0.09 !
    H202 H203
    ATOM H122 HGA3
    0.09 !
    \ /
    ATOM H123 HGA3
    0.09 !
    H201-C20
    GROUP
    !
    |
    ATOM C13 CG2DC2 0.00 !H121-C12--C13
    O29
    ATOM C14 CG2DC2 -0.15 !
    / |
    \\
    ||
    ATOM H141 HGA4
    0.15 !H122 H123
    C14--C15
    GROUP
    !
    /
    \
    ATOM C15 CG2O1 0.51 !
    H141
    N21-H211 (cis)
    ATOM O29 OG2D1 -0.51 !
    |
    GROUP
    !
    H132-C16-H131
    ATOM N21 NG2S1 -0.47 !
    |
    ATOM H211 HGP1
    0.28 !
    H133
    ATOM C16 CG331 -0.08
    ATOM H131 HGA3
    0.09
    ATOM H132 HGA3
    0.09

    ATOM H133
    GROUP
    ATOM C20
    ATOM H201
    ATOM H202
    ATOM H203

    HGA3

    BOND
    BOND
    BOND
    BOND
    BOND

    C13
    C20
    H131
    H121
    H201

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.09

    C12
    C13
    C16
    C12
    C20

    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !

    C12
    C13
    C14
    H121
    H121
    H121
    C14
    C15
    N21
    C16
    C15
    H131
    H131
    C12
    H201
    H201

    C14
    O29
    H132
    H122
    H202

    C14
    C15
    N21
    *C12
    *C12
    C13
    *C13
    *C14
    *C15
    *N21
    C16
    *C16
    *C16
    C20
    *C20
    *C20

    C15
    N21
    C16
    H122
    H123
    C14
    C20
    H141
    O29
    H211
    H131
    H132
    H133
    H201
    H202
    H203

    C13
    C14
    C15
    C13
    C13
    C12
    C12
    C13
    C14
    C15
    N21
    N21
    N21
    C13
    C13
    C13

    C13
    C15
    C16
    C12
    C20

    C14
    C14
    C16
    C12
    C20

    C15 C15 N21 N21 C16


    H141 N21 H211
    H133
    H123
    H203

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    PATCH FIRST NONE LAST NONE


    RESI PACP
    ATOM C14
    ATOM H141
    ATOM H142
    ATOM H143
    GROUP
    ATOM C15
    ATOM O29
    GROUP
    ATOM N21
    ATOM H211
    ATOM C22
    GROUP
    ATOM C23
    ATOM H231
    GROUP
    ATOM C24
    ATOM H241
    GROUP
    ATOM C26
    ATOM H261
    GROUP
    ATOM C27
    ATOM H271
    GROUP
    ATOM C25

    CG331
    HGA3
    HGA3
    HGA3
    CG2O1
    OG2D1
    NG2S1
    HGP1
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00 ! C8H9NO2 p-acetamide-phenol


    ! numbering as in fennretinide
    !
    -0.27 !
    H142
    0.09 !
    |
    0.09 !
    H141-C14-H143
    0.09 !
    |
    !
    C15=O29
    0.52 !
    |
    -0.52 !
    N21-H211
    !
    |
    -0.47 !
    C22
    0.33 !
    // \
    0.14 ! H231-C23 C27-H271
    !
    |
    ||
    -0.115! H241-C24 C26-H261
    0.115!
    \\ /
    !
    C25
    -0.115!
    |
    0.115!
    O28
    !
    \
    -0.115!
    H281
    0.115

    CG2R61 -0.115
    HGR61 0.115
    CG2R61 0.11

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM O28 OG311 -0.53


    ATOM H281 HGP1
    0.42
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C14
    C23
    C25
    C14
    C23

    C14
    C15
    N21
    C22
    C23
    H141
    H141
    H141
    N21
    C22
    C27
    C24
    C25
    O28
    C27
    C26
    C24

    C15
    C24
    O28
    H141
    H231
    C15
    N21
    C22
    C23
    C24
    C15
    C15
    C14
    C14
    C15
    N21
    C22
    C23
    C24
    C25
    C22
    C25

    C15
    C24
    O28
    C14
    C24

    N21
    C25
    H281
    H142
    H241

    N21
    C22
    C23
    C24
    C25
    *C14
    *C14
    C15
    *C15
    *N21
    *C22
    *C23
    *C24
    *C25
    *C26
    *C27
    O28

    N21
    C25
    N21
    C14
    C26

    C22
    C27
    C24
    C25
    O28
    H142
    H143
    N21
    O29
    H211
    C23
    H231
    H241
    C26
    H261
    H271
    H281

    C22 C22 C23 C15 O29


    C26 C26 C27 C27 C22
    H211
    H143
    H261 C27 H271
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    0.00
    180.00
    0.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI MECH
    GROUP
    ATOM C1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM C6
    GROUP
    ATOM C7
    ATOM H71
    ATOM C8
    ATOM H81
    ATOM H82
    GROUP
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    GROUP
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173

    0.00 ! C11H18 1,6,6-trimethyl-2-ethenyl-cyclohexene


    ! using retinol numbering
    CG301
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG2DC2
    CG2DC2

    0.00
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    0.00
    0.00

    CG2DC1
    HGA4
    CG2DC3
    HGA5
    HGA5

    -0.15
    0.15
    -0.42
    0.21
    0.21

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09

    !H162 H163 H171 H172


    !
    \ |
    | /
    !H161-C16
    C17-H173 H81
    !
    \ /
    |
    ! H21
    C1
    C8-H82
    !
    \ / \
    //
    ! H22-C2
    C6------C7
    !
    |
    ||
    \
    ! H31-C3
    C5 H181 H71
    !
    / \ / \ /
    ! H32
    C4
    C18-H18
    !
    / \
    \
    !
    H41 H42 H183
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183

    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !

    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C7
    H21
    H161
    H71

    C1
    C6
    C2
    C16
    C7

    C2
    C7
    C2
    C16
    C8

    C3
    C8
    H22
    H162
    H81

    C3
    C1
    C3
    C16
    C8

    C4
    C16
    H31
    H163
    H82

    !initial ring geometry is planar


    IC C1 C2 C3 C4 0.00 0.00
    IC C2 C3 C4 C5 0.00 0.00
    IC C3 C4 C5 C6 0.00 0.00
    IC C1 C3 *C2 H21 0.00 0.00
    IC C1 C3 *C2 H22 0.00 0.00
    IC C2 C4 *C3 H31 0.00 0.00
    IC C2 C4 *C3 H32 0.00 0.00
    IC C3 C5 *C4 H41 0.00 0.00
    IC C3 C5 *C4 H42 0.00 0.00
    IC C1 C5 *C6 C7 0.00 0.00
    IC C5 C6 C7 C8 0.00 0.00
    IC C6 C8 *C7 H71 0.00 0.00
    IC C6 C7 C8 H81 0.00 0.00
    IC C7 H81 *C8 H82 0.00 0.00
    IC C6 C2 *C1 C16 0.00 0.00
    IC C6 C2 *C1 C17 0.00 0.00
    IC C2 C1 C16 H161 0.00 0.00
    IC C1 H161 *C16 H162 0.00 0.00
    IC C1 H161 *C16 H163 0.00 0.00
    IC C2 C1 C17 H171 0.00 0.00
    IC C1 H171 *C17 H172 0.00 0.00
    IC C1 H171 *C17 H173 0.00 0.00
    IC C4 C6 *C5 C18 0.00 0.00
    IC C4 C5 C18 H181 0.00 0.00
    IC C5 H181 *C18 H182 0.00 0.00
    IC C5 H181 *C18 H183 0.00 0.00
    PATCH FIRST NONE LAST NONE
    RESI TMCH
    GROUP
    ATOM C1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM C6
    GROUP
    ATOM C7
    ATOM H71
    ATOM H72

    C4
    C1
    C3
    C17
    C18
    63.0
    -46.0
    15.0
    120.0
    -120.0
    120.0
    -120.0
    120.0
    -120.0
    180.0
    60.0
    180.0
    180.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    180.0
    120.0
    -120.0

    C5
    C17
    H32
    H171
    H181
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5
    C5
    C4
    C17
    C18

    C6
    C18
    H41
    H172
    H182

    C6

    C1

    C4 H42
    C17 H173
    C18 H183

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C10H18 1,2,6,6-tetramethylcyclohexene


    ! using retinol numbering
    CG301
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG2DC2
    CG2DC2

    0.00
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    0.00
    0.00

    !H162 H163 H171 H172


    !
    \ |
    | /
    !H161-C16
    C17-H173
    !
    \ /
    ! H21
    C1
    H71 H72
    !
    \ / \
    | /
    ! H22-C2
    C6------C7-H73
    !
    |
    ||
    ! H31-C3
    C5 H181
    !
    / \ / \ /
    ! H32
    C4
    C18-H18
    !
    / \
    \
    !
    H41 H42 H183
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !

    ATOM H73
    GROUP
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    GROUP
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173
    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183

    HGA3

    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C7
    H21
    H161
    H71

    C1
    C6
    C2
    C16
    C7

    0.09 !
    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    C2
    C1
    C2
    C16
    C7

    C3
    C16
    H22
    H162
    H72

    C3
    C1
    C3
    C16
    C7

    !initial geometry is planar


    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 C6 0.00
    IC C1 C3 *C2 H21 0.00
    IC C1 C3 *C2 H22 0.00
    IC C2 C4 *C3 H31 0.00
    IC C2 C4 *C3 H32 0.00
    IC C3 C5 *C4 H41 0.00
    IC C3 C5 *C4 H42 0.00
    IC C1 C5 *C6 C7 0.00
    IC C5 C6 C7 H71 0.00
    IC C6 H71 *C7 H72 0.00
    IC C6 H71 *C7 H73 0.00
    IC C6 C2 *C1 C16 0.00
    IC C6 C2 *C1 C17 0.00
    IC C2 C1 C16 H161 0.00
    IC C1 H161 *C16 H162 0.00
    IC C1 H161 *C16 H163 0.00
    IC C2 C1 C17 H171 0.00
    IC C1 H171 *C17 H172 0.00
    IC C1 H171 *C17 H173 0.00
    IC C4 C6 *C5 C18 0.00
    IC C4 C5 C18 H181 0.00
    IC C5 H181 *C18 H182 0.00
    IC C5 H181 *C18 H183 0.00
    PATCH FIRST NONE LAST NONE

    C4
    C17
    H31
    H163
    H73
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4
    C5
    C3
    C17
    C18
    -63.0
    46.0
    -13.0
    120.0
    -120.0
    120.0
    -120.0
    120.0
    -120.0
    180.0
    180.0
    120.0
    -120.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    120.0
    -120.0
    180.0
    180.0
    120.0
    -120.0

    C5
    C18
    H32
    H171
    H181

    C5

    C6

    C6

    C1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4 H41 C4 H42
    C17 H172 C17 H173
    C18 H182 C18 H183
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI FRET
    0.00 ! C26H33NO2 fennretinide, nomenclature consistent with re
    tinol
    !
    !
    !
    GROUP
    ATOM C1 CG301 0.00
    ATOM C2 CG321 -0.18
    ATOM H21 HGA2
    0.09

    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM C6
    GROUP
    ATOM C7
    ATOM H71
    ATOM C8
    ATOM H81
    ATOM C9
    ATOM C10
    ATOM H101
    GROUP
    ATOM C11
    ATOM H111
    ATOM C12
    ATOM H121
    ATOM C13
    ATOM C14
    ATOM H141
    GROUP
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    GROUP
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173
    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183
    GROUP
    ATOM C19
    ATOM H191
    ATOM H192
    ATOM H193
    GROUP
    ATOM C20
    ATOM H201
    ATOM H202
    ATOM H203
    GROUP
    ATOM C15
    ATOM O29
    GROUP
    ATOM N21
    ATOM H211
    ATOM C22
    GROUP
    ATOM C23
    ATOM H231

    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG2DC2
    CG2DC2

    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    0.00
    0.00

    CG2DC1
    HGA4
    CG2DC1
    HGA4
    CG2DC2
    CG2DC2
    HGA4

    -0.15
    0.15
    -0.15
    0.15
    0.00
    -0.15
    0.15

    CG2DC1
    HGA4
    CG2DC1
    HGA4
    CG2DC2
    CG2DC2
    HGA4

    -0.15
    0.15
    -0.15
    0.15
    0.00
    -0.15
    0.15

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09

    !H162 H163 H171 H172


    !
    \ |
    | /
    !H161-C16
    C17-H173
    H191 H192
    !
    \ /
    \ /
    ! H21
    C1
    H71
    H81
    C19
    !
    \ / \
    |
    |
    / \
    ! H22-C2
    C6------C7=====C8----C9
    H193
    !
    |
    ||
    ||
    ! H31-C3
    C5 H181
    C10-H101
    !
    / \ / \ /
    |
    ! H32
    C4
    C18-H182
    C11-H111
    !
    / \
    \
    ||
    !
    H41 H42 H183
    C12-H121 H201
    !
    |
    /
    !
    C13---C20-H202
    !
    ||
    \
    !
    C14-H141 H203
    !
    |
    !
    C15=O29
    !
    |
    !
    N21-H211
    !
    |
    !
    C22
    !
    // \
    !
    H231-C23 C27-H271
    !
    |
    ||
    !
    H241-C24 C26-H261
    !
    \\ /
    !
    C25
    !
    |
    !
    O28
    !
    \
    !
    H281
    ! charges from CROT
    !

    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG2O1 0.51
    OG2D1 -0.51

    NG2S1 -0.47 !
    HGP1
    0.33 ! charges from PACP
    CG2R61 0.14 !
    CG2R61 -0.115
    HGR61 0.115

    GROUP
    ATOM C24
    ATOM H241
    GROUP
    ATOM C26
    ATOM H261
    GROUP
    ATOM C27
    ATOM H271
    GROUP
    ATOM C25
    ATOM O28
    ATOM H281
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C6
    C12
    C23
    C1
    C25
    C2
    C7
    C16
    C18
    C20
    C23

    C1
    C2
    C6
    C1
    C6
    C7
    C2
    C2
    C3
    C3
    C4
    C4
    C5
    C5
    C5
    C8
    C9
    C10
    C8
    C11
    C9
    C12
    C10
    C13
    C11
    C14
    C12
    C15
    C6
    H161
    H161
    C6
    H171

    CG2R61 -0.115
    HGR61 0.115
    CG2R61 -0.115
    HGR61 0.115
    CG2R61 -0.115
    HGR61 0.115
    CG2R61 0.11
    OG311 -0.53
    HGP1
    0.42
    C2
    C7
    C13
    C24
    C16
    O28
    H21
    H71
    H161
    H181
    H201
    H231
    C2
    C3
    C1
    C6
    C7
    C8
    C6
    C6
    C1
    C1
    C2
    C2
    C3
    C3
    C1
    C6
    C7
    C8
    C9
    C9
    C10
    C10
    C11
    C11
    C12
    C12
    C13
    C13
    C1
    C1
    C1
    C1
    C1

    C2
    C7
    C13
    C24
    C1
    O28
    C2
    C8
    C16
    C18
    C20
    C24
    C3
    C4
    C2
    C7
    C8
    C9
    *C1
    *C1
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C6
    *C7
    *C8
    *C9
    C10
    *C10
    C11
    *C11
    C12
    *C12
    C13
    *C13
    C14
    *C14
    C16
    *C16
    *C16
    C17
    *C17

    C3
    C8
    C14
    C25
    C17
    H281
    H22
    H81
    H162
    H182
    H202
    H241
    C4
    C5
    C3
    C8
    C9
    C10
    C16
    C17
    H21
    H22
    H31
    H32
    H41
    H42
    C7
    H71
    H81
    C19
    C11
    H101
    C12
    H111
    C13
    H121
    C14
    C20
    C15
    H141
    H161
    H162
    H163
    H171
    H172

    C3
    C8
    C14
    C25
    C5
    N21
    C3
    C10
    C16
    C18
    C20
    C26

    C4
    C9
    C15
    C26
    C18
    H211
    H31
    H101
    H163
    H183
    H203
    H261
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C9
    C15
    C26
    C9

    C5
    C10
    N21
    C27
    C19

    C5
    C10
    N21
    C27
    C13

    C6
    C11
    C22
    C22
    C20

    C6 C1
    C11 C12
    C22 C23

    C3
    C11
    C17
    C19

    H32
    H111
    H171
    H191

    C4
    C12
    C17
    C19

    H41
    H121
    H172
    H192

    C4
    C14
    C17
    C19

    C15 O29
    H42
    H141
    H173
    H193

    C27 H271
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H171
    C6
    C4
    H181
    H181
    C8
    H191
    H191
    C12
    H201
    H201
    C13
    N21
    C14
    C22
    C15
    C27
    N21
    C24
    C22
    C25
    C23
    O28
    C27
    C26
    C24

    C1
    C4
    C5
    C5
    C5
    C9
    C9
    C9
    C13
    C13
    C13
    C14
    C14
    C15
    C15
    N21
    N21
    C22
    C22
    C23
    C23
    C24
    C24
    C25
    C22
    C25

    *C17
    *C5
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    C20
    *C20
    *C20
    C15
    *C15
    N21
    *N21
    C22
    *C22
    C23
    *C23
    C24
    *C24
    C25
    *C25
    *C26
    *C27
    O28

    H173
    C18
    H181
    H182
    H183
    H191
    H192
    H193
    H201
    H202
    H203
    N21
    O29
    C22
    H211
    C27
    C23
    C24
    H231
    C25
    H241
    O28
    C26
    H261
    H271
    H281

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI RTOL
    !
    GROUP
    ATOM C1
    ATOM C2
    ATOM H21
    ATOM H22
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM C6
    GROUP
    ATOM C7
    ATOM H71
    ATOM C8
    ATOM H81
    GROUP
    ATOM C9
    ATOM C10
    ATOM H101
    GROUP
    ATOM C11
    ATOM H111
    GROUP
    ATOM C12

    0.00 ! C20H30O retinol, nomenclature from PDB


    CG301 0.00
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321
    HGA2
    HGA2
    CG2DC2
    CG2DC2

    -0.18
    0.09
    0.09
    0.00
    0.00

    CG2DC1
    HGA4
    CG2DC1
    HGA4

    -0.15
    0.15
    -0.15
    0.15

    CG2DC2 0.00
    CG2DC2 -0.15
    HGA4
    0.15
    CG2DC1 -0.15
    HGA4
    0.15
    CG2DC1 -0.15

    ATOM H121
    GROUP
    ATOM C13
    ATOM C14
    ATOM H141
    GROUP
    ATOM C15
    ATOM H151
    ATOM H152
    ATOM OR
    ATOM HR
    GROUP
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    GROUP
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173
    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183
    GROUP
    ATOM C19
    ATOM H191
    ATOM H192
    ATOM H193
    GROUP
    ATOM C20
    ATOM H201
    ATOM H202
    ATOM H203

    HGA4

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C7
    C13
    C16
    H21
    H71
    H151
    H161
    H181
    H201

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C6
    C2
    C1
    C6
    C7
    C2
    C2
    C3
    C3
    C4
    C4

    C1
    C6
    C12
    C1
    C2
    C7
    C15
    C16
    C18
    C20

    0.15

    CG2DC2 0.00
    CG2DC2 -0.15 !
    HGA4
    0.15 !H162 H163 H171 H172
    !
    \ |
    | /
    CG321 0.05 !H161-C16
    C17-H173
    H191 H192
    HGA2
    0.09 !
    \ /
    \ /
    HGA2
    0.09 ! H21
    C1
    H71
    H81
    C19
    OG311 -0.65 !
    \ / \
    |
    |
    / \
    HGP1
    0.42 ! H22-C2
    C6------C7=====C8----C9
    H193
    !
    |
    ||
    ||
    CG331 -0.27 ! H31-C3
    C5 H181
    C10-H101
    HGA3
    0.09 !
    / \ / \ /
    |
    HGA3
    0.09 ! H32
    C4
    C18-H182
    C11-H111
    HGA3
    0.09 !
    / \
    \
    ||
    !
    H41 H42 H183
    C12-H121 H201
    CG331 -0.27 !
    |
    /
    HGA3
    0.09 !
    C13---C20-H202
    HGA3
    0.09 !
    ||
    \
    HGA3
    0.09 !
    C14-H141 H203
    !
    |
    CG331 -0.27 !
    H151-C15-H152
    HGA3
    0.09 !
    |
    HGA3
    0.09 !
    OR
    HGA3
    0.09 !
    \
    !
    HR
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    !
    CG331 -0.27 !
    HGA3
    0.09 !
    HGA3
    0.09 !
    HGA3
    0.09 !

    C2
    C1
    C3
    C6
    C7
    C8
    C6
    C6
    C1
    C1
    C2
    C2

    C2
    C7
    C13
    C1
    C2
    C8
    C15
    C16
    C18
    C20

    C3
    C8
    C14
    C17
    H22
    H81
    H152
    H162
    H182
    H202

    C3
    C2
    C4
    C7
    C8
    C9
    *C1
    *C1
    *C2
    *C2
    *C3
    *C3

    C4
    C3
    C5
    C8
    C9
    C10
    C16
    C17
    H21
    H22
    H31
    H32

    C3
    C8
    C14
    C5
    C3
    C10
    OR
    C16
    C18
    C20

    C4
    C9
    C15
    C18
    H31
    H101
    HR
    H163
    H183
    H203
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C9
    C15
    C9
    C3
    C11

    C5
    C10
    OR
    C19
    H32
    H111

    C5 C6 C6 C1
    C10 C11 C11 C12
    C13 C20
    C4 H41 C4 H42
    C12 H121 C14 H141

    C17 H171 C17 H172 C17 H173


    C19 H191 C19 H192 C19 H193
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C5
    C5
    C5
    C8
    C9
    C10
    C8
    C11
    C9
    C12
    C10
    C13
    C11
    C14
    C12
    C15
    C13
    OR
    OR
    C14
    C6
    H161
    H161
    C6
    H171
    H171
    C6
    C4
    H181
    H181
    C8
    H191
    H191
    C12
    H201
    H201

    C3
    C3
    C1
    C6
    C7
    C8
    C9
    C9
    C10
    C10
    C11
    C11
    C12
    C12
    C13
    C13
    C14
    C14
    C14
    C15
    C1
    C1
    C1
    C1
    C1
    C1
    C4
    C5
    C5
    C5
    C9
    C9
    C9
    C13
    C13
    C13

    *C4
    *C4
    *C6
    *C7
    *C8
    *C9
    C10
    *C10
    C11
    *C11
    C12
    *C12
    C13
    *C13
    C14
    *C14
    C15
    *C15
    *C15
    OR
    C16
    *C16
    *C16
    C17
    *C17
    *C17
    *C5
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    C20
    *C20
    *C20

    H41
    H42
    C7
    H71
    H81
    C19
    C11
    H101
    C12
    H111
    C13
    H121
    C14
    C20
    C15
    H141
    OR
    H151
    H152
    HR
    H161
    H162
    H163
    H171
    H172
    H173
    C18
    H181
    H182
    H183
    H191
    H192
    H193
    H201
    H202
    H203

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI RTAL
    !
    GROUP
    ATOM C1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM C6
    GROUP
    ATOM C7
    ATOM H71
    ATOM C8
    ATOM H81
    ATOM C9

    0.00 ! C20H28O retinal, nomenclature from PDB based on retinol


    CG301
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG2DC2
    CG2DC2

    0.00
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    0.00
    0.00

    CG2DC1
    HGA4
    CG2DC1
    HGA4
    CG2DC2

    -0.15
    0.15
    -0.15
    0.15
    0.00

    ATOM C10
    ATOM H101
    GROUP
    ATOM C11
    ATOM H111
    ATOM C12
    ATOM H121
    ATOM C13
    GROUP
    ATOM C14
    ATOM H141
    ATOM C15
    ATOM O15
    ATOM H15
    GROUP
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    GROUP
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173
    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183
    GROUP
    ATOM C19
    ATOM H191
    ATOM H192
    ATOM H193
    GROUP
    ATOM C20
    ATOM H201
    ATOM H202
    ATOM H203

    CG2DC2 -0.15
    HGA4
    0.15

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C7
    C13
    C16
    H21
    H71
    H161
    H181
    H201

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C2
    C6
    C1
    C6
    C7
    C8
    C2
    C2
    C3

    C1
    C6
    C12
    C1
    C2
    C7
    C16
    C18
    C20

    CG2DC1
    HGA4
    CG2DC1
    HGA4
    CG2DC2
    CG2DC2
    HGA4
    CG2O4
    OG2D1
    HGR52
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    C2
    C3
    C1
    C6
    C7
    C8
    C9
    C6
    C6
    C1

    -0.15
    0.15
    -0.15
    0.15 !
    0.00 !H162 H163 H171 H172
    !
    \ |
    | /
    -0.04 !H161-C16
    C17-H173
    H191 H192
    0.15 !
    \ /
    \ /
    0.27 ! H21
    C1
    H71
    H81
    C19
    -0.51 !
    \ / \
    |
    |
    / \
    0.13 ! H22-C2
    C6------C7=====C8----C9
    H193
    !
    |
    ||
    ||
    -0.27 ! H31-C3
    C5 H181
    C10-H101
    0.09 !
    / \ / \ /
    |
    0.09 ! H32
    C4
    C18-H182
    C11-H111
    0.09 !
    / \
    \
    ||
    !
    H41 H42 H183
    C12-H121 H201
    -0.27 !
    |
    /
    0.09 !
    C13---C20-H202
    0.09 !
    ||
    \
    0.09 !
    C14-H141 H203
    !
    |
    -0.27 !
    C15
    0.09 !
    / \\
    0.09 !
    H15 O15
    0.09 !
    !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !
    !
    -0.27 !
    0.09 !
    0.09 !
    0.09 !

    C2
    C7
    C13
    C1
    C2
    C8
    C16
    C18
    C20

    C3
    C8
    C14
    C17
    H22
    H81
    H162
    H182
    H202

    C3
    C4
    C2
    C7
    C8
    C9
    C10
    *C1
    *C1
    *C2

    C4
    C5
    C3
    C8
    C9
    C10
    C11
    C16
    C17
    H21

    C3
    C8
    C14
    C5
    C3
    C10
    C16
    C18
    C20

    C4
    C9
    C15
    C18
    H31
    H101
    H163
    H183
    H203
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C9
    C15
    C9
    C3
    C11
    C17
    C19

    C5
    C10
    O15
    C19
    H32
    H111
    H171
    H191
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5
    C10
    C15
    C13
    C4
    C12
    C17
    C19

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00

    C6
    C11
    H15
    C20
    H41
    H121
    H172
    H192

    C6 C1
    C11 C12
    C4
    C14
    C17
    C19
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H42
    H141
    H173
    H193
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C3
    C4
    C4
    C5
    C5
    C5
    C8
    C9
    C10
    C11
    C9
    C12
    C10
    C13
    C11
    C14
    C12
    C15
    C13
    O15
    C6
    H161
    H161
    C6
    H171
    H171
    C6
    C4
    H181
    H181
    C8
    H191
    H191
    C12
    H201
    H201

    C1
    C2
    C2
    C3
    C3
    C1
    C6
    C7
    C8
    C9
    C10
    C10
    C11
    C11
    C12
    C12
    C13
    C13
    C14
    C14
    C1
    C1
    C1
    C1
    C1
    C1
    C4
    C5
    C5
    C5
    C9
    C9
    C9
    C13
    C13
    C13

    *C2
    *C3
    *C3
    *C4
    *C4
    *C6
    *C7
    *C8
    *C9
    *C10
    C11
    *C11
    C12
    *C12
    C13
    *C13
    C14
    *C14
    C15
    *C15
    C16
    *C16
    *C16
    C17
    *C17
    *C17
    *C5
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    C20
    *C20
    *C20

    H22
    H31
    H32
    H41
    H42
    C7
    H71
    H81
    C19
    H101
    C12
    H111
    C13
    H121
    C14
    C20
    C15
    H141
    O15
    H15
    H161
    H162
    H163
    H171
    H172
    H173
    C18
    H181
    H182
    H183
    H191
    H192
    H193
    H201
    H202
    H203

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI RTAC
    !
    GROUP
    ATOM C1
    ATOM C16
    ATOM H161
    ATOM H162
    ATOM H163
    ATOM C17
    ATOM H171
    ATOM H172
    ATOM H173
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41

    -1.00 ! C20H27O2 all-trans-retinoic acid, nomenclature from PDB


    CG301 0.00
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321 -0.18
    HGA2
    0.09

    ATOM H42
    GROUP
    ATOM C5
    ATOM C6
    GROUP
    ATOM C18
    ATOM H181
    ATOM H182
    ATOM H183
    GROUP
    ATOM C7
    ATOM H71
    ATOM C8
    ATOM H81
    GROUP
    ATOM C9
    ATOM C19
    ATOM H191
    ATOM H192
    ATOM H193
    ATOM C10
    ATOM H101
    GROUP
    ATOM C11
    ATOM H111
    ATOM C12
    ATOM H121
    GROUP
    ATOM C13
    ATOM C20
    ATOM H201
    ATOM H202
    ATOM H203
    GROUP
    ATOM C14
    ATOM H141
    ATOM C15
    ATOM O29
    ATOM O29B

    HGA2

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C2
    C7
    C13
    C16
    H21
    H71
    H161
    H181
    H201

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C6
    C12
    C1
    C2
    C7
    C16
    C18
    C20

    C1
    C2
    C6
    C1
    C6
    C7
    C2
    C2
    C6
    H161

    0.09

    CG2DC2 0.00
    CG2DC2 0.00
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    CG2DC1
    HGA4
    CG2DC1
    HGA4

    -0.15
    0.15
    -0.15
    0.15

    CG2DC2
    CG331
    HGA3
    HGA3
    HGA3
    CG2DC2
    HGA4

    0.00
    -0.27
    0.09
    0.09
    0.09
    -0.15
    0.15

    CG2DC1
    HGA4
    CG2DC1
    HGA4

    -0.15
    0.15
    -0.15
    0.15

    CG2DC2
    CG331
    HGA3
    HGA3
    HGA3

    0.00
    -0.27
    0.09
    0.09
    0.09

    CG2DC2
    HGA4
    CG2O3
    OG2D2
    OG2D2

    -0.25
    0.15
    0.62
    -0.76
    -0.76

    C2
    C3
    C1
    C6
    C7
    C8
    C6
    C6
    C1
    C1

    C2
    C7
    C13
    C1
    C2
    C8
    C16
    C18
    C20
    C3
    C4
    C2
    C7
    C8
    C9
    *C1
    *C1
    C16
    *C16

    !H162 H163 H171 H172


    !
    \ |
    | /
    !H161-C16
    C17-H173
    H191 H192
    !
    \ /
    \ /
    ! H21
    C1
    H71
    H81
    C19
    !
    \ / \
    |
    |
    / \
    ! H22-C2
    C6------C7=====C8----C9
    H193
    !
    |
    ||
    ||
    ! H31-C3
    C5 H181
    C10-H101
    !
    / \ / \ /
    |
    ! H32
    C4
    C18-H182
    C11-H111
    !
    / \
    \
    ||
    !
    H41 H42 H183
    C12-H121 H201
    !
    |
    /
    !
    C13---C20-H202
    !
    ||
    \
    !
    C14-H141 H203
    !
    |
    !
    C15=O29
    !
    | (-)
    !
    O29B
    !

    C3
    C8
    C14
    C17
    H22
    H81
    H162
    H182
    H202
    C4
    C5
    C3
    C8
    C9
    C10
    C16
    C17
    H161
    H162

    C3
    C8
    C14
    C5
    C3
    C10
    C16
    C18
    C20

    C4
    C9
    C15
    C18
    H31
    H101
    H163
    H183
    H203
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C9
    C15
    C9
    C3
    C11
    C17
    C19

    C5
    C10
    O29
    C19
    H32
    H111
    H171
    H191
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5
    C10
    C15
    C13
    C4
    C12
    C17
    C19

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00

    C6
    C11
    O29B
    C20
    H41
    H121
    H172
    H192

    C6 C1
    C11 C12
    C4
    C14
    C17
    C19
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H42
    H141
    H173
    H193
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H161
    C6
    H171
    H171
    C3
    C3
    C4
    C4
    C5
    C5
    C6
    C4
    H181
    H181
    C5
    C8
    C9
    C10
    C8
    H191
    H191
    C8
    C11
    C9
    C12
    C10
    C13
    C11
    C14
    C12
    H201
    H201
    C12
    C15
    C13
    O29

    C1
    C1
    C1
    C1
    C1
    C1
    C2
    C2
    C3
    C3
    C4
    C5
    C5
    C5
    C1
    C6
    C7
    C8
    C9
    C9
    C9
    C9
    C9
    C10
    C10
    C11
    C11
    C12
    C12
    C13
    C13
    C13
    C13
    C13
    C14
    C14

    *C16
    C17
    *C17
    *C17
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C5
    C18
    *C18
    *C18
    *C6
    *C7
    *C8
    *C9
    C19
    *C19
    *C19
    C10
    *C10
    C11
    *C11
    C12
    *C12
    C13
    *C13
    C20
    *C20
    *C20
    C14
    *C14
    C15
    *C15

    H163
    H171
    H172
    H173
    H21
    H22
    H31
    H32
    H41
    H42
    C18
    H181
    H182
    H183
    C7
    H71
    H81
    C19
    H191
    H192
    H193
    C11
    H101
    C12
    H111
    C13
    H121
    C14
    C20
    H201
    H202
    H203
    C15
    H141
    O29
    O29B

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    PATCH FIRST NONE LAST NONE


    !naming convention changed in following model compounds to
    !standard double bond nomenclature, vs. conjugated double
    !bond nomenclature. Done due to the double bonds not being
    !conjugated with other double bonds.
    RESI PRAC
    !
    GROUP
    ATOM C1 CG2D2
    ATOM H11 HGA5
    ATOM H12 HGA5
    GROUP
    ATOM C2 CG2D1
    ATOM H21 HGA4
    ATOM CG CG2O3
    ATOM OD1 OG2D2
    ATOM OD2 OG2D2

    -1.00 ! C3H3O2 2-propenoic acid


    -0.42 !
    0.21 !
    0.21 ! H11
    OD1
    ! \
    ||
    -0.25 !
    C1 CG
    0.15 ! / \\ / \
    0.62 ! H12 C2 OD2 (-)
    -0.76 !
    |
    -0.76 !
    H21

    BOND C1 H11 C1 H12 C1 C2 C2


    BOND C2 CG CG OD1 CG OD2

    H21

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC

    C1
    OD1
    H11
    H11
    CG

    C2
    C2
    C1
    C2
    C1

    CG
    *CG
    C2
    *C1
    *C2

    OD1
    OD2
    CG
    H12
    H21

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI PROL
    0.00
    !
    GROUP
    ATOM C1 CG2D2 -0.42
    ATOM H11 HGA5
    0.21
    ATOM H12 HGA5
    0.21
    ATOM C2 CG2D1 -0.15
    ATOM H21 HGA4
    0.15
    GROUP
    ATOM C3 CG321
    0.05
    ATOM H31 HGA2
    0.09
    ATOM H32 HGA2
    0.09
    ATOM OR OG311 -0.65
    ATOM HR HGP1
    0.42
    BOND C1 C2 C2 C3
    BOND H11 C1 H12 C1
    BOND H32 C3
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C2
    H11
    H11
    C3
    OR
    OR

    C2
    C3
    C1
    C2
    C1
    C2
    C2

    C3
    OR
    C2
    *C1
    *C2
    *C3
    *C3

    ! C3H6O 3-propenol (1-hydroxy-2-propene)


    !
    ! H11
    H31
    ! \
    |
    ! C1
    C3-OR
    ! / \\ / | \
    ! H12 C2 H32 HR
    !
    |
    !
    H21

    C3 OR
    H21 C2

    OR
    HR
    C3
    H12
    H21
    H31
    H32

    OR HR
    H31 C3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    60.00
    180.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI PRAL
    GROUP
    ATOM C1 CG2D2
    ATOM H11 HGA5
    ATOM H12 HGA5
    ATOM C2 CG2D1
    ATOM H21 HGA4
    ATOM CG CG2O4
    ATOM OD1 OG2D1
    ATOM H HGR52

    0.00 ! C3H4O 2-propenal (acrolein)


    -0.42
    0.21
    0.21
    -0.04
    0.15
    0.27
    -0.51
    0.13

    !
    ! H11
    OD1
    ! \
    ||
    ! C1
    CG
    ! / \\ / \
    ! H12 C2 H
    !
    |
    !
    H21

    BOND C1 H11 C1 H12 C1 C2 C2 H21


    BOND C2 CG CG OD1 CG H
    IMPR CG C2 OD1 H
    IC
    IC
    IC
    IC
    IC

    C1
    H11
    H11
    CG
    OD1

    C2
    C1
    C2
    C1
    C2

    RESI SCH1
    GROUP
    ATOM C1 CG331

    CG
    C2
    *C1
    *C2
    *CG

    OD1
    CG
    H12
    H21
    H

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00

    0.00 ! C3H7N Schiff's base model compound 1, deprotonated


    -0.05 !

    H11

    H31

    ATOM H11
    ATOM H12
    ATOM H13
    ATOM N2
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43

    HGA3
    HGA3
    HGA3
    NG2D1
    CG2D1
    HGA4

    0.09
    0.09
    0.09
    -0.60
    0.23
    0.15

    !
    \
    /
    ! H12--C1-N2=C3
    H41
    !
    /
    \ /
    ! H13
    C4--H42
    !
    \
    !
    H43

    CG331
    HGA3
    HGA3
    HGA3

    !
    -0.27 !
    0.09 !
    0.09
    0.09

    BOND C1 H11 C1 H12 C1 H13


    BOND C1 N2 N2 C3 C3 H31
    BOND C3 C4 C4 H41 C4 H42 C4 H43
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    N2
    C3
    H11
    H11
    C4
    H41
    H41

    N2
    C3
    N2
    N2
    N2
    N2
    C3
    C3

    RESI SCH2
    GROUP
    ATOM C1 CG334
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    ATOM N2 NG2P1
    ATOM H21 HGP2
    ATOM C3 CG2D1
    ATOM H31 HGR52
    GROUP
    ATOM C4 CG331
    ATOM H41 HGA3
    ATOM H42 HGA3
    ATOM H43 HGA3

    C3
    C4
    C1
    *C1
    *C1
    *C3
    *C4
    *C4

    C4
    H41
    H11
    H12
    H13
    H31
    H42
    H43

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    0.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.00 ! C3H8N Schiff's base model compound 2, protonated


    0.18
    0.09
    0.09
    0.09
    -0.40
    0.38
    0.37
    0.20

    ! H11 H21
    H31
    !
    \ |
    /
    ! H12--C1-N2=C3
    H41
    !
    / (+) \ /
    ! H13
    C4--H42
    !
    \
    !
    H43
    ! hydrogen with intermediate VDW radius

    !
    -0.27 !
    0.09 !
    0.09
    0.09

    BOND C1 H11 C1 H12 C1 H13


    BOND C1 N2 N2 H21 N2 C3 C3 H31
    BOND C3 C4 C4 H41 C4 H42 C4 H43
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    N2
    C1
    C3
    H11
    H11
    C4
    H41
    H41

    N2
    C3
    C3
    N2
    N2
    N2
    N2
    C3
    C3

    RESI SCH3
    GROUP
    ATOM C1 CG334
    ATOM H11 HGA3
    ATOM H12 HGA3

    C3
    C4
    *N2
    C1
    *C1
    *C1
    *C3
    *C4
    *C4

    C4
    H41
    H21
    H11
    H12
    H13
    H31
    H42
    H43

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    0.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.00 ! C4H8N Schiff's base model compound 3, protonated


    0.18 ! H11 H21
    H31
    0.09 !
    \ |
    /
    0.09 ! H12--C1-N2=C3
    H51

    ATOM H13
    ATOM N2
    ATOM H21
    ATOM C3
    ATOM H31
    GROUP
    ATOM C4
    ATOM H41
    ATOM C5
    ATOM H51
    ATOM H52

    HGA3
    0.09 !
    / (+) \
    /
    NG2P1 -0.40 ! H13
    C4=C5
    HGP2
    0.38 !
    /
    \
    CG2DC1 0.37 !
    H41
    H52
    HGR52
    0.20 ! hydrogen with intermediate VDW radius

    BOND
    BOND
    BOND
    BOND

    H11
    N2
    C4
    C5

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C3
    C4

    CG2DC2 -0.15
    HGA4
    0.15
    CG2DC3 -0.42
    HGA5
    0.21
    HGA5
    0.21

    C1
    N2
    H11
    H11
    H11
    C3
    C4
    C5
    C3
    H51

    C1
    N2
    C4
    C5

    N2
    C3
    C1
    N2
    N2
    C1
    N2
    C3
    C4
    C4

    C3
    C4
    N2
    *C1
    *C1
    *N2
    *C3
    *C4
    C5
    *C5

    H12 C1 H13
    H21 N2 C3 C3 H31
    H41
    H51 C5 H52
    C4
    C5
    C3
    H12
    H13
    H21
    H31
    H41
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !/home/alex/param/general/Cyprus/toppar
    !toppar_all22_flavopyridol_apr05.str
    !piperidine models only
    RESI PIP1
    about the
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    ATOM H1C
    ATOM N1
    ATOM HNA
    ATOM C12
    ATOM H12A
    ATOM H12B
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C13
    ATOM H13A
    ATOM H13B
    GROUP
    ATOM C14
    ATOM H14A
    ATOM H14B
    GROUP
    ATOM C15
    ATOM H15A

    1.00 ! C6H14N N-methyl piperidinium


    !methyl axial to ring
    !Note that PIP1 and 2 only differ by the configuration
    N
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CG334
    HGA3
    HGA3
    HGA3
    NG3P1
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2

    0.15
    0.09
    0.09
    0.09
    -0.40
    0.32
    0.15
    0.09
    0.09
    0.15
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18 !
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18!
    0.09
    0.09

    CG321
    HGA2

    -0.18
    0.09

    C15--C16
    /

    \
    (+) N1--C1
    \
    /
    C13--C12

    C14

    ATOM
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H15B
    C1
    N1
    N1
    C12
    C13
    C15
    C16

    C16
    N1
    C12
    C13
    C12
    H1A
    H1A
    H1A
    C16
    C12
    C13
    H12A
    C15
    C15
    C14
    H13A
    C15
    H14A
    C14
    C14

    HGA2
    H1A
    HNA
    C16
    C13
    C14
    H15A
    H16B
    N1
    C12
    C13
    C14
    C16
    N1
    N1
    C1
    C1
    C1
    N1
    N1
    N1
    N1
    C12
    C12
    C13
    C13
    C16
    C16

    C12
    C13
    C14
    C15
    *N1
    *C1
    *C1
    N1
    *N1
    *N1
    *C12
    *C12
    *C16
    *C16
    *C13
    *C13
    *C14
    *C14
    *C15
    *C15

    0.09
    C1 H1B

    C1

    H1C

    C1

    N1
    C13
    C14
    C15

    C12
    C13
    C14
    C15

    H12A
    H13B
    H14B
    C16

    C12 H12B

    C12
    H13A
    H14A
    H15B

    C13
    C14
    C15
    C16
    C1
    H1B
    H1C
    C16
    C12
    HNA
    H12A
    H12B
    H16A
    H16B
    H13A
    H13B
    H14A
    H14B
    H15A
    H15B

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    60.00
    -60.00
    60.00
    -120.00
    120.00
    -120.00
    180.00
    -120.00
    -120.00
    120.00
    120.00
    120.00
    -120.00
    120.00
    120.00
    -120.00
    -120.00
    120.00
    -120.00

    N1

    C14 C15
    C16 H16A
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    PATCH FIRST NONE LAST NONE


    RESI PIP2
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    ATOM H1C
    ATOM N1
    ATOM HNA
    ATOM C12
    ATOM H12A
    ATOM H12B
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C13
    ATOM H13A
    ATOM H13B
    GROUP
    ATOM C14
    ATOM H14A
    ATOM H14B
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B

    1.00 ! C6H14N N-methyl piperidinium


    !methyl equitorial to ring
    CG334
    HGA3
    HGA3
    HGA3
    NG3P1
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2

    0.15
    0.09
    0.09
    0.09
    -0.40
    0.32
    0.15
    0.09
    0.09
    0.15
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    C15--C16
    /

    \
    (+) N1--C1
    \
    /
    C13--C12

    C14

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C1
    N1
    N1
    C12
    C13
    C15
    C16

    H1A
    HNA
    C16
    C13
    C14
    H15A
    H16B

    C1

    H1B

    C1

    H1C

    C1

    N1
    C13
    C14
    C15

    C12
    H13A
    H14A
    H15B

    C12
    C13
    C14
    C15

    H12A
    H13B
    H14B
    C16

    C12 H12B

    IC C16 N1
    C12 C13
    IC N1
    C12 C13 C14
    IC C12 C13 C14 C15
    IC C13 C14 C15 C16
    IC C12 C16 *N1 C1
    IC H1A N1
    *C1 H1B
    IC H1A N1
    *C1 H1C
    IC H1A C1
    N1
    C16
    IC C16 C1
    *N1 C12
    IC C12 C1
    *N1 HNA
    IC C13 N1
    *C12 H12A
    IC H12A N1
    *C12 H12B
    IC C15 N1
    *C16 H16A
    IC C15 N1
    *C16 H16B
    IC C14 C12 *C13 H13A
    IC H13A C12 *C13 H13B
    IC C15 C13 *C14 H14A
    IC H14A C13 *C14 H14B
    IC C14 C16 *C15 H15A
    IC C14 C16 *C15 H15B
    PATCH FIRST NONE LAST NONE
    RESI PIP3
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    ATOM H1C
    ATOM N1
    ATOM HNA
    ATOM C12
    ATOM H12A
    ATOM H12B
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C13
    ATOM H13
    ATOM O3
    ATOM HO3
    GROUP
    ATOM C14
    ATOM H14A
    ATOM H14B
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    BOND
    BOND
    BOND

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    N1

    C14 C15
    C16 H16A

    -60.00
    60.00
    -60.00
    60.00
    120.00
    120.00
    -120.00
    180.00
    -120.00
    120.00
    120.00
    120.00
    120.00
    -120.00
    120.00
    120.00
    -120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.00 ! C6H14NO 3-hydroxy-N-methyl piperidinium


    CG334
    HGA3
    HGA3
    HGA3
    NG3P1
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2

    0.15
    0.09
    0.09
    0.09
    -0.40
    0.32
    0.15
    0.09
    0.09
    0.15
    0.09
    0.09

    ! group charge should be 1.0


    !
    !
    C15--C16
    !
    /
    \
    !
    ----C14
    (+) N1--C1
    !
    \
    /
    !
    C13--C12
    !
    /
    !
    H-O3
    !
    !
    !

    CG311
    HGA1
    OG311
    HGP1

    0.14 !
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2
    C1
    N1
    N1

    -0.18
    0.09
    0.09
    H1A
    HNA
    C16

    C1

    H1B

    C1

    H1C

    C1

    N1

    N1

    C12

    C12

    H12A

    C12 H12B

    BOND
    C12 C13
    C13 H13
    C13 O3
    BOND
    C13 C14
    C14 H14A
    C14 H14B
    BOND
    C15 H15A
    C15 H15B
    C15 C16
    BOND
    C16 H16B
    IC C14 C15 C16 N1
    .0000
    .00 -60.00
    IC C15 C16 N1
    C12
    .0000
    .00 60.00
    IC C16 N1
    C12 C13
    .0000
    .00 -60.00
    IC N1
    C12 C13 C14
    .0000
    .00 60.00
    IC C12 C16 *N1 C1
    .0000
    .00 120.00
    IC C12 C16 *N1 HNA
    .0000
    .00 -120.00
    IC C16 N1
    C1
    H1A
    .0000
    .00 120.00
    IC H1A N1
    *C1 H1B
    .0000
    .00 120.00
    IC H1A N1
    *C1 H1C
    .0000
    .00 -120.00
    IC C13 N1
    *C12 H12A
    .0000
    .00 120.00
    IC C13 N1
    *C12 H12B
    .0000
    .00 -120.00
    IC C15 N1
    *C16 H16A
    .0000
    .00 120.00
    IC C15 N1
    *C16 H16B
    .0000
    .00 -120.00
    IC C12 C14 *C13 O3
    .0000
    .00 120.00
    IC C12 C14 *C13 H13
    .0000
    .00 -120.00
    IC C12 C13 O3
    HO3
    .0000
    .00 60.00
    IC C15 C13 *C14 H14A
    .0000
    .00 120.00
    IC C15 C13 *C14 H14B
    .0000
    .00 -120.00
    IC C14 C16 *C15 H15A
    .0000
    .00 120.00
    IC C14 C16 *C15 H15B
    .0000
    .00 -120.00
    PATCH FIRST NONE LAST NONE

    O3 HO3
    C14 C15
    C16 H16A
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00
    .00

    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000
    .0000

    !RESI DUM
    0.00 ! DUMMY ATOM
    !GROUP
    !ATOM DUM DUM 0.00
    !PATCHING FIRST NONE LAST NONE
    !RESI HE
    0.00 ! helium
    !GROUP
    !ATOM HE HE
    0.00
    !PATCHING FIRST NONE LAST NONE
    !RESI NE
    0.00 ! neon
    !GROUP
    !ATOM NE NE
    0.00
    !PATCHING FIRST NONE LAST NONE
    !adm jr(?), july2006
    RESI ALF4
    -1.00 ! AlF4 Aluminum tetraflouride, tetrahedral geometry
    GROUP
    ATOM AL1 ALG1
    1.16
    ATOM F1 FGP1
    -0.54
    ATOM F2 FGP1
    -0.54
    ATOM F3 FGP1
    -0.54
    ATOM F4 FGP1
    -0.54
    BOND AL1 F1 AL1 F2 AL1 F3 AL1 F4
    IC
    IC

    F2
    F2

    F1
    F1

    *AL1 F3
    *AL1 F4

    RESI FLUB
    0.00
    GROUP
    ATOM C1 CG2R61 -0.10
    ATOM H1 HGR62
    0.15 !

    0.0000
    0.0000

    0.00 120.00
    0.00 -120.00

    0.00
    0.00

    0.0000
    0.0000

    ! C6H5F fluorobenzene, adm jr.


    ! atom numbering based on difluorotoluene
    H5

    H4

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    H2
    C3
    H3
    C4
    H4
    C5
    H5
    C6
    F6
    C1
    C3
    C6
    C2
    C6
    C3
    C1
    C4
    C2
    C5
    C6
    C5

    RESI BROB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM BR
    BOND C1
    BOND C3
    BOND C6
    IC C2
    IC C6
    IC C3
    IC C1
    IC C4
    IC C2
    IC C5
    IC C6
    IC C5
    RESI CHLB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.10
    HGR62
    0.15
    CG2R66 0.11
    FGR1
    -0.21
    H1 C1 C2
    H3 C3 C4
    C1 C6 F6
    C6 *C1 H1
    C1 C2 C3
    C1 *C2 H2
    C2 C3 C4
    C2 *C3 H3
    C3 C4 C5
    C3 *C4 H4
    C4 *C5 H5
    C1 *C6 F6

    !
    \ ___ /
    !
    C5---C4
    !
    /
    \
    ! F6--C6
    C3--H3
    !
    \\
    //
    !
    C1---C2
    !
    /
    \
    !
    H1
    H2
    C2
    C4

    H2
    H4

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C2
    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C3
    C5

    C5

    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    180.00
    180.00

    0.000 ! C6H5Br bromobenzene


    !
    CG2R61 -0.06 !
    HGR62
    0.15 !
    H5
    H4
    CG2R61 -0.115 !
    \ ___ /
    HGR61
    0.115 !
    C5---C4
    CG2R61 -0.115 !
    /
    \
    HGR61
    0.115 ! BR--C6
    C3--H3
    CG2R61 -0.115 !
    \\ //
    HGR61
    0.115 !
    C1---C2
    CG2R61 -0.06 !
    /
    \
    HGR62
    0.15 !
    H1
    H2
    CG2R61 -0.08 !
    BRGR1 -0.10 !
    H1 C1 C2 C2 H2 C2 C3
    H3 C3 C4 C4 H4 C4 C5 C5
    C1 C6 BR
    C6 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 C4 C5 0.0000
    0.00
    0.00
    C3 *C4 H4 0.0000
    0.00 180.00
    C4 *C5 H5 0.0000
    0.00 180.00
    C1 *C6 BR 0.0000
    0.00 180.00

    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.000 ! C6H5Cl compound #


    !
    -0.10 !
    0.15 !
    H5
    H4
    -0.115 !
    \ ___ /
    0.115 !
    C5---C4
    -0.115 !
    /
    \
    0.115 ! CL--C6
    C3--H3
    -0.115 !
    \\ //
    0.115 !
    C1---C2

    H5

    C5

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    H5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5

    C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    : chlorobenzene

    ATOM
    ATOM
    ATOM
    ATOM
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C5
    H5
    C6
    CL
    C1
    C3
    C6
    C2
    C6
    C3
    C1
    C4
    C2
    C5
    C6
    C5

    RESI IODB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM I6
    BOND C1
    BOND C3
    BOND C6
    IC C2
    IC C6
    IC C3
    IC C1
    IC C4
    IC C2
    IC C5
    IC C6
    IC C5
    RESI UREA
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H31
    ATOM H32

    CG2R61 -0.10
    HGR62
    0.15
    CG2R61 0.03
    CLGR1 -0.13
    H1 C1 C2
    H3 C3 C4
    C1 C6 CL
    C6 *C1 H1
    C1 C2 C3
    C1 *C2 H2
    C2 C3 C4
    C2 *C3 H3
    C3 C4 C5
    C3 *C4 H4
    C4 *C5 H5
    C1 *C6 CL

    !
    !

    /
    H1

    \
    H2

    !
    !
    C2
    C4

    H2
    H4

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C2
    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C3
    C5

    C5

    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    180.00
    180.00

    0.000 ! C6H5I iodobenzene


    !
    CG2R61 -0.06 !
    HGR62
    0.14 !
    H5
    H4
    CG2R61 -0.115 !
    \ ___ /
    HGR61
    0.115 !
    C5---C4
    CG2R61 -0.115 !
    /
    \
    HGR61
    0.115 ! I--C6
    C3--H3
    CG2R61 -0.115 !
    \\ //
    HGR61
    0.115 !
    C1---C2
    CG2R61 -0.06 !
    /
    \
    HGR62
    0.14 !
    H1
    H2
    CG2R61 -0.08 !
    IGR1
    -0.08 !
    H1 C1 C2 C2 H2 C2 C3
    H3 C3 C4 C4 H4 C4 C5 C5
    C1 C6 I6
    C6 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 C4 C5 0.0000
    0.00
    0.00
    C3 *C4 H4 0.0000
    0.00 180.00
    C4 *C5 H5 0.0000
    0.00 180.00
    C1 *C6 I6 0.0000
    0.00 180.00
    0.00 ! CH4N2O Urea, adm
    NG2S2
    HGP1
    HGP1
    CG2O6
    OG2D1
    NG2S2
    HGP1
    HGP1

    -0.69
    0.34
    0.34
    0.60
    -0.58
    -0.69
    0.34
    0.34

    BOND C2 O2 C2 N1 C2 N3
    BOND N1 H11 N1 H12
    BOND N3 H31 N3 H32
    IMPR O2 N1 N3 C2

    H5

    C5

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    H5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5

    C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC

    O2
    H11
    H11
    N3
    N1
    H31

    C2
    C2
    N1
    N1
    C2
    C2

    N1
    *N1
    C2
    *C2
    N3
    *N3

    H11
    H12
    N3
    O2
    H31
    H32

    RESI PY01
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM C3
    ATOM H31
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM C6
    ATOM H61

    0.000 !
    !
    OG3R60 -0.32 !
    CG2D1O -0.04 !
    HGA4
    0.20 !
    CG2D1 -0.15 !
    HGA4
    0.15 !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    CG2D1 -0.15 !
    HGA4
    0.15 !
    CG2D1O -0.04 !
    HGA4
    0.20 !

    BOND O1
    BOND C3
    BOND C5

    C2
    C4
    C6

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C6
    O1
    C2
    C3
    C4
    C5
    C5
    C6
    C5

    O1
    C2
    C3
    O1
    C2
    C3
    C3
    C4
    O1

    C2
    C4
    C6
    C2
    C3
    C4
    *C2
    *C3
    *C4
    *C4
    *C5
    *C6

    RESI PY02
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM C4
    ATOM H41
    ATOM C5
    ATOM H51
    ATOM C6
    ATOM H61

    OG3R60
    CG321
    HGA2
    HGA2
    CG2DC2
    HGA4
    CG2DC2
    HGA4
    CG2DC1
    HGA4
    CG2D1O
    HGA4

    BOND O1
    BOND C3
    BOND C5

    C2
    C4
    C6

    C2
    C4
    C6

    !mp2/6-31g* ring
    IC C6 O1
    C2
    IC O1 C2
    C3
    IC C2 C3
    C4
    IC C3 C4
    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5H6O 4H-Pyran, maybridge list, adm


    new atom type!!
    new atom type!!
    O1
    / \
    H21-C2
    C6-H61
    ||
    ||
    H31-C3
    C5-H51
    \ /
    C4
    / \
    H41 H42

    H21 C2
    H41 C4
    H61 C6

    C3 C3
    H42 C4
    O1

    C3
    C4
    C5
    H21
    H31
    H41
    H42
    H51
    H61

    H31
    C5 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 !
    !
    -0.37 !
    0.00 !
    0.09 !
    0.09 !
    -0.15 !
    0.15 !
    -0.15 !
    0.15 !
    -0.15 !
    0.15 !
    0.00 !
    0.19 !

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H51

    0.00
    0.00
    0.00
    180.00
    180.00
    120.00
    240.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5H6O 2H-Pyran, maybridge list, adm


    Note use of conjugated C types

    H21

    O1
    \ / \
    H22-C2
    C6-H61
    |
    ||
    H31-C3
    C5-H51
    \\ /
    C4
    |
    H41

    H21 C2
    H41 C4
    H61 C6
    C3
    C4
    C5
    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H22 C2
    C5 C5
    O1
    0.0000
    0.0000
    0.0000
    0.0000

    C3 C3
    H51

    0.00 51.00
    0.00 -42.00
    0.00
    8.00
    0.00 18.00

    H31

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C4
    C5
    C3
    C3
    C4
    C5
    C6
    C5

    C5
    C6
    O1
    O1
    C2
    C3
    C4
    O1

    C6
    O1
    *C2
    *C2
    *C3
    *C4
    *C5
    *C6

    O1
    C2
    H21
    H22
    H31
    H41
    H51
    H61

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -8.00
    -27.00
    120.00
    240.00
    180.00
    180.00
    180.00
    180.00

    RESI NITB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM N6
    ATOM O6A
    ATOM O6B
    BOND C1
    BOND C3
    BOND C6
    IC C2
    IC C6
    IC C3
    IC C1
    IC C4
    IC C2
    IC C5
    IC C6
    IC C5
    IC C1
    IC O6A

    0.000 ! C6H5NO2 nitrobenzene


    !
    CG2R61 -0.18 !
    HGR61
    0.16 !
    H5
    H4
    CG2R61 -0.115 !
    \ ___ /
    HGR61
    0.115 ! O6A
    C5---C4
    CG2R61 -0.115 !
    \ +
    /
    \
    HGR61
    0.115 ! - N6--C6
    C3--H3
    CG2R61 -0.115 !
    /
    \\
    //
    HGR61
    0.115 ! O6B
    C1---C2
    CG2R61 -0.18 !
    /
    \
    HGR61
    0.16 !
    H1
    H2
    CG2R61 0.32 !
    NG2O1
    0.40 !
    OG2N1 -0.34 !
    OG2N1 -0.34 !
    H1 C1 C2 C2 H2 C2 C3
    H3 C3 C4 C4 H4 C4 C5 C5
    C1 C6 N6 N6 O6A N6 O6B
    C6 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 C4 C5 0.0000
    0.00
    0.00
    C3 *C4 H4 0.0000
    0.00 180.00
    C4 *C5 H5 0.0000
    0.00 180.00
    C1 *C6 N6 0.0000
    0.00 180.00
    C6 N6 O6A 0.0000
    0.00 180.00
    C6 *N6 O6B 0.0000
    0.00 180.00

    RESI PYRL
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM N5
    ATOM H5
    BOND C1
    BOND C3
    IC C2
    IC N5
    IC C3
    IC C1
    IC C4
    IC N5

    0.000 ! C4H5N pyrrole


    ! H2
    H1
    CG2R51 -0.04 !
    \ ____ /
    HGR52
    0.14 !
    C2----C1
    CG2R51 -0.25 !
    |
    \
    HGR51
    0.15 !
    |
    N5--H5
    CG2R51 -0.25 !
    |____ /
    HGR51
    0.15 !
    C3----C4
    CG2R51 -0.04 !
    /
    \
    HGR52
    0.14 ! H3
    H4
    NG2R51 -0.35 !
    HGP1
    0.35 !
    H1 C1 C2 C2 H2 C2 C3 C3
    C4 C4 H4 C4 N5 N5 H5 N5
    N5 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 *C4 H4 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H5

    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    H3
    C1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC

    C4

    C1

    *N5 H5

    0.0000

    0.00 180.00

    0.00

    0.0000

    RESI FURA
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM O5
    BOND C1
    BOND C3
    IC C2
    IC O5
    IC C3
    IC C1
    IC C4
    IC O5

    0.00 ! C4H4O furan


    ! H2
    H1
    CG2R51 0.10 !
    \ ____ /
    HGR52
    0.14 !
    C2----C1
    CG2R51 -0.25 !
    |
    \
    HGR51
    0.15 !
    |
    O5
    CG2R51 -0.25 !
    |____ /
    HGR51
    0.15 !
    C3----C4
    CG2R51 0.10 !
    /
    \
    HGR52
    0.14 ! H3
    H4
    OG2R50 -0.28 !
    H1 C1 C2 C2 H2 C2 C3
    H3 C3 C4 C4 H4 C4 O5 O5
    O5 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 *C4 H4 0.0000
    0.00 180.00

    C1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI THIP
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM S5
    BOND C1
    BOND C3
    IC C2
    IC S5
    IC C3
    IC C1
    IC C4
    IC S5
    !
    RESI OXAZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM O5
    BOND C1
    BOND N3
    IC C2
    IC O5
    IC N3
    IC C1
    IC O5
    !

    0.000 ! C4H4S thiophene


    !
    CG2R51 -0.06 ! H2
    H1
    HGR52
    0.18 !
    \ ____ /
    CG2R51 -0.24 !
    C2----C1
    HGR51
    0.17 !
    |
    \
    CG2R51 -0.24 !
    |
    S5
    HGR51
    0.17 !
    |____ /
    CG2R51 -0.06 !
    C3----C4
    HGR52
    0.18 !
    /
    \
    SG2R50 -0.10 ! H3
    H4
    H1 C1 C2 C2 H2 C2 C3
    H3 C3 C4 C4 H4 C4 S5 S5
    S5 *C1 H1 0.0000
    0.00 180.00
    C1 C2 C3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 C3 C4 0.0000
    0.00
    0.00
    C2 *C3 H3 0.0000
    0.00 180.00
    C3 *C4 H4 0.0000
    0.00 180.00

    C1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H3NO oxazole


    ! H2
    H1
    CG2R51 0.11 !
    \ ____ /
    HGR52
    0.12 !
    C2----C1
    CG2R51 0.15 !
    |
    \
    HGR52
    0.11 !
    |
    O5
    NG2R50 -0.61 !
    |____ /
    CG2R53 0.22 !
    N3----C4
    HGR52
    0.19 !
    \
    OG2R50 -0.29 !
    H4
    H1 C1 C2 C2 H2 C2 N3
    C4 C4 H4 C4 O5 O5 C1
    O5 *C1 H1 0.0000
    0.00 180.00
    C1 C2 N3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 N3 C4 0.0000
    0.00
    0.00
    N3 *C4 H4 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI ISOX
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM O5
    BOND C1
    BOND C3
    IC C1
    IC O5
    IC C2
    IC C3
    IC N4
    !
    RESI THAZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM S5
    BOND C1
    BOND N3
    IC C1
    IC S5
    IC C2
    IC N3
    IC S5
    !
    RESI ISOT
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM S5
    BOND C1
    BOND C3
    IC S5
    IC C1
    IC C2
    IC C3
    IC N4
    !
    RESI PYRZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2

    CG2R51
    HGR52
    CG2R51
    HGR51
    CG2R52
    HGR52
    NG2R50
    OG2R50

    0.000 ! C3H3NO isoxazole


    ! H2
    H1
    0.28 !
    \ ____ /
    0.13 !
    C2----C1
    -0.43 !
    |
    \
    0.18 !
    |
    O5
    0.35 !
    |____ /
    0.11 !
    C3----N4
    -0.45 !
    /
    -0.17 ! H3

    H1
    N4
    C2
    C1
    O5
    C1
    C2

    C1
    C3
    C3
    C2
    *C1
    *C2
    *C3

    C2
    H3
    N4
    C3
    H1
    H2
    H3

    C2 H2
    N4 O5
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C2
    O5
    0.00
    0.00
    0.00
    0.00
    0.00

    C3
    C1
    0.00
    0.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H3NS thiazole


    ! H2
    H1
    CG2R51 -0.30 !
    \ ____ /
    HGR52
    0.21 !
    C2----C1
    CG2R51 0.20 !
    |
    \
    HGR52
    0.13 !
    |
    S5
    NG2R50 -0.61 !
    |____ /
    CG2R53 0.22 !
    N3----C4
    HGR52
    0.14 !
    \
    SG2R50 0.01 !
    H4
    H1 C1 C2 C2 H2 C2 N3
    C4 C4 H4 C4 S5 S5 C1
    C2 N3 C4 0.0000
    0.00
    0.00
    C1 C2 N3 0.0000
    0.00
    0.00
    S5 *C1 H1 0.0000
    0.00 180.00
    C1 *C2 H2 0.0000
    0.00 180.00
    N3 *C4 H4 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H3NS isothiazole


    ! H2
    H1
    CG2R51 -0.04 !
    \ ____ /
    HGR52
    0.16 !
    C2----C1
    CG2R51 -0.20 !
    |
    \
    HGR51
    0.13 !
    |
    S5
    CG2R52 0.23 !
    |____ /
    HGR52
    0.11 !
    C3----N4
    NG2R50 -0.53 !
    /
    SG2R50 0.14 ! H3
    H1 C1 C2 C2 H2 C2 C3
    N4 C3 H3 N4 S5 S5 C1
    C1 C2 C3 0.0000
    0.00
    0.00
    C2 C3 N4 0.0000
    0.00
    0.00
    S5 *C1 H1 0.0000
    0.00 180.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 *C3 H3 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H4N2 pyrazole


    !
    CG2R51 -0.03 ! H2
    H1
    HGR52
    0.15 !
    \ ____ /
    CG2R51 -0.24 !
    C2----C1

    ATOM H2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM N5
    ATOM H5
    BOND C1
    BOND C3
    IC C1
    IC N5
    IC C2
    IC C3
    IC N4
    IC N4
    !
    RESI OXAD
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM N4
    ATOM O5
    BOND C1
    BOND N3
    IC C1
    IC C2
    IC N3
    IC O5
    IC C2
    IC N3
    !
    RESI TRZ3
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM N4
    ATOM N5
    ATOM H5
    BOND C1
    BOND N3
    IC C2
    IC N5
    IC N3
    IC C1
    IC N4
    !
    RESI TRZ4
    GROUP
    ATOM C1
    ATOM H1
    ATOM N2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM N5

    HGR51
    0.14
    CG2R52 0.14
    HGR52
    0.13
    NG2R50 -0.57
    NG2R51 -0.05
    HGP1
    0.33
    H1 C1 C2
    H3 C3 N4
    C2 C3 N4
    C1 C2 C3
    N5 *C1 H1
    C1 *C2 H2
    C2 *C3 H3
    C1 *N5 H5

    !
    |
    \
    !
    |
    N5--H5
    !
    |____ /
    !
    C3----N4
    !
    /
    ! H3
    C2 H2 C2 C3
    N4 N5 N5 H5 N5
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    C1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C2H2N2O oxadiazole123


    ! H2
    H1
    CG2R51 0.17 !
    \ ____ /
    HGR52
    0.14 !
    C2----C1
    CG2R51 0.19 !
    |
    \
    HGR52
    0.10 !
    |
    O5
    NG2R50 -0.32 !
    |____ /
    NG2R50 -0.10 !
    N3----N4
    OG2R50 -0.18 !
    H1 C1 C2 C2 H2 C2 N3
    N4 N4 O5 O5 C1
    C2 N3 N4 0.0000
    0.00
    0.00
    N3 N4 O5 0.0000
    0.00
    0.00
    N4 O5 C1 0.0000
    0.00
    0.00
    C1 C2 N3 0.0000
    0.00
    0.00
    O5 *C1 H1 0.0000
    0.00 180.00
    C1 *C2 H2 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C2H3N3 triazole123


    ! H2
    H1
    CG2R51 -0.35 !
    \ ____ /
    HGR52
    0.20 !
    C2----C1
    CG2R51 0.25 !
    |
    \
    HGR52
    0.11 !
    |
    N5--H5
    NG2R50 -0.41 !
    |____ /
    NG2R50 -0.37 !
    N3----N4
    NG2R51 0.28 !
    HGP1
    0.29 !
    H1 C1 C2 C2 H2 C2 N3
    N4 N4 N5 N5 H5 N5 C1
    N5 *C1 H1 0.0000
    0.00 180.00
    C1 C2 N3 0.0000
    0.00
    0.00
    C1 *C2 H2 0.0000
    0.00 180.00
    C2 N3 N4 0.0000
    0.00
    0.00
    C1 *N5 H5 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    CG2R52
    HGR52
    NG2R50
    CG2R52
    HGR52
    NG2R50
    NG2R51

    0.00 ! C2H3N3 triazole124


    !
    H1
    0.21 !
    ____ /
    0.16 !
    N2----C1
    -0.68 !
    |
    \
    0.45 !
    |
    N5--H5
    0.12 !
    |____ /
    -0.62 !
    C3----N4
    0.03 ! /

    ATOM H5

    HGP1

    BOND C1
    BOND C3
    IC C1
    IC N2
    IC N5
    IC N2
    IC N4
    IC N4
    !
    RESI TEAZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM N2
    ATOM N3
    ATOM N4
    ATOM N5
    ATOM H5
    BOND C1
    BOND N3
    IC C1
    IC N2
    IC N5
    IC N2
    IC N4
    !
    RESI TDAZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM N2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM S5

    H1
    N4
    N2
    C3
    C1
    N5
    N2
    C1

    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    !

    H1
    H4
    N2
    N3
    C1
    S5
    N3

    C1
    C4
    C1
    N2
    S5
    N2
    S5

    RESI PYRD
    GROUP
    ATOM N1
    ATOM N2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6

    0.33 ! H3
    C1
    N4
    C3
    N4
    N2
    *C1
    *C3
    *N5

    N2
    N5
    N4
    N5
    C3
    H1
    H3
    H5

    N2 C3
    N5 H5
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C3
    N5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H3
    C1
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! CH2N4 tetrazole


    !
    H1
    CG2R52 0.24 !
    ____ /
    HGR52
    0.14 !
    N2----C1
    NG2R50 -0.41 !
    |
    \
    NG2R50 -0.14 !
    |
    N5--H5
    NG2R50 -0.34 !
    |____ /
    NG2R51 0.23 !
    N3----N4
    HGP1
    0.28 !
    H1 C1 N2 N2 N3
    N4 N4 N5 N5 H5 N5 C1
    N2 N3 N4 0.0000
    0.00
    0.00
    N3 N4 N5 0.0000
    0.00
    0.00
    C1 N2 N3 0.0000
    0.00
    0.00
    N5 *C1 H1 0.0000
    0.00 180.00
    C1 *N5 H5 0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    CG2R52
    HGR52
    NG2R50
    NG2R50
    CG2R52
    HGR52
    SG2R50

    0.000 ! C2H2N2S thiadiazole 1,3,4


    !
    H1
    0.11 !
    ____ /
    0.27 !
    N2----C1
    -0.37 !
    |
    \
    -0.37 !
    |
    S5
    0.11 !
    |____ /
    0.27 !
    N3----C4
    -0.02 !
    \
    !
    H4

    C1
    C4
    N3
    C4
    N2
    *C1
    *C4

    N2
    S5
    C4
    S5
    N3
    H1
    H4

    N2 N3
    S5 C1
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    N3

    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00 180.00

    0.000 ! C4H4N2 pyridazine


    NG2R62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR62

    -0.44
    -0.44
    0.31
    0.11
    -0.16
    0.18
    -0.16
    0.18
    0.31
    0.11

    !
    !
    H5
    H6
    !
    \
    /
    !
    C5----C6
    !
    /
    \
    ! H4--C4
    N1
    !
    \\
    //
    !
    C3----N2
    !
    /
    !
    H3

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    BOND N1 N2
    BOND C3 H3
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1
    N2
    C6
    C4
    C5
    C6
    C5

    !
    RESI PYZN
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    BOND C6
    BOND C3
    IC N1
    IC C2
    IC C2
    IC C6
    IC C3
    IC N4
    IC C5
    IC N4
    !
    RESI PYRM
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    !
    BOND N1
    BOND C2
    !
    IC
    N1
    IC
    C2
    IC
    N3
    IC
    C6
    IC
    N3
    IC
    C5
    IC
    C6

    N2 C3
    C4 H4

    C5 C6

    C6 N1

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C4H4N2 pyrazine


    !
    NG2R60 -0.56 !
    H5
    H6
    CG2R61 0.18 !
    \ ____ /
    HGR62
    0.10 !
    C5----C6
    CG2R61 0.18 !
    /
    \
    HGR62
    0.10 !
    N4
    N1
    NG2R60 -0.56 !
    \\
    //
    CG2R61 0.18 !
    C3----C2
    HGR62
    0.10 !
    /
    \
    CG2R61 0.18 !
    H3
    H2
    HGR62
    0.10 !
    H6 C6 C5 C5 H5 C5 N4 N4
    H3 C3 C2 C2 H2 C2 N1 N1
    C2 C3 N4 0.0000
    0.00
    0.00
    C3 N4 C5 0.0000
    0.00
    0.00
    N1 C6 C5 0.0000
    0.00
    0.00
    N1 C2 C3 0.0000
    0.00
    0.00
    N1 *C2 H2 0.0000
    0.00 180.00
    C2 *C3 H3 0.0000
    0.00 180.00
    N1 *C6 H6 0.0000
    0.00 180.00
    C6 *C5 H5 0.0000
    0.00 180.00

    C3
    C6
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    N2
    C3
    N1
    N2
    C3
    C4
    N1

    C3
    C4
    N2
    *C3
    *C4
    *C5
    *C6

    C2
    N3
    C4
    N1
    N1
    N3
    C4

    C4
    C5
    C3
    H3
    H4
    H5
    H6

    C4 C5
    C6 H6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C4H4N2 pyrimidine


    !
    -0.73 !
    H5
    H6
    0.50 !
    \ ___ /
    0.14 !
    C5---C6
    -0.73 !
    /
    \
    0.29 ! H4--C4
    N1
    0.12 !
    \\
    //
    -0.115 !
    N3---C2
    0.115 !
    \
    0.29 !
    H2
    0.12 !

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    HGR62
    C2
    H2

    C3 C4
    C5 H5

    C2
    C4
    N3
    C4
    C5
    C2
    *C2
    *C4
    *C5

    N3
    H4
    C4
    C5
    C6
    N3
    H2
    H4
    H5

    N3
    C5

    C4
    H5

    C4
    C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5
    H6

    C5 C6 C6 N1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00 180.00
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    C5
    !
    RESI TRIA
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM N5
    ATOM C6
    ATOM H6
    !
    BOND C6
    BOND N3
    IC N1
    IC C2
    IC N3
    IC C6
    IC N3
    IC N5
    IC N5
    !
    RESI TRIB
    GROUP
    ATOM N1
    ATOM N2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    !

    N1

    *C6 H6

    0.0000

    0.00 180.00

    0.00

    0.00 ! C3H3N3 1,3,5-triazine


    !
    -0.88 !
    H6
    0.78 !
    ___ /
    0.10 !
    N5---C6
    -0.88 !
    /
    \
    0.78 ! H4--C4
    N1
    0.10 !
    \\
    //
    -0.88 !
    N3---C2
    0.78 !
    \
    0.10 !
    H2

    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2R64
    HGR62
    H6
    C2

    C6
    C2

    N5
    H2

    N5
    C2

    C4
    N1

    C2
    N3
    C4
    N1
    N1
    N3
    N1

    N3
    C4
    N5
    C2
    *C2
    *C4
    *C6

    C4
    N5
    C6
    N3
    H2
    H4
    H6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    N1

    H4
    C6

    C4

    N3

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00 180.00
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C3H3N3 1,2,4-triazine


    !
    -0.41 !
    H5
    H6
    -0.53 !
    \ ___ /
    0.72 !
    C5---C6
    0.09 !
    /
    \
    -0.75 !
    N4
    N1
    0.36 !
    \\
    //
    0.09 !
    C3---N2
    0.36 !
    /
    0.07 !
    H3

    NG2R62
    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    HGR62

    BOND N1 N2 N2 C3 C3 N4 N4 C5 C5 C6 C6 N1
    BOND C3 H3 C5 H5 C6 H6
    IC
    IC
    IC
    IC
    IC
    IC

    C6
    N1
    N2
    N4
    C6
    C5

    RESI THP
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C3
    ATOM H31

    N1
    N2
    C3
    N2
    N4
    N1

    N2
    C3
    N4
    *C3
    *C5
    *C6

    C3
    N4
    C5
    H3
    H5
    H6

    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    ! C5H10O tetrahydropyran sng

    OG3C61 -0.40
    CG321
    0.02 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    CG321
    0.02 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09

    O1
    /
    C6
    |
    C5
    \

    \
    C2
    |
    C3
    /
    C4

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H32
    C4
    H41
    H42
    C5
    H51
    H52

    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C6
    O1
    C2
    C3
    C3
    C5
    C5
    C4
    C4
    C5
    C5
    C4
    C4

    O1
    C2
    O1
    O1
    O1
    O1
    O1
    C2
    C2
    C3
    C3
    C6
    C6

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    O1
    C2
    C3
    C4
    C5
    C6

    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09

    C2
    H21
    H31
    H41
    H51
    H61

    C2
    C3
    C6
    *C2
    *C2
    *C6
    *C6
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    C2
    C2
    C3
    C4
    C5
    C6

    C3
    C4
    C5
    H21
    H22
    H61
    H62
    H31
    H32
    H41
    H42
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    60.00
    60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C3 C3 C4 C4 C5 C5 C6 C6 O1
    H22
    H32
    H42
    H52
    H62

    PATC FIRS NONE LAST NONE


    RESI DIOX
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM O4
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM C6
    ATOM H61
    ATOM H62

    0.00 ! C4H8O2 dioxane14


    !
    OG3C61 -0.40 !
    CG321
    0.02 !
    HGA2
    0.09 ! H52 H61 H62
    HGA2
    0.09 !
    \
    \ /
    CG321
    0.02 ! H51--C5---C6
    HGA2
    0.09 !
    /
    \
    HGA2
    0.09 !
    O4
    O1
    OG3C61 -0.40 !
    \
    /
    CG321
    0.02 ! H31--C3---C2
    HGA2
    0.09 !
    /
    / \
    HGA2
    0.09 ! H32 H21 H22
    CG321
    0.02 !
    HGA2
    0.09 !
    HGA2
    0.09 !

    BOND O1
    BOND C2
    BOND C6

    C2 C2
    H21 C2
    H61 C6

    C3 C3
    H22 C3
    H62 C5

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    C3
    O4
    C5
    C3
    C3
    O4
    O4

    O4
    C5
    C6
    O1
    H21
    H22
    H31
    H32

    O1
    C2
    C3
    O4
    O1
    O1
    C2
    C2

    C3
    O4
    C5
    C6
    *C2
    *C2
    *C3
    *C3

    O4 O4
    H31 C3
    H51 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5 C5
    H32
    H52
    60.00
    -60.00
    60.00
    -60.00
    120.00
    -120.00
    120.00
    -120.00

    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6 O1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC O4
    IC O4
    IC C5
    IC C5
    !
    RESI DIXB
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM O3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM C6
    ATOM H61
    ATOM H62

    C6
    C6
    O1
    O1

    BOND O1
    BOND C2
    BOND C6

    C2 C2
    H21 C2
    H61 C6

    O3 O3
    H22 C4
    H62 C5

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O1
    C2
    O3
    O1
    O1
    O3
    O3
    C4
    C4
    O1
    O1

    O3
    C4
    C5
    H21
    H22
    H41
    H42
    H51
    H52
    H61
    H62

    C6
    O1
    C2
    O3
    O3
    C5
    C5
    C6
    C6
    C5
    C5

    RESI PIP
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51

    *C5
    *C5
    *C6
    *C6

    H51
    H52
    H61
    H62

    0.0000
    0.0000
    0.0000
    0.0000

    0.00 !
    !
    OG3C61 -0.40 !
    CG321
    0.22 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    OG3C61 -0.40 !
    CG321
    0.02 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    CG321
    0.02 !
    HGA2
    0.09 !
    HGA2
    0.09 !

