Beruflich Dokumente
Kultur Dokumente
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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
--------------------------------------------------------------------------
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! -------------------------------------------------------------------------- !
!
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: 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
THIP, thiophene
sulfate sulfur
sulfur C-S-S-C type
thiolate sulfur (-1)
sulphur, SH, -S-
!
!
!
!
!
!
!
!
!
!
!
!
!
! dummy atom
! helium
! neon
! phosphorus
! pyrophosphate
! protonated pyrophosphate
! Aluminum, for ALF4, AlF4-
!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
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
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
\ /
N1 (+)
||
C
/ \
H21-N2 N3-H31
| |
H22 H32
H21
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
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
!
! 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
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
-0.27
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
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
-0.27
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
0.08 !
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
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
-0.27
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
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
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
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
HD1
HE1
|
/
ND1--CE1
/
||
ATOM
ATOM
ATOM
ATOM
ATOM
ND1
HD1
CE1
HE1
NE2
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
1.2987
1.3071
1.3165
1.3758
1.2854
1.5421
1.2987
1.0879
0.9770
1.0902
1.0000
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
0.000 !
!
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
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
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
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
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
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
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 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
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
108.00
108.00
108.00
108.00
108.00
108.00
108.00
0.00
0.00
0.00
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
-0.09 !
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
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
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
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
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
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
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
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
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
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
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
-0.600
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
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
CD1
CE2
CG
CE2
CD1
CG
CD2
HG
HE2
ND1
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
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
!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
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
CD1
CE2
CG
CD2
CE2
CD3
IC CG
!
O1
HG
!
\
|
! (-) ) CD3 CG
!
/ \ / \\
!
O2
CD1 CD2--HD2
!
||
|
!
HE1--CE1 CE2--HE2
!
\ //
!
NZ
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
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
-0.600
0.220
0.175
-0.115
0.180
-0.115
0.120
-0.215 !charge similar to difluorotoluene
0.115
0.115
0.120
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
! 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
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
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
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
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
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
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.
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
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
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
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
CD1
CE2
CG
CE1
CD1
CA3
CA6
CA2
CA5
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
0.0000
0.0000
0.0000
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
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
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
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
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
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
CG331
HGA3
HGA3
HGA3
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
-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
-0.18 !c12
0.09
0.09
-0.18 !c11
0.09
0.09
-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
-0.18 !c1
0.09
0.09
-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
-0.18 !c4
0.09
0.09
0.00 !c5
0.00 !c10
-0.18 !c1
0.09
0.09
-0.18 !c2
0.09
0.09
CG331
HGA3
HGA3
HGA3
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
-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
C5
C6
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
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
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
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
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
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
C2 CG2D1
-0.27
0.09
0.09
0.09
!
!
!
!
-0.15 !
H21
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
0.00
0.00
0.00
0.00
0.00
0.00
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
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
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
(+)
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
1.0797
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
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
0.0000
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
O3
O4
O1
C5
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
21-51 (1981)
(+)
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
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
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
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
0.0000
0.0000
0.0000
0.0000
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
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
!
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
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
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
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
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
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
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
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
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
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
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'
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'
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'
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
!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
!
! 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
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
!
! 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
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
!
! 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
!
! 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
!
! 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
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
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
!
! 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
1.3783 !chi
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0
0.0
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
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
!
! 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
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
!
! 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
!
! 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
!
! 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
!
! 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
\
\
\
*
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
!
! 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
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
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
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
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'
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'
!
-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'
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
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
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
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
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
!
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
-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
!
!
!
!
!
!
!
!
!
!
!
!
!
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
-0.40
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
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
0.0000
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
-0.40
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
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 !
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
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
! 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
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
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
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
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
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'
0.0000
0.0000
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
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
RESI TH5H
-2)
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
e
GROUP
ATOM O4' OG3C51
ATOM C1' CG3C52
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
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
!
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''
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
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
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 !
