Sie sind auf Seite 1von 430

*

*
*
*
*
*
*
*
*
*
*
*
*
36

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

*
*
*
*
*
*
*
*
*

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

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

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

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

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


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

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

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


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

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

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

CLET, DCLE, chloroethane, 1,1-dichloroethane


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

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

DEFA FIRS NONE LAST NONE


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

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

-1.00 ! C3H5O2 propionic acid


CG321
CG2O3
HGA2
HGA2

ATOM
ATOM
GROUP
ATOM
ATOM
ATOM
ATOM

CG331
HGA3
HGA3
HGA3

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

O1 OG2D2
O2 OG2D2

-0.28
0.62
0.09
0.09

C3
H31
H32
H33

BOND C1
BOND C2
BOND C3
DOUBLE
IMPR C1

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

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

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

C3
O2
H21
H22
O1
O2
H31
H32
H33
NONE

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
0.00
120.00
-120.00
180.00
180.00
180.00
120.00
-120.00

1.00 ! CH6N3 guandinium, K. Kuczera


0.64 !

H11 H12

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM N1 NG2P1 -0.80 !


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

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

H21

N2 H22 N3 H31 N3 H32

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

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

0.00 ! C2H5NO2 neutral glycine


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

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

HGA2
HGA2

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

126.10
113.44
113.44
107.16
110.99
111.22
110.0
110.0

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

1.2218
1.3958
1.5780
0.9565
1.0023
1.0030
1.1
1.1

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

1.00 ! C2H8N ethylammonium, adm jr.


0.21
-0.30
0.05
0.05

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

ATOM
ATOM
ATOM
ATOM
BOND
BOND
BOND

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

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

NZ
HE1
HE2
HZ1
HZ2
HZ3
H11
H12
H13
NONE

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

! CH4O methanol, adm jr.


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

0.0000 0.0000 180.0000 0.0000 0.0000


0.0000 0.0000 120.0000 0.0000 0.0000
0.0000 0.0000 -120.0000 0.0000 0.0000

-1.00 ! CH3O methoxide, adm jr.

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

ab initio

0.0000 0.0000
0.0000 0.0000
0.0000 0.0000

0.00 ! C2H6O Ethanol, adm jr.


0.05
-0.65
0.42
0.09
0.09

! H21 H11 H12


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

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

H21
H22
H23
H11
H12
HO1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

180.0000
120.0000
240.0000
240.0000
120.0000
180.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

-1.00 ! C2H5O Ethoxide, adm jr.


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

HA1 HB1 HB2


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

HB1 CB HB2
HA3

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

180.0000
180.0000
180.0000
180.0000
180.0000
60.0000
300.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC HA1 CA
IC HA1 CA

CB
CB

HB1
HB2

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

0.0000 0.0000 120.0000 0.0000 0.0000


0.0000 0.0000 240.0000 0.0000 0.0000

0.00 ! C3H8O 2-propanol, adm jr.


0.14
-0.65
0.42
0.09
-0.27
0.09
0.09
0.09

! H12 H13 H33 H32


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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

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

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! CH3NO formamide, adm jr.


HGR52
CG2O1
NG2S2
HGP1
HGP1
OG2D1

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

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

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

HT

N HA O
1.00

90.0

0. 124.70 1.352

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

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

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

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

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

IC C
IC C

CC C1 H12
CC C1 H13

0.0
0.0

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

O
H
O
N
N
N
C
C
C

C
N
C
C
C
C
N
N
N

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

N
C
N
CL
CL
CL
CR
CR
CR

0.0
0.0

60.
300.

0.0 0.0
0.0 0.0

! C3H7NO N-methylacetamide, Louis Kuchnir

H
CL
CR
HL1
HL2
HL3
HR1
HR2
HR3

HL3 CL !
N CR !
!
HR3 CR !

1.2233
0.9933
1.2233
1.3418
1.3418
1.3418
1.3418
1.3418
1.3418

122.84
119.23
122.84
116.25
116.25
116.25
122.57
122.57
122.57

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

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

119.23
116.25
122.57
109.3
109.3
109.3
110.7
110.7
110.7

0.9933
1.5118
1.4488
1.109
1.109
1.109
1.113
1.113
1.113

!
!
!
!
!
!
!
!
!

variable
variable
variable
variable
variable
variable
variable
variable
variable

1
8
8
2
3
4
5
6
7

0.00 ! C6H12N2O2 Alanine dipeptide


CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG2O1
OG2D1

0.51
-0.51

NG2S1
HGP1
CG311
HGA1

-0.47
0.31
0.07
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG2O1
OG2D1
NG2S1

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

HL1
\

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

ATOM
ATOM
ATOM
ATOM
ATOM

HR
CR
HR1
HR2
HR3

HGP1
CG331
HGA3
HGA3
HGA3

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

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

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

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

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

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

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

CA
CR

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

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

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

! Phi
! Psi
! Omega Left
! Omega Right

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

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

0.0 0.00 0.00

-1.00 ! CH3S methylthiolate, adm jr.