    C2
    O3
    C4
    *C2
    *C2
    *C4
    *C4
    *C5
    *C5
    *C6
    *C6

    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    C4H8O2 1,3-dioxane

    H52

    H61 H62
    \
    \ /
    H51--C5---C6
    /
    \
    H42-C4
    O1
    / \
    /
    H41 O3---C2
    / \
    H21 H22

    C4 C4
    H41 C4
    H51 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5 C5
    H42
    H52
    -60.00
    60.00
    60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6 O1

    NG3P2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2

    1.00 ! C5H12N piperidine


    !
    -0.40 !
    0.32 !
    0.32 !
    C5---C6
    H11
    0.20 !
    /
    \ /
    0.09 !
    C4
    (+) N1
    0.09 !
    \
    / \
    0.20 !
    C3---C2
    H12
    0.09 !
    0.09 !

    CG321
    HGA2
    HGA2

    -0.18 !
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18!
    0.09
    0.09

    CG321
    HGA2

    -0.18
    0.09

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM H52 HGA2


    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1
    N1
    C2
    C3
    C4
    C5
    C6

    C6
    N1
    C2
    C2
    C2
    C3
    C3
    C5
    C5
    C4
    C4
    C5
    C5
    C4
    C4

    C2
    H11
    H21
    H31
    H41
    H51
    H61

    C2
    N1
    C2
    C3
    C4
    C5
    C6

    N1
    C2
    N1
    C6
    C6
    N1
    N1
    N1
    N1
    C2
    C2
    C3
    C3
    C6
    C6

    RESI PIPZ
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM H61
    ATOM H62
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM N4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC

    0.09

    C6
    N1
    C2
    C2

    N1
    N1
    C2
    C3
    N4
    C5
    C6

    C2
    C3
    C6
    *N1
    *N1
    *C2
    *C2
    *C6
    *C6
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5

    C3 C3
    H12
    H22
    H32
    H42
    H52
    H62
    C3
    C4
    C5
    H11
    H12
    H21
    H22
    H61
    H62
    H31
    H32
    H41
    H42
    H51
    H52

    C4

    C4 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C6 C6 N1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    60.00
    60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    NG3P2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2

    2.00 ! C4H12N2 piperazine


    !
    -0.76 !
    0.50 !
    0.50 !
    H41
    C5---C6
    H11
    0.20 !
    \ /
    \ /
    0.09 !
    N4 (+) (+) N1
    0.09 !
    / \
    / \
    0.20 !
    H42
    C3---C2
    H12
    0.09 !
    0.09 !

    CG324
    HGA2
    HGA2
    NG3P2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2

    0.20 !
    0.09
    0.09
    -0.76
    0.50
    0.50
    0.20
    0.09
    0.09

    C2
    H11
    H21
    H31
    H41
    H51
    H61
    N1
    C2
    N1
    C6

    C2
    N1
    C2
    C3
    N4
    C5
    C6
    C2
    C3
    C6
    *N1

    C3 C3
    H12
    H22
    H32
    H42
    H52
    H62
    C3
    N4
    C5
    H11

    N4

    N4 C5

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C6 C6 N1

    0.00 -60.00
    0.00 60.00
    0.00 60.00
    0.00 120.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    C3
    C3
    C5
    C5
    N4
    N4
    C5
    C5
    N4
    N4

    C6
    N1
    N1
    N1
    N1
    C2
    C2
    C3
    C3
    C6
    C6

    *N1
    *C2
    *C2
    *C6
    *C6
    *C3
    *C3
    *N4
    *N4
    *C5
    *C5

    H12
    H21
    H22
    H61
    H62
    H31
    H32
    H41
    H42
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PATCH FIRST NONE LAST NONE


    RESI THPS
    GROUP
    ATOM S1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM C6
    ATOM H61
    ATOM H62

    SG311
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND

    C2
    H21
    H41
    H61

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    S1
    C2
    C3
    C6
    C3
    C3
    C4
    C4
    C5
    C5
    C6
    C6
    C5
    C5

    S1
    C2
    C4
    C6
    C2
    C3
    C4
    S1
    S1
    S1
    C2
    C2
    C3
    C3
    C4
    C4
    S1
    S1

    RESI DITH
    GROUP
    ATOM S1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3

    0.00 !
    !
    -0.24 !
    -0.06 !
    0.09 !
    0.09 !
    -0.18 !
    0.09 !
    0.09 !
    -0.18 !
    0.09 !
    0.09 !
    -0.18 !
    0.09 !
    0.09 !
    -0.06 !
    0.09 !
    0.09 !
    C2
    C2
    C4
    C6

    C3
    C4
    C5
    C2
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    *C6
    *C6

    SG311
    CG321
    HGA2
    HGA2
    CG321

    C5H10S tetrahydro-thiopyran (thiane)


    from ethylmethylsulfide (-0.09)

    H61 H62
    \
    \ /
    H51--C5---C6
    H41 /
    \
    \ /
    \
    C4
    S1
    / \
    /
    H42 \
    /
    H31--C3---C2
    /
    / \
    H32 H21 H22

    C3 C3
    H22 C3
    H42 C5
    H62

    H52

    C4
    C5
    C6
    C3
    H21
    H22
    H31
    H32
    H41
    H42
    H51
    H52
    H61
    H62

    C4 C4
    H31 C3
    H51 C5
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    H32
    H52
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    60.00
    -60.00
    60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    C6

    C6 S1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C4H8S2 1,4-dithiane


    !
    -0.22 ! from ethylmethylsulfide (-0.09)
    -0.07 !
    0.09 ! H52 H61 H62
    0.09 !
    \
    \ /
    -0.07 ! H51--C5---C6

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H31
    H32
    S4
    C5
    H51
    H52
    C6
    H61
    H62

    HGA2
    HGA2
    SG311
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND

    S1
    C2
    C5
    C6

    C2
    H21
    H51
    H61

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    S1
    C2
    C3
    C6
    C3
    C3
    S4
    S4
    C6
    C6
    C5
    C5

    C2
    C3
    S4
    S1
    S1
    S1
    C2
    C2
    S4
    S4
    S1
    S1

    0.09
    0.09
    -0.22
    -0.07
    0.09
    0.09
    -0.07
    0.09
    0.09
    C2
    C2
    C5
    C6

    SG311
    CG321
    HGA2
    HGA2
    SG311
    CG321
    HGA2
    HGA2
    SG311
    CG321
    HGA2
    HGA2

    BOND S1
    BOND C2
    BOND C6

    C2 C2
    H21 C2
    H61 C6

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    S1
    C2
    S3
    C6
    S3
    S3
    S5
    S5
    S5
    S5

    C3 C3
    H22 C3
    H52
    H62

    C3
    S4
    C5
    C2
    *C2
    *C2
    *C3
    *C3
    *C5
    *C5
    *C6
    *C6

    RESI TRIT
    GROUP
    ATOM S1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM S3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM S5
    ATOM C6
    ATOM H61
    ATOM H62

    C2
    S3
    C4
    S1
    S1
    S1
    S3
    S3
    S1
    S1

    !
    /
    \
    !
    /
    \
    !
    S4
    S1
    !
    \
    /
    !
    \
    /
    ! H31--C3---C2
    !
    /
    / \
    ! H32 H21 H22
    !

    S4
    C5
    C6
    C3
    H21
    H22
    H31
    H32
    H51
    H52
    H61
    H62

    S4 S4
    H31 C3

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    H32

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    -60.00
    60.00
    -60.00
    60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    C6 S1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C3H6S3 trithiane135


    !
    -0.18 !
    0.00 !
    H61 H62
    0.09 !
    \ /
    0.09 ! H41 S5---C6
    -0.18 !
    \ /
    \
    0.00 !
    C4
    S1
    0.09 !
    / \
    /
    0.09 ! H42 S3---C2
    -0.18 !
    / \
    0.00 !
    H21 H22
    0.09 !
    0.09 !

    S3
    C4
    S5
    C2
    *C2
    *C2
    *C4
    *C4
    *C6
    *C6

    S3 S3
    H22 C4
    H62
    C4
    S5
    C6
    S3
    H21
    H22
    H41
    H42
    H61
    H62

    C4 C4
    H41 C4
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    S5 S5
    H42
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    RESI MORP
    1.00 ! C4H10NO morpholine
    ATOM O1 OG3C61 -0.28 !

    60.00
    -60.00
    60.00
    -60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    C6

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    S1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    C2
    H21
    H22
    C3
    H31
    H32
    N4
    H41
    H42
    C5
    H51
    H52
    C6
    H61
    H62

    CG321
    HGA2
    HGA2
    CG324
    HGA2
    HGA2
    NG3P2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND

    O1
    C2
    N4
    C5

    C2
    H21
    H41
    H51

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O1
    C2
    C3
    C6
    C3
    C3
    N4
    N4
    C5
    C5
    C6
    C6
    C5
    C5

    -0.04
    0.09
    0.09
    0.20
    0.09
    0.09
    -0.46
    0.35
    0.35
    0.20
    0.09
    0.09
    -0.04
    0.09
    0.09
    C2
    C2
    N4
    C5

    C3 C3
    H22 C3
    H42
    H52 C6

    C2
    C3
    N4
    O1
    O1
    O1
    C2
    C2
    C3
    C3
    N4
    N4
    O1
    O1
    TMOR
    S1
    C2
    H21
    H22
    C3
    H31
    H32
    N4
    H41
    H42
    C5
    H51
    H52
    C6
    H61
    H62

    SG311
    CG321
    HGA2
    HGA2
    CG324
    HGA2
    HGA2
    NG3P2
    HGP2
    HGP2
    CG324
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND

    S1
    C2
    N4
    C5

    C2
    H21
    H41
    H51

    C3
    N4
    C5
    C2
    *C2
    *C2
    *C3
    *C3
    *N4
    *N4
    *C5
    *C5
    *C6
    *C6

    RESI
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    IC S1

    C2

    !
    ! H52 H61 H62
    !
    \
    \ /
    ! H51--C5---C6
    !H41 /
    \
    ! \ /
    \
    !
    N4 (+)
    O1
    ! / \
    /
    !H42 \
    /
    ! H31--C3---C2
    !
    /
    / \
    ! H32 H21 H22
    !
    !
    !

    N4
    C5
    C6
    C3
    H21
    H22
    H31
    H32
    H41
    H42
    H51
    H52
    H61
    H62

    1.00
    -0.12
    -0.12
    0.09
    0.09
    0.20
    0.09
    0.09
    -0.40
    0.32
    0.32
    0.20
    0.09
    0.09
    -0.12
    0.09
    0.09
    C2
    C2
    N4
    C5

    C5 C5
    H32

    H61 C6

    H62

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6

    C6

    60.00
    -30.00
    -30.00
    -30.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    O1

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! C4H10NS thiomorpholine
    !
    !
    ! H52 H61 H62
    !
    \
    \ /
    ! H51--C5---C6
    !H41 /
    \
    ! \ /
    \
    !
    N4 (+)
    S1
    ! / \
    /
    !H42 \
    /
    ! H31--C3---C2
    !
    /
    / \
    ! H32 H21 H22
    !
    !
    !

    C3 C3
    H22 C3
    H42
    H52 C6
    C3

    N4 N4
    H31 C3

    N4

    N4 N4
    H31 C3

    C5 C5
    H32

    H61 C6

    H62

    0.0000

    0.00

    C6

    60.00

    C6

    S1

    0.00

    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    C3
    C6
    C3
    C3
    N4
    N4
    C5
    C5
    C6
    C6
    C5
    C5

    RESI MGU1
    GROUP
    ATOM C
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM N2
    ATOM H21
    ATOM H22
    ATOM N3
    ATOM C4
    e
    ATOM H41
    ATOM H42
    ATOM H43
    BOND C
    BOND N1
    BOND C4
    IMPR C
    IMPR N1

    C3
    N4
    S1
    S1
    S1
    C2
    C2
    C3
    C3
    N4
    N4
    S1
    S1

    CG2N1
    NG321
    HGPAM2
    HGPAM2
    NG321
    HGPAM2
    HGPAM2
    NG2D1
    CG331

    N4
    C5
    C2
    *C2
    *C2
    *C3
    *C3
    *N4
    *N4
    *C5
    *C5
    *C6
    *C6

    C5
    C6
    C3
    H21
    H22
    H31
    H32
    H41
    H42
    H51
    H52
    H61
    H62

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    0.00
    0.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C2H7N3 deprotonated methyl-guanidinium


    ! Ne deprotonated
    0.66 !
    H11 H12
    -0.60 !
    \ /
    0.29 !
    N1
    0.29 !
    |
    -0.60 !
    C
    H41
    0.29 !
    / \\
    /
    0.29 ! H21-N2 N3--C4-H42
    -0.86 !
    |
    \
    -0.03 !
    H22
    H43 !extra charge on C4 to neutraliz

    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    N1 C N2
    C N3
    N3 C4
    H11 N1 H12 N2 H21 N2 H22
    H41 C4 H42 C4 H43
    N2 N1 N3
    H11 H12 C N2 H21 H22 C

    IC N3 C
    N1 H11
    IC H11 C
    *N1 H12
    IC N1 N3 *C N2
    IC N3 C
    N2 H21
    IC H21 C
    *N2 H22
    IC N1 C
    N3 C4
    IC C
    N3 C4 H41
    IC H41 N3 *C4 H42
    IC H41 N3 *C4 H43
    PATC FIRS NONE LAST NONE
    RESI MGU2
    GROUP
    ATOM C
    ATOM N1
    ATOM H11
    ATOM N2
    ATOM H21
    ATOM H22
    ATOM N3
    ATOM H31
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    150.00
    -120.00
    180.00
    150.00
    -120.00
    180.00
    -170.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C2H7N3 deprotonated methyl-guanidinium


    ! NH1-H12 (outer) deprotonated
    CG2N1
    0.59 !
    NG2D1 -0.91 !
    H11
    HGP1
    0.37 !
    \
    NG321 -0.60 !
    N1
    HGPAM2 0.33 !
    ||
    HGPAM2 0.33 !
    C
    H41
    NG311 -0.54 !
    / \
    /
    HGPAM1 0.36 ! H21-N2 N3--C4-H42
    CG331 -0.20 !
    | |
    \
    !carbon charge to neutralize
    HGA3
    0.09 !
    H22 H31 H43
    HGA3
    0.09
    HGA3
    0.09

    BOND
    BOND
    BOND
    IMPR
    IMPR

    C
    N1
    C4
    C
    N3

    N1
    H11
    H41
    N2
    C4

    C N2
    C N3 N3 C4
    N2 H21 N2 H22 N3 H31
    C4 H42 C4 H43
    N1 N3
    C H31 N2 H21 H22 C

    IC N3 C
    N1 H11
    IC N1 N3 *C N2
    IC N3 C
    N2 H21
    IC H21 C
    *N2 H22
    IC N1 C
    N3 C4
    IC C
    C4 *N3 H31
    IC C
    N3 C4 H41
    IC H41 N3 *C4 H42
    IC H41 N3 *C4 H43
    PATC FIRS NONE LAST NONE

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    150.00
    -120.00
    -120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !end adm jr(?), jul2006


    !start adm jr(?),
    RESI HDZ1
    GROUP
    ATOM C1 CG331
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    GROUP
    ATOM C2 CG2O1
    ATOM O2 OG2D1
    ATOM N3 NG2S1
    ATOM H3 HGP1
    ATOM N4 NG2D1
    ATOM C5 CG2D1
    ATOM H5 HGA4
    ATOM C6 CG331
    ATOM H61 HGA3
    ATOM H62 HGA3
    ATOM H63 HGA3

    dec2006
    0.00 ! C4H8N2O Hydrazone model compound
    !
    -0.27 !
    0.09 ! C1
    H3
    0.09 !
    \
    |
    0.09 !
    C2--N3
    H5
    !
    //
    \
    /
    0.58 !
    O2
    N4=C5
    -0.49 !
    \
    -0.34 !
    C6
    0.31
    -0.31
    -0.24
    0.24
    -0.02
    0.09
    0.09
    0.09

    BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 C2 N3 N3 H3


    BOND N3 N4 C5 H5 C5 C6 C6 H61 C6 H62 C6 H63
    BOND N4 C5
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    H11
    H11
    H11
    N3
    N4
    C2
    N3
    C6
    N4
    H61
    H61

    C2
    C2
    C2
    C1
    C1
    C2
    N3
    N4
    N4
    C5
    C5
    C5

    RESI HDZ2 0.00


    GROUP
    ATOM HG HGR51

    N3
    *C1
    *C1
    C2
    *C2
    *N3
    N4
    C5
    *C5
    C6
    *C6
    *C6

    N4
    H12
    H13
    N3
    O2
    H3
    C5
    C6
    H5
    H61
    H62
    H63

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ! C16H13N3O2 Hydrazone containing drug-like molecule


    0.14 !

    HE3

    ATOM CG CG2R51
    ATOM CD2 CG2RC0
    ATOM CD1 CG2R51
    ATOM HD1 HGR52
    ATOM NE1 NG2R51
    ATOM HE1 HGP1
    ATOM CE2 CG2RC0
    ATOM CE3 CG2R61
    ATOM HE3 HGR61
    ATOM CZ2 CG2R61
    ATOM CZ3 CG2R61
    ATOM HZ3 HGR61
    ATOM CH2 CG2R61
    ATOM HH2 HGR61
    GROUP
    ATOM C2 CG2O1
    ATOM O2 OG2D1
    ATOM N3 NG2S1
    ATOM H3 HGP1
    ATOM N4 NG2D1
    ATOM C5 CG2D1
    ATOM H5 HGA4
    !
    !Phenol moiety: P
    !
    ATOM CPG CG2R61
    GROUP
    ATOM CPD1 CG2R61
    ATOM HPD1 HGR61
    GROUP
    ATOM CPD2 CG2R61
    ATOM HPD2 HGR61
    GROUP
    ATOM CPE1 CG2R61
    ATOM HPE1 HGR61
    GROUP
    ATOM CPE2 CG2R61
    ATOM HPE2 HGR61
    GROUP
    ATOM CPZ CG2R61
    ATOM OPH OG311
    ATOM HPH HGP1

    -0.17
    0.11
    -0.15
    0.22
    -0.51
    0.37
    0.24
    -0.25
    0.17
    -0.11
    -0.20
    0.14
    -0.14
    0.14
    0.58
    -0.49
    -0.34
    0.31
    -0.31
    -0.24
    0.24

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    added to
    0.25 !
    !
    -0.115 !
    0.115 !
    !
    -0.115 !
    0.115 !
    !
    -0.115 !
    0.115

    |
    CE3
    \
    / \\
    CG-----CD2 CZ3-HZ3
    ||
    ||
    |
    CD1
    CE2 CH2-HH2
    / \ / \ //
    HD1
    NE1 CZ2
    |
    /
    HE1 /
    /
    /
    /
    ___________/
    \
    \
    H3
    \
    |
    C2--N3
    H5
    //
    \
    /
    O2
    N4=C5
    \
    ________________\
    |
    atom names to avoid conflicts with indole
    |
    | HPD1 HPE1
    |
    |
    |
    | CPD1--CPE1
    | //
    \\
    |--CPG
    CPZ--OPH
    \
    /
    \
    CPD2==CPE2
    HPH
    |
    |
    HPD2 HPE2
    HG

    -0.115
    0.115
    0.11
    -0.53
    0.42

    !indole section
    BOND CG HG CD2 CG NE1 CD1 CZ2 CE2
    BOND CZ3 CH2 CD2 CE3 NE1 CE2
    BOND CD1 HD1 NE1 HE1 CE3 HE3
    BOND CZ3 HZ3 CH2 HH2
    BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
    BOND CZ2 C2
    BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5
    BOND N4 C5 C5 CPG
    BOND CPD2 CPG CPE1 CPD1 CPZ CPE2
    BOND CPD1 HPD1 CPD2 HPD2 CPE1 HPE1
    BOND CPE2 HPE2 CPZ OPH OPH HPH
    BOND CPD1 CPG CPE2 CPD2 CPZ CPE1
    IC CG
    180.0
    IC CD2

    CD1

    NE1

    CE2

    0.0000

    0.00

    0.00

    0.00

    0.0000 !dihe from

    HG

    *CG

    CD1

    0.0000

    0.00 180.00

    0.00

    0.0000

    IC HG
    IC NE1
    IC CE2
    IC CE2
    IC CG
    IC CZ3
    IC CD2
    IC CD2
    180.0
    IC CH2
    IC CZ2
    IC CH2
    IC CE2
    IC N3
    IC CZ2
    IC N4
    IC C2
    IC N3
    IC CPG
    IC N4
    IC CPD1
    IC C5
    IC CPE1
    IC C5
    IC CPE2
    IC CPG
    80.0
    IC CPZ
    IC CPZ
    IC CPE2
    IC CPE1
    !end adm

    CG
    CG
    CD1
    CG
    CD2
    CD2
    NE1
    CE3

    CD1
    *CD1
    *NE1
    *CD2
    CE3
    *CE3
    *CE2
    CZ3

    NE1
    HD1
    HE1
    CE3
    CZ3
    HE3
    CZ2
    CH2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000 !dihe from

    CE3
    CZ3
    CE2
    CZ2
    CZ2
    C2
    C2
    N3
    N4
    N4
    C5
    C5
    CPG
    CPG
    CPG
    CPG
    CPD1

    *CZ3
    *CH2
    *CZ2
    C2
    *C2
    N3
    *N3
    N4
    C5
    *C5
    CPG
    *CPG
    CPD1
    *CPD1
    CPD2
    *CPD2
    CPE1

    HZ3
    HH2
    C2
    N3
    O2
    N4
    H3
    C5
    CPG
    H5
    CPD1
    CPD2
    CPE1
    HPD1
    CPE2
    HPD2
    CPZ

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000 !dihe from 1

    CPD1 *CPE1 HPE1


    CPD2 *CPE2 HPE2
    CPE1 *CPZ OPH
    CPZ OPH HPH
    jr(?), dec2006

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00

    0.0000
    0.0000

    !Continuation of
    RESI INDZ
    GROUP
    ATOM C1 CG2R51
    ATOM H1 HGR51
    ATOM C2 CG2R51
    ATOM H2 HGR51
    ATOM C3 CG2R51
    ATOM H3 HGR52
    ATOM N4 NG2RC0
    ATOM C5 CG2R61
    ATOM H5 HGR62
    ATOM C6 CG2R61
    ATOM H6 HGR61
    ATOM C7 CG2R61
    ATOM H7 HGR61
    ATOM C8 CG2R61
    ATOM H8 HGR61
    ATOM C9 CG2RC0

    Maybridge list, kevo, dec2006


    0.00 ! C8H7N indolizine, kevo

    BOND
    BOND
    BOND
    BOND

    C3
    C6
    H2
    H6

    IC C9
    IC C1

    C1
    N4
    C1
    C5

    C2
    C5
    H1
    H5
    C1
    C2

    C2
    C5
    C2
    C6

    -0.28
    0.23
    -0.23
    0.19
    0.07
    0.14
    -0.28
    -0.10
    0.24
    -0.14
    0.17
    -0.15
    0.18
    -0.22
    0.24
    -0.06

    C2
    C3

    C3
    C6
    C3
    C7
    C3
    N4

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    C5

    H3
    \

    / \\
    C3----N4
    C6-H6
    ||
    |
    |
    C2
    C9
    C7-H7
    / \ // \ //
    H2
    C1
    C8
    |
    |
    H1
    H8

    N4 N4 C9 C9 C1
    C7 C7 C8 C8 C9
    H3
    H7 C8 H8
    0.0000
    0.0000

    0.00
    0.00

    0.00
    0.00

    IC C3
    N4
    C5
    C6
    IC N4
    C5
    C6
    C7
    IC C5
    C6
    C7
    C8
    IC C2
    C9
    *C1 H1
    IC C3
    C1
    *C2 H2
    IC N4
    C2
    *C3 H3
    IC C9
    C3
    *N4 C5
    IC C6
    N4
    *C5 H5
    IC C7
    C5
    *C6 H6
    IC C8
    C6
    *C7 H7
    IC C9
    C7
    *C8 H8
    PATCH FIRST NONE LAST NONE
    RESI ISOI
    GROUP
    ATOM HG
    ATOM CG
    ATOM CD2
    ATOM ND1
    ATOM HD1
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM CE3
    ATOM HE3
    ATOM CZ2
    ATOM HZ2
    ATOM CZ3
    ATOM HZ3
    ATOM CH2
    ATOM HH2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H7N isoindole, kevo


    HGR52
    CG2R51
    CG2RC0
    NG2R51
    HGP1
    CG2R51
    HGR52
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.15
    -0.16
    0.17
    -0.29
    0.35
    -0.16
    0.15
    0.17
    -0.36
    0.23
    -0.36
    0.23
    -0.30
    0.24
    -0.30
    0.24

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    HE3
    |
    HG
    CE3
    \ _____ / \\
    CG-----CD2 CZ3-HZ3
    |
    |
    |
    ND1
    CE2 CH2-HH2
    / \ // \ //
    HD1
    CE1 CZ2
    |
    |
    HE1 HZ2

    BOND CD2 CE2


    BOND CE1 ND1 ND1 CG
    BOND CD2 CE3 CZ3 CH2 CZ2 CE2
    BOND CE1 HE1 ND1 HD1 CG HG
    BOND CE3 HE3 CZ3 HZ3 CH2 HH2 CZ2 HZ2
    DOUBLE CE2 CE1 CG CD2 CE3 CZ3 CH2 CZ2
    DONOR HD1 ND1
    IC CG ND1
    IC ND1 CG
    IC CD2 CG
    IC CE2 CG
    IC CE2 CD2
    IC CD2 CE3
    IC CE3 CZ3
    IC CZ3 CD2
    IC CH2 CE3
    IC CZ2 CZ3
    IC CE2 CH2
    IC ND1 CE2
    IC CG CE1
    IC ND1 CD2
    PATCH FIRST

    CE1 CE2 0.0000


    CD2 CE2 0.0000
    ND1 CE1 0.0000
    *CD2 CE3 0.0000
    CE3 CZ3 0.0000
    CZ3 CH2 0.0000
    CH2 CZ2 0.0000
    *CE3 HE3 0.0000
    *CZ3 HZ3 0.0000
    *CH2 HH2 0.0000
    *CZ2 HZ2 0.0000
    *CE1 HE1 0.0000
    *ND1 HD1 0.0000
    *CG HG
    0.0000
    NONE LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    RESI INDA
    0.00 ! C7H6N2 1H-indazole, kevo
    GROUP
    ATOM N1 NG2R51 -0.05 !
    H5
    ATOM H1 HGP1
    0.28 !
    |

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    N2
    C3
    H3
    C4
    C5
    H5
    C6
    H6
    C7
    H7
    C8
    H8
    C9

    NG2R50
    CG2R52
    HGR52
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    -0.60
    0.28
    0.09
    -0.11
    -0.43
    0.30
    -0.38
    0.28
    -0.26
    0.24
    -0.20
    0.15
    0.41

    !
    !
    !
    !
    !
    !
    !
    !
    !

    H3

    BOND C3 H3 C4 C3 N1 N2
    BOND C8 C9
    BOND C6 C7 C4 C5 N1 C9
    BOND N1 H1 C5 H5 C6 H6
    BOND C7 H7 C8 H8
    DOUBLE N2 C3 C9 C4 C7 C8 C6
    DONOR H1 N1
    IC C3 N2 N1 C9
    0.0000
    IC N1 N2 C3 C4
    0.0000
    IC N2 C3 C4 C9
    0.0000
    IC C9 C3 *C4 C5
    0.0000
    IC C9 C4 C5 C6
    0.0000
    IC C4 C5 C6 C7
    0.0000
    IC C5 C6 C7 C8
    0.0000
    IC C6 C4 *C5 H5
    0.0000
    IC C7 C5 *C6 H6
    0.0000
    IC C8 C6 *C7 H7
    0.0000
    IC C9 C7 *C8 H8
    0.0000
    IC N2 C9 *N1 H1
    0.0000
    IC N2 C4 *C3 H3
    0.0000
    PATCH FIRST NONE LAST NONE
    RESI ZIMI
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9

    C5
    / \\
    C3-----C4
    C6 -H6
    ||
    ||
    |
    N2
    C9
    C7 -H7
    \ / \ //
    N1
    C8
    |
    |
    H1
    H8

    C5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C7H6N2 benzimidazole, kevo


    NG2R51
    HGP1
    CG2R53
    HGR52
    NG2R50
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    -0.28
    0.31
    0.24
    0.14
    -0.72
    0.45
    -0.35
    0.23
    -0.19
    0.20
    -0.34
    0.24
    -0.32
    0.22
    0.17

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    C5
    / \\
    N3----C4
    C6 -H6
    ||
    ||
    |
    C2
    C9
    C7 -H7
    / \ / \ //
    H2
    N1
    C8
    |
    |
    H1
    H8

    BOND N1 H1 C2 H2
    BOND C5 H5 C6 H6 C7 H7 C8 H8
    BOND C9 N1 N1 C2 N3 C4
    BOND C4 C5 C6 C7 C8 C9
    DOUBLE C2 N3 C4 C9 C5 C6 C7 C8
    DONOR H1 N1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC N3 C2
    IC N1 C2
    IC C2 N3
    IC C9 N3
    IC C9 C4
    IC C4 C5
    IC C5 C6
    IC C6 C4
    IC C7 C5
    IC C8 C6
    IC C9 C7
    IC C2 C9
    IC N3 N1
    PATCH FIRST

    N1
    N3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *N1
    *C2
    NONE

    C9
    0.0000
    C4
    0.0000
    C9
    0.0000
    C5
    0.0000
    C6
    0.0000
    C7
    0.0000
    C8
    0.0000
    H5
    0.0000
    H6
    0.0000
    H7
    0.0000
    H8
    0.0000
    H1
    0.0000
    H2
    0.0000
    LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    RESI 2HPR
    GROUP
    ATOM N1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5

    NG2R50 -0.72 ! H5
    CG3C52 0.45 !
    \ ____
    HGA2
    0.09 !
    C5----N1 H21
    HGA2
    0.09 !
    |
    \ /
    CG2R51 -0.75 !
    |
    C2
    HGR51
    0.33 !
    |____ / \
    CG2R51 0.05 !
    C4----C3 H22
    HGR51
    0.15 !
    /
    \
    CG2R52 0.20 ! H4
    H3
    HGR52
    0.11

    BOND C2
    BOND N1
    DOUBLE C3
    IC C2
    IC C3
    IC C3
    IC C3
    IC C4
    IC C5
    IC N1

    H21
    C2
    C4
    C3
    C4
    N1
    N1
    C2
    C3
    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C4H5N 2H-pyrrole, kevo

    C2
    C2
    C5
    C4
    C5
    *C2
    *C2
    *C3
    *C4
    *C5

    H22
    C3
    N1
    C5
    N1
    H21
    H22
    H3
    H4
    H5

    RESI 2PRL
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3C51
    HGP1
    CG2R51
    HGR52
    CG2R51
    HGR51
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    BOND N1
    BOND C4
    BOND N1
    DOUBLE C2
    IC N1
    IC C2

    H1
    H41
    C2
    C3
    C2
    C3

    C3
    C4

    H3
    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H4

    C5

    0.00
    0.00
    120.00
    240.00
    180.00
    180.00
    180.00

    H5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00

    0.0000
    0.0000

    0.000 ! C4H7N 2-pyrroline, kevo


    -0.60
    0.32
    -0.01
    0.17
    -0.36
    0.20
    -0.10
    0.09
    0.09
    0.02
    0.09
    0.09

    ! H3
    H41 H42
    ! \
    | /
    !
    C3----C4
    !
    ||
    |
    !
    C2
    C5--H51
    ! / \ / \
    ! H2
    N1
    H52
    !
    |
    !
    H1

    C2
    C4
    C3

    H2 C3
    H42 C5
    C4 C4

    C3
    C4

    C4
    C5

    H3
    H51 C5
    C5 C5

    0.0000
    0.0000

    0.00
    0.00

    H52
    N1
    0.00
    20.00

    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    C3
    C4
    C5
    C5
    N1
    N1

    C5
    N1
    C2
    C3
    C3
    C4
    C4

    *N1
    *C2
    *C3
    *C4
    *C4
    *C5
    *C5

    H1
    H2
    H3
    H41
    H42
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.00
    180.00
    180.00
    120.00
    240.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 2PRZ
    0.000 ! C3H6N2 2-pyrazoline, kevo
    GROUP
    ATOM N1 NG3C51 -0.46
    ATOM H1 HGP1
    0.34 ! H3
    H41 H42
    ATOM N2 NG2R50 -0.49 ! \
    | /
    ATOM C3 CG2R52 0.32 !
    C3----C4
    ATOM H3 HGR52
    0.06 !
    ||
    |
    ATOM C4 CG3C52 -0.15 !
    N2
    C5--H51
    ATOM H41 HGA2
    0.09 !
    \ / \
    ATOM H42 HGA2
    0.09 !
    N1
    H52
    ATOM C5 CG3C52 0.02 !
    |
    ATOM H51 HGA2
    0.09 !
    H1
    ATOM H52 HGA2
    0.09
    !H[45][12] constrained at +0.09, pre1g
    BOND N1
    BOND C4
    BOND N1
    DOUBLE N2
    IC N1
    IC N2
    IC N2
    IC C4
    IC C5
    IC C5
    IC N1
    IC N1

    H1
    H41
    N2
    C3
    N2
    C3
    C5
    N2
    C3
    C3
    C4
    C4

    C3
    C4
    C3

    H3
    H42 C5
    C4 C4

    C3
    C4
    *N1
    *C3
    *C4
    *C4
    *C5
    *C5

    C4
    C5
    H1
    H3
    H41
    H42
    H51
    H52

    H51 C5
    C5 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H52
    N1
    0.00
    20.00
    120.00
    180.00
    120.00
    240.00
    120.00
    240.00

    RESI 2IMI
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3C51 -0.68
    HGP1
    0.32 !
    H41 H42
    CG2R53 0.61 !
    | /
    HGR52
    0.06 !
    N3----C4
    NG2R50 -0.79 !
    ||
    |
    CG3C52 0.12 !
    C2
    C5--H51
    HGA2
    0.09 ! / \ / \
    HGA2
    0.09 ! H2
    N1
    H52
    CG3C52 0.00 !
    |
    HGA2
    0.09 !
    H1
    HGA2
    0.09

    BOND N1
    BOND C4
    BOND N1
    DOUBLE C2
    IC N1
    IC C2
    IC C2
    IC N3
    IC C5
    IC C5

    H1
    H41
    C2
    N3
    C2
    N3
    C5
    N1
    N3
    N3

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H6N2 2-imidazoline, kevo

    C2
    C4
    N3

    H2
    H42 C5
    C4 C4

    N3
    C4
    *N1
    *C2
    *C4
    *C4

    C4
    C5
    H1
    H2
    H41
    H42

    H51 C5
    C5 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H52
    N1
    0.00
    20.00
    120.00
    180.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC N1 C4 *C5 H51 0.0000


    0.00 120.00
    0.00
    IC N1 C4 *C5 H52 0.0000
    0.00 240.00
    0.00
    !end continuation of Maybridge list, kevo, dec2006
    !Continuation of
    RESI PRLD
    GROUP
    ATOM N1 NG3C51
    ATOM H1 HGP1
    ATOM C2 CG3C52
    ATOM H21 HGA2
    ATOM H22 HGA2
    ATOM C3 CG3C52
    ATOM H31 HGA2
    ATOM H32 HGA2
    ATOM C4 CG3C52
    ATOM H41 HGA2
    ATOM H42 HGA2
    ATOM C5 CG3C52
    ATOM H51 HGA2
    ATOM H52 HGA2
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1
    N1
    C4
    C2
    C3
    C2
    C4
    C4
    C3
    C3
    N1
    N1
    N1
    N1

    RESI 3PRL
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H51
    ATOM H52
    BOND N1
    BOND C3
    BOND N1
    DOUBLE C3
    IC C2
    IC C3
    IC C2
    IC C4

    C2
    H1
    H41
    C3
    C4
    C5
    C2
    C2
    C5
    C5
    C3
    C3
    C4
    C4

    0.0000
    0.0000

    Maybridge list, kevo, may2007


    0.000 ! C4H9N pyrrolidine, kevo

    C2
    C2
    C4
    C4
    C5
    *N1
    *C3
    *C3
    *C4
    *C4
    *C2
    *C2
    *C5
    *C5

    -0.86
    0.36
    0.10
    0.09
    0.09
    -0.21
    0.09
    0.09
    -0.21
    0.09
    0.09
    0.10
    0.09
    0.09
    C3
    H21
    H42
    C5
    N1
    H1
    H31
    H32
    H41
    H42
    H21
    H22
    H51
    H52

    !
    !
    !
    !
    !
    !
    !
    !
    !

    H32

    H42
    \
    /
    H31--C3----C4--H41
    |
    |
    H21--C2
    C5--H51
    / \ / \
    H22
    N1
    H52
    |
    H1

    C3 C4
    C2 H22
    C5 H51
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C3
    C5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5 C5
    H31 C3
    H52
    10.00
    15.00
    120.00
    -120.00
    120.00
    120.00
    -120.00
    120.00
    -120.00
    -120.00
    120.00

    N1
    H32
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C4H7N 3-pyrroline, kevo


    NG3C51 -0.89
    HGP1
    0.37 ! H3
    H4
    CG3C52 0.17 !
    \ ____ /
    HGA2
    0.09 !
    C3----C4
    HGA2
    0.09 !
    |
    |
    CG2R51 -0.28 ! H21--C2
    C5--H52
    HGR51
    0.19 !
    / \ / \
    CG2R51 -0.28 ! H22
    N1
    H51
    HGR51
    0.19 !
    |
    CG3C52 0.17 !
    H1
    HGA2
    0.09
    HGA2
    0.09
    H1
    H3
    C2

    C2
    C4
    C2

    H21 C2
    H4 C5
    C3 C4

    C4
    C5
    *N1
    *C3

    C5
    N1
    H1
    H3

    H22
    H51 C5
    C5 C5

    H52
    N1

    C4
    C3
    C4
    C5
    C2

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00 20.00
    0.00 120.00
    0.00 180.00

    IC
    IC
    IC
    IC
    IC

    C3
    N1
    N1
    N1
    N1

    C5
    C3
    C3
    C4
    C4

    *C4
    *C2
    *C2
    *C5
    *C5

    RESI PRLP
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3P2
    HGP2
    HGP2
    CG3C54
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C54
    HGA2
    HGA2

    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H11
    H32
    C2
    C3
    C4
    C5
    C5
    C2
    C2
    C5
    C5
    C3
    C3
    C4
    C4

    N1
    C3
    N1
    C2
    C3
    C2
    C2
    C4
    C4
    C3
    C3
    N1
    N1
    N1
    N1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    240.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C4H10N pyrrolidine protonated, kevo


    -0.22
    0.34
    0.34
    -0.35
    0.28
    0.28
    -0.12
    0.09
    0.09
    -0.12
    0.09
    0.09
    -0.35
    0.28
    0.28

    N1
    C4
    C2
    C4
    C5
    *N1
    *N1
    *C3
    *C3
    *C4
    *C4
    *C2
    *C2
    *C5
    *C5

    RESI 3PRP
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H51
    ATOM H52

    NG3P2
    HGP2
    HGP2
    CG3C54
    HGA2
    HGA2
    CG2R51
    HGR51
    CG2R51
    HGR51
    CG3C54
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND

    H11 N1
    H3 C4
    C2 C2
    C4

    N1
    C3
    N1
    C3

    H4
    H21
    H22
    H51
    H52

    H12
    H41
    C3
    C5
    N1
    H11
    H12
    H31
    H32
    H41
    H42
    H21
    H22
    H51
    H52

    !
    !
    !
    !
    !
    !
    !
    !
    !

    H32

    H42
    \
    /
    H31--C3----C4--H41
    |
    |
    H21--C2
    C5--H51
    / \ / \
    H22
    N1(+) H52
    / \
    H11
    H12

    C2 H21
    C4 H42
    C3 C4
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C2
    C5
    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H22 C3
    H51 C5
    C5 C5
    40.00
    330.00
    120.00
    240.00
    240.00
    120.00
    120.00
    240.00
    120.00
    240.00
    240.00
    120.00

    H31
    H52
    N1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C4H8N 3-pyrroline protonated, kevo


    -0.40
    0.39
    0.39
    -0.17
    0.28
    0.28
    -0.33
    0.25
    -0.33
    0.25
    -0.17
    0.28
    0.28

    ! H3
    H4
    !
    \ ____ /
    !
    C3----C4
    !
    |
    |
    ! H21--C2
    C5--H51
    !
    / \ / \
    ! H22
    N1(+) H52
    !
    / \
    !
    H11
    H12

    H12 C2
    H4 C5
    C3 C4

    H21 C2
    H51 C5
    C5 C5

    H22
    H52
    N1

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2
    C3
    C5
    C5
    C4
    C3
    N1
    N1
    N1
    N1

    C3
    C4
    C2
    C2
    C2
    C5
    C3
    C3
    C4
    C4

    C4
    C5
    *N1
    *N1
    *C3
    *C4
    *C2
    *C2
    *C5
    *C5

    RESI 2PRP
    GROUP
    ATOM N1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3P2
    HGP2
    HGP2
    CG2R51
    HGR52
    CG2R51
    HGR51
    CG3C52
    HGA2
    HGA2
    CG3C54
    HGA2
    HGA2

    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H11
    H41
    C2
    C3
    C2
    C3
    C5
    C5
    N1
    C2
    C3
    C3
    C4
    C4

    N1
    C4
    N1
    C2
    N1
    C2
    C2
    C2
    C3
    C4
    C5
    C5
    N1
    N1

    C5
    N1
    H11
    H12
    H3
    H4
    H21
    H22
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    20.00
    120.00
    240.00
    180.00
    180.00
    120.00
    240.00
    240.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C4H8N 2-pyrroline protonated, kevo


    -0.13
    0.33
    0.33
    -0.18
    0.22
    -0.06
    0.20
    -0.12
    0.09
    0.09
    -0.33
    0.28
    0.28

    ! H3
    H41 H42
    ! \
    | /
    !
    C3----C4
    !
    ||
    |
    !
    C2
    C5--H51
    ! / \ / \
    ! H2
    N1(+) H52
    !
    / \
    ! H11
    H12

    N1
    C4
    C3

    H12 C2
    H42 C5
    C4 C4

    C3
    C4
    *N1
    *N1
    *C2
    *C3
    *C4
    *C4
    *C5
    *C5

    C4
    C5
    H11
    H12
    H2
    H3
    H41
    H42
    H51
    H52

    H2 C3
    H51 C5
    C5 C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H3
    H52
    N1
    0.00
    20.00
    120.00
    240.00
    180.00
    180.00
    120.00
    240.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 2IMP
    1.000 ! C3H7N2 2-imidazoline protonated, kevo
    GROUP
    ATOM N1 NG2R52 -0.35
    ATOM H1 HGP2
    0.38
    ATOM C2 CG2R53 0.52 ! H3
    H41 H42
    ATOM H2 HGR53
    0.12 !
    \
    | /
    ATOM N3 NG2R52 -0.35 ! (+) N3----C4
    ATOM H3 HGP2
    0.38 !
    ||
    |
    ATOM C4 CG3C54 -0.41 !
    C2
    C5--H51
    ATOM H41 HGA2
    0.28 !
    / \ / \
    ATOM H42 HGA2
    0.28 ! H2
    N1
    H52
    ATOM C5 CG3C54 -0.41 !
    |
    ATOM H51 HGA2
    0.28 !
    H1
    ATOM H52 HGA2
    0.28
    !H[2-5][12] constrained, pre1g
    BOND N1
    BOND C4

    H1 C2
    H41 C4

    H2 N3
    H42 C5

    H3
    H51 C5

    H52

    BOND N1
    DOUBLE C2
    IC N1
    IC C2
    IC C2
    IC N3
    IC C4
    IC C5
    IC C5
    IC N1
    IC N1
    RESI 2HPP
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    !End

    C2

    N3

    C4

    C4

    C5

    N3
    C4
    *N1
    *C2
    *N3
    *C4
    *C4
    *C5
    *C5

    C4
    C5
    H1
    H2
    H3
    H41
    H42
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5

    N1

    N3
    C2
    N3
    C5
    N1
    C2
    N3
    N3
    C4
    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    -12.00
    180.00
    180.00
    180.00
    120.00
    240.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C4H6N 2H-pyrrole protonated, kevo


    NG2R52
    HGP2
    CG3C54
    HGA2
    HGA2
    CG2R51
    HGR51
    CG2R51
    HGR51
    CG2R52
    HGR52

    -0.27
    0.39
    -0.19
    0.28
    0.28
    -0.08
    0.25
    -0.27
    0.25
    0.07
    0.29

    ! H5
    H1
    !
    \ ____ /
    !
    C5----N1 H21
    !
    | (+) \ /
    !
    |
    C2
    !
    |____ / \
    !
    C4----C3 H22
    !
    /
    \
    ! H4
    H3

    N1 H1 C2 H21 C2 H22 C3 H3 C4 H4 C5
    N1 C2 C2 C3 C3 C4 C4 C5 C5 N1
    C2 C3 C4 C5 0.0000
    0.00
    0.00
    0.00
    C3 C4 C5 N1 0.0000
    0.00
    0.00
    0.00
    C2 C5 *N1 H1 0.0000
    0.00 180.00
    0.00
    C3 N1 *C2 H21 0.0000
    0.00 120.00
    0.00
    C3 N1 *C2 H22 0.0000
    0.00 240.00
    0.00
    C4 C2 *C3 H3 0.0000
    0.00 180.00
    0.00
    C5 C3 *C4 H4 0.0000
    0.00 180.00
    0.00
    N1 C4 *C5 H5 0.0000
    0.00 180.00
    0.00
    continuation of Maybridge list, kevo, may2007

    H5
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Bile acids and related compounds, chayan, jul2006


    RESI BAM1
    0.00 ! C13H24 Bile Acid Model cmpd 1, chayan (to estimate di
    hedral rotational surface energy)
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9A
    ATOM H9B
    GROUP
    ATOM C8
    ATOM H8A
    ATOM H8B
    GROUP
    ATOM C14

    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    -0.18 !
    0.09 !
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3RC1 -0.09

    C21
    |
    C12 C18 C20--C22
    / \ | |
    C11 C13--C17
    |
    |
    |
    C9 C14 C16
    \ / \ /
    C8 C15
    Model Compound

    ATOM H14
    GROUP
    ATOM C13
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    ATOM H22C

    HGA1

    0.09

    CG3RC1

    0.00

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    H12A
    C11
    C9
    C8
    C14
    C15
    C16
    C17
    C13
    C18
    C20
    C21
    C22

    !
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C12
    C12
    C11
    C9
    C8
    C14
    C15
    C16
    C17
    C13
    C17
    C20
    C20

    C12
    C11
    C9
    C8
    C14
    C15
    C16
    C8
    C8
    C14
    C13

    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09
    HGA1
    0.09
    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    C11
    C9
    C8
    C14
    C15
    C16
    C17
    C14
    C14
    C13
    C8

    C12
    C11
    C9
    C8
    C14
    C15
    C16
    C17
    C13
    C18
    C20
    C21
    C22

    C9
    C8
    C14
    C15
    C16
    C17
    C13
    C13
    C13
    C12
    *C14

    H12B
    H11A
    H9A
    H8A
    H14
    H15A
    H16A
    H17
    C12
    H18A
    H20
    H21A
    H22A
    C8
    C14
    C15
    C16
    C17
    C13
    C12
    C12
    C17
    C11
    C15

    C11
    C9
    C8
    C14
    C15
    C16

    H11B
    H9B
    H8B
    C13
    H15B
    H16B

    C18 H18B C18 H18C


    C21 H21B C21 H21C
    C22 H22B C22 H22C

    R(I(J/K))
    1.5465
    1.5370
    1.5369
    1.5301
    1.5242
    1.5463
    1.5545
    1.5301
    1.5301
    1.5400
    1.5400

    T(I(JK/KJ)) PHI
    113.07 53.26
    111.97 -54.31
    108.19 179.63
    117.07 -157.35
    103.25 -1.62
    106.76 32.90
    98.76 -165.58
    113.89 -59.62
    113.89 -179.99
    108.36 54.13
    113.89 120.29

    T(JKL)
    111.97
    108.19
    117.07
    103.25
    106.76
    98.76
    115.64
    108.36
    97.80
    111.30
    117.07

    R(KL)
    1.5369
    1.5301
    1.5242
    1.5463
    1.5545
    1.5707
    1.5392
    1.5392
    1.5707
    1.5465
    1.5242

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C17
    C14
    H8A
    C8
    H9A
    C9
    H11A
    C14
    H12A
    C13
    C16
    H15A
    C17
    H16A
    C13
    C12
    C14
    H18A
    H18A
    C13
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    H22A
    H22A

    RESI CA
    GROUP
    ATOM C3
    ATOM O3
    ATOM H3'
    ATOM H3
    GROUP
    ATOM C4
    ATOM H4A
    ATOM H4B
    GROUP
    ATOM C5
    ATOM H5
    GROUP
    ATOM C6
    ATOM H6A
    ATOM H6B

    C14
    C9
    C9
    C11
    C11
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20

    *C13
    *C8
    *C8
    *C9
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22

    C12
    H8A
    H8B
    H9A
    H9B
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    H22A
    H22B
    H22C

    1.5707
    1.5301
    1.1090
    1.5369
    1.1138
    1.5370
    1.1127
    1.5400
    1.1064
    1.5400
    1.5463
    1.0999
    1.5545
    1.0991
    1.5707
    1.5392
    1.5400
    1.1059
    1.1059
    1.5707
    1.5545
    1.5428
    1.5383
    1.5593
    1.1069
    1.1069
    1.5593
    1.1105
    1.1105

    97.80
    108.19
    109.97
    111.97
    108.41
    113.07
    109.08
    108.36
    111.17
    113.89
    103.25
    111.17
    106.76
    110.63
    98.76
    108.36
    113.50
    111.90
    111.90
    98.76
    112.96
    107.68
    112.55
    112.55
    111.01
    111.01
    107.68
    110.13
    110.13

    120.38
    121.59
    118.57
    -119.77
    -117.69
    120.55
    117.14
    174.66
    119.56
    -118.75
    119.82
    119.44
    121.20
    117.46
    -113.04
    121.36
    109.24
    119.52
    -120.42
    126.23
    61.62
    119.44
    122.44
    76.43
    -121.83
    118.41
    177.17
    119.59
    -119.58

    108.36
    109.97
    109.82
    108.41
    109.98
    109.08
    109.30
    111.17
    108.93
    106.87
    111.17
    111.12
    110.63
    111.19
    109.96
    113.50
    111.90
    110.40
    111.60
    112.96
    107.68
    112.55
    110.57
    111.01
    110.68
    110.01
    110.13
    111.27
    110.32

    -1.00 ! C24H39O5 Cholic Acid, chayan


    CG311
    OG311
    HGP1
    HGA1

    0.14
    -0.65
    0.42
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09 !

    GROUP

    OE1

    ||

    ATOM C7

    CG311

    0.14 !

    OH

    ATOM O7

    OG311

    -0.65 !

    ATOM H7' HGP1


    -1)
    ATOM H7 HGA1
    GROUP

    1.5392
    1.1090
    1.1117
    1.1138
    1.1118
    1.1127
    1.1121
    1.1064
    1.1115
    1.1175
    1.0999
    1.0993
    1.0991
    1.0988
    1.1005
    1.5528
    1.1059
    1.1089
    1.1063
    1.5593
    1.5428
    1.5383
    1.1109
    1.1069
    1.1100
    1.1108
    1.1105
    1.1091
    1.1103

    0.42 !
    0.09 !
    !

    Me21

    C22

    \ / \ / \

    C12 Me18
    / \ |

    CD

    C20
    /

    C11 C13---C17

    CG

    OE2(

    ATOM C8

    CG311

    -0.09 !

    Me19 |

    ATOM H8

    HGA1

    0.09 !

    C1 | C9

    GROUP

    C2

    C10 C8

    ATOM H14 HGA1

    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12
    ATOM O12
    ATOM H12'
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP

    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG311
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311 -0.09
    HGA1
    0.09
    CG301

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    C14

    C16

    / \|/ \ / \ /

    ATOM C14 CG3RC1 -0.09 !


    0.09 !

    C15

    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH
    Cholic Acid (CA)

    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM CD
    ATOM OE1
    ATOM OE2

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.52
    -0.76
    -0.76

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    CD
    C23

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    CD

    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    H3'
    H4B

    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12 C12 O12 O12 H12'
    H11A C11 H11B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    O7 O7

    H7'

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    CD
    OE1

    H20
    H22A
    H23A
    OE1
    OE2

    C20
    C22
    C23
    CD

    C21 C21 H21A C21 H21B C21 H21C


    H22B
    H23B
    OE2

    !
    R(I(J/K)) T(I(JK/KJ)) PHI
    !ICs based on CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5324 111.68 -49.58
    IC C2 C3 C4 C5
    1.5336 111.85 43.65
    IC C3 C4 C5 C6
    1.5384 115.86 -174.25
    IC C4 C5 C6 C7
    1.5602 108.84 86.42
    IC C5 C6 C7 C8
    1.5528 115.04 38.94
    IC C7 C8 C9 C10 1.5297 113.41 59.71
    IC C8 C9 C10 C1
    1.5223 109.57 178.73
    IC C9 C10 C1 C2
    1.5432 111.89 63.50
    IC O3 C3 C4 C5
    1.4163 109.08 161.75
    IC C4 C2 *C3 O3
    1.5384 111.85 -119.36
    IC C4 C2 *C3 H3
    1.5384 111.85 121.41
    IC C9 C5 *C10 C19 1.5432 109.52 -123.19
    IC C2 C3 O3 H3' 1.5336 106.95 64.94
    IC C5 C3 *C4 H4A 1.5602 115.86 122.86

    T(JKL)
    111.85
    115.86
    108.84
    115.04
    113.04
    109.57
    111.89
    113.76
    115.86
    106.95
    109.41
    109.67
    104.68
    108.65

    R(KL)
    1.5384
    1.5602
    1.5528
    1.5449
    1.5297
    1.5432
    1.5560
    1.5324
    1.5602
    1.4163
    1.1143
    1.5560
    0.9611
    1.1110

    IC H4A
    IC C10
    IC C7
    IC H6A
    IC C2
    IC C2
    IC C1
    IC H2A
    !IC C1
    fig
    !IC C2
    fig
    !IC C3
    fig
    !IC C10
    fig
    !IC C4
    fig
    !IC C5
    fig
    IC C6
    IC C14
    IC C7
    IC C13
    IC C8
    IC C14
    IC C17
    IC C14
    !IC C2
    fig
    !IC C2
    fig
    !IC C1
    fig
    !IC H2A
    fig
    !IC C1
    fig
    !IC C4
    fig
    !IC O3
    fig
    !IC C2
    fig
    !IC C5
    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC O7
    IC C6
    IC C9
    IC C10
    IC C9

    C3
    C4
    C5
    C5
    C10
    C10
    C3
    C3
    C2

    *C4
    *C5
    *C6
    *C6
    *C1
    *C1
    *C2
    *C2
    C3

    H4B
    H5
    H6A
    H6B
    H1A
    H1B
    H2A
    H2B
    C4

    C3

    C4

    C4

    C5

    C4

    1.1110
    1.5283
    1.5449
    1.1112
    1.5324
    1.5324
    1.5324
    1.1118
    1.5383

    108.72
    105.10
    109.40
    108.30
    107.87
    110.13
    110.22
    108.75
    110.66

    1.1114
    1.1173
    1.1112
    1.1112
    1.1135
    1.1095
    1.1118
    1.1127
    1.5367 ! for trans con

    C5

    1.5311 110.66 -52.17 111.70

    1.5156 ! for trans con

    C10

    1.5367 111.70 -54.41 115.09

    1.5304 ! for trans con

    *C5 C6

    1.5304 115.09 -177.32 121.28

    1.3432 ! for trans con

    C5

    C6

    C7

    1.5156 121.28

    75.31 123.88

    1.5018 ! for trans con

    C6

    C7

    C8

    1.3432 123.88

    51.01 112.36

    1.5506 ! for trans con

    C7
    C7
    C8
    C8
    C14
    C15
    C14
    C13
    C10

    C8
    *C8
    C14
    *C14
    C15
    C16
    *C13
    C12
    *C1

    C14
    C9
    C13
    C15
    C16
    C17
    C12
    C11
    H1A

    109.07
    113.41
    112.73
    114.03
    103.48
    107.62
    106.82
    112.18
    109.26

    1.5517
    1.5223
    1.5504
    1.5268
    1.5369
    1.5513
    1.5557
    1.5515
    1.1104 ! for trans con

    C10 *C1 H1B

    1.5383 114.55 -120.71 108.29

    1.1134 ! for trans con

    C3

    *C2 H2A

    1.5383 110.44 121.16 109.41

    1.1119 ! for trans con

    C3

    *C2 H2B

    1.1119 109.41 118.30 109.70

    1.1112 ! for trans con

    C2

    C3

    O3

    1.1119 109.41 -175.00 109.70

    1.1112 ! for trans con

    C2

    *C3 O3

    1.5367 110.66 -120.28 109.14

    1.4158 ! for trans con

    C2

    *C3 H3

    1.4158 109.14 -118.92 109.40

    1.1155 ! for trans con

    C3

    O3

    1.5311 109.14

    60.00 105.39

    0.9593 ! for trans con

    C3

    *C4 H4A

    1.5156 111.70 121.99 109.16

    1.1099 ! for trans con

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C7
    C8
    C12

    *C7
    *C7
    O7
    *C8
    *C9
    *C11

    H3'

    O7
    H7
    H7'
    H8
    H9
    H11A

    1.5449
    1.5517
    1.5297
    1.5504
    1.5517
    1.5268
    1.5748
    1.5504
    1.5383

    108.65 115.61
    114.75 116.75
    115.04 -124.17
    109.40 -115.79
    113.76 119.42
    113.76 -124.15
    111.68 121.97
    110.22 117.25
    110.44 -62.22

    1.5297
    1.4213
    1.5449
    1.5223
    1.5432
    1.5553

    113.04 -167.24
    109.07 119.23
    109.07 -171.16
    112.73 117.19
    114.03 -155.98
    103.48
    2.71
    98.26 120.41
    106.82 50.62
    114.55 122.42

    113.04
    108.12
    108.12
    113.41
    109.57
    117.58

    -126.79
    -113.65
    170.74
    122.31
    -116.33
    122.21

    108.12
    106.95
    104.84
    106.89
    105.86
    106.83

    1.4213
    1.1162
    0.9615
    1.1063
    1.1163
    1.1096

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H11A
    C14
    O12
    C13
    C13
    C16
    H15A
    C17
    H16A
    C13
    C12
    C14
    H18A
    H18A
    C5
    H19A
    H19A
    C13
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    C23
    H22A
    C20
    CD
    CD
    C22
    OE1

    RESI DCA
    GROUP
    ATOM C3
    ATOM O3
    ATOM H3'
    ATOM H3
    GROUP
    ATOM C4
    ATOM H4A
    ATOM H4B
    GROUP
    ATOM C5
    ATOM H5
    GROUP
    ATOM C6
    ATOM H6A
    ATOM H6B
    GROUP
    ATOM C7
    ATOM H7A
    ATOM H7B
    GROUP
    ATOM C8
    ATOM H8
    GROUP
    ATOM C14

    C12
    C13
    C13
    C12
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23

    *C11
    C12
    *C12
    O12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    CD
    *CD

    H11B
    O12
    H12
    H12'
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    CD
    H23A
    H23B
    OE1
    OE2

    1.1096
    1.5504
    1.4228
    1.5557
    1.5504
    1.5369
    1.1006
    1.5513
    1.1007
    1.5748
    1.5557
    1.5504
    1.1055
    1.1055
    1.5283
    1.1077
    1.1077
    1.5748
    1.5513
    1.5487
    1.5408
    1.5616
    1.1068
    1.1068
    1.5616
    1.5494
    1.1125
    1.5487
    1.5299
    1.5299
    1.5494
    1.2584

    106.83
    106.82
    114.67
    114.67
    112.73
    103.48
    111.22
    107.62
    110.48
    100.22
    106.82
    113.69
    112.14
    112.14
    109.67
    111.22
    111.22
    100.22
    112.63
    108.94
    113.13
    113.13
    111.00
    111.00
    108.94
    113.97
    109.76
    113.97
    113.05
    113.05
    113.05
    116.54

    114.26
    -74.73
    -118.14
    -49.37
    -119.72
    119.05
    119.83
    120.90
    117.28
    -113.28
    122.03
    3.50
    119.59
    -120.84
    9.75
    120.95
    -119.64
    127.99
    71.02
    122.52
    121.15
    67.60
    -122.83
    118.17
    -161.91
    119.29
    117.37
    176.94
    119.90
    -119.56
    -178.02
    175.48

    107.91
    114.67
    108.61
    105.00
    109.55
    111.22
    112.45
    110.48
    111.71
    108.29
    113.69
    112.14
    111.31
    110.78
    111.22
    111.67
    110.71
    112.63
    108.94
    113.13
    109.02
    111.00
    111.01
    109.90
    113.97
    109.76
    110.00
    113.05
    111.01
    110.12
    116.54
    119.00

    1.1115
    1.4228
    1.1119
    0.9629
    1.1139
    1.1006
    1.0988
    1.1007
    1.1003
    1.1013
    1.5568
    1.1055
    1.1063
    1.1084
    1.1077
    1.1070
    1.1092
    1.5616
    1.5487
    1.5408
    1.1123
    1.1068
    1.1085
    1.1107
    1.5494
    1.1125
    1.1113
    1.5299
    1.1071
    1.1084
    1.2584
    1.2572

    -1.00 ! C24H39O4 deoxycholic acid(DCA), chayan


    CG311
    OG311
    HGP1
    HGA1
    CG321
    HGA2
    HGA2

    0.14
    -0.65
    0.42
    0.09

    -0.18
    0.09 !
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG3RC1 -0.09 !

    OE1
    ||
    OH
    Me21 C22 CD
    |
    \ / \ / \
    C12 Me18 C20 CG
    OE2(-1)
    / \ |
    /
    C11 C13---C17
    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ /
    OH C4 C6
    Deoxycholic acid (DCA)

    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12
    ATOM O12
    ATOM H12'
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23

    HGA1

    0.09 !
    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG311
    HGA1
    OG311
    HGP1

    0.14
    0.09
    -0.65
    0.42

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG301

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321

    -0.18

    ATOM H23A
    ATOM H23B
    GROUP
    ATOM CD
    ATOM OE1
    ATOM OE2

    HGA2
    HGA2

    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.52
    -0.76
    -0.76

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    CD
    C23

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    CD

    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    H3'
    H4B

    C6
    C7
    C8
    C9

    H6A C6
    H7A C7
    H8
    H9

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12 C12 O12 O12 H12'
    H11A C11 H11B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    H7B

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    CD
    OE1

    H20
    H22A
    H23A
    OE1
    OE2

    C20
    C22
    C23
    CD

    C21 C21 H21A C21 H21B C21 H21C


    H22B
    H23B
    OE2

    !
    R(I(J/K)) T(I(JK/KJ)) PHI
    !ICs based on CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5324 111.68 -49.58
    IC C2 C3 C4 C5
    1.5336 111.85 43.65
    IC C3 C4 C5 C6
    1.5384 115.86 -174.25
    IC C4 C5 C6 C7
    1.5602 108.84 86.42
    IC C5 C6 C7 C8
    1.5528 115.04 38.94
    IC C7 C8 C9 C10 1.5297 113.41 59.71
    IC C8 C9 C10 C1
    1.5223 109.57 178.73
    IC C9 C10 C1 C2
    1.5432 111.89 63.50
    IC O3 C3 C4 C5
    1.4163 109.08 161.75
    IC C4 C2 *C3 O3
    1.5384 111.85 -119.36
    IC C4 C2 *C3 H3
    1.5384 111.85 121.41
    IC C9 C5 *C10 C19 1.5432 109.52 -123.19
    IC C2 C3 O3 H3' 1.5336 106.95 64.94
    IC C5 C3 *C4 H4A 1.5602 115.86 122.86
    IC H4A C3 *C4 H4B 1.1110 108.65 115.61
    IC C10 C4 *C5 H5
    1.5283 114.75 116.75
    IC C7 C5 *C6 H6A 1.5449 115.04 -124.17
    IC H6A C5 *C6 H6B 1.1112 109.40 -115.79
    IC C2 C10 *C1 H1A 1.5324 113.76 119.42
    IC C2 C10 *C1 H1B 1.5324 113.76 -124.15
    IC C1 C3 *C2 H2A 1.5324 111.68 121.97
    IC H2A C3 *C2 H2B 1.1118 110.22 117.25
    !IC C1 C2 C3 C4
    1.5383 110.44 -62.22
    fig

    T(JKL)
    111.85
    115.86
    108.84
    115.04
    113.04
    109.57
    111.89
    113.76
    115.86
    106.95
    109.41
    109.67
    104.68
    108.65
    108.72
    105.10
    109.40
    108.30
    107.87
    110.13
    110.22
    108.75
    110.66

    R(KL)
    1.5384
    1.5602
    1.5528
    1.5449
    1.5297
    1.5432
    1.5560
    1.5324
    1.5602
    1.4163
    1.1143
    1.5560
    0.9611
    1.1110
    1.1114
    1.1173
    1.1112
    1.1112
    1.1135
    1.1095
    1.1118
    1.1127
    1.5367 ! for trans con

    !IC C2
    fig
    !IC C3
    fig
    !IC C10
    fig
    !IC C4
    fig
    !IC C5
    fig
    IC C6
    IC C14
    IC C7
    IC C13
    IC C8
    IC C14
    IC C17
    IC C14
    !IC C2
    fig
    !IC C2
    fig
    !IC C1
    fig
    !IC H2A
    fig
    !IC C1
    fig
    !IC C4
    fig
    !IC O3
    fig
    !IC C2
    fig
    !IC C5
    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC H7A
    IC C9
    IC C10
    IC C9
    IC H11A
    IC C14
    IC O12
    IC C13
    IC C13
    IC C16
    IC H15A
    IC C17
    IC H16A
    IC C13
    IC C12

    C3

    C4

    C5

    1.5311 110.66 -52.17 111.70

    1.5156 ! for trans con

    C4

    C5

    C10

    1.5367 111.70 -54.41 115.09

    1.5304 ! for trans con

    C4

    *C5 C6

    1.5304 115.09 -177.32 121.28

    1.3432 ! for trans con

    C5

    C6

    C7

    1.5156 121.28

    75.31 123.88

    1.5018 ! for trans con

    C6

    C7

    C8

    1.3432 123.88

    51.01 112.36

    1.5506 ! for trans con

    C7
    C7
    C8
    C8
    C14
    C15
    C14
    C13
    C10

    C8
    *C8
    C14
    *C14
    C15
    C16
    *C13
    C12
    *C1

    C14
    C9
    C13
    C15
    C16
    C17
    C12
    C11
    H1A

    109.07
    113.41
    112.73
    114.03
    103.48
    107.62
    106.82
    112.18
    109.26

    1.5517
    1.5223
    1.5504
    1.5268
    1.5369
    1.5513
    1.5557
    1.5515
    1.1104 ! for trans con

    C10 *C1 H1B

    1.5383 114.55 -120.71 108.29

    1.1134 ! for trans con

    C3

    *C2 H2A

    1.5383 110.44 121.16 109.41

    1.1119 ! for trans con

    C3

    *C2 H2B

    1.1119 109.41 118.30 109.70

    1.1112 ! for trans con

    C2

    C3

    O3

    1.1119 109.41 -175.00 109.70

    1.1112 ! for trans con

    C2

    *C3 O3

    1.5367 110.66 -120.28 109.14

    1.4158 ! for trans con

    C2

    *C3 H3

    1.4158 109.14 -118.92 109.40

    1.1155 ! for trans con

    C3

    O3

    1.5311 109.14

    60.00 105.39

    0.9593 ! for trans con

    C3

    *C4 H4A

    1.5156 111.70 121.99 109.16

    1.1099 ! for trans con

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C8
    C12
    C12
    C13
    C13
    C12
    C8
    C14
    C14
    C15
    C15
    C16
    C14

    *C7
    *C7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    O12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13

    H3'

    H7A
    H7B
    H8
    H9
    H11A
    H11B
    O12
    H12
    H12'
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18

    1.5449
    1.5517
    1.5297
    1.5504
    1.5517
    1.5268
    1.5748
    1.5504
    1.5383

    1.5383
    1.1119
    1.5223
    1.5432
    1.5553
    1.1096
    1.5504
    1.4228
    1.5557
    1.5504
    1.5369
    1.1006
    1.5513
    1.1007
    1.5748
    1.5557

    113.04 -167.24
    109.07 119.23
    109.07 -171.16
    112.73 117.19
    114.03 -155.98
    103.48
    2.71
    98.26 120.41
    106.82 50.62
    114.55 122.42

    113.44
    109.41
    113.41
    109.57
    117.58
    106.83
    106.82
    114.67
    114.67
    112.73
    103.48
    111.22
    107.62
    110.48
    100.22
    106.82

    -126.79
    -113.65
    122.31
    -116.33
    122.21
    114.26
    -74.73
    -118.14
    -49.37
    -119.72
    119.05
    119.83
    120.90
    117.28
    -113.28
    122.03

    109.41
    109.70
    106.89
    105.86
    106.83
    107.91
    114.67
    108.61
    105.00
    109.55
    111.22
    112.45
    110.48
    111.71
    108.29
    113.69

    1.1119
    1.1112
    1.1063
    1.1163
    1.1096
    1.1115
    1.4228
    1.1119
    0.9629
    1.1139
    1.1006
    1.0988
    1.1007
    1.1003
    1.1013
    1.5568

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C14
    H18A
    H18A
    C5
    H19A
    H19A
    C13
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    C23
    H22A
    C20
    CD
    CD
    C22
    OE1

    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23

    RESI LCA
    GROUP
    ATOM C3
    ATOM O3
    ATOM H3'
    ATOM H3
    GROUP
    ATOM C4
    ATOM H4A
    ATOM H4B
    GROUP
    ATOM C5
    ATOM H5
    GROUP
    ATOM C6
    ATOM H6A
    ATOM H6B
    GROUP
    ATOM C7
    ATOM H7A
    ATOM H7B
    GROUP
    ATOM C8
    ATOM H8
    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17

    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    CD
    *CD

    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    CD
    H23A
    H23B
    OE1
    OE2

    1.5504
    1.1055
    1.1055
    1.5283
    1.1077
    1.1077
    1.5748
    1.5513
    1.5487
    1.5408
    1.5616
    1.1068
    1.1068
    1.5616
    1.5494
    1.1125
    1.5487
    1.5299
    1.5299
    1.5494
    1.2584

    113.69
    112.14
    112.14
    109.67
    111.22
    111.22
    100.22
    112.63
    108.94
    113.13
    113.13
    111.00
    111.00
    108.94
    113.97
    109.76
    113.97
    113.05
    113.05
    113.05
    116.54

    3.50
    119.59
    -120.84
    9.75
    120.95
    -119.64
    127.99
    71.02
    122.52
    121.15
    67.60
    -122.83
    118.17
    -161.91
    119.29
    117.37
    176.94
    119.90
    -119.56
    -178.02
    175.48

    112.14
    111.31
    110.78
    111.22
    111.67
    110.71
    112.63
    108.94
    113.13
    109.02
    111.00
    111.01
    109.90
    113.97
    109.76
    110.00
    113.05
    111.01
    110.12
    116.54
    119.00

    1.1055
    1.1063
    1.1084
    1.1077
    1.1070
    1.1092
    1.5616
    1.5487
    1.5408
    1.1123
    1.1068
    1.1085
    1.1107
    1.5494
    1.1125
    1.1113
    1.5299
    1.1071
    1.1084
    1.2584
    1.2572

    -1.00 ! C24H39O3 LITHOCHOLIC ACID (LCA), chayan


    CG311
    OG311
    HGP1
    HGA1

    0.14
    -0.65
    0.42
    0.09

    CG321
    HGA2
    HGA2

    -0.18 !
    0.09 !
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG3RC1 -0.09 !
    HGA1
    0.09 !
    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09

    OE1
    ||
    H
    Me21 C22 CD
    |
    \ / \ / \
    C12 Me18 C20 CG
    OE2(-1)
    / \ |
    /
    C11 C13---C17
    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ /
    OH C4 C6
    Lithocholic acid (LCA)

    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM CD
    ATOM OE1
    ATOM OE2

    HGA1

    0.09

    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    BOND
    BOND
    BOND
    BOND
    BOND

    O3
    C4
    C5
    C10
    C1

    C3
    C3
    C4
    C5
    C10

    CG301

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.52
    -0.76
    -0.76
    C3
    C4
    C5
    C10
    C1

    H3
    H4A
    H5
    C19
    H1A

    O3
    C4

    H3'
    H4B

    C19 H19A C19 H19B C19 H19C


    C1 H1B

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    CD

    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    CD
    C23

    C2

    H2A C2

    H2B

    C6
    C7
    C8
    C9

    H6A C6
    H7A C7
    H8
    H9

    H6B
    H7B

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12A C12 H12B
    H11A C11 H11B

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    CD
    OE1

    H20
    H22A
    H23A
    OE1
    OE2

    C20
    C22
    C23
    CD

    C21 C21 H21A C21 H21B C21 H21C


    H22B
    H23B
    OE2

    !
    R(I(J/K)) T(I(JK/KJ)) PHI
    !ICs based on CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5337 112.03 -49.25
    IC C2 C3 C4 C5
    1.5350 111.84 44.83
    IC C3 C4 C5 C6
    1.5388 114.98 -175.73
    IC C4 C5 C6 C7
    1.5580 110.26 75.60
    IC C5 C6 C7 C8
    1.5462 112.05 52.55
    IC C7 C8 C9 C10 1.5462 111.19 57.34
    IC C8 C9 C10 C1
    1.5356 111.05 -177.00
    IC C9 C10 C1 C2
    1.5448 112.40 64.20
    IC O3 C3 C4 C5
    1.4166 109.16 163.09
    IC C4 C2 *C3 O3
    1.5388 111.84 -119.52
    IC C4 C2 *C3 H3
    1.5388 111.84 121.28
    IC C9 C5 *C10 C19 1.5448 110.02 -122.97
    IC C2 C3 O3 H3' 1.5350 107.04 60.89
    IC C5 C3 *C4 H4A 1.5580 114.98 122.28
    IC H4A C3 *C4 H4B 1.1112 108.66 116.01
    IC C10 C4 *C5 H5
    1.5336 114.85 117.05
    IC C7 C5 *C6 H6A 1.5329 112.05 -122.19
    IC H6A C5 *C6 H6B 1.1114 109.68 -117.56
    IC C2 C10 *C1 H1A 1.5337 114.05 119.68
    IC C2 C10 *C1 H1B 1.5337 114.05 -124.22
    IC C1 C3 *C2 H2A 1.5337 112.03 122.06
    IC H2A C3 *C2 H2B 1.1113 110.32 117.22
    !IC C1 C2 C3 C4
    1.5383 110.44 -62.22
    fig
    !IC C2 C3 C4 C5
    1.5311 110.66 -52.17
    fig
    !IC C3 C4 C5 C10 1.5367 111.70 -54.41
    fig
    !IC C10 C4 *C5 C6
    1.5304 115.09 -177.32
    fig
    !IC C4 C5 C6 C7
    1.5156 121.28 75.31
    fig
    !IC C5 C6 C7 C8
    1.3432 123.88 51.01
    fig
    IC C6 C7 C8 C14 1.5329 111.32 -170.02
    IC C14 C7 *C8 C9
    1.5454 106.39 115.37

    T(JKL)

    R(KL)

    111.84
    114.98
    110.26
    112.05
    111.32
    111.05
    112.40
    114.05
    114.98
    107.04
    109.34
    109.85
    105.08
    108.66
    108.59
    105.40
    109.68
    109.38
    107.55
    110.15
    110.32
    108.67
    110.66

    1.5388
    1.5580
    1.5462
    1.5329
    1.5462
    1.5448
    1.5563
    1.5337
    1.5580
    1.4166
    1.1145
    1.5545
    0.9602
    1.1112
    1.1102
    1.1171
    1.1114
    1.1121
    1.1136
    1.1090
    1.1113
    1.1129
    1.5367 ! for trans con

    111.70

    1.5156 ! for trans con

    115.09

    1.5304 ! for trans con

    121.28

    1.3432 ! for trans con

    123.88

    1.5018 ! for trans con

    112.36

    1.5506 ! for trans con

    106.39
    111.19

    1.5454
    1.5356

    IC C7
    IC C13
    IC C8
    IC C14
    IC C17
    IC C14
    !IC C2
    fig
    !IC C2
    fig
    !IC C1
    fig
    !IC H2A
    fig
    !IC C1
    fig
    !IC C4
    fig
    !IC O3
    fig
    !IC C2
    fig
    !IC C5
    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC H7A
    IC C9
    IC C10
    IC C9
    IC H11A
    IC C14
    IC H12A
    IC C13
    IC C16
    IC H15A
    IC C17
    IC H16A
    IC C13
    IC C12
    IC C14
    IC H18A
    IC H18A
    IC C5
    IC H19A
    IC H19A
    IC C13
    IC C16
    IC C22
    IC C21
    IC C17
    IC H21A
    IC H21A

    C8
    C8
    C14
    C15
    C14
    C13
    C10

    112.55
    116.48
    103.50
    106.89
    108.13
    111.21
    109.26

    1.5432
    1.5277
    1.5439
    1.5535
    1.5348
    1.5444
    1.1104 ! for trans con

    C10 *C1 H1B

    1.5383 114.55 -120.71 108.29

    1.1134 ! for trans con

    C3

    *C2 H2A

    1.5383 110.44 121.16 109.41

    1.1119 ! for trans con

    C3

    *C2 H2B

    1.1119 109.41 118.30 109.70

    1.1112 ! for trans con

    C2

    C3

    O3

    1.1119 109.41 -175.00 109.70

    1.1112 ! for trans con

    C2

    *C3 O3

    1.5367 110.66 -120.28 109.14

    1.4158 ! for trans con

    C2

    *C3 H3

    1.4158 109.14 -118.92 109.40

    1.1155 ! for trans con

    C3

    O3

    1.5311 109.14

    60.00 105.39

    0.9593 ! for trans con

    C3

    *C4 H4A

    1.5156 111.70 121.99 109.16

    1.1099 ! for trans con

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C8
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20

    C14
    *C14
    C15
    C16
    *C13
    C12
    *C1

    *C7
    *C7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21

    C13
    C15
    C16
    C17
    C12
    C11
    H1A

    H3'

    H7A
    H7B
    H8
    H9
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C

    1.5462
    1.5432
    1.5454
    1.5277
    1.5722
    1.5432
    1.5383

    1.5462
    1.1112
    1.5356
    1.5448
    1.5521
    1.1097
    1.5432
    1.1120
    1.5432
    1.5439
    1.0997
    1.5535
    1.0992
    1.5722
    1.5348
    1.5432
    1.1058
    1.1058
    1.5336
    1.1083
    1.1083
    1.5722
    1.5535
    1.5506
    1.5401
    1.5637
    1.1071
    1.1071

    106.39 -177.38
    112.55 118.10
    116.48 -154.70
    103.50 -1.82
    98.05 120.18
    108.13 53.76
    114.55 122.42

    111.32
    109.56
    111.19
    111.05
    113.16
    109.10
    108.13
    108.72
    112.55
    103.50
    111.24
    106.89
    110.90
    98.51
    108.13
    113.93
    111.83
    111.83
    109.85
    111.07
    111.07
    98.51
    111.95
    109.13
    112.87
    112.87
    110.62
    110.62

    -120.76
    -117.60
    124.30
    -116.65
    121.96
    116.39
    -66.12
    -119.32
    -119.67
    119.46
    119.60
    121.34
    117.31
    -112.99
    121.73
    -4.01
    120.17
    -120.74
    -8.12
    120.82
    -119.70
    127.11
    70.28
    121.97
    121.21
    73.29
    -122.03
    118.43