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
RESI T3PH
C3'
H21'
O1P
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C3'
C3'
C3'
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
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
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
H21'
O1P
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C3'
C3'
C3'
O3'
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
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
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
.
! 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'
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0
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
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
! 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'
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'
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
! 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
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'
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
-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
RESI TMFU
p) on c2'
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
s
! taken from Daxu Yin's thesis (monofluoroethane).
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
OG3C51
CG3C52
HGA2
HGA2
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
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
-0.40
0.02
0.02
0.09
0.09
0.09
0.09
!
!
!
!
!
0.14 !
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
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
0.09
0.09
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
BOND
BOND
BOND
BOND
BOND
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'
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
-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
!
!
!
!
!
!
!
!
!
!
!
!
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'
-0.40
0.11
0.09
0.02
0.09
0.09
!
!
!
!
!
!
!
-0.18 !
0.09 !
0.09 !
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
CG
CG
ND1
CD2
C1'
HD2
HE1
HG
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
-0.40
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
RESI RIBO
GROUP
ATOM O4'
ATOM C1'
ATOM C4'
ATOM H11'
CG
CD2
HD2
HG
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
!
!
!
!
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'
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
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
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
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
0.28
-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'
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
-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
-0.02
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
-0.34 !
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
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
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'
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
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 !
-0.40
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'
-0.40
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
on C3'
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
!
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'
-0.40
0.11
0.09
0.11
0.09
!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Thymine
!
\ / \ /
-0.18 ! H42'--C4' C1'--H12'
0.09 !
|
|
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
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
-0.40
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
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
-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
-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
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
C3'
C3'
P
C3T
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'
1.5346
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
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
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
0.09
0.09
0.09
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-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
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
O12 0.0000
P1 O14
O11 C1
P2 O24
O22 H22
000.00
180.0
000.00
0.0000
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
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
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
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
0.0000
0.0000
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
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
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
AC6
AN1
AC5
AN6
NC7
NN7
NC3
NC7
NN7 NO7
NH72 NH71
NC5
NC6
NC4
NH5
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
0.0
0.0
120.
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
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
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
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
-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
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
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
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
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
-0.30
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
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
0.14
-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
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
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
CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1
CG2
CD1
CG2
CE1
CG2
CE2
CG1
CZ1
CZ1
CE2
CD1
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
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
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
SUBS--CZ1
0.115 !
!
CG2R61 -0.115 !
HGR61
0.115 !
!
CG2R61 -0.115 !
HGR61
0.115 !
!
!
!
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
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
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
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
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
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
-0.42
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
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
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
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
0.0000
0.0000
0.0000
0.0000
0.0000
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
CG331
HGA3
HGA3
HGA3
CG2O1
OG2D1
NG2S1
HGP1
CG2R61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
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
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
0.00
0.00
0.00
0.00
0.00
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
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
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
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
-0.18
0.09
0.09
-0.18
0.09
0.09
-0.18
0.09
0.09
0.00
0.00
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
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
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
-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
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
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
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
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
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
C1
C2
H11
H11
C3
OR
OR
C2
C3
C1
C2
C1
C2
C2
C3
OR
C2
*C1
*C2
*C3
*C3
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
!
! H11
OD1
! \
||
! C1
CG
! / \\ / \
! H12 C2 H
!
|
!
H21
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
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
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
! 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
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
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
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
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
0.15
0.09
0.09
0.09
-0.40
0.32
0.15
0.09
0.09
0.15
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
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
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
CG2R61
HGR62
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
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
-0.69
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
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
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
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
0.00
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
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
!
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
0.00
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
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
0.00
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
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
0.00
0.00
0.00
0.00
0.00
0.00
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.00
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
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
0.00
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
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
-0.44
-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
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
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
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
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
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
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
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
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
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
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
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
0.0000
0.0000
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
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
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
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
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
C1
H11
H11
H11
N3
N4
C2
N3
C6
N4
H61
H61
C2
C2
C2
C1
C1
C2
N3
N4
N4
C5
C5
C5
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
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
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
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
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
0.15
-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
0.00
0.00
0.00
0.00
0.00
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
-0.28
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
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
! 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
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
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
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
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
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
! 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
! 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
-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
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
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
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 !