SG302
CG323
HGA3
HGA3
HGA3

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

-0.80
-0.47
0.09
0.09
0.09

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

0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000

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

1.8281

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

*C1
*C1
*C1
C2
C2
C2
NONE

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

109.72
109.72
108.57
114.02
114.02
114.02

118.35
-125.21
-114.71
-180.00
59.57
-59.57

105.91
108.57
108.57
110.65
109.98
109.98

1.1131
1.5315
1.1131
1.1089
1.1111
1.1111

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

CM1 CG321
S2 SG301

0.00 ! C4H10S2 diethyldisulfide, adm jr.


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

S3
CM4
H4
H5

SG301
CG321
HGA2
HGA2

CM0
H01
H02
H03

CG331
HGA3
HGA3
HGA3

CM5
H51
H52
H53

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09

H1
S2
CM4
CM0

CM1
S3
CM5
H01

H2
S3

CM1
CM4

CM1 CM0
CM4 H4

CM0 H02

CM0 H03

CM1 S2
CM4 H5

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

CM5 H51

CM5 H52

CM0 CM1 S2 S3 0.00


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

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

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

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

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

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

0.00 ! C3H4N2 Imidazole, adm jr.


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

HD1
HE1
|
/
ND1--CE1
/
||

ATOM
ATOM
ATOM
ATOM
ATOM

ND1
HD1
CE1
HE1
NE2

NG2R51 -0.36 ! HG-CG


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

HD1
HD2
HE1
HG

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

109.79
110.31
105.82
108.68
105.39
131.52
109.79
119.57
123.39
118.30

1.2987
1.3071
1.3165
1.3758
1.2854
1.5421
1.2987
1.0879
0.9770
1.0902

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

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

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

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

1.2987
1.3165
1.3071
1.5421
0.0
0.0
0.0
1.3758
1.3071
1.3165
1.3165

110.31
105.82
110.31
131.52
0.0
0.0
0.0
105.39
105.82
108.68
108.68

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

105.82
119.57
123.39
118.30
0.0
0.0
0.0
109.79
108.68
105.39
131.52

1.3165
1.0879
0.9770
1.0902
0.0
0.0
0.0
1.2987
1.3758
1.2854
1.5421

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

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

HE2

109.79
110.31
105.82
108.68
105.39
131.52
109.79
119.57
123.39
118.30
125.00

1.00 ! C5H9N2 Ethyl-Imidazolium, adm jr.


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

1.2987
1.3071
1.3165
1.3758
1.2854
1.5421
1.2987
1.0879
0.9770
1.0902
1.0000

! KEEPS HYDROGENS IN RING PLANE


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

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

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

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

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

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

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

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

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C8H10 ethylbenzene, adm jr.

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

HB1

HD1 HE1
|
|
CD1--CE1

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

HGR61

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

CD1
CE2
CG
CE2
CB
CA

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

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

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

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

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

CG
CE1
HD1
HZ
HB2
HA2

CE1 CD1
CZ CE2
CD2 HD2 CE1 HE1

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

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

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

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

0.00 ! C6H6O phenol, adm jr.


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

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

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

ATOM CE2 CG2R61 -0.115


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

CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61

HE1
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
180.0000
180.0000
180.0000
180.0000
180.0000
180.0000
180.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C8H10O p-ethylphenol, adm jr.


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

CG2R61 0.11
OG311 -0.53
HGP1
0.42
CG321
HGA2
HGA2

-0.18
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

BOND CD2 CG CE1 CD1


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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

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

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

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

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

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI AP2
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

N
CA
CB
CG
CD
CY
OY
C
HA

NG2S0
CG3C51
CG3C52
CG3C52
CG3C52
CG2O1
OG2D1
CG2O1
HGA1

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

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

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

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

0.00 ! C7H12N2O2 acetyl-prolineamide, R. Dunbrack


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

ATOM HB1 HGA2


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

HB2 CB

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

!Omega
!Omega
!Psi
!Phi

IC OY CY CAY HY1 0.00


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

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

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

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

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

0.00 0.00
0.00 0.00
0.00 0.00

0.00 ! C8H14N2O2 proline dipeptide


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

BOND CY N CAY HY1


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

0.00 90.00
0.00 120.00
0.00 -120.00

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

CAY
CA
HG2
NT
CR

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

HY2
CB
CG
HT1
HR3

CAY
CB
HD1
NT

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

C5H11N2O prolineamide, R. Dunbrack

HN1 HD1 HD2


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

0.00 120.00
0.00 120.00

0.00 0.00
0.00 0.00

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

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

120.00
-120.00

0.00 0.00
0.00 0.00

180.0

0.00 0.00

29.25
-36.72
29.50
-11.61
-11.17

103.67
103.63
103.28
112.90
103.34

0.00
0.00
0.00
0.00
0.00

120.00 108.00 0.00


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

108.00
108.00
108.00
108.00
108.00
108.00
108.00
0.00
0.00
0.00

0.00 ! C2H6 ethane

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.09
0.09
0.09
-0.27

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

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

0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0

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

!Phi

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

C3
C2
H31
H31
C2
H11
H11
C3
C3

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

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

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

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

0.00 ! C4H10 Iso-butane, S. Fischer


CG311
HGA1
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3

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

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

ATOM C3 CG331 -0.27


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

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

HT

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

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.00 ! C5H12 pentane, adm jr.