    109.56
    109.24
    109.39
    106.44
    109.10
    107.43
    108.72
    111.59
    108.40
    111.24
    111.35
    110.90
    111.27
    110.29
    113.93
    111.83
    111.33
    110.60
    111.07
    111.82
    110.58
    111.95
    109.13
    112.87
    109.11
    110.62
    110.43
    110.33

    1.1112
    1.1114
    1.1045
    1.1137
    1.1097
    1.1100
    1.1120
    1.1062
    1.1145
    1.0997
    1.0990
    1.0992
    1.0993
    1.1004
    1.5529
    1.1058
    1.1067
    1.1083
    1.1083
    1.1063
    1.1092
    1.5637
    1.5506
    1.5401
    1.1116
    1.1071
    1.1097
    1.1098

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C17
    C23
    H22A
    C20
    CD
    CD
    C22
    OE1

    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23

    RESI CDCA
    GROUP
    ATOM C3
    ATOM O3
    ATOM H3'
    ATOM H3
    GROUP
    ATOM C4
    ATOM H4A
    ATOM H4B
    GROUP
    ATOM C5
    ATOM H5
    GROUP
    ATOM C6
    ATOM H6A
    ATOM H6B
    GROUP
    ATOM C7
    ATOM O7
    ATOM H7'
    ATOM H7
    GROUP
    ATOM C8
    ATOM H8
    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B

    C22
    *C22
    *C22
    C23
    *C23
    *C23
    CD
    *CD

    C23
    H22A
    H22B
    CD
    H23A
    H23B
    OE1
    OE2

    1.5637
    1.5502
    1.1115
    1.5506
    1.5303
    1.5303
    1.5502
    1.2588

    109.13
    114.04
    110.02
    114.04
    113.25
    113.25
    113.25
    116.56

    -161.00
    119.37
    117.32
    177.56
    119.99
    -119.65
    -178.85
    177.44

    114.04
    110.02
    109.74
    113.25
    110.96
    110.01
    116.56
    119.16

    1.5502
    1.1115
    1.1112
    1.5303
    1.1070
    1.1083
    1.2588
    1.2573

    -1.00 ! C24H39O4 CHENODEOXYCHOLIC ACID, chayan


    CG311
    OG311
    HGP1
    HGA1

    0.14
    -0.65
    0.42
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09 !
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG311
    0.14 !
    OG311 -0.65 !
    HGP1
    0.42 !
    HGA1
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG3RC1 -0.09 !
    HGA1
    0.09 !
    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09

    OE1
    ||
    H
    Me21 C22 CD
    |
    \ / \ / \
    C12 Me18 C20 CG
    OE2(-1)
    / \ |
    /
    C11 C13---C17
    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH
    Chenodeoxycholic acid (CDCA)

    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09

    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM CD
    ATOM OE1
    ATOM OE2
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG301

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.52
    -0.76
    -0.76

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9

    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    H3'
    H4B

    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12A C12 H12B
    H11A C11 H11B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    O7 O7

    H7'

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    CD

    C15
    C16
    C17
    C13
    C20
    C22
    C23
    CD
    C23

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    CD
    OE1

    H20
    H22A
    H23A
    OE1
    OE2

    C20
    C22
    C23
    CD

    C21 C21 H21A C21 H21B C21 H21C


    H22B
    H23B
    OE2

    !
    R(I(J/K)) T(I(JK/KJ)) PHI
    !ICs based on CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5325 111.74 -49.21
    IC C2 C3 C4 C5
    1.5341 111.88 43.74
    IC C3 C4 C5 C6
    1.5385 115.69 -175.10
    IC C4 C5 C6 C7
    1.5597 109.04 85.37
    IC C5 C6 C7 C8
    1.5520 114.98 38.83
    IC C7 C8 C9 C10 1.5290 114.20 57.90
    IC C8 C9 C10 C1
    1.5325 109.53 179.78
    IC C9 C10 C1 C2
    1.5437 112.01 63.19
    IC O3 C3 C4 C5
    1.4164 109.06 161.96
    IC C4 C2 *C3 O3
    1.5385 111.88 -119.42
    IC C4 C2 *C3 H3
    1.5385 111.88 121.34
    IC C9 C5 *C10 C19 1.5437 109.64 -123.44
    IC C2 C3 O3 H3' 1.5341 107.04 68.70
    IC C5 C3 *C4 H4A 1.5597 115.69 122.74
    IC H4A C3 *C4 H4B 1.1111 108.67 115.74
    IC C10 C4 *C5 H5
    1.5278 114.69 116.72
    IC C7 C5 *C6 H6A 1.5440 114.98 -124.18
    IC H6A C5 *C6 H6B 1.1112 109.41 -115.81
    IC C2 C10 *C1 H1A 1.5325 113.83 119.45
    IC C2 C10 *C1 H1B 1.5325 113.83 -124.31
    IC C1 C3 *C2 H2A 1.5325 111.74 122.10
    IC H2A C3 *C2 H2B 1.1113 110.26 117.21
    !IC C1 C2 C3 C4
    1.5383 110.44 -62.22
    fig
    !IC C2 C3 C4 C5
    1.5311 110.66 -52.17
    fig
    !IC C3 C4 C5 C10 1.5367 111.70 -54.41
    fig
    !IC C10 C4 *C5 C6
    1.5304 115.09 -177.32
    fig
    !IC C4 C5 C6 C7
    1.5156 121.28 75.31
    fig
    !IC C5 C6 C7 C8
    1.3432 123.88 51.01
    fig
    IC C6 C7 C8 C14 1.5440 113.15 -166.48
    IC C14 C7 *C8 C9
    1.5543 108.55 119.88
    IC C7 C8 C14 C13 1.5290 108.55 -174.00
    IC C13 C8 *C14 C15 1.5423 113.09 118.54
    IC C8 C14 C15 C16 1.5543 116.41 -154.98
    IC C14 C15 C16 C17 1.5290 103.52 -2.21
    IC C17 C14 *C13 C12 1.5726 98.14 119.76
    IC C14 C13 C12 C11 1.5423 107.63 55.01
    !IC C2 C10 *C1 H1A 1.5383 114.55 122.42
    fig
    !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71
    fig
    !IC C1 C3 *C2 H2A 1.5383 110.44 121.16
    fig

    T(JKL)

    R(KL)

    111.88
    115.69
    109.04
    114.98
    113.15
    109.53
    112.01
    113.83
    115.69
    107.04
    109.37
    109.56
    104.78
    108.67
    108.84
    105.05
    109.41
    108.31
    107.75
    110.15
    110.26
    108.67
    110.66

    1.5385
    1.5597
    1.5520
    1.5440
    1.5290
    1.5437
    1.5562
    1.5325
    1.5597
    1.4164
    1.1144
    1.5561
    0.9606
    1.1111
    1.1112
    1.1175
    1.1112
    1.1113
    1.1136
    1.1092
    1.1113
    1.1128
    1.5367 ! for trans con

    111.70

    1.5156 ! for trans con

    115.09

    1.5304 ! for trans con

    121.28

    1.3432 ! for trans con

    123.88

    1.5018 ! for trans con

    112.36

    1.5506 ! for trans con

    108.55
    114.20
    113.09
    116.41
    103.52
    106.91
    107.63
    111.17
    109.26

    1.5543
    1.5325
    1.5423
    1.5290
    1.5436
    1.5527
    1.5335
    1.5432
    1.1104 ! for trans con

    108.29

    1.1134 ! for trans con

    109.41

    1.1119 ! for trans con

    !IC H2A
    fig
    !IC C1
    fig
    !IC C4
    fig
    !IC O3
    fig
    !IC C2
    fig
    !IC C5
    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC O7
    IC C6
    IC C9
    IC C10
    IC C9
    IC H11A
    IC C14
    IC H12A
    IC C13
    IC C16
    IC H15A
    IC C17
    IC H16A
    IC C13
    IC C12
    IC C14
    IC H18A
    IC H18A
    IC C5
    IC H19A
    IC H19A
    IC C13
    IC C16
    IC C22
    IC C21
    IC C17
    IC H21A
    IC H21A
    IC C17
    IC C23
    IC H22A
    IC C20
    IC CD
    IC CD
    IC C22
    IC OE1

    C3

    *C2 H2B

    1.1119 109.41 118.30 109.70

    1.1112 ! for trans con

    C2

    C3

    O3

    1.1119 109.41 -175.00 109.70

    1.1112 ! for trans con

    C2

    *C3 O3

    1.5367 110.66 -120.28 109.14

    1.4158 ! for trans con

    C2

    *C3 H3

    1.4158 109.14 -118.92 109.40

    1.1155 ! for trans con

    C3

    O3

    1.5311 109.14

    60.00 105.39

    0.9593 ! for trans con

    C3

    *C4 H4A

    1.5156 111.70 121.99 109.16

    1.1099 ! for trans con

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C7
    C8
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23

    RESI UDCA

    *C7
    *C7
    O7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    CD
    *CD

    H3'

    O7
    H7
    H7'
    H8
    H9
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    CD
    H23A
    H23B
    OE1
    OE2

    1.5290
    1.4217
    1.5440
    1.5325
    1.5437
    1.5549
    1.1092
    1.5423
    1.1122
    1.5423
    1.5436
    1.1003
    1.5527
    1.0995
    1.5726
    1.5335
    1.5423
    1.1055
    1.1055
    1.5278
    1.1078
    1.1078
    1.5726
    1.5527
    1.5504
    1.5400
    1.5638
    1.1072
    1.1072
    1.5638
    1.5501
    1.1115
    1.5504
    1.5306
    1.5306
    1.5501
    1.2588

    113.15
    108.08
    108.08
    114.20
    109.53
    114.17
    108.68
    107.63
    108.84
    113.09
    103.52
    111.14
    106.91
    110.94
    98.49
    107.63
    114.21
    111.99
    111.99
    109.56
    111.20
    111.20
    98.49
    111.91
    109.15
    112.87
    112.87
    110.64
    110.64
    109.15
    114.01
    110.01
    114.01
    113.21
    113.21
    113.21
    116.45

    -126.97
    -113.63
    176.29
    122.49
    -117.14
    122.57
    115.77
    -64.93
    -119.33
    -118.19
    118.98
    119.93
    121.32
    117.27
    -113.15
    121.99
    -3.87
    120.12
    -120.94
    4.64
    121.08
    -119.52
    127.01
    69.89
    122.01
    121.24
    73.30
    -122.05
    118.42
    -160.90
    119.25
    117.37
    177.00
    120.02
    -119.58
    -177.88
    173.57

    108.08
    107.20
    104.82
    107.19
    106.58
    108.68
    107.30
    108.84
    111.64
    108.50
    111.14
    112.23
    110.94
    111.30
    110.37
    114.21
    111.99
    111.33
    110.59
    111.20
    112.01
    110.63
    111.91
    109.15
    112.87
    109.18
    110.64
    110.45
    110.32
    114.01
    110.01
    109.82
    113.21
    110.96
    110.04
    116.45
    119.02

    1.4217
    1.1165
    0.9615
    1.1068
    1.1136
    1.1092
    1.1109
    1.1122
    1.1063
    1.1148
    1.1003
    1.0983
    1.0995
    1.0996
    1.1004
    1.5526
    1.1055
    1.1067
    1.1084
    1.1078
    1.1062
    1.1093
    1.5638
    1.5504
    1.5400
    1.1115
    1.1072
    1.1097
    1.1099
    1.5501
    1.1115
    1.1111
    1.5306
    1.1069
    1.1084
    1.2588
    1.2574

    -1.00 ! C24H39O4 URSODEOXYCHOLIC ACID (UDCA), chayan

    GROUP
    ATOM C3
    ATOM O3
    ATOM H3'
    ATOM H3
    GROUP
    ATOM C4
    ATOM H4A
    ATOM H4B
    GROUP
    ATOM C5
    ATOM H5
    GROUP
    ATOM C6
    ATOM H6A
    ATOM H6B
    GROUP
    ATOM C7
    ATOM O7
    ATOM H7'
    ATOM H7
    GROUP
    ATOM C8
    ATOM H8
    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19

    CG311
    OG311
    HGP1
    HGA1

    0.14
    -0.65
    0.42
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09 !
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG321 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG311
    0.14 !
    OG311 -0.65 !
    HGP1
    0.42 !
    HGA1
    0.09 !
    !
    CG311 -0.09 !
    HGA1
    0.09 !
    !
    CG3RC1 -0.09 !
    HGA1
    0.09 !
    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09

    OE1
    ||
    H
    Me21 C22 CD
    |
    \ / \ / \
    C12 Me18 C20 CG
    OE2(-1)
    / \ |
    /
    C11 C13---C17
    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH (above the plane of the ring)
    Ursodeoxycholic acid (UDCA)

    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG301

    0.00 ! no hydrogen

    CG331

    -0.27 !methyl at c10

    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM CD
    ATOM OE1
    ATOM OE2

    HGA3
    HGA3
    HGA3

    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O3
    OG2D2
    OG2D2

    0.52
    -0.76
    -0.76

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    CD
    C23

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    CD

    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    H3'
    H4B

    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12A C12 H12B
    H11A C11 H11B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    O7 O7

    H7'

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    CD
    OE1

    H20
    H22A
    H23A
    OE1
    OE2

    C20
    C22
    C23
    CD

    C21 C21 H21A C21 H21B C21 H21C


    H22B
    H23B
    OE2

    R(I(J/K)) T(I(JK/KJ)) PHI

    T(JKL)

    R(KL)

    !ICs based on CHARMM optimized structure


    IC C1 C2 C3 C4
    1.5325 111.74 -49.21
    IC C2 C3 C4 C5
    1.5341 111.88 43.74
    IC C3 C4 C5 C6
    1.5385 115.69 -175.10
    IC C4 C5 C6 C7
    1.5597 109.04 85.37
    IC C5 C6 C7 C8
    1.5520 114.98 38.83
    IC C7 C8 C9 C10 1.5290 114.20 57.90
    IC C8 C9 C10 C1
    1.5325 109.53 179.78
    IC C9 C10 C1 C2
    1.5437 112.01 63.19
    IC O3 C3 C4 C5
    1.4164 109.06 161.96
    IC C4 C2 *C3 O3
    1.5385 111.88 -119.42
    IC C4 C2 *C3 H3
    1.5385 111.88 121.34
    IC C9 C5 *C10 C19 1.5437 109.64 -123.44
    IC C2 C3 O3 H3' 1.5341 107.04 68.70
    IC C5 C3 *C4 H4A 1.5597 115.69 122.74
    IC H4A C3 *C4 H4B 1.1111 108.67 115.74
    IC C10 C4 *C5 H5
    1.5278 114.69 116.72
    IC C7 C5 *C6 H6A 1.5440 114.98 -124.18
    IC H6A C5 *C6 H6B 1.1112 109.41 -115.81
    IC C2 C10 *C1 H1A 1.5325 113.83 119.45
    IC C2 C10 *C1 H1B 1.5325 113.83 -124.31
    IC C1 C3 *C2 H2A 1.5325 111.74 122.10
    IC H2A C3 *C2 H2B 1.1113 110.26 117.21
    !IC C1 C2 C3 C4
    1.5383 110.44 -62.22
    fig
    !IC C2 C3 C4 C5
    1.5311 110.66 -52.17
    fig
    !IC C3 C4 C5 C10 1.5367 111.70 -54.41
    fig
    !IC C10 C4 *C5 C6
    1.5304 115.09 -177.32
    fig
    !IC C4 C5 C6 C7
    1.5156 121.28 75.31
    fig
    !IC C5 C6 C7 C8
    1.3432 123.88 51.01
    fig
    IC C6 C7 C8 C14 1.5440 113.15 -166.48
    IC C14 C7 *C8 C9
    1.5543 108.55 119.88
    IC C7 C8 C14 C13 1.5290 108.55 -174.00
    IC C13 C8 *C14 C15 1.5423 113.09 118.54
    IC C8 C14 C15 C16 1.5543 116.41 -154.98
    IC C14 C15 C16 C17 1.5290 103.52 -2.21
    IC C17 C14 *C13 C12 1.5726 98.14 119.76
    IC C14 C13 C12 C11 1.5423 107.63 55.01
    !IC C2 C10 *C1 H1A 1.5383 114.55 122.42
    fig
    !IC C2 C10 *C1 H1B 1.5383 114.55 -120.71
    fig
    !IC C1 C3 *C2 H2A 1.5383 110.44 121.16
    fig
    !IC H2A C3 *C2 H2B 1.1119 109.41 118.30
    fig
    !IC C1 C2 C3 O3
    1.1119 109.41 -175.00
    fig
    !IC C4 C2 *C3 O3
    1.5367 110.66 -120.28
    fig
    !IC O3 C2 *C3 H3
    1.4158 109.14 -118.92
    fig
    !IC C2 C3 O3 H3' 1.5311 109.14 60.00
    fig
    !IC C5 C3 *C4 H4A 1.5156 111.70 121.99

    111.88
    115.69
    109.04
    114.98
    113.15
    109.53
    112.01
    113.83
    115.69
    107.04
    109.37
    109.56
    104.78
    108.67
    108.84
    105.05
    109.41
    108.31
    107.75
    110.15
    110.26
    108.67
    110.66

    1.5385
    1.5597
    1.5520
    1.5440
    1.5290
    1.5437
    1.5562
    1.5325
    1.5597
    1.4164
    1.1144
    1.5561
    0.9606
    1.1111
    1.1112
    1.1175
    1.1112
    1.1113
    1.1136
    1.1092
    1.1113
    1.1128
    1.5367 ! for trans con

    111.70

    1.5156 ! for trans con

    115.09

    1.5304 ! for trans con

    121.28

    1.3432 ! for trans con

    123.88

    1.5018 ! for trans con

    112.36

    1.5506 ! for trans con

    108.55
    114.20
    113.09
    116.41
    103.52
    106.91
    107.63
    111.17
    109.26

    1.5543
    1.5325
    1.5423
    1.5290
    1.5436
    1.5527
    1.5335
    1.5432
    1.1104 ! for trans con

    108.29

    1.1134 ! for trans con

    109.41

    1.1119 ! for trans con

    109.70

    1.1112 ! for trans con

    109.70

    1.1112 ! for trans con

    109.14

    1.4158 ! for trans con

    109.40

    1.1155 ! for trans con

    105.39

    0.9593 ! for trans con

    109.16

    1.1099 ! for trans con

    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC H7
    IC C6
    IC C9
    IC C10
    IC C9
    IC H11A
    IC C14
    IC H12A
    IC C13
    IC C16
    IC H15A
    IC C17
    IC H16A
    IC C13
    IC C12
    IC C14
    IC H18A
    IC H18A
    IC C5
    IC H19A
    IC H19A
    IC C13
    IC C16
    IC C22
    IC C21
    IC C17
    IC H21A
    IC H21A
    IC C17
    IC C23
    IC H22A
    IC C20
    IC CD
    IC CD
    IC C22
    IC OE1

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C7
    C8
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23

    *C7
    *C7
    O7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    CD
    *CD

    H7
    O7
    H7'
    H8
    H9
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    CD
    H23A
    H23B
    OE1
    OE2

    1.5322
    1.1146
    1.5418
    1.5325
    1.5437
    1.5549
    1.1092
    1.5423
    1.1122
    1.5423
    1.5436
    1.1003
    1.5527
    1.0995
    1.5726
    1.5335
    1.5423
    1.1055
    1.1055
    1.5278
    1.1078
    1.1078
    1.5726
    1.5527
    1.5504
    1.5400
    1.5638
    1.1072
    1.1072
    1.5638
    1.5501
    1.1115
    1.5504
    1.5306
    1.5306
    1.5501
    1.2588

    112.88
    108.52
    106.42
    114.20
    109.53
    114.17
    108.68
    107.63
    108.84
    113.09
    103.52
    111.14
    106.91
    110.94
    98.49
    107.63
    114.21
    111.99
    111.99
    109.56
    111.20
    111.20
    98.49
    111.91
    109.15
    112.87
    112.87
    110.64
    110.64
    109.15
    114.01
    110.01
    114.01
    113.21
    113.21
    113.21
    116.45

    -121.61
    -118.80
    -178.10
    122.49
    -117.14
    122.57
    115.77
    -64.93
    -119.33
    -118.19
    118.98
    119.93
    121.32
    117.27
    -113.15
    121.99
    -3.87
    120.12
    -120.94
    4.64
    121.08
    -119.52
    127.01
    69.89
    122.01
    121.24
    73.30
    -122.05
    118.42
    -160.90
    119.25
    117.37
    177.00
    120.02
    -119.58
    -177.88
    173.57

    108.52
    106.42
    104.63
    107.19
    106.58
    108.68
    107.30
    108.84
    111.64
    108.50
    111.14
    112.23
    110.94
    111.30
    110.37
    114.21
    111.99
    111.33
    110.59
    111.20
    112.01
    110.63
    111.91
    109.15
    112.87
    109.18
    110.64
    110.45
    110.32
    114.01
    110.01
    109.82
    113.21
    110.96
    110.04
    116.45
    119.02

    1.1146
    1.4215
    0.9612
    1.1068
    1.1136
    1.1092
    1.1109
    1.1122
    1.1063
    1.1148
    1.1003
    1.0983
    1.0995
    1.0996
    1.1004
    1.5526
    1.1055
    1.1067
    1.1084
    1.1078
    1.1062
    1.1093
    1.5638
    1.5504
    1.5400
    1.1115
    1.1072
    1.1097
    1.1099
    1.5501
    1.1115
    1.1111
    1.5306
    1.1069
    1.1084
    1.2588
    1.2574

    PRES GYCO
    -1.00 ! C3H3NO3 previously PRES GLYC, chayan
    ! patch combination:
    ! core residue cholic acid (CA) >> glycocholic acid (GCA)
    ! core residue deoxycholic acid (DCA) >> glycodeoxycholic acid (GDCA)
    ! core residue lithocholic acid (LCA) >> glycolithocholic acid (GLCA)
    ! core residue chenodeoxycholic acid (CDCA) >> glycochenodeoxycholic acid (GCDCA
    )
    ! core residue ursodeoxycholic acid (UDCA) >> glycoursodeoxycholic acid (GUDCA)
    !
    OEG1
    !

    ||
    !

    OE1

    ||

    CDG--OEG2(-1)
    |
    DELETE ATOM OE2
    G
    ATOM CD CG2O1

    OH

    0.51

    ATOM OE1 OG2D1

    -0.51

    C12 Me18

    ATOM N

    NG2S1

    -0.47

    / \ |

    ATOM HN
    ATOM CG

    HGP1
    CG321

    0.47
    -0.28

    !
    !

    C11 C13---C17
    Me19 |
    |
    |

    ATOM HG1 HGA2


    ATOM HG2 HGA2

    0.09
    0.09

    !
    !

    C1 | C9
    C14 C16
    / \|/ \ / \ /

    ATOM CDG CG2O3


    ATOM OEG1 OG2D2

    0.62
    -0.76

    !
    !

    ATOM OEG2 OG2D2

    -0.76

    !
    !
    !

    BOND CD

    HN

    BOND
    BOND
    IMPR
    IMPR

    CG
    CDG
    C23
    CG

    CG
    CDG
    N
    OEG1

    HG1 CG HG2 !
    OEG1 CDG OEG2 !
    OE1 N
    CD CG
    OEG2

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N
    CG
    CD
    CDG

    OE1
    C23
    CG
    CD
    CDG
    CDG
    N
    OEG1

    C23
    CD
    CD
    N
    N
    N
    CG
    CG

    *CD
    N
    *N
    CG
    *CG
    *CG
    CDG
    *CDG

    N
    CG
    HN
    CDG
    HG1
    HG2
    OEG1
    OEG2

    C2
    |

    Me21

    C22

    CD

    \ / \ / \ /

    C10 C8
    |
    |

    C20

    C23

    NH

    C15

    C3 C5 C7
    / \ / \ / \
    HO

    C4

    C6

    OH

    1.2267
    1.5039
    1.4497
    1.3368
    1.5483
    1.5483
    1.4497
    1.2549

    119.93
    116.52
    130.72
    130.72
    104.28
    104.28
    104.28
    116.21

    Glycocholic acid (GCA)


    HN
    177.01
    -173.26
    170.32
    168.60
    117.38
    -117.58
    148.60
    -149.85

    116.52
    130.72
    124.06
    104.28
    111.67
    112.23
    116.21
    112.75

    1.3368
    1.4497
    1.0161
    1.5483
    1.1092
    1.1082
    1.2549
    1.2749

    !end bile acid related compounds, chayan, jul2006


    !bile acid related compounds, chayan, dec2006
    RESI GA
    -2.00 ! C29H45NO7 GLUTAMIC ACID CDCA AMIDE, chayan
    GROUP
    ATOM C3 CG311
    0.14 !
    ATOM O3 OG311 -0.65 !
    ATOM H3' HGP1
    0.42 !
    ATOM H3 HGA1
    0.09 !
    GROUP
    !
    )
    ATOM C4 CG321 -0.18 !
    ATOM H4A HGA2
    0.09 !
    O24
    -0.5)
    ATOM H4B HGA2
    0.09 !
    ||
    GROUP
    !
    H
    Me21 C22 C24

    OA2(-0.5
    |
    CA--OA1(
    |
    CC1

    CC3

    OG1(-0.5)
    ATOM C5 CG311
    /
    ATOM H5 HGA1
    CG
    GROUP
    \
    ATOM C6 CG321
    OG2(-0.5)
    ATOM H6A HGA2
    ATOM H6B HGA2
    GROUP
    ATOM C7 CG311
    ATOM O7 OG311
    ATOM H7' HGP1
    ATOM H7 HGA1
    GROUP
    ATOM C8 CG311
    ATOM H8 HGA1
    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP

    -0.09 !

    0.09 !

    \ / \ / \ / \ / \

    C12 Me18

    / \ |

    C20

    C11 C13---C17

    0.09 !
    0.09 !
    !
    0.14 !
    -0.65 !
    0.42 !
    0.09 !
    !
    -0.09 !
    0.09 !

    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH

    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c13


    0.09
    0.09
    0.09

    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG301

    0.00 ! no hydrogen

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    NH

    CC2

    -0.18 !

    !
    CG3RC1 -0.09 !
    HGA1
    0.09 !
    !
    CG3C52 -0.18 !
    HGA2
    0.09 !
    HGA2
    0.09 !
    !
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09

    C23

    Glutamic Acid CDCA Amide (GA)

    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM C24
    ATOM O24
    ATOM N
    ATOM HN
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    GROUP
    ATOM CC2
    ATOM HC2A
    ATOM HC2B
    GROUP
    ATOM CC3
    ATOM HC3A
    ATOM HC3B
    ATOM CG
    ATOM OG1
    ATOM OG2

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O1
    OG2D1
    NG2S1
    HGP1

    0.51
    -0.51
    -0.47
    0.47

    CG311
    HGA1
    CG2O3
    OG2D2
    OG2D2

    -0.19
    0.09
    0.62
    -0.76
    -0.76

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2
    CG2O3
    OG2D2
    OG2D2

    -0.28
    0.09
    0.09
    0.62
    -0.76
    -0.76

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14

    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    H3'
    H4B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    O7 O7

    H7'

    C14 H14
    C13 C18 C18 H18A C18 H18B C18 H18C

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR

    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    C24
    N
    CC1
    CC3
    C24
    CA

    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    C24
    N
    CC1
    CC2
    HC3A
    C23
    CC1

    C12 H12A C12 H12B


    C11 H11A C11 H11B
    C15 H15A C15 H15B
    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    C24
    N
    CC1
    CC2
    CC3
    N
    OA2

    H20
    H22A
    H23A
    O24
    HN
    HC1
    HC2A
    HC3B
    O24
    OA1

    C20 C21 C21 H21A C21 H21B C21 H21C


    C22 H22B
    C23 H23B
    CC1
    CC2
    CC3
    N
    CG

    CA
    HC2B
    CG
    C24
    CC3

    CA
    CC2
    CG
    CC1
    OG2

    OA1
    CC3
    OG1
    HN
    OG1

    CA OA2
    CG OG2

    !
    R(I(J/K)) T(I(JK/KJ)) PHI T(JKL)
    !ICs based on arbitrary CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5325 111.83 -48.81 111.97
    IC C2 C3 C4 C5
    1.5343 111.97 43.31 115.75
    IC C3 C4 C5 C6
    1.5386 115.75 -175.01 109.03
    IC C4 C5 C6 C7
    1.5595 109.03 85.21 115.02
    IC C5 C6 C7 C8
    1.5520 115.02 38.61 113.11
    IC C7 C8 C9 C10 1.5276 114.59 57.44 109.36
    IC C8 C9 C10 C1
    1.5364 109.36 -179.93 112.02
    IC C9 C10 C1 C2
    1.5436 112.02 62.99 113.75
    IC O3 C3 C4 C5
    1.4166 108.95 161.43 115.75
    IC C4 C2 *C3 O3
    1.5386 111.97 -119.29 106.97
    IC C4 C2 *C3 H3
    1.5386 111.97 121.36 109.36
    IC C9 C5 *C10 C19 1.5436 109.73 -123.35 109.59
    IC C2 C3 O3 H3' 1.5343 106.97 70.81 104.29
    IC C5 C3 *C4 H4A 1.5595 115.75 122.78 108.78
    IC H4A C3 *C4 H4B 1.1109 108.78 115.85 108.94
    IC C10 C4 *C5 H5
    1.5280 114.66 116.76 105.20
    IC C7 C5 *C6 H6A 1.5438 115.02 -124.32 109.59
    IC H6A C5 *C6 H6B 1.1107 109.59 -115.96 108.35
    IC C2 C10 *C1 H1A 1.5325 113.75 119.62 107.69
    IC C2 C10 *C1 H1B 1.5325 113.75 -124.21 109.99
    IC C1 C3 *C2 H2A 1.5325 111.83 121.96 110.22
    IC H2A C3 *C2 H2B 1.1114 110.22 117.27 108.72
    !IC C1 C2 C3 C4
    1.5383 110.44 -62.22 110.66
    fig
    !IC C2 C3 C4 C5
    1.5311 110.66 -52.17 111.70
    fig
    !IC C3 C4 C5 C10 1.5367 111.70 -54.41 115.09
    fig
    !IC C10 C4 *C5 C6
    1.5304 115.09 -177.32 121.28
    fig
    !IC C4 C5 C6 C7
    1.5156 121.28 75.31 123.88
    fig
    !IC C5 C6 C7 C8
    1.3432 123.88 51.01 112.36
    fig
    IC C6 C7 C8 C14 1.5438 113.11 -165.92 108.46
    IC C14 C7 *C8 C9
    1.5523 108.46 119.72 114.59
    IC C7 C8 C14 C13 1.5276 108.46 -173.32 111.50
    IC C13 C8 *C14 C15 1.5366 111.50 118.16 117.80
    IC C8 C14 C15 C16 1.5523 117.80 -150.82 103.90
    IC C14 C15 C16 C17 1.5346 103.90 -5.86 105.47

    R(KL)
    1.5386
    1.5595
    1.5520
    1.5438
    1.5276
    1.5436
    1.5561
    1.5325
    1.5595
    1.4166
    1.1143
    1.5558
    0.9610
    1.1109
    1.1114
    1.1172
    1.1107
    1.1117
    1.1133
    1.1093
    1.1114
    1.1125
    1.5367 ! for trans con
    1.5156 ! for trans con
    1.5304 ! for trans con
    1.3432 ! for trans con
    1.5018 ! for trans con
    1.5506 ! for trans con
    1.5523
    1.5364
    1.5366
    1.5346
    1.5511
    1.5512

    IC C17
    IC C14
    !IC C2
    fig
    !IC C2
    fig
    !IC C1
    fig
    !IC H2A
    fig
    !IC C1
    fig
    !IC C4
    fig
    !IC O3
    fig
    !IC C2
    fig
    !IC C5
    fig
    !IC H4A
    fig
    !IC C10
    fig
    !IC C7
    fig
    !IC H6A
    fig
    IC C8
    IC O7
    IC C6
    IC C9
    IC C10
    IC C9
    IC H11A
    IC C14
    IC H12A
    IC C13
    IC C16
    IC H15A
    IC C17
    IC H16A
    IC C13
    IC C12
    IC C14
    IC H18A
    IC H18A
    IC C5
    IC H19A
    IC H19A
    IC C13
    IC C16
    IC C22
    IC C21
    IC C17
    IC H21A
    IC H21A
    IC C17
    IC C23
    IC H22A

    C14 *C13 C12 1.5566 98.22 118.19 109.26 1.5283


    C13 C12 C11 1.5366 109.26 55.66 110.30 1.5429
    C10 *C1 H1A 1.5383 114.55 122.42 109.26 1.1104 ! for trans con
    C10 *C1 H1B

    1.5383 114.55 -120.71 108.29

    1.1134 ! for trans con

    C3

    *C2 H2A

    1.5383 110.44 121.16 109.41

    1.1119 ! for trans con

    C3

    *C2 H2B

    1.1119 109.41 118.30 109.70

    1.1112 ! for trans con

    C2

    C3

    O3

    1.1119 109.41 -175.00 109.70

    1.1112 ! for trans con

    C2

    *C3 O3

    1.5367 110.66 -120.28 109.14

    1.4158 ! for trans con

    C2

    *C3 H3

    1.4158 109.14 -118.92 109.40

    1.1155 ! for trans con

    C3

    O3

    1.5311 109.14

    60.00 105.39

    0.9593 ! for trans con

    C3

    *C4 H4A

    1.5156 111.70 121.99 109.16

    1.1099 ! for trans con

    C3

    *C4 H4B

    1.1099 109.16 115.03 107.34

    1.1142 ! for trans con

    C4

    *C5 H5

    1.5000 111.00 -120.00 110.10

    1.1110 ! for trans con

    C5

    *C6 H6A

    1.5018 110.10 -120.00 110.10

    1.1001 ! for trans con

    C5

    *C6 H6B

    1.1110 110.10 -120.00 110.10

    1.1110 ! for trans con

    C6
    C6
    C7
    C7
    C8
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20

    *C7
    *C7
    O7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22

    H3'

    O7
    H7
    H7'
    H8
    H9
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B

    1.5276
    1.4225
    1.5438
    1.5364
    1.5436
    1.5599
    1.1091
    1.5366
    1.1119
    1.5366
    1.5511
    1.1022
    1.5512
    1.1009
    1.5566
    1.5283
    1.5366
    1.1075
    1.1075
    1.5280
    1.1078
    1.1078
    1.5566
    1.5512
    1.5470
    1.5439
    1.5606
    1.1095
    1.1095
    1.5606
    1.5506
    1.1166

    113.11
    108.31
    108.31
    114.59
    109.36
    114.19
    108.67
    109.26
    108.77
    111.50
    103.90
    111.42
    105.47
    108.43
    98.62
    109.26
    114.19
    112.02
    112.02
    109.59
    111.26
    111.26
    98.62
    118.99
    112.57
    107.65
    107.65
    110.43
    110.43
    112.57
    114.81
    108.00

    -126.99
    -113.92
    -176.31
    122.91
    -116.93
    122.19
    115.84
    -63.53
    -118.49
    -117.92
    118.25
    120.29
    121.54
    116.18
    -112.31
    123.58
    4.73
    118.46
    -121.96
    4.28
    120.71
    -119.86
    124.35
    -1.33
    123.04
    117.51
    56.27
    -120.25
    120.00
    -177.70
    119.77
    116.45

    108.31
    107.38
    103.73
    107.14
    106.27
    108.67
    107.52
    108.77
    110.35
    108.42
    111.42
    112.58
    108.43
    112.44
    108.27
    114.19
    112.02
    111.31
    111.70
    111.26
    111.90
    110.79
    118.99
    112.57
    107.65
    109.34
    110.43
    109.86
    110.54
    114.81
    108.00
    108.68

    1.4225
    1.1176
    0.9623
    1.1079
    1.1129
    1.1091
    1.1100
    1.1119
    1.1099
    1.1139
    1.1022
    1.0964
    1.1009
    1.0973
    1.1016
    1.5536
    1.1075
    1.1080
    1.1059
    1.1078
    1.1071
    1.1088
    1.5606
    1.5470
    1.5439
    1.1119
    1.1095
    1.1109
    1.1093
    1.5506
    1.1166
    1.1124

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C20
    C24
    C24
    C22
    N
    C23
    CC1
    C24
    CA
    HC1
    N
    OA1
    N
    CC3
    HC2A
    CC1
    CG
    HC3A
    CC2
    OG1

    C22
    C22
    C22
    C23
    C23
    C24
    C24
    N
    N
    N
    CC1
    CC1
    CC1
    CC1
    CC1
    CC2
    CC2
    CC2
    CC3
    CC3

    C23
    *C23
    *C23
    C24
    *C24
    N
    *N
    CC1
    *CC1
    *CC1
    CA
    *CA
    CC2
    *CC2
    *CC2
    CC3
    *CC3
    *CC3
    CG
    *CG

    C24
    H23A
    H23B
    N
    O24
    CC1
    HN
    CA
    HC1
    CC2
    OA1
    OA2
    CC3
    HC2A
    HC2B
    CG
    HC3A
    HC3B
    OG1
    OG2

    1.5470
    1.4987
    1.4987
    1.5506
    1.3366
    1.4987
    1.4417
    1.3366
    1.5535
    1.1093
    1.4417
    1.2563
    1.4417
    1.5576
    1.1108
    1.5587
    1.5329
    1.1056
    1.5576
    1.2602

    114.81
    110.40
    110.40
    110.40
    115.40
    115.40
    129.84
    129.84
    104.17
    110.25
    104.17
    120.14
    109.79
    114.87
    109.65
    114.87
    114.28
    110.64
    114.28
    118.59

    166.35
    121.19
    -118.13
    46.22
    -179.81
    -163.64
    178.15
    -156.03
    116.15
    122.36
    160.24
    -176.18
    58.95
    122.98
    116.68
    -160.82
    119.62
    118.51
    -112.88
    -177.02

    110.40
    111.13
    109.46
    115.40
    120.30
    129.84
    124.42
    104.17
    110.25
    109.79
    120.14
    115.58
    114.87
    109.65
    107.14
    114.28
    110.64
    109.05
    118.59
    117.98

    1.4987
    1.1081
    1.1111
    1.3366
    1.2285
    1.4417
    1.0052
    1.5535
    1.1093
    1.5587
    1.2563
    1.2715
    1.5576
    1.1108
    1.1137
    1.5329
    1.1056
    1.1085
    1.2602
    1.2616

    PRES AMGA
    0.00 ! C3H4O2 chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha-Methyl Glu Acid CDCA Amide
    !
    !
    OA1
    !

    ||

    O24

    CA--OA2--C

    ||

    C24

    CC1

    H3(M)
    !
    OG1(-0.5)
    ATOM CC1 CG311
    /
    ATOM HC1 HGA1
    G
    ATOM CA CG2O2
    \
    ATOM OA1 OG2D1
    OG2(-0.5)
    ATOM OA2 OG302
    ATOM CM

    CG331

    OH

    Me21

    0.17 !

    0.09 !

    C12 Me18

    0.90 !

    Me19 |

    -0.31 !

    C1 | C9

    ATOM HM1 HGA3

    0.09 !

    ATOM HM2 HGA3

    0.09 !

    C2

    C10 C8

    ATOM HM3 HGA3

    0.09 !

    C3

    C5

    C7

    C14

    C16

    / \|/ \ / \ /

    C20

    C11 C13---C17

    -0.49 !

    C15

    / \ / \ / \
    HO

    C4

    C6

    CC3

    \ / \ / \ / \ / \

    / \ |

    -0.63 !

    C22

    OH

    C23

    NH

    CC2

    !
    BOND OA2 CM
    BOND CM HM1 CM
    IC
    IC
    IC
    IC

    CC1
    HM1
    HM2
    HM3

    CA
    CM
    CM
    CM

    OA2
    OA2
    OA2
    OA2

    HM2
    CM
    CA
    CA
    CA

    Alpha-Methyl Glutamic Acid CDCA Amide

    CM
    1.5285
    1.1113
    1.1136
    1.1135

    HM3
    111.09 -178.91 115.08
    109.28 179.56 115.08
    110.99 60.48 115.08
    110.99 -61.17 115.08

    1.4371
    1.3429
    1.3429
    1.3429

    PRES GMGA
    0.00 ! C3H5O2 chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Methyl Glu Acid CDCA Amide
    !
    !
    OA1(-0.5)
    !

    O24

    CA--OA2(-0

    ||

    C24

    CC1

    .5)
    !

    OH

    Me21

    C22

    CC3

    OG1
    //
    ATOM CC3 CG321
    G
    ATOM HC3A HGA2
    \
    ATOM HC3B HGA2
    OG2--CM3(M)
    ATOM CG CG2O2
    ATOM OG1 OG2D1
    ATOM OG2 OG302
    ATOM CM CG331
    ATOM HM1 HGA3
    ATOM HM2 HGA3
    ATOM HM3 HGA3

    0.08 !

    CC3
    HM1
    HM2
    HM3

    CG
    CM
    CM
    CM

    OG2
    OG2
    OG2
    OG2

    C23

    NH

    CC2

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    C11 C13---C17
    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH
    Gamma-Methyl Glutamic Acid CDCA Amide

    HM2 CM
    CM
    CG
    CG
    CG

    C20

    / \ |

    0.09 !

    BOND OG2 CM
    BOND CM HM1 CM
    IC
    IC
    IC
    IC

    C12 Me18

    0.09 !

    0.90
    -0.63
    -0.49
    -0.31
    0.09
    0.09
    0.09

    \ / \ / \ / \ / \

    1.5001
    1.1114
    1.1140
    1.1136

    HM3
    109.42 178.80 114.93
    109.43 179.48 114.93
    110.99 60.32 114.93
    111.06 -61.13 114.93

    1.4378
    1.3439
    1.3439
    1.3439

    PRES DMGA
    0.00 ! C6H9O4 chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dimethyl Glu Acid CD
    CA Amide
    !

    ATOM CC1 CG311

    0.17 !

    OA1

    ATOM HC1 HGA1

    0.09 !

    ||

    ATOM CA CG2O2
    (M)
    ATOM OA1 OG2D1

    0.90 !

    O24

    CA--OA2--CH3

    -0.63 !

    ||

    C24

    CC1

    ATOM OA2 OG302


    OG1
    ATOM CM CG331
    /
    ATOM HM1 HGA3

    -0.49 !

    OH

    -0.31 !

    ATOM HM2 HGA3

    0.09 !

    ATOM HM3 HGA3


    OG2--CM3(N)
    ATOM CC3 CG321

    0.09 !
    0.08 !

    Me19 |

    ATOM HC3A HGA2

    0.09 !

    C1 | C9

    ATOM HC3B HGA2

    0.09 !

    ATOM CG

    CG2O2

    0.90 !

    C2

    C10 C8

    ATOM OG1 OG2D1

    -0.63 !

    ATOM OG2 OG302

    -0.49 !

    C3

    C5

    C7

    ATOM CN

    -0.31 !

    CG331

    0.09 !

    ATOM HN1 HGA3

    0.09 !

    ATOM HN2 HGA3

    0.09 !

    ATOM HN3 HGA3


    de

    0.09 !

    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OA2
    CM
    OG2
    CN

    CC1
    HM1
    HM2
    HM3
    CC3
    HN1
    HN2
    HN3

    CM
    HM1 CM
    CN
    HN1 CN
    CA
    CM
    CM
    CM
    CG
    CN
    CN
    CN

    OA2
    OA2
    OA2
    OA2
    OG2
    OG2
    OG2
    OG2

    CC3

    \ / \ / \ / \ / \ /
    C20

    / \ |

    C23

    NH

    CC2

    CG
    \

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /
    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    Alpha,Gamma-Dimethyl Glutamic Acid CDCA Ami

    HM3

    HN2 CN

    HN3

    PRES AMGT
    0.00
    ! patch combination:
    ! core residue Glutamic
    lu Acid CDCA Amide
    !
    ATOM CC1 CG311
    0.17
    ATOM HC1 HGA1
    0.09

    C22

    C12 Me18

    HM2 CM

    CM
    CA
    CA
    CA
    CN
    CG
    CG
    CG

    Me21

    1.5215
    1.1119
    1.1147
    1.1148
    1.5036
    1.1119
    1.1144
    1.1141

    109.43
    109.81
    111.25
    111.21
    109.18
    109.57
    111.15
    111.21

    -179.14
    179.92
    60.55
    -60.74
    178.54
    179.75
    60.57
    -60.90

    114.39
    114.39
    114.39
    114.39
    114.99
    114.99
    114.99
    114.99

    1.4397
    1.3481
    1.3481
    1.3481
    1.4389
    1.3378
    1.3378
    1.3378

    ! C9H15O4 chayan
    Acid CDCA Amide (GA) >> Alpha Methyl, Gamma Tert.Butyl G
    !
    !

    OA1

    ATOM
    ATOM
    3(M)
    ATOM
    ATOM
    OG1
    ATOM
    //
    ATOM

    CA CG2O2
    OA1 OG2D1

    0.90 !
    -0.63 !

    OA2 OG302
    CM CG331

    -0.49 !
    -0.31 !

    OH

    HM1 HGA3

    0.09 !

    0.09 !

    C12 Me18

    HM2 HGA3
    CB1
    ATOM HM3 HGA3
    \
    |
    ATOM CC3 CG321
    OG2--CT--CB2
    ATOM HC3A HGA2
    |
    ATOM HC3B HGA2
    CB3
    ATOM CG CG2O2
    ATOM OG1 OG2D1
    ATOM OG2 OG302
    ATOM CT CG301
    ATOM CB1 CG331
    ATOM HB11 HGA3
    ATOM HB12 HGA3

    0.09 !

    ATOM HB13 HGA3


    d CDCA Amide
    ATOM CB2 CG331
    ATOM HB21 HGA3
    ATOM HB22 HGA3
    ATOM HB23 HGA3
    ATOM CB3 CG331
    ATOM HB31 HGA3
    ATOM HB32 HGA3
    ATOM HB33 HGA3
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OA2
    CM
    OG2
    CT
    CT
    CT

    CC1
    HM1
    HM2
    HM3
    CC3
    CB1
    CB2
    CB3
    HB11
    HB12
    HB13
    HB21
    HB22
    HB23
    HB31
    HB32

    CM
    HM1
    CT
    CB1
    CB2
    CB3
    CA
    CM
    CM
    CM
    CG
    CT
    CT
    CT
    CB1
    CB1
    CB1
    CB2
    CB2
    CB2
    CB3
    CB3

    Me19 |

    0.09 !

    C1 | C9

    !
    !
    !
    !
    !
    !
    !

    C20

    C23

    CC2

    CG

    C14

    C16

    Alpha Methyl,Gamma Tert.Butyl Glutamic Aci

    !
    !
    !
    !
    !
    !
    !
    !

    HM2 CM

    CM
    CA
    CA
    CA
    CT
    CG
    CG
    CG
    OG2
    OG2
    OG2
    OG2
    OG2
    OG2
    OG2
    OG2

    NH

    HM3

    CB1 HB11 CB1 HB12 CB1 HB13


    CB2 HB21 CB2 HB22 CB2 HB23
    CB3 HB31 CB3 HB32 CB3 HB33
    OA2
    OA2
    OA2
    OA2
    OG2
    OG2
    OG2
    OG2
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    CT

    CC3

    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH

    0.09 !

    CM

    |
    CC1

    C11 C13---C17

    0.09 !

    -0.27
    0.09
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    ||
    C24

    C22

    ||
    CA--OA2--CH

    \ / \ / \ / \ / \

    / \ |

    0.08 !

    0.90
    -0.63
    -0.49
    -0.04
    -0.27
    0.09
    0.09

    Me21

    O24

    1.5216
    1.1119
    1.1147
    1.1147
    1.5056
    1.5308
    1.5354
    1.5354
    1.1097
    1.1088
    1.1105
    1.1098
    1.1099
    1.1092
    1.1098
    1.1094

    109.43
    109.81
    111.24
    111.21
    108.23
    105.14
    111.04
    110.89
    110.37
    110.29
    110.19
    109.96
    110.24
    111.27
    109.90
    111.09

    -179.07
    179.90
    60.54
    -60.74
    179.34
    179.25
    62.01
    -63.42
    -179.27
    60.60
    -59.24
    171.88
    52.17
    -68.59
    -171.74
    68.88

    114.39
    114.39
    114.39
    114.39
    121.50
    121.50
    121.50
    121.50
    105.14
    105.14
    105.14
    111.04
    111.04
    111.04
    110.89
    110.89

    1.4397
    1.3481
    1.3481
    1.3481
    1.4254
    1.3210
    1.3210
    1.3210
    1.4254
    1.4254
    1.4254
    1.4254
    1.4254
    1.4254
    1.4254
    1.4254

    IC HB33 CB3 CT

    OG2

    PRES ATGM
    0.00
    ! patch combination:
    ! core residue Glutamic
    lu Acid CDCA Amide
    !
    ATOM CC1 CG311
    0.17
    ATOM HC1 HGA1
    0.09
    ATOM CA CG2O2
    0.90
    CB2
    ATOM OA1 OG2D1 -0.63
    /
    ATOM OA2 OG302 -0.49
    --CB3
    ATOM CT CG301 -0.04
    ATOM CB1 CG331 -0.27
    OG1
    ATOM HB11 HGA3
    0.09
    //
    ATOM HB12 HGA3
    0.09

    1.1092 110.31 -51.87 110.89

    ! C9H15O4 chayan
    Acid CDCA Amide (GA) >> Gamma Methyl, Alpha Tert.Butyl G
    !
    !
    !

    OA1

    ||

    !
    !
    !

    OH

    C12 Me18

    ATOM HB13 HGA3


    \
    ATOM CB2 CG331
    OG2--CH3(M)
    ATOM HB21 HGA3

    -0.27 !
    0.09 !

    Me19 |

    ATOM HB22 HGA3

    0.09 !

    C1 | C9

    ATOM HB23 HGA3

    0.09 !

    ATOM CB3 CG331

    -0.27 !

    C2

    C10 C8

    ATOM HB31 HGA3

    0.09 !

    ATOM HB32 HGA3

    0.09 !

    C3

    C5

    C7

    ATOM HB33 HGA3

    0.09 !

    ATOM CC3 CG321


    ATOM HC3A HGA2

    0.08 !
    0.09 !

    ATOM HC3B HGA2


    d CDCA Amide
    ATOM CG CG2O2
    ATOM OG1 OG2D1
    ATOM OG2 OG302
    ATOM CM CG331
    ATOM HM1 HGA3
    ATOM HM2 HGA3
    ATOM HM3 HGA3

    0.09 !

    BOND
    BOND
    BOND
    BOND
    BOND

    OA2
    CT
    CT
    CT
    OG2

    0.09 !

    0.90
    -0.63
    -0.49
    -0.31
    0.09
    0.09
    0.09

    1.4254

    Me21

    CB1
    \

    CA--OA2--CT

    ||
    C24

    |
    CC1

    C22

    O24

    CC3

    \ / \ / \ / \ / \
    C20

    / \ |

    C23

    NH

    CC2

    CG

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /
    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    Gamma Methyl, Alpha Tert.Butyl Glutamic Aci

    !
    !
    !
    !
    !
    !
    !

    CT
    CB1 CB1 HB11 CB1 HB12 CB1 HB13
    CB2 CB2 HB21 CB2 HB22 CB2 HB23
    CB3 CB3 HB31 CB3 HB32 CB3 HB33
    CM

    BOND CM
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    CB1
    CB2
    CB3
    HB11
    HB12
    HB13
    HB21
    HB22
    HB23
    HB31
    HB32
    HB33
    CC3
    HM1
    HM2
    HM3

    HM1 CM
    CA
    CT
    CT
    CT
    CB1
    CB1
    CB1
    CB2
    CB2
    CB2
    CB3
    CB3
    CB3
    CG
    CM
    CM
    CM

    OA2
    OA2
    OA2
    OA2
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    OG2
    OG2
    OG2
    OG2

    HM2 CM
    CT
    CA
    CA
    CA
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    CM
    CG
    CG
    CG

    PRES ABGA
    0.00
    ! patch combination:
    ! core residue Glutamic
    ATOM CC1 CG311
    0.17
    CD1--CE1
    ATOM HC1 HGA1
    0.09
    //
    \\
    ATOM CA CG2O2
    0.90
    CB--CZ
    CP
    ATOM OA1 OG2D1 -0.63
    \ __ /
    ATOM OA2 OG302 -0.49
    CD2--CE2
    ATOM CB CG321 -0.22

    1.5243
    1.5313
    1.5354
    1.5351
    1.1105
    1.1099
    1.1100
    1.1101
    1.1093
    1.1095
    1.1101
    1.1095
    1.1095
    1.5032
    1.1119
    1.1145
    1.1141

    108.15
    105.10
    111.03
    111.02
    110.10
    110.43
    110.42
    109.87
    110.56
    111.28
    109.93
    111.24
    110.50
    109.19
    109.57
    111.16
    111.21

    1.4251
    1.3318
    1.3318
    1.3318
    1.4251
    1.4251
    1.4251
    1.4251
    1.4251
    1.4251
    1.4251
    1.4251
    1.4251
    1.4389
    1.3378
    1.3378
    1.3378

    ||

    O24

    CA--OA2--

    ||

    C24

    CM1

    OH

    C12 Me18

    !
    !

    Me19 |

    0.115 !

    C1 | C9

    C10 C8

    ATOM CE1 CG2R61 -0.115 !

    ATOM HE1 HGR61

    C3

    C5

    C7

    0.115 !

    ATOM CE2 CG2R61 -0.115 !

    CG2R61 -0.115 !

    ATOM HP

    HGR61

    0.115 !

    CC3

    \ / \ / \ / \ / \
    C20

    C23

    NH

    CC2

    C14

    C16

    / \|/ \ / \ /

    0.115 !

    ATOM CP

    C22

    C11 C13---C17

    0.115 !

    Me21

    / \ |

    C2

    ATOM HE2 HGR61

    121.38
    121.38
    121.38
    121.38
    105.10
    105.10
    105.10
    111.03
    111.03
    111.03
    111.02
    111.02
    111.02
    114.98
    114.98
    114.98
    114.98

    Acid CDCA Amide (GA) >> Alpha-Benzyl Glu Acid CDCA Amide
    !
    OA1

    ATOM CD2 CG2R61 -0.115 !


    ATOM HD2 HGR61

    -178.31
    179.75
    62.52
    -62.94
    -179.76
    60.50
    -60.01
    172.54
    52.80
    -68.22
    -172.01
    68.69
    -52.18
    178.53
    179.56
    60.39
    -61.08

    ! C9H8O2 chayan

    ATOM HB1 HGA2


    0.09
    CG--OG1(-0.5)
    ATOM HB2 HGA2
    0.09
    |
    ATOM CZ CG2R61 0.00
    OG2(-0.5)
    ATOM CD1 CG2R61 -0.115
    ATOM HD1 HGR61

    HM3

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    Alpha-Benzyl Glutamic Acid CDCA Amide

    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OA2
    CB
    CZ
    CP

    CC1
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1

    CB
    HB1 CB HB2 CB CZ
    CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP
    CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ
    CA
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2

    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP

    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP

    1.5276
    1.1152
    1.1140
    1.5060
    1.4042
    1.4055
    1.4055
    1.4042
    1.4042
    1.5060
    1.5060
    1.4055
    1.4022
    1.4018
    1.4022
    1.4001
    1.4018
    1.4008
    1.4018

    110.26
    110.81
    109.30
    114.53
    119.63
    120.89
    119.47
    119.63
    119.63
    120.89
    119.63
    120.21
    119.99
    119.98
    120.21
    120.33
    119.99
    120.02
    119.98

    -175.22
    49.30
    -69.99
    168.41
    -39.76
    141.67
    -178.59
    82.33
    -161.94
    178.93
    -178.66
    -0.33
    0.00
    0.28
    179.92
    -179.34
    -179.96
    -179.26
    -179.91

    CP

    115.99
    115.99
    115.99
    115.99
    114.53
    114.53
    119.63
    105.44
    108.22
    120.21
    120.33
    119.99
    119.98
    120.02
    119.72
    119.97
    120.00
    119.27
    119.82

    HP
    1.4474
    1.3364
    1.3364
    1.3364
    1.4474
    1.4474
    1.5060
    1.1152
    1.1140
    1.4022
    1.4001
    1.4018
    1.4008
    1.4001
    1.0791
    1.0825
    1.0797
    1.0807
    1.0797

    PRES GBGA
    0.00 ! C9H9O2 chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Gamma-Benzyl Glu Acid CDCA Amide
    ATOM CC3 CG321
    0.08 !
    OA1(-0.5)
    ATOM HC3A HGA2

    0.09 !

    ATOM HC3B HGA2


    0.5)
    ATOM CG CG2O2

    0.09 !

    O24

    CA--OA2(-

    0.90 !

    ||

    C24

    CC1

    ATOM OG1 OG2D1

    -0.63 !
    CD1--CE1
    ATOM OG2 OG302 -0.49 !
    //
    \\
    ATOM CB CG321 -0.22 !
    CG--OG2--CB--CZ
    CP
    ATOM HB1 HGA2
    0.09 !
    ||
    \ __ /
    ATOM HB2 HGA2
    0.09 !
    OG1
    CD2--CE2
    ATOM CZ CG2R61 0.00 !

    Me19 |

    ATOM CD1 CG2R61 -0.115 !

    C1 | C9

    ATOM HD1 HGR61

    OH
    |

    C20
    /

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    ATOM HD2 HGR61

    C3

    C5

    C7

    CC3

    \ / \ / \ / \ / \

    / \ |

    ATOM CD2 CG2R61 -0.115 !

    ATOM CE1 CG2R61 -0.115 !

    C22

    C12 Me18

    0.115 !

    0.115 !

    Me21

    C15

    C23

    NH

    CC2

    ATOM HE1 HGR61

    0.115 !

    ATOM CE2 CG2R61 -0.115 !


    ATOM HE2 HGR61

    / \ / \ / \
    HO

    C4

    C6

    OH

    0.115 !

    ATOM CP

    CG2R61 -0.115 !

    ATOM HP

    HGR61

    BOND
    BOND
    BOND
    BOND

    CB
    HB1 CB HB2 CB CZ
    CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP
    CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG2
    CB
    CZ
    CP

    CC3
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1

    CG
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2

    OG2
    OG2
    OG2
    OG2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP

    Gamma-Benzyl Glutamic Acid CDCA Amide

    0.115

    CB
    CG
    CG
    CG
    OG2
    OG2
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP

    1.5019
    1.1166
    1.1126
    1.5090
    1.4043
    1.4036
    1.4036
    1.4043
    1.4043
    1.5090
    1.5090
    1.4036
    1.4014
    1.4016
    1.4014
    1.4015
    1.4016
    1.4017
    1.4016

    110.25
    111.80
    107.85
    115.77
    120.63
    119.72
    119.63
    120.63
    120.63
    119.72
    120.63
    120.22
    119.95
    120.04
    120.22
    120.19
    119.95
    119.96
    120.04

    -178.87
    -40.89
    -156.53
    84.56
    -105.67
    73.22
    178.88
    21.27
    134.60
    -179.56
    179.55
    0.20
    0.28
    -0.28
    179.19
    -178.97
    179.43
    -179.44
    -179.29

    116.50
    116.50
    116.50
    116.50
    115.77
    115.77
    120.63
    108.88
    106.33
    120.22
    120.19
    119.95
    120.04
    119.96
    119.50
    119.56
    119.88
    119.89
    120.00

    CP

    HP
    1.4500
    1.3367
    1.3367
    1.3367
    1.4500
    1.4500
    1.5090
    1.1166
    1.1126
    1.4014
    1.4015
    1.4016
    1.4017
    1.4015
    1.0802
    1.0802
    1.0801
    1.0800
    1.0800

    PRES DBGA
    0.00 ! C18H17O4 chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha,Gamma-Dibenzyl Glu Acid CD
    CA Amide
    !
    ATOM CC1 CG311
    0.17 !
    ATOM HC1 HGA1
    0.09 !
    OA1
    CJ1--CK1
    ATOM CA CG2O2
    0.90 !
    ||
    //
    \\
    ATOM OA1 OG2D1 -0.63 !
    O24 CA--OA2--CH2
    (B)--CY
    CQ
    ATOM OA2 OG302 -0.49 !
    ||
    |
    \ __ /
    ATOM CB CG321 -0.22 !
    OH
    Me21 C22 C24 CC1 CC3
    CJ2--CK2 CD1--CE1
    ATOM HB1 HGA2
    0.09 !
    |
    \ / \ / \ / \ / \
    //
    \\
    ATOM HB2 HGA2
    0.09 !
    C12 Me18 C20 C23 NH
    CC2 CG-OG2--CH2(N)--CZ
    CP
    ATOM CY CG2R61 0.00 !
    / \ |
    /
    ||
    \ __ /
    ATOM CJ1 CG2R61 -0.115 !
    C11 C13---C17
    OG1
    CD2--CE2
    ATOM HJ1 HGR61
    0.115 !
    Me19 |
    |
    |

    ATOM CJ2 CG2R61 -0.115 !


    ATOM HJ2 HGR61

    C1 | C9

    0.115 !

    C14

    / \|/ \ / \ /

    ATOM CK1 CG2R61 -0.115 !

    C2

    C10 C8

    ATOM HK1 HGR61

    C3

    C5

    C7

    0.115 !

    ATOM CK2 CG2R61 -0.115 !


    ATOM HK2 HGR61

    0.115 !

    ATOM CQ

    CG2R61 -0.115 !

    ATOM HQ

    HGR61

    0.115 !

    ATOM
    de
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CC3 CG321

    0.08 !

    HC3A
    HC3B
    CG
    OG1
    OG2
    CN
    HN1
    HN2
    CZ
    CD1
    HD1
    CD2
    HD2
    CE1
    HE1
    CE2
    HE2
    CP
    HP

    HGA2
    HGA2
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    OA2
    CB
    CY
    CQ
    OG2
    CN
    CZ
    CP

    CB
    HB1
    CJ1
    CK2
    CN
    HN1
    CD1
    CE2

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY

    CA
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1

    0.09
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09
    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    C16

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    Alpha,Gamma-Dibenzyl Glutamic Acid CDCA Ami

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CB HB2 CB CY
    CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ
    CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY

    CQ

    HQ

    CN HN2 CN CZ
    CD1 HD1 CD1 CE1 CE1 HE1 CE1 CP
    CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ

    CP

    HP

    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1

    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ

    1.5206
    1.1132
    1.1177
    1.5069
    1.4050
    1.4039
    1.4039
    1.4050
    1.4050
    1.5069
    1.5069
    1.4039

    108.90
    108.27
    112.85
    114.70
    120.48
    119.88
    119.62
    120.48
    120.48
    119.88
    120.48
    120.21

    105.00
    147.25
    31.14
    -93.16
    -91.04
    87.42
    178.47
    29.17
    142.14
    -178.91
    178.97
    0.12

    116.86
    116.86
    116.86
    116.86
    114.70
    114.70
    120.48
    107.16
    108.03
    120.21
    120.16
    119.97

    1.4507
    1.3434
    1.3434
    1.3434
    1.4507
    1.4507
    1.5069
    1.1132
    1.1177
    1.4011
    1.4016
    1.4012

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1
    CC3
    HN1
    HN2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CN
    CN
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1

    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2
    CG
    CN
    CN
    CN
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2

    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    OG2
    OG2
    OG2
    OG2
    CN
    CN
    *CZ
    CN
    CN
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP

    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    CN
    CG
    CG
    CG
    OG2
    OG2
    CN
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP

    1.4011
    1.4012
    1.4011
    1.4016
    1.4012
    1.4013
    1.4012
    1.5035
    1.1127
    1.1172
    1.5070
    1.4041
    1.4041
    1.4041
    1.4041
    1.4041
    1.5070
    1.5070
    1.4041
    1.4013
    1.4014
    1.4013
    1.4013
    1.4014
    1.4014
    1.4014

    119.97
    120.06
    120.21
    120.16
    119.97
    119.97
    120.06
    108.85
    108.18
    112.24
    115.12
    120.43
    119.89
    119.66
    120.43
    120.43
    119.89
    120.43
    120.18
    119.96
    120.06
    120.18
    120.17
    119.96
    119.97
    120.06

    0.13
    -0.07
    179.67
    179.94
    179.94
    179.97
    -179.96
    -165.00
    -45.00
    75.00
    -165.00
    180.00
    0.00
    178.41
    -88.94
    -83.96
    -179.11
    179.10
    0.23
    0.23
    -0.23
    179.46
    -179.25
    179.64
    -179.65
    -179.54

    120.06
    119.97
    119.77
    119.94
    119.95
    120.09
    120.02
    116.75
    116.75
    116.75
    116.75
    115.12
    115.12
    120.43
    130.32
    118.87
    120.18
    120.17
    119.96
    120.06
    119.97
    119.82
    119.77
    120.04
    119.97
    119.96

    1.4013
    1.4016
    1.0809
    1.0795
    1.0807
    1.0805
    1.0806
    1.4498
    1.3348
    1.3348
    1.3348
    1.4498
    1.4498
    1.5070
    7.6318
    8.2110
    1.4013
    1.4013
    1.4014
    1.4014
    1.4013
    1.0792
    1.0805
    1.0805
    1.0805
    1.0805

    PRES AL
    1.00 ! C3H9N chayan
    ! patch combination:
    ! core residue Glutamic Acid CDCA Amide (GA) >> Alpha Lysine CDCA Amide
    !
    !
    OA1(-0.5)
    !
    5)
    DELETE ATOM CG
    DELETE ATOM OG1
    CC5
    DELETE ATOM OG2
    / \
    ATOM CC3 CG321
    4
    NH3(+1)
    ATOM HC3A HGA2

    O24

    CA--OA2(-0.

    ||

    C24

    CC1

    OH

    -0.18 !

    Me21

    C22

    \ / \ / \ / \ / \

    C12 Me18

    0.09 !

    C20

    / \ |

    ATOM HC3B HGA2

    0.09 !

    ATOM CC4 CG321

    -0.18 !

    Me19 |

    ATOM HC4A HGA2

    0.09 !

    C1 | C9

    ATOM HC4B HGA2

    0.09 !

    ATOM CC5 CG324

    0.13 !

    C2

    C10 C8

    ATOM HC5A HGA2

    0.09 !

    ATOM HC5B HGA2

    0.09 !

    C3

    C5

    C7

    CC3

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /
    C15

    C23

    NH

    CC2

    CC

    ATOM NL

    NG3P3

    -0.30 !

    ATOM HL1 HGP2

    0.33 !

    ATOM HL2 HGP2

    0.33 !

    ATOM HL3 HGP2

    0.33 !

    / \ / \ / \
    HO

    C4

    C6

    Alpha Lysine CDCA Amide

    BOND CC3 CC4 CC4 HC4A CC4 HC4B


    BOND CC4 CC5 CC5 HC5A CC5 HC5B
    BOND CC5 NL NL HL1 NL HL2 NL
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    CC2
    CC5
    HC4A
    CC3
    NL
    NL
    HL1
    HL2
    HL3

    CC2
    CC3
    CC3
    CC3
    CC4
    CC4
    CC4
    NL
    NL
    NL

    CC3
    CC4
    *CC4
    *CC4
    CC5
    *CC5
    *CC5
    CC5
    CC5
    CC5

    CC4
    CC5
    HC4A
    HC4B
    NL
    HC5A
    HC5B
    CC4
    CC4
    CC4

    PRES ALME
    1.00
    ! patch combination:
    ! core residue Glutamic
    mide
    !
    DELETE ATOM CG
    DELETE ATOM OG1
    DELETE ATOM OG2
    ATOM CC1 CG311
    0.17
    ATOM HC1 HGA1
    0.09
    ATOM CA

    1.5561
    1.5463
    1.5430
    1.1129
    1.5479
    1.4822
    1.4822
    1.0369
    1.0708
    1.0308

    OH

    114.54
    116.18
    115.63
    108.29
    115.63
    111.91
    111.91
    112.46
    105.60
    115.27

    HL3
    179.98
    -57.56
    -123.18
    -115.77
    -52.00
    119.56
    -121.02
    -11.49
    100.09
    -141.75

    116.18
    115.63
    108.29
    107.94
    111.91
    110.77
    110.60
    111.91
    111.91
    111.91

    1.5479
    1.5430
    1.1129
    1.1143
    1.4822
    1.1051
    1.1019
    1.5430
    1.5430
    1.5430

    ! C6H13NO2 chayan
    Acid CDCA Amide (GA) >> Alpha Lysine Methyl Ester CDCA A
    !
    !
    !
    !
    !

    OA1

    CG2O2

    0.90 !

    ||

    ATOM OA1 OG2D1


    3(M)
    ATOM OA2 OG302

    -0.63 !

    O24

    CA--OA2--CH

    -0.49 !

    ||

    ATOM CM CG331
    CC5
    ATOM HM1 HGA3
    / \
    ATOM HM2 HGA3
    4
    NH3(+1)
    ATOM HM3 HGA3

    -0.31 !

    OH

    C24

    CC1

    0.09 !

    0.09 !

    C12 Me18

    ATOM CC3 CG321

    -0.18 !

    ATOM HC3A HGA2

    0.09 !

    Me19 |

    ATOM HC3B HGA2

    0.09 !

    C1 | C9

    ATOM CC4 CG321

    -0.18 !

    ATOM HC4A HGA2

    0.09 !

    0.09 !

    Me21

    C22

    \ / \ / \ / \ / \
    C20

    / \ |

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    CC3

    C15

    C23

    NH

    CC2

    CC

    ATOM HC4B HGA2

    0.09 !

    ATOM CC5 CG324

    0.13 !

    C3

    C5

    C7

    ATOM HC5A HGA2

    0.09 !

    ATOM HC5B HGA2

    0.09 !

    ATOM NL

    NG3P3

    / \ / \ / \
    HO

    0.33 !

    ATOM HL2 HGP2


    ATOM HL3 HGP2

    0.33 !
    0.33 !

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OA2
    CC3
    CC4
    CC5

    CC1
    HM1
    HM2
    HM3
    CC1
    CC2
    CC5
    HC4A
    CC3
    NL
    NL
    HL1
    HL2
    HL3

    CM
    CC4
    CC5
    NL
    CA
    CM
    CM
    CM
    CC2
    CC3
    CC3
    CC3
    CC4
    CC4
    CC4
    NL
    NL
    NL

    C6

    OH

    -0.30 !

    ATOM HL1 HGP2

    BOND
    BOND
    BOND
    BOND

    C4

    CM
    CC4
    CC5
    NL
    OA2
    OA2
    OA2
    OA2
    CC3
    CC4
    *CC4
    *CC4
    CC5
    *CC5
    *CC5
    CC5
    CC5
    CC5

    HM1
    HC4A
    HC5A
    HL1

    Alpha Lysine Methyl Ester CDCA Amide

    CM
    CA
    CA
    CA
    CC4
    CC5
    HC4A
    HC4B
    NL
    HC5A
    HC5B
    CC4
    CC4
    CC4

    CM
    CC4
    CC5
    NL

    HM2 CM
    HC4B
    HC5B
    HL2 NL

    1.5257
    1.1130
    1.1137
    1.1147
    1.5577
    1.5429
    1.5434
    1.1138
    1.5433
    1.4903
    1.4903
    1.0382
    1.0532
    1.0388

    109.81
    109.51
    111.53
    111.32
    114.43
    114.31
    113.71
    108.53
    113.71
    111.29
    111.29
    110.29
    109.68
    111.18

    HM3
    HL3
    -179.93
    -178.65
    62.15
    -60.00
    -162.39
    -58.57
    -122.33
    -116.24
    -46.10
    119.98
    -120.90
    -57.73
    61.17
    -179.42

    115.57
    115.57
    115.57
    115.57
    114.31
    113.71
    108.53
    108.97
    111.29
    110.79
    110.69
    111.29
    111.29
    111.29

    1.4395
    1.3318
    1.3318
    1.3318
    1.5433
    1.5434
    1.1138
    1.1147
    1.4903
    1.1033
    1.1030
    1.5434
    1.5434
    1.5434

    !end bile acids, chayan, dec2006


    !Bile acids and related compounds, chayan, may2007
    RESI BAB1
    -1.00 ! C29H47N2O6 Bile Acid Basic moiety 1 (BASE FOR NEW COMP
    OUNDS), chayan
    GROUP
    !
    ATOM C3 CG311
    0.14 !
    OG
    ATOM O3

    OG311

    -0.65 !

    ||

    ATOM H3' HGP1

    0.42 !

    CG--NT--HT2

    ATOM H3

    0.09 !

    CC3

    -0.18 !

    HGA1

    GROUP
    ATOM C4

    CG321

    ATOM H4A HGA2

    0.09 !

    O24

    CC2

    ATOM H4B HGA2

    0.09 !

    ||

    GROUP

    Me21

    C22

    C24

    CC1

    HT1

    ATOM C5

    CG311

    -0.09 !

    ATOM H5
    0.5)
    GROUP

    HGA1

    0.09 !

    ATOM C6

    CG321

    |
    C12 Me18

    0.09 !

    Me19 |

    ATOM H6B HGA2

    0.09 !

    C1 | C9

    !
    CG311

    0.14 !

    C2

    C10 C8

    ATOM O7

    OG311

    -0.65 !

    ATOM H7' HGP1

    0.42 !

    C3

    C5

    C7

    ATOM H7

    0.09 !
    !

    ATOM C8

    CG311

    -0.09 !

    ATOM H8

    HGA1

    0.09 !

    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9

    !
    CG3RC1 -0.09 !
    HGA1
    0.09

    HO

    C4

    C6

    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09
    HGA1
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    0.00
    -0.27 !methyl at c13
    0.09
    0.09
    0.09

    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    C14

    C16

    C15

    / \ / \ / \

    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09

    CG3RC1

    / \|/ \ / \ /

    ATOM C7

    GROUP

    C11 C13---C17

    ATOM H6A HGA2

    HGA1

    C20

    / \ |

    -0.18 !

    GROUP

    \ / \ / \ / \

    OH

    BAB1

    C23

    NH

    CA--OA1 (|
    OA2 (-0.5)

    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP
    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM C24
    ATOM O24
    ATOM N
    ATOM HN
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    GROUP
    ATOM CC2
    ATOM HC2A
    ATOM HC2B
    GROUP
    ATOM CC3
    ATOM HC3A
    ATOM HC3B
    GROUP
    ATOM CG
    ATOM OG
    ATOM NT
    ATOM HT1
    ATOM HT2
    BOND C3
    BOND C3
    BOND C4

    CG301

    0.00

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O1
    OG2D1
    NG2S1
    HGP1

    0.51
    -0.51
    -0.47
    0.47

    CG311
    HGA1
    CG2O3
    OG2D2
    OG2D2

    -0.19
    0.09
    0.62
    -0.76
    -0.76

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O1
    OG2D1
    NG2S2
    HGP1
    HGP1

    0.55
    -0.55
    -0.62
    0.32
    0.30

    O3
    C4
    C5

    C3
    C4
    C5

    H3 O3
    H4A C4
    H5

    H3'
    H4B

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR

    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13
    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    C24
    N
    CC2
    CC3
    CG
    C24
    CG
    CA

    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12
    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    C24
    N
    CC1
    HC2A
    HC3A
    OG
    C23
    CC3
    CC1

    C10 C19 C19 H19A C19 H19B C19 H19C


    C1 H1A C1 H1B
    C2 H2A C2 H2B
    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    H6B
    O7 O7

    C14
    C13
    C12
    C11

    H14
    C18 C18 H18A C18 H18B C18 H18C
    H12A C12 H12B
    H11A C11 H11B

    H7'

    C15 H15A C15 H15B


    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    C24
    N
    CC1
    CC2
    CC3
    CG
    N
    NT
    OA2

    H20
    H22A
    H23A
    O24
    HN
    HC1
    HC2B
    HC3B
    NT
    O24
    OG
    OA1

    C20 C21 C21 H21A C21 H21B C21 H21C


    C22 H22B
    C23 H23B
    CC1
    CC2
    CC3
    NT
    N
    NT

    CC2
    CC3
    CG
    HT1
    C24
    CG

    CC1 CA

    CA

    OA1 CA

    OA2

    NT HT2
    CC1 HN
    HT2 HT1

    !
    R(I(J/K)) T(I(JK/KJ)) PHI T(JKL)
    !ICs based on arbitrary CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5325 111.68 -49.45 111.84
    IC C2 C3 C4 C5
    1.5339 111.84 43.93 115.68
    IC C3 C4 C5 C6
    1.5383 115.68 -175.10 109.02
    IC C4 C5 C6 C7
    1.5598 109.02 85.47 114.98
    IC C5 C6 C7 C8
    1.5521 114.98 39.04 113.05
    IC C7 C8 C9 C10 1.5290 114.08 58.26 109.48
    IC C8 C9 C10 C1
    1.5323 109.48 179.67 111.99
    IC C9 C10 C1 C2
    1.5439 111.99 63.33 113.83
    IC O3 C3 C4 C5
    1.4163 109.09 162.18 115.68
    IC C4 C2 *C3 O3
    1.5383 111.84 -119.44 107.07
    IC C4 C2 *C3 H3
    1.5383 111.84 121.33 109.38
    IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53
    IC C2 C3 O3 H3' 1.5339 107.07 70.05 104.87
    IC C5 C3 *C4 H4A 1.5598 115.68 122.75 108.69
    IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82
    IC C10 C4 *C5 H5
    1.5279 114.70 116.72 105.03
    IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39
    IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33
    IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74
    IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18
    IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21
    IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66
    IC C6 C7 C8 C14 1.5441 113.05 -166.95 108.56
    IC C14 C7 *C8 C9
    1.5542 108.56 119.93 114.08
    IC C7 C8 C14 C13 1.5290 108.56 -174.20 113.13
    IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30
    IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56

    R(KL)
    1.5383
    1.5598
    1.5521
    1.5441
    1.5290
    1.5439
    1.5563
    1.5325
    1.5598
    1.4163
    1.1144
    1.5562
    0.9608
    1.1111
    1.1113
    1.1175
    1.1113
    1.1112
    1.1137
    1.1091
    1.1113
    1.1128
    1.5542
    1.5323
    1.5425
    1.5285
    1.5435

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C14
    C17
    C14
    C8
    O7
    C6
    C9
    C10
    C9
    H11A
    C14
    H12A
    C13
    C16
    H15A
    C17
    H16A
    C13
    C12
    C14
    H18A
    H18A
    C9
    C5
    H19A
    H19A
    C13
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    C23
    H22A
    C20
    C24
    H23A
    C22
    N
    C23
    CC1
    C24
    CA
    HC1
    N
    OA1
    N
    CC3
    HC2A
    CC1
    CG
    HC3A
    CC2
    NT
    CC3
    HT2

    C15
    C14
    C13
    C6
    C6
    C7
    C7
    C8
    C12
    C12
    C13
    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C5
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23
    C24
    C24
    N
    N
    N
    CC1
    CC1
    CC1
    CC1
    CC1
    CC2
    CC2
    CC2
    CC3
    CC3
    CG
    CG

    PRES G4MP

    C16
    *C13
    C12
    *C7
    *C7
    O7
    *C8
    *C9
    *C11
    *C11
    C12
    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    *C10
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    C24
    *C24
    N
    *N
    CC1
    *CC1
    *CC1
    CA
    *CA
    CC2
    *CC2
    *CC2
    CC3
    *CC3
    *CC3
    CG
    *CG
    NT
    *NT

    C17
    C12
    C11
    O7
    H7
    H7'
    H8
    H9
    H11A
    H11B
    H12A
    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    C19
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    C24
    H23A
    H23B
    N
    O24
    CC1
    HN
    CA
    HC1
    CC2
    OA1
    OA2
    CC3
    HC2A
    HC2B
    CG
    HC3A
    HC3B
    NT
    OG
    HT2
    HT1

    1.5285
    1.5731
    1.5425
    1.5290
    1.4218
    1.5441
    1.5323
    1.5439
    1.5547
    1.1090
    1.5425
    1.1059
    1.5425
    1.5435
    1.1002
    1.5533
    1.0992
    1.5731
    1.5340
    1.5425
    1.1064
    1.1064
    1.5439
    1.5279
    1.1079
    1.1079
    1.5731
    1.5533
    1.5519
    1.5396
    1.5649
    1.1079
    1.1079
    1.5649
    1.5524
    1.1127
    1.5519
    1.5029
    1.1097
    1.5524
    1.3364
    1.5029
    1.4446
    1.3364
    1.5482
    1.1102
    1.4446
    1.2534
    1.4446
    1.5552
    1.1118
    1.5536
    1.5034
    1.1125
    1.5552
    1.3503
    1.5034
    0.9905

    103.56
    98.18
    107.46
    113.05
    107.98
    107.98
    114.08
    109.48
    114.18
    108.77
    107.46
    111.88
    113.13
    103.56
    111.17
    106.91
    110.78
    98.41
    107.46
    114.21
    111.38
    111.38
    109.64
    109.53
    111.17
    111.17
    98.41
    111.83
    108.75
    112.90
    112.90
    110.45
    110.45
    108.75
    113.67
    108.15
    113.67
    114.01
    110.50
    114.01
    116.58
    116.58
    130.40
    130.40
    102.83
    109.50
    102.83
    119.90
    113.47
    115.05
    109.17
    115.05
    115.32
    108.25
    115.32
    118.71
    118.71
    118.60

    -2.52
    119.81
    55.26
    -126.94
    -113.62
    177.77
    122.47
    -117.10
    122.66
    115.79
    175.99
    119.47
    -118.30
    119.15
    119.82
    121.49
    117.20
    -112.89
    121.97
    116.84
    119.04
    -120.17
    -123.44
    5.08
    121.06
    -119.50
    127.01
    71.96
    122.38
    120.78
    71.88
    -121.55
    118.45
    -163.10
    119.92
    116.44
    176.63
    120.77
    118.82
    0.05
    -179.90
    178.79
    -174.70
    -170.40
    114.75
    123.68
    178.79
    177.56
    60.10
    126.07
    114.51
    107.73
    119.05
    117.32
    -46.42
    -179.05
    -177.78
    177.52

    106.91
    107.46
    111.18
    107.98
    107.19
    105.26
    107.18
    106.56
    108.77
    107.30
    111.88
    108.82
    108.46
    111.17
    112.08
    110.78
    110.97
    110.39
    114.21
    111.38
    110.59
    111.91
    109.53
    111.17
    112.01
    110.64
    111.83
    108.75
    112.90
    108.89
    110.45
    110.43
    110.89
    113.67
    108.15
    108.31
    114.01
    110.50
    109.42
    116.58
    119.94
    130.40
    123.77
    102.83
    109.50
    113.47
    119.90
    115.53
    115.05
    109.17
    106.60
    115.32
    108.25
    110.47
    118.71
    119.96
    118.60
    119.35

    1.00 ! C7H14N2O (01OH03), chayan

    1.5533
    1.5340
    1.5432
    1.4218
    1.1164
    0.9614
    1.1067
    1.1138
    1.1090
    1.1111
    1.1059
    1.1125
    1.1150
    1.1002
    1.0988
    1.0992
    1.0999
    1.1009
    1.5526
    1.1064
    1.1085
    1.1058
    1.5562
    1.1079
    1.1061
    1.1093
    1.5649
    1.5519
    1.5396
    1.1119
    1.1079
    1.1103
    1.1089
    1.5524
    1.1127
    1.1133
    1.5029
    1.1097
    1.1112
    1.3364
    1.2265
    1.4446
    1.0138
    1.5482
    1.1102
    1.5536
    1.2534
    1.2691
    1.5552
    1.1118
    1.1142
    1.5034
    1.1125
    1.1095
    1.3503
    1.2327
    0.9905
    1.0169

    ! This compund has 4-methylamine piperidine at gamma-position


    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    CG2--CG3 HG41
    ATOM OG OG2D1 -0.51 !
    /
    \ /
    ATOM NT NG2S1 -0.47 !
    T--CG1
    NG4 (+)
    ATOM HT1 HGP1
    0.47 !
    \
    / \
    GROUP
    !
    CG6--CG5 HG42
    ATOM CGT CG321 -0.18 !