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
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
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
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
/ \|/ \ / \ /
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
H7'
H20
H22A
H23A
OE1
OE2
C20
C22
C23
CD
!
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
C10
*C5 C6
C5
C6
C7
1.5156 121.28
75.31 123.88
C6
C7
C8
1.3432 123.88
51.01 112.36
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
C3
*C2 H2A
C3
*C2 H2B
C2
C3
O3
C2
*C3 O3
C2
*C3 H3
C3
O3
1.5311 109.14
60.00 105.39
C3
*C4 H4A
C3
*C4 H4B
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
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
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
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
H20
H22A
H23A
OE1
OE2
C20
C22
C23
CD
!
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
C4
C5
C10
C4
*C5 C6
C5
C6
C7
1.5156 121.28
75.31 123.88
C6
C7
C8
1.3432 123.88
51.01 112.36
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
C3
*C2 H2A
C3
*C2 H2B
C2
C3
O3
C2
*C3 O3
C2
*C3 H3
C3
O3
1.5311 109.14
60.00 105.39
C3
*C4 H4A
C3
*C4 H4B
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
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
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
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
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
H20
H22A
H23A
OE1
OE2
C20
C22
C23
CD
!
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
115.09
121.28
123.88
112.36
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
C3
*C2 H2A
C3
*C2 H2B
C2
C3
O3
C2
*C3 O3
C2
*C3 H3
C3
O3
1.5311 109.14
60.00 105.39
C3
*C4 H4A
C3
*C4 H4B
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
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
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
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
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
H20
H22A
H23A
OE1
OE2
C20
C22
C23
CD
!
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
115.09
121.28
123.88
112.36
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
109.41
!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
C2
C3
O3
C2
*C3 O3
C2
*C3 H3
C3
O3
1.5311 109.14
60.00 105.39
C3
*C4 H4A
C3
*C4 H4B
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
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
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
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
H7'
H20
H22A
H23A
OE1
OE2
C20
C22
C23
CD
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
115.09
121.28
123.88
112.36
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
109.41
109.70
109.70
109.14
109.40
105.39
109.16
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
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
-0.51
C12 Me18
ATOM N
NG2S1
-0.47
/ \ |
ATOM HN
ATOM CG
HGP1
CG321
0.47
-0.28
!
!
C11 C13---C17
Me19 |
|
|
0.09
0.09
!
!
C1 | C9
C14 C16
/ \|/ \ / \ /
0.62
-0.76
!
!
-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
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
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
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
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
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
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
H20
H22A
H23A
O24
HN
HC1
HC2A
HC3B
O24
OA1
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
C3
*C2 H2A
C3
*C2 H2B
C2
C3
O3
C2
*C3 O3
C2
*C3 H3
C3
O3
1.5311 109.14
60.00 105.39
C3
*C4 H4A
C3
*C4 H4B
C4
*C5 H5
C5
*C6 H6A
C5
*C6 H6B
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
0.09 !
0.09 !
C2
C10 C8
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
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
!
0.17 !
OA1
0.09 !
||
ATOM CA CG2O2
(M)
ATOM OA1 OG2D1
0.90 !
O24
CA--OA2--CH3
-0.63 !
||
C24
CC1
-0.49 !
OH
-0.31 !
0.09 !
0.09 !
0.08 !
Me19 |
0.09 !
C1 | C9
0.09 !
ATOM CG
CG2O2
0.90 !
C2
C10 C8
-0.63 !
-0.49 !
C3
C5
C7
ATOM CN
-0.31 !
CG331
0.09 !
0.09 !
0.09 !
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
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 !
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
!
!
!
!
!
!
!
!
HM2 CM
CM
CA
CA
CA
CT
CG
CG
CG
OG2
OG2
OG2
OG2
OG2
OG2
OG2
OG2
NH
HM3
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
! C9H15O4 chayan
Acid CDCA Amide (GA) >> Gamma Methyl, Alpha Tert.Butyl G
!