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

C2
C1
C3
C5

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

C4
H13
H41

C4
C2
C4

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

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

C5
H21
H42

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

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

IC C4 H51 *C5 H52 0.0000


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

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

0.00 120.00
0.00 -120.00

0.00
0.00

0.0000
0.0000

0.00 ! C8H18O OCTANOL


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

C2
C6
C1
C3
C6
C8

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

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

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

C5
O1
H22
H42
H71

O1

HO1

C5
C7

H51
H72

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

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

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

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

RESI CO2
GROUP
ATOM C
ATOM OC1
ATOM OC2
BOND OC1

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! CO2 Carbon Dioxide, John Straub


CG2O7
0.60
OG2D5 -0.30
OG2D5 -0.30
C OC2 C

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

C1
C3
C3
C3
C3

C2
C2
C2
C1
C1

C3
*C1
*C1
*C2
*C2

H31
H11
H12
H21
H22

0.00
0.00

0.0000
0.0000 !redundant defi

C3H6 Cyclopropane Model Compound


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

0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00

-120.00
120.00
-120.00
-120.00
120.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

IC C2
IC C2

C1 *C3 H31
C1 *C3 H32

0.0000
0.0000

0.00 120.00
0.00 -120.00

0.00
0.00

0.0000
0.0000

PATCHING FIRST NONE LAST NONE


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

1.1053
1.2074
1.2074
1.5462

0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

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

180.0
0.0
0.0
120.0
120.0

0.0
0.0
0.0
0.0
0.0

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


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

0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

PATC FIRS NONE LAST NONE


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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

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

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

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00

0.00 ! C5H6N2 4-aminopyridine


NG2R60
CG2R61
CG2R61
CG2R61
CG2R61
CG2R61
NG2S3

-0.600
0.180
-0.115
0.050
0.180
-0.115
-0.850

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

HE1
HD1
HD2
HE2
HG11
HG12

BOND
BOND
BOND
BOND
BOND

CD1
CE2
CD1
CE2
CG

HGR62
HGR61
HGR61
HGR62
HGP4
HGP4
CG
CD2
HD1
HE2
NG

0.120
0.115
0.115
0.120
0.400
0.400

CD2 CG CE1 CD1


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

IMPR NG CG HG11 HG12


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

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

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

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

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

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

RESI 3APY

0.00 ! C5H6N2 3-aminopyridine


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

CD1
CE2
CG
CE2
CD1

CG
CD2
HG
HE2
ND1

CD2 CG CE1 CD1


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

!delete this line IMPR HD11 CD1 HD12 ND1


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

0.0000 0.0000
0.0000 0.0000

0.0000 0.0000 0.0000


0.0000 0.0000 0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CE1
CD1
CE1
CE2
NZ
NZ
CE1
HD11
NZ
CE2

NZ
CD2
CG
CG
CD1
CD2
CD1
CD1
CE1
NZ

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

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

CD1
CE2
CD2
CE2
CD1
CG

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

CD2
HG
ND1
HD2
HE1
HE2
HD11
HD12
CG
CD1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
180.0000
180.0000
180.0000
180.0000
180.0000
0.0000
180.0000
0.0000
0.0000

CD2 CG CE1 CD1


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

IMPR HD11 CD1 HD12 ND1


IMPR HG11 CG HG12 NG
HD12
HG12

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

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

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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


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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

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

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

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

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

PATCH FIRST NONE LAST NONE


RESI 3CPY
GROUP

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

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

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

BOND
BOND
BOND
BOND
BOND
DOUB
IMPR

CD1
CE2
CG
CE2
CD1
CD3
CD3

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

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

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

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

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

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

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

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

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

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

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

-1.00 ! C7H5O2 benzoate


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

CD1
CE2
CG
CD2
CE2
CD3

IC CG

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

CG CD2 CG CE1 CD1


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

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

BOND
BOND
BOND
BOND
BOND
DOUB

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

CG
CD2
HG
HD2
HE2
O2

CD2
CZ
CD1
CE1
CZ

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

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

CG CE1 CD1
CE1 CZ CE2
CD3 CD3 O1
HE1
HZ

CD1 CE1 CZ

0.0000 0.0000

0.0000 0.0000 0.0000

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

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

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

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

CD1
CE2
CG
CE2

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

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

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

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

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

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

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

0.00 ! C5H4FN 3-fluoropyridine


NG2R60
CG2R61
CG2R66
CG2R61
CG2R61
CG2R61
HGR62
FGR1
HGR62
HGR61
HGR62

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

CG CD2 CG CE1 CD1


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

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

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
180.0000
180.0000
180.0000
180.0000
180.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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


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

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

BOND
BOND
BOND
BOND
BOND
DOUB

CD1
CE2
CG
CE2
CD1
CD3

CG
CD2
HG
HE2
CD3
O1

CD2 CG CE1 CD1


NZ CE1 NZ CE2
CD2 HD2 CE1 HE1
CD3 H3

IMPR CD3 CD1 O1 H3


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

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

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

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

CD1
CE2
CG
CE1

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

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

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

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

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

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

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

0.000 ! C5H5NO 3-hydroxypyridine


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

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

CD2
NZ
CD1
CE2

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

CE1
NZ
CD2
OH

CD1
CE2
HD2
HO1

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
180.0000
180.0000
180.0000
180.0000
180.0000
0.0000
0.0000
0.0000