    OG
    ||
    CG---NT--CG
    /

    HT1

    CC3
    \

    ATOM HGT1 HGA2

    0.09 !

    O24

    CC2

    ATOM HGT2 HGA2

    0.09 !

    ||

    GROUP

    ATOM CG1 CG311

    -0.09 !

    ATOM HG1 HGA1


    0.5)
    GROUP

    0.09 !

    ATOM CG2 CG321

    -0.18 !

    ATOM HG21 HGA2

    0.09 !

    Me19 |

    ATOM HG22 HGA2

    0.09 !

    C1 | C9

    GROUP

    C20

    C23

    C11 C13---C17
    |

    C14

    C16

    / \|/ \ / \ /

    0.20 !

    C2

    C10 C8

    ATOM HG31 HGA2

    0.09 !

    ATOM HG32 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM NG4 NG3P2

    -0.40 !

    ATOM HG41 HGP2

    0.32 !

    ATOM HG42 HGP2

    0.32 !

    ATOM CG5 CG324

    0.20 !

    CG321
    HGA2
    HGA2

    C24

    C15

    / \ / \ / \
    HO

    C4

    C6

    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    BOND NT CGT CGT HGT1 CGT HGT2 CGT CG1


    BOND CG1 HG1 CG1 CG2
    BOND CG2 HG21 CG2 HG22 CG2 CG3

    CC1

    \ / \ / \ / \

    / \ |

    HGA2
    HGA2

    C22

    C12 Me18

    ATOM CG3 CG324

    ATOM HG51
    ATOM HG52
    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62

    Me21

    OH

    G4MP (01OH03)

    NH

    CA--OA1 (|
    OA2 (-0.5)

    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG3
    NG4
    CG5
    CG6
    NT

    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    NG4
    NG4
    CG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    HG31
    HG41
    HG51
    HG61
    CG
    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    CG3
    CG3
    CG3
    NG4
    NG4
    NG4
    CG1
    CG1

    CG3
    NG4
    CG5
    CG6
    CG1

    HG32
    HG42
    HG52
    HG62
    HT1

    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3
    NG4
    *NG4
    *NG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    CG3
    NG4
    CG5
    CG6

    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    NG4
    CG5
    CG6
    CG1
    1.2271
    1.3456
    1.1142
    1.1142
    1.4538
    1.1164
    1.1164
    1.5450
    1.5201
    1.5201
    1.5436
    1.5017
    1.5017
    1.5201
    1.5048
    1.5048
    1.5017
    1.5264
    1.5264
    1.5264
    1.5264

    121.41
    121.99
    107.55
    107.55
    115.04
    107.27
    107.27
    111.92
    113.31
    113.31
    113.31
    108.23
    108.23
    108.23
    112.36
    112.36
    112.36
    109.26
    109.26
    111.91
    111.91

    13.20
    88.64
    -116.19
    121.44
    77.21
    -117.50
    118.24
    -173.65
    123.02
    -119.66
    55.01
    116.95
    -117.23
    -61.48
    118.67
    -125.21
    62.10
    121.78
    -121.65
    -121.76
    121.65

    121.99
    107.55
    111.07
    115.04
    107.27
    111.92
    109.86
    113.31
    108.94
    109.16
    108.23
    112.61
    113.22
    112.36
    107.00
    110.67
    109.26
    105.74
    105.59
    108.69
    108.91

    1.4538
    1.1142
    1.1174
    1.5450
    1.1164
    1.5436
    1.5466
    1.5201
    1.1140
    1.1145
    1.5017
    1.1038
    1.1028
    1.5048
    1.0106
    1.0050
    1.5264
    1.1029
    1.1034
    1.1133
    1.1129

    PRES G4MPAB
    1.00 ! C16H22N2O3 (010203D), chayan
    ! This compound has 4-methylamine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    CG2--CG3 HG41
    ATOM NT NG2S1 -0.47 !
    /
    \ /
    ATOM HT1 HGP1
    0.47 !
    -CG1
    NG4 (+)
    GROUP
    !
    \
    / \
    ATOM CGT CG321 -0.18 !
    CG6--CG5 HG42
    ATOM HGT1 HGA2
    0.09 !
    ATOM HGT2 HGA2
    GROUP
    ATOM CG1 CG311
    CD1--CE1
    ATOM HG1 HGA1
    //
    \\
    GROUP
    -CZ
    CP
    ATOM CG2 CG321
    \ __ /

    0.09 !

    0.09 !

    !
    -0.18 !

    Me21

    CG---NT--CGT/

    HT1

    CC3
    \
    CC2

    ||

    C22

    C24

    CC1

    \ / \ / \ / \

    C12 Me18
    / \ |

    ||

    O24

    !
    -0.09 !

    OG

    C20
    /

    C23

    NH

    CA--OA2--CB||

    ATOM HG21 HGA2


    CD2--CE2
    ATOM HG22 HGA2

    0.09 !

    C11 C13---C17

    0.09 !

    Me19 |

    C1 | C9

    GROUP
    ATOM CG3 CG324

    0.20 !

    ATOM HG31 HGA2

    0.09 !

    C2

    C10 C8

    ATOM HG32 HGA2

    0.09 !

    ATOM NG4 NG3P2

    -0.40 !

    C3

    C5

    C7

    ATOM HG41 HGP2

    0.32 !

    ATOM HG42 HGP2

    0.32 ! HO

    ATOM CG5 CG324

    0.20 !

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52
    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP

    HGA2

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    CD1
    CE2
    CG

    NT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    OA2
    CZ
    CP
    NT

    C16

    C15

    C4

    C6

    OH

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    G4MPAB (010203D)

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    HGT1
    CG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HB1
    HD1
    HE2
    HT1

    C14

    / \ / \ / \

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    CGT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CB
    CD1
    CE2
    CGT

    / \|/ \ / \ /

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG321
    HGA2
    HGA2

    OA1

    CGT HGT2 CGT CG1


    CG2
    CG3
    NG4
    CG5
    CG6
    CB
    CD1
    CE2

    CG3
    NG4
    CG5
    CG6
    CG1
    HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ

    CP

    HP

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    CA
    CA
    CA
    OA2
    OA2
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    NG4
    NG4
    CG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    CA
    OA2
    OA2
    OA2
    CB
    CB
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    CG3
    CG3
    CG3
    NG4
    NG4
    NG4
    CG1
    CG1

    OA2
    CB
    CB
    CB
    CZ
    CZ
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3
    NG4
    *NG4
    *NG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    CB
    HB1
    CZ
    HB2
    CD2
    CD1
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5235
    1.3360
    1.3360
    1.3360
    1.4472
    1.4472
    1.4048
    1.4060
    1.4060
    1.5063
    1.5063
    1.4048
    1.4015
    1.4007
    1.4015
    1.4018
    1.4007
    1.4005
    1.4007
    1.2237
    1.3437
    1.1140
    1.1140
    1.4463
    1.1180
    1.1180
    1.5425
    1.5296
    1.5296
    1.5449
    1.5090
    1.5090
    1.5296
    1.5087
    1.5087
    1.5090
    1.5282
    1.5282
    1.5282
    1.5282

    109.54
    116.53
    116.53
    116.53
    113.68
    113.68
    119.48
    121.22
    121.22
    119.30
    121.22
    120.29
    119.94
    120.09
    120.29
    120.19
    119.94
    120.00
    120.09
    121.80
    123.40
    109.15
    109.15
    113.44
    106.98
    106.98
    112.49
    110.63
    110.63
    110.63
    110.03
    110.03
    110.03
    113.44
    113.44
    113.44
    109.66
    109.66
    110.78
    110.78

    -176.41
    -64.48
    176.13
    54.52
    -117.39
    62.45
    179.84
    121.02
    5.79
    179.52
    -179.50
    0.00
    0.62
    -0.61
    -179.48
    179.40
    -179.57
    179.35
    -179.52
    2.70
    165.76
    -116.48
    121.76
    57.56
    -118.28
    116.87
    179.28
    122.32
    -120.00
    55.35
    117.95
    -117.03
    -57.44
    120.02
    -123.98
    57.59
    122.28
    -121.41
    -122.43
    120.30

    116.53
    110.30
    113.68
    110.72
    121.22
    119.30
    121.22
    106.39
    107.87
    120.29
    120.19
    119.94
    120.09
    120.00
    119.81
    120.20
    120.13
    120.25
    119.77
    123.40
    109.15
    109.48
    113.44
    106.98
    112.49
    111.08
    110.63
    109.32
    109.52
    110.03
    113.07
    112.44
    113.44
    108.22
    110.17
    109.66
    105.76
    105.40
    109.37
    108.99

    1.4472
    1.1156
    1.5063
    1.1160
    1.4060
    1.4048
    1.5063
    1.1156
    1.1160
    1.4015
    1.4018
    1.4007
    1.4005
    1.4018
    1.0800
    1.0796
    1.0809
    1.0815
    1.0816
    1.4463
    1.1140
    1.1169
    1.5425
    1.1180
    1.5449
    1.5446
    1.5296
    1.1119
    1.1129
    1.5090
    1.1028
    1.1041
    1.5087
    1.0087
    1.0071
    1.5282
    1.1029
    1.1040
    1.1120
    1.1138

    PRES G4P
    1.00 ! C6H12N2O (01OH02), chayan
    ! This compound has 4-amine piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    G2--CG3 HG41
    ATOM OG OG2D1 -0.51 !
    \ /
    ATOM NT NG2S1 -0.47 !
    NG4
    ATOM HT1 HGP1
    0.47 !
    / \
    GROUP
    !
    G6--CG5 HG42
    ATOM CG1 CG311 -0.09 !
    ATOM HG1 HGA1

    0.09 !

    OG

    ||

    CG--NT--CG1
    /
    CC3
    \
    O24

    CC2

    HT1

    \
    C

    GROUP

    ||

    ATOM CG2 CG321

    -0.18 !

    ATOM HG21 HGA2

    0.09 !

    ATOM HG22 HGA2


    .5)
    GROUP

    0.09 !

    C12 Me18

    ATOM CG3 CG324

    0.20 !

    ATOM HG31 HGA2

    0.09 !

    Me19 |

    ATOM HG32 HGA2

    0.09 !

    C1 | C9

    ATOM NG4 NG3P2

    -0.40 !

    ATOM HG41 HGP2

    0.32 !

    C2

    C10 C8

    ATOM HG42 HGP2

    0.32 !

    ATOM CG5 CG324

    0.20 !

    C3

    C5

    C7

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52 HGA2

    0.09 ! HO

    GROUP

    C24

    CC1

    C20

    C23

    NH

    C14

    C16

    OA2 (-0.5)

    / \|/ \ / \ /
    C15

    / \ / \ / \
    C4

    C6

    OH

    ATOM HG61 HGA2


    ATOM HG62 HGA2

    0.09 !
    0.09 !

    NT
    CG2
    CG3
    NG4
    CG5
    CG6
    NT

    OG
    CG
    HG1
    HG1
    NT
    CG3
    CG3
    CG1
    NG4
    NG4
    CG2
    CG5
    CG5
    CG3
    CG6
    CG6

    CG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG
    CG
    NT
    NT
    NT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    CG3
    CG3
    CG3
    NG4
    NG4
    NG4

    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CG1
    NT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3
    NG4
    *NG4
    *NG4
    CG5
    *CG5
    *CG5

    G4P (01OH02)

    HG1
    HG22
    HG32
    HG42
    HG52
    HG62
    HT1
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52

    CG1
    CG2
    CG3
    NG4
    CG5
    CG6

    CG2
    CG3
    NG4
    CG5
    CG6
    CG1
    1.2252
    1.3388
    1.1178
    1.1178
    1.4376
    1.5415
    1.5415
    1.5451
    1.5035
    1.5035
    1.5415
    1.5102
    1.5102
    1.5035
    1.5345
    1.5345

    121.32
    125.38
    107.87
    107.87
    109.63
    112.88
    112.88
    112.88
    112.58
    112.58
    112.58
    115.17
    115.17
    115.17
    111.60
    111.60

    5.10
    -51.92
    -118.28
    120.36
    -92.37
    121.50
    -121.67
    27.90
    118.55
    -117.34
    -56.71
    117.55
    -129.75
    21.27
    121.58
    -123.20

    CA--OA1 (-0
    |

    C11 C13---C17

    -0.18 !

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C22

    \ / \ / \ / \

    / \ |

    ATOM CG6 CG321

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    Me21

    125.38
    107.87
    109.63
    111.16
    112.88
    108.63
    109.79
    112.58
    112.20
    112.10
    115.17
    107.51
    113.29
    111.60
    104.25
    105.77

    1.4376
    1.1178
    1.5451
    1.5418
    1.5415
    1.1130
    1.1112
    1.5035
    1.1031
    1.1033
    1.5102
    1.0298
    1.0008
    1.5345
    1.1051
    1.1005

    IC CG5
    IC CG5

    CG1
    CG1

    *CG6 HG61
    *CG6 HG62

    1.5345 110.88 -120.54 109.69


    1.5345 110.88 122.25 109.27

    1.1126
    1.1110

    PRES G4PAB
    1.00 ! C15H20N2O3 (010202D), chayan
    ! This compound has 4-amine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    CG2--CG3 HG41
    ATOM NT NG2S1 -0.47 !
    /
    \ /
    ATOM HT1 HGP1
    0.47 !
    CG1
    NG4 (+)
    GROUP
    !
    \
    / \
    ATOM CG1 CG311 -0.09 !
    CG6--CG5 HG42
    ATOM HG1 HGA1
    0.09 !
    GROUP

    ||
    CG--NT-/

    \
    O24

    CC2

    ||

    -0.18 !

    ATOM HG21 HGA2


    CD1--CE1
    ATOM HG22 HGA2
    //
    \\
    GROUP
    --CB--CZ
    CP
    ATOM CG3 CG324
    \ __ /
    ATOM HG31 HGA2
    CD2--CE2
    ATOM HG32 HGA2

    0.09 !

    0.09 !

    Me19 |

    ATOM NG4 NG3P2

    -0.40 !

    C1 | C9

    ATOM HG41 HGP2

    0.32 !

    ATOM HG42 HGP2

    0.32 !

    C2

    C10 C8

    ATOM CG5 CG324

    0.20 !

    ATOM HG51 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG52 HGA2

    0.09 !

    -0.18 !

    ATOM HG61 HGA2

    0.09 !

    ATOM HG62 HGA2


    GROUP
    ATOM CC1 CG311
    ATOM HC1 HGA1

    0.09 !
    !
    0.17 !
    0.09 !

    C24

    C20

    C23

    C11 C13---C17

    0.09 !

    ATOM CG6 CG321

    C22

    C14

    C16

    / \|/ \ / \ /
    C15

    / \ / \ / \
    HO

    C4

    C6

    CC1

    \ / \ / \ / \

    / \ |

    0.09 !

    Me21

    C12 Me18

    0.20 !

    HT1

    CC3

    ATOM CG2 CG321

    GROUP

    OG

    OH

    G4PAB (010202D)

    NH

    CA--OA2
    ||
    OA1

    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP

    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    HB1
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG2
    CG3
    NG4
    CG5
    CG6
    OA2
    CB
    CZ
    CP
    NT

    CC1
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    OG
    CG
    HG1
    HG1
    NT
    CG3
    CG3
    CG1
    NG4
    NG4

    CA
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT
    NT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CG1
    CG2
    CG3
    NG4
    CG5
    CG6

    HG1
    HG22
    HG32
    HG42
    HG52
    HG62

    CB
    CD1
    CE2
    CG1

    HB2 CB CZ
    HD1 CD1 CE1 CE1 HE1 CE1 CP
    HE2 CE2 CD2 CD2 HD2 CD2 CZ
    HT1

    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3

    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32

    CG1
    CG2
    CG3
    NG4
    CG5
    CG6

    CG2
    CG3
    NG4
    CG5
    CG6
    CG1

    1.5231
    1.1156
    1.1156
    1.5059
    1.4060
    1.4048
    1.4048
    1.4060
    1.4060
    1.5059
    1.5059
    1.4048
    1.4015
    1.4006
    1.4015
    1.4018
    1.4006
    1.4005
    1.4006
    1.2229
    1.3417
    1.1209
    1.1209
    1.4328
    1.5271
    1.5271
    1.5409
    1.5089
    1.5089

    109.59
    110.71
    110.36
    113.59
    121.17
    119.33
    119.49
    121.17
    121.17
    119.33
    121.17
    120.28
    119.94
    120.09
    120.28
    120.18
    119.94
    120.00
    120.09
    121.22
    123.49
    108.39
    108.39
    110.90
    110.81
    110.81
    110.81
    109.54
    109.54

    -176.73
    55.90
    -63.25
    177.35
    -112.96
    66.62
    179.58
    10.10
    125.42
    179.62
    -179.61
    0.06
    0.67
    -0.65
    -179.55
    179.50
    -179.64
    179.44
    -179.41
    -0.98
    42.04
    -119.14
    118.05
    179.86
    122.78
    -120.05
    56.29
    117.78
    -116.99

    CP

    116.72
    116.72
    116.72
    116.72
    113.59
    113.59
    121.17
    107.80
    106.41
    120.28
    120.18
    119.94
    120.09
    120.00
    119.88
    120.27
    120.14
    120.29
    119.77
    123.49
    108.39
    110.90
    110.60
    110.81
    109.51
    109.07
    109.54
    113.14
    112.54

    HP

    1.4465
    1.3350
    1.3350
    1.3350
    1.4465
    1.4465
    1.5059
    1.1156
    1.1156
    1.4015
    1.4018
    1.4006
    1.4005
    1.4018
    1.0800
    1.0795
    1.0810
    1.0816
    1.0817
    1.4328
    1.1209
    1.5409
    1.5391
    1.5271
    1.1117
    1.1144
    1.5089
    1.1028
    1.1039

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    CG3
    CG3
    CG3
    NG4
    NG4
    NG4
    CG1
    CG1

    NG4
    *NG4
    *NG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5271
    1.5096
    1.5096
    1.5089
    1.5304
    1.5304
    1.5304
    1.5304

    109.54
    113.50
    113.50
    113.50
    110.03
    110.03
    110.58
    110.58

    -57.03
    120.09
    -124.10
    56.82
    122.41
    -121.42
    -122.01
    120.54

    113.50
    108.06
    110.07
    110.03
    105.69
    105.25
    109.49
    109.24

    1.5096
    1.0087
    1.0071
    1.5304
    1.1028
    1.1040
    1.1127
    1.1133

    PRES G3PR
    1.00 ! C6H12N2O (01OH04(R)), chayan ! Check IC table
    ! This compound has 3-amine piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    HG31
    ATOM OG OG2D1 -0.51 !
    |
    ATOM NT NG2S1 -0.47 !
    OG
    CG2--NG3(+1)--HG32
    ATOM HT1 HGP1
    0.47 !
    ||
    /
    \
    GROUP
    !
    CG--NT--CG
    1
    CG4
    ATOM CG1 CG311 -0.09 !
    / HT1 \
    /
    ATOM HG1 HGA1
    0.09 !
    CC3
    CG6--CG5
    GROUP
    !
    \
    ATOM CG2 CG324

    0.20 !

    O24

    CC2

    ATOM HG21 HGA2

    0.09 !

    ||

    ATOM HG22 HGA2

    0.09 !

    ATOM NG3 NG3P2

    -0.40 !

    ATOM HG31 HGP2


    -0.5)
    ATOM HG32 HGP2

    0.32 !

    ATOM CG4 CG324


    )
    ATOM HG41 HGA2

    0.20 !
    0.09 !

    Me19 |

    ATOM HG42 HGA2

    0.09 !

    C1 | C9

    GROUP

    0.32 !

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52 HGA2

    0.09 !

    C3

    C5

    C7

    !
    -0.18 !

    C20

    C11 C13---C17

    C15

    / \ / \ / \
    HO

    C4

    C6

    C24

    CC1

    \ / \ / \ / \

    / \ |

    -0.18 !

    ATOM CG6 CG321

    C22

    C12 Me18

    ATOM CG5 CG321

    GROUP

    Me21

    OH

    C23

    NH

    CA--OA1 (
    |
    OA2 (-0.5

    ATOM HG61 HGA2

    0.09 !

    ATOM HG62 HGA2

    0.09 !

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    ig
    IC
    ig
    IC
    ig
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    NT

    CG1
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CG1

    CG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HT1

    G3PR (01OH04(R))

    CG2
    NG3
    CG4
    CG5
    CG6

    NG3
    CG4
    CG5
    CG6
    CG1

    CC3
    CG
    HG1

    CG
    NT
    NT

    NT
    CG1
    CG1 HG1
    *CG1 CG2

    1.5047 118.90 -176.48 124.61


    1.3378 124.61 -36.75 108.87
    1.1179 108.87 119.19 110.98

    1.4438
    1.1179
    1.5420 ! for R conf

    HG1

    NT

    *CG1 CG6

    1.1179 108.87 -118.11 109.81

    1.5506 ! for R conf

    NT

    CG1

    CG2

    NG3

    1.4438 110.98

    1.5058 ! for R conf

    NG3
    NG3
    CG1
    CG4
    CG4
    CG2
    CG5
    CG5
    NG3
    CG6
    CG6
    CG5
    CG5

    CG1
    CG1
    CG2
    CG2
    CG2
    NG3
    NG3
    NG3
    CG4
    CG4
    CG4
    CG1
    CG1

    *CG2
    *CG2
    NG3
    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5058
    1.5058
    1.5420
    1.5046
    1.5046
    1.5058
    1.5355
    1.5355
    1.5046
    1.5411
    1.5411
    1.5411
    1.5411

    110.11
    110.11
    110.11
    115.65
    115.65
    115.65
    111.13
    111.13
    111.13
    110.56
    110.56
    113.66
    113.66

    74.30 110.11
    118.33
    -116.73
    58.73
    131.36
    -117.57
    -9.08
    123.33
    -121.08
    -47.06
    122.13
    -120.28
    -123.82
    119.91

    113.56
    111.83
    115.65
    112.19
    105.76
    111.13
    105.76
    104.21
    110.56
    110.68
    109.02
    109.48
    108.64

    1.0998
    1.1032
    1.5046
    1.0010
    1.0308
    1.5355
    1.1009
    1.1056
    1.5411
    1.1119
    1.1129
    1.1121
    1.1155

    PRES G3PS
    1.00 ! C6H12N2O (01OH04(S)), chayan ! Check IC table
    ! This compound has 3-amine piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    HG31
    ATOM OG OG2D1 -0.51 !
    |
    ATOM NT NG2S1 -0.47 !
    OG
    CG2--NG3(+1)--HG32
    ATOM HT1 HGP1
    0.47 !
    ||
    /
    \
    GROUP
    !
    CG--NT--CG
    1
    CG4
    ATOM CG1 CG311 -0.09 !
    / HT1 \
    /
    ATOM HG1 HGA1
    0.09 !
    CC3
    CG6--CG5
    GROUP
    !
    \
    ATOM CG2 CG324
    0.20 !
    O24
    CC2
    ATOM HG21 HGA2
    0.09 !
    ||
    /

    ATOM HG22
    ATOM NG3
    ATOM HG31
    -0.5)
    ATOM HG32
    ATOM CG4
    )
    ATOM HG41
    ATOM HG42
    GROUP
    ATOM CG5
    ATOM HG51
    ATOM HG52
    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62

    HGA2
    NG3P2
    HGP2

    0.09 !
    -0.40 !
    0.32 !

    HGP2
    CG324

    0.32 !
    0.20 !

    / \ |
    /
    C11 C13---C17

    HGA2
    HGA2

    CG321
    HGA2
    HGA2

    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    Me19 |
    |
    |
    C1 | C9
    C14 C16
    / \|/ \ / \ /
    C2 C10 C8
    C15
    |
    |
    |
    C3 C5 C7
    / \ / \ / \
    HO C4 C6
    OH

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CG1
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG

    CG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HT1

    IC
    IC
    IC
    ig
    IC
    ig
    IC
    ig
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    NT

    CG321
    HGA2
    HGA2

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CG1

    H
    Me21 C22 C24 CC1
    |
    \ / \ / \ / \
    C12 Me18 C20 C23 NH
    CA--OA1 (
    |
    OA2 (-0.5

    G3PS (01OH04(S))

    CG2
    NG3
    CG4
    CG5
    CG6

    NG3
    CG4
    CG5
    CG6
    CG1

    CC3
    CG
    HG1

    CG
    NT
    NT

    NT
    CG1
    CG1 HG1
    *CG1 CG2

    1.5067 118.82 -168.68 125.46


    1.3336 125.46 -54.62 108.34
    1.1153 108.34 -120.60 110.10

    1.4406
    1.1153
    1.5378 ! for S conf

    HG1

    NT

    *CG1 CG6

    1.1153 108.34 119.57 110.63

    1.5471 ! for S conf

    NT

    CG1

    CG2

    NG3

    1.4406 110.10 -175.03 112.25

    1.5062 ! for S conf

    NG3
    NG3
    CG1
    CG4
    CG4
    CG2
    CG5
    CG5
    NG3
    CG6
    CG6
    CG5
    CG5

    CG1
    CG1
    CG2
    CG2
    CG2
    NG3
    NG3
    NG3
    CG4
    CG4
    CG4
    CG1
    CG1

    *CG2
    *CG2
    NG3
    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5062
    1.5062
    1.5378
    1.5047
    1.5047
    1.5062
    1.5284
    1.5284
    1.5047
    1.5380
    1.5380
    1.5380
    1.5380

    1.1050
    1.1009
    1.5047
    1.0062
    1.0067
    1.5284
    1.1051
    1.1021
    1.5380
    1.1129
    1.1129
    1.1151
    1.1123

    112.25
    112.25
    112.25
    112.03
    112.03
    112.03
    109.25
    109.25
    109.25
    110.27
    110.27
    112.70
    112.70

    116.92
    -120.00
    58.60
    122.85
    -120.61
    -59.03
    120.95
    -122.37
    57.37
    120.37
    -121.28
    -121.55
    122.04

    111.42
    112.62
    112.03
    109.11
    108.23
    109.25
    105.28
    105.83
    110.27
    109.44
    110.59
    108.33
    109.35

    PRES G3PABR
    1.00 ! C15H20N2O3 (010204(R)D), chayan ! check IC table
    ! This compound has 3-amine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    HG31

    ATOM HT1 HGP1


    0.47
    |
    GROUP
    CG2--NG3(+1)--HG32
    ATOM CG1 CG311 -0.09
    /
    \
    ATOM HG1 HGA1
    0.09
    CG1
    CG4
    GROUP
    \
    /
    ATOM CG2 CG324
    0.20
    CG6--CG5
    ATOM HG21 HGA2
    0.09

    !
    !

    OG

    ||

    CG---NT--

    CC3

    HT1

    ATOM HG22 HGA2

    0.09 !

    O24

    CC2

    ATOM NG3 NG3P2

    -0.40 !

    ||

    ATOM HG31 HGP2


    0.32
    CD1--CE1
    ATOM HG32 HGP2
    0.32
    //
    \\
    ATOM CG4 CG324
    0.20
    ---CB--CZ
    CP
    ATOM HG41 HGA2
    0.09
    \ __ /
    ATOM HG42 HGA2
    0.09
    CD2--CE2
    GROUP

    C12 Me18

    !
    !

    ATOM CG5 CG321

    -0.18 !

    C1 | C9

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52 HGA2

    0.09 !

    ATOM HG61 HGA2

    0.09 !

    ATOM HG62 HGA2

    0.09 !

    GROUP

    C23

    C14

    C16

    C2

    C10 C8

    C3

    C5

    C7

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    ATOM CC1 CG311


    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2

    C20

    / \|/ \ / \ /

    !
    -0.18 !

    C24

    C11 C13---C17
    Me19 |

    ATOM CG6 CG321

    C22

    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17 !
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61 0.00
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CC1

    \ / \ / \ / \

    / \ |

    GROUP

    Me21

    G3PABR (010204(R)D)

    NH

    CA---OA2
    ||
    OA1

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HD2
    CE1
    HE1
    CE2
    HE2
    CP
    HP

    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    NT
    CG2
    NG3
    CG4
    CG5
    CG6
    OA2
    CZ
    CP
    NT

    CG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    ig
    IC
    ig
    IC
    ig
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2
    CG1

    HG1
    HG22
    HG32
    HG42
    HG52
    HG62
    HB1
    HD1
    HE2
    HT1
    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CG1
    HG1
    CG2

    CC1
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    CC3
    CG
    HG1

    CA
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT

    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT
    CG1
    *CG1

    HG1

    NT

    NT
    NG3
    NG3
    CG1
    CG4
    CG4
    CG2
    CG5
    CG5
    NG3
    CG6
    CG6
    CG5
    CG5

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2

    CG2
    NG3
    CG4
    CG5
    CG6
    CG1
    HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    1.5247
    1.1153
    1.1158
    1.5068
    1.4048
    1.4063
    1.4063
    1.4048
    1.4048
    1.5068
    1.5068
    1.4063
    1.4018
    1.4005
    1.4018
    1.4014
    1.4005
    1.4006
    1.4005
    1.5011
    1.3471
    1.1192

    109.30
    110.11
    110.89
    113.78
    119.29
    121.26
    119.45
    119.29
    119.29
    121.26
    119.29
    120.20
    120.00
    120.09
    120.20
    120.31
    120.00
    119.94
    120.09
    116.88
    129.61
    103.59

    HP

    116.76
    116.76
    116.76
    116.76
    113.78
    113.78
    119.29
    106.30
    107.79
    120.20
    120.31
    120.00
    120.09
    119.94
    120.24
    119.81
    120.29
    120.12
    120.13
    129.61
    103.59
    117.90

    1.4477
    1.3346
    1.3346
    1.3346
    1.4477
    1.4477
    1.5068
    1.1153
    1.1158
    1.4018
    1.4014
    1.4005
    1.4006
    1.4014
    1.0794
    1.0801
    1.0816
    1.0810
    1.0815
    1.4554
    1.1192
    1.5488 ! for R conf

    *CG1 CG6

    1.1192 103.59 -114.20 112.24

    1.5460 ! for R conf

    CG1

    CG2

    NG3

    1.4554 117.90

    1.5102 ! for R conf

    CG1
    CG1
    CG2
    CG2
    CG2
    NG3
    NG3
    NG3
    CG4
    CG4
    CG4
    CG1
    CG1

    *CG2
    *CG2
    NG3
    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5102
    1.5102
    1.5488
    1.5050
    1.5050
    1.5102
    1.5325
    1.5325
    1.5050
    1.5405
    1.5405
    1.5405
    1.5405

    110.69
    110.69
    110.69
    114.54
    114.54
    114.54
    109.28
    109.28
    109.28
    111.03
    111.03
    112.67
    112.67

    -176.15
    -68.10
    51.00
    172.70
    56.49
    -123.70
    179.81
    -64.86
    179.89
    -179.38
    179.41
    0.03
    -0.52
    0.55
    179.30
    -179.45
    179.28
    -179.51
    179.59
    179.73
    -155.34
    116.28

    CP

    78.28 110.69
    116.99
    -118.04
    56.48
    128.88
    -116.54
    -57.39
    121.77
    -121.69
    55.18
    121.20
    -121.12
    -120.64
    122.50

    112.30
    112.47
    114.54
    111.74
    104.32
    109.28
    105.46
    105.58
    111.03
    109.59
    109.77
    108.98
    109.46

    1.1021
    1.1014
    1.5050
    1.0037
    1.0232
    1.5325
    1.1028
    1.1031
    1.5405
    1.1130
    1.1134
    1.1142
    1.1133

    PRES G3PABS
    1.00 ! C15H20N2O3 (010204(S)D), chayan ! check IC table
    ! This compound has 3-amine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    ! Relative position of CG2 and CG6 wrt CG1 dictates (R/S) configuration
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    HG31
    ATOM HT1 HGP1
    0.47 !
    |
    GROUP
    !
    OG
    CG2--NG3(+1)--HG32
    ATOM CG1 CG311 -0.09 !
    ||
    /
    \
    ATOM HG1 HGA1
    0.09 !
    CG---NT-CG1
    CG4
    GROUP
    !
    /
    HT1
    \
    /
    ATOM CG2 CG324
    0.20 !
    CC3
    CG6--CG5
    ATOM HG21 HGA2
    0.09 !
    \
    ATOM HG22 HGA2

    0.09 !

    O24

    CC2

    ATOM NG3 NG3P2

    -0.40 !

    ||

    ATOM HG31 HGP2


    0.32
    CD1--CE1
    ATOM HG32 HGP2
    0.32
    //
    \\
    ATOM CG4 CG324
    0.20
    ---CB--CZ
    CP
    ATOM HG41 HGA2
    0.09
    \ __ /
    ATOM HG42 HGA2
    0.09
    CD2--CE2
    GROUP

    C12 Me18

    !
    !

    ATOM CG5 CG321

    -0.18 !

    C1 | C9

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52 HGA2

    0.09 !

    ATOM HG61 HGA2

    0.09 !

    ATOM HG62 HGA2

    0.09 !

    GROUP

    C20

    C23

    C14

    C16

    / \|/ \ / \ /

    !
    -0.18 !

    C24

    C11 C13---C17
    Me19 |

    ATOM CG6 CG321

    C22

    C2

    C10 C8

    C3

    C5

    C7

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    ATOM CC1 CG311

    0.17 !

    ATOM HC1 HGA1

    0.09 !

    CC1

    \ / \ / \ / \

    / \ |

    GROUP

    Me21

    G3PABS (010204(R)D)

    NH

    CA---OA2
    ||
    OA1

    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP

    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    ig
    IC
    ig
    IC
    ig
    IC
    IC
    IC

    NT
    CG2
    NG3
    CG4
    CG5
    CG6
    OA2
    CZ
    CP
    NT

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2
    CG1

    HG1
    HG22
    HG32
    HG42
    HG52
    HG62
    HB1
    HD1
    HE2
    HT1
    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CG1
    HG1
    CG2

    CC1
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    CC3
    CG
    HG1

    CA
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT

    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT
    CG1
    *CG1

    HG1

    NT

    NT
    NG3
    NG3
    CG1

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2

    CG2
    NG3
    CG4
    CG5
    CG6
    CG1
    HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    110.33
    107.66
    110.84
    117.67
    119.99
    120.38
    119.50
    119.99
    119.99
    120.38
    119.99
    120.09
    120.04
    120.04
    120.09
    120.33
    120.04
    119.98
    120.04
    118.65
    125.29
    106.27

    173.10
    -159.94
    -45.26
    81.14
    -124.81
    59.26
    -175.97
    115.14
    2.48
    174.84
    -174.60
    0.17
    0.53
    -0.28
    -177.48
    177.84
    -177.24
    178.76
    178.32
    -174.99
    72.25
    -120.59

    HP

    116.65
    116.65
    116.65
    116.65
    117.67
    117.67
    119.99
    105.50
    109.03
    120.09
    120.33
    120.04
    120.04
    119.98
    119.41
    119.72
    120.45
    119.77
    119.79
    125.29
    106.27
    116.06

    1.4498
    1.3360
    1.3360
    1.3360
    1.4498
    1.4498
    1.5124
    1.1133
    1.1172
    1.4034
    1.4000
    1.4001
    1.4004
    1.4000
    1.0806
    1.0808
    1.0791
    1.0812
    1.0802
    1.4513
    1.1180
    1.5481 ! for S conf

    *CG1 CG6

    1.1180 106.27 116.21 109.65

    1.5438 ! for S conf

    CG1

    CG2

    1.4513 116.06 -178.87 111.82

    1.5083 ! for S conf

    CG1
    CG1
    CG2

    *CG2 HG21
    *CG2 HG22
    NG3 CG4

    1.5083 111.82 118.34 112.32


    1.5083 111.82 -117.38 113.04
    1.5481 111.82 58.07 113.36

    1.1010
    1.1005
    1.5025

    NG3

    1.5355
    1.1133
    1.1172
    1.5124
    1.4046
    1.4055
    1.4055
    1.4046
    1.4046
    1.5124
    1.5124
    1.4055
    1.4034
    1.4001
    1.4034
    1.4000
    1.4001
    1.4004
    1.4001
    1.4955
    1.3420
    1.1180

    CP

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG4
    CG4
    CG2
    CG5
    CG5
    NG3
    CG6
    CG6
    CG5
    CG5

    CG2
    CG2
    NG3
    NG3
    NG3
    CG4
    CG4
    CG4
    CG1
    CG1

    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.5025
    1.5025
    1.5083
    1.5325
    1.5325
    1.5025
    1.5423
    1.5423
    1.5423
    1.5423

    113.36
    113.36
    113.36
    109.81
    109.81
    109.81
    112.00
    112.00
    112.61
    112.61

    123.57
    -121.13
    -55.74
    121.56
    -122.34
    53.37
    121.73
    -121.07
    -121.49
    121.00

    108.79
    108.70
    109.81
    105.19
    105.61
    112.00
    109.45
    109.56
    109.20
    109.29

    1.0183
    1.0090
    1.5325
    1.1030
    1.1031
    1.5423
    1.1131
    1.1110
    1.1133
    1.1144

    !end bile acids, chayan, may2007


    !fatty acid binding protein inhibitors, chayan, may2007
    RESI FBIB
    -1.00 ! C12H15O3 Fatty acid Binding protein Inhibitor B, chay
    an
    ! This is a phenyl derivative having
    ! dimethyl at 2 and ethyl acetate at 4 position
    GROUP
    !
    ATOM CG CG2R61 0.00 !
    HD1 HE1
    GROUP
    !
    |
    |
    ATOM CD1 CG2R61 -0.115 !
    (-0.5)OD1 HA1 HB1 CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    \
    | |
    //
    \\
    GROUP
    !
    CD--CA--CB--CG
    CZ--OH
    ATOM CD2 CG2R61 -0.115 !
    /
    | |
    \ __ /
    \
    ATOM HD2 HGR61
    0.115 !
    (-0.5)OD2 HA2 HB2 CD2--CE2
    HH
    GROUP
    !
    |
    |
    ATOM CE1 CG2R61 -0.115 !
    HD2 CC--C1(Me)
    ATOM HE1 HGR61
    0.115 !
    |
    GROUP
    !
    C2(Me)
    ATOM CE2 CG2R61 0.00 !
    GROUP
    !
    COMPOUND "FBIB"
    ATOM CC CG311 -0.09 !
    ATOM HC HGA1
    0.09
    ATOM C1 CG331 -0.27
    ATOM H1A HGA3
    0.09
    ATOM H1B HGA3
    0.09
    ATOM H1C HGA3
    0.09
    ATOM C2 CG331 -0.27
    ATOM H2A HGA3
    0.09
    ATOM H2B HGA3
    0.09
    ATOM H2C HGA3
    0.09
    GROUP
    ATOM CZ CG2R61 0.11
    ATOM OH OG311 -0.53
    ATOM HH HGP1
    0.42
    GROUP
    ATOM CB CG321 -0.18
    ATOM HB1 HGA2
    0.09
    ATOM HB2 HGA2
    0.09
    GROUP
    ATOM CA CG321 -0.28
    ATOM HA1 HGA2
    0.09
    ATOM HA2 HGA2
    0.09
    ATOM CD CG2O3
    0.62
    ATOM OD1 OG2D2 -0.76
    ATOM OD2 OG2D2 -0.76
    BOND CG CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ
    BOND CG CD2 CD2 HD2 CD2 CE2 CE2 CC CE2 CZ

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CA
    CC
    C1
    C2
    CZ

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CD2
    C1
    C1
    CE2
    H1A
    H1A
    CE2
    H2A
    H2A
    CE1
    CE1
    CD2
    CD2
    CD2
    CG
    CG
    CG
    CB
    OD1

    CB
    HA1
    HC
    H1A
    H2A
    OH
    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CE2
    CE2
    CC
    CC
    CC
    CC
    CC
    CC
    CE2
    CZ
    CG
    CG
    CG
    CB
    CB
    CB
    CA
    CA

    CB
    CA
    CC
    C1
    C2
    OH
    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    CC
    *CC
    *CC
    C1
    *C1
    *C1
    C2
    *C2
    *C2
    *CZ
    OH
    CB
    CB
    CB
    CA
    CA
    CA
    CD
    *CD

    HB1
    HA2
    C1
    H1B
    H2B
    HH
    CZ
    CE2
    CD2
    CB
    HD1
    HD2
    HE1
    CC
    C1
    C2
    HC
    H1A
    H1B
    H1C
    H2A
    H2B
    H2C
    OH
    HH
    HB1
    HB2
    CA
    HA1
    HA2
    CD
    OD1
    OD2

    CB
    CA
    CC
    C1
    C2

    HB2 CB CA
    CD CD OD1 CD OD2
    C2
    H1C
    H2C
    1.4003
    1.4003
    1.3984
    1.4003
    1.4003
    1.4085
    1.3984
    1.4166
    1.4085
    1.5426
    1.5426
    1.5244
    1.1101
    1.1101
    1.5244
    1.1103
    1.1103
    1.3984
    1.3984
    1.4003
    1.4003
    1.4003
    1.5048
    1.5048
    1.5048
    1.5472
    1.2587

    119.98
    120.25
    120.56
    119.77
    119.98
    121.14
    120.25
    118.30
    119.43
    108.96
    108.96
    108.96
    110.22
    110.22
    109.20
    110.11
    110.11
    120.56
    117.60
    119.58
    119.58
    119.58
    109.99
    109.99
    109.99
    111.18
    117.29

    -0.26
    -0.01
    0.13
    -179.27
    -179.56
    179.42
    -179.58
    179.70
    -61.92
    122.45
    -118.75
    -177.62
    120.09
    -119.54
    177.34
    119.41
    -120.01
    179.54
    176.63
    -159.98
    -41.93
    79.08
    61.87
    -59.13
    -179.13
    124.07
    167.13

    120.25
    120.56
    118.30
    119.58
    119.47
    118.28
    119.97
    119.43
    108.96
    109.20
    112.03
    110.22
    110.82
    111.08
    110.11
    111.04
    110.78
    121.85
    106.54
    109.56
    108.74
    109.99
    110.80
    110.94
    111.18
    117.29
    117.17

    1.3984
    1.4166
    1.4085
    1.5048
    1.0801
    1.0793
    1.0797
    1.5244
    1.5426
    1.5429
    1.1131
    1.1101
    1.1111
    1.1110
    1.1103
    1.1107
    1.1110
    1.4123
    0.9574
    1.1132
    1.1119
    1.5472
    1.1089
    1.1090
    1.5290
    1.2587
    1.2586

    PRES FBIA
    0.00 ! CH3 Fatty acid Binding protein Inhibitor A, chayan
    ! This is a phenyl derivative having
    ! methyl at 2 and ethyl acetate at 4 position
    ! patch combination:
    ! core residue Compound "FBIB" >> Compound "FBIA"
    !
    DELETE ATOM CC
    !
    HD1 HE1
    DELETE ATOM HC

    DELETE ATOM C1

    (-0.5)OD1

    DELETE ATOM H1A

    DELETE ATOM H1B

    DELETE ATOM H1C

    DELETE ATOM C2
    DELETE ATOM H2A
    DELETE ATOM H2B
    DELETE ATOM H2C
    GROUP
    ATOM CM CG331
    ATOM HM1 HGA3

    !
    !
    !
    !
    !
    -0.27 !
    0.09 !

    (-0.5)OD2

    HA1 HB1
    |

    CD1--CE1
    //

    CD--CA--CB--CG

    \\

    HA2 HB2

    CZ--OH

    \ __ /
    CD2--CE2
    |
    |
    HD2 CM(Me)

    COMPOUND "FBIA"

    \
    HH

    ATOM HM2 HGA3


    ATOM HM3 HGA3

    0.09 !
    0.09 !

    BOND CE2 CM CM HM1 CM HM2 CM HM3


    IC
    IC
    IC
    IC

    CZ
    CD2
    HM1
    HM1

    CD2
    CE2
    CE2
    CE2

    *CE2
    CM
    *CM
    *CM

    CM
    HM1
    HM2
    HM3

    1.4166
    1.4085
    1.1426
    1.1426

    118.30
    119.43
    108.96
    108.96

    179.70
    -118.92
    122.45
    -118.75

    119.43
    108.96
    109.20
    112.03

    1.5244
    1.1426
    1.1429
    1.1131

    !PRES FBICR
    0.00 ! Fatty acid Binding protein Inhibitor, R-isomer, chaya
    n
    PRES FBICS
    0.00 ! C2H5 Fatty acid Binding protein Inhibitor, S-isomer, c
    hayan
    ! This is a phenyl derivative having
    ! 2-methyl ethyl acetate at 4 position
    ! core residue "FBIB" >> Compound "FBICR" or Compound "FBICS"
    ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration
    ! Specific configuration can be obtained by commenting/uncommenting correspondin
    g IC values
    ! as described in the IC table
    DELETE ATOM CB
    !
    HD1 HE1
    DELETE ATOM HB1
    !
    |
    |
    DELETE ATOM HB2
    ! (-0.5)OD1 HA1 CM
    CD1--CE1
    DELETE ATOM CC
    !
    \
    | |
    //
    \\
    DELETE ATOM HC
    !
    CD--CA--CBA--CG
    CZ--OH
    DELETE ATOM C1
    !
    /
    | |
    \ __ /
    \
    DELETE ATOM H1A
    ! (-0.5)OD2 HA2 HBA
    CD2--CE2
    HH
    DELETE ATOM H1B
    !
    |
    |
    DELETE ATOM H1C
    !
    HD2 HE2
    DELETE ATOM C2
    !
    DELETE ATOM H2A
    !
    COMPOUND "FBICR" OR "FBICS"
    DELETE ATOM H2B
    !
    DELETE ATOM H2C
    !
    GROUP
    !
    ATOM HE2 HGR61
    0.00 !
    GROUP
    !
    ATOM CBA CG311 -0.09 !
    ATOM HBA HGA1
    0.09 !
    ATOM CM CG331 -0.27 !
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    BOND CE2 HE2
    BOND CG CBA CBA HBA CBA CM CM HM1 CM HM2 CM HM3
    BOND CBA CA
    IC CZ CD2 *CE2 HE2
    IC CD1 CD2 *CG CBA
    !IC CD2 CG CBA CM
    !IC CD2 CG CBA HBA
    IC CD2 CG CBA CM
    IC CD2 CG CBA HBA
    IC CG CBA CM HM1
    IC HM1 CBA *CM HM2
    IC HM1 CBA *CM HM3
    !End fatty acid binding

    1.4028
    1.4029
    1.4036
    1.4036
    1.4036
    1.4036
    1.4978
    1.1093
    1.1093
    protein

    119.93 -179.94 119.66 1.0804


    119.56 179.52 120.59 1.4978
    120.59 178.00 110.88 1.1144 ! for r-isomer
    120.59 -60.83 109.72 1.5424 ! for r-isomer
    120.59 -60.83 109.72 1.5424 ! for s-isomer
    120.59 178.00 110.88 1.1144 ! for s-isomer
    109.72 65.78 111.17 1.1093
    111.17 120.55 110.04 1.1140
    111.17 -120.83 110.06 1.1096
    inhibitors, chayan, may2007

    !BCL-6 inhibitor project, kevo, may2007

    RESI 2PDO
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM O2
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    !End

    0.000 ! C4H7NO 2-pyrrolidinone, kevo


    NG2R53
    HGP1
    CG2R53
    OG2D1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    -0.58
    0.36
    0.30
    -0.49
    -0.01
    0.09
    0.09
    -0.19
    0.09
    0.09
    0.07
    0.09
    0.09

    ! H32
    H42
    !
    \
    /
    ! H31--C3----C4--H41
    !
    |
    |
    !
    C2
    C5--H51
    !
    // \ / \
    !
    O2 N1
    H52
    !
    |
    !
    H1

    N1 H1 C2 O2 C3 H31 C3 H32
    C4 H41 C4 H42 C5 H51 C5 H52
    N1 C2 C2 C3 C3 C4 C4 C5 C5
    C2 C3 N1 O2
    C5 N1 C2 C3 0.0000
    0.00
    0.00
    N1 C2 C3 C4 0.0000
    0.00 15.00
    C2 C5 *N1 H1 0.0000
    0.00 200.00
    C3 N1 *C2 O2 0.0000
    0.00 181.00
    C4 C2 *C3 H31 0.0000
    0.00 120.00
    C4 C2 *C3 H32 0.0000
    0.00 240.00
    C5 C3 *C4 H41 0.0000
    0.00 120.00
    C5 C3 *C4 H42 0.0000
    0.00 240.00
    N1 C4 *C5 H51 0.0000
    0.00 120.00
    N1 C4 *C5 H52 0.0000
    0.00 240.00
    BCL-6 inhibitor project, kevo, may2007

    N1
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Acyclic ethers from top_all27_carb_jul2o.inp


    RESI DMEE
    0.0000 ! C2H6O Dimethylether, viv 2006
    GROUP
    ATOM C1 CG331 -0.10 !
    H12
    H32
    ATOM H11 HGA3
    0.09 !
    |
    |
    ATOM H12 HGA3
    0.09 ! H11--C1---O2---C3--H31
    ATOM H13 HGA3
    0.09 !
    |
    |
    ATOM O2 OG301 -0.34 !
    H13
    H33
    ATOM C3 CG331 -0.10
    ATOM H31 HGA3
    0.09
    ATOM H32 HGA3
    0.09
    ATOM H33 HGA3
    0.09
    BOND C1 O2 O2
    BOND C1 H11 C1
    BOND C3 H31 C3
    IC C1 O2 C3
    IC H31 O2 *C3
    IC H31 O2 *C3
    IC C3 O2 C1
    IC H11 O2 *C1
    IC H11 O2 *C1
    RESI METE
    GROUP
    ATOM C1 CG331
    ATOM H11 HGA3
    ATOM H12 HGA3

    C3
    H12 C1 H13
    H32 C3 H33
    H31
    0.0000
    H32
    0.0000
    H33
    0.0000
    H11
    0.0000
    H12
    0.0000
    H13
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000 ! C3H8O Methyl ethyl ether, viv 2006


    -0.27 !
    H12 H21
    H42
    0.09 !
    |
    |
    |
    0.09 ! H11--C1---C2---O3---C4--H41

    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM O3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43

    HGA3
    CG321
    HGA2
    HGA2
    OG301
    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 C2 C2
    BOND C1 H11 C1
    BOND C2 H21 C2
    BOND C4 H41 C4
    IC C4 O3 C2
    IC C1 O3 *C2
    IC C1 O3 *C2
    IC C2 O3 C4
    IC H41 O3 *C4
    IC H41 O3 *C4
    IC O3 C2 C1
    IC H11 C2 *C1
    IC H11 C2 *C1
    RESI DETE
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM O3
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53

    0.09 !
    !
    -0.01
    0.09
    0.09
    -0.34
    -0.10
    0.09
    0.09
    0.09

    |
    |
    H13 H22

    O3 O3 C4
    H12 C1 H13
    H22
    H42 C4 H43
    C1
    0.0000
    H21
    0.0000
    H22
    0.0000
    H41
    0.0000
    H42
    0.0000
    H43
    0.0000
    H11
    0.0000
    H12
    0.0000
    H13
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    |
    H43

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000 ! C4H10O Diethylether, viv 2006


    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2
    OG301
    CG321
    HGA2
    HGA2

    -0.01
    0.09
    0.09
    -0.34
    -0.01
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    BOND C1 C2 C2
    BOND C1 H11 C1
    BOND C2 H21 C2
    BOND C4 H41 C4
    BOND C5 H51 C5
    IC C1 C2 O3
    IC C2 O3 C4
    IC H11 C2 *C1
    IC H11 C2 *C1
    IC H11 C1 C2
    IC O3 C1 *C2
    IC O3 C1 *C2
    IC C5 O3 *C4
    IC C5 O3 *C4
    IC O3 C4 C5

    !
    H11 H21
    H41 H51
    !
    |
    |
    |
    |
    ! H13--C1---C2---O3---C4---C5--H53
    !
    |
    |
    |
    |
    !
    H12 H22
    H42 H52

    O3 O3 C4 C4
    H12 C1 H13
    H22
    H42
    H52 C5 H53
    C4
    0.0000
    C5
    0.0000
    H12
    0.0000
    H13
    0.0000
    O3
    0.0000
    H21
    0.0000
    H22
    0.0000
    H41
    0.0000
    H42
    0.0000
    H51
    0.0000

    C5

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC H51 C4 *C5 H52


    IC H51 C4 *C5 H53
    RESI DME
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM O2
    ATOM C3
    ATOM H31
    ATOM H32
    GROUP
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM O5
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM H63

    0.0000
    0.0000

    0.00 120.00
    0.00 -120.00

    0.00
    0.00

    0.0000
    0.0000

    0.0000 ! C4H10O2 Dimethoxyethane, adm jr.


    CG331
    HGA3
    HGA3
    HGA3
    OG301
    CG321
    HGA2
    HGA2

    -0.10
    0.09
    0.09
    0.09
    -0.34
    -0.01
    0.09
    0.09

    CG321
    HGA2
    HGA2
    OG301
    CG331
    HGA3
    HGA3
    HGA3

    -0.01
    0.09
    0.09
    -0.34
    -0.10
    0.09
    0.09
    0.09

    BOND C1 H11 C1
    BOND C1 O2 O2
    BOND C3 H31 C3
    BOND C4 H41 C4
    BOND C4 O5 O5
    BOND C6 H61 C6
    IC C1 O2 C3
    IC H11 O2 *C1
    IC H11 O2 *C1
    IC H11 C1 O2
    IC C4 O2 *C3
    IC C4 O2 *C3
    o
    IC O2 C3 C4
    IC O5 C3 *C4
    IC O5 C3 *C4
    o
    IC C3 C4 O5
    IC C4 O5 C6
    IC H61 O5 *C6
    IC H61 O5 *C6
    RESI MPRE
    GROUP
    ATOM C1 CG331
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    ATOM O2 OG301
    ATOM C3 CG321
    ATOM H31 HGA2
    ATOM H32 HGA2
    GROUP
    ATOM C4 CG321
    ATOM H41 HGA2
    ATOM H42 HGA2
    GROUP

    ! H12 H11
    !
    \ /
    ! H13-C1 H31 H32 H61 H62
    !
    \ \ /
    \ /
    !
    O2--C3
    C6-H63
    !
    \
    /
    !
    H41-C4-O5
    !
    |
    !
    H42

    H12 C1 H13
    C3
    H32 C3 C4
    H42
    C6
    H62 C6 H63
    C4
    0.0000
    H12
    0.0000
    H13
    0.0000
    C3
    0.0000
    H31
    0.0000
    H32
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000 !corrected by kev

    O5
    H41
    H42

    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000 !corrected by kev

    C6
    H61
    H62
    H63

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    180.00
    180.00
    120.00
    -120.00

    0.0000 ! C4H10O Methyl Propyl Ether, 9/29/06 viv


    -0.10
    0.09
    0.09
    0.09
    -0.34
    -0.01
    0.09
    0.09
    -0.18
    0.09
    0.09

    !
    H11
    H31
    !
    |
    |
    ! H11 - C1 - O2 - C3 !
    |
    |
    !
    H12
    H32

    H41
    |
    C4 |
    H42

    H51
    |
    C5 - H53
    |
    H52

    ATOM
    ATOM
    ATOM
    ATOM

    C5
    H51
    H52
    H53

    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 H11 C1
    BOND O2 C3 C3
    BOND C4 H41 C4
    BOND C5 H51 C5
    IC O2 C3 C4
    IC C4 C3 O2
    IC O2 C4 *C3
    IC O2 C4 *C3
    IC C3 C5 *C4
    IC C3 C5 *C4
    IC C3 C4 C5
    IC C4 H51 *C5
    IC C4 H51 *C5
    IC C3 O2 C1
    IC H11 O2 *C1
    IC H11 O2 *C1
    RESI MBUE
    GROUP
    ATOM C1 CG331
    ATOM H11 HGA3
    ATOM H12 HGA3
    ATOM H13 HGA3
    ATOM O2 OG301
    ATOM C3 CG321
    ATOM H31 HGA2
    ATOM H32 HGA2
    GROUP
    ATOM C4 CG321
    ATOM H41 HGA2
    ATOM H42 HGA2
    GROUP
    ATOM C5 CG321
    ATOM H51 HGA2
    ATOM H52 HGA2
    GROUP
    ATOM C6 CG331
    ATOM H61 HGA3
    ATOM H62 HGA3
    ATOM H63 HGA3
    BOND C1 H11 C1
    BOND O2 C3 C3
    BOND C4 H41 C4
    BOND C5 H51 C5
    BOND C6 H61 C6
    IC O2 C3 C4
    IC C4 C3 O2
    IC C3 C4 C5
    IC O2 C4 *C3
    IC O2 C4 *C3
    IC C3 C5 *C4
    IC C3 C5 *C4
    IC C4 C6 *C5
    IC C4 C6 *C5

    -0.27
    0.09
    0.09
    0.09
    H12
    H31
    H42
    H52
    C5
    C1
    H31
    H32
    H41
    H42
    H51
    H52
    H53
    H11
    H12
    H13

    C1
    C3
    C4
    C5

    H13 C1
    H32 C3
    C5
    H53
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    O2
    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000 ! C5H12O Methyl Butyl Ether, 9/30/06 viv


    -0.10
    0.09
    0.09
    0.09
    -0.34
    -0.01
    0.09
    0.09

    !
    H11
    H31
    !
    |
    |
    ! H11 - C1 - O2 - C3 !
    |
    |
    !
    H12
    H32

    H41
    |
    C4 |
    H42

    H51 H6A
    | |
    C5 - C6 - H6C
    | |
    H52 H6B

    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    H12
    H31
    H42
    H52
    H62
    C5
    C1
    C6
    H31
    H32
    H41
    H42
    H51
    H52

    C1
    C3
    C4
    C5
    C6

    H13 C1
    H32 C3
    C5
    C6
    H63
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    O2
    C4

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC

    C4
    C5
    C5
    C3
    H11
    H11

    C5
    H61
    H61
    O2
    O2
    O2

    RESI EPRE
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM O3
    ATOM C4
    ATOM H41
    ATOM H42
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM H63

    C6
    *C6
    *C6
    C1
    *C1
    *C1

    H61
    H62
    H63
    H11
    H12
    H13

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000 ! C5H12O Ethyl propyl ether, viv 9/30/06


    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2
    OG301
    CG321
    HGA2
    HGA2

    -0.01
    0.09
    0.09
    -0.34
    -0.01
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    BOND C1 C2 C2
    BOND C4 C5 C5
    BOND C1 H11 C1
    BOND C2 H21 C2
    BOND C4 H41 C4
    BOND C5 H51 C5
    BOND C6 H61 C6
    IC C2 O3 C4
    IC C4 O3 C2
    IC O3 C4 C5
    IC C1 O3 *C2
    IC C1 O3 *C2
    IC O3 C5 *C4
    IC O3 C5 *C4
    IC C4 C6 *C5
    IC C4 C6 *C5
    IC C4 C5 C6
    IC C5 H61 *C6
    IC C5 H61 *C6
    IC O3 C2 C1
    IC H11 C2 *C1
    IC H11 C2 *C1

    !
    !
    !
    !
    !

    H11 H21
    H41 H51 H61
    |
    |
    |
    |
    |
    H13 - C1 - C2 - O3 - C4 - C5 - C6 - H63
    |
    |
    |
    |
    |
    H12 H22
    H42 H52 H62

    O3 O3 C4
    C6
    H12 C1 H13
    H22
    H42
    H52
    H62 C6 H63
    C5
    0.0000
    C1
    0.0000
    C6
    0.0000
    H21
    0.0000
    H22
    0.0000
    H41
    0.0000
    H42
    0.0000
    H51
    0.0000
    H52
    0.0000
    H61
    0.0000
    H62
    0.0000
    H63
    0.0000
    H11
    0.0000
    H12
    0.0000
    H13
    0.0000

    !<<<<<<<<<<<<PEG>>>>>>>>>>>>
    DECL -C2
    DECL -O1
    DECL +C1
    AUTOGENERATE ANGLE DIHE
    DEFAULT FIRST HYD1 LAST HYD2

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI PEGM
    2006
    GROUP
    ATOM C1
    ATOM H12
    ATOM H11
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22

    0.0000 ! C2H4O Peg monomer for polymer construction, viv Nov


    CG321 -0.01
    HGA2
    0.09 !
    H11
    H21
    HGA2
    0.09 !
    |
    |
    OG301 -0.34 ! (-C2) - C1 - O1 - C2 CG321 -0.01 !
    |
    |
    HGA2
    0.09 !
    H12
    H22
    HGA2
    0.09

    BOND C1 H11 C1 H12


    BOND O1 C2
    C2 H21
    BOND C1 -C2
    IC -O1 -C2 C1 O1
    IC -C2 C1 O1 C2
    IC C1 O1 C2 +C1
    IC -C2 O1 *C1 H11
    IC -C2 O1 *C1 H12
    IC O1 +C1 *C2 H21
    IC O1 +C1 *C2 H22
    PRES
    ATOM
    ATOM
    ATOM
    ATOM

    HYD1
    H13
    C1
    H11
    H12

    HGA3
    CG331
    HGA3
    HGA3

    HYD2
    H23
    C2
    H21
    H22

    HGA3
    CG331
    HGA3
    HGA3

    ATOM
    ATOM
    ATOM
    ATOM

    CE
    HE1
    HE2
    HE3

    BOND CE
    IC C2
    IC CE
    IC CE
    IC O1
    IC HE3
    IC HE3

    CG331
    HGA3
    HGA3
    HGA3
    C1
    O1
    O1
    O1
    C1
    C1
    C1

    CE
    C1
    *C1
    *C1
    CE
    *CE
    *CE

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    0.1700 ! CH3 Complete terminal methyl group adjacent to OCE


    0.09
    -0.10 ! H23 0.09
    0.09

    BOND H23 C2
    IC C1 O1 C2 H23
    IC O1 H23 *C2 H21
    IC O1 H23 *C2 H22
    PRES MET1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.1700 ! CH3 Complete terminal methyl group adjacent to OCE


    0.09
    -0.10 ! H13 0.09
    0.09

    BOND H13 C1
    IC C2 O1 C1 H13
    IC H13 O1 *C1 H11
    IC H13 O1 *C1 H12
    PRES
    ATOM
    ATOM
    ATOM
    ATOM

    C1 O1
    C2 H22

    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    0.0000 ! CH3 Append terminal methyl group adjacent to CH2


    !
    HE2
    -0.27 !
    |
    0.09 ! HE3 - CE 0.09 !
    |
    0.09 !
    HE1
    HE1 CE HE2 CE HE3
    CE
    0.0000
    0.00
    H11
    0.0000
    0.00
    H12
    0.0000
    0.00
    HE3
    0.0000
    0.00
    HE1
    0.0000
    0.00
    HE2
    0.0000
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    PRES MET2
    ATOM
    ATOM
    ATOM
    ATOM

    CA
    HA1
    HA2
    HA3

    CG331
    HGA3
    HGA3
    HGA3

    0.0000 ! CH3 Append terminal methyl group adjacent to CH2


    !
    HA3
    -0.27 !
    |
    0.09 ! HA2 - CA 0.09 !
    |
    0.09 !
    HA1

    BOND CA C2
    IC C1 O1
    IC O1 CA
    IC O1 CA
    IC C1 C2
    IC C2 HA3
    IC C2 HA3

    CA
    C2
    *C2
    *C2
    CA
    *CA
    *CA

    HA1 CA HA2 CA HA3


    CA
    0.0000
    0.00
    H21
    0.0000
    0.00
    H22
    0.0000
    0.00
    HA3
    0.0000
    0.00
    HA1
    0.0000
    0.00
    HA2
    0.0000
    0.00

    180.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    DEFAULT FIRST NONE LAST NONE


    !<<<<<<<<<<<</PEG>>>>>>>>>>>>
    !End acyclic ethers from top_all27_carb_jul2o.inp
    !New compounds from the sugar force field
    RESI ACO
    0.0000 ! C3H6O Acetone, adm, Oct 08
    GROUP
    ATOM O1 OG2D3 -0.48
    ATOM C1 CG2O5
    0.40
    ATOM C2 CG331 -0.23 !
    O1
    ATOM C3 CG331 -0.23 !
    ||
    ATOM H21 HGA3
    0.09 !
    C1
    ATOM H22 HGA3
    0.09 !
    / \
    ATOM H23 HGA3
    0.09 !
    H21--C2
    C3--H31
    ATOM H31 HGA3
    0.09 !
    / |
    | \
    ATOM H32 HGA3
    0.09 !
    H22 H32 H33 H32
    ATOM H33 HGA3
    0.09
    BOND
    BOND
    BOND
    DOUBLE
    IMPR
    ACCE
    IC C2
    IC O1
    IC O1
    IC O1
    IC C3
    IC O1
    IC O1
    IC O1

    C1
    C2
    C3
    O1
    C1
    O1
    C1
    C1
    C1
    C1
    C1
    C1
    C1
    C1

    RESI IPAA
    GROUP
    ATOM CL
    ATOM HL1
    ATOM HL2
    ATOM HL3
    GROUP
    ATOM C
    ATOM O
    ATOM N
    ATOM H
    ATOM CR

    C2 C1 C3
    H21 C2 H22
    H31 C3 H32
    C1
    C2 C3 O1
    C3
    C3
    C3
    C3
    C2
    C2
    C2
    C2

    CG331
    HGA3
    HGA3
    HGA3
    CG2O1
    OG2D1
    NG2S1
    HGP1
    CG311

    H31
    H31
    H32
    H33
    H21
    H21
    H22
    H23

    C2 H23
    C3 H33

    1.5366
    1.2237
    1.2237
    1.2237
    1.5233
    1.2237
    1.2237
    1.2237

    110.58
    122.95
    122.95
    122.95
    110.58
    126.42
    126.42
    126.42

    135.22
    -42.47
    77.28
    -161.85
    -153.74
    23.85
    148.26
    -90.21

    109.51
    109.51
    104.63
    105.76
    111.52
    111.52
    114.11
    101.67

    1.1328
    1.1328
    1.1325
    1.0732
    1.1204
    1.1204
    1.1296
    1.1375

    0.00 ! C5H11NO og isopropyl acetamide, based on NMA


    !
    n.b.: CL, HL, CR, HR vdw params != c22
    -0.27 ! ??? this molecule needs optimization
    0.09
    0.09 !
    H211 H212 H213
    0.09 !
    \ | /
    !
    C21
    0.51 !
    HL1\
    O
    /
    -0.51 !
    HL2-- CL -- C -- N -- CR --HR
    -0.47 !
    HL3/
    H
    \
    0.31 !
    C22
    0.07 !
    / | \

    ATOM HR HGA1
    GROUP
    ATOM C21 CG331
    ATOM H211 HGA3
    ATOM H212 HGA3
    ATOM H213 HGA3
    GROUP
    ATOM C22 CG331
    ATOM H221 HGA3
    ATOM H222 HGA3
    ATOM H223 HGA3
    BOND HL1 CL HL2
    BOND CL C
    C
    BOND N H
    BOND HR CR C21
    BOND C21 H211 C21
    BOND C22 H221 C22
    DOUBLE C O
    IMPR N C CR H
    IMPR C CL N O
    !
    I
    J
    K
    IC O
    C
    N
    IC H
    N
    C
    IC O
    C
    N
    IC N
    C
    CL
    IC N
    C
    CL
    IC N
    C
    CL
    IC C
    N
    CR
    IC C
    N
    CR
    IC C
    N
    CR
    IC N
    CR C21
    IC N
    CR C21
    IC N
    CR C21
    IC N
    CR C22
    IC N
    CR C22
    IC N
    CR C22

    0.09 !