!
!
OA1
||
!
!
!
OH
C12 Me18
-0.27 !
0.09 !
Me19 |
0.09 !
C1 | C9
0.09 !
-0.27 !
C2
C10 C8
0.09 !
0.09 !
C3
C5
C7
0.09 !
0.08 !
0.09 !
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
!
!
!
!
!
!
!
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
C3
C5
C7
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
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
-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
HM3
C15
/ \ / \ / \
HO
C4
C6
OH
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 !
0.09 !
O24
CA--OA2(-
0.90 !
||
C24
CC1
-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 |
C1 | C9
OH
|
C20
/
C11 C13---C17
|
C14
C16
/ \|/ \ / \ /
C2
C10 C8
C3
C5
C7
CC3
\ / \ / \ / \ / \
/ \ |
C22
C12 Me18
0.115 !
0.115 !
Me21
C15
C23
NH
CC2
0.115 !
/ \ / \ / \
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
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 |
|
|
C1 | C9
0.115 !
C14
/ \|/ \ / \ /
C2
C10 C8
C3
C5
C7
0.115 !
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
!
!
!
!
!
!
!
!
!
!
!
!
!
!
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
/ \ |
0.09 !
-0.18 !
Me19 |
0.09 !
C1 | C9
0.09 !
0.13 !
C2
C10 C8
0.09 !
0.09 !
C3
C5
C7
CC3
C11 C13---C17
|
C14
C16
/ \|/ \ / \ /
C15
C23
NH
CC2
CC
ATOM NL
NG3P3
-0.30 !
0.33 !
0.33 !
0.33 !
/ \ / \ / \
HO
C4
C6
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 !
||
-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
-0.18 !
0.09 !
Me19 |
0.09 !
C1 | C9
-0.18 !
0.09 !
0.09 !
Me21
C22
\ / \ / \ / \ / \
C20
/ \ |
C11 C13---C17
|
C14
C16
/ \|/ \ / \ /
C2
C10 C8
CC3
C15
C23
NH
CC2
CC
0.09 !
0.13 !
C3
C5
C7
0.09 !
0.09 !
ATOM NL
NG3P3
/ \ / \ / \
HO
0.33 !
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 !
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
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
OG311
-0.65 !
||
0.42 !
CG--NT--HT2
ATOM H3
0.09 !
CC3
-0.18 !
HGA1
GROUP
ATOM C4
CG321
0.09 !
O24
CC2
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 |
0.09 !
C1 | C9
!
CG311
0.14 !
C2
C10 C8
ATOM O7
OG311
-0.65 !
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
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
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
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'
H20
H22A
H23A
O24
HN
HC1
HC2B
HC3B
NT
O24
OG
OA1
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
1.5533
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
OG
||
CG---NT--CG
/
HT1
CC3
\
0.09 !
O24
CC2
0.09 !
||
GROUP
-0.09 !
0.09 !
-0.18 !
0.09 !
Me19 |
0.09 !
C1 | C9
GROUP
C20
C23
C11 C13---C17
|
C14
C16
/ \|/ \ / \ /
0.20 !
C2
C10 C8
0.09 !
0.09 !
C3
C5
C7
-0.40 !
0.32 !
0.32 !
0.20 !
CG321
HGA2
HGA2
C24
C15
/ \ / \ / \
HO
C4
C6
0.09 !
0.09 !
!
-0.18 !
0.09 !
0.09 !
CC1
\ / \ / \ / \
/ \ |
HGA2
HGA2
C22
C12 Me18
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||
0.09 !
C11 C13---C17
0.09 !
Me19 |
C1 | C9
GROUP
ATOM CG3 CG324
0.20 !
0.09 !
C2
C10 C8
0.09 !
-0.40 !
C3
C5
C7
0.32 !
0.32 ! HO
0.20 !
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
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
||
-0.18 !