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

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

BOND
BOND
BOND
BOND
BOND

CD1
CE2
CG
CE1
CD3

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

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

CD2
NZ
CD1
CE2
CD3

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

CD1
CE2
CG
CE1
CD3
H21

CG
CE1
CD3
HE2
H32

CE1 CD1
NZ CE2
CD2 HD2
CD3 H33

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

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

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

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

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

0.00 ! C7H9N ethylpyridine


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

CD2
NZ
CD1
CE2
CD3
H22

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

!aliphatic, corresponds to new CT2, HA2


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

CE1 CD1
NZ CE2
CD2 HD2
CD3 C2
H23 C2

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

CD1
CE2
CG
CD1
CD3
C2
C3
C4

CG
CD1
CE1
CD1
CE2
NZ
NZ
NZ

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

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

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

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

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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C9H13N butylpyridine


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

CD1
CE1
NZ
CD2
CG
CD1
CD2
CE1

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

CD2
NZ
CD2
CD3
C2
C2
C3
C4

CG
CE1
HD2
H11
C3
H22
H32
H42

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

NZ
CE2
CD2
HG
HD2
HE1
HE2
CG

CE1
NZ
CE1
CD3
C3

CD1
CE2
HE1 CE2 HE2
H12
C4

C4 H43
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
180.0000
180.0000
180.0000
180.0000
0.0000

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

CE1 CD1 0.0000


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

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

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

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

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

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

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

!ATOM NZ NG2R60 -0.600


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

CD1
CE2
CG
CE1
CD1
C3N

CG
CD1
CE1
CD1

CG
CD2
HG
HE1
C3N
N3C
CD1
CE1
NZ
CD2

CD2
NZ
CD2
CE2

CE1
NZ
CE2
*CG

CG CE1 CD1
CE1 NZ CE2
HD2
HE2

NZ
CE2
CD2
HG

0.0000
0.0000
0.0000
0.0000

0.0000 0.000
0.0000 0.0000
0.0000 0.0000
0.0000 180.0000

0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000

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

*CD2 HD2 0.0000


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

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

180.0000
180.0000
180.0000
180.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

CD1
CE2
CG
CE1
CD1
HC1
C

IMPR C

CG
CD2
HG
HE1
C
CH3
O

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

CD1 CH3 O

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

CD2
NZ
CD2
CE2
C
HC2

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

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

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

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

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

0.00 ! C6H6N2O Really just unprotonated oxidized nicotinamid


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

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

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

BOND
BOND
BOND
BOND
BOND
BOND
DOUB

CD1
CE2
CG
CE1
CD1
HC
C

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

IMPR C

CG
CD2
HG
HE1
C
N
O

CD1 N

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

CD2
NZ
CD2
CE2
C
HT

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

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

CG CE1 CD1
CE1 NZ CE2
HD2
HE2
N
N
O

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

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

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

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

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

0.00 ! C6H7NO carbinol-pyridine, by daxu


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

0.05 !aliphatic, corresponds to new CT2, HA2


0.09
0.09
-0.65
0.42

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

CD1
CE2
CG
CE1
CD1
CD3

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

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

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

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

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

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

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

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

PATCH FIRST NONE LAST NONE


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

CD1
CE2
CG
CE1
CD1
CA3
CA6
CA2
CA5

0.00 ! C11H9N 3-phenyl-pyridine


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

CD2
NZ
CD2
CE2
CA1
CA4

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

CE1 CD1
NZ CE2
CA2 CA3
CA6 CA5

CA3 HA3 CA4 HA4


CA6 HA6

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

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

CD1
CE2
CG
CE1
CD1
C
CA1
CA3
CA6
CA2
CA5

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

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

CD2
NZ
CD2
CE2
C
C
CA2
CA4

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

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

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

0.00 ! C12H11N 3-benzyl-pyridine


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

CA3 HA3 CA4 HA4


CA6 HA6

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

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

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

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

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

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

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

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

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

HGA2

0.09

CG311
HGA1

-0.09
0.09

CG311

0.00

CG331
HGA3
HGA3
HGA3

-0.27 !methyl at c13


0.09
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG311
HGA1

-0.09
0.09

CG311

0.00

CG331
HGA3
HGA3
HGA3

-0.27 !methyl at c10


0.09
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG311
HGA1

-0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18 !beyond this nomenclature may not be correct


0.09
0.09

CG311
HGA1

-0.09 !c25
0.09

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

CG331
HGA3
HGA3
HGA3

-0.27 !terminal methyl, c26


0.09
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27 !terminal methyl, c27