    H221 H222 H223

    -0.27
    0.09
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    CL HL3 CL
    N
    N CR
    CR C22 CR
    H212 C21 H213
    H222 C22 H223

    L
    H
    CL
    CR
    HL1
    HL2
    HL3
    HR
    C21
    C22
    H211
    H212
    H213
    H221
    H222
    H223

    RESI AMOP
    -1.00 !
    GROUP
    ATOM C1 CG311 -0.02 !
    ATOM C2 CG2O3
    0.62 !
    ATOM H1 HGA1
    0.09 !
    ATOM OM OG301 -0.34 !
    ATOM CM CG331 -0.10 !
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    ATOM O1 OG2D2 -0.76 !
    ATOM O2 OG2D2 -0.76 !
    GROUP
    !
    ATOM C0 CG331 -0.27 !
    ATOM H01 HGA3
    0.09 !
    ATOM H02 HGA3
    0.09 !
    ATOM H03 HGA3
    0.09 !
    BOND C1 H1 C1 OM C1 C0
    BOND C1 C2 C2 O1
    BOND C0 H01 C0 H02 C0 H03
    BOND OM CM
    BOND CM HM1 CM HM2 CM HM3
    DOUBLE C2 O2

    R(IK)
    1.2240
    0.9902
    1.2240
    1.3414
    1.3414
    1.3414
    1.3414
    1.3414
    1.3414
    1.4315
    1.4315
    1.4315
    1.4315
    1.4315
    1.4315

    T(IKJ)
    124.40
    118.74
    124.40
    115.46
    115.46
    115.46
    125.23
    125.23
    125.23
    112.40
    112.40
    112.40
    112.40
    112.40
    112.40

    PHI
    -180.00
    0.00
    0.00
    180.00
    60.56
    -60.56
    180.00
    64.21
    -64.21
    53.31
    -66.48
    173.88
    66.48
    -53.31
    -173.88

    T(JKL)
    118.74
    115.46
    125.23
    109.20
    110.24
    110.24
    105.39
    112.40
    112.40
    110.44
    110.16
    110.46
    110.16
    110.44
    110.46

    R(KL)
    0.9902
    1.4817
    1.4315
    1.1119
    1.1102
    1.1102
    1.1185
    1.5343
    1.5343
    1.1098
    1.1110
    1.1098
    1.1110
    1.1098
    1.1098

    C4H7O3 alpha-methoxy-propionic acid, og


    CT1 HM1 HM2 HM3
    CC
    \ | /
    HA
    CM
    ethers
    |
    CT3
    OM
    O1 (-)
    HA
    |
    /
    HA
    H1--C1--C2
    HA
    |
    \\
    OC
    |
    O2
    OC H01--C0
    | \
    CT3
    H02 H03
    HA
    HA
    HA

    IMPR C2 C1 O2 O1
    IC C2
    C1
    OM
    CM
    IC OM
    C2
    *C1 C0
    IC OM
    C2
    *C1 H1
    IC C1
    OM
    CM
    HM1
    IC HM1 OM
    *CM HM2
    IC HM1 OM
    *CM HM3
    IC H1
    C1
    C2
    O1
    IC O1
    C1
    *C2 O2
    IC H1
    C1
    C0
    H01
    IC H01 C1
    *C0 H02
    IC H01 C1
    *C0 H03
    PATC FIRS NONE LAST NONE
    !End new compounds from the

    1.5370
    1.4224
    1.4224
    1.4224
    1.1106
    1.1106
    1.1094
    1.2599
    1.1094
    1.1106
    1.1106

    107.76
    107.76
    107.76
    111.65
    109.96
    109.96
    106.67
    118.57
    109.13
    109.93
    109.93

    -154.77
    123.63
    -117.54
    60.37
    -120.84
    119.38
    177.14
    -179.67
    -60.43
    -118.90
    120.54

    111.65
    111.13
    106.67
    109.96
    110.46
    109.38
    118.57
    117.64
    109.93
    109.59
    111.13

    1.4194
    1.5565
    1.1094
    1.1106
    1.1094
    1.1097
    1.2599
    1.2609
    1.1106
    1.1115
    1.1077

    sugar force field

    !Special project, og, feb2008


    RESI CUME
    0.0000 ! C9H12 Cumene (aka. isopropylbenzene), Olgun Guvench
    GROUP
    ATOM CA1 CG2R61 -0.115 !
    HA1
    ATOM HA1 HGR61
    0.115 !
    |
    GROUP
    !
    CA1
    ATOM CA2 CG2R61 -0.115 !
    // \
    ATOM HA2 HGR61
    0.115 ! HA6--CA6
    CA2--HA2
    GROUP
    !
    |
    ||
    ATOM CA3 CG2R61 -0.115 !
    |
    ||
    ATOM HA3 HGR61
    0.115 ! HA5--CA5
    CA3--HA3
    GROUP
    !
    \\ /
    ATOM CA4 CG2R61 0.0 !
    CA4
    GROUP
    !
    |
    ATOM CA5 CG2R61 -0.115 !
    |
    ATOM HA5 HGR61
    0.115 !
    |
    GROUP
    !
    -------C4-------ATOM CA6 CG2R61 -0.115 !
    |
    |
    |
    ATOM HA6 HGR61
    0.115 !
    |
    H41
    |
    GROUP
    ! H52-C5-H51
    H31-C3-H32
    ATOM C4 CG311 -0.09 !
    |
    |
    ATOM H41 HGA1
    0.09 !
    H53
    H33
    GROUP
    ATOM C3 CG331 -0.27
    ATOM H31 HGA3
    0.09
    ATOM H32 HGA3
    0.09
    ATOM H33 HGA3
    0.09
    GROUP
    ATOM C5 CG331 -0.27
    ATOM H51 HGA3
    0.09
    ATOM H52 HGA3
    0.09
    ATOM H53 HGA3
    0.09
    BOND CA1 HA1
    BOND CA1 CA2 CA2 HA2
    BOND CA3 HA3 CA3 CA4
    BOND CA5 HA5 CA5 CA6
    BOND CA6 HA6
    DOUBLE CA6 CA1 CA4 CA5 CA2 CA3
    BOND C3 H31 C3 H32 C3 H33
    BOND CA4 C4
    BOND C3 C4
    BOND C4 H41
    BOND C4 C5
    BOND C5 H51 C5 H52 C5 H53
    IC CA6 HA1 *CA1 CA2
    1.4195 121.85 177.84 121.53 1.4194

    IC HA1 CA1 CA2 CA3


    IC CA3 CA1 *CA2 HA2
    IC CA1 CA2 CA3 CA4
    IC CA4 CA2 *CA3 HA3
    IC HA1 CA1 CA6 CA5
    IC CA5 CA1 *CA6 HA6
    IC CA4 CA6 *CA5 HA5
    IC CA5 CA3 *CA4 C4
    IC CA3 CA4 C4 C3
    IC C3 CA4 *C4 C5
    IC C3 CA4 *C4 H41
    IC CA4 C4 C3 H31
    IC H31 C4 *C3 H32
    IC H31 C4 *C3 H33
    IC CA4 C4 C5 H51
    IC H51 C4 *C5 H52
    IC H51 C4 *C5 H53
    PATCHING FIRST NONE LAST

    1.0800
    1.3982
    1.4194
    1.4029
    1.0800
    1.3985
    1.4036
    1.4036
    1.4029
    1.5411
    1.5411
    1.5147
    1.1098
    1.1098
    1.5147
    1.1098
    1.1098
    NONE

    121.53
    121.60
    121.60
    120.92
    121.85
    121.61
    120.87
    118.40
    120.23
    109.64
    109.64
    109.64
    110.17
    110.17
    109.66
    110.16
    110.16

    -178.93
    -179.91
    0.43
    179.85
    178.93
    179.93
    -179.85
    179.75
    0.00
    -124.08
    117.96
    176.65
    119.90
    -119.93
    -176.66
    119.93
    -119.89

    121.60
    119.41
    120.92
    119.25
    121.61
    119.45
    119.09
    120.23
    109.64
    109.66
    107.55
    110.17
    110.84
    110.47
    110.16
    110.47
    110.84

    1.3982
    1.0825
    1.4029
    1.0788
    1.3985
    1.0824
    1.0786
    1.5147
    1.5411
    1.5411
    1.1143
    1.1098
    1.1103
    1.1115
    1.1098
    1.1114
    1.1103

    RESI BSAT
    -1.0000 ! C6H5O3S Benzenesulfonate, Olgun Guvench
    GROUP
    ATOM S
    SG3O1
    1.35 !
    O1
    ATOM O1 OG2P1 -0.65 !
    |
    ATOM O2 OG2P1 -0.65 !
    O2--S--O3
    ATOM O3 OG2P1 -0.65 !
    |
    ATOM CA1 CG2R61 -0.40 !
    CA1
    GROUP
    !
    // \
    ATOM CA2 CG2R61 -0.21 ! HA6--CA6
    CA2--HA2
    ATOM HA2 HGR61
    0.21 !
    |
    ||
    GROUP
    !
    |
    ||
    ATOM CA3 CG2R61 -0.115 ! HA5--CA5
    CA3--HA3
    ATOM HA3 HGR61
    0.115 !
    \\ /
    GROUP
    !
    CA4
    ATOM CA4 CG2R61 -0.115 !
    |
    ATOM HA4 HGR61
    0.115 !
    HA4
    GROUP
    ATOM CA5 CG2R61 -0.115
    ATOM HA5 HGR61
    0.115
    GROUP
    ATOM CA6 CG2R61 -0.21
    ATOM HA6 HGR61
    0.21
    BOND S O1 S O2 S O3
    BOND S CA1
    BOND CA1 CA2 CA2 HA2
    BOND CA3 HA3 CA3 CA4
    BOND CA4 HA4
    BOND CA5 HA5 CA5 CA6
    BOND CA6 HA6
    DOUBLE CA6 CA1 CA4 CA5 CA2 CA3
    ACCEPTOR O1 S
    ACCEPTOR O2 S
    ACCEPTOR O3 S
    IC O1 CA1 *S O2
    1.4520 103.94 119.83 106.18 1.4544
    IC O1 CA1 *S O3
    1.4520 103.94 -119.70 105.93 1.4543
    IC O1 S
    CA1 CA6
    1.4520 103.94 -90.93 121.85 1.4195
    IC CA6 S
    *CA1 CA2
    1.4195 121.85 177.84 121.53 1.4194
    IC S
    CA1 CA2 CA3
    1.6322 121.53 -178.93 121.60 1.3982
    IC CA3 CA1 *CA2 HA2
    1.3982 121.60 -179.91 119.41 1.0825
    IC CA1 CA2 CA3 CA4
    1.4194 121.60
    0.43 120.92 1.4029
    IC CA4 CA2 *CA3 HA3
    1.4029 120.92 179.85 119.25 1.0788

    IC S
    CA1 CA6 CA5
    1.6322 121.85
    IC CA5 CA1 *CA6 HA6
    1.3985 121.61
    IC CA4 CA6 *CA5 HA5
    1.4036 120.87
    IC CA5 CA3 *CA4 HA4
    1.4036 118.40
    PATCHING FIRST NONE LAST NONE
    !End special project, og, feb2008

    178.93
    179.93
    -179.85
    179.75

    121.61
    119.45
    119.09
    120.23

    1.3985
    1.0824
    1.0786
    1.0800

    !Polli's bile acids, chayan, feb2008


    RESI 2MPA
    1.00 ! C8H17N2O 2-Methyl Piperidine Amide
    ! Made in order to build Polli's compounds (Pablo)
    GROUP
    !
    ATOM CG1 CG314
    0.29 !
    ATOM HG1 HGA1
    0.09 !
    HG21 HG22
    ATOM NG2 NG3P2 -0.40 !
    \ /
    ATOM HG21 HGP2
    0.32 !
    OG HT
    (+1)NG2--CG3
    ATOM HG22 HGP2
    0.32 !
    || |
    /
    \
    ATOM CG3 CG324
    0.20 !
    CG---NT--CGT--CG1
    CG4
    ATOM HG31 HGA2
    0.09 !
    /
    \
    /
    ATOM HG32 HGA2
    0.09 ! HM1--CM--HM3
    CG6--CG5
    GROUP
    !
    |
    ATOM CG4 CG321 -0.18 !
    HM2
    ATOM HG41 HGA2
    0.09 !
    ATOM HG42 HGA2
    0.09 !
    2MPA
    GROUP
    !
    ATOM CG5 CG321 -0.18 !
    ATOM HG51 HGA2
    0.09 !
    ATOM HG52 HGA2
    0.09 !
    GROUP
    !
    ATOM CG6 CG321 -0.18 !
    ATOM HG61 HGA2
    0.09 !
    ATOM HG62 HGA2
    0.09 !
    GROUP
    ATOM CM CG331 -0.27 !
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    ATOM HT HGP1
    0.47 !
    GROUP
    !
    ATOM CGT CG321 -0.18 !
    ATOM HGT1 HGA2
    0.09 !
    ATOM HGT2 HGA2
    0.09 !
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CM
    CG
    NT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    NT

    HM1
    OG
    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG

    IC CM
    CG
    IC CG
    NT
    IC HGT1 NT

    CM
    CG
    CGT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    CGT

    HM2
    NT
    HGT1
    NG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HT

    CM HM3 CM CG
    NT HT
    CGT HGT2 CGT CG1

    NT
    CGT
    CGT HGT1
    *CGT HGT2

    NG2
    CG3
    CG4
    CG5
    CG6

    CG3
    CG4
    CG5
    CG6
    CG1
    1.4784 116.17 178.50 125.70
    1.3412 125.70 -174.52 107.65
    1.1160 107.65 114.70 109.82

    1.4627
    1.1160
    1.1155

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HGT1
    NT
    HM1
    HM1
    CM
    OG
    CG
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    CG4
    CG4
    NG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    NT
    CG
    CG
    CG
    NT
    CG
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    NG2
    NG2
    NG2
    CG3
    CG3
    CG3
    CG4
    CG4
    CG4
    CG1
    CG1

    *CGT
    CM
    *CM
    *CM
    *CG
    NT
    CGT
    CG1
    *CG1
    *CG1
    NG2
    *NG2
    *NG2
    CG3
    *CG3
    *CG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    CG1
    HM1
    HM2
    HM3
    OG
    HT
    CG1
    HG1
    NG2
    CG6
    CG3
    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    !Pablo's Compounds
    RESI BPIP
    1.00
    n
    GROUP
    ATOM CB CG324
    0.15
    ATOM HB1 HGA2
    0.09
    ATOM HB2 HGA2
    0.09
    ATOM N1 NG3P1
    -0.40
    ATOM H1 HGP2
    0.32
    ATOM C2 CG324
    0.15
    ATOM H21 HGA2
    0.09
    ATOM H22 HGA2
    0.09
    ATOM C6 CG324
    0.15
    ATOM H61 HGA2
    0.09
    ATOM H62 HGA2
    0.09
    GROUP
    ATOM C3 CG321
    -0.18
    ATOM H31 HGA2
    0.09
    ATOM H32 HGA2
    0.09
    GROUP
    ATOM C4 CG321
    -0.18
    ATOM H41 HGA2
    0.09
    ATOM H42 HGA2
    0.09
    GROUP
    ATOM C5 CG321
    -0.18
    ATOM H51 HGA2
    0.09
    ATOM H52 HGA2
    0.09
    GROUP
    ATOM CZ CG2R61 0.090
    GROUP
    ATOM CD1 CG2R61 -0.115
    ATOM HD1 HGR61
    0.115
    GROUP

    1.1160
    1.3412
    1.1111
    1.1111
    1.4784
    1.2240
    1.3412
    1.4627
    1.1056
    1.1056
    1.5494
    1.5001
    1.5001
    1.5010
    1.5313
    1.5313
    1.5001
    1.5394
    1.5394
    1.5313
    1.5411
    1.5411
    1.5411
    1.5411

    107.65
    116.17
    110.69
    110.69
    116.17
    122.13
    125.70
    116.84
    109.99
    109.99
    109.74
    115.30
    115.30
    115.30
    108.63
    108.63
    108.63
    110.88
    110.88
    110.88
    111.72
    111.72
    110.92
    110.92

    -119.46
    -62.83
    -119.06
    121.66
    170.21
    175.26
    66.02
    36.30
    -114.94
    124.49
    176.09
    122.39
    -125.48
    59.26
    122.04
    -121.53
    -54.12
    120.82
    -121.31
    54.58
    121.65
    -121.21
    -121.44
    120.54

    116.84
    110.69
    109.32
    110.83
    122.13
    115.36
    116.84
    109.99
    109.74
    113.69
    115.30
    107.69
    107.03
    108.63
    105.77
    105.49
    110.88
    109.89
    109.72
    111.72
    109.56
    109.32
    110.01
    109.46

    1.5494
    1.1111
    1.1131
    1.1107
    1.2240
    0.9985
    1.5494
    1.1056
    1.5010
    1.5350
    1.5001
    1.0058
    1.0184
    1.5313
    1.1032
    1.1034
    1.5394
    1.1138
    1.1134
    1.5411
    1.1147
    1.1144
    1.1127
    1.1130

    ! C12H18N Model compound for N-benzyl piperidine, chaya


    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    C3---C2
    /

    CD1--CE1
    //
    \\

    C4

    N1--CB--CZ
    \

    /
    C5---C6
    BPIP

    CP
    \

    __ /
    CD2--CE2

    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CP
    ATOM HP

    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    H1
    C3
    C4
    C5
    C6
    CB
    CD1
    CD2
    CP

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1
    C2
    C3
    C4
    C5
    N1
    CZ
    CZ
    CE1
    C6
    N1
    C2
    C3
    C2
    HB1
    HB1
    HB1
    C6
    C2
    C3
    H21
    C5
    C5
    C4
    H31
    C5
    H41
    C4
    C4
    C2
    N1
    N1
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    N1
    C2
    C3
    C4
    C6
    N1
    N1
    CB
    CB
    CB
    N1
    N1
    N1
    N1
    C2
    C2
    C3
    C3
    C6
    C6
    N1
    CB
    CB
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2

    N1
    C3
    C4
    C5
    C6
    CB
    CD1
    CD2
    CP
    C2
    C3
    C4
    C5
    *N1
    *CB
    *CB
    N1
    *N1
    *N1
    *C2
    *C2
    *C6
    *C6
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    CB
    CZ
    CZ
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP

    C2
    H31
    H41
    H51
    H61
    HB1
    HD1
    HD2
    HP
    C3
    C4
    C5
    C6
    CB
    HB2
    CZ
    C6
    C2
    H1
    H21
    H22
    H61
    H62
    H31
    H32
    H41
    H42
    H51
    H52
    CZ
    CD2
    CD1
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP

    C2
    C3
    C4
    C5
    C6
    CB
    CD1
    CD2
    CP

    H21
    H32
    H42
    H52
    H62
    HB2
    CE1
    CE2
    CE2
    1.5157
    1.5157
    1.5319
    1.5362
    1.5157
    1.1028
    1.1028
    1.1028
    1.5157
    1.5157
    1.5319
    1.1025
    1.5319
    1.5319
    1.5362
    1.1137
    1.5362
    1.1145
    1.5362
    1.5362
    1.5157
    1.5015
    1.5015
    1.4109
    1.4109
    1.4109
    1.4889
    1.4889
    1.4109
    1.4001
    1.3993
    1.4001
    1.4001
    1.3993
    1.3993
    1.3993

    C2

    H22

    C6
    CB
    CE1
    CE2

    N1
    CZ
    HE1
    HE2

    110.13
    110.11
    110.44
    111.24
    110.13
    107.08
    107.08
    107.08
    116.61
    116.61
    110.11
    105.72
    110.11
    110.11
    110.44
    109.65
    111.24
    109.83
    110.44
    110.44
    116.61
    107.59
    107.59
    118.75
    120.51
    120.51
    120.51
    120.51
    120.52
    120.00
    120.12
    120.52
    120.52
    120.00
    120.00
    120.12

    -60.42
    57.37
    -54.84
    54.84
    135.82
    -120.06
    119.97
    173.55
    132.96
    113.52
    121.51
    116.75
    121.75
    -121.51
    120.70
    118.12
    -121.82
    -117.39
    121.18
    -120.70
    66.48
    -92.75
    92.75
    -174.60
    24.38
    150.12
    177.83
    -177.83
    -1.31
    -0.66
    0.66
    -179.79
    179.79
    -179.18
    179.18
    178.89

    110.11
    110.44
    111.24
    110.44
    116.61
    107.08
    107.59
    116.61
    116.61
    105.15
    105.72
    105.78
    105.78
    105.72
    109.65
    110.23
    109.83
    109.30
    110.23
    109.65
    107.59
    120.51
    120.51
    120.51
    111.50
    111.50
    120.52
    120.52
    120.00
    120.12
    120.00
    120.55
    120.55
    120.30
    120.30
    119.94

    1.5319
    1.5362
    1.5362
    1.5319
    1.5015
    1.1028
    1.4889
    1.5157
    1.5157
    1.0496
    1.1025
    1.1018
    1.1018
    1.1025
    1.1137
    1.1131
    1.1145
    1.1147
    1.1131
    1.1137
    1.4889
    1.4109
    1.4109
    1.4889
    1.1028
    1.1028
    1.4001
    1.4001
    1.3993
    1.3993
    1.4001
    1.0802
    1.0802
    1.0822
    1.0822
    1.0821

    PRES BPAB
    1.00 ! C22H26N2O3 Gamma N-benzyl piperidine, alpha benzyl CDC
    A amide (010201P), chayan
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    OG
    CG
    3--CG3
    CJ1--CK1
    ATOM CG CG2O1
    0.51 !
    ||
    /
    \
    //
    \\
    ATOM OG OG2D1 -0.51 !
    CG---NT--CG4
    NG1(+1) CY
    CQ
    ATOM NT NG2S1 -0.47 !
    /
    HT1 \
    / \ / \ __ /
    ATOM HT1 HGP1
    0.47 !
    CC3
    CG
    5--CG6
    CBG CJ2--CK2
    GROUP
    !
    \
    ATOM CG4 CG311

    -0.09 !

    O24

    CC2

    ATOM HG4 HGA1

    0.09 !

    ||

    GROUP

    !
    CD1--CE1
    ATOM CG3 CG321 -0.18 !
    //
    \\
    ATOM HG31 HGA2
    0.09 !
    CB--CZ
    CP
    ATOM HG32 HGA2
    0.09 !
    \ __ /
    GROUP
    !
    CD2--CE2
    ATOM CG2 CG324 0.15 !
    ATOM HG21 HGA2

    0.09 !

    ATOM HG22 HGA2

    0.09 !

    H
    |

    Me19 |

    HGP2

    0.32 !

    ATOM CBG

    CG324

    0.15 !

    C3

    C5

    C7

    ATOM HBG1 HGA2

    0.09 !

    ATOM HBG2 HGA2

    0.09 ! HO

    ATOM CG6

    0.15 !

    CG321
    HGA2
    HGA2

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG2R61

    0.090

    CG2R61 -0.115
    HGR61
    0.115

    C14

    C16

    / \|/ \ / \ /

    ATOM HG1

    HGA2

    C23

    C1 | C9

    C10 C8

    ATOM HG62
    GROUP
    ATOM CG5
    ATOM HG51
    ATOM HG52
    GROUP
    ATOM CY
    GROUP
    ATOM CJ1
    ATOM HJ1

    C20

    C11 C13---C17

    C2

    0.09 !

    C24

    C15

    / \ / \ / \
    C4

    C6

    CC1

    \ / \ / \ / \

    / \ |

    NG3P1 -0.40 !

    ATOM HG61 HGA2

    C22

    C12 Me18

    ATOM NG1

    CG324

    Me21

    OH

    BPAB (010201P)

    NH

    CA---OA2--||
    OA1

    GROUP
    ATOM CJ2
    ATOM HJ2
    GROUP
    ATOM CK1
    ATOM HK1
    GROUP
    ATOM CK2
    ATOM HK2
    GROUP
    ATOM CQ
    ATOM HQ
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CY
    CQ
    OA2
    CZ
    CP
    NT
    CC1
    HB1
    HB2
    CZ
    CD2
    CD1
    CD1
    CD2
    CD2
    CB
    CB
    CZ

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CG4
    HG31
    HG21
    HG1
    HG61
    HG51
    HBG1
    CJ1
    CK2
    CB
    CD1
    CE2
    CG
    CA
    CB
    CB
    CB
    CZ
    CZ
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1

    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2
    CB
    CD1
    CE2
    CG4
    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CZ
    CB
    CB
    CD1
    CD2
    CE1

    HG4
    HG32
    HG22
    CBG
    HG62
    HG52
    HBG2
    HJ1
    HK2
    HB1
    HD1
    HE2
    HT1
    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CE1
    CE2
    CP

    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2
    CB
    CD1
    CE2

    CG3
    CG2
    NG1
    CG6
    CG5
    CG4
    CY
    CK1
    CJ2
    HB2
    CE1
    CD2
    1.5234
    1.1167
    1.1142
    1.5069
    1.4041
    1.4045
    1.4045
    1.4041
    1.4041
    1.5069
    1.5069
    1.4045

    CK1
    CJ2
    CB
    CE1
    CD2

    HK1
    HJ2
    CZ
    HE1
    HD2

    109.38
    112.82
    108.54
    113.23
    120.59
    119.58
    119.68
    120.59
    120.59
    119.58
    120.59
    120.14

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CE1 CP
    CD2 CZ

    CP

    HP

    -153.04
    -38.66
    -155.51
    86.00
    -99.33
    76.21
    175.54
    27.27
    141.22
    -176.05
    175.62
    0.56

    116.99
    116.99
    116.99
    116.99
    113.23
    113.23
    120.59
    109.20
    106.86
    120.14
    120.15
    119.98

    1.4484
    1.3347
    1.3347
    1.3347
    1.4484
    1.4484
    1.5069
    1.1167
    1.1142
    1.4008
    1.4011
    1.4008

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    HT1
    CG
    CG3
    CG3
    NT
    CG4
    CG4
    CG4
    NG1
    NG1
    CG3
    CG6
    CG6
    CG2
    CG5
    CG5
    CG6
    CG6
    CG6
    HBG1
    CG2
    NG1
    NG1
    CBG
    CBG
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1

    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT
    NT
    CG4
    CG2
    CG2
    CG3
    CG3
    CG3
    CG2
    CG2
    CG2
    CG3
    NG1
    NG1
    CG4
    CG4
    NG1
    NG1
    NG1
    CBG
    CBG
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2

    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    *NT
    CG4
    *CG4
    *CG4
    CG3
    *CG3
    *CG3
    CG2
    *CG2
    *CG2
    NG1
    *NG1
    *NG1
    CG4
    *CG6
    *CG6
    *CG5
    *CG5
    CBG
    *CBG
    CBG
    CY
    CY
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ

    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CG4
    CG3
    HG4
    CG5
    CG2
    HG31
    HG32
    NG1
    HG21
    HG22
    CG6
    HG1
    CBG
    CG5
    HG61
    HG62
    HG51
    HG52
    HBG1
    HBG2
    CY
    CJ2
    CJ1
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ

    1.4008
    1.4008
    1.4008
    1.4011
    1.4008
    1.4012
    1.4008
    1.0054
    1.3416
    1.5378
    1.5378
    1.4381
    1.5378
    1.5378
    1.5378
    1.5202
    1.5202
    1.5352
    1.5109
    1.5109
    1.5352
    1.5266
    1.5266
    1.5266
    1.5266
    1.5109
    1.1032
    1.5202
    1.4972
    1.4972
    1.4862
    1.4862
    1.4090
    1.4003
    1.3998
    1.4003
    1.4003
    1.3998
    1.3998
    1.3998

    119.98
    120.07
    120.14
    120.15
    119.98
    119.97
    120.07
    116.40
    124.61
    110.67
    110.67
    110.67
    111.85
    111.85
    111.85
    111.06
    111.06
    111.06
    110.73
    110.73
    111.85
    110.48
    110.48
    111.10
    111.10
    111.45
    107.08
    117.47
    105.98
    105.98
    120.17
    120.62
    120.32
    120.02
    120.16
    120.32
    120.29
    120.02
    120.02
    120.16

    -0.25
    -0.13
    179.88
    -179.36
    -179.84
    179.92
    179.63
    -172.83
    170.00
    -117.93
    122.73
    70.05
    121.71
    -120.95
    55.34
    118.37
    -118.11
    -56.33
    112.39
    -129.60
    -54.87
    121.09
    -122.70
    121.26
    -122.01
    -69.57
    121.43
    -60.45
    -74.47
    108.23
    179.26
    -179.21
    -0.80
    -0.38
    0.42
    179.90
    179.62
    -179.40
    179.37
    179.20

    120.07
    119.97
    120.03
    120.10
    120.09
    120.22
    119.91
    124.61
    110.67
    107.34
    112.97
    111.85
    109.54
    109.60
    111.06
    110.41
    113.59
    110.73
    104.22
    117.47
    109.15
    105.90
    105.64
    109.77
    109.21
    107.08
    107.67
    105.98
    120.62
    120.17
    120.32
    120.29
    120.02
    120.16
    120.02
    120.54
    120.62
    120.26
    120.29
    119.92

    1.4012
    1.4011
    1.0802
    1.0785
    1.0803
    1.0812
    1.0813
    1.4381
    1.5378
    1.1204
    1.5408
    1.5352
    1.1122
    1.1132
    1.5202
    1.1001
    1.1007
    1.5109
    1.0469
    1.4972
    1.5408
    1.1028
    1.1023
    1.1128
    1.1123
    1.1032
    1.1023
    1.4862
    1.4104
    1.4090
    1.4003
    1.4003
    1.3998
    1.3998
    1.4003
    1.0806
    1.0803
    1.0821
    1.0822
    1.0821

    PRES BPAT
    1.00 ! C19H28N2O3 Gamma N-benzyl piperidine, alpha tert.butyl
    CDCA amide (010101P), chayan
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    OG
    CG
    3--CG3
    CJ1--CK1
    ATOM CG CG2O1
    0.51 !
    ||
    /
    \
    //
    \\
    ATOM OG OG2D1 -0.51 !
    CG---NT--CG4
    NG1(+1) CY
    CQ
    ATOM NT NG2S1 -0.47 !
    /
    HT1 \
    / \ / \ __ /
    ATOM HT1 HGP1
    0.47 !
    CC3
    CG
    5--CG6
    CBG CJ2--CK2
    GROUP
    !
    \
    ATOM CG4 CG311

    -0.09 !

    O24

    CC2

    ATOM HG4 HGA1


    GROUP
    CT1
    ATOM CG3
    /
    ATOM HG31
    CT--CT2
    ATOM HG32
    \
    GROUP
    CT3
    ATOM CG2

    0.09 !

    ||

    CG321

    -0.18 !

    HGA2

    0.09 !

    HGA2

    0.09 !

    ATOM HG21 HGA2

    0.09 !

    C1 | C9

    ATOM HG22 HGA2

    0.09 !

    NG3P1 -0.40 !

    C2

    C10 C8

    ATOM HG1

    HGP2

    0.32 !

    ATOM CBG

    CG324

    0.15 !

    C3

    C5

    C7

    ATOM HBG1 HGA2

    0.09 !

    ATOM HBG2 HGA2

    0.09 ! HO

    ATOM CG6

    0.15 !

    ATOM HG62
    GROUP
    ATOM CG5
    ATOM HG51
    ATOM HG52
    GROUP
    ATOM CY
    GROUP
    ATOM CJ1
    ATOM HJ1
    GROUP
    ATOM CJ2
    ATOM HJ2
    GROUP
    ATOM CK1
    ATOM HK1
    GROUP
    ATOM CK2
    ATOM HK2
    GROUP
    ATOM CQ
    ATOM HQ
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2

    HGA2
    CG321
    HGA2
    HGA2

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG2R61

    0.090

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG311
    HGA1
    CG2O2
    OG2D1
    OG302

    0.17
    0.09
    0.90
    -0.63
    -0.49

    C23

    C14

    C16

    / \|/ \ / \ /

    ATOM NG1

    0.09 !

    C20

    C11 C13---C17
    Me19 |

    ATOM HG61 HGA2

    C24

    C15

    / \ / \ / \
    C4

    C6

    CC1

    \ / \ / \ / \

    / \ |

    0.15 !

    CG324

    C22

    C12 Me18

    !
    CG324

    Me21

    OH

    BPAT (010101P)

    NH

    CA---OA2--||
    OA1

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CT
    CT1
    HT11
    HT12
    HT13
    CT2
    HT21
    HT22
    HT23
    CT3
    HT31
    HT32
    HT33

    CG301
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    NT
    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CY
    CQ
    OA2
    CT
    CT
    CT
    NT

    CG4
    HG4
    HG31
    HG21
    HG1
    HG61
    HG51
    HBG1
    CJ1
    CK2
    CT
    CT1
    CT2
    CT3
    CG

    CC1
    CT1
    CT2
    CT3
    HT11
    HT12
    HT13
    HT21
    HT22
    HT23
    HT31
    HT32
    HT33
    HT1
    CG
    CG3
    CG3
    NT
    CG4
    CG4
    CG4
    NG1
    NG1
    CG3
    CG6
    CG6
    CG2
    CG5
    CG5
    CG6

    CA
    CT
    CT
    CT
    CT1
    CT1
    CT1
    CT2
    CT2
    CT2
    CT3
    CT3
    CT3
    CG
    NT
    NT
    NT
    CG4
    CG2
    CG2
    CG3
    CG3
    CG3
    CG2
    CG2
    CG2
    CG3
    NG1
    NG1
    CG4

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    -0.04
    -0.27
    0.09
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2

    CG3
    HG32
    HG22
    CBG
    HG62
    HG52
    HBG2
    HJ1
    HK2

    CT1
    CT2
    CT3
    CG4

    HT11 CT1 HT12 CT1 HT13


    HT21 CT2 HT22 CT2 HT23
    HT31 CT3 HT32 CT3 HT33
    HT1

    OA2
    OA2
    OA2
    OA2
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    CT
    *NT
    CG4
    *CG4
    *CG4
    CG3
    *CG3
    *CG3
    CG2
    *CG2
    *CG2
    NG1
    *NG1
    *NG1
    CG4
    *CG6
    *CG6
    *CG5

    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2

    CT
    CA
    CA
    CA
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    OA2
    CG4
    CG3
    HG4
    CG5
    CG2
    HG31
    HG32
    NG1
    HG21
    HG22
    CG6
    HG1
    CBG
    CG5
    HG61
    HG62
    HG51

    CG2
    NG1
    CG6
    CG5
    CG4
    CY
    CK1 CK1 HK1 CK1 CQ
    CJ2 CJ2 HJ2 CJ2 CY

    1.5234
    1.5352
    1.5347
    1.5307
    1.1112
    1.1067
    1.1101
    1.1108
    1.1080
    1.1104
    1.1107
    1.1106
    1.1099
    1.0045
    1.3436
    1.5381
    1.5381
    1.4390
    1.5381
    1.5381
    1.5381
    1.5200
    1.5200
    1.5350
    1.5109
    1.5109
    1.5350
    1.5267
    1.5267
    1.5267

    109.10
    110.85
    111.07
    105.00
    109.61
    111.59
    110.52
    109.79
    111.70
    110.28
    110.25
    110.46
    110.69
    117.45
    124.06
    110.90
    110.90
    110.90
    111.99
    111.99
    111.99
    111.05
    111.05
    111.05
    110.70
    110.70
    111.99
    110.50
    110.50
    111.14

    -173.96
    62.78
    -62.73
    179.91
    171.34
    -69.34
    52.23
    -171.93
    68.38
    -52.79
    179.66
    60.01
    -60.47
    -173.12
    168.56
    -117.89
    122.85
    70.34
    121.82
    -120.93
    55.21
    118.37
    -118.12
    -56.35
    112.41
    -129.56
    -54.61
    121.09
    -122.70
    121.28

    CQ

    122.03
    122.03
    122.03
    122.03
    110.85
    110.85
    110.85
    111.07
    111.07
    111.07
    105.00
    105.00
    105.00
    124.06
    110.90
    107.42
    112.85
    111.99
    109.60
    109.55
    111.05
    110.38
    113.66
    110.70
    104.22
    117.44
    109.17
    105.89
    105.62
    109.72

    HQ

    1.4239
    1.3222
    1.3222
    1.3222
    1.4239
    1.4239
    1.4239
    1.4239
    1.4239
    1.4239
    1.4239
    1.4239
    1.4239
    1.4390
    1.5381
    1.1207
    1.5408
    1.5350
    1.1121
    1.1133
    1.5200
    1.1001
    1.1004
    1.5109
    1.0468
    1.4972
    1.5408
    1.1029
    1.1023
    1.1128

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG6
    CG6
    HBG1
    CG2
    NG1
    NG1
    CBG
    CBG
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1

    CG4
    NG1
    NG1
    NG1
    CBG
    CBG
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2

    *CG5
    CBG
    *CBG
    CBG
    CY
    CY
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ

    HG52
    HBG1
    HBG2
    CY
    CJ2
    CJ1
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ

    1.5267
    1.5109
    1.1032
    1.5200
    1.4972
    1.4972
    1.4862
    1.4862
    1.4090
    1.4003
    1.3998
    1.4003
    1.4003
    1.3998
    1.3998
    1.3998

    111.14
    111.46
    107.08
    117.44
    105.99
    105.99
    120.17
    120.62
    120.32
    120.02
    120.16
    120.32
    120.29
    120.02
    120.02
    120.16

    -122.01
    -69.49
    121.42
    -60.42
    -74.52
    108.18
    179.26
    -179.21
    -0.80
    -0.38
    0.42
    179.88
    179.63
    -179.41
    179.38
    179.21

    109.20
    107.08
    107.67
    105.99
    120.62
    120.17
    120.32
    120.29
    120.02
    120.16
    120.02
    120.54
    120.62
    120.26
    120.29
    119.92

    1.1124
    1.1032
    1.1023
    1.4862
    1.4104
    1.4090
    1.4003
    1.4003
    1.3998
    1.3998
    1.4003
    1.0806
    1.0803
    1.0821
    1.0822
    1.0821

    PRES GBP
    1.00 ! C13H18N2O Gamma N-benzyl piperidine CDCA amide (01OH01
    ), chayan
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    OG
    CG
    3--CG3
    CJ1--CK1
    ATOM CG CG2O1
    0.51 !
    ||
    /
    \
    //
    \\
    ATOM OG OG2D1 -0.51 !
    CG---NT--CG4
    NG1(+1) CY
    CQ
    ATOM NT NG2S1 -0.47 !
    /
    HT1 \
    / \ / \ __ /
    ATOM HT1 HGP1
    0.47 !
    CC3
    CG
    5--CG6
    CBG CJ2--CK2
    GROUP
    !
    \
    ATOM CG4 CG311

    -0.09 !

    O24

    CC2

    ATOM HG4 HGA1

    0.09 !

    ||

    GROUP

    ATOM CG3 CG321

    -0.18 !

    ATOM HG31 HGA2

    0.09 !

    ATOM HG32 HGA2

    0.09 !

    GROUP
    ATOM CG2

    C22

    C20

    / \ |

    C11 C13---C17

    0.15 !

    Me19 |

    ATOM HG21 HGA2

    0.09 !

    C1 | C9

    ATOM HG22 HGA2

    0.09 !

    C14

    C16

    / \|/ \ / \ /

    ATOM NG1

    NG3P1 -0.40 !

    C2

    C10 C8

    ATOM HG1

    HGP2

    0.32 !

    ATOM CBG

    CG324

    0.15 !

    C3

    C5

    C7

    C24

    CC1

    \ / \ / \ / \

    C12 Me18

    !
    CG324

    Me21

    C15

    C23

    NH

    CA---OA2
    ||
    OA1

    ATOM HBG1 HGA2

    0.09 !

    ATOM HBG2 HGA2

    0.09 ! HO

    ATOM CG6

    0.15 !

    CG324

    ATOM HG61 HGA2


    ATOM HG62
    GROUP
    ATOM CG5
    ATOM HG51
    ATOM HG52
    GROUP
    ATOM CY
    GROUP
    ATOM CJ1
    ATOM HJ1
    GROUP
    ATOM CJ2
    ATOM HJ2
    GROUP
    ATOM CK1
    ATOM HK1
    GROUP
    ATOM CK2
    ATOM HK2
    GROUP
    ATOM CQ
    ATOM HQ
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CY
    CQ
    NT
    HT1
    CG
    CG3
    CG3
    NT
    CG4
    CG4
    CG4
    NG1
    NG1
    CG3
    CG6
    CG6
    CG2
    CG5
    CG5
    CG6

    / \ / \ / \
    C4

    C6

    0.09 !

    HGA2

    OH

    CG321
    HGA2
    HGA2

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG2R61

    0.090

    GBP (01OH01)

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG4
    HG4
    HG31
    HG21
    HG1
    HG61
    HG51
    HBG1
    CJ1
    CK2
    CG
    CG
    NT
    NT
    NT
    CG4
    CG2
    CG2
    CG3
    CG3
    CG3
    CG2
    CG2
    CG2
    CG3
    NG1
    NG1
    CG4

    CG4
    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2
    CG4
    *NT
    CG4
    *CG4
    *CG4
    CG3
    *CG3
    *CG3
    CG2
    *CG2
    *CG2
    NG1
    *NG1
    *NG1
    CG4
    *CG6
    *CG6
    *CG5

    CG3
    HG32
    HG22
    CBG
    HG62
    HG52
    HBG2
    HJ1
    HK2
    HT1

    CG3
    CG2
    NG1
    CG6
    CG5
    CBG
    CJ1
    CK2

    CG4
    CG3
    HG4
    CG5
    CG2
    HG31
    HG32
    NG1
    HG21
    HG22
    CG6
    HG1
    CBG
    CG5
    HG61
    HG62
    HG51

    CG2
    NG1
    CG6
    CG5
    CG4
    CY
    CK1 CK1 HK1 CK1 CQ
    CJ2 CJ2 HJ2 CJ2 CY
    1.0266
    1.3473
    1.5369
    1.5369
    1.4492
    1.5369
    1.5369
    1.5369
    1.5205
    1.5205
    1.5253
    1.5195
    1.5195
    1.5253
    1.5363
    1.5363
    1.5363

    118.64
    121.63
    112.24
    112.24
    112.24
    110.04
    110.04
    110.04
    111.15
    111.15
    111.15
    113.22
    113.22
    110.04
    113.88
    113.88
    113.37

    -178.12
    69.87
    -119.04
    122.72
    63.89
    120.66
    -121.42
    61.26
    118.11
    -118.76
    -51.59
    114.22
    -126.12
    -62.01
    122.63
    -123.87
    121.63

    CQ

    121.63
    112.24
    107.41
    113.59
    110.04
    109.41
    110.77
    111.15
    110.13
    113.26
    113.22
    104.34
    117.02
    107.88
    105.32
    104.60
    109.05

    HQ

    1.4492
    1.5369
    1.1206
    1.5392
    1.5253
    1.1118
    1.1110
    1.5205
    1.0998
    1.0984
    1.5195
    1.0416
    1.4977
    1.5392
    1.1016
    1.0916
    1.1130

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG6
    CG6
    HBG1
    CG2
    NG1
    NG1
    CBG
    CBG
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1

    CG4
    NG1
    NG1
    NG1
    CBG
    CBG
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2

    *CG5
    CBG
    *CBG
    CBG
    CY
    CY
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ

    HG52
    HBG1
    HBG2
    CY
    CJ2
    CJ1
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ

    1.5363
    1.5195
    1.1054
    1.5205
    1.4977
    1.4977
    1.4811
    1.4811
    1.4082
    1.3993
    1.4003
    1.3993
    1.4006
    1.4003
    1.4003
    1.4003

    113.37
    107.66
    106.80
    117.02
    108.23
    108.23
    119.67
    121.06
    120.36
    120.02
    120.13
    120.36
    120.27
    120.02
    120.00
    120.13

    -121.40
    -53.18
    120.32
    -43.82
    -74.54
    108.39
    177.88
    -178.43
    0.02
    -0.22
    -0.37
    -179.98
    179.99
    179.98
    179.79
    -179.96

    108.53
    106.80
    107.39
    108.23
    121.06
    119.67
    120.36
    120.27
    120.02
    120.13
    120.00
    119.89
    120.44
    119.90
    119.85
    120.17

    1.1122
    1.1054
    1.1012
    1.4811
    1.4098
    1.4082
    1.3993
    1.4006
    1.4003
    1.4003
    1.4006
    1.0829
    1.0799
    1.0816
    1.0816
    1.0809

    PRES 3MSB
    1.00 ! C16H22N2O3 (010206(S)D), chayan
    ! This compound has 3-methylamine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    ATOM HT1 HGP1
    0.47 !
    HG31 HG32
    GROUP
    !
    \ /
    ATOM CGT CG321 -0.18 !
    CG2--NG3 (+1)
    ATOM HGT1 HGA2
    0.09 !
    /
    \
    ATOM HGT2 HGA2
    0.09 !
    GT--CG1
    CG4
    GROUP
    !
    \
    /
    ATOM CG1 CG311 -0.09 !
    CG6--CG5
    ATOM HG1 HGA1
    0.09 !
    GROUP
    ATOM CG2 CG324

    ||
    CG---NT--C
    /

    \
    O24

    CC2

    ||

    0.20 !
    !

    C12 Me18

    !
    !

    Me21

    C22

    C20
    /

    C11 C13---C17
    Me19 |

    0.09 !

    C1 | C9

    C24

    CC1

    \ / \ / \ / \

    / \ |

    HT1

    CC3

    ATOM HG21 HGA2


    0.09
    CD1--CE1
    ATOM HG22 HGA2
    0.09
    //
    \\
    ATOM NG3 NG3P2 -0.40
    --CB--CZ
    CP
    ATOM HG31 HGP2
    0.32
    \ __ /
    ATOM HG32 HGP2
    0.32
    CD2--CE2
    ATOM CG4 CG324
    0.20
    ATOM HG41 HGA2

    OG

    C14

    C16

    C23

    NH

    CA---OA2||
    OA1

    ATOM HG42 HGA2

    0.09 !

    GROUP

    / \|/ \ / \ /

    C2

    C10 C8

    ATOM CG5 CG321

    -0.18 !

    ATOM HG51 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG52 HGA2

    0.09 !

    GROUP

    / \ / \ / \

    !
    -0.18 !

    ATOM HG61 HGA2

    0.09 !

    HO

    ATOM CG6 CG321

    ATOM HG62
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP

    HGA2

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    OA2
    CZ
    CP
    NT

    CC1
    CA
    CA
    CA
    OA2
    OA2
    CD1
    CD2

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CA
    OA2
    OA2
    OA2
    CB
    CB
    CD2
    CZ

    HGT1
    CG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HB1
    HD1
    HE2
    HT1

    OA2
    CB
    CB
    CB
    CZ
    CZ
    *CZ
    CB

    CB
    HB1
    CZ
    HB2
    CD2
    CD1
    CB
    HB1

    C4

    C6

    OH

    3MSB (010206(S)D)

    0.09 !
    !
    0.17 !
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CGT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2
    CGT

    C15

    CGT HGT2 CGT CG1


    CG2
    NG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2

    NG3
    CG4
    CG5
    CG6
    CG1
    HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    1.5242
    1.3349
    1.3349
    1.3349
    1.4476
    1.4476
    1.4048
    1.4061

    109.43
    116.64
    116.64
    116.64
    113.76
    113.76
    119.46
    121.23

    -175.98
    -66.79
    173.93
    52.26
    -121.85
    58.24
    -179.91
    116.69

    CP

    116.64
    110.19
    113.76
    110.81
    121.23
    119.30
    121.23
    106.33

    HP

    1.4476
    1.1154
    1.5066
    1.1160
    1.4061
    1.4048
    1.5066
    1.1154

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    NG3
    NG3
    CG1
    CG4
    CG4
    CG2
    CG5
    CG5
    NG3
    CG6
    CG6
    CG5
    CG5

    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    NG3
    NG3
    NG3
    CG4
    CG4
    CG4
    CG1
    CG1

    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    NG3
    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    NG3
    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.4061
    1.5066
    1.5066
    1.4048
    1.4015
    1.4007
    1.4015
    1.4017
    1.4007
    1.4005
    1.4007
    1.2239
    1.3478
    1.1149
    1.1149
    1.4536
    1.1153
    1.1153
    1.5521
    1.5116
    1.5116
    1.5358
    1.5084
    1.5084
    1.5116
    1.5314
    1.5314
    1.5084
    1.5395
    1.5395
    1.5395
    1.5395

    121.23
    119.30
    121.23
    120.30
    119.94
    120.09
    120.30
    120.20
    119.94
    120.00
    120.09
    122.72
    127.00
    108.33
    108.33
    117.09
    107.48
    107.48
    111.66
    109.85
    109.85
    109.85
    113.58
    113.58
    113.58
    109.83
    109.83
    109.83
    110.96
    110.96
    111.48
    111.48

    1.46
    179.43
    -179.39
    -0.06
    0.59
    -0.55
    -179.46
    179.33
    -179.52
    179.30
    -179.58
    8.77
    -166.41
    -115.07
    122.64
    69.36
    -120.14
    117.07
    179.38
    117.59
    -116.95
    58.38
    124.95
    -119.78
    -56.76
    121.43
    -122.30
    54.36
    121.27
    -120.76
    -121.73
    120.99

    107.82
    120.30
    120.20
    119.94
    120.09
    120.00
    119.80
    120.22
    120.13
    120.26
    119.77
    127.00
    108.33
    108.53
    117.09
    107.48
    111.66
    111.60
    109.85
    112.64
    113.19
    113.58
    110.23
    107.15
    109.83
    105.28
    105.71
    110.96
    109.75
    109.94
    109.49
    109.18

    1.1160
    1.4015
    1.4017
    1.4007
    1.4005
    1.4017
    1.0800
    1.0796
    1.0809
    1.0816
    1.0816
    1.4536
    1.1149
    1.1163
    1.5521
    1.1153
    1.5358
    1.5466
    1.5116
    1.1015
    1.1017
    1.5084
    1.0062
    1.0101
    1.5314
    1.1036
    1.1029
    1.5395
    1.1134
    1.1139
    1.1129
    1.1142

    PRES 3MPS
    1.00 ! C7H14N2O (01OH06(S)D), chayan
    ! This compound has 3-methylamine piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    ATOM HT1 HGP1
    0.47 !
    HG31 HG32
    GROUP
    !
    \ /
    ATOM CGT CG321 -0.18 !
    CG2--NG3 (+1)
    ATOM HGT1 HGA2
    0.09 !
    /
    \
    ATOM HGT2 HGA2
    0.09 !
    GT--CG1
    CG4
    GROUP
    !
    \
    /
    ATOM CG1 CG311 -0.09 !
    CG6--CG5
    ATOM HG1 HGA1
    0.09 !
    GROUP

    OG
    ||
    CG---NT--C
    /
    CC3
    \
    O24

    CC2

    HT1

    ATOM CG2 CG324

    0.20 !

    ATOM HG21 HGA2

    0.09 !

    ATOM HG22 HGA2

    0.09 !

    ATOM NG3 NG3P2

    -0.40 !

    ATOM HG31 HGP2

    0.32 !

    ATOM HG32 HGP2

    0.32 !

    ATOM CG4 CG324

    0.20 !

    Me19 |

    ATOM HG41 HGA2

    0.09 !

    C1 | C9

    ATOM HG42 HGA2

    0.09 !

    GROUP

    ||

    C2

    C10 C8
    |

    ATOM HG51 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG52 HGA2

    0.09 !

    -0.18 !

    ATOM HG61 HGA2

    0.09 !

    ATOM HG62 HGA2

    0.09 !

    HO

    ATOM CG6 CG321

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    NG3
    NG3
    CG1
    CG4
    CG4
    CG2
    CG5
    CG5
    NG3

    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    NG3
    NG3
    NG3
    CG4

    HGT1
    CG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HT1
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    NG3
    *NG3
    *NG3
    CG4
    *CG4
    *CG4
    CG5

    C23

    NH

    CA---OA2
    ||

    C14

    C16

    OA1

    C15

    / \ / \ / \

    CGT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    CGT

    C20

    / \|/ \ / \ /

    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG

    CC1

    C11 C13---C17

    -0.18 !

    NT
    CG1
    CG2
    NG3
    CG4
    CG5
    CG6
    NT

    C24

    \ / \ / \ / \

    / \ |

    ATOM CG5 CG321

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    C22

    C12 Me18

    GROUP

    Me21

    C4

    C6

    OH

    3MPS (01OH06(S)D)

    CGT HGT2 CGT CG1


    CG2
    NG3
    CG4
    CG5
    CG6
    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    NG3
    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6

    NG3
    CG4
    CG5
    CG6
    CG1
    1.2256
    1.3392
    1.1137
    1.1137
    1.4530
    1.1140
    1.1140
    1.5501
    1.5027
    1.5027
    1.5302
    1.4981
    1.4981
    1.5027
    1.5348
    1.5348
    1.4981

    121.47
    124.59
    107.85
    107.85
    112.47
    108.38
    108.38
    107.80
    116.62
    116.62
    116.62
    112.51
    112.51
    112.51
    109.73
    109.73
    109.73

    0.79
    149.80
    -116.73
    120.07
    83.79
    -117.58
    121.37
    -170.55
    118.47
    -118.49
    51.23
    122.69
    -123.39
    -54.57
    121.15
    -122.63
    58.52

    124.59
    107.85
    111.18
    112.47
    108.38
    107.80
    112.80
    116.62
    110.90
    111.67
    112.51
    105.66
    108.44
    109.73
    105.11
    105.65
    111.11

    1.4530
    1.1137
    1.1160
    1.5501
    1.1140
    1.5302
    1.5449
    1.5027
    1.1061
    1.1051
    1.4981
    1.0135
    1.0051
    1.5348
    1.1047
    1.1024
    1.5422

    IC
    IC
    IC
    IC

    CG6
    CG6
    CG5
    CG5

    CG4
    CG4
    CG1
    CG1

    *CG5
    *CG5
    *CG6
    *CG6

    HG51
    HG52
    HG61
    HG62

    1.5422
    1.5422
    1.5422
    1.5422

    111.11
    111.11
    112.06
    112.06

    120.57
    -121.30
    -120.86
    122.05

    109.36
    110.16
    108.98
    109.12

    1.1130
    1.1129
    1.1136
    1.1131

    PRES 2MRB
    1.00 ! C16H22N2O3 (010207(R)D), chayan
    ! This compound has 2-methylamine piperidine at gamma position
    ! and benzyl at alpha position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    HG21 HG22
    ATOM OG OG2D1 -0.51 !
    \ /
    ATOM NT NG2S1 -0.47 !
    +1)NG2--CG3
    ATOM HT1 HGP1
    0.47 !
    /
    \
    GROUP
    !
    -CG1
    CG4
    ATOM CGT CG321 -0.18 !
    \
    /
    ATOM HGT1 HGA2
    0.09 !
    CG6--CG5
    ATOM HGT2 HGA2
    0.09 !
    GROUP

    ATOM CG1 CG314

    0.29 !

    ATOM HG1 HGA1


    CD1--CE1
    ATOM NG2 NG3P2
    //
    \\
    ATOM HG21 HGP2
    B--CZ
    CP
    ATOM HG22 HGP2
    \ __ /
    ATOM CG3 CG324
    CD2--CE2
    ATOM HG31 HGA2

    0.09 !

    -0.40 !

    ATOM HG32 HGA2


    GROUP

    0.32 !
    0.32 !

    Me19 |

    0.09 !

    C1 | C9

    C2

    C10 C8

    ATOM HG41 HGA2

    0.09 !

    ATOM HG42 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG51 HGA2

    C14

    C16

    C15

    / \ / \ / \

    -0.18 ! HO
    0.09 !

    / \|/ \ / \ /

    -0.18 !

    ATOM CG5 CG321

    C20

    C11 C13---C17

    0.09 !

    C4

    C6

    CG---NT--CGT/

    HT1

    CC3
    \
    CC2

    ||

    C24

    CC1

    \ / \ / \ / \

    / \ |

    0.20 !

    ||

    O24

    C22

    C12 Me18

    ATOM CG4 CG321

    GROUP

    Me21

    OG

    OH

    C23

    NH

    CA---OA2---C
    ||
    OA1

    ATOM HG52 HGA2


    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CP
    ATOM HP
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    NT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    OA2
    CZ
    CP
    NT

    CC1
    CA
    CA
    CA
    OA2
    OA2
    CD1
    CD2
    CD2
    CB
    CB
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1
    OG

    0.09 !

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    !
    -0.18 !
    0.09 !
    0.09 !
    !
    0.17 !
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    2MRB (010207(R)D)

    CG321
    HGA2
    HGA2

    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CB
    CD1
    CE2
    CG
    CA
    OA2
    OA2
    OA2
    CB
    CB
    CD2
    CZ
    CZ
    CZ
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2
    CG

    CGT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2
    CGT

    HGT1
    NG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HB1
    HD1
    HE2
    HT1

    OA2
    CB
    CB
    CB
    CZ
    CZ
    *CZ
    CB
    CB
    CD1
    CD2
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP
    NT

    CB
    HB1
    CZ
    HB2
    CD2
    CD1
    CB
    HB1
    HB2
    CE1
    CE2
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP
    CGT

    CGT HGT2 CGT CG1


    NG2
    CG3
    CG4
    CG5
    CG6
    CB
    CD1
    CE2

    CG3
    CG4
    CG5
    CG6
    CG1
    HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    1.5251
    1.3348
    1.3348
    1.3348
    1.4475
    1.4475
    1.4048
    1.4063
    1.4063
    1.5068
    1.5068
    1.4048
    1.4013
    1.4006
    1.4013
    1.4018
    1.4006
    1.4005
    1.4006
    1.2258

    109.19
    116.84
    116.84
    116.84
    113.76
    113.76
    119.45
    121.29
    121.29
    119.26
    121.29
    120.31
    119.94
    120.09
    120.31
    120.20
    119.94
    119.99
    120.09
    121.77

    -176.53
    -68.03
    172.79
    51.08
    -124.12
    56.05
    -179.83
    114.56
    -0.72
    179.46
    -179.43
    -0.08
    0.52
    -0.49
    -179.47
    179.31
    -179.52
    179.29
    -179.60
    -9.07

    CP

    116.84
    110.09
    113.76
    110.88
    121.29
    119.26
    121.29
    106.29
    107.81
    120.31
    120.20
    119.94
    120.09
    119.99
    119.81
    120.24
    120.12
    120.29
    119.79
    126.25

    HP

    1.4475
    1.1153
    1.5068
    1.1157
    1.4063
    1.4048
    1.5068
    1.1153
    1.1157
    1.4013
    1.4018
    1.4006
    1.4005
    1.4018
    1.0801
    1.0794
    1.0810
    1.0816
    1.0814
    1.4608

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    CG4
    CG4
    NG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    NG2
    NG2
    NG2
    CG3
    CG3
    CG3
    CG4
    CG4
    CG4
    CG1
    CG1

    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    NG2
    *NG2
    *NG2
    CG3
    *CG3
    *CG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HGT1
    HGT2
    CG1
    HG1
    NG2
    CG6
    CG3
    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    1.3453
    1.1149
    1.1149
    1.4608
    1.1148
    1.1148
    1.5520
    1.5017
    1.5017
    1.4997
    1.5329
    1.5329
    1.5017
    1.5388
    1.5388
    1.5329
    1.5388
    1.5388
    1.5388
    1.5388

    126.25
    109.68
    109.68
    116.89
    109.62
    109.62
    110.19
    115.54
    115.54
    115.54
    109.20
    109.20
    109.20
    110.62
    110.62
    110.62
    111.04
    111.04
    112.23
    112.23

    -63.13
    -114.42
    125.80
    35.97
    -115.37
    123.79
    177.33
    122.50
    -125.48
    58.81
    122.16
    -121.59
    -54.65
    120.78
    -121.22
    54.76
    121.50
    -121.04
    -121.77
    120.96

    109.68
    107.29
    116.89
    109.62
    110.19
    114.12
    115.54
    107.57
    106.76
    109.20
    105.67
    105.38
    110.62
    109.91
    109.75
    111.04
    109.70
    109.48
    109.64
    109.15

    1.1149
    1.1157
    1.5520
    1.1148
    1.4997
    1.5387
    1.5017
    1.0057
    1.0184
    1.5329
    1.1031
    1.1034
    1.5388
    1.1136
    1.1132
    1.5388
    1.1146
    1.1142
    1.1131
    1.1133

    PRES 2MPR
    1.00 ! C7H14N2O (01OH07(R)D), chayan
    ! This compound has 3-methylamine piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    ATOM CG CG2O1
    0.51 !
    ATOM OG OG2D1 -0.51 !
    ATOM NT NG2S1 -0.47 !
    HG31 HG32
    ATOM HT1 HGP1
    0.47 !
    \ /
    GROUP
    !
    +1) NG2--CG3
    ATOM CGT CG321 -0.18 !
    /
    \
    ATOM HGT1 HGA2
    0.09 !
    --CG1
    CG4
    ATOM HGT2 HGA2
    0.09 !
    \
    /
    GROUP
    !
    CG6--CG5
    ATOM CG1 CG314
    0.29 !

    OG
    ||

    CG---NT--CGT
    /

    HT1

    CC3
    \

    ATOM HG1 HGA1

    0.09 !

    O24

    CC2

    ATOM NG2 NG3P2

    -0.40 !

    ||

    ATOM HG21 HGP2

    0.32 !

    ATOM HG22 HGP2

    0.32 !

    ATOM CG3 CG324

    0.20 !

    C12 Me18

    ATOM HG31 HGA2

    0.09 !

    ATOM HG32 HGA2

    0.09 !

    GROUP

    Me21

    C22

    C24

    CC1

    \ / \ / \ / \
    C20

    / \ |

    C11 C13---C17
    Me19 |

    C23

    NH

    CA---OA2
    ||
    OA1

    ATOM CG4 CG321

    -0.18 !

    ATOM HG41 HGA2

    0.09 !

    ATOM HG42 HGA2

    0.09 !

    GROUP

    C1 | C9

    ATOM CG5 CG321

    -0.18 !

    ATOM HG51 HGA2

    0.09 !

    ATOM HG52 HGA2

    0.09 ! HO

    C10 C8

    C3

    C5

    C7

    C15

    C4

    C6

    OH

    !
    -0.18 !

    ATOM HG61 HGA2


    ATOM HG62 HGA2

    0.09 !
    0.09 !

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C2

    / \ / \ / \

    ATOM CG6 CG321

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    C16

    / \|/ \ / \ /

    GROUP

    C14

    NT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    NT

    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    CG4
    CG4
    NG2
    CG5
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5

    CGT
    HG1
    HG21
    HG31
    HG41
    HG51
    HG61
    CG
    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    NG2
    NG2
    NG2
    CG3
    CG3
    CG3
    CG4
    CG4
    CG4
    CG1
    CG1

    CGT
    CG1
    NG2
    CG3
    CG4
    CG5
    CG6
    CGT
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    NG2
    *NG2
    *NG2
    CG3
    *CG3
    *CG3
    CG4
    *CG4
    *CG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6

    HGT1
    NG2
    HG22
    HG32
    HG42
    HG52
    HG62
    HT1

    2MPR (01OH07(R)D)

    CGT HGT2 CGT CG1

    CGT
    HGT1
    HGT2
    CG1
    HG1
    NG2
    CG6
    CG3
    HG21
    HG22
    CG4
    HG31
    HG32
    CG5
    HG41
    HG42
    CG6
    HG51
    HG52
    HG61
    HG62

    NG2
    CG3
    CG4
    CG5
    CG6

    CG3
    CG4
    CG5
    CG6
    CG1
    1.2249
    1.3396
    1.1163
    1.1163
    1.4568
    1.1157
    1.1157
    1.5472
    1.5005
    1.5005
    1.4973
    1.5319
    1.5319
    1.5005
    1.5379
    1.5379
    1.5319
    1.5379
    1.5379
    1.5379
    1.5379

    120.85
    124.27
    110.37
    110.37
    114.28
    109.88
    109.88
    109.66
    116.32
    116.32
    116.32
    110.16
    110.16
    110.16
    110.24
    110.24
    110.24
    110.68
    110.68
    112.67
    112.67

    2.25
    30.47
    -116.64
    122.29
    59.06
    -114.17
    124.35
    -178.06
    127.76
    -119.58
    55.95
    123.18
    -121.78
    -54.81
    120.63
    -121.15
    56.12
    121.42
    -120.66
    -121.48
    121.55

    124.27
    110.37
    108.59
    114.28
    109.88
    109.66
    113.41
    116.32
    109.81
    107.88
    110.16
    105.12
    104.60
    110.24
    109.71
    109.61
    110.68
    109.84
    109.46
    109.11
    108.86

    PRES GPBZ
    0.00 ! C14H17N2O2 (01OH08), chayan
    ! This compound has 4-benzamide piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    CG2--CG3
    CD1--CE1

    1.4568
    1.1163
    1.1139
    1.5472
    1.1157
    1.4973
    1.5401
    1.5005
    1.0015
    1.0283
    1.5319
    1.1032
    1.1046
    1.5379
    1.1131
    1.1124
    1.5379
    1.1137
    1.1142
    1.1130
    1.1125

    OG

    ATOM CG CG2O1
    0.51 !
    /
    \
    //
    \\
    ATOM OG OG2D1 -0.51 !
    --CG1
    NG4--CQ--CZ
    CP
    ATOM NT NG2S1 -0.47 !
    \
    /
    || \ __ /
    ATOM HT1 HGP1
    0.47 !
    CG6--CG5
    OQ CD2--CE2
    GROUP
    !

    ||
    CG---NT--CGT
    /

    HT1

    CC3
    \

    ATOM CGT CG321

    -0.18 !

    O24

    CC2

    ATOM HGT1 HGA2

    0.09 !

    ||

    ATOM HGT2 HGA2

    0.09 !

    GROUP
    ATOM CG1 CG311

    -0.09 !

    ATOM HG1 HGA1

    0.09 !

    GROUP

    Me19 |

    ATOM HG21 HGA2

    0.09 !

    C1 | C9

    ATOM HG22 HGA2

    0.09 !

    C2

    C10 C8

    ATOM CG3 CG321

    0.06 !

    ATOM HG31 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG32 HGA2

    0.09 !

    0.09 !

    ATOM HG52
    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62
    GROUP
    ATOM CQ
    ATOM OQ
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1

    HGA2
    CG321
    HGA2
    HGA2

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG2O1
    OG2D1

    0.51
    -0.51

    CG2R61 0.00
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    C14

    C16

    C15

    / \ / \ / \

    -0.48 ! HO

    ATOM HG51 HGA2

    C23

    / \|/ \ / \ /

    0.06 !

    C20

    C11 C13---C17

    -0.18 !

    ATOM CG5 CG321

    C24

    C4

    C6

    CC1

    \ / \ / \ / \

    / \ |

    ATOM CG2 CG321

    ATOM NG4 NG2S1

    C22

    C12 Me18

    GROUP

    Me21

    OH

    GPBZ (01OH08)

    NH

    CA---OA2
    ||
    OA1

    ATOM
    ATOM
    ATOM
    ATOM

    CE2
    HE2
    CP
    HP

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    NT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CQ
    CZ
    CP
    NT

    CGT
    HG1
    HG21
    HG31
    CG5
    HG51
    HG61
    OQ
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    NG4
    NG4
    CG2
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5
    CG3
    NG4
    NG4
    NG4
    CQ
    CQ
    CZ
    CZ
    CZ
    CD1
    CD1
    CD2
    CE1

    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    CG3
    CG3
    NG4
    NG4
    NG4
    CG1
    CG1
    NG4
    CZ
    CQ
    CQ
    CZ
    CZ
    CE1
    CE2
    CD1
    CE1
    CP
    CP
    CE2

    CGT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CQ
    CD1
    CE2
    CGT
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3
    NG4
    *NG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6
    CQ
    *CQ
    CZ
    CZ
    CD1
    CD2
    *CD1
    *CD2
    CE1
    CP
    *CE1
    *CE2
    *CP

    HGT1
    CG2
    HG22
    HG32
    CQ
    HG52
    HG62
    CZ
    HD1
    HE2
    HT1

    CGT HGT2 CGT CG1


    CG2 CG3
    CG3 NG4
    CG5 CG6
    CG6 CG1

    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32
    CG5
    CQ
    CG6
    HG51
    HG52
    HG61
    HG62
    CZ
    OQ
    CD1
    CD2
    CE1
    CE2
    HD1
    HD2
    CP
    CE2
    HE1
    HE2
    HP

    CD1 CE1 CE1 HE1 CE1 CP


    CE2 CD2 CD2 HD2 CD2 CZ
    1.2285
    1.3432
    1.1137
    1.1137
    1.4478
    1.1160
    1.1160
    1.5405
    1.5382
    1.5382
    1.5394
    1.4496
    1.4496
    1.5382
    1.4504
    1.4496
    1.5322
    1.5322
    1.5322
    1.5322
    1.4496
    1.3663
    1.3663
    1.3663
    1.5086
    1.5086
    1.4130
    1.4106
    1.4130
    1.4000
    1.4000
    1.4005
    1.3994

    122.33
    124.79
    108.53
    108.53
    112.32
    107.50
    107.50
    112.81
    112.85
    112.85
    112.85
    112.63
    112.63
    112.63
    111.69
    111.69
    112.24
    112.24
    111.44
    111.44
    119.66
    121.12
    121.12
    121.12
    122.19
    119.29
    120.74
    120.75
    120.74
    120.02
    120.02
    120.04
    120.00

    -0.06
    128.92
    -117.40
    120.10
    53.30
    -118.96
    118.24
    -174.32
    120.61
    -122.07
    52.71
    123.49
    -121.08
    -55.66
    -157.27
    58.25
    123.62
    -118.88
    -120.03
    121.81
    -172.03
    175.96
    36.02
    -148.04
    178.23
    -178.39
    179.21
    179.73
    -0.87
    -0.51
    179.42
    -179.55
    179.25

    CP

    124.79
    108.53
    111.38
    112.32
    107.50
    112.81
    111.56
    112.85
    108.70
    109.93
    112.63
    106.93
    108.70
    111.69
    119.66
    112.24
    113.36
    108.26
    108.75
    109.36
    121.12
    118.45
    122.19
    119.29
    120.74
    120.75
    119.10
    119.18
    120.02
    120.00
    120.07
    120.09
    120.00

    PRES GPMB
    0.00 ! C15H19N2O2 (01OH09), chayan
    ! This compound has 4-benzyl piperidine at gamma position
    ! core residue Bile Acid Basic moiety 1 (BAB1)
    DELETE ATOM HT2
    !
    GROUP
    !
    CG2--CG3
    CD1--CE1
    ATOM CG CG2O1
    0.51 !
    /
    \
    //
    \\

    HP

    1.4478
    1.1137
    1.1153
    1.5405
    1.1160
    1.5394
    1.5378
    1.5382
    1.1120
    1.1117
    1.4496
    1.1175
    1.1134
    1.4504
    1.3663
    1.5322
    1.1116
    1.1150
    1.1120
    1.1109
    1.5086
    1.2305
    1.4130
    1.4106
    1.4000
    1.4005
    1.0814
    1.0819
    1.3994
    1.3995
    1.0806
    1.0804
    1.0804

    OG
    ||

    ATOM OG OG2D1 -0.51 !


    --CG1
    NG4--CQ--CB--CZ
    CP
    ATOM NT NG2S1 -0.47 !
    \
    /
    ||
    \ __ /
    ATOM HT1 HGP1
    0.47 !
    CG6--CG5
    OQ
    CD2--CE2
    GROUP
    !

    CG---NT--CGT
    /

    HT1

    CC3
    \

    ATOM CGT CG321

    -0.18 !

    O24

    CC2

    ATOM HGT1 HGA2

    0.09 !

    ||

    ATOM HGT2 HGA2

    0.09 !

    GROUP
    ATOM CG1 CG311

    -0.09 !

    ATOM HG1 HGA1

    0.09 !

    GROUP

    Me19 |

    ATOM HG21 HGA2

    0.09 !

    C1 | C9

    ATOM HG22 HGA2

    0.09 !

    C2

    C10 C8

    ATOM CG3 CG321

    0.06 !

    ATOM HG31 HGA2

    0.09 !

    C3

    C5

    C7

    ATOM HG32 HGA2

    0.09 !

    0.09 !

    ATOM HG52
    GROUP
    ATOM CG6
    ATOM HG61
    ATOM HG62
    GROUP
    ATOM CQ
    ATOM OQ
    GROUP
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CZ
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2

    HGA2
    CG321
    HGA2
    HGA2

    0.09 !
    !
    -0.18 !
    0.09 !
    0.09 !

    CG2O1
    OG2D1

    0.51
    -0.51

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2R61 0.00
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    C14

    C16

    C15

    / \ / \ / \

    -0.48 ! HO

    ATOM HG51 HGA2

    C23

    / \|/ \ / \ /

    0.06 !

    C20

    C11 C13---C17

    -0.18 !

    ATOM CG5 CG321

    C24

    C4

    C6

    CC1

    \ / \ / \ / \

    / \ |

    ATOM CG2 CG321

    ATOM NG4 NG2S1

    C22

    C12 Me18

    GROUP

    Me21

    OH

    GPBZ (01OH08)

    NH

    CA---OA2
    ||
    OA1

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CE1
    HE1
    CE2
    HE2
    CP
    HP

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    NT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CQ
    CZ
    CP
    NT

    CGT
    HG1
    HG21
    HG31
    CG5
    HG51
    HG61
    OQ
    CD1
    CE2
    CG

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG
    CG
    HGT1
    HGT1
    NT
    HG1
    HG1
    CGT
    CG3
    CG3
    CG1
    NG4
    NG4
    CG2
    CG5
    CG3
    CG6
    CG6
    CG5
    CG5
    CG3
    NG4
    NG4
    CQ
    CQ
    CQ
    CQ
    CB
    CB
    CZ
    CZ
    CZ
    CD1
    CD1
    CD2
    CE1

    CG
    NT
    NT
    NT
    CGT
    CGT
    CGT
    CG1
    CG1
    CG1
    CG2
    CG2
    CG2
    CG3
    CG3
    NG4
    NG4
    NG4
    CG1
    CG1
    NG4
    CB
    CQ
    CZ
    CZ
    CB
    CB
    CZ
    CZ
    CE1
    CE2
    CD1
    CE1
    CP
    CP
    CE2

    CGT
    CG1
    CG2
    CG3
    NG4
    CG5
    CG6
    CQ
    CD1
    CE2
    CGT
    NT
    CGT
    *CGT
    *CGT
    CG1
    *CG1
    *CG1
    CG2
    *CG2
    *CG2
    CG3
    *CG3
    *CG3
    NG4
    *NG4
    CG5
    *CG5
    *CG5
    *CG6
    *CG6
    CQ
    *CQ
    CB
    *CB
    *CB
    CZ
    CZ
    CD1
    CD2
    *CD1
    *CD2
    CE1
    CP
    *CE1
    *CE2
    *CP

    HGT1
    CG2
    HG22
    HG32
    CQ
    HG52
    HG62
    CB
    HD1
    HE2
    HT1

    CGT HGT2 CGT CG1


    CG2 CG3
    CG3 NG4

    CGT
    HGT1
    HGT2
    CG1
    HG1
    CG2
    CG6
    CG3
    HG21
    HG22
    NG4
    HG31
    HG32
    CG5
    CQ
    CG6
    HG51
    HG52
    HG61
    HG62
    CB
    OQ
    CZ
    HB1
    HB2
    CD1
    CD2
    CE1
    CE2
    HD1
    HD2
    CP
    CE2
    HE1
    HE2
    HP

    CG5
    CG6
    CB
    CD1
    CE2

    CG6
    CG1
    HB1 CB HB2 CB CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    1.2285
    1.3432
    1.1137
    1.1137
    1.4478
    1.1159
    1.1159
    1.5405
    1.5378
    1.5378
    1.5379
    1.4510
    1.4510
    1.5378
    1.4510
    1.4510
    1.5341
    1.5341
    1.5341
    1.5341
    1.4510
    1.3625
    1.3625
    1.5054
    1.5054
    1.5054
    1.5054
    1.5140
    1.5140
    1.4073
    1.4047
    1.4073
    1.4008
    1.4008
    1.4012
    1.4006

    122.33
    124.78
    108.54
    108.54
    112.32
    107.52
    107.52
    112.83
    112.65
    112.65
    112.65
    113.09
    113.09
    113.09
    112.54
    112.54
    112.72
    112.72
    111.80
    111.80
    120.07
    120.00
    120.00
    125.27
    125.27
    125.27
    125.27
    122.41
    118.39
    120.37
    120.47
    120.37
    120.00
    120.00
    119.94
    120.02

    -0.09
    129.33
    -117.40
    120.10
    53.04
    -119.17
    118.39
    -175.41
    120.60
    -121.96
    52.69
    124.04
    -120.86
    -53.58
    -162.86
    55.30
    122.23
    -119.44
    -120.02
    121.99
    178.19
    172.13
    57.32
    -122.00
    125.08
    5.90
    -174.94
    -179.94
    179.98
    -179.93
    179.78
    -0.43
    -0.14
    179.88
    -179.94
    179.81

    CP

    124.78
    108.54
    111.37
    112.32
    107.52
    112.83
    111.58
    112.65
    108.78
    109.96
    113.09
    106.80
    108.45
    112.54
    120.07
    112.72
    113.35
    108.34
    108.69
    109.45
    120.00
    118.37
    125.27
    105.23
    106.72
    122.41
    118.39
    120.37
    120.47
    119.41
    119.94
    120.00
    120.02
    120.19
    120.02
    120.08

    HP

    1.4478
    1.1137
    1.1153
    1.5405
    1.1159
    1.5379
    1.5364
    1.5378
    1.1119
    1.1117
    1.4510
    1.1174
    1.1134
    1.4510
    1.3625
    1.5341
    1.1122
    1.1144
    1.1121
    1.1109
    1.5054
    1.2266
    1.5140
    1.1143
    1.1126
    1.4073
    1.4047
    1.4008
    1.4012
    1.0805
    1.0797
    1.4006
    1.4009
    1.0807
    1.0802
    1.0803

    !End of Pablo's compounds


    !Start of Rana's and Swan's compounds
    RESI 2AMP

    0.00 ! C7H8N2O 2-acetamide pyridine, Chayan

    ! Made in
    GROUP
    ATOM NZ
    GROUP
    ATOM CE1
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM NE
    ATOM HE
    ATOM C
    ATOM O
    ATOM CM
    ATOM HM1
    ATOM HM2
    ATOM HM3
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    NZ
    CE1
    C
    C

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CD1
    C
    CE1
    CM
    O
    O
    O

    order to build Polli's compounds (Rana & Swan)


    NG2R60 -0.600 !
    !
    CG2R61 0.600 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    CG2R61 0.180 !
    HGR62
    0.120 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    NG2S1 -0.620 !
    HGP1
    0.320 !
    CG2O1
    0.550 !
    OG2D1 -0.550 !
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09
    HG
    CE2
    NE
    CM
    CM

    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CE1
    CE1
    NE
    NE
    C
    C
    C

    CG
    CE2
    NE
    CM
    NE
    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    NE
    *NE
    C
    *C
    CM
    CM
    CM

    CD1
    HE2
    HE
    HM1
    O
    NZ
    CE2
    CD2
    HG
    HD1
    HD2
    NE
    HE2
    C
    HE
    CM
    O
    HM1
    HM2
    HM3

    CD1
    CE2
    NE
    CM
    NE

    O
    NZ---CE2
    ||
    //
    \\
    CM--C--NE--CE1
    CD2
    |
    \ ___ /
    HE
    CD1---CG
    2AMP

    HD1
    CD2
    C
    HM2
    C

    1.4062
    1.4051
    1.3330
    1.4062
    1.4051
    1.4013
    1.3330
    1.3284
    1.4051
    1.3256
    1.3987
    1.4775
    1.2197
    1.2197
    1.2197

    CD1
    CD2
    C
    CM
    CE1
    118.77
    121.31
    120.60
    118.83
    118.77
    118.04
    121.31
    122.45
    127.83
    128.89
    128.89
    115.52
    120.61
    120.61
    120.61

    CE1 CE1 NZ
    HD2 CD2 CG
    O
    HM3
    HE
    0.00
    0.00
    0.00
    -180.00
    180.00
    -180.00
    -180.00
    -180.00
    0.00
    180.00
    180.00
    -180.00
    119.56
    0.00
    -119.56

    121.31
    120.60
    122.45
    120.71
    119.96
    121.24
    127.83
    122.15
    128.89
    109.18
    115.52
    123.87
    110.14
    109.25
    110.14

    1.3330
    1.3284
    1.4013
    1.0807
    1.0752
    1.0783
    1.3987
    1.0814
    1.3256
    0.9866
    1.4775
    1.2197
    1.1102
    1.1117
    1.1102

    RESI 3AMP
    0.00 ! C7H8N2O 3-acetamide pyridine, Chayan
    ! Made in order to build Polli's compounds (Rana & Swan)
    ! Taken from Acetamide and 4-Amino pyridine
    GROUP
    ATOM NZ NG2R60 -0.600 !
    GROUP
    !
    ATOM CE1 CG2R61 0.180 !
    ATOM HE1 HGR62
    0.120 !
    O
    CE1--NZ
    GROUP
    !
    ||
    //
    \\
    ATOM CE2 CG2R61 0.180 !
    CM--C--ND--CD1
    CE2
    ATOM HE2 HGR62
    0.120 !
    |
    \ ___ /

    GROUP
    ATOM CD1
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CG
    ATOM HG
    GROUP
    ATOM ND
    ATOM HD
    ATOM C
    ATOM O
    ATOM CM
    ATOM HM1
    ATOM HM2
    ATOM HM3
    BOND
    BOND
    BOND
    BOND
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    !
    0.300 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    !
    NG2S1 -0.620 !
    HGP1
    0.320 !
    CG2O1
    0.550 !
    OG2D1 -0.550 !
    CG331 -0.27
    HGA3
    0.09
    HGA3
    0.09
    HGA3
    0.09

    HD

    CG---CD2

    CG
    NZ
    CD1
    C
    C

    CG2R61

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CE1
    C
    CD1
    CM
    O
    O
    O

    HG
    CE2
    ND
    CM
    CM
    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CD1
    CD1
    ND
    ND
    C
    C
    C

    CG
    CE2
    ND
    CM
    ND
    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    ND
    *ND
    C
    *C
    CM
    CM
    CM

    CD1
    HE2
    HD
    HM1
    O
    NZ
    CE2
    CD2
    HG
    ND
    HD2
    HE1
    HE2
    C
    HD
    CM
    O
    HM1
    HM2
    HM3

    CD1
    CE2
    ND
    CM
    ND

    3AMP

    CE1
    CD2
    C
    HM2
    C

    1.4078
    1.4129
    1.3381
    1.4078
    1.4129
    1.4035
    1.3381
    1.3292
    1.4129
    1.3351
    1.4213
    1.4776
    1.2198
    1.2198
    1.2198

    CE1
    CD2
    C
    CM
    CD1
    116.24
    123.96
    118.93
    120.04
    116.24
    118.00
    123.96
    122.82
    127.27
    126.90
    126.90
    115.67
    120.73
    120.73
    120.73

    HE1 CE1 NZ
    HD2 CD2 CG
    O
    HM3
    HD
    0.00
    0.00
    0.00
    -180.00
    -180.00
    180.00
    180.00
    -180.00
    0.00
    -180.00
    -180.00
    180.00
    119.43
    0.00
    -119.43

    123.96
    118.93
    122.82
    120.23
    116.49
    121.42
    121.22
    122.14
    126.90
    115.12
    115.67
    123.60
    110.22
    109.14
    110.22

    1.3381
    1.3292
    1.4035
    1.0783
    1.4213
    1.0782
    1.0791
    1.0813
    1.3351
    0.9890
    1.4776
    1.2198
    1.1101
    1.1120
    1.1101

    RESI 2AMF
    0.00 ! C8H9NO2 2-acetamide phenol, Chayan
    ! Made in order to build Polli's compounds (Rana & Swan)
    GROUP
    ATOM CM
    ATOM HM1
    ATOM HM2
    ATOM HM3
    GROUP
    ATOM C
    ATOM O
    GROUP
    ATOM N
    ATOM H
    ATOM CZ
    GROUP
    ATOM CD1
    ATOM OD
    ATOM HOD
    GROUP

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG2O1
    OG2D1

    0.52
    -0.52

    NG2S1 -0.47
    HGP1
    0.33
    CG2R61 0.14
    CG2R61 0.11
    OG311 -0.53
    HGP1
    0.42

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    O
    CD2--CE2
    ||
    //
    \\
    CM--C--N---CZ
    CP
    |
    \ ___ /
    H
    CD1---CE2
    |
    OH(D)
    2AMF

    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CP
    ATOM HP
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2

    CG2R61 -0.115 !
    HGR61
    0.115 !

    BOND
    BOND
    BOND
    BOND

    HM1
    O
    CD1
    HP

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CM
    C
    CZ
    CP

    N
    HM1
    HM1
    N
    CM
    CZ
    C
    CD1
    N
    CE1
    CZ
    CZ
    CP
    CD1
    CE2
    CD2
    CE2
    HM1
    HM1
    HM1
    N
    CM
    CZ
    C
    CD1
    N
    CE1
    CZ
    CZ
    CP
    CD1
    CE2
    CD2
    CE2

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    C
    C
    C
    CM
    C
    C
    N
    N
    CZ
    CZ
    CD1
    CD1
    CD1
    CE1
    CE1
    CP
    CZ
    C
    C
    CM
    CM
    C
    C
    N
    N
    CZ
    CZ
    CD1
    CD1
    CD1
    CE1
    CE1
    CP
    CZ

    CM
    C
    CD1
    CP
    CM
    *CM
    *CM
    *C
    N
    *N
    CZ
    *CZ
    CD1
    *CD1
    OD
    CE1
    *CE1
    CP
    *CP
    *CE2
    *CD2
    *CM
    *CM
    C
    *C
    N
    *N
    CZ
    *CZ
    CD1
    *CD1
    OD
    CE1
    *CE1
    CP
    *CP
    *CE2
    *CD2

    HM2
    N
    OD
    CE2
    HM1
    HM2
    HM3
    O
    CZ
    H
    CD1
    CD2
    CE1
    OD
    HOD
    CP
    HE1
    CE2
    HP
    HE2
    HD2
    HM2
    HM3
    N
    O
    CZ
    H
    CD1
    CD2
    CE1
    OD
    HOD
    CP
    HE1
    CE2
    HP
    HE2
    HD2

    PRES 2APP
    0.00
    Amide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2

    CM
    N
    OD
    CE2

    HM3
    H
    HOD
    HE2

    1.3407
    1.1118
    1.1118
    1.3407
    1.4807
    1.4232
    1.3407
    1.4149
    1.4232
    1.4002
    1.4149
    1.4149
    1.4013
    1.4002
    1.3995
    1.4022
    1.4022
    1.1118
    1.1118
    1.1118
    1.3407
    1.4807
    1.4232
    1.3407
    1.4149
    1.4232
    1.4002
    1.4149
    1.4149
    1.4013
    1.4002
    1.3995
    1.4022
    1.4022

    CM
    N
    CD1
    CE2
    115.20
    109.20
    109.20
    115.20
    115.20
    130.65
    130.65
    115.77
    115.77
    120.37
    120.75
    120.37
    120.00
    120.00
    119.97
    120.11
    120.52
    109.20
    109.20
    109.20
    115.20
    115.20
    130.65
    130.65
    115.77
    115.77
    120.37
    120.75
    120.37
    120.00
    120.00
    119.97
    120.11
    120.52

    C
    CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    180.00
    119.48
    -119.48
    -180.00
    -180.00
    180.00
    180.00
    -180.00
    -180.00
    180.00
    -180.00
    0.00
    180.00
    0.00
    180.00
    180.00
    180.00
    119.48
    -119.48
    180.00
    -180.00
    -180.00
    180.00
    180.00
    -180.00
    -180.00
    180.00
    -180.00
    0.00
    180.00
    0.00
    180.00
    180.00
    180.00

    109.20
    110.20
    110.20
    119.94
    130.65
    118.72
    115.77
    125.20
    120.37
    120.75
    107.60
    120.00
    120.56
    119.97
    120.14
    120.11
    120.79
    110.20
    110.20
    115.20
    119.94
    130.65
    118.72
    115.77
    125.20
    120.37
    120.75
    107.60
    120.00
    120.56
    119.97
    120.14
    120.11
    120.79

    1.1118
    1.1102
    1.1102
    1.2226
    1.4232
    0.9928
    1.4149
    1.4017
    1.4002
    1.4188
    0.9602
    1.4013
    1.0796
    1.3995
    1.0810
    1.0811
    1.0784
    1.1102
    1.1102
    1.3407
    1.2226
    1.4232
    0.9928
    1.4149
    1.4017
    1.4002
    1.4188
    0.9602
    1.4013
    1.0796
    1.3995
    1.0810
    1.0811
    1.0784

    ! C16H15N2O3 Alpha-Benzyl Gamma-2-Amino Pyridine GA CDCA


    Acid CDCA Amide (GA)
    !
    !

    GROUP
    ATOM CC3 CG321
    ATOM HC3A HGA2
    CJ1--CK1
    ATOM HC3B HGA2
    //
    \\
    GROUP
    CY
    CJ
    ATOM CG CG2O1
    / \ __ /
    ATOM OG OG2D1
    CJ2--CK2
    GROUP

    !
    -0.18 !
    0.09 !
    0.09 !
    !

    OA1

    0.52 !

    -0.52 !

    ATOM NG NG2S1 -0.47 !


    NG
    NZ---CE2
    ATOM HG HGP1
    0.33 !
    \ //
    \\
    ATOM CZ CG2R61 0.44 !
    CZ
    CP
    GROUP
    !
    \ __ /
    ATOM CD1 CG2R61 -0.115 !
    CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    GROUP

    OH

    ATOM NZ

    Me19 |

    ATOM HE2 HGR62

    0.120 !

    GROUP

    !
    CG2R61 -0.115 !
    HGR61
    0.115
    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61 0.00
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115

    C14

    C16

    / \|/ \ / \ /

    !
    0.180 !

    C1 | C9

    NG2R60 -0.600 !