0.09 !
0.09 !
C12 Me18
0.20 !
0.09 !
Me19 |
0.09 !
C1 | C9
-0.40 !
0.32 !
C2
C10 C8
0.32 !
0.20 !
C3
C5
C7
0.09 !
0.09 ! HO
GROUP
C24
CC1
C20
C23
NH
C14
C16
OA2 (-0.5)
/ \|/ \ / \ /
C15
/ \ / \ / \
C4
C6
OH
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
\ / \ / \ / \
/ \ |
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
1.1126
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 !
0.09 !
0.09 !
Me19 |
-0.40 !
C1 | C9
0.32 !
0.32 !
C2
C10 C8
0.20 !
0.09 !
C3
C5
C7
0.09 !
-0.18 !
0.09 !
0.09 !
!
0.17 !
0.09 !
C24
C20
C23
C11 C13---C17
0.09 !
C22
C14
C16
/ \|/ \ / \ /
C15
/ \ / \ / \
HO
C4
C6
CC1
\ / \ / \ / \
/ \ |
0.09 !
Me21
C12 Me18
0.20 !
HT1
CC3
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
0.09 !
||
0.09 !
-0.40 !
0.32 !
0.20 !
0.09 !
Me19 |
0.09 !
C1 | C9
GROUP
0.32 !
C14
C16
/ \|/ \ / \ /
C2
C10 C8
0.09 !
0.09 !
C3
C5
C7
!
-0.18 !
C20
C11 C13---C17
C15
/ \ / \ / \
HO
C4
C6
C24
CC1
\ / \ / \ / \
/ \ |
-0.18 !
C22
C12 Me18
GROUP
Me21
OH
C23
NH
CA--OA1 (
|
OA2 (-0.5
0.09 !
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
1.4438
1.1179
1.5420 ! for R conf
HG1
NT
*CG1 CG6
NT
CG1
CG2
NG3
1.4438 110.98
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
1.4406
1.1153
1.5378 ! for S conf
HG1
NT
*CG1 CG6
NT
CG1
CG2
NG3
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
!
!
OG
||
CG---NT--
CC3
HT1
0.09 !
O24
CC2
-0.40 !
||
C12 Me18
!
!
-0.18 !
C1 | C9
0.09 !
0.09 !
0.09 !
0.09 !
GROUP
C23
C14
C16
C2
C10 C8
C3
C5
C7
C15
/ \ / \ / \
HO
C4
C6
OH
C20
/ \|/ \ / \ /
!
-0.18 !
C24
C11 C13---C17
Me19 |
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
CG1
CG2
NG3
1.4554 117.90
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
-0.40 !
||
C12 Me18
!
!
-0.18 !
C1 | C9
0.09 !
0.09 !
0.09 !
0.09 !
GROUP
C20
C23
C14
C16
/ \|/ \ / \ /
!
-0.18 !
C24
C11 C13---C17
Me19 |
C22
C2
C10 C8
C3
C5
C7
C15
/ \ / \ / \
HO
C4
C6
OH
0.17 !
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
CG1
CG2
CG1
CG1
CG2
*CG2 HG21
*CG2 HG22
NG3 CG4
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
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 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
0.09 !
0.09 !
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
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
-0.58
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
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
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
-0.27
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
0.0000
0.0000
0.00 120.00
0.00 -120.00
0.00
0.00
0.0000
0.0000
-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
!
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
!
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
-0.27
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
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
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
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
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
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
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
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
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 !
-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
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
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
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
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
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 !
0.09 !
H
|
Me19 |
HGP2
0.32 !
ATOM CBG
CG324
0.15 !
C3
C5
C7
0.09 !
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 !
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
0.09 !
||
CG321
-0.18 !
HGA2
0.09 !
HGA2
0.09 !
0.09 !
C1 | C9
0.09 !
NG3P1 -0.40 !
C2
C10 C8
ATOM HG1
HGP2
0.32 !
ATOM CBG
CG324
0.15 !