0.09
0.09
0.09

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

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

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

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

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

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

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

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

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

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

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

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

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

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

! correct
GROUP
ATOM C1
ATOM O1
ATOM HO1
ATOM H1

cholesterol nomenclature
CG311
OG311
HGP1
HGA1

0.14 !c3
-0.65
0.42
0.09

ATOM C2 CG321
ATOM H2 HGA2
ATOM H2' HGA2

-0.18 !c4
0.09
0.09

ATOM C3
ATOM C4
ATOM H4

CG2D1
CG2D1
HGA4

0.00 !c5
-0.15 !c6
0.15

ATOM C5 CG321
ATOM H5 HGA2
ATOM H5' HGA2

-0.18 !c7
0.09
0.09

ATOM C6
ATOM H6
GROUP
ATOM C7
ATOM H7

CG311
HGA1

-0.09 !c8
0.09

CG311
HGA1

-0.09 !c14
0.09

ATOM C8 CG321
ATOM H8 HGA2
ATOM H8' HGA2

-0.18 !c15
0.09
0.09

ATOM C9 CG321
ATOM H9 HGA2
ATOM H9' HGA2

-0.18 !c16
0.09
0.09

ATOM C10 CG311


ATOM H10 HGA1

-0.09 !c17
0.09

ATOM C11
GROUP
ATOM CC11
ATOM H111
ATOM H112
ATOM H113

CG311
CG331
HGA3
HGA3
HGA3

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

ATOM C12 CG321


ATOM H12 HGA2
ATOM H12' HGA2

-0.18 !c12
0.09
0.09

ATOM C13 CG321


ATOM H13 HGA2
ATOM H13' HGA2

-0.18 !c11
0.09
0.09

ATOM C14 CG311


ATOM H14 HGA1

-0.09 !c9
0.09

ATOM C15
GROUP
ATOM CC15
ATOM H151
ATOM H152
ATOM H153

CG311
CG331
HGA3
HGA3
HGA3

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

ATOM C16 CG321


ATOM H16 HGA2
ATOM H16' HGA2

-0.18 !c1
0.09
0.09

ATOM C17 CG321


ATOM H17 HGA2
ATOM H17' HGA2

-0.18 !c2
0.09
0.09

ATOM
ATOM
ATOM
ATOM

-0.27 !c20
0.09
0.09
0.09

C18
H181
H182
H183

CG331
HGA3
HGA3
HGA3

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

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

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

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

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

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

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

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

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

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

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

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

RESI CHM1

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

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

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

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

0.00 ! C11H18O cholesterol analog with only rings 1 and 2


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

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

ATOM C16 CG321


ATOM H16 HGA2
ATOM H16' HGA2

-0.18 !c1
0.09
0.09

ATOM C17 CG321

-0.18 !c2

ATOM H17 HGA2


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

0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27 !c19, methyl at c10


0.09
0.09
0.09

CG2D1
HGA4

-0.15 !c6
0.15

ATOM C5 CG321
ATOM H5 HGA2
ATOM H5' HGA2

-0.18 !c7
0.09
0.09

ATOM C6 CG321
ATOM H6 HGA2
ATOM H6' HGA2

-0.18 !c8
0.09
0.09

ATOM C14 CG321


ATOM H14 HGA2
ATOM H14' HGA2

-0.18 !c9
0.09
0.09

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

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

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

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

C2
O1
C2
CC15
C16
C17

C3 C3 C15 C15 C16 C16 C17 C17 C1


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

C5

C6

C6 C14 C14 C15

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

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

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

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

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

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

IC
IC
IC
IC

C14
C14
C6
C6

C5
C5
C15
C15

*C6
*C6
*C14
*C14

H6
H6'
H14
H14'

0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00

120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

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

OM

OM

C2

H12
H22

C1
C2

H13
H23

from experiment for


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

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

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

1.437
1.437
1.334
1.334
1.334
1.334
1.334
1.334

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
O
H11
H12
H13
C21
H22
H23
H211
H212
H213

C
C
C1
C1
C1
C2
C2
C2
C21
C21
C21

114.8
114.8
109.0
109.0
109.0
114.8
114.8
114.8
116.7
116.7
116.7

1.437
1.437
1.334
1.334
1.334
1.334
1.334
1.334
1.437
1.437
1.437

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

1.437
1.437
1.334
1.334
1.334
1.334
1.334
1.334
1.520
1.520
1.520

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

OM
OM
C
C
C
OM
OM
OM
C2
C2
C2

SG3O1
OG303
OG2P1
OG2P1
OG2P1
CG331
HGA3
HGA3
HGA3

C2
C2
OM
OM
OM
C
C
C
OM
OM
OM

1.520
1.200
1.1
1.1
1.1
1.520
1.0802
1.0802
1.1
1.1
1.1

109.0
125.9
108.9
109.75
109.75
109.94
110.50
110.50
108.90
108.90
108.90

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

-1.00 ! CH3O4S Methylsulfate


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

BOND S OS1 S OS2 S OS3 S OS4 OS1 C1

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

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

C1 H11 C1 H12 C1 H13


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

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

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

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

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

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

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

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

0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00

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

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

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

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

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

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

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

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

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

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

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

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

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

C2H4 ethylene, yin/adm jr.


H11
\

H21
/
C1=C2

/
H12

121.37
121.37
121.37
121.37

\
H22

180.00 121.37
180.00 121.37
180.00 121.37
-180.00 31.37

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

1.1036
1.1036
1.1036
1.8845

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

! C4H8 2-Butene, yin/adm jr.


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

H13

H43

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
NONE

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
0.0
120.0
-120.0
180.0
180.0
0.0
120.0
-120.0

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

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

C1
H11
H12
H13

jr.