    ATOM CE2 CG2R61

    C20

    C11 C13---C17

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    C24

    CC1

    C2

    C10 C8

    C3

    C5

    C7

    C15

    / \ / \ / \
    HO

    C4

    C6

    CC3

    \ / \ / \ / \ / \ /

    / \ |

    0.115 !

    GROUP

    ATOM CP
    ATOM HP
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2

    ||
    C22

    C12 Me18

    ATOM CE1 CG2R61 -0.115 !

    GROUP

    Me21

    ATOM HE1 HGR61

    CA--OA2---CB

    O24

    OH

    2APP

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HJ2
    CK1
    HK1
    CK2
    HK2
    CQ
    HQ

    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    OA2
    CB
    CY
    CQ
    CG
    CZ
    CP
    CG

    CB
    HB1
    CJ1
    CK2
    OG
    NZ
    CE1
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1
    CC2
    NG
    CG
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CZ
    CD1
    CE1
    CP

    CA
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2
    CC3
    CC3
    CZ
    CG
    NG
    CZ
    CD1
    CE1
    CP
    CE1
    CP
    CE2
    NZ

    CB
    CJ1
    CK2
    CG
    NZ
    CE1
    NG
    OA2
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    CG
    *CG
    *NG
    NG
    CZ
    CD1
    CE1
    CP
    CE2
    *CD1
    *CE1
    *CP
    *CE2

    HB2
    HJ1
    HK2
    NG
    CE2
    HE1
    OG
    CB
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    NG
    OG
    HG
    CZ
    CD1
    CE1
    CP
    CE2
    NZ
    HD1
    HE1
    HP
    HE2

    PRES 3APP
    0.00
    Amide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18
    CJ1--CK1

    CB
    CJ1
    CK2
    NG
    CE2
    CE1
    NG
    1.5262
    1.1154
    1.1163
    1.5059
    1.4053
    1.4046
    1.4046
    1.4053
    1.4053
    1.5059
    1.5059
    1.4046
    1.4013
    1.4011
    1.4013
    1.4021
    1.4011
    1.4014
    1.4011
    1.5506
    1.3339
    1.3339
    1.4983
    1.3339
    1.4019
    1.4046
    1.4059
    1.4033
    1.4046
    1.4059
    1.4033
    1.4015

    CY
    CK1
    CJ2
    HG
    HE2
    CD1
    CG

    CK1
    CJ2
    NG
    CE2
    CD1
    CZ

    109.01
    110.02
    110.83
    113.59
    121.33
    119.17
    119.50
    121.33
    121.33
    119.17
    121.33
    120.30
    119.97
    120.01
    120.30
    120.18
    119.97
    120.03
    120.01
    112.89
    116.27
    129.72
    116.27
    129.72
    127.25
    118.62
    118.91
    118.00
    118.62
    118.91
    118.00
    122.46

    HK1
    HJ2
    CZ
    CP
    HD1
    HG

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CP HP
    CD1 CZ

    178.05
    65.56
    -53.21
    -172.68
    -117.38
    62.26
    179.63
    5.26
    120.54
    180.00
    -179.83
    -0.04
    0.26
    -0.08
    -179.72
    179.57
    -179.63
    179.68
    179.51
    -51.60
    -171.32
    179.61
    -177.09
    -1.35
    -179.67
    0.11
    0.05
    0.00
    -179.85
    -179.93
    -179.93
    -179.90

    116.10
    116.10
    116.10
    116.10
    113.59
    113.59
    121.33
    108.43
    106.20
    120.30
    120.18
    119.97
    120.01
    120.03
    119.65
    120.00
    120.04
    120.00
    120.01
    116.27
    119.51
    108.48
    129.72
    127.25
    118.62
    118.91
    118.00
    122.46
    120.00
    120.66
    120.73
    115.36

    1.4465
    1.3439
    1.3439
    1.3439
    1.4465
    1.4465
    1.5059
    1.1154
    1.1163
    1.4013
    1.4021
    1.4011
    1.4014
    1.4021
    1.0800
    1.0798
    1.0806
    1.0809
    1.0810
    1.3339
    1.2231
    0.9872
    1.4019
    1.4046
    1.4059
    1.4033
    1.4015
    1.3291
    1.0758
    1.0804
    1.0781
    1.0811

    ! C16H15N2O3 Alpha-Benzyl Gamma-3-Amino Pyridine GA CDCA


    Acid CDCA Amide (GA)
    !
    !
    !
    !

    ATOM HC3A HGA2


    //
    \\
    ATOM HC3B HGA2
    Y
    CJ
    GROUP
    \ __ /
    ATOM CG CG2O1
    CJ2--CK2
    ATOM OG OG2D1

    0.09 !
    0.09 !

    OA1

    |
    O24

    CA--OA2---CB

    -0.52 !

    ||

    C24

    CC1

    OH

    Me19 |

    C14

    C16

    C1 | C9

    / \|/ \ / \ /
    C10 C8

    ATOM HE1 HGR61

    C3

    C5

    C7

    0.115 !
    !

    ATOM CP

    CG2R61

    0.180 !

    ATOM HP

    HGR62

    0.120 ! HO

    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2
    ATOM HJ2
    ATOM CK1
    ATOM HK1

    C20

    C11 C13---C17

    C2

    C15

    / \ / \ / \
    C4

    C6

    OH

    !
    NG2R60 -0.600 !
    !
    CG2R61
    HGR62
    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.180
    0.120
    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61 0.00
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    CC3

    NG

    \ / \ / \ / \ / \ /

    / \ |

    ATOM CE1 CG2R61 -0.115 !

    GROUP

    C22

    C12 Me18

    GROUP

    Me21

    0.115 !

    GROUP

    ATOM NZ

    0.52 !

    GROUP
    !
    CD2---NZ
    ATOM NG NG2S1 -0.47 !
    \ //
    \\
    ATOM HG HGP1
    0.33 !
    CZ
    CP
    ATOM CZ CG2R61 0.14 !
    \ __ /
    GROUP
    !
    CD1--CE1
    ATOM CD1 CG2R61 -0.115 !
    ATOM HD1 HGR61

    3APP

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM
    ATOM
    ATOM
    ATOM

    CK2
    HK2
    CQ
    HQ

    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    OA2
    CB
    CY
    CQ
    CG
    CZ
    CP
    CG

    CB
    HB1
    CJ1
    CK2
    OG
    CD2
    CE1
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    HC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1
    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD2
    NZ
    CZ
    CZ
    NZ
    CP

    CA
    CC1
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2
    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD2
    NZ
    CP
    NZ
    CE1
    CE1
    CD1

    CB
    CJ1
    CK2
    CG
    CD2
    CE1
    NG
    OA2
    CA
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    CG
    *NG
    *CG
    NG
    CZ
    CD2
    NZ
    CP
    CE1
    *CD2
    *CD1
    *CP
    *CE1

    HB2
    HJ1
    HK2
    NG
    HD2
    HE1
    OG
    CB
    OA2
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    NG
    HG
    OG
    CZ
    CD2
    NZ
    CP
    CE1
    CD1
    HD2
    HD1
    HP
    HE1

    PRES 4APP
    0.00
    A Amide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18
    CJ1--CK1
    ATOM HC3A HGA2
    0.09
    //
    \\

    CB
    CJ1
    CK2
    NG
    CD2
    CE1
    NG
    1.5266
    1.1142
    1.1155
    1.1162
    1.5060
    1.4052
    1.4048
    1.4048
    1.4052
    1.4052
    1.5060
    1.5060
    1.4048
    1.4013
    1.4010
    1.4013
    1.4020
    1.4010
    1.4014
    1.4010
    1.5518
    1.3433
    1.3433
    1.5020
    1.3433
    1.4225
    1.4111
    1.3358
    1.3292
    1.4111
    1.4072
    1.3292
    1.4031

    CY
    CK1
    CJ2
    HG
    NZ
    CD1
    CG

    CK1
    CJ2
    NG
    NZ
    CD1
    CZ

    108.91
    106.59
    110.00
    110.85
    113.54
    121.32
    119.18
    119.50
    121.32
    121.32
    119.18
    121.32
    120.31
    119.96
    120.01
    120.31
    120.18
    119.96
    120.03
    120.01
    114.60
    128.03
    117.28
    117.28
    128.03
    126.45
    123.66
    119.08
    122.82
    123.66
    119.79
    122.82
    118.00

    HK1
    HJ2
    CZ
    CP
    HD1
    HG

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CP HP
    CD1 CZ

    178.06
    -130.75
    65.28
    -53.55
    -173.02
    -119.04
    60.58
    179.62
    3.54
    118.88
    -179.91
    -179.85
    -0.14
    0.31
    -0.07
    -179.69
    179.59
    -179.53
    179.71
    179.51
    -1.21
    179.74
    179.83
    -180.00
    0.97
    -179.92
    0.08
    0.01
    -0.03
    179.94
    179.97
    -179.97
    -179.98

    116.23
    108.91
    116.23
    116.23
    116.23
    113.54
    113.54
    121.32
    108.43
    106.21
    120.31
    120.18
    119.96
    120.01
    120.03
    119.67
    120.02
    120.06
    119.99
    120.00
    117.28
    114.63
    119.35
    128.03
    126.45
    123.66
    119.08
    122.82
    118.00
    114.79
    120.05
    122.13
    121.40

    1.4463
    1.3434
    1.3434
    1.3434
    1.3434
    1.4463
    1.4463
    1.5060
    1.1155
    1.1162
    1.4013
    1.4020
    1.4010
    1.4014
    1.4020
    1.0799
    1.0799
    1.0806
    1.0809
    1.0810
    1.3433
    0.9895
    1.2229
    1.4225
    1.4111
    1.3358
    1.3292
    1.4031
    1.4059
    1.0796
    1.0788
    1.0811
    1.0780

    ! C16H15N2O3 Alpha-Benzyl Gamma-4-Amino Pyridine GA CDC


    Acid CDCA Amide (GA)
    !
    !
    !
    !
    !

    ATOM HC3B HGA2


    CY
    CJ
    GROUP
    / \ __ /
    ATOM CG CG2O1
    B
    CJ2--CK2
    ATOM OG OG2D1
    GROUP
    NG
    CD2--CE2
    ATOM NG NG2S1
    / \ //
    \\
    ATOM HG HGP1
    CZ
    NZ
    ATOM CZ CG2R61
    \ __ /
    GROUP
    CD1--CE1
    ATOM CD1 CG2R61
    ATOM HD1 HGR61

    0.09 !

    OA1

    0.52 !

    O24

    CA--OA2---C

    -0.52 !

    ||

    C24

    CC1

    OH

    -0.47 !

    0.33 !

    Me19 |

    0.115 !

    C1 | C9

    !
    0.180 !

    C2

    C10 C8

    ATOM HE1 HGR62

    0.120 !

    C3

    C5

    C7

    !
    NG2R60 -0.600 !

    GROUP

    ATOM CE2 CG2R61

    0.180 !

    ATOM HE2 HGR62

    0.120 !

    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2
    ATOM HJ2
    ATOM CK1
    ATOM HK1
    ATOM CK2
    ATOM HK2

    CG2R61 -0.115
    HGR61
    0.115
    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    C14

    C16

    / \|/ \ / \ /

    ATOM CE1 CG2R61

    ATOM NZ

    C20

    C11 C13---C17

    -0.115 !

    C15

    / \ / \ / \
    HO

    C4

    C6

    CC3

    \ / \ / \ / \ / \

    / \ |

    GROUP

    C22

    C12 Me18

    0.14 !

    GROUP

    Me21

    OH

    4APP

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM CQ
    ATOM HQ

    CG2R61 -0.115
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CB
    HB1
    CJ1
    CK2
    OG
    CD1
    CE2
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OA2
    CB
    CY
    CQ
    CG
    CZ
    NZ
    CG

    CC1
    HC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ
    CK1
    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CE1
    CE2
    NZ
    NZ

    CA
    CC1
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2
    CK2
    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    NZ
    CZ
    CZ
    CD1
    CD2

    CB
    CJ1
    CK2
    CG
    CD1
    CE2
    NG
    OA2
    CA
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    CG
    *NG
    *CG
    NG
    CZ
    CD1
    CE1
    NZ
    CE2
    *CD1
    *CD2
    *CE1
    *CE2

    HB2
    HJ1
    HK2
    NG
    HD1
    HE2
    OG
    CB
    OA2
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    NG
    HG
    OG
    CZ
    CD1
    CE1
    NZ
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2

    PRES 2APD
    0.00
    eprotected), Chayan
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18

    CB
    CJ1
    CK2
    NG
    CD1
    CE2
    NG
    1.5239
    1.1142
    1.1164
    1.1163
    1.5039
    1.4046
    1.4046
    1.4046
    1.4046
    1.4046
    1.5039
    1.5039
    1.4046
    1.4015
    1.4011
    1.4015
    1.4014
    1.4011
    1.4013
    1.4011
    1.5519
    1.3446
    1.3446
    1.5018
    1.3446
    1.4198
    1.4032
    1.4006
    1.3294
    1.4006
    1.4002
    1.3294
    1.3282

    CK1
    CJ2
    NG
    CE1
    CD2
    CZ

    109.11
    106.36
    110.53
    110.59
    113.58
    120.24
    120.15
    119.59
    120.24
    120.24
    120.15
    120.24
    120.20
    119.97
    120.05
    120.20
    120.19
    119.97
    119.98
    120.05
    114.52
    129.26
    116.90
    116.90
    129.26
    125.21
    118.21
    122.53
    119.84
    118.21
    118.32
    122.53
    122.41

    HK1
    HJ2
    CZ
    HE1
    HD2
    HG

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CE1 NZ
    CD2 CZ

    -178.78
    -134.92
    59.14
    -59.32
    179.91
    -90.36
    88.42
    178.79
    32.16
    147.07
    -179.79
    179.88
    0.22
    0.48
    -0.39
    -179.58
    179.62
    -179.63
    179.84
    -179.99
    13.37
    179.52
    179.10
    -179.26
    13.81
    -179.01
    0.20
    0.20
    -0.22
    -179.44
    -179.68
    180.00
    -179.87

    115.31
    109.11
    115.31
    115.31
    115.31
    113.58
    113.58
    120.24
    107.39
    107.36
    120.20
    120.19
    119.97
    120.05
    119.98
    119.84
    119.87
    120.04
    119.99
    119.97
    116.90
    114.04
    119.13
    129.26
    125.21
    118.21
    122.53
    119.84
    122.41
    122.09
    121.19
    122.17
    122.39

    1.4471
    1.3428
    1.3428
    1.3428
    1.3428
    1.4471
    1.4471
    1.5039
    1.1164
    1.1163
    1.4015
    1.4014
    1.4011
    1.4013
    1.4014
    1.0799
    1.0801
    1.0807
    1.0807
    1.0807
    1.3446
    0.9891
    1.2233
    1.4198
    1.4032
    1.4006
    1.3294
    1.3282
    1.4002
    1.0759
    1.0764
    1.0810
    1.0812

    ! C7H7N2O Gamma-2-Amino Pyridine GA CDCA Amide (alpha d


    Acid CDCA Amide (GA)
    !
    !
    !
    !

    ATOM HC3A HGA2

    0.09 !

    ATOM HC3B HGA2

    0.09 !

    GROUP

    CY
    CK1
    CJ2
    HG
    CE1
    CD2
    CG

    OA1
    |
    O24

    CA--OA2

    ||

    ATOM CG CG2O1
    0.52 !
    NZ---CE2
    ATOM OG OG2D1 -0.52 !
    \ //
    \\
    GROUP
    !
    CZ
    CP
    ATOM NG NG2S1 -0.47 !
    \ __ /
    ATOM HG HGP1
    0.33 !
    CD1--CE1
    ATOM CZ CG2R61 0.44 !
    GROUP

    OH
    |

    Me19 |

    C2

    C10 C8

    ATOM HE2 HGR62

    0.120 !

    C3

    C5

    C7

    NG

    C23

    NH

    C14

    C16

    CC2

    CGP
    ||
    OGP

    C15

    CG2R61 -0.115 ! HO

    ATOM HP

    HGR61

    / \ / \ / \

    ATOM CP

    C4

    C6

    OH

    0.115 !

    GROUP

    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CD1
    ATOM HD1

    CG2R61 -0.115 !
    HGR62
    0.115 !

    BOND
    BOND
    BOND
    IMPR

    OG
    NZ
    CE1
    CC3

    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CZ
    CD1
    CE1
    CP

    CM3

    / \|/ \ / \ /

    0.180 !

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C20

    C1 | C9

    ATOM CE2 CG2R61

    CG
    CZ
    CP
    CG

    CC1

    C11 C13---C17

    GROUP

    C24

    \ / \ / \ / \ / \ /

    / \ |

    NG2R60 -0.600 !

    GROUP

    C22

    C12 Me18

    ATOM NZ

    Me21

    2APD

    CG2R61 -0.115
    HGR61
    0.115

    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CP
    CE1
    CP
    CE2
    NZ

    CG
    NZ
    CE1
    NG
    CG
    *NG
    *CG
    NG
    CZ
    CD1
    CE1
    CP
    CE2
    *CD1
    *CE1
    *CP
    *CE2

    NG
    CE2
    HE1
    OG
    NG
    HG
    OG
    CZ
    CD1
    CE1
    CP
    CE2
    NZ
    HD1
    HE1
    HP
    HE2

    NG
    CE2
    CE1
    NG
    1.5492
    1.3349
    1.3349
    1.4933
    1.3349
    1.4027
    1.4060
    1.4057
    1.4029
    1.4060
    1.4057
    1.4029
    1.4010

    HG
    HE2
    CD1
    CG

    NG
    CE2
    CD1
    CZ

    112.40
    129.91
    115.58
    115.58
    129.91
    126.80
    118.92
    118.91
    117.98
    118.92
    118.91
    117.98
    122.23

    CZ
    CP CP HP
    HD1 CD1 CZ
    HG
    -59.01
    179.75
    -178.53
    179.53
    -0.74
    -179.83
    0.05
    0.03
    0.00
    -179.87
    -179.95
    -179.95
    -179.94

    115.58
    110.72
    120.70
    129.91
    126.80
    118.92
    118.91
    117.98
    122.23
    119.87
    120.76
    120.75
    115.28

    1.3349
    0.9908
    1.2263
    1.4027
    1.4060
    1.4057
    1.4029
    1.4010
    1.3271
    1.0753
    1.0796
    1.0774
    1.0808

    PRES 3APD
    0.00 ! C7H7N2O Gamma-3-Amino Pyridine GA CDCA Amide (alpha d
    eprotected), Chayan
    ! core residue Glutamic Acid CDCA Amide (GA)

    DELETE ATOM OG1


    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321

    !
    !
    !
    -0.18 !

    ATOM HC3A HGA2

    0.09 !

    ATOM HC3B HGA2

    0.09 !

    GROUP

    OA1
    |

    ATOM CG CG2O1
    0.52 !
    NG
    CD2---NZ
    ATOM OG OG2D1 -0.52 !
    \ //
    \\
    GROUP
    !
    CZ
    CP
    ATOM NG NG2S1 -0.47 !
    \ __ /
    ATOM HG HGP1
    0.33 !
    CD1--CE1
    ATOM CZ CG2R61 0.14 !
    GROUP

    OH

    0.180 !

    ATOM HD2 HGR62

    0.120 !

    GROUP

    ||

    C24

    CC1

    Me19 |

    CG2R61

    0.180 !

    ATOM HP

    HGR62

    0.120 !

    GROUP

    C14

    C16

    C10 C8

    C3

    C5

    C7

    C4

    C6

    CG2R61 -0.115 !
    HGR62
    0.115 !

    BOND
    BOND
    BOND
    IMPR

    OG
    CD2
    CE1
    CC3

    CG
    CZ
    CP
    CG

    C15

    OH

    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD2

    3APD

    CG2R61 -0.115
    HGR61
    0.115

    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD2
    NZ

    CG
    CD2
    CE1
    NG
    CG
    *NG
    *CG
    NG
    CZ
    CD2
    NZ
    CP

    NG
    HD2
    HE1
    OG
    NG
    HG
    OG
    CZ
    CD2
    NZ
    CP
    CE1

    NG
    CD2
    CE1
    NG
    1.5535
    1.3422
    1.3422
    1.5030
    1.3422
    1.4197
    1.4108
    1.3390

    HG
    NZ
    CD1
    CG

    NG
    NZ
    CD1
    CZ

    114.91
    128.46
    117.54
    117.54
    128.46
    126.55
    124.13
    118.24

    CZ
    CP CP HP
    HD1 CD1 CZ
    HG
    -48.02
    -179.57
    -179.06
    -179.13
    -3.17
    179.85
    -0.43
    0.10

    117.54
    113.64
    119.46
    128.46
    126.55
    124.13
    118.24
    123.37

    CC2

    CGP

    OGP

    / \ / \ / \
    HO

    NH

    ||

    / \|/ \ / \ /

    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CD1
    ATOM HD1

    C23

    C1 | C9

    ATOM CP

    C20

    C11 C13---C17

    C2

    CM3

    \ / \ / \ / \ / \ /

    / \ |

    NG2R60 -0.600 !

    GROUP

    C22

    C12 Me18

    ATOM NZ

    Me21

    ATOM CD2 CG2R61

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CA--OA2

    O24

    1.3422
    1.0156
    1.2281
    1.4197
    1.4108
    1.3390
    1.3305
    1.4034

    IC
    IC
    IC
    IC
    IC

    NZ
    CZ
    CZ
    NZ
    CP

    CP
    NZ
    CE1
    CE1
    CD1

    CE1
    *CD2
    *CD1
    *CP
    *CE1

    CD1
    HD2
    HD1
    HP
    HE1

    PRES 4APD
    0.00
    protected), Chayan
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18

    1.3305
    1.4108
    1.4056
    1.3305
    1.4034

    123.37
    124.13
    119.87
    123.37
    117.85

    117.85
    114.91
    120.63
    121.76
    121.01

    1.4044
    1.0790
    1.0809
    1.0804
    1.0770

    ! C7H7N2O Gamma-4-Amino Pyridine GA CDCA Amide (alpha-de


    Acid CDCA Amide (GA)
    !
    !
    !
    !

    ATOM HC3A HGA2

    0.09 !

    ATOM HC3B HGA2

    0.09 !

    GROUP

    OA1
    |
    O24

    CA--OA2

    ||

    C24

    CC1

    ATOM CG CG2O1
    0.52 !
    NG
    CD2--CE2
    ATOM OG OG2D1 -0.52 !
    \ //
    \\
    GROUP
    !
    CZ
    NZ
    ATOM NG NG2S1 -0.47 !
    \ __ /
    ATOM HG HGP1
    0.33 !
    CD1--CE1
    ATOM CZ CG2R61 0.14 !
    GROUP

    OH

    Me19 |

    0.180 !

    ATOM HE1 HGR62

    0.120 !

    GROUP

    C14

    C16

    C1 | C9

    / \|/ \ / \ /

    ATOM CE1 CG2R61

    C20

    C11 C13---C17

    C2

    C10 C8

    C3

    C5

    C7

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    NG2R60 -0.600 !

    GROUP

    CC3

    \ / \ / \ / \ / \ /

    / \ |

    0.115 !

    GROUP

    C22

    C12 Me18

    ATOM HD1 HGR61

    Me21

    ATOM CD1 CG2R61 -0.115 !

    ATOM NZ

    0.07
    -179.72
    -179.90
    179.97
    179.97

    4APD

    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2

    CG2R61
    HGR62

    0.180 !
    0.120 !

    BOND CG
    BOND CZ
    BOND NZ

    OG CG NG NG HG NG CZ
    CD1 CD1 HD1 CD1 CE1 CE1 HE1 CE1 NZ
    CE2 CE2 HE2 CE2 CD2 CD2 HD2 CD2 CZ

    CG2R61 -0.115
    HGR61
    0.115

    C23

    NH

    CC2

    CG
    ||
    OG

    IMPR CG
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CE1
    CE2
    NZ
    NZ

    CC3 NG
    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    NZ
    CZ
    CZ
    CD1
    CD2

    CG
    *NG
    *CG
    NG
    CZ
    CD1
    CE1
    NZ
    CE2
    *CD1
    *CD2
    *CE1
    *CE2

    OG
    NG
    HG
    OG
    CZ
    CD1
    CE1
    NZ
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2

    PRES 2AFP
    0.00
    mide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18
    CJ1--CK1
    ATOM HC3A HGA2
    0.09
    //
    \\
    ATOM HC3B HGA2
    0.09
    CY
    CJ
    GROUP
    / \ __ /
    ATOM CG CG2O1
    0.52
    CJ2--CK2
    ATOM OG OG2D1 -0.52

    NG

    CG

    1.5535
    1.3441
    1.3441
    1.5032
    1.3441
    1.4177
    1.4027
    1.4012
    1.3307
    1.4012
    1.3990
    1.3307
    1.3315

    CZ
    114.98
    129.78
    117.27
    117.27
    129.78
    125.48
    118.11
    123.10
    118.95
    118.11
    118.37
    123.10
    122.87

    -47.60
    -179.11
    -178.79
    -179.47
    -75.00
    178.96
    -0.21
    -0.04
    -0.04
    179.50
    179.96
    -179.94
    179.77

    !
    !

    OA1

    O24

    CA--OA2---CB

    ||

    C24

    CC1

    OH

    C22

    C20

    / \ |

    C11 C13---C17
    Me19 |

    C14

    C16

    C1 | C9

    / \|/ \ / \ /

    ATOM CE1 CG2R61 -0.115 !

    ATOM HE1 HGR61

    C3

    C5

    C7

    0.115 !
    !

    C15

    / \ / \ / \
    HO

    C4

    C6

    CC3

    \ / \ / \ / \ / \ /

    C12 Me18

    CG2R61 -0.115 !

    Me21

    C10 C8

    ATOM CP

    1.3441
    1.0148
    1.2283
    1.4177
    1.4027
    1.4012
    1.3307
    1.3315
    1.3990
    1.0751
    1.0785
    1.0804
    1.0804

    Acid CDCA Amide (GA)


    !
    !
    !
    !

    C2

    GROUP

    117.27
    112.90
    119.11
    129.78
    125.48
    118.11
    123.10
    118.95
    122.87
    121.85
    120.58
    121.79
    121.77

    ! C17H16NO4 Alpha-Benzyl Gamma-2-Amino Phenol GA CDCA A

    GROUP
    !
    NG
    CD2--CE2
    ATOM NG NG2S1 -0.47 !
    \ //
    \\
    ATOM HG HGP1
    0.33 !
    CZ
    CP
    ATOM CZ CG2R61 0.14 !
    \ __ /
    GROUP
    !
    CD1--CE1
    ATOM CD1 CG2R61 0.11 !
    |
    ATOM OD OG311 -0.53 !
    OH(D)
    ATOM HOD HGP1
    0.42 !
    GROUP

    HG

    OH

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM HP

    HGR61

    0.115 !

    GROUP

    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2
    ATOM HJ2
    ATOM CK1
    ATOM HK1
    ATOM CK2
    ATOM HK2
    ATOM CQ
    ATOM HQ

    CG2R61 -0.115 !
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CB
    HB1
    CJ1
    CK2
    OG
    CD1
    HP
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG2R61 -0.115
    HGR61
    0.115

    OA2
    CB
    CY
    CQ
    CG
    CZ
    CP
    CG

    CC1
    HC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ
    CQ

    2AFP

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CA
    CC1
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1
    CJ2

    CB
    CJ1
    CK2
    CG
    CD1
    CP
    NG
    OA2
    CA
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1
    *CK2

    HB2
    HJ1
    HK2
    NG
    OD
    CE2
    OG
    CB
    OA2
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1
    HK2

    CB
    CJ1
    CK2
    NG
    OD
    CE2
    NG
    1.5213
    1.1144
    1.1133
    1.1175
    1.5072
    1.4049
    1.4040
    1.4040
    1.4049
    1.4049
    1.5072
    1.5072
    1.4040
    1.4011
    1.4012
    1.4011
    1.4015
    1.4012
    1.4013

    CY
    CK1
    CJ2
    HG
    HOD
    HE2
    CG

    CK1
    CJ2
    NG
    CD1
    CE2
    CZ

    109.18
    106.26
    108.22
    112.74
    114.91
    120.41
    119.97
    119.61
    120.41
    120.41
    119.97
    120.41
    120.21
    119.97
    120.06
    120.21
    120.17
    119.97
    119.97

    HK1
    HJ2
    CZ
    CE1
    CD2
    HG

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CE1 HE1 CE1 CP


    CD2 HD2 CD2 CZ

    176.21
    -147.37
    148.39
    32.40
    -92.05
    -89.66
    89.00
    178.67
    30.54
    143.47
    -179.11
    179.16
    0.12
    0.14
    -0.07
    179.64
    179.97
    179.91
    -179.99

    116.81
    109.18
    116.81
    116.81
    116.81
    114.91
    114.91
    120.41
    107.06
    108.08
    120.21
    120.17
    119.97
    120.06
    119.97
    119.77
    119.92
    119.96
    120.08

    1.4508
    1.3426
    1.3426
    1.3426
    1.3426
    1.4508
    1.4508
    1.5072
    1.1133
    1.1175
    1.4011
    1.4015
    1.4012
    1.4013
    1.4015
    1.0808
    1.0795
    1.0806
    1.0805

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CK1
    CC2
    CG
    HG
    CC3
    CG
    NG
    CZ
    NG
    CZ
    CD1
    CE1
    CD1
    CE2
    CP
    CP

    CK2
    CC3
    CZ
    NG
    CG
    NG
    CZ
    CD1
    CZ
    CD1
    CE1
    CP
    CD2
    CZ
    CD1
    CD2

    *CQ
    CG
    *NG
    CG
    NG
    CZ
    CD1
    OD
    CD1
    CE1
    CP
    CE2
    *CP
    *CD2
    *CE1
    *CE2

    HQ
    NG
    HG
    OG
    CZ
    CD1
    OD
    HOD
    CE1
    CP
    CE2
    CD2
    HP
    HD2
    HE1
    HE2

    PRES 3AFP
    0.00
    mide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18
    CJ1--CK1
    ATOM HC3A HGA2
    0.09
    //
    \\
    ATOM HC3B HGA2
    0.09
    CY
    CJ
    GROUP
    / \ __ /
    ATOM CG CG2O1
    0.52
    CJ2--CK2
    ATOM OG OG2D1 -0.52

    1.4012
    1.5538
    1.3413
    0.9900
    1.5004
    1.3413
    1.4278
    1.4180
    1.4278
    1.4180
    1.4002
    1.3996
    2.4326
    1.3997
    1.3996
    1.3982

    120.06
    115.11
    130.29
    116.53
    117.38
    130.29
    127.51
    124.65
    127.51
    119.88
    120.65
    119.87
    60.10
    120.98
    120.65
    119.87

    ATOM OE

    OG311

    ATOM HOE HGP1


    GROUP

    120.01
    117.38
    113.17
    123.61
    130.29
    127.51
    124.65
    106.30
    119.88
    120.65
    119.87
    119.87
    150.25
    119.69
    119.51
    120.17

    1.0806
    1.3413
    0.9900
    1.2237
    1.4278
    1.4180
    1.4137
    0.9750
    1.4002
    1.3996
    1.3982
    1.3997
    1.0810
    1.0796
    1.0809
    1.0811

    ! C17H16NO4 Alpha-Benzyl Gamma-3-Amino Phenol GA CDCA A


    Acid CDCA Amide (GA)
    !
    !
    !
    !
    !
    !

    OA1

    O24

    CA--OA2---CB

    ||

    C24

    CC1

    GROUP
    !
    NG
    CD2--CE2
    ATOM NG NG2S1 -0.47 !
    \ //
    \\
    ATOM HG HGP1
    0.33 !
    CZ
    CP
    ATOM CZ CG2R61 0.14 !
    \ __ /
    GROUP
    !
    CD1--CE1
    ATOM CD1 CG2R61 -0.115 !
    |
    ATOM HD1 HGR61
    0.115 !
    OH(E)
    GROUP
    !
    ATOM CE1 CG2R61

    -179.91
    -15.46
    178.93
    176.72
    175.23
    -22.14
    -0.04
    20.40
    -178.75
    -0.93
    0.22
    0.26
    179.91
    -179.92
    -179.71
    -179.89

    OH
    |

    C22

    C20

    / \ |

    C11 C13---C17
    Me19 |

    C14

    C16

    C1 | C9

    / \|/ \ / \ /
    C2

    C10 C8

    -0.53 !

    0.42 !

    C3

    C5

    C7

    CC3

    \ / \ / \ / \ / \ /

    C12 Me18

    0.11 !

    Me21

    / \ / \ / \

    C15

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM CP

    CG2R61 -0.115 !

    ATOM HP

    HGR61

    C4

    C6

    OH

    0.115 !

    GROUP

    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2
    ATOM HJ2
    ATOM CK1
    ATOM HK1
    ATOM CK2
    ATOM HK2
    ATOM CQ
    ATOM HQ

    CG2R61 -0.115 !
    HGR61
    0.115

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CB
    HB1
    CJ1
    CK2
    OG
    CD1
    HP
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HO

    CG2R61 -0.115
    HGR61
    0.115

    OA2
    CB
    CY
    CQ
    CG
    CZ
    CP
    CG

    CC1
    HC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1
    CK1
    CK2
    CQ

    3AFP

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CA
    CC1
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CJ1

    CB
    CJ1
    CK2
    CG
    CD1
    CP
    NG
    OA2
    CA
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2
    *CJ1
    *CJ2
    *CK1

    HB2
    HJ1
    HK2
    NG
    HD1
    CE2
    OG
    CB
    OA2
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2
    HJ1
    HJ2
    HK1

    CB
    CJ1
    CK2
    NG
    CD1
    CE2
    NG
    1.5213
    1.1144
    1.1133
    1.1175
    1.5073
    1.4049
    1.4040
    1.4040
    1.4049
    1.4049
    1.5073
    1.5073
    1.4040
    1.4011
    1.4012
    1.4011
    1.4015
    1.4012

    CY
    CK1
    CJ2
    HG
    CE1
    HE2
    CG

    CK1
    CJ2
    NG
    CE1
    CE2
    CZ

    109.19
    106.19
    108.20
    112.72
    114.94
    120.41
    119.97
    119.61
    120.41
    120.41
    119.97
    120.41
    120.22
    119.97
    120.06
    120.22
    120.17
    119.97

    HK1
    HJ2
    CZ
    OE
    CD2
    HG

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    OE HOE CE1 CP
    CD2 HD2 CD2 CZ

    176.53
    -147.97
    148.28
    32.34
    -92.14
    -89.70
    89.00
    178.70
    30.50
    143.43
    -179.14
    179.20
    0.11
    0.14
    -0.08
    179.64
    179.98
    179.91

    116.82
    109.19
    116.82
    116.82
    116.82
    114.94
    114.94
    120.41
    107.07
    108.09
    120.22
    120.17
    119.97
    120.06
    119.97
    119.75
    119.90
    119.95

    1.4508
    1.3424
    1.3424
    1.3424
    1.3424
    1.4508
    1.4508
    1.5073
    1.1133
    1.1175
    1.4011
    1.4015
    1.4012
    1.4013
    1.4015
    1.0808
    1.0795
    1.0806

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CQ
    CK1
    CC2
    CG
    HG
    CC3
    CG
    NG
    CZ
    CD1
    CZ
    CD1
    CE1
    CD1
    CE1
    CE2
    CP

    CJ2
    CK2
    CC3
    CZ
    NG
    CG
    NG
    CZ
    CD1
    CE1
    CD1
    CE1
    CP
    CD2
    CZ
    CZ
    CD2

    *CK2
    *CQ
    CG
    *NG
    CG
    NG
    CZ
    CD1
    CE1
    OE
    CE1
    CP
    CE2
    *CP
    *CD1
    *CD2
    *CE2

    HK2
    HQ
    NG
    HG
    OG
    CZ
    CD1
    CE1
    OE
    HOE
    CP
    CE2
    CD2
    HP
    HD1
    HD2
    HE2

    PRES 4AFP
    0.00
    mide, Chayan
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18
    CJ1--CK1
    ATOM HC3A HGA2
    0.09
    //
    \\
    ATOM HC3B HGA2
    0.09
    CY
    CJ
    GROUP
    / \ __ /
    ATOM CG CG2O1
    0.52
    CB
    CJ2--CK2
    ATOM OG OG2D1 -0.52

    1.4013
    1.4012
    1.5550
    1.3442
    0.9888
    1.5026
    1.3442
    1.4221
    1.4019
    1.3983
    1.4019
    1.3983
    1.3988
    2.4258
    1.3983
    1.4012
    1.4012

    119.97
    120.06
    116.14
    129.55
    116.71
    117.40
    129.55
    125.65
    120.47
    119.61
    120.47
    120.28
    119.83
    59.83
    120.47
    120.77
    119.70

    GROUP

    1.0805
    1.0806
    1.3442
    0.9888
    1.2224
    1.4221
    1.4019
    1.3983
    1.4070
    0.9583
    1.3988
    1.4012
    1.4012
    1.0795
    1.0774
    1.0794
    1.0810

    Acid CDCA Amide (GA)


    !
    !
    !
    !
    !
    !

    OA1

    O24

    CA--OA2---

    ||

    C24

    CC1

    OH

    C20
    /

    C11 C13---C17
    Me19 |
    C1 | C9

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    ATOM HE1 HGR61

    C3

    C5

    C7

    CC3

    \ / \ / \ / \ / \

    / \ |

    C22

    C12 Me18

    0.115 !

    0.115 !

    Me21

    ATOM CE1 CG2R61 -0.115 !

    GROUP

    120.07
    120.01
    117.40
    113.63
    124.09
    129.55
    125.65
    120.47
    119.61
    107.72
    120.28
    119.83
    119.70
    149.86
    121.26
    119.71
    120.15

    ! C17H16NO4 Alpha-Benzyl Gamma-4-Amino Phenol GA CDCA A

    GROUP
    !
    NG
    CD2--CE2
    ATOM NG NG2S1 -0.47 !
    / \ //
    \\
    ATOM HG HGP1
    0.33 !
    G
    CZ
    CP--OH(P)
    ATOM CZ CG2R61 0.14 !
    |
    \ __ /
    GROUP
    !
    G
    CD1--CE1
    ATOM CD1 CG2R61 -0.115 !
    ATOM HD1 HGR61

    -179.99
    -179.90
    -6.99
    175.98
    177.69
    171.67
    8.58
    -176.91
    -179.93
    173.29
    0.29
    0.19
    -0.22
    -179.40
    -179.99
    -179.35
    -179.76

    C15

    C23

    NH

    CC2

    C
    |
    O

    ATOM CE2 CG2R61 -0.115 !


    ATOM HE2 HGR61

    0.115 !

    / \ / \ / \

    GROUP

    HO

    C4

    C6

    OH

    ATOM CD2 CG2R61 -0.115 !


    ATOM HD2
    GROUP
    ATOM CP
    ATOM OP
    ATOM HOP
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    ATOM CB
    ATOM HB1
    ATOM HB2
    GROUP
    ATOM CY
    ATOM CJ1
    ATOM HJ1
    ATOM CJ2
    ATOM HJ2
    ATOM CK1
    ATOM HK1
    ATOM CK2
    ATOM HK2
    ATOM CQ
    ATOM HQ

    HGR61

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR

    CB
    HB1
    CJ1
    CK2
    OG
    CD1
    CE2
    OP
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.115 !
    !
    CG2R61 0.11
    OG311 -0.53
    HGP1
    0.42

    OA2
    CB
    CY
    CQ
    CG
    CZ
    CP
    CP
    CG

    CC1
    HC1
    HB1
    HB2
    CY
    CJ2
    CJ1
    CJ1
    CJ2
    CJ2
    CB
    CB
    CY
    CJ1
    CK1

    4AFP

    CG311
    HGA1
    CG2O2
    OG2D1
    OG302
    CG321
    HGA2
    HGA2

    0.17
    0.09
    0.90
    -0.63
    -0.49
    -0.22
    0.09
    0.09

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CA
    CC1
    CB
    CB
    CB
    CY
    CY
    CJ2
    CY
    CY
    CY
    CY
    CJ1
    CK1
    CQ

    CB
    CJ1
    CK2
    CG
    CD1
    CE2
    OP
    NG
    OA2
    CA
    OA2
    OA2
    OA2
    CB
    CB
    *CY
    CB
    CB
    CJ1
    CJ2
    CK1
    CQ
    CK2

    HB2
    HJ1
    HK2
    NG
    HD1
    HE2
    HOP
    OG
    CB
    OA2
    CA
    CA
    CA
    OA2
    OA2
    CB
    HB1
    HB2
    CK1
    CK2
    CQ
    CK2
    CJ2

    CB
    CJ1
    CK2
    NG
    CD1
    CE2

    CY
    CK1
    CJ2
    HG
    CE1
    CD2

    CK1
    CJ2
    NG
    CE1
    CD2

    HK1
    HJ2
    CZ
    HE1
    HD2

    NG

    CG

    CZ

    HG

    1.5236
    1.1142
    1.1165
    1.1162
    1.5038
    1.4045
    1.4046
    1.4046
    1.4045
    1.4045
    1.5038
    1.5038
    1.4046
    1.4015
    1.4011

    109.09
    106.35
    110.58
    110.53
    113.57
    120.04
    120.35
    119.60
    120.04
    120.04
    120.35
    120.04
    120.19
    119.97
    120.06

    CK1 CQ
    CJ2 CY

    CQ

    HQ

    CE1 CP
    CD2 CZ

    -178.41
    -136.56
    58.38
    -60.09
    178.93
    -86.50
    92.29
    178.79
    35.94
    150.86
    -179.80
    179.88
    0.22
    0.49
    -0.40

    115.32
    109.09
    115.32
    115.32
    115.32
    113.57
    113.57
    120.04
    107.19
    107.55
    120.19
    120.20
    119.97
    120.06
    119.97

    1.4470
    1.3425
    1.3425
    1.3425
    1.3425
    1.4470
    1.4470
    1.5038
    1.1165
    1.1162
    1.4015
    1.4014
    1.4011
    1.4013
    1.4014

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CK1
    CK2
    CQ
    CQ
    CK1
    CC2
    CG
    NG
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CD1
    CE1
    CE1
    CE2
    CP
    CP

    CY
    CY
    CJ1
    CJ2
    CK2
    CC3
    CZ
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CP
    CE1
    CP
    CZ
    CZ
    CD1
    CD2

    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    CG
    *NG
    *CG
    NG
    CZ
    CD1
    CE1
    CP
    OP
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2

    HJ1
    HJ2
    HK1
    HK2
    HQ
    NG
    HG
    OG
    CZ
    CD1
    CE1
    CP
    OP
    HOP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2

    PRES 2AFD
    0.00
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18

    1.4015
    1.4014
    1.4011
    1.4013
    1.4011
    1.5522
    1.3446
    1.3446
    1.5020
    1.3446
    1.4209
    1.4023
    1.4040
    1.3974
    1.4040
    1.3974
    1.4040
    1.4034
    1.3974
    1.3995

    ATOM HC3B HGA2

    0.09 !

    1.0799
    1.0802
    1.0807
    1.0807
    1.0807
    1.3446
    0.9886
    1.2231
    1.4209
    1.4023
    1.4040
    1.3974
    1.4076
    0.9582
    1.3995
    1.4034
    1.0783
    1.0792
    1.0802
    1.0794

    OA1 (-0.5)

    CG2O1

    0.52 !

    O24

    CA--OA2 (-0.

    OG2D1

    -0.52 !

    ||

    C24

    CC1

    GROUP
    !
    NG
    CD2--CE2
    ATOM NG NG2S1 -0.47 !
    \ //
    \\
    ATOM HG HGP1
    0.33 !
    CZ
    CP
    ATOM CZ CG2R61 0.14 !
    \ __ /
    GROUP
    !
    CD1--CE1
    ATOM CD1 CG2R61 0.11 !
    |
    ATOM OD OG311 -0.53 !
    OH(D)
    ATOM HOD HGP1
    0.42 !
    GROUP

    119.87
    119.84
    120.03
    119.99
    119.97
    116.85
    113.69
    118.95
    129.70
    125.34
    120.44
    120.10
    119.57
    107.83
    120.00
    119.77
    120.86
    119.68
    120.20
    119.80

    Acid CDCA Amide (GA)


    !
    !
    !
    !

    0.09 !

    ATOM CG
    5)
    ATOM OG

    -179.59
    179.63
    -179.64
    179.84
    -179.97
    9.31
    -179.80
    179.97
    178.94
    -12.00
    179.30
    -0.30
    -179.94
    179.31
    0.00
    0.08
    179.44
    179.81
    -179.87
    179.92

    ! C8H8NO2 Gamma-2-Amino Phenol GA CDCA Amide, Chayan

    ATOM HC3A HGA2

    GROUP

    120.19
    120.20
    119.97
    119.97
    120.06
    114.66
    129.70
    116.85
    116.85
    129.70
    125.34
    120.44
    120.10
    119.57
    120.10
    120.00
    120.44
    120.68
    120.10
    119.77

    ATOM CE1 CG2R61 -0.115 !

    OH

    Me21

    C22

    \ / \ / \ / \ / \ /

    C12 Me18

    C20

    / \ |

    C11 C13---C17
    Me19 |
    C1 | C9

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    CC3

    C15

    C23

    NH

    CC2

    CG
    ||
    OG

    ATOM HE1 HGR61

    0.115 !

    GROUP

    ATOM CP

    CG2R61 -0.115 !

    ATOM HP

    HGR61

    C5

    C7

    / \ / \ / \
    HO

    C4

    C6

    OH

    0.115 !

    GROUP

    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2

    CG2R61 -0.115 !
    HGR61
    0.115

    BOND
    BOND
    BOND
    IMPR

    OG
    CD1
    HP
    CC3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C3

    CG
    CZ
    CP
    CG

    CC2
    CG
    HG
    CC3
    CG
    NG
    CZ
    NG
    CZ
    CD1
    CE1
    CD1
    CE2
    CP
    CP

    CG2R61 -0.115
    HGR61
    0.115

    CC3
    CZ
    NG
    CG
    NG
    CZ
    CD1
    CZ
    CD1
    CE1
    CP
    CD2
    CZ
    CD1
    CD2

    CG
    CD1
    CP
    NG
    CG
    *NG
    CG
    NG
    CZ
    CD1
    OD
    CD1
    CE1
    CP
    CE2
    *CP
    *CD2
    *CE1
    *CE2

    NG
    OD
    CE2
    OG
    NG
    HG
    OG
    CZ
    CD1
    OD
    HOD
    CE1
    CP
    CE2
    CD2
    HP
    HD2
    HE1
    HE2

    PRES 3AFD
    0.00
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP
    ATOM CC3 CG321 -0.18

    NG
    OD
    CE2
    NG

    NG
    CD1
    CE2
    CZ

    114.79
    131.49
    116.38
    117.53
    131.49
    128.16
    124.84
    128.16
    120.02
    120.69
    119.77
    59.99
    121.28
    120.69
    119.83

    CZ
    CE1 CE1 HE1 CE1 CP
    CD2 CD2 HD2 CD2 CZ
    HG
    -49.84
    -179.00
    178.36
    -179.31
    -17.12
    -0.87
    13.21
    -180.00
    -0.79
    0.09
    0.21
    -179.98
    -179.74
    -179.78
    -179.85

    117.53
    112.13
    123.50
    131.49
    128.16
    124.84
    105.74
    120.02
    120.69
    119.77
    119.83
    150.22
    119.14
    119.40
    119.73

    1.3436
    1.0158
    1.2277
    1.4281
    1.4178
    1.4130
    0.9771
    1.4012
    1.3997
    1.3979
    1.3990
    1.0801
    1.0814
    1.0802
    1.0805

    ! C8H8NO2 Gamma-3-Amino Phenol GA CDCA Amide, Chayan


    Acid CDCA Amide (GA)
    !
    !
    !
    !

    0.09 !

    ATOM HC3B HGA2

    0.09 !

    GROUP

    HG
    HOD
    HE2
    CG

    1.5527
    1.3436
    1.0158
    1.5021
    1.3436
    1.4281
    1.4178
    1.4281
    1.4178
    1.4012
    1.3997
    2.4340
    1.3990
    1.3997
    1.3979

    ATOM HC3A HGA2

    ATOM CG
    5)
    ATOM OG

    2AFD

    OA1 (-0.5)

    CG2O1

    0.52 !

    O24

    CA--OA2 (-0.

    OG2D1

    -0.52 !

    ||

    GROUP
    NG
    CD2--CE2
    ATOM NG NG2S1
    \ //
    \\

    C24

    CC1

    -0.47 !

    OH
    |

    Me21

    C22

    CC3

    \ / \ / \ / \ / \ /

    ATOM HG HGP1
    0.33 !
    CZ
    CP
    ATOM CZ CG2R61 0.14 !
    \ __ /
    GROUP
    !
    CD1--CE1
    ATOM CD1 CG2R61 -0.115 !
    |
    ATOM HD1 HGR61
    0.115 !
    OH(E)
    GROUP
    !
    ATOM CE1 CG2R61
    ATOM OE

    Me19 |

    0.42 !

    C3

    C5

    C7

    !
    CG2R61 -0.115 !

    ATOM HP

    HGR61

    C14

    C16

    ||
    OG

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2

    CG2R61 -0.115 !
    HGR61
    0.115

    BOND
    BOND
    BOND
    IMPR

    OG
    CD1
    HP
    CC3

    CC2
    CG
    HG
    CC3
    CG
    NG
    CZ
    CD1
    CZ
    CD1
    CE1
    CD1
    CE1
    CE2
    CP

    CG

    0.115 !

    GROUP

    CG
    CZ
    CP
    CG

    CC2

    / \|/ \ / \ /

    -0.53 !

    ATOM CP

    NH

    C1 | C9

    C10 C8

    GROUP

    C23

    C11 C13---C17

    C2

    OG311

    C20

    / \ |

    0.11 !

    ATOM HOE HGP1

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C12 Me18

    3AFD

    CG2R61 -0.115
    HGR61
    0.115

    CC3
    CZ
    NG
    CG
    NG
    CZ
    CD1
    CE1
    CD1
    CE1
    CP
    CD2
    CZ
    CZ
    CD2

    CG
    CD1
    CP
    NG
    CG
    *NG
    CG
    NG
    CZ
    CD1
    CE1
    OE
    CE1
    CP
    CE2
    *CP
    *CD1
    *CD2
    *CE2

    NG
    HD1
    CE2
    OG
    NG
    HG
    OG
    CZ
    CD1
    CE1
    OE
    HOE
    CP
    CE2
    CD2
    HP
    HD1
    HD2
    HE2

    PRES 4AFD
    0.00
    ! patch combination:
    ! core residue Glutamic
    DELETE ATOM OG1
    DELETE ATOM OG2
    GROUP

    NG
    CD1
    CE2
    NG
    1.5535
    1.3441
    1.0143
    1.5033
    1.3441
    1.4190
    1.4020
    1.3993
    1.4020
    1.3993
    1.4003
    2.4274
    1.3993
    1.4004
    1.4014

    HG
    CE1
    HE2
    CG

    NG
    CE1
    CE2
    CZ

    114.97
    129.77
    117.35
    117.22
    129.77
    125.45
    120.37
    120.07
    120.37
    120.24
    119.87
    59.83
    120.37
    120.84
    119.63

    CZ
    OE OE HOE CE1 CP
    CD2 CD2 HD2 CD2 CZ
    HG
    -47.53
    -178.97
    177.56
    -179.94
    -14.90
    179.05
    179.48
    179.46
    -0.43
    0.04
    0.07
    -179.94
    179.29
    -179.99
    179.99

    117.22
    112.88
    123.74
    129.77
    125.45
    120.37
    120.07
    107.22
    120.24
    119.87
    119.63
    149.75
    120.63
    119.02
    119.74

    1.3441
    1.0143
    1.2279
    1.4190
    1.4020
    1.3993
    1.4087
    0.9566
    1.4003
    1.4014
    1.4004
    1.0785
    1.0774
    1.0816
    1.0802

    ! C8H8NO2 Gamma-4-Amino Phenol GA CDCA Amide, Chayan


    Acid CDCA Amide (GA)
    !
    !
    !

    ATOM CC3 CG321

    -0.18 !

    ATOM HC3A HGA2

    0.09 !

    ATOM HC3B HGA2

    0.09 !

    GROUP

    OA1 (-0.5)

    ATOM CG
    0.5)
    ATOM OG

    CG2O1

    0.52 !

    O24

    CA--OA2 (-

    OG2D1

    -0.52 !

    ||

    C24

    CC1

    GROUP
    !
    NG
    CD2--CE2
    ATOM NG NG2S1 -0.47 !
    / \ //
    \\
    ATOM HG HGP1
    0.33 !
    G
    CZ
    CP--OH(P)
    ATOM CZ CG2R61 0.14 !
    |
    \ __ /
    GROUP
    !
    G
    CD1--CE1
    ATOM CD1 CG2R61 -0.115 !
    ATOM HD1 HGR61

    OH
    |

    Me19 |

    ATOM HE1 HGR61

    C3

    C5

    C7

    0.115 !
    !

    ATOM CE2 CG2R61 -0.115 !

    C14

    C16

    0.115 !

    HO

    C4

    C6

    C15

    OH

    ATOM HD2
    GROUP
    ATOM CP
    ATOM OP
    ATOM HOP

    HGR61

    BOND
    BOND
    BOND
    BOND
    IMPR

    OG
    CD1
    CE2
    OP
    CC3

    CG
    CZ
    CP
    CP
    CG

    CC2
    CG
    NG
    CC3
    CG
    NG

    4AFP

    0.115 !
    !
    CG2R61 0.11
    OG311 -0.53
    HGP1
    0.42

    CC3
    CZ
    CC3
    CG
    NG
    CZ

    CG
    CD1
    CE2
    OP
    NG
    CG
    *NG
    *CG
    NG
    CZ
    CD1

    NG
    HD1
    HE2
    HOP
    OG
    NG
    HG
    OG
    CZ
    CD1
    CE1

    NG HG NG CZ
    CD1 CE1 CE1 HE1 CE1 CP
    CE2 CD2 CD2 HD2 CD2 CZ
    NG
    1.5534
    1.3442
    1.3442
    1.5032
    1.3442
    1.4190

    CG

    CZ
    114.96
    129.81
    117.22
    117.22
    129.81
    125.44

    HG
    -47.72
    -179.00
    -178.69
    -179.68
    -13.97
    178.96

    117.22
    112.85
    119.03
    129.81
    125.44
    120.46

    CC2

    / \ / \ / \

    ATOM CD2 CG2R61 -0.115 !

    IC
    IC
    IC
    IC
    IC
    IC

    NH

    / \|/ \ / \ /
    C10 C8

    GROUP

    C23

    C1 | C9

    C2

    ATOM HE2 HGR61

    C20

    C11 C13---C17

    ATOM CE1 CG2R61 -0.115 !

    CC3

    \ / \ / \ / \ / \

    / \ |

    GROUP

    C22

    C12 Me18

    0.115 !

    GROUP

    Me21

    1.3442
    1.0143
    1.2282
    1.4190
    1.4028
    1.4048

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CZ
    CD1
    CE1
    CD1
    CE1
    CE1
    CE2
    CP
    CP

    CD1
    CE1
    CP
    CE1
    CP
    CZ
    CZ
    CD1
    CD2

    RESI GABD
    e, Chayan
    GROUP
    ATOM C3
    D1--CE1
    ATOM O3
    \\
    ATOM HO3
    CP
    ATOM H3
    __ /
    GROUP
    D2--CE2
    ATOM C4

    CE1
    CP
    OP
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2

    CP
    OP
    HOP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2

    1.4028
    1.4048
    1.3982
    1.4048
    1.3982
    1.4048
    1.4022
    1.3982
    1.3994

    120.46
    120.02
    120.03
    120.02
    120.03
    120.46
    120.80
    120.02
    119.74

    -0.32
    -179.99
    -179.80
    -0.03
    0.06
    179.35
    179.99
    -179.92
    179.94

    120.02
    120.03
    106.81
    120.03
    119.74
    120.40
    119.04
    120.17
    119.33

    1.3982
    1.4082
    0.9579
    1.3994
    1.4022
    1.0778
    1.0815
    1.0792
    1.0788

    -1.00 ! C35H51N2O6 Gamma amino benzene glutamic acid CDCA amid


    CG311

    !
    0.14 !

    OG

    OG311

    -0.65 !

    ||

    //

    HGP1

    0.42 !

    CG--NG--CZ

    HGA1

    0.09 !

    CC3

    -0.18 !

    CG321

    HG

    ATOM H4A HGA2

    0.09 !

    O24

    CC2

    ATOM H4B HGA2

    0.09 !

    ||

    GROUP

    H
    |

    ATOM C5

    CG311

    -0.09 !

    ATOM H5
    0.5)
    GROUP

    HGA1

    0.09 !

    ATOM C6

    CG321

    -0.18 !

    Me19 |

    ATOM H6B HGA2

    0.09 !

    C1 | C9

    !
    CG311

    0.14 !

    C2

    C10 C8

    ATOM O7

    OG311

    -0.65 !

    ATOM HO7 HGP1

    0.42 !

    C3

    C5

    C7

    ATOM H7

    0.09 !
    !

    ATOM C8

    CG311

    -0.09 !

    ATOM H8

    HGA1

    0.09 !

    C14

    C16

    / \|/ \ / \ /

    ATOM C7

    GROUP

    C20

    C11 C13---C17

    0.09 !

    C15

    / \ / \ / \
    HO

    C4

    C6

    C24

    CC1

    \ / \ / \ / \

    / \ |

    ATOM H6A HGA2

    HGA1

    C22

    C12 Me18

    GROUP

    Me21

    OH

    GABD

    C23

    NH

    CA--OA1 (|
    OA2 (-0.5)

    GROUP
    ATOM C14
    ATOM H14
    GROUP
    ATOM C15
    ATOM H15A
    ATOM H15B
    GROUP
    ATOM C16
    ATOM H16A
    ATOM H16B
    GROUP
    ATOM C17
    ATOM H17
    GROUP
    ATOM C13
    GROUP
    ATOM C18
    ATOM H18A
    ATOM H18B
    ATOM H18C
    GROUP
    ATOM C12
    ATOM H12A
    ATOM H12B
    GROUP
    ATOM C11
    ATOM H11A
    ATOM H11B
    GROUP
    ATOM C9
    ATOM H9
    GROUP
    ATOM C10
    GROUP
    ATOM C19
    ATOM H19A
    ATOM H19B
    ATOM H19C
    GROUP
    ATOM C1
    ATOM H1A
    ATOM H1B
    GROUP
    ATOM C2
    ATOM H2A
    ATOM H2B
    GROUP
    ATOM C20
    ATOM H20
    GROUP
    ATOM C21
    ATOM H21A
    ATOM H21B
    ATOM H21C
    GROUP
    ATOM C22
    ATOM H22A
    ATOM H22B
    GROUP

    !
    CG3RC1 -0.09 !
    HGA1
    0.09
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C52 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG3C51 -0.09
    HGA1
    0.09
    CG3RC1
    CG331
    HGA3
    HGA3
    HGA3

    0.00
    -0.27 !methyl at c13
    0.09
    0.09
    0.09

    CG321 -0.18
    HGA2
    0.09
    HGA2
    0.09
    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG301

    0.00

    CG331
    HGA3
    HGA3
    HGA3

    -0.27 !methyl at c10


    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG311
    HGA1

    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    ATOM C23
    ATOM H23A
    ATOM H23B
    GROUP
    ATOM C24
    ATOM O24
    ATOM N
    ATOM HN
    GROUP
    ATOM CC1
    ATOM HC1
    ATOM CA
    ATOM OA1
    ATOM OA2
    GROUP
    ATOM CC2
    ATOM HC2A
    ATOM HC2B
    GROUP
    ATOM CC3
    ATOM HC3A
    ATOM HC3B
    GROUP
    ATOM CG
    ATOM OG
    GROUP
    ATOM NG
    ATOM HG
    ATOM CZ
    GROUP
    ATOM CD1
    ATOM HD1
    GROUP
    ATOM CE1
    ATOM HE1
    GROUP
    ATOM CP
    ATOM HP
    GROUP
    ATOM CE2
    ATOM HE2
    GROUP
    ATOM CD2
    ATOM HD2

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O1
    OG2D1
    NG2S1
    HGP1

    0.51
    -0.51
    -0.47
    0.47

    CG311
    HGA1
    CG2O3
    OG2D2
    OG2D2

    -0.19
    0.09
    0.62
    -0.76
    -0.76

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG321
    HGA2
    HGA2

    -0.18
    0.09
    0.09

    CG2O1
    OG2D1

    0.52
    -0.52

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    O3
    C4
    C5
    C10
    C1
    C2
    C3
    C6
    C7
    C8
    C9
    C10
    C14
    C13
    C12

    C3
    C3
    C4
    C5
    C10
    C1
    C2
    C5
    C6
    C7
    C8
    C9
    C8
    C14
    C13

    NG2S1 -0.47
    HGP1
    0.33
    CG2R61 0.14
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 -0.115
    HGR62
    0.115
    CG2R61 -0.115
    HGR61
    0.115
    C3
    C4
    C5
    C10
    C1
    C2

    H3
    H4A
    H5
    C19
    H1A
    H2A

    O3
    C4

    C6
    C7
    C8
    C9

    H6A C6
    H7 C7
    H8
    H9

    HO3
    H4B

    C19 H19A C19 H19B C19 H19C


    C1 H1B
    C2 H2B
    H6B
    O7 O7

    HO7

    C14 H14
    C13 C18 C18 H18A C18 H18B C18 H18C
    C12 H12A C12 H12B

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR

    C12
    C11
    C14
    C15
    C16
    C17
    C17
    C20
    C22
    C23
    C24
    N
    CC2
    CC3
    CG
    CZ
    CP
    C24
    CG

    C11
    C9
    C15
    C16
    C17
    C13
    C20
    C22
    C23
    C24
    N
    CC1
    HC2A
    HC3A
    OG
    CD1
    CE2
    C23
    CC3

    C11 H11A C11 H11B


    C15 H15A C15 H15B
    C16 H16A C16 H16B
    C17 H17
    C20
    C22
    C23
    C24
    N
    CC1
    CC2
    CC3
    CG
    CD1
    CE2
    N
    NG

    H20
    H22A
    H23A
    O24
    HN
    HC1
    HC2B
    HC3B
    NG
    HD1
    HE2
    O24
    OG

    C20 C21 C21 H21A C21 H21B C21 H21C


    C22 H22B
    C23 H23B
    CC1
    CC2
    CC3
    NG
    CD1
    CE2
    N
    NG

    CC2
    CC3
    CG
    HG
    CE1
    CD2
    C24
    CG

    CC1 CA
    NG
    CE1
    CD2
    CC1
    CZ

    CA

    OA1 CA

    OA2

    CZ
    HE1 CE1 CP CP HP
    HD2 CD2 CZ
    HN
    HG

    !
    R(I(J/K)) T(I(JK/KJ)) PHI T(JKL)
    !ICs based on arbitrary CHARMM optimized structure
    IC C1 C2 C3 C4
    1.5325 111.68 -49.44 111.84
    IC C2 C3 C4 C5
    1.5339 111.84 43.92 115.68
    IC C3 C4 C5 C6
    1.5383 115.68 -175.08 109.02
    IC C4 C5 C6 C7
    1.5598 109.02 85.48 114.98
    IC C5 C6 C7 C8
    1.5521 114.98 39.05 113.05
    IC C7 C8 C9 C10 1.5291 114.07 58.27 109.47
    IC C8 C9 C10 C1
    1.5323 109.47 179.67 111.99
    IC C9 C10 C1 C2
    1.5439 111.99 63.32 113.83
    IC O3 C3 C4 C5
    1.4163 109.09 162.16 115.68
    IC C4 C2 *C3 O3
    1.5383 111.84 -119.44 107.07
    IC C4 C2 *C3 H3
    1.5383 111.84 121.33 109.38
    IC C9 C5 *C10 C19 1.5439 109.64 -123.44 109.53
    IC C2 C3 O3 HO3 1.5339 107.07 70.15 104.87
    IC C5 C3 *C4 H4A 1.5598 115.68 122.76 108.69
    IC H4A C3 *C4 H4B 1.1111 108.69 115.73 108.82
    IC C10 C4 *C5 H5
    1.5279 114.71 116.72 105.03
    IC C7 C5 *C6 H6A 1.5441 114.98 -124.16 109.39
    IC H6A C5 *C6 H6B 1.1113 109.39 -115.80 108.33
    IC C2 C10 *C1 H1A 1.5325 113.83 119.39 107.74
    IC C2 C10 *C1 H1B 1.5325 113.83 -124.36 110.18
    IC C1 C3 *C2 H2A 1.5325 111.68 122.11 110.21
    IC H2A C3 *C2 H2B 1.1113 110.21 117.20 108.66
    IC C6 C7 C8 C14 1.5441 113.05 -166.97 108.56
    IC C14 C7 *C8 C9
    1.5542 108.56 119.93 114.07
    IC C7 C8 C14 C13 1.5291 108.56 -174.23 113.13
    IC C13 C8 *C14 C15 1.5425 113.13 118.56 116.30
    IC C8 C14 C15 C16 1.5542 116.30 -154.74 103.56
    IC C14 C15 C16 C17 1.5285 103.56 -2.52 106.91
    IC C17 C14 *C13 C12 1.5731 98.17 119.81 107.46
    IC C14 C13 C12 C11 1.5425 107.46 55.27 111.17
    IC C8 C6 *C7 O7
    1.5291 113.05 -126.94 107.98
    IC O7 C6 *C7 H7
    1.4218 107.98 -113.62 107.19
    IC C6 C7 O7 HO7 1.5441 107.98 178.15 105.27
    IC C9 C7 *C8 H8
    1.5323 114.07 122.48 107.18
    IC C10 C8 *C9 H9
    1.5439 109.47 -117.09 106.55
    IC C9 C12 *C11 H11A 1.5547 114.18 122.66 108.77
    IC H11A C12 *C11 H11B 1.1090 108.77 115.79 107.30
    IC C14 C13 C12 H12A 1.5425 107.46 175.99 111.87

    R(KL)
    1.5383
    1.5598
    1.5521
    1.5441
    1.5291
    1.5439
    1.5563
    1.5325
    1.5598
    1.4163
    1.1144
    1.5562
    0.9608
    1.1111
    1.1113
    1.1175
    1.1113
    1.1112
    1.1137
    1.1091
    1.1113
    1.1128
    1.5542
    1.5323
    1.5425
    1.5285
    1.5435
    1.5532
    1.5340
    1.5431
    1.4218
    1.1164
    0.9614
    1.1067
    1.1138
    1.1090
    1.1111
    1.1059

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H12A
    C13
    C16
    H15A
    C17
    H16A
    C13
    C12
    C14
    H18A
    H18A
    C9
    C5
    H19A
    H19A
    C13
    C16
    C22
    C21
    C17
    H21A
    H21A
    C17
    C23
    H22A
    C20
    C24
    H23A
    C22
    N
    C23
    CC1
    C24
    CA
    HC1
    N
    OA1
    N
    CC3
    HC2A
    CC1
    CG
    HC3A
    CC2
    NG
    CC3
    CC3
    CG
    NG
    CZ
    CD1
    CE1
    CE1
    CE2
    CP
    CP
    CE1

    C13
    C8
    C14
    C14
    C15
    C15
    C16
    C14
    C13
    C13
    C13
    C5
    C10
    C10
    C10
    C16
    C17
    C17
    C17
    C20
    C20
    C20
    C20
    C20
    C20
    C22
    C22
    C22
    C23
    C23
    C24
    C24
    N
    N
    N
    CC1
    CC1
    CC1
    CC1
    CC1
    CC2
    CC2
    CC2
    CC3
    CC3
    CG
    CG
    NG
    CZ
    CD1
    CE1
    CP
    CZ
    CZ
    CD1
    CD2
    CE2

    PRES 4FBD

    *C12
    *C14
    *C15
    *C15
    *C16
    *C16
    *C17
    *C13
    C18
    *C18
    *C18
    *C10
    C19
    *C19
    *C19
    *C17
    C20
    *C20
    *C20
    C21
    *C21
    *C21
    C22
    *C22
    *C22
    C23
    *C23
    *C23
    C24
    *C24
    N
    *N
    CC1
    *CC1
    *CC1
    CA
    *CA
    CC2
    *CC2
    *CC2
    CC3
    *CC3
    *CC3
    CG
    *CG
    NG
    NG
    CZ
    CD1
    CE1
    CP
    CE2
    *CD1
    *CD2
    *CE1
    *CE2
    *CP

    H12B
    H14
    H15A
    H15B
    H16A
    H16B
    H17
    C18
    H18A
    H18B
    H18C
    C19
    H19A
    H19B
    H19C
    C20
    C22
    C21
    H20
    H21A
    H21B
    H21C
    C23
    H22A
    H22B
    C24
    H23A
    H23B
    N
    O24
    CC1
    HN
    CA
    HC1
    CC2
    OA1
    OA2
    CC3
    HC2A
    HC2B
    CG
    HC3A
    HC3B
    NG
    OG
    HG
    CZ
    CD1
    CE1
    CP
    CE2
    CD2
    HD1
    HD2
    HE1
    HE2
    HP

    1.1059
    1.5425
    1.5435
    1.1002
    1.5532
    1.0992
    1.5731
    1.5340
    1.5425
    1.1064
    1.1064
    1.5439
    1.5279
    1.1079
    1.1079
    1.5731
    1.5532
    1.5518
    1.5396
    1.5649
    1.1079
    1.1079
    1.5649
    1.5524
    1.1129
    1.5518
    1.5026
    1.1095
    1.5524
    1.3359
    1.5026
    1.4436
    1.3359
    1.5637
    1.1100
    1.4436
    1.2563
    1.4436
    1.5540
    1.1120
    1.5529
    1.4995
    1.1109
    1.5540
    1.3423
    1.4995
    1.4995
    1.3423
    1.4189
    1.4022
    1.4034
    1.4008
    1.4034
    1.4007
    1.4008
    1.4004
    1.4008

    111.87
    113.13
    103.56
    111.17
    106.91
    110.78
    98.41
    107.46
    114.21
    111.39
    111.39
    109.64
    109.53
    111.17
    111.17
    98.41
    111.84
    108.71
    112.90
    112.90
    110.45
    110.45
    108.71
    113.72
    108.17
    113.72
    113.87
    110.57
    113.87
    116.55
    116.55
    130.34
    130.34
    103.53
    109.79
    103.53
    117.28
    112.57
    114.17
    108.53
    114.17
    114.11
    109.21
    114.11
    116.06
    116.06
    116.06
    130.53
    125.50
    120.55
    119.96
    119.92
    120.55
    120.81
    119.96
    119.80
    119.92

    119.48
    -118.31
    119.14
    119.82
    121.49
    117.18
    -112.88
    121.96
    116.77
    119.05
    -120.16
    -123.44
    5.11
    121.06
    -119.50
    127.02
    71.76
    122.37
    120.80
    71.89
    -121.56
    118.40
    -163.91
    119.83
    116.47
    174.68
    120.96
    118.91
    6.38
    -179.98
    -179.82
    -176.24
    -166.57
    115.21
    123.30
    -162.71
    152.11
    56.12
    126.04
    114.46
    119.76
    120.83
    118.15
    -53.86
    -178.54
    0.87
    -179.02
    -7.10
    179.36
    -0.19
    0.01
    0.02
    179.64
    179.97
    -179.93
    179.93
    179.95

    108.83
    108.46
    111.17
    112.08
    110.78
    110.97
    110.39
    114.21
    111.39
    110.59
    111.91
    109.53
    111.17
    112.01
    110.64
    111.84
    108.71
    112.90
    108.91
    110.45
    110.44
    110.88
    113.72
    108.17
    108.28
    113.87
    110.57
    109.38
    116.55
    120.03
    130.34
    124.18
    103.53
    109.79
    112.57
    117.28
    113.14
    114.17
    108.53
    107.25
    114.11
    109.21
    110.34
    116.06
    119.61
    115.97
    130.53
    125.50
    120.55
    119.96
    119.92
    119.80
    120.41
    119.00
    119.80
    119.74
    119.93

    1.1125
    1.1150
    1.1002
    1.0988
    1.0992
    1.0998
    1.1009
    1.5526
    1.1064
    1.1085
    1.1058
    1.5562
    1.1079
    1.1062
    1.1093
    1.5649
    1.5518
    1.5396
    1.1119
    1.1079
    1.1103
    1.1089
    1.5524
    1.1129
    1.1132
    1.5026
    1.1095
    1.1114
    1.3359
    1.2265
    1.4436
    1.0134
    1.5637
    1.1100
    1.5529
    1.2563
    1.2722
    1.5540
    1.1120
    1.1137
    1.4995
    1.1109
    1.1107
    1.3423
    1.2286
    1.0167
    1.4189
    1.4022
    1.4034
    1.4008
    1.4004
    1.4007
    1.0774
    1.0814
    1.0798
    1.0797
    1.0796

    0.00 ! C3H2F Gamma 4-Fluoro amino benzene glutamic acid CDCA

    amide, Chayan
    !To be patched with residue GABD
    DELETE ATOM HP
    !
    ATOM CE1 CG2R61 -0.100 !
    ATOM HE1 HGR62
    0.150 !
    ATOM CP CG2R66 0.110 !
    ATOM FP FGR1
    -0.210 !
    ATOM CE2 CG2R61 -0.100 !
    ATOM HE2 HGR62
    0.150 !
    BOND CP FP
    IC CE1 CE2 *CP FP
    1.4008 119.92 179.96 119.93

    1.0796

    PRES 3FBD
    0.00 ! C3H2F Gamma 3-Fluoro amino benzene glutamic acid CDCA
    amide, Chayan
    !To be patched with residue GABD
    DELETE ATOM HE1
    !
    ATOM CD1 CG2R61 -0.100 !
    ATOM HD1 HGR62
    0.150 !
    ATOM CE1 CG2R66 0.110 !
    ATOM FE1 FGR1
    -0.210 !
    ATOM CP CG2R61 -0.100 !
    ATOM HP HGR62
    0.150 !
    BOND CE1 FE1
    IC CP CD1 *CE1 FE1 1.4008 119.96 -179.93 119.80 1.0798
    PRES 2FBD
    0.14 ! C3HF Gamma 2-Fluoro amino benzene glutamic acid CDCA
    amide, Chayan
    !To be patched with residue GABD
    DELETE ATOM HD1
    !
    ATOM CE1 CG2R61 -0.100 !
    ATOM HE1 HGR62
    0.150 !
    ATOM CD1 CG2R66 0.110 !
    ATOM FD1 FGR1
    -0.210 !
    ATOM CZ CG2R61 0.190 !
    BOND CD1 FD1
    IC CE1 CZ *CD1 FD1 1.3985 122.02 176.60 121.03 1.3368
    PRES 4FBP
    0.00 ! C12H10FO2 Alpha benzyl, Gamma 4-Fluoro amino benzene
    glutamic acid CDCA amide, Chayan
    !To be patched with residue GABD
    DELETE ATOM HP
    !
    GROUP
    !
    OG
    CD1--CE1
    ATOM CC1 CG311
    0.17 !
    ||
    /
    /
    \\
    ATOM HC1 HGA1
    0.09 !
    CG--NG--CZ
    CP--FP
    ATOM CA CG2O2
    0.90 !
    / HG
    \ __ /
    ATOM OA1 OG2D1 -0.63 !
    CC3
    CD2--CE2
    ATOM OA2 OG302 -0.49 !
    \
    ATOM CB

    CG321

    ATOM HB1 HGA2

    -0.22 !

    O24

    CC2

    0.09 !

    ||

    ATOM HB2 HGA2

    0.09 !

    GROUP

    ATOM CY CG2R61 0.00 !


    CJ1--CK1
    ATOM CJ1 CG2R61 -0.115 !
    //
    \\
    ATOM HJ1 HGR61
    0.115 !
    CY
    CQ
    ATOM CJ2 CG2R61 -0.115 !
    \ __ /
    ATOM HJ2 HGR61
    0.115 !
    CJ2--CK2
    ATOM CK1 CG2R61 -0.115 !
    ATOM HK1 HGR61

    Me19 |

    ATOM HK2 HGR61

    C3

    C5

    C7

    0.115 !

    GROUP

    C14

    C16

    NH

    CA--OA1
    |
    OA2--CB--

    C15

    / \ / \ / \
    HO

    C4

    C6

    OH

    ATOM CE1 CG2R61 -0.100 !

    4FBP

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HE1
    CP
    FP
    CE2
    HE2

    HGR62
    0.150 !
    CG2R66 0.110 !
    FGR1
    -0.210 !
    CG2R61 -0.100 !
    HGR62
    0.150 !

    BOND
    BOND
    BOND
    BOND
    BOND

    OA2
    CB
    CY
    CQ
    CP

    CB
    HB1 CB HB2 CB CY
    CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ
    CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY
    FP

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1

    / \|/ \ / \ /

    0.115 !

    C23

    C1 | C9

    ATOM CK2 CG2R61 -0.115 !

    HGR61

    C20

    C11 C13---C17

    C10 C8

    ATOM HQ

    C24

    \ / \ / \ / \ __

    / \ |

    C2

    CG2R61 -0.115 !

    C22

    C12 Me18

    0.115 !

    ATOM CQ

    Me21

    CC1
    HB1
    HB2
    CA
    CJ1
    CB
    CY
    CJ1
    CK1
    CB
    CK1
    CK2
    CQ
    CQ
    CK1
    CE1

    CA
    CB
    CB
    OA2
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CY
    CJ1
    CJ2
    CK2
    CE2

    PRES 3FBP

    OA2
    OA2
    OA2
    CB
    CB
    CJ1
    CK1
    CQ
    CK2
    CJ2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    *CP

    CB
    CA
    CA
    CY
    OA2
    CK1
    CQ
    CK2
    CJ2
    CK2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    FP

    1.5349
    1.1146
    1.1156
    1.3430
    1.4037
    1.5061
    1.4037
    1.4016
    1.4012
    1.5061
    1.4016
    1.4012
    1.4012
    1.4009
    1.4012
    1.3937

    110.60
    109.86
    110.43
    114.63
    119.63
    119.63
    120.28
    119.99
    120.04
    120.87
    120.28
    120.33
    119.99
    119.92
    120.04
    122.13

    -171.93
    61.07
    -57.63
    -177.12
    48.09
    177.33
    0.19
    -0.03
    -0.22
    -177.55
    -179.34
    179.00
    -179.93
    179.15
    179.61
    178.58

    114.63
    114.63
    114.63
    115.21
    115.21
    120.28
    119.99
    120.04
    119.92
    120.33
    119.52
    119.92
    119.95
    120.02
    119.92
    118.94

    CQ

    HQ

    1.4514
    1.3430
    1.3430
    1.5061
    1.4514
    1.4016
    1.4012
    1.4009
    1.4012
    1.4012
    1.0802
    1.0789
    1.0805
    1.0814
    1.0812
    1.3320

    0.00 ! C12H10FO2 Alpha benzyl, Gamma 3-Fluoro amino benzene

    glutamic acid CDCA amide, Chayan


    !To be patched with residue GABD
    DELETE ATOM HE1
    !
    GROUP
    !
    CD1--CE1--FE1
    ATOM CC1 CG311
    0.17 !
    /
    \\
    ATOM HC1 HGA1
    0.09 !
    CP
    ATOM CA CG2O2
    0.90 !
    \ __ /
    ATOM OA1 OG2D1 -0.63 !
    CD2--CE2
    ATOM OA2 OG302 -0.49 !
    ATOM CB

    CG321

    OG
    ||

    CG--NG--CZ
    /

    HG

    CC3
    \

    -0.22 !

    O24

    CC2

    ATOM HB1 HGA2

    0.09 !

    ||

    ATOM HB2 HGA2

    0.09 !

    GROUP

    ATOM CY CG2R61 0.00 !


    CJ1--CK1
    ATOM CJ1 CG2R61 -0.115 !
    //
    \\
    ATOM HJ1 HGR61
    0.115 !
    CY
    CQ
    ATOM CJ2 CG2R61 -0.115 !
    \ __ /
    ATOM HJ2 HGR61
    0.115 !
    CJ2--CK2
    ATOM CK1 CG2R61 -0.115 !
    ATOM HK1 HGR61

    Me19 |

    ATOM HK2 HGR61

    C3

    C5

    C7

    0.115 !

    GROUP

    0.115 !

    C23

    C14

    C16

    C4

    C6

    C15

    OH

    ATOM CD1 CG2R61 -0.100 !

    3FBP

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HD1
    CE1
    FE1
    CP
    HP

    HGR62
    0.150 !
    CG2R66 0.110 !
    FGR1
    -0.210 !
    CG2R61 -0.100 !
    HGR62
    0.150 !