C3
C5
C7
0.09 !
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 |
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
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
0.09 !
||
GROUP
-0.18 !
0.09 !
0.09 !
GROUP
ATOM CG2
C22
C20
/ \ |
C11 C13---C17
0.15 !
Me19 |
0.09 !
C1 | C9
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
0.09 !
0.09 ! HO
ATOM CG6
0.15 !
CG324
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
OG
C14
C16
C23
NH
CA---OA2||
OA1
0.09 !
GROUP
/ \|/ \ / \ /
C2
C10 C8
-0.18 !
0.09 !
C3
C5
C7
0.09 !
GROUP
/ \ / \ / \
!
-0.18 !
0.09 !
HO
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
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
0.20 !
0.09 !
0.09 !
-0.40 !
0.32 !
0.32 !
0.20 !
Me19 |
0.09 !
C1 | C9
0.09 !
GROUP
||
C2
C10 C8
|
0.09 !
C3
C5
C7
0.09 !
-0.18 !
0.09 !
0.09 !
HO
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
\ / \ / \ / \
/ \ |
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IMPR
C22
C12 Me18
GROUP
Me21
C4
C6
OH
3MPS (01OH06(S)D)
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
0.29 !
0.09 !
-0.40 !
0.32 !
0.32 !
Me19 |
0.09 !
C1 | C9
C2
C10 C8
0.09 !
0.09 !
C3
C5
C7
C14
C16
C15
/ \ / \ / \
-0.18 ! HO
0.09 !
/ \|/ \ / \ /
-0.18 !
C20
C11 C13---C17
0.09 !
C4
C6
CG---NT--CGT/
HT1
CC3
\
CC2
||
C24
CC1
\ / \ / \ / \
/ \ |
0.20 !
||
O24
C22
C12 Me18
GROUP
Me21
OG
OH
C23
NH
CA---OA2---C
||
OA1
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
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
\
0.09 !
O24
CC2
-0.40 !
||
0.32 !
0.32 !
0.20 !
C12 Me18
0.09 !
0.09 !
GROUP
Me21
C22
C24
CC1
\ / \ / \ / \
C20
/ \ |
C11 C13---C17
Me19 |
C23
NH
CA---OA2
||
OA1
-0.18 !
0.09 !
0.09 !
GROUP
C1 | C9
-0.18 !
0.09 !
0.09 ! HO
C10 C8
C3
C5
C7
C15
C4
C6
OH
!
-0.18 !
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
/ \ / \ / \
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
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
\
-0.18 !
O24
CC2
0.09 !
||
0.09 !
GROUP
ATOM CG1 CG311
-0.09 !
0.09 !
GROUP
Me19 |
0.09 !
C1 | C9
0.09 !
C2
C10 C8
0.06 !
0.09 !
C3
C5
C7
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
C23
/ \|/ \ / \ /
0.06 !
C20
C11 C13---C17
-0.18 !
C24
C4
C6
CC1
\ / \ / \ / \
/ \ |
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
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
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
||
CG---NT--CGT
/
HT1
CC3
\
-0.18 !
O24
CC2
0.09 !
||
0.09 !
GROUP
ATOM CG1 CG311
-0.09 !
0.09 !
GROUP
Me19 |
0.09 !
C1 | C9
0.09 !
C2
C10 C8
0.06 !
0.09 !
C3
C5
C7
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
C23
/ \|/ \ / \ /
0.06 !
C20
C11 C13---C17
-0.18 !
C24
C4
C6
CC1
\ / \ / \ / \
/ \ |
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
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
! 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
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
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 !
OH
ATOM NZ
Me19 |
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 !
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
GROUP
Me21
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
0.09 !
0.09 !
OA1
|
O24
CA--OA2---CB
-0.52 !
||
C24
CC1
OH
Me19 |
C14
C16
C1 | C9
/ \|/ \ / \ /
C10 C8
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
\ / \ / \ / \ / \ /
/ \ |
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
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
0.120 !
C3
C5
C7
!