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

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


CG331
HGA3
HGA3
HGA3

C2 CG2D1

-0.27
0.09
0.09
0.09

!
!
!
!

-0.15 !

H21

H31 H51 H61

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

H21 HGA4

C4 CG321
H41 HGA2
H42 HGA2

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

C5 CG2D1
H51 HGA4

-0.15
0.15

C6 CG2D1
H61 HGA4

-0.15
0.15

C7
H71
H72
H73

-0.27
0.09
0.09
0.09

C3 CG2D1
H31 HGA4

CG331
HGA3
HGA3
HGA3

BOND C1 H11 C1 H12 C1 H13


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

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

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


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

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

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

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

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09

BOND C1 H11 C1 H12


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

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

C1 H13

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

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

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

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

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

1.00 ! C4H12N tetramethylammonium


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

(+)

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

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

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

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

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

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

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

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

analog

1.5217
1.4950
1.4950
1.0809
1.0809
1.0795
1.0773
1.0797
1.0795
1.0773

IC
IC
IC
IC
IC
IC
IC

C1
C1
C1
C1
N
N
N

1.5176
1.5176
1.5176
1.5176
1.5176
1.5176
1.5176

111.12
107.80
107.80
107.80
115.98
115.98
115.98

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

choline

RESI ACHO

N
N
N
N
C1
C1
C1

C3
C4
C4
C4
C5
C5
C5

H33
H41
H42
H43
H51
H52
H53

54.79
180.00
60.03
-60.03
180.00
62.29
-62.29

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

109.07
109.11
109.12
109.12
107.05
112.91
112.91

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

1.00 ! C7H16NO2 acetylcholine

1.0797
1.0793
1.0793
1.0793
1.0836
1.0820
1.0820

(+)

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

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

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

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

(+)

C4

OM

C5

C7

H73

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

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

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

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

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

IC H73

C7

OM

0.0000 000.00 -60.4

000.00

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

0.00 ! C6H16NO4P phosphatidylcholine


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

0.0000

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

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

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

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

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

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

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

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

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

O2

C6

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

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

N
N
C1
C5
O3
O4
O1
H61
H62
H63

C1
C1
C5
O1
P1
P1
P1
C6
C6
C6

C5
C5
O1
P1
O1
O1
O2
O2
O2
O2

H52
O1
P1
O2
C5
C5
C6
P1
P1
P1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

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

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

BOND C5 H51 C5 H52


BOND P O1 P O2

O3

O4

O1

C5

! internal coordinates for analysis


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

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

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

-0.27
0.09
0.09
0.09
-0.27

0.
0.
0.
0.

!
!
!
!

t1
t2
t3
t3

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

!
!
!
!
!
!
!
!

a1
a2
a3
a4
a5
a6
a6
a6

C8H20N tetra ethylammonium (TEA)


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

methyl groups, the atom type HAL


to HGA3 . adm jr.
-0.27
0.09
0.09
0.09

21-51 (1981)

(+)

ATOM H71 HGA3


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

NG3P3
HGP2
HGP2
HGP2
CG324
HGA2
HGA2
CG321
HGA2
HGA2
OG311

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

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

1.00 ! C2H8NO ethanolamine


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

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

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

ATOM HO1 HGP1


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

107.86
104.92
108.35
112.05
112.39
000.00
000.00
000.00
000.00

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

104.92
111.99
107.86
107.86
107.86
000.00
000.00
000.00
000.00

1.3987
0.9495
1.5191
1.5191
1.5191
0.0000
0.0000
0.0000
0.0000

0.00 ! C7H12O4 Model compound for glycerol headgroup the


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

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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

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

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

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

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

!was giving an error


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

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

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

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

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

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

C8H14O8P Model compound for glycerol headgroup the


aliphatic tail linker region, phosphorylated

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

P1 OP3 P1 OP4
CP1 HP13 OP2 C3

OP1 CP1

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

0.00 ! C5H10O2 methyl-butyrate


-0.27
0.09
0.09
0.09
-0.18
0.09
0.09

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

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

BOND C2 C3 C3 H31 C3 H32


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

! C6H4F2 1,3-difluorobenzene aka m-difluorobenzene


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

H5

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

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

F4
|
C4

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

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

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

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

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

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

ATOM H103 HGA3


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

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

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

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

BOND
BOND
BOND
BOND

C4'
H11'
H31'
H52'

O4'
C1'
C3'
C5'

0.09 !
P3
O9
O82
H12
H62

P3
O9

O4
C10

O4
P3

C5
O31

C5
P3

C6
O32

C6

O7

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

C1 H13 C5 H51 C5 H52


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

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

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

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

0.00 ! C5H10O3 abasic deoxyribose nucleoside (susil)


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

BILD O4' C1' C2' C3'


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

C1'
H12'
O3'
H5T
1.433
1.521
1.525

C4'
C1'
O3'
C2'
104.1
100.9
102.6

C5'
C2'
H32'
C3'
41.2
325.1
257.8

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

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

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

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

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

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

PG1
OG2P1
OG2P1
OG303
NG2S3
HGP1

ATOM
ATOM
ATOM
ATOM

C1
H11
H12
H13

CG331
HGA3
HGA3
HGA3

ATOM
ATOM
ATOM
ATOM

C2
H21
H22
H23

CG331
HGA3
HGA3
HGA3

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

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

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

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

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

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

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

-1.00 ! C2H7NO3P Phosphoramidate (backbone for DNA)


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

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

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

H1 O2
H23

C1

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

OG3C51
CG3C52
HGA2
HGA2

-0.40 ! Note: has 1 asymmetric carbon.