    BOND
    BOND
    BOND
    BOND
    BOND

    OA2
    CB
    CY
    CQ
    CE1

    CB
    HB1 CB HB2 CB CY
    CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ
    CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY
    FE1

    NH

    CA--OA1

    OA2--CB--

    / \ / \ / \
    HO

    CC1

    / \|/ \ / \ /

    HGR61

    C20

    C1 | C9

    ATOM CK2 CG2R61 -0.115 !

    ATOM HQ

    C24

    C11 C13---C17

    C10 C8

    CG2R61 -0.115 !

    C22

    \ / \ / \ / \ __

    / \ |

    C2

    ATOM CQ

    Me21

    C12 Me18

    0.115 !

    CQ

    HQ

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CC1
    HB1
    HB2
    CA
    CJ1
    CB
    CY
    CJ1
    CK1
    CB
    CK1
    CK2
    CQ
    CQ
    CK1
    CD1

    CA
    CB
    CB
    OA2
    CY
    CY
    CJ1
    CK1
    CQ
    CY
    CY
    CY
    CJ1
    CJ2
    CK2
    CP

    OA2
    OA2
    OA2
    CB
    CB
    CJ1
    CK1
    CQ
    CK2
    CJ2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    *CE1

    CB
    CA
    CA
    CY
    OA2
    CK1
    CQ
    CK2
    CJ2
    CK2
    HJ1
    HJ2
    HK1
    HK2
    HQ
    FE1

    1.5310
    1.1151
    1.1156
    1.3407
    1.4053
    1.5054
    1.4053
    1.4017
    1.4010
    1.5054
    1.4017
    1.4002
    1.4010
    1.4000
    1.4010
    1.3934

    110.63
    110.56
    109.57
    114.31
    119.56
    119.56
    120.29
    119.95
    119.94
    120.97
    120.29
    120.26
    119.95
    120.12
    119.94
    122.09

    -175.15
    55.87
    -63.30
    175.76
    164.70
    177.79
    -0.37
    0.24
    0.14
    -177.38
    -179.60
    178.59
    -179.67
    178.86
    179.70
    178.24

    114.31
    114.31
    114.31
    116.12
    116.12
    120.29
    119.95
    119.94
    120.12
    120.26
    119.80
    119.81
    120.07
    119.82
    119.90
    118.96

    1.4534
    1.3407
    1.3407
    1.5054
    1.4534
    1.4017
    1.4010
    1.4000
    1.4002
    1.4002
    1.0797
    1.0794
    1.0804
    1.0784
    1.0807
    1.3332

    PRES 2FBP
    0.14 ! C12H9FO2 Alpha benzyl, Gamma 2-Fluoro amino benzene g
    lutamic acid CDCA amide, Chayan
    !To be patched with residue GABD
    DELETE ATOM HD1
    !
    GROUP
    !
    F
    D1
    ATOM CC1 CG311
    0.17 !
    |
    ATOM HC1
    D1--CE1
    ATOM CA
    \\
    ATOM OA1
    CP
    ATOM OA2
    __ /
    ATOM CB
    D2--CE2
    ATOM HB1

    HGA1

    0.09 !

    OG

    CG2O2

    0.90 !

    ||

    //

    OG2D1

    -0.63 !

    CG--NG--CZ

    OG302

    -0.49 !

    CG321

    -0.22 !

    CC3

    HGA2

    0.09 !

    ATOM HB2 HGA2

    0.09 !

    GROUP
    ATOM CY

    0.00 !

    ATOM CJ1 CG2R61 -0.115 !

    ATOM HJ1 HGR61


    0.115 !
    CJ1--CK1
    ATOM CJ2 CG2R61 -0.115 !
    //
    \\
    ATOM HJ2 HGR61
    0.115 !
    Y
    CQ
    ATOM CK1 CG2R61 -0.115 !
    \ __ /
    ATOM HK1 HGR61
    0.115 !
    CJ2--CK2
    ATOM CK2 CG2R61 -0.115 !

    C12 Me18

    ATOM HK2 HGR61

    0.115 !

    Me21

    CC2

    ||

    C22

    C20
    /

    C11 C13---C17

    C1 | C9

    C14

    C16

    / \|/ \ / \ /
    C2

    C10 C8

    CC1

    \ / \ / \ / \ __

    / \ |

    Me19 |

    C24

    \
    C

    O24

    !
    CG2R61

    HG

    C15

    C23

    NH

    CA--OA1
    |
    OA2--CB--C

    ATOM CQ

    CG2R61 -0.115 !

    ATOM HQ

    HGR61

    C3

    C5

    C7

    GROUP

    0.115 !
    !

    ATOM CE1 CG2R61 -0.100 ! HO

    / \ / \ / \

    ATOM HE1 HGR62

    0.150 !

    ATOM CD1 CG2R66

    0.110 !

    C4

    C6

    OH

    2FBP

    ATOM FD1 FGR1


    -0.210 !
    ATOM CZ CG2R61 0.190 !
    BOND
    BOND
    BOND
    BOND
    BOND

    OA2
    CB
    CY
    CQ
    CD1

    CB
    HB1 CB HB2 CB CY
    CJ1 CJ1 HJ1 CJ1 CK1 CK1 HK1 CK1 CQ
    CK2 CK2 HK2 CK2 CJ2 CJ2 HJ2 CJ2 CY
    FD1

    IC CC1 CA
    IC HB1 CB
    IC HB2 CB
    IC CA OA2
    IC CJ1 CY
    IC CB CY
    IC CY CJ1
    IC CJ1 CK1
    IC CK1 CQ
    IC CB CY
    IC CK1 CY
    IC CK2 CY
    IC CQ CJ1
    IC CQ CJ2
    IC CK1 CK2
    IC CZ CE1
    !End Polli's

    OA2
    OA2
    OA2
    CB
    CB
    CJ1
    CK1
    CQ
    CK2
    CJ2
    *CJ1
    *CJ2
    *CK1
    *CK2
    *CQ
    *CD1
    bile

    CB
    1.5324 110.58 -171.81
    CA
    1.1152 109.67 65.73
    CA
    1.1162 110.77 -52.90
    CY
    1.3429 114.58 -172.25
    OA2 1.4051 121.08 -129.13
    CK1 1.5055 121.08 -177.36
    CQ
    1.4051 120.29
    0.38
    CK2 1.4015 119.93 -0.45
    CJ2 1.4010 120.04
    0.10
    CK2 1.5055 119.39 177.05
    HJ1 1.4015 120.29 179.02
    HJ2 1.4014 120.28 -179.17
    HK1 1.4010 119.93 179.08
    HK2 1.4010 119.98 -179.89
    HQ
    1.4010 120.04 -179.60
    FD1 1.4058 122.69 179.26
    acids, chayan, feb2008

    114.58
    114.58
    114.58
    114.95
    114.95
    120.29
    119.93
    120.04
    119.98
    120.28
    119.81
    119.50
    120.10
    119.95
    120.00
    117.93

    CQ

    HQ

    1.4510
    1.3429
    1.3429
    1.5055
    1.4510
    1.4015
    1.4010
    1.4010
    1.4014
    1.4014
    1.0790
    1.0802
    1.0810
    1.0805
    1.0812
    1.3368

    !Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008


    !Model compound to optimize aromatic-aliphatic ether
    RESI MEOB
    0.00 ! C7H8O Methoxybenzene (aka anisole, phenyl-methyl ethe
    r), Chayan
    ATOM CG CG2R61 -0.115 !
    ATOM HG HGR61
    0.115 !
    HD1 HE1
    GROUP
    !
    |
    |
    ATOM CD1 CG2R61 -0.115 !
    CD1--CE1
    ATOM HD1 HGR61
    0.115 !
    /
    \
    GROUP
    ! HG--CG
    CZ--OZ--CM
    ATOM CD2 CG2R61 -0.115 !
    \
    /
    ATOM HD2 HGR61
    0.115 !
    CD2--CE2
    GROUP
    !
    |
    |
    ATOM CE1 CG2R61 -0.115 !
    HD2 HE2
    ATOM HE1 HGR61
    0.115
    GROUP
    ATOM CE2 CG2R61 -0.115
    ATOM HE2 HGR61
    0.115
    GROUP
    ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    OZ
    CM
    HM1
    HM2
    HM3

    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE2
    CM

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    OG301
    CG331
    HGA3
    HGA3
    HGA3

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CE2
    CZ
    HM1
    HM1

    CG
    CD2
    HG
    HE2
    HM1
    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CZ
    OZ
    OZ
    OZ

    CD2
    CZ
    CD1
    CZ
    CM

    CD1
    CE2
    CG
    CE2
    C1
    C2

    CG
    CD2
    HG
    HE2
    H1A
    H2A

    CG
    CE1
    HD1
    OZ
    HM2

    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    OZ
    CM
    *CM
    *CM

    RESI ETOB
    er), Chayan
    ATOM CG CG2R61
    ATOM HG HGR61
    GROUP
    ATOM CD1 CG2R61
    ATOM HD1 HGR61
    GROUP
    ATOM CD2 CG2R61
    ATOM HD2 HGR61
    GROUP
    ATOM CE1 CG2R61
    ATOM HE1 HGR61
    GROUP
    ATOM CE2 CG2R61
    ATOM HE2 HGR61
    GROUP
    ATOM CZ CG2R61
    ATOM OZ OG301
    ATOM C1 CG321
    ATOM H1A HGA2
    ATOM H1B HGA2
    GROUP
    ATOM C2 CG331
    ATOM H2A HGA3
    ATOM H2B HGA3
    ATOM H2C HGA3
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    -0.39 ! RESI C36 and Igor's ethers should


    -0.10 ! be better than analogy to phenol!
    0.09
    0.09
    0.09

    CD2
    CZ
    CD1
    CZ
    C1
    C2

    CE1
    CZ
    CD2
    OZ
    CM

    CZ
    CE2
    CD2
    HG
    HD1
    HD2
    HE1
    HE2
    OZ
    CM
    HM1
    HM2
    HM3

    CD1
    CE2
    HD2 CE1 HE1
    CM
    HM3
    1.3999
    1.4007
    1.3997
    1.3999
    1.4007
    1.4039
    1.3997
    1.4128
    1.3997
    1.4128
    1.4094
    1.1121
    1.1121

    119.78
    121.00
    118.94
    119.98
    119.78
    120.17
    121.00
    120.14
    118.94
    123.32
    117.32
    110.78
    110.78

    0.00
    0.00
    0.00
    180.00
    180.00
    -180.00
    -180.00
    -180.00
    -180.00
    0.00
    -61.22
    122.45
    -118.78

    121.00
    118.94
    120.14
    120.06
    120.21
    119.86
    120.31
    117.62
    123.32
    117.32
    110.78
    110.78
    108.75

    1.3997
    1.4128
    1.4039
    1.0805
    1.0804
    1.0805
    1.0797
    1.0763
    1.4094
    1.4272
    1.1121
    1.1121
    1.1112

    0.00 ! C8H10O Ethoxybenzene (aka phenetole, phenyl-ethyl eth


    -0.115 !
    0.115 !
    HD1 HE1
    !
    |
    |
    -0.115 !
    CD1--CE1
    0.115 !
    /
    \
    ! HG--CG
    CZ--OZ--C1--C2(Me)
    -0.115 !
    \
    /
    0.115 !
    CD2--CE2
    !
    |
    |
    -0.115 !
    HD2 HE2
    0.115
    -0.115
    0.115
    0.22 ! Corrected by kevo: combination of
    -0.39 ! RESI C36 and Igor's ethers should
    -0.01 ! be better than analogy to phenol!
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09
    CG
    CE1
    HD1
    OZ
    H1B
    H2B

    CE1
    CZ
    CD2
    OZ
    C1
    C2

    CD1
    CE2
    HD2 CE1 HE1
    C1
    C2
    H2C

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CE2
    CZ
    H1A
    H1A
    OZ
    H2A
    H2A

    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CZ
    OZ
    OZ
    OZ
    C1
    C1
    C1

    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    OZ
    C1
    *C1
    *C1
    C2
    *C2
    *C2

    CZ
    CE2
    CD2
    HG
    HD1
    HD2
    HE1
    HE2
    OZ
    C1
    H1A
    H1B
    C2
    H2A
    H2B
    H2C

    1.4001
    1.4009
    1.3995
    1.4001
    1.4009
    1.4036
    1.3995
    1.4120
    1.3995
    1.4120
    1.4086
    1.1142
    1.1142
    1.4239
    1.1094
    1.1094

    119.79
    120.95
    118.98
    119.98
    119.79
    120.12
    120.95
    120.18
    118.98
    123.18
    117.39
    110.26
    110.26
    107.48
    110.94
    110.94

    0.00
    0.00
    0.00
    -180.00
    180.00
    -180.00
    180.00
    180.00
    -180.00
    0.00
    -60.67
    121.34
    -119.33
    180.00
    120.60
    -120.60

    120.95
    118.98
    120.18
    120.05
    120.21
    119.88
    120.34
    117.95
    123.18
    117.39
    110.26
    110.26
    107.48
    110.94
    109.82
    109.82

    1.3995
    1.4120
    1.4036
    1.0805
    1.0804
    1.0805
    1.0797
    1.0763
    1.4086
    1.4239
    1.1142
    1.1142
    1.5257
    1.1094
    1.1110
    1.1110

    PRES FBID
    0.00 ! C3H6O Fatty acid Binding protein Inhibitor D, chayan
    ! This is a phenyl-methyl ether derivative having
    ! methyl at 2 and ethyl acetate at 4 position
    ! patch combination:
    ! core residue Compound "FBIB" >> Compound "FBID"
    !
    DELETE ATOM CC
    !
    HD1 HE1
    DELETE ATOM HC
    !
    |
    |
    DELETE ATOM C1
    !
    (-0.5)OD1 HA1 HB1 CD1--CE1
    DELETE ATOM H1A
    !
    \
    | |
    //
    \\
    DELETE ATOM H1B
    !
    CD--CA--CB--CG
    CZ--OH
    DELETE ATOM H1C
    !
    /
    | |
    \ __ /
    \
    DELETE ATOM C2
    !
    (-0.5)OD2 HA2 HB2 CD2--CE2
    CN(Me)
    DELETE ATOM H2A
    !
    |
    |
    DELETE ATOM H2B
    !
    HD2 CM(Me)
    DELETE ATOM H2C
    !
    DELETE ATOM HH
    !
    GROUP
    !
    ATOM CM CG331 -0.27 !
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    GROUP
    ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of
    ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should
    ATOM CN CG331 -0.10 ! be better than analogy to phenol!
    ATOM HN1 HGA3
    0.09
    ATOM HN2 HGA3
    0.09
    ATOM HN3 HGA3
    0.09
    BOND CE2 CM CM HM1 CM HM2 CM HM3
    BOND OH CN CN HN1 CN HN2 CN HN3
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CZ
    CD2
    HM1
    HM1
    CE1
    CZ
    HN1
    HN1

    CD2
    CE2
    CE2
    CE2
    CZ
    OH
    OH
    OH

    *CE2
    CM
    *CM
    *CM
    OH
    CN
    *CN
    *CN

    CM
    HM1
    HM2
    HM3
    CN
    HN1
    HN2
    HN3

    1.4150
    1.4035
    1.1101
    1.1101
    1.4096
    1.4137
    1.1113
    1.1113

    119.45
    118.38
    108.56
    108.56
    121.48
    115.06
    110.63
    110.63

    178.47
    -73.69
    120.14
    -119.98
    33.49
    -76.12
    122.41
    -118.58

    118.38
    108.56
    109.17
    109.71
    115.06
    110.63
    111.24
    108.69

    1.5035
    1.1101
    1.1105
    1.1110
    1.4278
    1.1113
    1.1132
    1.1108

    PRES FBIE
    0.00 ! C2H4O Fatty acid Binding protein Inhibitor D, chayan
    ! This is a phenyl-methyl ether derivative having
    ! ethyl acetate at 4 position
    ! patch combination:
    ! core residue Compound "FBIB" >> Compound "FBIE"
    !
    DELETE ATOM CC
    !
    HD1 HE1
    DELETE ATOM HC
    !
    |
    |
    DELETE ATOM C1
    !
    (-0.5)OD1 HA1 HB1 CD1--CE1
    DELETE ATOM H1A
    !
    \
    | |
    //
    \\
    DELETE ATOM H1B
    !
    CD--CA--CB--CG
    CZ--OH
    DELETE ATOM H1C
    !
    /
    | |
    \ __ /
    \
    DELETE ATOM C2
    !
    (-0.5)OD2 HA2 HB2 CD2--CE2
    CM(Me)
    DELETE ATOM H2A
    !
    |
    |
    DELETE ATOM H2B
    !
    HD2 HE2
    DELETE ATOM H2C
    !
    DELETE ATOM HH
    !
    GROUP
    !
    ATOM HE2 HGR61
    0.00 !
    GROUP
    !
    ATOM CZ CG2R61 0.22 ! Corrected by kevo: combination of
    ATOM OH OG301 -0.39 ! RESI C36 and Igor's ethers should
    ATOM CM CG331 -0.10 ! be better than analogy to phenol!
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    BOND CE2 HE2
    BOND OH CM CM HM1 CM HM2 CM HM3
    IC
    IC
    IC
    IC
    IC

    CZ
    CE1
    CZ
    HM1
    HM1

    CD2
    CZ
    OH
    OH
    OH

    *CE2
    OH
    CM
    *CM
    *CM

    HE2
    CM
    HM1
    HM2
    HM3

    1.4159
    1.4005
    1.4145
    1.1126
    1.1126

    120.13
    117.83
    116.32
    110.84
    110.84

    -179.81
    171.75
    -56.84
    122.15
    -118.98

    117.32
    116.32
    110.84
    110.67
    108.83

    1.0785
    1.4272
    1.1126
    1.1120
    1.1108

    PRES FBIFR
    -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, R-isomer,
    chayan
    ! This is IBUPROFEN (phenyl derivative having
    ! 2-methyl ethyl acetate at 4 position)
    ! core residue "FBIB" >> Compound "FBIFR"
    ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration
    DELETE ATOM CA
    !
    DELETE ATOM HA1
    !
    DELETE ATOM HA2
    !
    DELETE ATOM CB
    !
    DELETE ATOM HB1
    !
    DELETE ATOM HB2
    !
    HD1 HE1
    DELETE ATOM CC
    !
    |
    |
    DELETE ATOM HC
    ! (-0.5)OD1 CMG
    CD1--CE1
    CN1
    DELETE ATOM C1
    !
    \
    |
    //
    \\
    /
    DELETE ATOM H1A
    !
    CD--CBG--CG
    CZM--CM1--CM2
    DELETE ATOM H1B
    !
    /
    |
    \ __ /
    \
    DELETE ATOM H1C
    ! (-0.5)OD2 HBG
    CD2--CE2
    CN2
    DELETE ATOM C2
    !
    |
    |
    DELETE ATOM H2A
    !
    HD2 HE2
    DELETE ATOM H2B
    !
    DELETE ATOM H2C
    !
    COMPOUND "FBIFR" OR "FBIFS"

    DELETE ATOM CZ
    DELETE ATOM OH
    DELETE ATOM HH
    GROUP
    ATOM HE2 HGR61
    GROUP
    ATOM CBG CG311
    ATOM HBG HGA1
    ATOM CMG CG331
    ATOM HMG1 HGA3
    ATOM HMG2 HGA3
    ATOM HMG3 HGA3
    GROUP
    ATOM CZM CG2R61
    GROUP
    ATOM CM1 CG321
    ATOM HM1A HGA2
    ATOM HM1B HGA2
    GROUP
    ATOM CM2 CG311
    ATOM HM2 HGA1
    GROUP
    ATOM CN1 CG331
    ATOM HN1A HGA3
    ATOM HN1B HGA3
    ATOM HN1C HGA3
    GROUP
    ATOM CN2 CG331
    ATOM HN2A HGA3
    ATOM HN2B HGA3
    ATOM HN2C HGA3
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    0.00

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    -0.19
    0.09
    -0.27
    0.09
    0.09
    0.09
    0.00
    -0.18
    0.09
    0.09
    -0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    CE2
    CG
    CE1
    CM1
    CM2

    HE2
    CBG
    CZM
    CM2
    CN2

    CBG
    CE2
    CM2
    CN2

    CG
    CZM
    CE2
    CD2
    CD2
    CG
    HMG1
    HMG1
    CMG
    CG
    OD1
    CE1
    CE1
    HM1A
    HM1A
    CZM
    HM2
    HM2
    CM1
    HN1A
    HN1A
    CM1

    CD1
    CD2
    CD2
    CG
    CG
    CBG
    CBG
    CBG
    CG
    CBG
    CBG
    CE2
    CZM
    CZM
    CZM
    CM1
    CM1
    CM1
    CM2
    CM2
    CM2
    CM2

    CE1
    *CE2
    CG
    CBG
    CBG
    CMG
    *CMG
    *CMG
    *CBG
    CD
    *CD
    CZM
    CM1
    *CM1
    *CM1
    CM2
    *CM2
    *CM2
    CN1
    *CN1
    *CN1
    CN2

    -0.27
    0.09
    0.09
    0.09
    CD
    CZM
    HM2
    HN2A
    CZM
    HE2
    CBG
    CMG
    HBG
    HMG1
    HMG2
    HMG3
    CD
    OD1
    OD2
    CM1
    HM1A
    HM1B
    CM2
    HM2
    CN1
    CN2
    HN1A
    HN1B
    HN1C
    HN2A

    CBG
    CZM
    CM2
    CN2

    HBG
    CM1
    CN1
    HN2B

    1.4074
    1.4038
    1.4008
    1.4107
    1.4107
    1.5308
    1.1099
    1.1099
    1.5638
    1.5308
    1.2585
    2.4229
    1.4018
    1.1109
    1.1109
    1.5097
    1.1171
    1.1171
    1.5467
    1.1105
    1.1105
    1.5467

    CBG
    CM1
    CN1
    CN2

    121.22
    120.33
    120.74
    123.82
    123.82
    111.99
    110.42
    110.42
    111.99
    113.97
    120.65
    30.26
    119.74
    107.54
    107.54
    111.69
    108.58
    108.58
    110.34
    110.14
    110.14
    112.25

    CMG CMG HMG1 CMG HMG2 CMG HMG3


    HM1A CM1 HM1B
    HN1A CN1 HN1B CN1 HN1C
    HN2C
    0.25
    -179.97
    178.69
    -15.87
    -132.75
    68.31
    118.37
    -121.91
    126.26
    1.93
    172.14
    178.92
    50.63
    117.28
    -120.94
    56.61
    117.56
    -119.29
    61.99
    119.99
    -119.88
    60.91

    120.04
    119.65
    123.82
    111.99
    108.39
    110.42
    109.28
    110.96
    113.97
    120.65
    115.78
    120.81
    107.54
    109.24
    111.69
    108.58
    110.34
    112.25
    110.14
    110.39
    110.33
    110.56

    1.4018
    1.0800
    1.5308
    1.5638
    1.1103
    1.1099
    1.1117
    1.1084
    1.5510
    1.2585
    1.2623
    1.5097
    1.1109
    1.1111
    1.5467
    1.1171
    1.5373
    1.5383
    1.1105
    1.1102
    1.1105
    1.1111

    IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.90 110.46


    IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.87 110.24

    1.1099
    1.1101

    PRES FBIFS
    -0.10 ! C7H14 Fatty acid Binding protein Inhibitor, S-isomer,
    chayan
    ! This is IBUPROFEN (phenyl derivative having
    ! 2-methyl ethyl acetate at 4 position)
    ! core residue "FBIB" >> Compound "FBIFS"
    ! Orientation of the methyl group on ehtyl acetate dictates R/S configuration
    DELETE ATOM CA
    !
    DELETE ATOM HA1
    !
    DELETE ATOM HA2
    !
    DELETE ATOM CB
    !
    DELETE ATOM HB1
    !
    DELETE ATOM HB2
    !
    DELETE ATOM CC
    !
    HD1 HE1
    DELETE ATOM HC
    !
    |
    |
    DELETE ATOM C1
    ! (-0.5)OD1 CMG
    CD1--CE1
    CN1
    DELETE ATOM H1A
    !
    \
    |
    //
    \\
    /
    DELETE ATOM H1B
    !
    CD--CBG--CG
    CZM--CM1--CM2
    DELETE ATOM H1C
    !
    /
    |
    \ __ /
    \
    DELETE ATOM C2
    ! (-0.5)OD2 HBG
    CD2--CE2
    CN2
    DELETE ATOM H2A
    !
    |
    |
    DELETE ATOM H2B
    !
    HD2 HE2
    DELETE ATOM H2C
    !
    DELETE ATOM CZ
    !
    COMPOUND "FBIFR" OR "FBIFS"
    DELETE ATOM OH
    !
    DELETE ATOM HH
    !
    GROUP
    !
    ATOM HE2 HGR61
    0.00 !
    GROUP
    !
    ATOM CBG CG311 -0.19 !
    ATOM HBG HGA1
    0.09 !
    ATOM CMG CG331 -0.27 !
    ATOM HMG1 HGA3
    0.09 !
    ATOM HMG2 HGA3
    0.09 !
    ATOM HMG3 HGA3
    0.09 !
    GROUP
    ATOM CZM CG2R61 0.00
    GROUP
    ATOM CM1 CG321 -0.18
    ATOM HM1A HGA2
    0.09
    ATOM HM1B HGA2
    0.09
    GROUP
    ATOM CM2 CG311 -0.09
    ATOM HM2 HGA1
    0.09
    GROUP
    ATOM CN1 CG331 -0.27
    ATOM HN1A HGA3
    0.09
    ATOM HN1B HGA3
    0.09
    ATOM HN1C HGA3
    0.09
    GROUP
    ATOM CN2 CG331 -0.27
    ATOM HN2A HGA3
    0.09
    ATOM HN2B HGA3
    0.09
    ATOM HN2C HGA3
    0.09
    BOND CE2 HE2
    BOND CG CBG CBG HBG CBG CD

    CBG CMG CMG HMG1 CMG HMG2 CMG HMG3

    BOND CE1 CZM CE2 CZM CZM CM1 CM1 HM1A CM1 HM1B
    BOND CM1 CM2 CM2 HM2 CM2 CN1 CN1 HN1A CN1 HN1B CN1 HN1C
    BOND CM2 CN2 CN2 HN2A CN2 HN2B CN2 HN2C
    IC CG CD1 CE1 CZM 1.4067 120.82
    0.59 120.10 1.4030
    IC CZM CD2 *CE2 HE2 1.4050 120.15 -179.82 119.75 1.0799
    IC CE2 CD2 CG CBG 1.3998 120.76 178.17 119.92 1.5233
    IC CD2 CG CBG CMG 1.4058 119.92 -112.06 107.62 1.5610 ! S-isomer
    IC CD2 CG CBG HBG 1.4058 119.92
    5.06 110.49 1.1095 ! S-isomer
    IC CG CBG CMG HMG1 1.5233 107.62 55.81 110.88 1.1088
    IC HMG1 CBG *CMG HMG2 1.1088 110.88 119.89 109.40 1.1116
    IC HMG1 CBG *CMG HMG3 1.1088 110.88 -121.32 110.59 1.1099
    IC CMG CG *CBG CD
    1.5610 107.62 -124.32 115.01 1.5504
    IC CG CBG CD OD1 1.5233 115.01 -1.31 120.84 1.2583
    IC OD1 CBG *CD OD2 1.2583 120.84 -175.49 115.85 1.2621
    IC CE1 CE2 CZM CM1 2.4256 30.23 179.20 120.79 1.5096
    IC CE1 CZM CM1 HM1A 1.4030 119.71 50.70 107.54 1.1109
    IC HM1A CZM *CM1 HM1B 1.1109 107.54 117.31 109.24 1.1110
    IC HM1A CZM *CM1 CM2 1.1109 107.54 -120.92 111.68 1.5467
    IC CZM CM1 CM2 HM2 1.5096 111.68 56.65 108.57 1.1172
    IC HM2 CM1 *CM2 CN1 1.1172 108.57 117.56 110.34 1.5373
    IC HM2 CM1 *CM2 CN2 1.1172 108.57 -119.28 112.26 1.5383
    IC CM1 CM2 CN1 HN1A 1.5467 110.34 62.00 110.14 1.1105
    IC HN1A CM2 *CN1 HN1B 1.1105 110.14 119.98 110.39 1.1103
    IC HN1A CM2 *CN1 HN1C 1.1105 110.14 -119.89 110.33 1.1105
    IC CM1 CM2 CN2 HN2A 1.5467 112.26 60.95 110.56 1.1111
    IC HN2A CM2 *CN2 HN2B 1.1111 110.56 119.89 110.46 1.1099
    IC HN2A CM2 *CN2 HN2C 1.1111 110.56 -119.88 110.25 1.1101
    !End Shapiro's Fatty acid Binding protein Inhibitors, chayan, feb2008
    !Fundamental functional groups, kevo, feb2008
    RESI ACN
    0.000 ! C2H3N acetonitrile, kevo
    GROUP
    ATOM C1 CG331 -0.17
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    ATOM C2 CG1N1
    0.36
    ATOM N3 NG1T1 -0.46
    BOND
    BOND
    IC
    IC
    IC

    C1 C2 C2 N3
    C1 H11 C1 H12 C1
    N3 C2 C1 H11
    C2 H11 *C1 H12
    C2 H11 *C1 H13

    RESI 2BTY
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM C2
    GROUP
    ATOM C3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43

    H13
    0.0000 179.90
    0.00
    0.0000
    0.00 120.00
    0.0000
    0.00 240.00

    0.000 ! C4H6 2-butyne, kevo


    CG331
    HGA3
    HGA3
    HGA3
    CG1T1

    -0.19
    0.09
    0.09
    0.09
    -0.08

    CG1T1
    CG331
    HGA3
    HGA3
    HGA3

    -0.08
    -0.19
    0.09
    0.09
    0.09

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    BOND C1 C2 C2 C3 C3 C4
    BOND C1 H11 C1 H12 C1 H13
    BOND C4 H41 C4 H42 C4 H43
    !!Just a test
    !DIHE H11 C2 C3 H41
    !DIHE H11 C2 C3 H42
    !DIHE H11 C2 C3 H43
    !DIHE H12 C2 C3 H41
    !DIHE H12 C2 C3 H42
    !DIHE H12 C2 C3 H43
    !DIHE H13 C2 C3 H41
    !DIHE H13 C2 C3 H42
    !DIHE H13 C2 C3 H43
    IC C1 C2 C3 C4 0.0000 179.90
    0.00 179.90
    IC C3 C2 C1 H11 0.0000 179.90
    0.00
    0.00
    IC C2 H11 *C1 H12 0.0000
    0.00 120.00
    0.00
    IC C2 H11 *C1 H13 0.0000
    0.00 240.00
    0.00
    IC C2 C3 C4 H41 0.0000 179.90
    0.00
    0.00
    IC C3 H41 *C4 H42 0.0000
    0.00 120.00
    0.00
    IC C3 H41 *C4 H43 0.0000
    0.00 240.00
    0.00
    !End fundamental functional groups, kevo, feb2008

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Continuation of Maybridge list, kevo, feb2008


    RESI 3HPR
    0.000 ! C4H5N 3H-pyrrole, kevo
    GROUP
    ATOM N1 NG2R50 -0.60
    ATOM C2 CG2R52 0.10
    ATOM H2 HGR52
    0.13 ! H31
    H4
    ATOM C3 CG3C52 0.05 !
    \
    /
    ATOM H31 HGA2
    0.09 ! H32--C3---C4
    ATOM H32 HGA2
    0.09 !
    |
    ||
    ATOM C4 CG2R51 -0.30 !
    C2 C5
    ATOM H4 HGR51
    0.18 !
    / \\ / \
    ATOM C5 CG2R51 0.12 ! H2 N1
    H5
    ATOM H5 HGR52
    0.14
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1 C2 C2 C3 C3
    C2 H2 C3 H31 C3
    C3 C4 C5 N1
    C4 C5 N1 C2
    C3 N1 *C2 H2
    C4 C2 *C3 H31
    C4 C2 *C3 H32
    C5 C3 *C4 H4
    N1 C4 *C5 H5

    RESI 3HIN
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7

    C4 C4 C5 C5 N1
    H32 C4 H4 C5 H5
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 120.00
    0.0000
    0.00 240.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.000 ! C8H7N 3H-indole, kevo


    NG2R50
    CG2R52
    HGR52
    CG3C52
    HGA2
    HGA2
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    -0.61
    0.18
    0.11
    -0.09
    0.09
    0.09
    0.25
    -0.36
    0.20
    -0.22
    0.21
    -0.21

    !
    H5
    !
    |
    ! H31
    C5
    !
    \
    / \\
    ! H32--C3---C4 C6--H6
    !
    |
    ||
    |
    !
    C2 C9 C7--H7
    !
    / \\ / \ //
    ! H2 N1
    C8

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM

    H7
    C8
    H8
    C9

    BOND N1
    BOND C6
    BOND C2
    BOND C5
    IC N1
    IC C2
    IC C9
    IC C9
    IC C4
    IC C5
    IC C6
    IC C7
    IC C8
    IC C9
    IC C3
    IC C4
    IC C4

    HGR61
    0.21 !
    CG2R61 -0.34 !
    HGR61
    0.26
    CG2RC0 0.23
    C2
    C7
    H2
    H5
    C2
    C3
    C3
    C4
    C5
    C6
    C4
    C5
    C6
    C7
    N1
    C2
    C2

    RESI INDI
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    BOND N1
    BOND C6
    BOND N1
    BOND C5
    IC N1
    IC C2
    IC C9
    IC C9
    IC C4
    IC C5
    IC C6
    IC C7
    IC C8
    IC C9
    IC C9
    IC C3

    C2
    C7
    C3
    C6
    C3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *C2
    *C3
    *C3

    C3 C3
    C8 C8
    H31 C3
    H6 C7
    C4
    C9
    C5
    C6
    C7
    C8
    H5
    H6
    H7
    H8
    H2
    H31
    H32

    |
    H8

    C4 C4 C5 C5 C6
    C9 C9 N1 C4 C9
    H32
    H7 C8 H8
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 120.00
    0.0000
    0.00 240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C8H9N indoline, kevo


    NG3C51
    HGP1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    C2
    C7
    H1
    H5
    C2
    C3
    C3
    C4
    C5
    C6
    C4
    C5
    C6
    C7
    C2
    N1

    C2
    C7
    C2
    C6
    C3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *N1
    *C2

    -0.68
    0.33
    0.00
    0.09
    0.09
    -0.12
    0.09
    0.09
    0.11
    -0.40
    0.24
    -0.27
    0.22
    -0.20
    0.20
    -0.29
    0.21
    0.29
    C3 C3
    C8 C8
    H21 C2
    H6 C7
    C4
    C9
    C5
    C6
    C7
    C8
    H5
    H6
    H7
    H8
    H1
    H21

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    H31
    C5
    \
    / \\
    H32--C3---C4 C6--H6
    |
    ||
    |
    H22--C2 C9 C7--H7
    / \ / \ //
    H21 N1
    C8
    |
    |
    H1
    H8

    C4 C4
    C9 C9
    H22 C3
    H7 C8
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    N1 C4
    H31 C3
    H8
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6
    C9
    H32
    330.00
    20.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    120.00
    120.00

    IC C3
    IC C4
    IC C4

    N1
    C2
    C2

    RESI ZFUR
    GROUP
    ATOM O1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    BOND O1
    BOND C6
    BOND C2
    BOND C5
    IC O1
    IC C2
    IC C9
    IC C9
    IC C4
    IC C5
    IC C6
    IC C7
    IC C8
    IC C9
    IC C3
    IC C4

    *C2 H22
    *C3 H31
    *C3 H32

    0.00 240.00
    0.00 120.00
    0.00 240.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    0.000 ! C8H6O benzofuran (there's only 1 benzofuran), kevo


    OG2R50
    CG2R51
    HGR52
    CG2R51
    HGR51
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    C2
    C7
    H2
    H5
    C2
    C3
    C3
    C4
    C5
    C6
    C4
    C5
    C6
    C7
    O1
    C2

    RESI ZTHP
    kevo
    GROUP
    ATOM S1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9

    0.0000
    0.0000
    0.0000

    C2
    C7
    C3
    C6
    C3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *C2
    *C3

    -0.28
    0.02
    0.18
    -0.40
    0.25
    0.15
    -0.33
    0.24
    -0.28
    0.23
    -0.21
    0.22
    -0.34
    0.24
    0.31

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    H3
    C5
    \
    / \\
    C3---C4 C6--H6
    || ||
    |
    C2 C9 C7--H7
    / \ / \ //
    H2 O1
    C8
    |
    H8

    C3 C3 C4 C4 C5 C5 C6
    C8 C8 C9 C9 O1 C4 C9
    H3
    H6 C7 H7 C8 H8
    C4
    0.0000
    0.00
    0.00
    C9
    0.0000
    0.00
    0.00
    C5
    0.0000
    0.00 180.00
    C6
    0.0000
    0.00
    0.00
    C7
    0.0000
    0.00
    0.00
    C8
    0.0000
    0.00
    0.00
    H5
    0.0000
    0.00 180.00
    H6
    0.0000
    0.00 180.00
    H7
    0.0000
    0.00 180.00
    H8
    0.0000
    0.00 180.00
    H2
    0.0000
    0.00 180.00
    H3
    0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C8H6S benzothiophene (there's only 1 benzothiophene),


    SG2R50
    CG2R51
    HGR52
    CG2R51
    HGR51
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    -0.16
    -0.09
    0.18
    -0.28
    0.21
    0.17
    -0.34
    0.24
    -0.29
    0.24
    -0.21
    0.21
    -0.23
    0.24
    0.11

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    H3
    C5
    \
    / \\
    C3---C4 C6--H6
    || ||
    |
    C2 C9 C7--H7
    / \ / \ //
    H2 S1
    C8
    |
    H8

    BOND S1 C2 C2 C3 C3 C4 C4 C5 C5 C6
    BOND C6 C7 C7 C8 C8 C9 C9 S1 C4 C9

    BOND C2
    BOND C5
    IC S1
    IC C2
    IC C9
    IC C9
    IC C4
    IC C5
    IC C6
    IC C7
    IC C8
    IC C9
    IC C3
    IC C4

    H2
    H5
    C2
    C3
    C3
    C4
    C5
    C6
    C4
    C5
    C6
    C7
    S1
    C2

    RESI ZTHZ
    GROUP
    ATOM S1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    BOND S1
    BOND C6
    BOND C2
    BOND C5
    IC S1
    IC C2
    IC C9
    IC C9
    IC C4
    IC C5
    IC C6
    IC C7
    IC C8
    IC C9
    IC N3

    H3
    H6 C7 H7 C8 H8
    C4
    0.0000
    0.00
    C9
    0.0000
    0.00
    C5
    0.0000
    0.00
    C6
    0.0000
    0.00
    C7
    0.0000
    0.00
    C8
    0.0000
    0.00
    H5
    0.0000
    0.00
    H6
    0.0000
    0.00
    H7
    0.0000
    0.00
    H8
    0.0000
    0.00
    H2
    0.0000
    0.00
    H3
    0.0000
    0.00

    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C7H5NS benzothiazole, kevo


    SG2R50
    CG2R53
    HGR52
    NG2R50
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    C2
    C7
    H2
    H5
    C2
    N3
    N3
    C4
    C5
    C6
    C4
    C5
    C6
    C7
    S1

    RESI PUR9
    GROUP
    ATOM C5
    ATOM N7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM H9
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3

    C3
    C6
    C3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *C2
    *C3

    -0.25
    0.16
    0.18
    -0.69
    0.64
    -0.46
    0.26
    -0.29
    0.26
    -0.38
    0.26
    -0.24
    0.22
    0.33

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    C5
    / \\
    N3---C4 C6--H6
    || ||
    |
    C2 C9 C7--H7
    / \ / \ //
    H2 S1
    C8
    |
    H8

    C2 N3 N3 C4 C4 C5 C5 C6
    C7 C8 C8 C9 C9 S1 C4 C9
    C6
    N3
    C4
    *C4
    C5
    C6
    C7
    *C5
    *C6
    *C7
    *C8
    *C2

    H6 C7 H7 C8 H8
    C4
    0.0000
    0.00
    C9
    0.0000
    0.00
    C5
    0.0000
    0.00
    C6
    0.0000
    0.00
    C7
    0.0000
    0.00
    C8
    0.0000
    0.00
    H5
    0.0000
    0.00
    H6
    0.0000
    0.00
    H7
    0.0000
    0.00
    H8
    0.0000
    0.00
    H2
    0.0000
    0.00

    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H4N4 purine (N9H-tautomer), kevo


    CG2RC0
    NG2R50
    CG2R53
    HGR52
    NG2R51
    HGP1
    NG2R62
    CG2R64
    HGR62
    NG2R62

    0.30
    -0.73
    0.37
    0.09
    -0.19
    0.29
    -0.73
    0.50
    0.14
    -0.77

    !
    !
    !
    !
    !
    !
    !
    !

    H6
    |
    C6
    //
    N1
    |
    C2
    / \\

    \
    C5--N7\\
    ||
    C8-H8
    C4--N9/
    /
    \

    ATOM C4
    ATOM C6
    ATOM H6

    CG2RC0
    CG2R61
    HGR62

    0.44 ! H2 N3
    H9
    0.09 ! Was: CG2R64. See: PYRM.
    0.20

    BOND N1 C2 C2 N3 N3
    BOND C5 N7 N7 C8 C8
    BOND C2 H2 C6 H6 C8
    !Ihis improper may only
    !IMPR C6 N1 C5 H6
    IC N7 C8 N9 C4
    IC N9 C8 N7 C5
    IC C8 N7 C5 C4
    IC C4 N7 *C5 C6
    IC C4 C5 C6 N1
    IC C5 C6 N1 C2
    IC C6 N1 C2 N3
    IC N1 C5 *C6 H6
    IC N3 N1 *C2 H2
    IC C8 C4 *N9 H9
    IC N7 N9 *C8 H8
    RESI PUR7
    GROUP
    ATOM C5
    ATOM N7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM C6
    ATOM H6

    C4 C4 C5 C5 C6 C6 N1
    N9 N9 C4
    H8 N9 H9
    be relevant if a heavy atom is bound to C6.
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H4N4 purine (N7H-tautomer), kevo


    CG2RC0
    NG2R51
    HGP1
    CG2R53
    HGR52
    NG2R50
    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2RC0
    CG2R61
    HGR62

    0.23
    -0.22
    0.26
    0.32
    0.12
    -0.57
    -0.78
    0.48
    0.13
    -0.58
    0.21
    0.31
    0.09

    !
    H6
    !
    |
    !
    C6
    H7
    !
    // \
    /
    !
    N1 C5--N7\
    !
    |
    ||
    C8-H8
    !
    C2 C4--N9//
    ! / \\ /
    ! H2 N3

    BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1
    BOND C5 N7 N7 C8 C8 N9 N9 C4
    BOND C2 H2 C6 H6 C8 H8 N7 H7
    !Ihis improper may only be relevant if a heavy atom is bound to C6.
    !IMPR C6 N1 C5 H6
    IC N7 C8 N9 C4
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC N9 C8 N7 C5
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC C8 N7 C5 C4
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC C4 N7 *C5 C6
    0.0000
    0.00 180.00
    0.00 0.0000
    IC C4 C5 C6 N1
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC C5 C6 N1 C2
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC C6 N1 C2 N3
    0.0000
    0.00
    0.00
    0.00 0.0000
    IC N1 C5 *C6 H6
    0.0000
    0.00 180.00
    0.00 0.0000
    IC N3 N1 *C2 H2
    0.0000
    0.00 180.00
    0.00 0.0000
    IC C5 C8 *N7 H7
    0.0000
    0.00 180.00
    0.00 0.0000
    IC N7 N9 *C8 H8
    0.0000
    0.00 180.00
    0.00 0.0000
    !End continuation of Maybridge list, kevo, feb2008
    !Continuation of Maybridge list, kevo and erh, jun2008
    RESI CPDE
    0.000 ! C5H6 cyclopentadiene, kevo
    ATOM C1 CG3C52 0.10
    ATOM H11 HGA2
    0.09 !
    H3
    H4
    ATOM H12 HGA2
    0.09 !
    \
    /

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    C2
    H2
    C3
    H3
    C4
    H4
    C5
    H5

    BOND C1
    BOND C5
    BOND C2
    IC C1
    IC C2
    IC C5
    IC C5
    IC C1
    IC C2
    IC C3
    IC C4

    CG2R51
    HGR51
    CG2R51
    HGR51
    CG2R51
    HGR51
    CG2R51
    HGR51
    C2
    C1
    H2
    C2
    C3
    C2
    C2
    C3
    C4
    C5
    C1

    RESI INDE
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM C5
    ATOM H5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    BOND C1
    BOND C5
    BOND C4
    BOND C1
    BOND C5
    IC C9
    IC C3
    IC C3
    IC C4
    IC C9
    IC C4
    IC C9
    IC C9
    IC C1
    IC C2
    IC C4
    IC C5
    IC C6
    IC C7

    C2
    C1
    C3
    C3
    C4
    *C1
    *C1
    *C2
    *C3
    *C4
    *C5

    -0.36
    0.22
    -0.22
    0.22
    -0.22
    0.22
    -0.36
    0.22
    C3 C3
    H11 C1
    H3 C4
    C4
    C5
    H11
    H12
    H2
    H3
    H4
    H5

    !
    !
    !
    !
    !
    !
    !

    C3----C4
    ||
    ||
    C2
    C5
    / \ / \
    H2
    C1
    H5
    /\
    H11 H12

    C4 C4 C5
    H12
    H4 C5 H5
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00

    0.00
    0.00
    120.00
    240.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C9H8 indene, kevo


    CG3C52
    HGA2
    HGA2
    CG2R51
    HGR51
    CG2R51
    HGR51
    CG2RC0
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0

    C2
    C6
    C9
    H11
    H5
    C4
    C4
    C9
    C1
    C4
    C9
    C2
    C2
    C3
    C4
    C6
    C7
    C8
    C9

    C2
    C6
    C9
    C1
    C6
    C3
    C9
    *C4
    *C9
    C5
    C8
    *C1
    *C1
    *C2
    *C3
    *C5
    *C6
    *C7
    *C8

    0.02
    0.09
    0.09
    -0.30
    0.22
    -0.43
    0.26
    0.24
    -0.33
    0.22
    -0.19
    0.20
    -0.22
    0.21
    -0.36
    0.22
    0.06
    C3 C3
    C7 C7
    C1
    H12 C2
    H6 C7
    C2
    C1
    C5
    C8
    C6
    C7
    H11
    H12
    H2
    H3
    H5
    H6
    H7
    H8

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H5
    |
    C5

    H3
    \

    / \\
    C3----C4
    C6 -H6
    ||
    ||
    |
    C2
    C9
    C7 -H7
    / \ / \ //
    H2
    C1
    C8
    /\
    |
    H11 H12 H8

    C4 C4 C5
    C8 C8 C9
    H2 C3 H3
    H7 C8 H8
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00

    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    120.00
    240.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI CRBZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM H10
    ATOM C11
    ATOM N12
    ATOM H12
    ATOM C13

    0.00 ! C12H9N Carbazole, erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R67
    CG2R67
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0
    NG2R51
    HGP1
    CG2RC0

    BOND C1 C2
    BOND C6 C7
    BOND C11 N12
    BOND C1 H1
    BOND C8 H8
    IC C5 C13
    IC C1 C13
    IC C13 C5
    IC C1 C5
    IC C4 C13
    IC C13 C5
    IC N12 C6
    IC C5 C11
    IC C11 C6
    IC C6 C11
    IC C13 C2
    IC C1 C3
    IC C2 C4
    IC C3 C5
    IC C6 C8
    IC C7 C9
    IC C8 C10
    IC C9 C11
    IC C11 C13
    RESI FLRN
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4

    -0.180
    0.180
    -0.180
    0.180
    -0.180
    0.180
    -0.270
    0.270
    -0.200
    -0.200
    -0.270
    0.270
    -0.180
    0.180
    -0.180
    0.180
    -0.180
    0.180
    0.200
    -0.300
    0.300
    0.200

    C2 C3 C3
    C7 C8 C8
    N12 C13 C13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C13 N12
    *C5 C6
    C6
    C11
    *C11 C10
    *C6 C7
    C7
    C8
    C10 C9
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H4
    *C7 H7
    *C8 H8
    *C9 H9
    *C10 H10
    *N12 H12

    !
    H4
    H7
    !
    |
    |
    !
    C4
    C7
    !
    // \
    / \\
    ! H3--C3
    C5----C6
    C8--H8
    !
    |
    ||
    ||
    |
    ! H2--C2
    C13 C11 C9--H9
    !
    \\ / \ / \ //
    !
    C1
    N12 C10
    !
    |
    |
    |
    !
    H1
    H12 H10

    C4 C4
    C9 C9
    C1 C5
    H3 C4
    H10 N12
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C13 C6
    H4 C7
    H12
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6
    C11
    C11
    H7
    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00 ! C13H10 Fluorene, erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    -0.140
    0.140
    -0.170
    0.170
    -0.190
    0.190
    -0.280 !

    H4

    H7

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H4
    C5
    C6
    C7
    H7
    C8
    H8
    C9
    H9
    C10
    H10
    C11
    C12
    H21
    H22
    C13

    HGR61
    CG2R67
    CG2R67
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2RC0
    CG3C52
    HGA2
    HGA2
    CG2RC0

    0.280
    -0.240
    -0.240
    -0.280
    0.280
    -0.190
    0.190
    -0.170
    0.170
    -0.140
    0.140
    0.240
    -0.180
    0.090
    0.090
    0.240

    BOND C1 C2 C2 C3 C3
    BOND C6 C7 C7 C8 C8
    BOND C11 C12 C12 C13 C13
    BOND C1 H1 C2 H2 C3
    BOND C8 H8 C9 H9 C10
    IC C5 C13 C1
    C2
    IC C1 C13 C5
    C4
    IC C13 C5 C4
    C3
    IC C1 C5 *C13 C12
    IC C4 C13 *C5 C6
    IC C13 C5 C6
    C11
    storsion!
    IC C5 C11 *C6 C7
    to make above work
    IC C7 C6 C11 C10
    to make above work
    IC C11 C6 C7
    C8
    IC C6 C11 C10 C9
    IC C13 C2 *C1 H1
    IC C1 C3 *C2 H2
    IC C2 C4 *C3 H3
    IC C3 C5 *C4 H4
    IC C6 C8 *C7 H7
    IC C7 C9 *C8 H8
    IC C8 C10 *C9 H9
    IC C9 C11 *C10 H10
    IC C11 C13 *C12 H21
    IC C11 C13 *C12 H22
    RESI NAFT
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7

    !
    |
    |
    !
    C4
    C7
    !
    // \
    / \\
    ! H3--C3
    C5----C6
    C8--H8
    !
    |
    ||
    ||
    |
    ! H2--C2
    C13 C11 C9--H9
    !
    \\ / \ / \ //
    !
    C1
    C12 C10
    !
    |
    / \
    |
    !
    H1 H21 H22 H10

    C4 C4
    C9 C9
    C1 C5
    H3 C4
    H10 C12
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C13 C6
    H4 C7
    H21 C12
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6
    C11
    C11
    H7
    H22
    0.00
    0.00
    0.00
    180.00
    180.00
    5.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000 ! Deliberate di

    0.0000

    0.00 180.00

    0.00

    0.0000 ! Deviating def

    0.0000

    0.00

    0.00

    0.00

    0.0000 ! Deviating def

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C10H8 Naphtalene, kevo


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115

    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H7
    C8
    H8
    C9
    H9
    C10

    BOND C1
    BOND C5
    BOND C9
    BOND C1
    BOND C6
    IC C5
    IC C1
    IC C10
    IC C1
    IC C4
    IC C10
    IC C5
    IC C10
    IC C1
    IC C2
    IC C3
    IC C5
    IC C6
    IC C7
    IC C8

    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.115
    HGR61
    0.115
    CG2R61 0.000
    C2
    C6
    C10
    H1
    H6
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    C2
    C3
    C4
    C5
    C7
    C8
    C9
    C10

    RESI QINL
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    BOND N1
    BOND C5
    BOND C9
    BOND C2
    BOND C6
    IC C5
    IC N1
    IC C10
    IC N1
    IC C4
    IC C10
    IC C5

    C2 C3 C3
    C6 C7 C7
    C5 C10 C1
    C2 H2 C3
    C7 H7 C8
    C1
    C2
    C5
    C4
    C4
    C3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H4
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    C1
    |
    H1

    C4 C4
    C8 C8
    C10
    H3 C4
    H8 C9
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C9
    |
    H9

    C5
    C9
    H4
    H9
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C9H7N Quinoline, kevo and erh


    NG2R60
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    C2
    C6
    C10
    H2
    H6
    C10
    C10
    C5
    C5
    C10
    C5
    C10

    -0.640
    0.160
    0.140
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.340

    C2 C3 C3
    C6 C7 C7
    C5 C10 N1
    C3 H3 C4
    C7 H7 C8
    N1
    C2
    C5
    C4
    C4
    C3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //
    N1
    C9
    |
    H9

    C4 C4 C5
    C8 C8 C9
    C10
    H4
    H8 C9 H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N1
    C2
    C3
    C5
    C6
    C7
    C8

    C3
    C4
    C5
    C7
    C8
    C9
    C10

    RESI IQIN
    GROUP
    ATOM C1
    ATOM H1
    ATOM N2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    BOND C1
    BOND C5
    BOND C9
    BOND C1
    BOND C6
    IC C5
    IC C1
    IC C10
    IC C1
    IC C4
    IC C10
    IC C5
    IC C10
    IC N2
    IC C3
    IC C5
    IC C6
    IC C7
    IC C8

    H2
    H3
    H4
    H6
    H7
    H8
    H9

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C9H7N Isoquinoline, erh


    CG2R61
    HGR62
    NG2R60
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    N2
    C6
    C10
    H1
    H6
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    N2
    C4
    C5
    C7
    C8
    C9
    C10

    RESI CINL
    GROUP
    ATOM N1
    ATOM N2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7

    *C2
    *C3
    *C4
    *C6
    *C7
    *C8
    *C9

    0.17
    0.15
    -0.61
    0.12
    0.14
    -0.115
    0.115
    0.05
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.02

    N2 C3 C3
    C6 C7 C7
    C5 C10 C1
    C3 H3 C4
    C7 H7 C8
    C1
    N2
    C5
    C4
    C4
    C3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C1 H1
    *C3 H3
    *C4 H4
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    N2
    C10 C8--H8
    \\ / \ //
    C1
    C9
    |
    |
    H1
    H9

    C4 C4 C5
    C8 C8 C9
    C10
    H4
    H8 C9 H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00 ! C8H6N2 Cinnoline, erh

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    NG2R62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61

    -0.500
    -0.450
    0.350
    0.070
    -0.160
    0.180
    0.000
    -0.115
    0.115
    -0.115

    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    N2
    C10 C8--H8
    \\ / \ //

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H7
    C8
    H8
    C9
    H9
    C10

    BOND N1
    BOND C5
    BOND C9
    BOND C3
    BOND C7
    IC C5
    IC N1
    IC C10
    IC N1
    IC C4
    IC C10
    IC C5
    IC N2
    IC C3
    IC C5
    IC C6
    IC C7
    IC C8

    HGR61
    0.115 !
    CG2R61 -0.115 !
    HGR61
    0.115 !
    CG2R61 -0.160
    HGR61
    0.180
    CG2R61 0.490
    N2
    C6
    C10
    H3
    H7
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    C4
    C5
    C7
    C8
    C9
    C10

    RESI FTAZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM N2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    BOND C1
    BOND C5
    BOND C9
    BOND C1
    BOND C7
    IC C5
    IC C1
    IC C10
    IC C1
    IC C4
    IC C10
    IC C5
    IC C10
    IC N3
    IC C5

    N2 C3 C3
    C6 C7 C7
    C5 C10 N1
    C4 H4 C6
    C8 H8 C9
    N1
    N2
    C5
    C4
    C4
    C3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C3 H3
    *C4 H4
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    N1

    C9
    |
    H9

    C4 C4 C5
    C8 C8 C9
    C10
    H6
    H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H6N2 Phthalazine, erh


    CG2R61
    HGR62
    NG2R62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    N2
    C6
    C10
    H1
    H7
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    N2
    C5
    C7

    0.340
    0.080
    -0.490
    -0.490
    0.340
    0.080
    0.070
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.070

    N2 N3 N3
    C6 C7 C7
    C5 C10 C1
    C4 H4 C6
    C8 H8 C9
    C1
    N2
    C5
    C4
    C4
    N3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C1 H1
    *C4 H4
    *C6 H6

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    N3
    C5
    C7--H7
    |
    ||
    |
    N2
    C10 C8--H8
    \\ / \ //
    C1
    C9
    |
    |
    H1
    H9

    C4 C4 C5
    C8 C8 C9
    C10
    H6
    H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    IC C6
    IC C7
    IC C8

    C8 *C7
    C9 *C8
    C10 *C9

    RESI QINZ
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    BOND N1
    BOND C5
    BOND C9
    BOND C2
    BOND C7
    IC C5
    IC N1
    IC C10
    IC N1
    IC C4
    IC C10
    IC C5
    IC N1
    IC N3
    IC C5
    IC C6
    IC C7
    IC C8

    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 180.00
    0.00 180.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    0.00 ! C8H6N2 Quinazoline, erh


    NG2R62
    CG2R64
    HGR62
    NG2R62
    CG2R61
    HGR62
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    C2
    C6
    C10
    H2
    H7
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    N3
    C5
    C7
    C8
    C9
    C10

    RESI QINX
    GROUP
    ATOM N1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM N4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10

    H7
    H8
    H9

    -0.810
    0.520
    0.140
    -0.750
    0.280
    0.130
    0.020
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.470

    C2 N3 N3
    C6 C7 C7
    C5 C10 N1
    C4 H4 C6
    C8 H8 C9
    N1
    C2
    C5
    C4
    C4
    N3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C2 H2
    *C4 H4
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    N3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //
    N1
    C9
    |
    H9

    C4 C4 C5
    C8 C8 C9
    C10
    H6
    H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00 ! C8H6N2 Quinoxaline, erh

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    NG2R60
    CG2R61
    HGR62
    CG2R61
    HGR62
    NG2R60
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    -0.580
    0.090
    0.160
    0.090
    0.160
    -0.580
    0.330
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.330

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H6
    |
    C6

    N4
    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //
    N1
    C9
    |
    H9

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    BOND N1
    BOND C5
    BOND C9
    BOND C2
    BOND C7
    IC C5
    IC N1
    IC C10
    IC N1
    IC N4
    IC C10
    IC C5
    IC N1
    IC C2
    IC C5
    IC C6
    IC C7
    IC C8

    C2
    C6
    C10
    H2
    H7
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    C3
    N4
    C7
    C8
    C9
    C10

    C2 C3 C3
    C6 C7 C7
    C5 C10 N1
    C3 H3 C6
    C8 H8 C9
    N1
    C2
    C5
    N4
    N4
    C3
    *C10 C9
    *C5 C6
    C6
    C7
    C9
    C8
    *C2 H2
    *C3 H3
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    RESI 18NFD
    GROUP
    ATOM N1 NG2R62
    ATOM C2 CG2R61
    ATOM H2 HGR62
    ATOM C3 CG2R61
    ATOM H3 HGR61
    ATOM C4 CG2R61
    ATOM H4 HGR61
    ATOM C5 CG2R61
    ATOM C6 CG2R61
    ATOM H6 HGR61
    ATOM C7 CG2R61
    ATOM H7 HGR61
    ATOM C8 CG2R61
    ATOM H8 HGR62
    ATOM N9 NG2R62
    ATOM C10 CG2R64
    BOND N1
    BOND C5
    BOND N9
    BOND C2
    BOND C6
    IC C5
    IC N1
    IC C10
    IC N1
    IC C4
    IC C10
    IC C5
    IC N1
    IC C2
    IC C3
    IC C5
    IC C6
    IC C7

    C2
    C6
    C10
    H2
    H6
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    C3
    C4
    C5
    C7
    C8
    N9

    RESI PTID
    GROUP

    N4 N4 C5
    C8 C8 C9
    C10
    H6
    H9
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H6N2 1,8-naphthyridine, erh


    -0.660
    0.330
    0.090
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115
    0.115
    0.330
    0.090
    -0.660
    0.480

    C2 C3 C3
    C6 C7 C7
    C5 C10 N1
    C3 H3 C4
    C7 H7 C8
    N1
    C2
    C5
    C4
    C4
    C3
    *C10 N9
    *C5 C6
    C6
    C7
    N9
    C8
    *C2 H2
    *C3 H3
    *C4 H4
    *C6 H6
    *C7 H7
    *C8 H8

    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //
    N1
    N9

    C4 C4 C5
    C8 C8 N9
    C10
    H4
    H8
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00 ! C6H4N4 pteridine, erh

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM N1
    ATOM C2
    ATOM H2
    ATOM N3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM N6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM N9
    ATOM C10
    ! Manual
    BOND N1
    BOND C5
    BOND N9
    BOND C2
    IC C5
    IC N1
    IC C10
    IC N1
    IC C4
    IC C10
    IC C5
    IC N1
    IC N3
    IC N6
    IC C7

    NG2R62 -0.710
    CG2R64 0.500
    HGR62
    0.140
    NG2R62 -0.700 !
    H4
    CG2R61 0.110 !
    |
    HGR62
    0.180 !
    C4
    N6
    CG2R61 0.450 !
    // \ / \\
    NG2R60 -0.640 !
    N3
    C5
    C7--H7
    CG2R61 0.185 !
    |
    ||
    |
    HGR62
    0.105 ! H2--C2
    C10 C8--H8
    CG2R61 0.320 !
    \\ / \ //
    HGR62
    0.090 !
    N1
    N9
    NG2R62 -0.650
    CG2R64 0.620
    init guess (analogy to PYZN, PYRM, PUR9 and PUR7)
    C2
    N6
    C10
    H2
    C10
    C10
    C5
    C5
    C10
    C5
    C10
    N3
    C5
    C8
    N9

    C2 N3 N3
    N6 C7 C7
    C5 C10 N1
    C4 H4 C7
    N1
    C2
    C5
    C4
    C4
    N3
    *C10 N9
    *C5 N6
    N6
    C7
    N9
    C8
    *C2 H2
    *C4 H4
    *C7 H7
    *C8 H8

    C4 C4 C5
    C8 C8 N9
    C10
    H7 C8 H8
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI 4HQI
    0.00 ! C9H9N 4H-Quinolizine, kevo
    !CG2DC2 and CG2DC1 are not symmetric for this class of compounds
    !we could do 16HP and 2M1HP first, but they're not perfectly relevant;
    !the system is significantly deformed (unlike 2M1HP) and
    !the nitrogen is quite planar (unlike 16HP). We used NG2R61, which can
    !be assigned automatically because all atoms in the right ring are sp2
    GROUP
    ATOM C1 CG2DC1 -0.27
    ATOM H1 HGA4
    0.17
    ATOM C2 CG2DC2 -0.34
    ATOM H2 HGA4
    0.24
    ATOM C3 CG2DC2 -0.44 !
    H41 H42 H6
    ATOM H3 HGA4
    0.22 !
    \ / |
    ATOM C4 CG321
    0.02 !
    C4
    C6
    ATOM H41 HGA2
    0.09 !
    / \ / \\
    ATOM H42 HGA2
    0.09 ! H3--C3
    N5
    C7--H7
    ATOM N5 NG2R61 0.27 !
    ||
    |
    |
    ATOM C6 CG2D1O -0.32 ! H2--C2
    C10 C8--H8
    ATOM H6 HGA4
    0.26 !
    \ // \ //
    ATOM C7 CG2DC1 -0.24 !
    C1
    C9
    ATOM H7 HGA4
    0.20 !
    |
    |
    ATOM C8 CG2DC2 -0.22 !
    H1
    H9
    ATOM H8 HGA4
    0.22
    ATOM C9 CG2DC2 -0.24
    ATOM H9 HGA4
    0.19
    ATOM C10 CG2D1O 0.10
    BOND C1 C2 C2 C3 C3 C4 C4 N5

    BOND N5
    BOND C9
    BOND C1
    BOND C6
    IC N5
    IC C1
    IC C10
    IC C1
    IC C4
    IC C10
    IC N5
    IC C10
    IC C1
    IC C2
    IC C3
    IC C3
    IC N5
    IC C6
    IC C7
    IC C8

    C6
    C10
    H1
    H6
    C10
    C10
    N5
    N5
    C10
    N5
    C10
    C2
    C3
    C4
    N5
    N5
    C7
    C8
    C9
    C10

    RESI ANTR
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM H10
    ATOM C11
    ATOM H11
    ATOM C12
    ATOM C13
    ATOM H13
    ATOM C14

    C6 C7 C7
    N5 C10 C1
    C2 H2 C3
    C7 H7 C8
    C1
    C2
    N5
    C4
    C4
    C3
    *C10 C9
    *N5 C6
    C6
    C7
    C9
    C8
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H41
    *C4 H42
    *C6 H6
    *C7 H7
    *C8 H8
    *C9 H9

    C8 C8 C9
    C10
    H3 C4 H41 C4 H42
    H8 C9 H9
    0.0000
    0.00 16.00
    0.0000
    0.00 22.00
    0.0000
    0.00 -51.00
    0.0000
    0.00 170.00
    0.0000
    0.00 170.00
    0.0000
    0.00
    0.00
    0.0000
    0.00
    0.00
    0.0000
    0.00 -160.00
    0.0000
    0.00 -160.00
    0.0000
    0.00 -160.00
    0.0000
    0.00 120.00
    0.0000
    0.00 -120.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00
    0.0000
    0.00 180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C14H10 Anthracene, kevo and erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61

    BOND C1 C2
    BOND C6 C7
    BOND C11 C12
    BOND C1 H1
    BOND C8 H8
    IC C5 C14
    IC C1 C14
    IC C14 C5
    IC C1 C5
    IC C4 C14
    IC C14 C5
    IC C5 C14

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    0.000

    C2 C3 C3
    C7 C8 C8
    C12 C13 C13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C14 C13
    *C5 C6
    C6
    C7
    C13 C12

    !
    H4
    H6
    H8
    !
    |
    |
    |
    !
    C4
    C6
    C8
    !
    // \ / \\ / \\
    ! H3--C3
    C5
    C7
    C9--H9
    !
    |
    ||
    |
    |
    ! H2--C2
    C14 C12 C10-H10
    !
    \\ / \ // \ //
    !
    C1
    C13 C11
    !
    |
    |
    |
    !
    H1
    H13 H11

    C4 C4
    C9 C9
    C14 C14
    H3 C4
    H10 C11
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C1 C5
    H4 C6
    H11 C13
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6
    C11
    C14 C7 C12
    H6
    H13
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    0.00
    180.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C13
    C6
    C12
    C7
    C14
    C1
    C2
    C3
    C5
    C7
    C8
    C9
    C10
    C12

    C7
    C12
    C7
    C12
    C2
    C3
    C4
    C5
    C7
    C9
    C10
    C11
    C12
    C14

    RESI ACRD
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM H10
    ATOM C11
    ATOM H11
    ATOM C12
    ATOM N13
    ATOM C14

    *C12
    *C7
    C8
    C11
    *C1
    *C2
    *C3
    *C4
    *C6
    *C8
    *C9
    *C10
    *C11
    *C13

    C11
    C8
    C9
    C10
    H1
    H2
    H3
    H4
    H6
    H8
    H9
    H10
    H11
    H13

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C13H9N Acridine, erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    NG2R60
    CG2R61

    BOND C1 C2
    BOND C6 C7
    BOND C11 C12
    BOND C1 H1
    BOND C8 H8
    IC C5 C14
    IC C1 C14
    IC C14 C5
    IC C1 C5
    IC C4 C14
    IC C14 C5
    IC C5 C14
    IC N13 C7
    IC C6 C12
    IC C12 C7
    IC C7 C12
    IC C14 C2
    IC C1 C3
    IC C2 C4

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.345
    -0.690
    0.345

    C2 C3 C3
    C7 C8 C8
    C12 N13 N13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C14 N13
    *C5 C6
    C6
    C7
    N13 C12
    *C12 C11
    *C7 C8
    C8
    C9
    C11 C10
    *C1 H1
    *C2 H2
    *C3 H3

    !
    H4
    H6
    H8
    !
    |
    |
    |
    !
    C4
    C6
    C8
    !
    // \ / \\ / \\
    ! H3--C3
    C5
    C7
    C9--H9
    !
    |
    ||
    |
    |
    ! H2--C2
    C14 C12 C10-H10
    !
    \\ / \ // \ //
    !
    C1
    N13 C11
    !
    |
    |
    !
    H1
    H11

    C4 C4
    C9 C9
    C14 C14
    H3 C4
    H10 C11
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C1 C5
    H4 C6
    H11
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6
    C11
    C14 C7 C12
    H6
    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC

    C3
    C5
    C7
    C8
    C9
    C10

    C5
    C7
    C9
    C10
    C11
    C12

    RESI FENZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM N6
    ATOM C7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM H10
    ATOM C11
    ATOM H11
    ATOM C12
    ATOM N13
    ATOM C14

    *C4
    *C6
    *C8
    *C9
    *C10
    *C11

    H4
    H6
    H8
    H9
    H10
    H11

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C12H8N2 Phenazine, erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    NG2R60
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    NG2R60
    CG2R61

    BOND C1 C2
    BOND N6 C7
    BOND C11 C12
    BOND C1 H1
    BOND C8 H8
    IC C5 C14
    IC C1 C14
    IC C14 C5
    IC C1 C5
    IC C4 C14
    IC C14 C5
    IC C5 C14
    IC N13 C7
    IC N6 C12
    IC C12 C7
    IC C7 C12
    IC C14 C2
    IC C1 C3
    IC C2 C4
    IC C3 C5
    IC C7 C9
    IC C8 C10
    IC C9 C11
    IC C10 C12

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.320
    -0.640
    0.320
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.320
    -0.640
    0.320

    C2 C3 C3
    C7 C8 C8
    C12 N13 N13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C14 N13
    *C5 N6
    N6
    C7
    N13 C12
    *C12 C11
    *C7 C8
    C8
    C9
    C11 C10
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H4
    *C8 H8
    *C9 H9
    *C10 H10
    *C11 H11

    !
    H4
    H8
    !
    |
    |
    !
    C4
    N6
    C8
    !
    // \ / \\ / \\
    ! H3--C3
    C5
    C7
    C9--H9
    !
    |
    ||
    |
    |
    ! H2--C2
    C14 C12 C10-H10
    !
    \\ / \ // \ //
    !
    C1
    N13 C11
    !
    |
    |
    !
    H1
    H11

    C4 C4
    C9 C9
    C14 C14
    H3 C4
    H10 C11
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C1 C5
    H4
    H11
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    N6
    C11
    C14 C7 C12
    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    RESI FEOZ
    0.00 ! C12H9NO Phenoxazine, erh & kevo
    GROUP
    ATOM C1 CG2R61 -0.115

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H1
    C2
    H2
    C3
    H3
    C4
    H4
    C5
    O6
    C7
    C8
    H8
    C9
    H9
    C10
    H10
    C11
    H11
    C12
    N13
    H13
    C14

    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    OG3R60
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    NG311
    HGPAM1
    CG2R61

    BOND C1 C2
    BOND O6 C7
    BOND C11 C12
    BOND C1 H1
    BOND C8 H8
    IC C5 C14
    IC C1 C14
    IC C14 C5
    IC C1 C5
    IC C4 C14
    IC C14 C5
    IC C5 C14
    IC N13 C7
    IC O6 C12
    IC C12 C7
    IC C7 C12
    IC C14 C2
    IC C1 C3
    IC C2 C4
    IC C3 C5
    IC C7 C9
    IC C8 C10
    IC C9 C11
    IC C10 C12
    IC C12 C14
    RESI FETZ
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5

    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.130
    -0.260
    0.130
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.040
    -0.470
    0.390
    0.040

    C2 C3 C3
    C7 C8 C8
    C12 N13 N13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C14 N13
    *C5 O6
    O6
    C7
    N13 C12
    *C12 C11
    *C7 C8
    C8
    C9
    C11 C10
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H4
    *C8 H8
    *C9 H9
    *C10 H10
    *C11 H11
    *N13 H13

    !
    H4
    H8
    !
    |
    |
    !
    C4
    O6
    C8
    !
    // \ / \ / \\
    ! H3--C3
    C5
    C7
    C9--H9
    !
    |
    ||
    ||
    |
    ! H2--C2
    C14 C12 C10-H10
    !
    \\ / \ / \ //
    !
    C1
    N13 C11
    !
    |
    |
    |
    !
    H1
    H13 H11

    C4 C4
    C9 C9
    C14 C14
    H3 C4
    H10 C11
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C1 C5
    H4
    H11 N13
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    O6
    C11
    C14 C7 C12
    H13
    0.00
    0.00
    0.00
    180.00
    180.00
    -30.00
    30.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00 ! C12H9NS Phenothiazine, erh


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115 !
    0.115 !
    0.130 !

    H4
    |
    C4

    S6

    H8
    |
    C8

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    S6
    C7
    C8
    H8
    C9
    H9
    C10
    H10
    C11
    H11
    C12
    N13
    H13
    C14

    SG311
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    NG311
    HGPAM1
    CG2R61

    BOND C1 C2
    BOND S6 C7
    BOND C11 C12
    BOND C1 H1
    BOND C8 H8
    IC C5 C14
    IC C1 C14
    IC C14 C5
    IC C1 C5
    IC C4 C14
    IC C14 C5
    IC C5 C14
    IC N13 C7
    IC C11 C12
    IC C12 C7
    IC C7 C12
    IC C14 C2
    IC C1 C3
    IC C2 C4
    IC C3 C5
    IC C7 C9
    IC C8 C10
    IC C9 C11
    IC C10 C12
    IC C12 C14

    -0.240
    0.130
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.010
    -0.360
    0.360
    -0.010

    C2 C3 C3
    C7 C8 C8
    C12 N13 N13
    C2 H2 C3
    C9 H9 C10
    C1
    C2
    C5
    C4
    C4
    C3
    *C14 N13
    *C5 S6
    S6
    C7
    N13 C12
    *C12 C11
    C7
    C8
    C8
    C9
    C11 C10
    *C1 H1
    *C2 H2
    *C3 H3
    *C4 H4
    *C8 H8
    *C9 H9
    *C10 H10
    *C11 H11
    *N13 H13

    !
    // \ / \ / \\
    ! H3--C3
    C5
    C7
    C9--H9
    !
    |
    ||
    ||
    |
    ! H2--C2
    C14 C12 C10-H10
    !
    \\ / \ / \ //
    !
    C1
    N13 C11
    !
    |
    |
    |
    !
    H1
    H13 H11

    C4 C4
    C9 C9
    C14 C14
    H3 C4
    H10 C11
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5 C5
    C10 C10
    C1 C5
    H4
    H11 N13
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    S6
    C11
    C14 C7 C12
    H13
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    0.00
    180.00
    0.00
    -30.00 99.00
    30.00 114.00
    180.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    120.00
    0.00

    RESI DIOL
    GROUP
    ATOM O1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM O3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    OG3C51 -0.40
    CG3C52 0.16 !
    H42
    HGA2
    0.09 !
    /
    HGA2
    0.09 !
    O3----C4--H41
    OG3C51 -0.40 !
    |
    |
    CG3C52 0.05 ! H21--C2
    C5--H51
    HGA2
    0.09 !
    / \ / \
    HGA2
    0.09 ! H22
    O1
    H52
    CG3C52 0.05
    HGA2
    0.09
    HGA2
    0.09

    BOND
    BOND
    BOND
    BOND
    IC

    C2
    C5
    H21
    H51
    C5

    O1
    C4
    C2
    C5
    C4

    0.0000
    0.0000
    0.0000
    1.4300
    0.0000
    0.0000
    1.4300
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.000 ! C3H6O2 1,3-Dioxolane, erh

    C2
    C5
    C2
    C5
    O1

    O3 O3 C4
    O1
    H22 C4 H41 C4 H42
    H52
    C2 0.0000
    0.00 30.00

    0.00

    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC

    O1
    O1
    O1
    O3
    O3
    O1
    O1

    C5
    O3
    O3
    C5
    C5
    C4
    C4

    C4
    *C2
    *C2
    *C4
    *C4
    *C5
    *C5

    RESI IMDP
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM N3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3C51
    HGP1
    CG3C54
    HGA2
    HGA2
    NG3P2
    HGP2
    HGP2
    CG3C54
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    H1
    H41
    C2
    N3
    C4
    C5
    C2
    C2
    C5
    C5
    N3
    N3
    C4
    C4

    N1
    C4
    N1
    C2
    N3
    C2
    C4
    C4
    N3
    N3
    N1
    N1
    N1
    N1

    O3
    H21
    H22
    H41
    H42
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C3H9N2 Imidazolidine protonated, erh and kevo

    C2
    C4
    C2
    C4
    C5
    *N1
    *N3
    *N3
    *C4
    *C4
    *C2
    *C2
    *C5
    *C5

    -0.89
    0.50
    0.16
    0.28
    0.28
    -0.89
    0.54
    0.54
    -0.22
    0.28
    0.28
    -0.04
    0.09
    0.09

    RESI PRZP
    GROUP
    ATOM N1
    ATOM H1
    ATOM N2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    ATOM H52

    NG3C51
    HGP1
    NG3P2
    HGP2
    HGP2
    CG3C54
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    BOND N1
    BOND C4
    BOND N1

    H1 N2
    H41 C4
    N2 N2

    !>=.89
    !<=.50
    ! H32
    H42
    !
    \(+)
    /
    ! H31--N3----C4--H41
    !x
    |
    |
    !xH21--C2
    C5--H51
    !
    / \ / \
    ! H22
    N1
    H52
    !
    |
    !
    H1

    H21
    H42
    N3
    C5
    N1
    H1
    H31
    H32
    H41
    H42
    H21
    H22
    H51
    H52

    C2 H22
    C5 H51
    C4 C5
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    N3
    C5
    C5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    H31 N3
    H52
    N1 N3
    -20.00
    40.00
    120.00
    -120.00
    120.00
    120.00
    -120.00
    120.00
    -120.00
    -120.00
    120.00

    H32
    C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.000 ! C3H9N2 Pyrazolidine protonated, kevo


    -0.47
    0.35
    -0.18
    0.37
    0.37
    -0.30
    0.28
    0.28
    -0.18
    0.09
    0.09
    0.12
    0.09
    0.09

    !
    !
    !
    !
    !
    !
    !
    !
    !

    H42
    \
    /
    H31--C3----C4--H41
    |
    |
    H21--N2(+) C5--H51
    / \ / \
    H22
    N1
    H52
    |
    H1

    H21 N2
    H42 C5
    C3 C4

    H32

    H22 C3
    H51 C5
    C5 C5

    H31 C3
    H52
    N1 C3

    H32
    C4

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    N2
    C3
    N2
    C4
    C4
    C3
    C3
    N1
    N1
    N1
    N1

    RESI QINU
    GROUP
    ATOM N1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM C7
    ATOM H71
    ATOM H72
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM C8
    ATOM H81
    ATOM H82

    C3
    C4
    C5
    N2
    N2
    C5
    C5
    C3
    C3
    C4
    C4

    BOND N1
    BOND C6
    BOND N1
    BOND C2
    BOND C5
    BOND C7
    IC C6
    IC N1
    IC C2
    IC C2
    IC C2
    IC C6
    IC C3
    IC C3
    IC C4
    IC C4
    IC C4
    IC C4
    IC C5
    IC C5
    IC N1
    IC N1
    IC C7

    C4
    C5
    *N1
    *C3
    *C3
    *C4
    *C4
    *N2
    *N2
    *C5
    *C5

    C5
    N1
    H1
    H31
    H32
    H41
    H42
    H21
    H22
    H51
    H52

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -20.00
    40.00
    120.00
    -120.00
    120.00
    120.00
    -120.00
    120.00
    -120.00
    -120.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.00 ! C7H14N Quinuclidine, kevo


    NG3P1
    HGP2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2
    CG324
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG311
    HGA1
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    C2
    N1
    H1
    H21
    H51
    H71
    N1
    C2
    N1
    C6
    C6
    N1
    N1
    N1
    C2
    C2
    C6
    C6
    N1
    N1
    C8
    C8
    C4

    0.13
    0.19
    0.03
    0.09
    0.09
    0.03
    0.09
    0.09
    0.03
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.04
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    C2
    N1
    C4
    C2
    C5
    C7
    C2
    C3
    C6
    *N1
    *N1
    C7
    *C2
    *C2
    *C3
    *C3
    *C5
    *C5
    *C6
    *C6
    *C7
    *C7
    *C8

    C3
    C7
    H4
    H22
    H52
    H72
    C3
    C4
    C5
    C7
    H1
    C8
    H21
    H22
    H31
    H32
    H51
    H52
    H61
    H62
    H71
    H72
    H81

    !
    !
    !
    !
    !