NG2R60 -0.600 !
GROUP
0.180 !
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 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
0.09 !
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
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
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)
!
!
!
-0.18 !
0.09 !
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 !
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
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
0.09 !
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 !
0.120 !
GROUP
C14
C16
C1 | C9
/ \|/ \ / \ /
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
Me21
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
/ \|/ \ / \ /
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
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
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
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
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
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
OA1
O24
CA--OA2---
||
C24
CC1
OH
C20
/
C11 C13---C17
Me19 |
C1 | C9
C14
C16
/ \|/ \ / \ /
C2
C10 C8
C3
C5
C7
CC3
\ / \ / \ / \ / \
/ \ |
C22
C12 Me18
0.115 !
0.115 !
Me21
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
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
0.115 !
/ \ / \ / \
GROUP
HO
C4
C6
OH
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
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
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
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
OH
Me21
C22
\ / \ / \ / \ / \ /
C12 Me18
C20
/ \ |
C11 C13---C17
Me19 |
C1 | C9
C14
C16
/ \|/ \ / \ /
C2
C10 C8
CC3
C15
C23
NH
CC2
CG
||
OG
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
0.09 !
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 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 !
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
-0.18 !
0.09 !
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 |
C3
C5
C7
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
/ \ / \ / \
IC
IC
IC
IC
IC
IC
NH
/ \|/ \ / \ /
C10 C8
GROUP
C23
C1 | C9
C2
C20
C11 C13---C17
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
!
0.14 !
OG
OG311
-0.65 !
||
//
HGP1
0.42 !
CG--NG--CZ
HGA1
0.09 !
CC3
-0.18 !
CG321
HG
0.09 !
O24
CC2
0.09 !
||
GROUP
H
|
ATOM C5
CG311
-0.09 !
ATOM H5
0.5)
GROUP
HGA1
0.09 !
ATOM C6
CG321
-0.18 !
Me19 |
0.09 !
C1 | C9
!
CG311
0.14 !
C2
C10 C8
ATOM O7
OG311
-0.65 !
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
\ / \ / \ / \
/ \ |
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
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
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
H20
H22A
H23A
O24
HN
HC1
HC2B
HC3B
NG
HD1
HE2
O24
OG
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
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
-0.22 !
O24
CC2
0.09 !
||
0.09 !
GROUP
Me19 |
C3
C5
C7
0.115 !
GROUP
C14
C16
NH
CA--OA1
|
OA2--CB--
C15
/ \ / \ / \
HO
C4
C6
OH
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
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
CG321
OG
||
CG--NG--CZ
/
HG
CC3
\
-0.22 !
O24
CC2
0.09 !
||
0.09 !
GROUP
Me19 |
C3
C5
C7
0.115 !
GROUP
0.115 !
C23
C14
C16
C4
C6
C15
OH
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 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 !
0.09 !
GROUP
ATOM CY
0.00 !
C12 Me18
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 !
!
/ \ / \ / \
0.150 !
0.110 !
C4
C6
OH
2FBP
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
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
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
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
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
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
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
-0.19
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
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
-0.61
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
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
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
-0.16
-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
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
0.30
-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
0.23
-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
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
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
-0.140
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
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
0.00
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
-0.115
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
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
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
0.00
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
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
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
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
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
0.00
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
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
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
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
-0.115
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
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
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
!
!
!
!
!
!
!
!
!
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
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
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
-0.09
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
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
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
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
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
-0.27
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
-0.65
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
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
-0.23
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
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
-0.27
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
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
-0.18
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
-0.40
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
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
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
-0.115
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
!
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
0.000
-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
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
-0.115
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
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
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
!
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
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
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
0.000
-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
!
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
0.110
-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
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
-0.18
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
0.03
-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
!
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
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
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
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
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
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
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
!
!
!
!
!
!
!
!
!
!
!
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
!
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
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
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
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
0.00
0.00
0.00
0.00
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
0.00
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
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
0.00
0.00
0.00
0.00
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