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

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

CG3C52
HGA2
HGA2

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

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

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

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

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

C2'
C1'
N1
C5'

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

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

C3' C4' C4' O4' C3'


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

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

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

PATC FIRS NONE LAST NONE


RESI THNI
imidazole
GROUP

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

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

OG3C51
CG3C51
HGA1
CG3C51
HGA1

-0.40 ! Note: has 3 asymmetric carbons.


0.11 ! Abs. config is arbitrary.
0.09
0.11
0.09

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

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

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

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

O4'
O4'
C4'

0.0 0.0 -59.66 0.0 0.0


0.0 0.0 59.68 0.0 0.0
0.0 0.0 59.68 0.0 0.0

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

Methyl group on C4'


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

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

OG2P1
OG2P1
OG303
CG331
HGA3
HGA3
HGA3

-0.820
-0.820
-0.560
-0.190
0.090
0.090
0.090

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

C2' C2' C3'


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

O3
O4
O5
C5
H51
H52
H53

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

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

O4

O5

guess:
1.4055 108.09
1.4127 106.18

C5
23.45 106.18
3.96 103.11

1.5457
1.5346

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

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

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

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

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

103.11 -26.93 100.86


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

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

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

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

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

C4
C2
C4

C5
H22
H42

C5

C1

note initial planar geometry


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

0.00 ! C5H10 cyclopentane, adm jr.


! with south atom types

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

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

C4
C2
C4

C5
H22
H42

C5

C1

note initial planar geometry


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

IC
IC
IC
IC
IC
IC
PATC

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

RESI BPNP

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00

120.0
240.0
120.0
240.0
120.0
240.0

0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

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


! used to parameterize epsilon

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

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

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

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

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

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

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

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

PATC FIRS NONE LAST NONE


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

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

C3
C6
H21
H62
H31
O2P
H52'

C3
C6
C2
C4
C3
P
C5'

C4
C1
H22
H41
O3'
O5'
H53'

C4
C4

C5
H42

O3' P
O5' C5'

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

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

PATC FIRS NONE LAST NONE


RESI CSAD

0.00 ! C11H13N5 carbocyclic sugar with adenine base, south


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

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

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

HGA2
HGA2
CG3RC1
CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.00
0.28
-0.71
0.34
0.12
-0.05

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

N1
C2
H2
N3
C4
C6
N6
H61
H62

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64
NG2S3
HGP4
HGP4

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

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
DOUB

C1S
C5S
C2S
C4S
C6S
N9
C6
C5
N1

C2S
C1S
H21S
H41S
H62S
C4
N6
N7
C6

IMPR H62 C6

0.09 !
0.09 !

C2S
C5S
C2S
C4S
C1S
N9
N6
C8
C2
H61 N6

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

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

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

C3S
C6S
H22S
H42S
N9
C8
H61
H8
N3
N6

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C4
N6
C2
C4

N3
H62
H2
C5

C2
C6

N1
C5

N7

C8

N1

C5

C3S H32S
C6S H61S

C6

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

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

1.5251
1.4896
1.376
1.367
0.0
0.0
0.0
1.376
1.409
1.337
1.01

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

120.00
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0

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

125.59
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00

IC
IC
IC
IC
IC
PATC

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

RESI CSGU

1.409
1.337
1.01
0.0
0.0

117.6 -180.0
119.0
0.0
119.0 180.0
0.0 180.0
0.0 180.0

119.0
119.0
121.00
0.0
0.0

0.00 ! C11H13N5O carbocyclic sugar with guanine base, south


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

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

C1S
C5S
C2S
C4S

1.337
1.01
1.01
0.0
0.0

C2S
C1S
H21S
H41S

C2S
C5S
C2S
C4S

C3S
C6S
H22S
H42S

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S
C3S H32S
C6S H61S

BOND
BOND
BOND
BOND
BOND

C6S
N9
C4
N2
C5

H62S
C4
C5
H22
N7

IMPR N2

N3

DONO
DONO
DONO
ACCE
ACCE
ACCE

N2
N2
N1
C6

H21
H22
H1
O6
N3
N7

C1S
N9
N3
N1
N7
N1

C2

N9
C8
C2
H1
C8

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

O6

C4
C2
N1

N3
N2
C6

N1

C5

C8
C2
C6
C6

H8
N1
O6

N2
C6

H22 H21 C2

H21
C5
N2

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

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

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

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

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

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

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

PATC FIRS NONE LAST NONE


RESI CSTH

0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, south


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

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

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

C1S
C5S
C2S
C4S
C6S
N1
C2
C5
C5M

CG3RC1
HGA1

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

CG3C31
HGA2
HGA2

-0.18 !
0.09 !
0.09 !