    C5---C6
    /
    \ (+)
    H4--C4--C8-C7--N1--H1
    \
    /
    C3---C2

    C3
    C7

    C4
    C8

    C4
    C8

    C5
    C4

    C5

    C3
    C6
    C8

    H31 C3 H32
    H61 C6 H62
    H81 C8 H82
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00

    C6

    60.00
    0.00
    -60.00
    120.00
    -120.00
    -60.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC C7
    IC C5
    RESI NORB
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM C7
    ATOM H71
    ATOM H72

    C4
    C3

    *C8
    *C4

    H82
    H4

    0.0000
    0.0000

    0.00 -120.00
    0.00 -120.00

    0.00
    0.00

    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C7H12 Norbornane, kevo

    BOND C1
    BOND C5
    BOND C1
    BOND C2
    BOND C5
    IC C6
    IC C1
    IC C2
    IC C2
    IC C2
    IC C5
    IC C1
    IC C1
    IC C3
    IC C3
    IC C4
    IC C4
    IC C4
    IC C4
    IC C5
    IC C5

    CG3RC1
    HGA1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3RC1
    HGA1
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2

    RESI ADAM
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5

    C2
    C6
    H1
    H21
    H51
    C1
    C2
    C1
    C6
    C6
    C3
    C4
    C4
    C1
    C1
    C2
    C2
    C6
    C6
    C1
    C1

    C2
    C6
    C4
    C2
    C5
    C2
    C3
    C6
    *C1
    *C1
    *C4
    *C7
    *C7
    *C2
    *C2
    *C3
    *C3
    *C5
    *C5
    *C6
    *C6

    -0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    C3
    C1
    H4
    H22
    H52
    C3
    C4
    C5
    C7
    H1
    H4
    H71
    H72
    H21
    H22
    H31
    H32
    H51
    H52
    H61
    H62

    !
    !
    !
    !
    !

    C3
    C1
    C7
    C3
    C6

    C5---C6
    /
    \
    H4--C4---C7---C1--H1
    \
    /
    C3---C2

    C4 C4
    C7 C7
    H71 C7
    H31 C3
    H61 C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5
    C4
    H72
    H32
    H62
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    60.00
    0.00
    -60.00
    120.00
    -120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00 ! C10H16 Adamantane, kevo and erh


    CG311
    HGA1
    CG321
    HGA2
    HGA2
    CG311
    HGA1
    CG321
    HGA2
    HGA2
    CG311

    -0.09
    0.09
    -0.18
    0.09
    0.09
    -0.09
    0.09
    -0.18
    0.09 !
    _C1_
    0.09 ! _- \ -_
    -0.09 ! C2
    \ C8

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H5
    C6
    H61
    H62
    C7
    H7
    C8
    H81
    H82
    C9
    H91
    H92
    C10
    H101
    H102

    BOND C1
    BOND C5
    BOND C3
    BOND C1
    BOND C2
    BOND C6
    BOND C9
    IC C1
    IC C3
    IC C2
    IC C2
    IC C2
    IC C9
    IC C9
    IC C8
    IC C8
    IC C2
    IC C4
    IC C1
    IC C1
    IC C3
    IC C3
    IC C5
    IC C5
    IC C7
    IC C7
    IC C3
    IC C3
    IC C5
    IC C5

    HGA1
    CG321
    HGA2
    HGA2
    CG311
    HGA1
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    C2
    C6
    C9
    H1
    H21
    H61
    H91
    C2
    C2
    C1
    C9
    C9
    C8
    C8
    C2
    C2
    C3
    C6
    C3
    C3
    C5
    C5
    C7
    C7
    C1
    C1
    C7
    C7
    C1
    C1

    0.09
    -0.18
    0.09
    0.09
    -0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    C2
    C6
    C9
    C3
    C2
    C6
    C9
    C3
    C1
    C8
    *C3
    *C3
    *C7
    *C7
    *C1
    *C1
    C4
    *C5
    *C2
    *C2
    *C4
    *C4
    *C6
    *C6
    *C8
    *C8
    *C9
    *C9
    *C10
    *C10

    !
    !
    !
    !
    !
    !
    !
    !

    |
    C10 |
    |
    | |
    C3_
    |_C7
    \ -_ _+ \
    \ C9 | \
    \
    C5_ \
    \ / -_ \
    C4
    -C6

    C3 C3
    C7 C7
    C7 C5
    H3 C5
    H22 C4
    H62 C8
    H92 C10
    C9
    C8
    C7
    C4
    H3
    C6
    H7
    C10
    H1
    C5
    H5
    H21
    H22
    H41
    H42
    H61
    H62
    H81
    H82
    H91
    H92
    H101
    H102

    C4 C4
    C8 C8
    C10 C10
    H5 C7
    H41 C4
    H81 C8
    H101 C10
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C5
    C1
    C1
    H7
    H42
    H82
    H102
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    -60.00
    60.00
    -60.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -60.00
    120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    RESI AZUL
    0.00 ! C10H8 azulene, kevo
    !QM has exteremly low freq for 7-ring. In CHARMM, it's way too rigid,
    !despite drastically pulling down all force constants. However,
    !The final result is more or less in line with naftalene (NAFT).
    GROUP
    ATOM C1 CG2R51 -0.30
    ATOM H1 HGR51
    0.20
    ATOM C2 CG2R51 -0.17
    ATOM H2 HGR51
    0.20
    ATOM C3 CG2R51 -0.30 !
    H5
    ATOM H3 HGR51
    0.20 !
    H3
    |
    H6
    ATOM C4 CG2RC7 0.07 !
    |
    C5-_ /
    ATOM C5 CG2R71 -0.24 !
    C3-_ //
    -C6

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H5
    C6
    H6
    C7
    H7
    C8
    H8
    C9
    H9
    C10

    HGR71
    CG2R71
    HGR71
    CG2R71
    HGR71
    CG2R71
    HGR71
    CG2R71
    HGR71
    CG2RC7

    0.23
    -0.15
    0.18
    -0.22
    0.21
    -0.15
    0.18
    -0.24
    0.23
    0.07

    !
    //
    -C4
    \\
    ! H2--C2
    |
    C7--H7
    !
    \ _=C10
    /
    !
    C1=\ _=C8
    !
    |
    C9=- \
    !
    H1
    |
    H8
    !
    H9

    BOND C1 C2 C2 C3 C3 C4 C4 C5
    BOND C5 C6 C6 C7 C7 C8 C8 C9
    BOND C9 C10 C10 C1 C4 C10
    BOND C1 H1 C2 H2 C3 H3 C5 H5
    BOND C6 H6 C7 H7 C8 H8 C9 H9
    IC C4 C10 C1
    C2
    0.0000
    0.00
    0.00
    IC C1 C10 C4
    C3
    0.0000
    0.00
    0.00
    IC C1 C4 *C10 C9
    0.0000
    0.00 180.00
    IC C3 C10 *C4 C5
    0.0000
    0.00 180.00
    IC C10 C4 C5
    C6
    0.0000
    0.00
    0.00
    IC C4 C10 C9
    C8
    0.0000
    0.00
    0.00
    IC C4 C5 C6
    C7
    0.0000
    0.00
    0.00
    IC C10 C2 *C1 H1
    0.0000
    0.00 180.00
    IC C1 C3 *C2 H2
    0.0000
    0.00 180.00
    IC C2 C4 *C3 H3
    0.0000
    0.00 180.00
    IC C4 C6 *C5 H5
    0.0000
    0.00 180.00
    IC C5 C7 *C6 H6
    0.0000
    0.00 180.00
    IC C6 C8 *C7 H7
    0.0000
    0.00 180.00
    IC C7 C9 *C8 H8
    0.0000
    0.00 180.00
    IC C8 C10 *C9 H9
    0.0000
    0.00 180.00
    !End continuation of Maybridge list, kevo and erh,
    !Team Sugar, og, jun2008
    RESI AMOL
    -1.00 !
    GROUP
    ATOM C1 CG301
    0.30 !
    ATOM C2 CG2O3
    0.30 !
    ATOM OH OG311 -0.65 !
    ATOM HO HGP1
    0.42 !
    ATOM OM OG301 -0.34 !
    ATOM CM CG331 -0.10 !
    ATOM HM1 HGA3
    0.09 !
    ATOM HM2 HGA3
    0.09 !
    ATOM HM3 HGA3
    0.09 !
    ATOM O1 OG2D2 -0.60 !
    ATOM O2 OG2D2 -0.60 !
    GROUP
    !
    ATOM C0 CG331 -0.27 !
    ATOM H01 HGA3
    0.09 !
    ATOM H02 HGA3
    0.09 !
    ATOM H03 HGA3
    0.09 !
    BOND C1 OH OH HO C1 OM
    BOND C1 C2 C2 O1
    BOND C0 H01 C0 H02 C0 H03
    BOND OM CM
    BOND CM HM1 CM HM2 CM HM3
    BOND C2 O2
    IMPR C2 C1 O2 O1
    IC C2
    C1
    OM
    CM

    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    0.00 0.0000
    jun2008

    C4H7O4 alpha-methoxy-lactic acid, og


    CT1 HM1 HM2 HM3
    CC
    \ | /
    OH1
    CM
    H
    |
    ethers
    OM
    O1 (-)
    CT3
    |
    /
    HA
    OH--C1--C2
    HA /
    |
    \\
    HA HO
    |
    O2
    OC H01--C0
    OC
    | \
    H02 H03
    CT3
    HA
    HA
    HA
    C1 C0

    1.5530 103.90 -179.96 113.60

    1.4233

    IC OM
    C2
    *C1 C0
    1.4292
    IC OM
    C2
    *C1 OH
    1.4292
    IC C2
    C1
    OH
    HO
    1.5530
    IC C1
    OM
    CM
    HM1
    1.4292
    IC HM1 OM
    *CM HM2
    1.1100
    IC HM1 OM
    *CM HM3
    1.1100
    IC OH
    C1
    C2
    O1
    1.4253
    IC O1
    C1
    *C2 O2
    1.2616
    IC OH
    C1
    C0
    H01
    1.4253
    IC H01 C1
    *C0 H02
    1.1112
    IC H01 C1
    *C0 H03
    1.1112
    PATC FIRS NONE LAST NONE
    !End team Sugar, og, jun2008

    103.90
    103.90
    107.58
    113.60
    110.67
    110.67
    107.58
    118.67
    108.18
    109.95
    109.95

    120.03
    -122.26
    -175.04
    51.98
    -121.80
    119.24
    116.60
    -179.94
    -61.82
    -118.40
    120.36

    110.17
    107.58
    105.92
    110.67
    110.69
    109.06
    118.67
    118.34
    109.95
    109.70
    111.60

    1.5625
    1.4253
    0.9600
    1.1100
    1.1095
    1.1099
    1.2616
    1.2627
    1.1112
    1.1104
    1.1074

    !Opioid preparation, kevo, jun2008


    RESI CHXE
    0.00 ! C6H10 cyclohexene, kevo
    GROUP
    ! Based on RESI TMCH .
    ATOM C1 CG321 -0.18 ! We don't really want to optimize it.
    ATOM H11 HGA2
    0.09
    ATOM H12 HGA2
    0.09
    ATOM C2 CG321 -0.18 !
    H11
    H12
    ATOM H21 HGA2
    0.09 !
    \ /
    ATOM H22 HGA2
    0.09 ! H21
    C1
    H6
    ATOM C3 CG321 -0.18 !
    \ / \ /
    ATOM H31 HGA2
    0.09 ! H22-C2
    C6
    ATOM H32 HGA2
    0.09 !
    |
    ||
    ATOM C4 CG321 -0.18 ! H31-C3
    C5
    ATOM H41 HGA2
    0.09 !
    / \ / \
    ATOM H42 HGA2
    0.09 ! H32
    C4
    H5
    ATOM C5 CG2D1 -0.15 !
    / \
    ATOM H5 HGA4
    0.15 !
    H41 H42
    ATOM C6 CG2D1 -0.15
    ATOM H6 HGA4
    0.15
    BOND C1
    BOND C6
    BOND C3

    C2 C2
    H6 C1
    H31 C3

    C3 C3
    H11 C1
    H32 C4

    IC C1 C2 C3 C4 0.00
    IC C2 C3 C4 C5 0.00
    IC C3 C4 C5 C6 0.00
    IC C6 C2 *C1 H11 0.00
    IC C6 C2 *C1 H12 0.00
    IC C1 C3 *C2 H21 0.00
    IC C1 C3 *C2 H22 0.00
    IC C2 C4 *C3 H31 0.00
    IC C2 C4 *C3 H32 0.00
    IC C3 C5 *C4 H41 0.00
    IC C3 C5 *C4 H42 0.00
    IC C4 C6 *C5 H5 0.00
    IC C1 C5 *C6 H6 0.00
    PATCH FIRST NONE LAST NONE
    RESI 2DHF
    GROUP
    ATOM O1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3

    C4 C4
    H12 C2
    H41 C4
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5 C5
    H21 C2
    H42 C5

    -63.0
    46.0
    -13.0
    120.0
    -120.0
    120.0
    -120.0
    120.0
    -120.0
    120.0
    -120.0
    180.0
    180.0

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C6 C6
    H22
    H5

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.000 ! C4H6O 2,3-dihydrofuran, kevo


    OG3C51 -0.33
    CG2R51 -0.06
    HGR52
    0.20 ! H3
    H41 H42
    CG2R51 -0.41 ! \
    | /
    HGR51
    0.24 !
    C3----C4

    C1

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    C4
    H41
    H42
    C5
    H51
    H52

    CG3C52 -0.08 !
    ||
    |
    HGA2
    0.09 !
    C2
    C5--H51
    HGA2
    0.09 ! / \ / \
    CG3C52 0.08 ! H2
    O1
    H52
    HGA2
    0.09
    HGA2
    0.09

    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    !End

    O1 C2 C2 C3
    C2 H2 C3 H3
    C4 H41 C4 H42
    O1 C2 C3 C4
    C2 C3 C4 C5
    C3 O1 *C2 H2
    C4 C2 *C3 H3
    C5 C3 *C4 H41
    C5 C3 *C4 H42
    O1 C4 *C5 H51
    O1 C4 *C5 H52
    opioid preparation,

    C3

    C4

    C4

    C5 H51 C5
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    0.0000
    0.00
    kevo, jun2008

    C5

    C5

    O1

    H52
    0.00
    20.00
    180.00
    180.00
    120.00
    240.00
    120.00
    240.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Compounds for GSK/IBM collaboration, kevo, jun2008


    RESI 9MAD
    0.00 ! C6H7N5 9-Methyl-Adenine, kevo for gsk/ibm
    GROUP
    ATOM C1 CG331
    -0.27
    ATOM H11 HGA3
    0.09
    ATOM H12 HGA3
    0.09
    ATOM H13 HGA3
    0.09
    GROUP
    ATOM N9 NG2R51 -0.05 ! H61
    H62
    ATOM C5 CG2RC0
    0.28 !
    \ /
    ATOM N7 NG2R50 -0.71 !
    N6
    ATOM C8 CG2R53
    0.34 !
    |
    ATOM H8 HGR52
    0.12 !
    C6
    ATOM N1 NG2R62 -0.74 !
    // \
    ATOM C2 CG2R64
    0.50 !
    N1 C5--N7\\
    ATOM H2 HGR62
    0.13 !
    |
    ||
    C8-H8
    ATOM N3 NG2R62 -0.75 !
    C2 C4--N9/
    ATOM C4 CG2RC0
    0.43 ! / \\ /
    \
    ATOM C6 CG2R64
    0.46 ! H2 N3
    C1--H13
    ATOM N6 NG2S3
    -0.77 !
    / \
    ATOM H61 HGP4
    0.38 !
    H11
    H12
    ATOM H62 HGP4
    0.38
    BOND C1
    BOND N9
    BOND C2
    BOND N6
    BOND C8
    DOUBLE
    IMPR N6
    IC C4
    IC C4
    IC C4
    IC N9
    IC N9
    IC C8
    IC C8
    IC N7
    IC C5
    IC N9

    N9
    C1
    C4
    N9
    N1
    C6
    H61
    N6
    H8
    C2
    N1 C6
    C2
    C6 H61 H62
    N9 C8 N7
    C8 *N9 C1
    N9 C1 H11
    H11 *C1 H12
    H11 *C1 H13
    N9 C4 C5
    N7 C5 C6
    C5 C6 N1
    C6 N1 C2
    C5 *C4 N3

    H11
    C8
    N6
    H62
    H2
    N3

    C1
    C4

    H12
    N3

    C1

    H13

    C6

    C5

    C5

    N7

    C4 C5
    N1 C5 N6
    106.0
    0.0
    0.0 180.0
    0.0 180.0
    0.0 120.0
    0.0 -120.0
    106.0
    0.0
    0.0 180.0
    0.0 180.0
    0.0
    0.0
    105.6 -180.0

    N7

    C8

    C6
    1.376
    0.0
    0.0
    0.0
    0.0
    1.367
    0.0
    0.0
    0.0
    1.376

    113.6
    0.0
    0.0
    0.0
    0.0
    105.6
    0.0
    0.0
    0.0
    126.9

    1.312
    0.0
    0.0
    0.0
    0.0
    1.382
    0.0
    0.0
    0.0
    1.342

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C5
    N1
    H61
    C5
    N1
    H61
    N9
    N1

    N1
    C6
    C6
    N1
    C6
    C6
    N7
    N3

    RESI 1MTH
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM N1
    ATOM C6
    ATOM H6
    ATOM C2
    ATOM O2
    ATOM N3
    ATOM H3
    ATOM C4
    ATOM O4
    ATOM C5
    ATOM C5M
    ATOM H51
    ATOM H52
    ATOM H53

    *C6
    N6
    *N6
    *C6
    N6
    *N6
    *C8
    *C2

    BOND C1
    BOND N1
    BOND C2
    BOND C5
    DOUBLE
    IMPR C2
    IC C2
    IC C2
    IC C2
    IC N1
    IC N1
    IC C6
    IC N1
    IC N1
    IC C5
    IC C2
    IC C4
    IC N1
    IC C6
    IC C5
    IC H51

    1.409
    1.337
    1.01
    1.409
    1.337
    1.01
    0.0
    0.0

    117.6 -180.0
    121.2
    0.0
    119.0 180.0
    117.6 -180.0
    119.0
    0.0
    119.0 180.0
    0.0 180.0
    0.0 180.0

    121.2
    119.0
    119.00
    119.0
    119.0
    121.00
    0.0
    0.0

    1.337
    1.01
    1.01
    1.337
    1.01
    1.01
    0.0
    0.0

    0.00 ! C6H8N2O2 1-Methyl-Thymine, kevo for gsk/ibm


    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    NG2R61
    CG2R62
    HGR62
    CG2R63
    OG2D4
    NG2R61
    HGP1
    CG2R63
    OG2D4
    CG2R62
    CG331
    HGA3
    HGA3
    HGA3

    -0.34
    0.17
    0.17
    0.51
    -0.41
    -0.46
    0.36
    0.50
    -0.45
    -0.15
    -0.11
    0.07
    0.07
    0.07

    N1
    C2
    N3
    C5M
    C2

    O2
    N1

    N1
    C6
    N1
    H11
    H11
    N1
    N3
    C2
    N3
    C4
    C6
    C5
    C5
    H51
    H52

    RESI PROH
    GROUP
    ATOM O1
    ATOM HO1
    ATOM C1
    ATOM H11
    ATOM H12

    N6
    H61
    H62
    N6
    H61
    H62
    H8
    H2

    N3
    C6
    *N1
    C1
    *C1
    *C1
    C2
    *C2
    N3
    *C4
    *N3
    *C5
    *C6
    C5M
    *C5M
    *C5M

    C1
    N1
    N3
    C5M
    C4
    O2
    C5
    C1
    H11
    H12
    H13
    N3
    O2
    C4
    O4
    H3
    C5M
    H6
    H51
    H52
    H53

    !
    H51
    O4
    !
    |
    ||
    ! H52-C5M C4
    H3
    !
    | \ / \ /
    !
    H53 C5 N3
    !
    || |
    !
    H6-C6 C2
    !
    \ / \\
    !
    N1 O2
    !
    |
    !
    H11--C1--H13
    !
    |
    !
    H12
    H11
    C6
    H3
    H51
    O4
    C4
    1.3746
    0.0
    0.0
    0.0
    0.0
    1.3704
    1.3746
    1.3746
    1.4439
    1.3813
    1.4439
    0.0
    0.0
    0.0
    0.0

    C1
    N3
    C5M
    C5
    N3
    122.08
    0.0
    0.0
    0.0
    0.0
    122.08
    115.38
    115.38
    114.07
    126.46
    120.78
    0.0
    0.0
    0.0
    0.0

    H12

    C1

    H13

    C4
    H52
    C6
    C5 O4
    -0.02
    180.0
    180.0
    120.0
    -120.0
    0.06
    -179.95
    -0.07
    179.98
    180.00
    -179.94
    180.0
    0.0
    115.0
    -115.0

    C4 C5
    C5M H53
    C5
    121.23
    0.0
    0.0
    0.0
    0.0
    115.38
    121.70
    126.46
    120.59
    116.77
    121.63
    0.0
    0.0
    0.0
    0.0

    C6
    C4 C6
    1.3432
    0.0
    0.0
    0.0
    0.0
    1.3813
    1.2191
    1.3795
    1.2327
    1.0900
    1.5000
    0.0
    0.0
    0.0
    0.0

    0.00 ! C3H8O n-propanol, kevo for gsk/ibm


    OG311
    HGP1
    CG321
    HGA2
    HGA2

    -0.65
    0.42
    0.05
    0.09
    0.09

    H6
    C5M

    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM H33
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    O1 HO1 O1 C1 C1 H11 C1 H12


    C1 C2 C2 H21 C2 H22
    C2 C3 C3 H31 C3 H32 C3 H33
    C1 C2 C3 H33 0.0000
    C3 C2 C1 O1 0.0000
    C2 C1 O1 HO1 0.0000
    O1 C2 *C1 H11 0.0000
    O1 C2 *C1 H12 0.0000
    C1 C3 *C2 H21 0.0000
    C1 C3 *C2 H22 0.0000
    C2 H33 *C3 H31 0.0000
    C2 H33 *C3 H32 0.0000

    RESI PRSH
    GROUP
    ATOM S1
    ATOM HS1
    ATOM C1
    ATOM H11
    ATOM H12
    GROUP
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM H33
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3

    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C3H8S n-thiopropanol, kevo for gsk/ibm


    SG311
    HGP3
    CG321
    HGA2
    HGA2

    -0.23
    0.16
    -0.11
    0.09
    0.09

    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3

    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    S1 HS1 S1 C1 C1 H11 C1 H12


    C1 C2 C2 H21 C2 H22
    C2 C3 C3 H31 C3 H32 C3 H33
    C1 C2 C3 H33 0.0000
    C3 C2 C1 S1 0.0000
    C2 C1 S1 HS1 0.0000
    S1 C2 *C1 H11 0.0000
    S1 C2 *C1 H12 0.0000
    C1 C3 *C2 H21 0.0000
    C1 C3 *C2 H22 0.0000
    C2 H33 *C3 H31 0.0000
    C2 H33 *C3 H32 0.0000

    RESI 2BOH
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    GROUP
    ATOM O2
    ATOM HO2

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C4H10O (S)-2-butanol, kevo for gsk/ibm


    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    OG311
    HGP1

    -0.65
    0.42

    ATOM C2
    ATOM H2
    GROUP
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG311
    HGA1

    0.14
    0.09

    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3

    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    C1 C2 C1
    O2 HO2 O2
    C2 C3 C3
    C3 C4 C4
    C2 C3
    C4 C3
    C3 C2
    C1 C3
    C1 C3
    C3 C2
    H13 C2
    H13 C2
    C2 C4
    C2 C4
    C3 H43
    C3 H43

    RESI NEOP
    GROUP
    ATOM C
    ATOM C1
    ATOM C2
    ATOM C3
    ATOM C4
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM H21
    ATOM H22
    ATOM H23
    ATOM H31
    ATOM H32
    ATOM H33
    ATOM H41
    ATOM H42
    ATOM H43

    H11
    C2
    H31
    H41
    C4
    C2
    C1
    *C2
    *C2
    O2
    *C1
    *C1
    *C3
    *C3
    *C4
    *C4

    C1 H12 C1 H13
    C2 H2
    C3 H32
    C4 H42 C4 H43
    H43 0.0000
    C1 0.0000
    H13 0.0000
    O2 0.0000
    H2 0.0000
    HO2 0.0000
    H11 0.0000
    H12 0.0000
    H31 0.0000
    H32 0.0000
    H41 0.0000
    H42 0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    -120.00
    120.00
    180.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000 ! S
    0.0000 ! S
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C5H12 neopentane, kevo for gsk/ibm


    CG301
    CG331
    CG331
    CG331
    CG331
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3
    HGA3

    BOND C C1 C
    BOND C1 H11
    BOND C2 H21
    BOND C3 H31
    BOND C4 H41
    IC C2 C
    IC C
    H11
    IC C
    H11
    IC C2 C1
    IC C2 C1
    IC C3 C
    IC C
    H21

    0.00
    -0.27
    -0.27
    -0.27
    -0.27
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09
    0.09

    C2 C C3 C
    C1 H12 C1
    C2 H22 C2
    C3 H32 C3
    C4 H42 C4
    C1 H11
    *C1 H12
    *C1 H13
    *C C3
    *C C4
    C2 H21
    *C2 H22

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    C4
    H13
    H23
    H33
    H43
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    H32
    |
    H31-C3-H33
    H23
    |
    H41
    |
    |
    |
    H22-C2------C------C4-H42
    |
    |
    |
    H21
    |
    H43
    H11-C1-H13
    |
    H12

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    180.0000
    120.0000
    -120.0000
    120.0000
    -120.0000
    180.0000
    120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C
    C4
    C
    C
    C1
    C
    C

    H21
    C
    H31
    H31
    C
    H41
    H41

    RESI MCPE
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM C5
    ATOM H51
    GROUP
    ATOM C6
    ATOM H61
    ATOM H62
    ATOM H63
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C3
    C5
    C1
    C2
    C3
    C5
    C5
    C1
    C1
    C2
    C2
    C3
    C3
    C4
    C4
    C4
    C5
    C5

    RESI DMTF
    GROUP
    ATOM O4'
    ATOM C1'
    ATOM C2'
    ATOM C3'
    ATOM C4'
    ATOM H11'
    ATOM H21'

    *C2
    C3
    *C3
    *C3
    C4
    *C4
    *C4

    H23
    H31
    H32
    H33
    H41
    H42
    H43

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    -120.0000
    180.0000
    120.0000
    -120.0000
    180.0000
    120.0000
    -120.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H12 methylcyclopentane, kevo for gsk/ibm


    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C52
    HGA2
    HGA2
    CG3C51
    HGA1

    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    C2
    H11
    H31
    H51
    C2
    C3
    C4
    C2
    C2
    C3
    C3
    C4
    C4
    C5
    C5
    C1
    C1
    C5
    H63
    H63

    C3
    C4
    C5
    *C1
    *C1
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4
    *C5
    *C5
    C6
    *C6
    *C6

    C2
    C1
    C3
    C5
    C4
    C5
    C1
    H11
    H12
    H21
    H22
    H31
    H32
    H41
    H42
    H51
    C6
    H63
    H61
    H62

    !
    H61
    H62
    !
    \ /
    !
    H51 C6--H63
    !
    \ /
    ! H41 C5 H11
    !
    \ / \ /
    ! H42--C4
    C1--H12
    !
    |
    |
    ! H31--C3----C2--H21
    !
    |
    |
    !
    H32
    H22

    C3
    H12
    H32
    C6

    C3
    C2
    C4
    C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    H21
    H41
    H61
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C4
    C2
    C4
    C6
    0.0
    -20.0
    40.0
    120.0
    240.0
    120.0
    240.0
    120.0
    240.0
    120.0
    240.0
    120.0
    240.0
    180.0
    120.0
    240.0

    C5
    H22
    H42
    H62
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5

    C6 H63
    0.0000
    0.0000 ! equatorial
    0.0000 ! equatorial
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H12O (S,R)-dimethyl-tetrahydrofuran


    OG3C51
    CG3C51
    CG3C52
    CG3C52
    CG3C51
    HGA1
    HGA2

    -0.40
    0.11
    -0.18
    -0.18
    0.11
    0.09
    0.09

    ! H52
    H53 H11
    H12
    !
    \ /
    \ /
    ! H51--C5
    O4'
    C1--H13
    !
    \ / \ /
    ! H42'--C4'
    C1'--H11'

    C1

    ATOM H22'
    ATOM H31'
    ATOM H32'
    ATOM H42'
    GROUP
    ATOM C5
    ATOM H51
    ATOM H52
    ATOM H53
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13

    HGA2
    HGA2
    HGA2
    HGA1

    0.09
    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    CG331
    HGA3
    HGA3
    HGA3

    -0.27
    0.09
    0.09
    0.09

    BOND C1' O4' C1'


    BOND C1' H11' C2'
    BOND C4' H42' C5
    BOND C1' C1 C1
    IC C4' O4' C1'
    IC C2' O4' *C1'
    IC C2' O4' *C1'
    IC O4' C1' C2'
    IC C3' C1' *C2'
    IC C3' C1' *C2'
    IC C4' C2' *C3'
    IC C4' C2' *C3'
    IC C3' O4' *C4'
    IC C3' O4' *C4'
    IC O4' C4' C5
    IC H51 C4' *C5
    IC H51 C4' *C5
    IC O4' C1' C1
    IC C1' H13 *C1
    IC C1' H13 *C1
    RESI TOLU
    gsk/ibm
    GROUP
    ATOM CG
    ATOM HG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM CT
    ATOM H11
    ATOM H12
    ATOM H13
    BOND
    BOND
    BOND
    BOND
    BOND

    C2'
    H21'
    H51
    H11
    C2'
    H11'
    C1
    C3'
    H21'
    H22'
    H31'
    H32'
    C5
    H42'
    H51
    H52
    H53
    H13
    H11
    H12

    !
    !
    !
    !

    |
    |
    H31'--C3'----C2'--H21'
    /
    \
    H32'
    H22'

    C2' C3'
    C2' H22'
    C5 H52
    C1 H12
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C3' C4' C4' O4' C4'


    C3' H31' C3' H32'
    C5 H53
    C1 H13
    0.00 -40.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 20.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 180.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 180.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00

    C5

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !
    !
    !
    !

    equatorial
    S
    S
    equatorial

    ! R
    ! R

    0.00 ! C7H8 toluene, copied from pedro/toppar_aromatics.str for


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090

    CD1 CG CD2 CG CE1


    CE2 CD2 CZ CE1 CZ
    CG HG CD1 HD1 CD2
    CE2 HE2 CZ CT
    CT H11 CT H12 CT

    !
    HD1 HE1
    !
    |
    |
    !
    CD1--CE1
    H11
    !
    /
    \
    /
    ! HG--CG
    CZ--CT--H12
    !
    \
    /
    \
    !
    CD2--CE2
    H13
    !
    |
    |
    !
    HD2 HE2

    CD1
    CE2
    HD2 CE1 HE1
    H13

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    CZ
    CZ
    CE1
    CE1
    CZ
    CZ

    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CZ
    H11
    H11

    RESI BBEN
    GROUP
    ATOM CG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM HZ
    GROUP
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM C4
    ATOM H41
    ATOM H42
    ATOM H43

    CE1
    CZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    *CZ
    CT
    *CT
    *CT

    CZ
    CE2
    CD2
    HG
    HD1
    HD2
    HE1
    HE2
    CT
    H11
    H12
    H13

    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100

    0.00 ! C10H14 butylbenzene, kevo for gsk/ibm


    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG331
    HGA3
    HGA3
    HGA3

    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.27
    0.09
    0.09
    0.09

    BOND CD1 CG
    BOND CE2 CD2
    BOND CG C1
    BOND CD1 HD1
    BOND C1 H11
    BOND C3 H31
    IC CG CD1
    IC CD1 CE1
    IC CE1 CZ
    IC CD1 CD2
    IC CD2 CG
    IC CG C1
    IC C1 C2
    IC C2 C3
    IC CE1 CG
    IC CE2 CG
    IC CZ CD1
    IC CZ CD2
    IC CE1 CE2

    !
    HD1 HE1
    !
    |
    |
    !
    H41 H31 H21 H11
    CD1--CE1
    !
    |
    |
    |
    |
    /
    \
    ! H43--C4---C3---C2---C1---CG
    CZ--HZ
    !
    |
    |
    |
    |
    \
    /
    !
    H42 H32 H22 H12
    CD2--CE2
    !
    |
    |
    !
    HD2 HE2

    CD2 CG CE1 CD1


    CZ CE1 CZ CE2
    C1 C2 C2 C3 C3 C4
    CD2 HD2 CE1 HE1 CE2 HE2 CZ
    C1 H12 C2 H21 C2 H22
    C3 H32 C4 H41 C4 H42 C4
    CE1 CZ
    0.0000
    0.00
    CZ CE2 0.0000
    0.00
    CE2 CD2 0.0000
    0.00
    *CG C1
    0.0000
    0.00
    C1 C2
    0.0000
    0.00
    C2 C3
    0.0000
    0.00
    C3 C4
    0.0000
    0.00
    C4 H43 0.0000
    0.00
    *CD1 HD1 0.0000
    0.00
    *CD2 HD2 0.0000
    0.00
    *CE1 HE1 0.0000
    0.00
    *CE2 HE2 0.0000
    0.00
    *CZ HZ
    0.0000
    0.00

    HZ
    H43
    0.00
    0.00
    0.00
    180.00
    90.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CG
    C1
    C1
    C2
    C2
    C3
    C3

    C2
    C2
    C3
    C3
    C4
    C4
    H43
    H43

    RESI OXYL
    GROUP
    ATOM CG
    ATOM HG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM CZ
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23

    *C1
    *C1
    *C2
    *C2
    *C3
    *C3
    *C4
    *C4

    H11
    H12
    H21
    H22
    H31
    H32
    H41
    H42

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C8H10 o-xylene, kevo for gsk/ibm


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090

    BOND CD1 CG CD2 CG CE1


    BOND CE2 CD2 CZ CE1 CZ
    BOND CG HG CD1 HD1 CD2
    BOND CE2 C2 CZ C1
    BOND C1 H11 C1 H12 C1
    BOND C2 H21 C2 H22 C2
    IC CG CD1 CE1 CZ
    IC CD1 CE1 CZ CE2
    IC CE1 CZ CE2 CD2
    IC CD1 CD2 *CG HG
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 HD2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 C2
    IC CE1 CE2 *CZ C1
    IC CE1 CZ C1 H11
    IC CZ H11 *C1 H12
    IC CZ H11 *C1 H13
    IC CZ CE2 C2 H21
    IC CE2 H21 *C2 H22
    IC CE2 H21 *C2 H23
    RESI MXYL
    GROUP
    ATOM CG
    ATOM HG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM CE1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !
    HD1 HE1
    !
    |
    |
    !
    CD1--CE1
    H11
    !
    /
    \
    /
    ! HG--CG
    CZ--C1--H12
    !
    \
    /
    \
    !
    CD2--CE2
    H13
    !
    |
    \
    !
    HD2
    C2--H21
    !
    | \
    !
    H23 H22

    CD1
    CE2
    HD2 CE1 HE1
    H13
    H23
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000
    1.4000
    1.5000
    1.5000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    120.00
    109.50
    109.50

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50
    109.50
    109.50
    109.50

    0.00 ! C8H10 m-xylene, kevo for gsk/ibm

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100

    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61

    -0.115
    0.115
    -0.115
    0.115
    0.000 !
    -0.115 !

    HD1 HE1
    |
    |

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    HE1
    CE2
    HE2
    CZ
    C1
    H11
    H12
    H13
    C2
    H21
    H22
    H23

    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090

    BOND CD1 CG CD2 CG CE1


    BOND CE2 CD2 CZ CE1 CZ
    BOND CG HG CD1 HD1 CD2
    BOND CE2 HE2 CZ C1
    BOND C1 H11 C1 H12 C1
    BOND C2 H21 C2 H22 C2
    IC CG CD1 CE1 CZ
    IC CD1 CE1 CZ CE2
    IC CE1 CZ CE2 CD2
    IC CD1 CD2 *CG HG
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 C2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 HE2
    IC CE1 CE2 *CZ C1
    IC CE1 CZ C1 H11
    IC CZ H11 *C1 H12
    IC CZ H11 *C1 H13
    IC CE2 CD2 C2 H21
    IC CD2 H21 *C2 H22
    IC CD2 H21 *C2 H23

    !
    CD1--CE1
    H11
    !
    /
    \
    /
    !
    HG--CG
    CZ--C1--H12
    !
    \
    /
    \
    !
    CD2--CE2
    H13
    !
    /
    \
    ! H21--C2
    HE2
    !
    / |
    !
    H22 H23

    RESI PXYL
    GROUP
    ATOM CG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    C2 CE1 HE1
    H13
    H23
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000
    1.4000
    1.5000
    1.5000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    120.00
    109.50
    109.50

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00
    -90.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50
    109.50
    109.50
    109.50

    0.00 ! C8H10 p-xylene, kevo for gsk/ibm

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100

    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090

    !
    HD1 HE1
    !
    |
    |
    ! H21
    CD1--CE1
    H11
    !
    \
    /
    \
    /
    ! H22--C2--CG
    CZ--C1--H12
    !
    /
    \
    /
    \
    ! H23
    CD2--CE2
    H13
    !
    |
    |
    !
    HD2 HE2

    CD1 CG CD2 CG CE1 CD1


    CE2 CD2 CZ CE1 CZ CE2
    CG C2 CD1 HD1 CD2 HD2 CE1 HE1
    CE2 HE2 CZ C1

    BOND C1
    BOND C2
    IC CG
    IC CD1
    IC CE1
    IC CD1
    IC CE1
    IC CE2
    IC CZ
    IC CZ
    IC CE1
    IC CE1
    IC CZ
    IC CZ
    IC CD2
    IC CG
    IC CG

    H11
    H21
    CD1
    CE1
    CZ
    CD2
    CG
    CG
    CD1
    CD2
    CE2
    CZ
    H11
    H11
    CG
    H21
    H21

    RESI PSCU
    k/ibm
    GROUP
    ATOM CG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM CZ
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23
    ATOM C3
    ATOM H31
    ATOM H32
    ATOM H33

    C1 H12 C1
    C2 H22 C2
    CE1 CZ
    CZ CE2
    CE2 CD2
    *CG C2
    *CD1 HD1
    *CD2 HD2
    *CE1 HE1
    *CE2 HE2
    *CZ C1
    C1 H11
    *C1 H12
    *C1 H13
    C2 H21
    *C2 H22
    *C2 H23

    H13
    H23
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000
    1.4000
    1.5000
    1.5000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    120.00
    109.50
    109.50

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00
    -90.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50
    109.50
    109.50
    109.50

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100

    0.00 ! C9H12 pseudocumene (1,2,4-trimethylbenzene), kevo for gs


    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090

    BOND CD1 CG CD2 CG CE1


    BOND CE2 CD2 CZ CE1 CZ
    BOND CG C3 CD1 HD1 CD2
    BOND CE2 C2 CZ C1
    BOND C1 H11 C1 H12 C1
    BOND C2 H21 C2 H22 C2
    BOND C3 H31 C3 H32 C3
    IC CG CD1 CE1 CZ
    IC CD1 CE1 CZ CE2
    IC CE1 CZ CE2 CD2
    IC CD1 CD2 *CG C3
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 HD2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 C2
    IC CE1 CE2 *CZ C1
    IC CE1 CZ C1 H11

    !
    HD1 HE1
    !
    |
    |
    ! H31
    CD1--CE1
    H11
    !
    \
    /
    \
    /
    ! H32--C3--CG
    CZ--C1--H12
    !
    /
    \
    /
    \
    ! H33
    CD2--CE2
    H13
    !
    |
    \
    !
    HD2
    C2--H21
    !
    | \
    !
    H23 H22

    CD1
    CE2
    HD2 CE1 HE1
    H13
    H23
    H33
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CZ
    CZ
    CZ
    CE2
    CE2
    CD2
    CG
    CG

    H11
    H11
    CE2
    H21
    H21
    CG
    H31
    H31

    RESI PCRO
    GROUP
    ATOM CG
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM C1
    ATOM H11
    ATOM H12
    ATOM H13
    ATOM O2
    ATOM H2

    *C1
    *C1
    C2
    *C2
    *C2
    C3
    *C3
    *C3

    H12
    H13
    H21
    H22
    H23
    H31
    H32
    H33

    109.50
    109.50
    120.00
    109.50
    109.50
    120.00
    109.50
    109.50

    120.00
    -120.00
    180.00
    120.00
    -120.00
    90.00
    120.00
    -120.00

    109.50
    109.50
    109.50
    109.50
    109.50
    109.50
    109.50
    109.50

    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100
    1.1100

    0.00 ! C7H8O p-cresol, kevo for gsk/ibm


    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    OG311
    HGP1

    0.110
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.530
    0.420

    BOND CD1 CG CD2 CG CE1


    BOND CE2 CD2 CZ CE1 CZ
    BOND CG O2 CD1 HD1 CD2
    BOND CE2 HE2 CZ C1 O2
    BOND C1 H11 C1 H12 C1
    IC CG CD1 CE1 CZ
    IC CD1 CE1 CZ CE2
    IC CE1 CZ CE2 CD2
    IC CD1 CD2 *CG O2
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 HD2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 HE2
    IC CE1 CE2 *CZ C1
    IC CE1 CZ C1 H11
    IC CZ H11 *C1 H12
    IC CZ H11 *C1 H13
    IC CD2 CG
    O2 H2
    RESI PNPO
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM O3
    ATOM H3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM H5

    1.5000
    1.5000
    1.4000
    1.5000
    1.5000
    1.4000
    1.5000
    1.5000

    !
    HD1 HE1
    !
    |
    |
    !
    CD1--CE1
    H11
    !
    /
    \
    /
    ! H2--O2--CG
    CZ--C1--H12
    !
    \
    /
    \
    !
    CD2--CE2
    H13
    !
    |
    |
    !
    HD2 HE2

    CD1
    CE2
    HD2 CE1
    H2
    H13
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000
    1.4000

    HE1
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    120.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00
    0.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50
    109.50

    1.4000
    1.4000
    1.4000
    1.0800
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100
    0.9600

    0.000 ! C6H5NO3 p-nitrophenol, kevo for gsk/ibm


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    OG311
    HGP1
    CG2R61
    HGR61
    CG2R61
    HGR61

    -0.18
    0.16
    -0.115
    0.115
    0.110
    -0.53
    0.42
    -0.115
    0.115
    -0.18
    0.16

    !
    H5
    H4
    !
    \ ___ /
    ! O6A
    C5---C4
    !
    \ +
    /
    \
    ! - N6--C6
    C3--O3--H3
    !
    /
    \\
    //
    ! O6B
    C1---C2
    !
    /
    \

    ATOM
    ATOM
    ATOM
    ATOM

    C6
    N6
    O6A
    O6B

    CG2R61 0.32 !
    NG2O1
    0.40
    OG2N1 -0.34
    OG2N1 -0.34

    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    O3
    C6
    C2
    C6
    C3
    C1
    C4
    C2
    C5
    C6
    C5
    C1
    O6A
    C2

    H1
    H3
    C1
    C6
    C1
    C1
    C2
    C2
    C3
    C3
    C4
    C1
    C6
    C6
    C3

    RESI PCLT
    GROUP
    ATOM CG
    ATOM CL
    ATOM CD1
    ATOM HD1
    ATOM CD2
    ATOM HD2
    ATOM CE1
    ATOM HE1
    ATOM CE2
    ATOM HE2
    ATOM CZ
    ATOM CT
    ATOM H11
    ATOM H12
    ATOM H13

    C1
    C3
    C6
    *C1
    C2
    *C2
    C3
    *C3
    C4
    *C4
    *C5
    *C6
    N6
    *N6
    O3

    C2
    C4
    N6
    H1
    C3
    H2
    C4
    O3
    C5
    H4
    H5
    N6
    O6A
    O6B
    H3

    C2 H2
    C4 H4
    N6 O6A
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    H1

    H2

    C2
    C4
    N6
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C3 C3
    C5 C5
    O6B
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00

    O3
    H5
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    C5

    C6
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C7H7Cl p-chlorotoluene, kevo for gsk/ibm


    CG2R61
    CLGR1
    CG2R61
    HGR62
    CG2R61
    HGR62
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3

    0.03
    -0.13
    -0.10
    0.15
    -0.10
    0.15
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090

    BOND CD1 CG CD2 CG CE1


    BOND CE2 CD2 CZ CE1 CZ
    BOND CG CL CD1 HD1 CD2
    BOND CE2 HE2 CZ CT
    BOND CT H11 CT H12 CT
    IC CG CD1 CE1 CZ
    IC CD1 CE1 CZ CE2
    IC CE1 CZ CE2 CD2
    IC CD1 CD2 *CG CL
    IC CE1 CG *CD1 HD1
    IC CE2 CG *CD2 HD2
    IC CZ CD1 *CE1 HE1
    IC CZ CD2 *CE2 HE2
    IC CE1 CE2 *CZ CT
    IC CE1 CZ CT H11
    IC CZ H11 *CT H12
    IC CZ H11 *CT H13

    !
    HD1 HE1
    !
    |
    |
    !
    CD1--CE1
    H11
    !
    /
    \
    /
    ! CL--CG
    CZ--CT--H12
    !
    \
    /
    \
    !
    CD2--CE2
    H13
    !
    |
    |
    !
    HD2 HE2

    CD1
    CE2
    HD2 CE1 HE1
    H13
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.4000
    1.5000
    1.5000

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00

    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    120.00
    109.50
    109.50
    109.50

    1.4000
    1.4000
    1.4000
    1.7400
    1.0800
    1.0800
    1.0800
    1.0800
    1.5000
    1.1100
    1.1100
    1.1100

    RESI 34MP
    0.00 ! C7H9N 3,4-dimethylpyridine, kevo for gsk/ibm
    GROUP
    ATOM NZ NG2R60 -0.600

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    CE1
    CD1
    CG
    CD2
    CE2
    HE1
    HD2
    HE2
    C3
    H31
    H32
    H33
    C2
    H21
    H22
    H23

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1
    C2
    C3

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR62
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CD2
    CG
    CG
    CG
    CD1
    CD1

    CG
    CD2
    C2
    HE1
    H21
    H31
    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CG
    H21
    H21
    CD1
    H31
    H31

    RESI 4MEP
    GROUP
    ATOM NZ
    ATOM CE1
    ATOM CD1
    ATOM CG
    ATOM CD2
    ATOM CE2
    ATOM HE1
    ATOM HD1
    ATOM HD2
    ATOM HE2
    ATOM C2
    ATOM H21
    ATOM H22
    ATOM H23
    BOND
    BOND
    BOND
    BOND

    CD1
    CE2
    CG
    CE1

    0.180
    0.000
    0.000
    -0.115
    0.180
    0.120
    0.115
    0.120
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090

    !
    H32 H33
    !
    \ /
    ! H31--CD3
    HE1
    !
    \
    |
    ! H21
    CD1--CE1
    !
    \
    /
    \
    ! H22--C2--CG
    NZ
    !
    /
    \
    /
    ! H23
    CD2--CE2
    !
    |
    |
    !
    HD2 HE2

    CD2 CG CE1 CD1


    NZ CE1 NZ CE2
    CD1 C3 CD2 HD2
    CE2 HE2
    C2 H22 C2 H23
    C3 H32 C3 H33
    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    C2
    *C2
    *C2
    C3
    *C3
    *C3

    NZ
    CE2
    CD2
    C2
    C3
    HD2
    HE1
    HE2
    H21
    H22
    H23
    H31
    H32
    H33

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    0.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C6H7N 4-methylpyridine, kevo for gsk/ibm


    NG2R60
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR62
    HGR61
    HGR61
    HGR62
    CG331
    HGA3
    HGA3
    HGA3
    CG
    CD2
    C2
    HE1

    CD2
    NZ
    CD1
    CE2

    -0.600
    0.180
    -0.115
    0.000
    -0.115
    0.180
    0.120
    0.115
    0.115
    0.120
    -0.270
    0.090
    0.090
    0.090

    !
    HD1 HE1
    !
    |
    |
    ! H21
    CD1--CE1
    !
    \
    /
    \
    ! H22--C2--CG
    NZ
    !
    /
    \
    /
    ! H23
    CD2--CE2
    !
    |
    |
    !
    HD2 HE2

    CG CE1 CD1
    CE1 NZ CE2
    HD1 CD2 HD2
    HE2

    BOND C2 H21 C2 H22 C2 H23


    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    CG
    CD1
    CE1
    CD1
    CE1
    CE2
    NZ
    NZ
    CD2
    CG
    CG

    CD1
    CE1
    NZ
    CD2
    CG
    CG
    CD1
    CD2
    CG
    H21
    H21

    RESI 23MN
    GROUP
    ATOM C1
    ATOM H1
    ATOM C2
    ATOM C3
    ATOM C4
    ATOM H4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM C21
    ATOM H211
    ATOM H212
    ATOM H213
    ATOM C31
    ATOM H311
    ATOM H312
    ATOM H313

    CE1
    NZ
    CE2
    *CG
    *CD1
    *CD2
    *CE1
    *CE2
    C2
    *C2
    *C2

    NZ
    CE2
    CD2
    C2
    HD1
    HD2
    HE1
    HE2
    H21
    H22
    H23

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    90.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C12H12 2,3-dimethylnaphtalene, kevo for gsk/ibm


    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 C2 C2
    BOND C5 C6 C6
    BOND C9 C10 C5
    BOND C1 H1 C2
    BOND C6 H6 C7
    BOND C21 H211 C21
    BOND C31 H311 C31
    IC C5 C10 C1
    IC C1 C10 C5
    IC C10 C5 C4
    IC C1 C5 *C10
    IC C4 C10 *C5
    IC C10 C5 C6
    IC C5 C10 C9
    IC C10 C2 *C1
    IC C1 C3 *C2
    IC C2 C4 *C3
    IC C3 C5 *C4
    IC C5 C7 *C6

    -0.115
    0.115
    0.000
    0.000
    -0.115
    0.115
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090
    C3
    C7
    C10
    C21
    H7
    H212
    H312
    C2
    C4
    C3
    C9
    C6
    C7
    C8
    H1
    C21
    C31
    H4
    H6

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H4
    |
    C4

    H6
    |
    C6

    H312 H311
    \ |
    // \ / \\
    H313--C31---C3
    C5
    C7--H7
    |
    ||
    |
    H211--C21---C2
    C10 C8--H8
    / |
    \\ / \ //
    H212 H213
    C1
    C9
    |
    |
    H1
    H9

    C3 C4
    C7 C8
    C1 C10
    C3 C31
    C8 H8
    C21 H213
    C31 H313
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C8

    C5
    C9

    C4
    C9

    H4
    H9

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C6
    C7
    C8
    C1
    C2
    C2
    C2
    C3
    C3

    C8
    C9
    C10
    C2
    H211
    H211
    C3
    H311
    H311

    RESI 14MN
    GROUP
    ATOM C1
    ATOM C2
    ATOM H2
    ATOM C3
    ATOM H3
    ATOM C4
    ATOM C5
    ATOM C6
    ATOM H6
    ATOM C7
    ATOM H7
    ATOM C8
    ATOM H8
    ATOM C9
    ATOM H9
    ATOM C10
    ATOM C11
    ATOM H111
    ATOM H112
    ATOM H113
    ATOM C41
    ATOM H411
    ATOM H412
    ATOM H413

    *C7
    *C8
    *C9
    C21
    *C21
    *C21
    C31
    *C31
    *C31

    H7
    H8
    H9
    H211
    H212
    H213
    H311
    H312
    H313

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    180.00
    180.00
    0.00
    120.00
    -120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00 ! C12H12 1,4-dimethylnaphtalene, kevo for gsk/ibm


    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    CG331
    HGA3
    HGA3
    HGA3
    CG331
    HGA3
    HGA3
    HGA3

    BOND C1 C2 C2
    BOND C5 C6 C6
    BOND C9 C10 C5
    BOND C1 C11 C2
    BOND C6 H6 C7
    BOND C11 H111 C11
    BOND C41 H411 C41
    IC C5 C10 C1
    IC C1 C10 C5
    IC C10 C5 C4
    IC C1 C5 *C10
    IC C4 C10 *C5
    IC C10 C5 C6
    IC C5 C10 C9
    IC C10 C2 *C1
    IC C1 C3 *C2
    IC C2 C4 *C3
    IC C3 C5 *C4
    IC C5 C7 *C6
    IC C6 C8 *C7
    IC C7 C9 *C8
    IC C8 C10 *C9
    IC C10 C1 C11

    0.000
    -0.115
    0.115
    -0.115
    0.115
    0.000
    0.000
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    0.000
    -0.270
    0.090
    0.090
    0.090
    -0.270
    0.090
    0.090
    0.090
    C3
    C7
    C10
    H2
    H7
    H112
    H412
    C2
    C4
    C3
    C9
    C6
    C7
    C8
    C11
    H2
    H3
    C41
    H6
    H7
    H8
    H9
    H111

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !

    H412 H411
    \ |
    H413--C41
    H6
    |
    |
    C4
    C6
    // \ / \\
    H3--C3
    C5
    C7--H7
    |
    ||
    |
    H2--C2
    C10 C8--H8
    \\ / \ //
    C1
    C9
    |
    |
    H111--C11
    H9
    / |
    H112 H113

    C3 C4
    C7 C8
    C1 C10
    C3 H3
    C8 H8
    C11 H113
    C41 H413
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    C4
    C8

    C5
    C9

    C4
    C9

    C41
    H9

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    180.00
    180.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC C1 H111 *C11
    IC C1 H111 *C11
    IC C3 C4 C41
    IC C4 H411 *C41
    IC C4 H411 *C41
    !End compounds for

    H112 0.0000
    0.00 120.00
    0.00
    H113 0.0000
    0.00 -120.00
    0.00
    H411 0.0000
    0.00
    0.00
    0.00
    H412 0.0000
    0.00 120.00
    0.00
    H413 0.0000
    0.00 -120.00
    0.00
    GSK/IBM collaboration, kevo, jun2008

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Drug-like molecules, S. Zhong, jun2008


    RESI AMDN
    1.00 ! C2H7N2 amidinium cation, S.Zhong
    GROUP
    ATOM C1 CG2N2
    0.66
    ATOM C2 CG331 -0.15 !
    H3 H4 H5
    ATOM H3 HGA3
    0.09 !
    \| /
    ATOM H4 HGA3
    0.09 !
    C2
    ATOM H5 HGA3
    0.09 !
    |
    ATOM N6 NG2P1 -0.69 !
    +) C1
    ATOM H7 HGP2
    0.40 !
    // \
    ATOM H8 HGP2
    0.40 !
    H7-N6 N9-H10
    ATOM N9 NG2P1 -0.69 !
    |
    |
    ATOM H10 HGP2
    0.40 !
    H8 H11
    ATOM H11 HGP2
    0.40
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1 C2 C2 H3 C2
    C1 N6 N6 H7 N6
    C1 N9 N9 H10 N9
    C1 N6 N9 C2
    N6 H7 H8 C1
    N9 H10 H11 C1
    N6 C1 C2 H3
    C1 H3 *C2 H4
    C1 H3 *C2 H5
    N6 C2 *C1 N9
    H7 N6 C1 N9
    H7 C1 *N6 H8
    H10 N9 C1 N6
    H10 C1 *N9 H11

    RESI BAMI
    GROUP
    ATOM C1
    ATOM H2
    ATOM C3
    ATOM H4
    ATOM C5
    ATOM H6
    ATOM C7
    ATOM H8
    ATOM C9
    ATOM H10
    GROUP
    ATOM C11
    ATOM C12
    ATOM N13
    ATOM H14
    ATOM H15
    ATOM N16
    ATOM H17
    ATOM H18

    H4 C2 H5
    H8
    H11

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    90.00
    120.00
    -120.00
    180.00
    180.00
    180.00
    180.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    1.00 ! C7H9N2 Benzamidinium cation, S.Zhong


    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    !
    CG2R61 0.19 !
    CG2N2
    0.73 !
    NG2P1 -0.60
    HGP2
    0.32
    HGP2
    0.32
    NG2P1 -0.60
    HGP2
    0.32
    HGP2
    0.32

    BOND C1 H2

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C1
    C11
    C12
    N13
    N16
    C12
    C1
    C3
    C5
    C11
    C9
    C7
    C7
    C1
    C3
    C11
    C9
    C5
    C5
    N13
    C11
    H14
    C11
    H17

    C3 C3 H4 C3
    C7 C7 H8 C7
    C5 C11 C12 C11
    N13 N13 H14 N13
    H14 H15 C12
    H17 H18 C12
    N13 N16 C11
    C3 C5 C11
    C5 C11 C9
    C11 C9 C7
    C9 C7 C1
    C7 C1 C3
    C1 C3 C5
    C3 *C1 H2
    C5 *C3 H4
    C11 *C5 H6
    C7 *C9 H10
    C1 *C7 H8
    C9 *C11 C12
    C11 C12 N13
    C11 *C12 N16
    C12 N13 H14
    C12 *N13 H15
    C12 N16 H17
    C12 *N16 H18

    RESI PNTM
    ne, S.Zhong
    GROUP
    ATOM C1 CG321
    ATOM H2 HGA2
    ATOM H3 HGA2
    ATOM C4 CG321
    ATOM H5 HGA2
    ATOM H6 HGA2
    ATOM C7 CG321
    ATOM H8 HGA2
    ATOM H9 HGA2
    GROUP
    ATOM C10 CG321
    ATOM H11 HGA2
    ATOM H12 HGA2
    ATOM O13 OG301
    ATOM C14 CG2R61
    GROUP
    ATOM C15 CG2R61
    ATOM H16 HGR61
    ATOM C17 CG2R61
    ATOM H18 HGR61
    ATOM C19 CG2R61
    ATOM H20 HGR61
    ATOM C21 CG2R61
    ATOM H22 HGR61
    GROUP
    ATOM C23 CG2R61
    ATOM C24 CG2N2
    ATOM N25 NG2P1
    ATOM H26 HGP2
    ATOM H27 HGP2
    ATOM N28 NG2P1

    C5 C5 H6
    C9 C9 H10
    C9
    H15 C12 N16 N16 H17 N16 H18

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    45.00
    180.00
    0.00
    180.00
    0.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    2.00 ! C19H26N4O2 1,5-bis(p-Amidinophenoxy)pentane,Pentamidi


    ! based on PENT, ETOB, PAMI/ARG,
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.18
    0.09
    0.09
    -0.01
    0.09
    0.09
    -0.39
    0.22
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    !
    H11 H5 H2 H8 H32
    !
    \
    | | | /
    !
    H12-C10-C4--C1--C7--C31-H33
    !
    /
    | | | \
    !
    O13 H6 H3 H9
    O34
    !
    |
    |
    !
    H20-C19==C14
    C35==C40-H41
    !
    /
    \
    /
    \
    ! H22-C21
    C15-H16
    H37-C36
    C42-H43
    !
    \\
    //
    \\
    //
    !
    C23--C17-H18
    H39-C38--C44
    !
    /
    \
    !
    (+) C24
    C45 (+)
    !
    // \
    / \\
    ! H29-N28 N25-H26
    H47-N46 N49-H50
    !
    | |
    | |
    !
    H30 H27
    H48 H51

    ! one positive charge on this group which is from PAMI


    0.19
    0.73
    -0.60
    0.32
    0.32
    -0.60

    ATOM H29
    ATOM H30
    GROUP
    ATOM C31
    ATOM H32
    ATOM H33
    ATOM O34
    ATOM C35
    GROUP
    ATOM C36
    ATOM H37
    ATOM C38
    ATOM H39
    ATOM C40
    ATOM H41
    ATOM C42
    ATOM H43
    GROUP
    ATOM C44
    ATOM C45
    ATOM N46
    ATOM H47
    ATOM H48
    ATOM N49
    ATOM H50
    ATOM H51
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IMPR
    IMPR
    IMPR
    IMPR
    IMPR
    IMPR
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    HGP2
    HGP2

    0.32
    0.32
    ! This group is from ETOB

    CG321 -0.01
    HGA2
    0.09
    HGA2
    0.09
    OG301 -0.39
    CG2R61 0.22
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    ! one positive charge on this group (PAMI)

    CG2R61 0.19
    CG2N2
    0.73
    NG2P1 -0.60
    HGP2
    0.32
    HGP2
    0.32
    NG2P1 -0.60
    HGP2
    0.32
    HGP2
    0.32

    C1 H2 C1 H3 C1 C4 C4 H5 C4 H6 C1 C7 C7
    C4 C10 C10 H11 C10 H12 C10 O13 O13 C14
    C14 C15 C15 H16 C15 C17 C17 H18
    C14 C19 C19 H20 C19 C21 C21 H22
    C17 C23 C21 C23 C23 C24 C24 N25 C24 N28
    N25 H26 N25 H27 N28 H29 N28 H30
    C7 C31 C31 H32 C31 H33 C31 O34 O34 C35
    C35 C36 C36 H37 C36 C38 C38 H39
    C35 C40 C40 H41 C40 C42 C42 H43
    C38 C44 C42 C44 C44 C45 C45 N46 C45 N49
    N46 H47 N46 H48 N49 H50 N49 H51
    C24 N25 N28 C23
    N25 H26 H27 C24
    N28 H29 H30 C24
    C45 N46 N49 C44
    N46 H47 H48 C45
    N49 H50 H51 C45
    C10 C4 C1 C7 0.0000
    0.00 180.00
    O13 C10 C4 C1 0.0000
    0.00 180.00
    C14 O13 C10 C4 0.0000
    0.00 180.00
    C10 O13 C14 C15 0.0000
    0.00
    0.00
    C4 C1 C7 C31 0.0000
    0.00 180.00
    C1 C7 C31 O34 0.0000
    0.00 180.00
    C7 C31 O34 C35 0.0000
    0.00 180.00
    C31 O34 C35 C36 0.0000
    0.00
    0.00
    C4 C7 *C1 H2 0.0000
    0.00 120.00
    C4 C7 *C1 H3 0.0000
    0.00 -120.00
    C1 C10 *C4 H5 0.0000
    0.00 120.00
    C1 C10 *C4 H6 0.0000
    0.00 -120.00
    O13 C4 *C10 H11 0.0000
    0.00 120.00
    O13 C4 *C10 H12 0.0000
    0.00 -120.00
    C31 C1 *C7 H8 0.0000
    0.00 120.00
    C31 C1 *C7 H9 0.0000
    0.00 -120.00

    H8 C7 H9

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C7
    C7
    C14
    C15
    C17
    C23
    C21
    C19
    C14
    C15
    C17
    C23
    C21
    C19
    C17
    C23
    C23
    C24
    C23
    C24
    C35
    C36
    C38
    C44
    C42
    C40
    C35
    C36
    C38
    C44
    C42
    C40
    C38
    C44
    C44
    C45
    C44
    C45

    ! DMSO is
    RESI DMSO
    GROUP
    ATOM O1
    ATOM S2
    ATOM C3
    ATOM H4
    ATOM H5
    ATOM H6
    ATOM C7
    ATOM H8
    ATOM H9
    ATOM H10

    O34
    O34
    C15
    C17
    C23
    C21
    C19
    C14
    C17
    C23
    C21
    C19
    C14
    C15
    C23
    N25
    C24
    H26
    C24
    H29
    C36
    C38
    C44
    C42
    C40
    C35
    C38
    C44
    C42
    C40
    C35
    C36
    C44
    N46
    C45
    H47
    C45
    H50

    *C31
    *C31
    C17
    C23
    C21
    C19
    C14
    C15
    *C15
    *C17
    *C23
    *C21
    *C19
    *C14
    C24
    *C24
    N25
    *N25
    N28
    *N28
    C38
    C44
    C42
    C40
    C35
    C36
    *C36
    *C38
    *C44
    *C42
    *C40
    *C35
    C45
    *C45
    N46
    *N46
    N49
    *N49

    H32
    H33
    C23
    C21
    C19
    C14
    C15
    C17
    H16
    H18
    C24
    H22
    H20
    O13
    N25
    N28
    H26
    H27
    H29
    H30
    C44
    C42
    C40
    C35
    C36
    C38
    H37
    H39
    C45
    H43
    H41
    O34
    N46
    N49
    H47
    H48
    H50
    H51

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    120.00
    -120.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    45.00
    180.00
    0.00
    180.00
    0.00
    180.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    180.00
    180.00
    180.00
    180.00
    180.00
    180.00
    45.00
    180.00
    0.00
    180.00
    0.00
    180.00

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    taken from literature JPC2002-A106-1074, S.Zhong


    0.00 ! C2H6OS dimethylsulfoxide
    OG2P1 -0.55 ! ? SG3O2
    0.0 -0.3500 2.0000 (JPC2002-A106-1074)
    SG3O1 0.31 ! charges: ML Strader, SE Feller, JPC-A106(6),1074(2002)
    CG331 -0.15
    HGA3
    0.09 !
    O1
    HGA3
    0.09 !
    ||
    HGA3
    0.09 !
    S2
    CG331 -0.15 !
    / \
    HGA3
    0.09 !
    H4--C3 C7--H10
    HGA3
    0.09 !
    / | | \
    HGA3
    0.09 !
    H5 H6 H8 H9

    BOND O1 S2 S2 C3 S2 C7
    BOND C3 H4 C3 H5 C3 H6
    BOND C7 H8 C7 H9 C7 H10
    IC C3
    O1
    *S2 C7
    IC O1
    S2
    C3
    H4
    IC H4
    S2
    *C3 H5
    IC H4
    S2
    *C3 H6

    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00

    120.00
    180.00
    120.00
    -120.00

    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000

    IC O1
    IC H8
    IC H8
    RESI FORA
    GROUP
    ATOM C1
    ATOM O2
    ATOM O3
    ATOM H4

    S2
    S2
    S2

    C7
    *C7
    *C7

    H8
    H9
    H10

    0.0000
    0.0000
    0.0000

    0.00 180.00
    0.00 120.00
    0.00 -120.00

    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000

    -1.00 ! CHO2 formate, from acetate, sz & kevo


    CG2O3
    OG2D2
    OG2D2
    HGR52

    0.52
    -0.76
    -0.76
    0.00

    !
    H
    !
    C
    !
    / \\
    ! -O O

    BOND C1 H4
    BOND C1 O2 C1 O3
    IMPR C1 O3 O2 H4
    IC O3 O2 *C1 H4 0.00 0.00 180.0 0.0 0.0
    IC H4 O3 *C1 O2 0.00 0.00 180.0 0.0 0.0 !redundant definition needed to en
    able seeding.
    RESI PMHA
    GROUP
    ATOM C1
    ATOM C2
    ATOM H3
    ATOM C4
    ATOM CL5
    ATOM C6
    ATOM H7
    ATOM C8
    ATOM H9
    ATOM C10
    ATOM H11
    ATOM N12
    ATOM H13
    ATOM C14
    ATOM O15
    ATOM C16
    ATOM H17
    ATOM H18
    ATOM C19
    ATOM H20
    ATOM H21
    ATOM C22
    ATOM O23
    ATOM N24
    ATOM H25
    ATOM N26
    ATOM C27
    ATOM H28
    ATOM C29
    ATOM C30
    ATOM C31
    ATOM C32
    ATOM H33
    ATOM C34
    ATOM C35
    ATOM C36
    ATOM H37
    ATOM C38
    ATOM H39
    ATOM C40

    CG2R61
    CG2R61
    HGR61
    CG2R61
    CLGR1
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    NG2S1
    HGP1
    CG2O1
    OG2D1
    CG321
    HGA2
    HGA2
    CG321
    HGA2
    HGA2
    CG2O1
    OG2D1
    NG2S1
    HGP1
    NG2D1
    CG2D1
    HGA4
    CG2R61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    CG2R61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61

    0.00 !
    !
    0.10
    -0.14 !
    0.22 !
    0.10 !
    -0.18 !
    -0.16 !
    0.19 !
    -0.12 !
    0.12 !
    -0.16 !
    0.19 !
    -0.47 !
    0.31 !
    0.51 !
    -0.51 !
    -0.18 !
    0.09 !
    0.09 !
    -0.18
    0.09
    0.09
    0.58 !
    -0.49
    -0.34
    0.31
    -0.31
    -0.24
    0.24
    0.25
    0.00 !
    0.00
    -0.115
    0.115
    0.00
    0.00
    -0.115
    0.115
    -0.115
    0.115
    -0.115

    C25H20ClN3O2 3-(N-(3-chloroPhenyl)carnoMoyl)propionyl
    Anthracene-9-carbaldehyde Hydrazone,
    S.Zhong
    H49
    H47
    \
    /
    H9
    C48--C46
    |
    //
    \\
    C8 H11
    H51-C50
    C44-H45
    / \\ /
    \
    /
    H7--C6 C10 O15 H20 H21 H25 H28
    C30--C31
    ||
    |
    ||
    \ /
    |
    |
    //
    \\
    Cl5-C4 C1
    C14
    C19 N24 C27--C29
    C32-H33
    \ // \ / \ / \ / \ //
    \
    /
    C2 N12 C16
    C22 N26
    C35==C34
    |
    |
    / \
    ||
    /
    \
    H3 H13 H17 H18 O23
    H37-C36
    C42-H43
    \\
    //
    Group 2
    C38--C40
    /
    \
    H39
    H41

    Group 3

    Group 4

    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM
    ATOM

    H41
    C42
    H43
    C44
    H45
    C46
    H47
    C48
    H49
    C50
    H51

    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    BOND
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC

    C1
    C4
    C8
    N12
    C16
    C22
    C27
    C29
    C30
    C31
    C34
    C35
    C1
    C2
    C4
    C6
    C8
    C10
    C1
    C2
    C4
    C6
    C8
    C10
    C14
    C14
    O15
    O15
    C19
    C19
    C19
    C22
    C16
    C16
    O23
    N24
    N26
    N26
    C27
    C29
    C29
    C30
    C31
    C32
    C34
    C31
    C35
    C31

    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61
    CG2R61
    HGR61

    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115
    -0.115
    0.115

    C2 C2 H3 C2
    C6 C6 H7 C6
    C10 C10 H11 C10
    H13 N12 C14 C14
    H17 C16 H18 C16
    O23 C22 N24 N24
    C29
    C30 C30 C31 C31
    C50 C50 H51 C50
    C44 C44 H45 C44
    C42 C42 H43 C42
    C36 C36 H37 C36
    C2 C4 C6
    C4 C6 C8
    C6 C8 C10
    C8 C10 C1
    C10 C1 C2
    C1 C2 C4
    C4 *C2 H3
    C6 *C4 CL5
    C8 *C6 H7
    C10 *C8 H9
    C1 *C10 H11
    C2 *C1 N12
    N12 C1 C10
    C1 *N12 H13
    C14 N12 H13
    N12 *C14 C16
    C16 C14 O15
    C14 *C16 H17
    C14 *C16 H18
    C19 C16 C14
    C22 *C19 H20
    C22 *C19 H21
    C22 C19 C16
    O23 *C22 C19
    C22 *N24 H25
    N24 C22 O23
    N26 N24 C22
    N26 *C27 H28
    C27 N26 N24
    C29 C27 N26
    C30 C29 C27
    C31 C30 C29
    C32 C31 C30
    C34 *C32 H33
    C34 C32 C31
    C29 *C30 C50

    C4
    C8
    C1
    O15
    C19
    H25

    C4
    C8
    C1
    C14
    C19
    N24

    C32 C32
    C48 C48
    C46 C46
    C40 C40
    C38 C38
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    CL5
    H9
    N12
    C16
    H20 C19 H21 C19 C22
    N26 N26 C27 C27 H28
    H33 C32 C34 C34 C35 C35
    H49 C48 C46
    H47
    H41 C40 C38
    H39
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 90.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00
    0.00
    0.00 120.00
    0.00
    0.00 -120.00
    0.00
    0.00 180.00
    0.00
    0.00 -120.00
    0.00
    0.00 120.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 180.00
    0.00
    0.00 90.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00
    0.00
    0.00
    0.00
    0.00 180.00
    0.00

    C29

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    IC
    !End

    C32 C30 *C31 C44 0.0000


    0.00 180.00
    C48 C50 C30 C31 0.0000
    0.00
    0.00
    C46 C44 C31 C30 0.0000
    0.00
    0.00
    C48 C30 *C50 H51 0.0000
    0.00 180.00
    C46 C50 *C48 H49 0.0000
    0.00 180.00
    C44 C48 *C46 H47 0.0000
    0.00 180.00
    C31 C46 *C44 H45 0.0000
    0.00 180.00
    C34 C29 *C35 C36 0.0000
    0.00 180.00
    C32 C35 *C34 C42 0.0000
    0.00 180.00
    C38 C36 C35 C34 0.0000
    0.00
    0.00
    C40 C42 C34 C35 0.0000
    0.00
    0.00
    C38 C35 *C36 H37 0.0000
    0.00 180.00
    C40 C36 *C38 H39 0.0000
    0.00 180.00
    C42 C38 *C40 H41 0.0000
    0.00 180.00
    C34 C40 *C42 H43 0.0000
    0.00 180.00
    drug-like molecules, S. Zhong, jun2008

    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    !Hydrazine, E. Darian, jun2008


    RESI HDZN
    0.00 ! N2H4 Hydrazine neutral, Eva Darian
    GROUP
    ATOM N1 NG3N1 -0.78 !
    ATOM H11 HGP1
    0.39 !
    H11
    H21
    ATOM H12 HGP1
    0.39 !
    \
    /
    GROUP
    !
    N1--N2
    ATOM N2 NG3N1 -0.78 !
    /
    \
    ATOM H21 HGP1
    0.39 !
    H12
    H22
    ATOM H22 HGP1
    0.39 !
    BOND N1 H11 N1 H12 N1 N2 N2 H21 N2 H22
    IC H11 N1 N2 H21 0.0000 0.0000 60.0000 0.0000
    IC N2 H11 *N1 H12 0.0000 0.0000 130.0000 0.0000
    IC H21 N1 *N2 H22 0.0000 0.0000 -120.0000 0.0000
    !End hydrazine, E. Darian, jun2008

    0.0000
    0.0000
    0.0000

    !halogenated ethanes, Nov08, adm


    RESI CLET
    0.00 ! C2H5Cl chloroethane, adm jr.
    GROUP
    ATOM C1
    CG321
    0.07 ! CL11 H12 H13
    ATOM CL11 CLGA1 -0.10 !
    \ | /
    ATOM H12 HGA2
    0.14 !
    C1
    ATOM H13 HGA2
    0.14 !
    |
    ATOM C2
    CG331 -0.52 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 CL11 C1 H12 C1 H13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC CL11 C1
    C2
    H21
    0.0000
    0.00 180.00
    IC C2
    CL11
    *C1
    H12
    0.0000
    0.00 120.00
    IC C2
    CL11
    *C1
    H13
    0.0000
    0.00 -120.00
    IC H21
    C1
    *C2
    H22
    0.0000
    0.00 120.00
    IC H21
    C1
    *C2
    H23
    0.0000
    0.00 -120.00
    PATC FIRS NONE LAST NONE
    RESI DCLE
    GROUP
    ATOM C1
    CG311
    ATOM CL11 CLGA1
    ATOM CL12 CLGA1

    0.00 ! C2H4Cl2 1,1-dichloroethane, adm jr.

    0.00
    0.00
    0.00
    0.00
    0.00

    0.12 ! CL11 CL12 H13


    -0.04 !
    \ | /
    -0.04 !
    C1

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    ATOM H13 HGA1


    0.22 !
    |
    ATOM C2
    CG331 -0.53 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 CL11 C1 CL12 C1 H13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC CL11 C1
    C2
    H21
    0.0000
    IC C2
    CL11
    *C1
    CL12
    0.0000
    IC C2
    CL11
    *C1
    H13
    0.0000
    IC H21
    C1
    *C2
    H22
    0.0000
    IC H21
    C1
    *C2
    H23
    0.0000
    PATC FIRS NONE LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    120.00
    -120.00

    RESI TCLE
    0.00 ! C2H3Cl3 1,1,1-trichloroethane, adm
    GROUP
    ATOM C1
    CG301 -0.24 ! CL11 CL12 CL13
    ATOM CL11 CLGA3
    0.14 !
    \ | /
    ATOM CL12 CLGA3
    0.14 !
    C1
    ATOM CL13 CLGA3
    0.14 !
    |
    ATOM C2
    CG331 -0.45 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 CL11 C1 CL12 C1 CL13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC CL11 C1
    C2
    H21
    0.0000
    0.00 180.00
    IC C2
    CL11
    *C1
    CL12
    0.0000
    0.00 120.00
    IC C2
    CL11
    *C1
    CL13
    0.0000
    0.00 -120.00
    IC H21
    C1
    *C2
    H22
    0.0000
    0.00 120.00
    IC H21
    C1
    *C2
    H23
    0.0000
    0.00 -120.00
    PATC FIRS NONE LAST NONE
    RESI BRET
    0.00 ! C2H5Br bromoethane, adm
    GROUP
    ATOM C1
    CG321
    0.07 ! BR11 H12 H13
    ATOM BR11 BRGA1 -0.10 !
    \ | /
    ATOM H12 HGA2
    0.14 !
    C1
    ATOM H13 HGA2
    0.14 !
    |
    ATOM C2
    CG331 -0.52 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 BR11 C1 H12 C1 H13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC BR11 C1
    C2
    H21
    0.0000
    0.00
    IC C2
    BR11
    *C1
    H12
    0.0000
    0.00
    IC C2
    BR11
    *C1
    H13
    0.0000
    0.00
    IC H21
    C1
    *C2
    H22
    0.0000
    0.00
    IC H21
    C1
    *C2
    H23
    0.0000
    0.00
    PATC FIRS NONE LAST NONE
    RESI DBRE
    GROUP
    ATOM C1
    CG311
    ATOM BR11 BRGA2

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    jr.

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    jr.

    180.00
    120.00
    -120.00
    120.00
    -120.00

    0.00 ! C2H4Br2 1,1-dibromoethane, adm jr.


    0.10 ! BR11 BR12 H13
    -0.04 !
    \ | /

    0.00
    0.00
    0.00
    0.00
    0.00

    ATOM BR12 BRGA2 -0.04 !


    C1
    ATOM H13 HGA1
    0.22 !
    |
    ATOM C2
    CG331 -0.51 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 BR11 C1 BR12 C1 H13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC BR11 C1
    C2
    H21
    0.0000
    IC C2
    BR11
    *C1
    BR12
    0.0000
    IC C2
    BR11
    *C1
    H13
    0.0000
    IC H21
    C1
    *C2
    H22
    0.0000
    IC H21
    C1
    *C2
    H23
    0.0000
    PATC FIRS NONE LAST NONE

    0.00
    0.00
    0.00
    0.00
    0.00

    180.00
    120.00
    -120.00
    120.00
    -120.00

    RESI TBRE
    0.00 ! C2H3Br3 1,1,1-tribromoethane, adm
    GROUP
    ATOM C1
    CG301 -0.12 ! BR11 BR12 BR13
    ATOM BR11 BRGA3 -0.01 !
    \ | /
    ATOM BR12 BRGA3 -0.01 !
    C1
    ATOM BR13 BRGA3 -0.01 !
    |
    ATOM C2
    CG331 -0.12 !
    C2
    ATOM H21 HGA3
    0.09 !
    / | \
    ATOM H22 HGA3
    0.09 ! H21 H22 H23
    ATOM H23 HGA3
    0.09
    BOND C1 BR11 C1 BR12 C1 BR13
    BOND C1 C2
    BOND C2 H21 C2 H22 C2 H23
    IC BR11 C1
    C2
    H21
    0.0000
    0.00 180.00
    IC C2
    BR11
    *C1
    BR12
    0.0000
    0.00 120.00
    IC C2
    BR11
    *C1
    BR13
    0.0000
    0.00 -120.00
    IC H21
    C1
    *C2
    H22
    0.0000
    0.00 120.00
    IC H21
    C1
    *C2
    H23
    0.0000
    0.00 -120.00
    PATC FIRS NONE LAST NONE
    END

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

    jr.

    0.00
    0.00
    0.00
    0.00
    0.00

    0.0000
    0.0000
    0.0000
    0.0000
    0.0000

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