CG3RC1
NG2R61
CG2R62
HGR62

0.00
-0.30
0.17
0.13

CG2R63
OG2D4
NG2R61
HGP1

0.57
-0.47
-0.46
0.36

CG2R63
OG2D4
CG2R62
CG331
HGA3
HGA3
HGA3

0.54
-0.49
-0.15
-0.11
0.07
0.07
0.07

CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

C2S
C1S
H21S
H41S
H62S
C2
N3
C5M
H52

IMPR O2

N1

DONO H3
ACCE O2
ACCE O4

N3
C2
C4

C2S
C5S
C2S
C4S
C1S
N1
N3
C5
C5M
N3

C2

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

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

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

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

C3S
C6S
H22S
H42S
N1
C6
H3
C6
H53
O4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C2
N3
C6

O2
C4
H6

C4 C5
C4 O4
C5M H51

N3

C5

C3S H32S
C6S H61S

C4

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

C5M C4

0.00
0.00
0.00
0.00
0.00
0.00
120.00
0.00

C6

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5

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

C1S C3S *C2S


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

H22S
H31S
H32S
H41S
H42S
H51S
N1

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

240.0
120.0
240.0
120.0
240.0
120.0
147.80

0.00
0.00
0.00
0.00
0.00
0.00
120.00

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

0.0000 120.00 -130.0 125.59


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

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

PATC FIRS NONE LAST NONE


RESI CSCY

0.00 ! C10H13N3O carbocyclic sugar with cytosine base, south


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

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

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

NG2R62
CG2R64

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2S
C1S
H21S
H41S
H62S
C2
N3
C5

C1S
C5S
C2S
C4S
C6S
N1
C2
C4

NG2S3
HGP4
HGP4
CG2R62
HGR62

IMPR O2 N1
IMPR H42 C4
DONO
DONO
ACCE
ACCE

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

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

N3 C2
H41 N4

C3S
C6S
H22S
H42S
N1
C6
C4
C6
N4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C2
C4
C5

O2
N4
H5

N3

C5

C4S C5S
C3S H32S
C6S H61S
N4
C6

H41
H6

N4

H42

C4

H42 N4
H41 N4
O2 C2
N3

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

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

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

0.0000 120.00 -130.0 125.59


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

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

PATC FIRS NONE LAST NONE


RESI CNAD

0.00 ! C11H13N5 carbocyclic sugar with adenine base, north


! base attached to C2 of carbocyclic sugar

! used to parameterize chi


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

C1S
C5S
C1S
C4S
C6S
N9
N6

C2S
C1S
H11S
H41S
H62S
C4
H61

C2S
C5S
C2S
C4S
C2S
N9
N6

C3S
C6S
H21S
H42S
N9
C8
H62

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C4
C6

N3
C5

C2
C5

N1
N7

N1

C6

C2

N3

C4

C5

N7

C8

IMPR H62 C6

H61 N6

N1

C5

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

N6
0.0000
0.0000

0.00
0.00

C3S H32S
C6S H61S
C6
C8

C6
0.0
0.0

0.00
0.00

0.0000
0.0000

N6
H8

C2

IC C3S C4S C5S C1S


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

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

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

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

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

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

0.00 ! C11H13N5O carbocyclic sugar with guanine base, north


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

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

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

CG3RC1
HGA1

-0.09 !
0.09 !

NG2R51
CG2RC0

CG2R63
OG2D4
CG2RC0

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

NG2R50
CG2R53
HGR52

-0.69
0.41
0.28

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2S
C1S
H11S
H41S
H62S
C4
C5
H22
N7

C1S
C5S
C1S
C4S
C6S
N9
C4
N2
C5

NG2R62
CG2R64
NG2R61
HGP1
NG2S3
HGP4
HGP4

IMPR N2

N3

DONO
DONO
DONO
ACCE
ACCE
ACCE

N2
N2
N1
C6

H21
H22
H1
O6
N3
N7

C2S
C5S
C2S
C4S
C2S
N9
N3
N1
N7
N1

C2

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

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

C3S
C6S
H21S
H42S
N9
C8
C2
H1
C8
O6

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C4
C2
N1

N3
N2
C6

C8
C2
C6

N1

C5

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

C3S H32S
C6S H61S

C6

H8
N1
O6

N2
C6

H22 H21 C2

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

1.5251 113.71 -120.00 125.59

H21
C5
N2

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

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

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

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

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

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

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

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

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

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

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

PATCH FIRST NONE LAST NONE


RESI CNTH

0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


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

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

CG2R62
HGR62

ATOM
ATOM
ATOM
ATOM

C2
O2
N3
H3

CG2R63
OG2D4
NG2R61
HGP1

ATOM C4
ATOM O4
ATOM C5

CG2R63
OG2D4
CG2R62

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

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

ATOM
ATOM
ATOM
ATOM

C5M
H51
H52
H53

CG331
HGA3
HGA3
HGA3

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C1S
C5S
C1S
C4S
C6S
N1
C2
C5
C5M

C2S
C1S
H11S
H41S
H62S
C2
N3
C5M
H52

IMPR O2

N1

DONO H3
ACCE O2
ACCE O4

N3
C2
C4

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

C3S
C6S
H21S
H42S
N1
C6
H3
C6
H53

C2

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

O4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C2
N3
C6

O2
C4
H6

C4 C5
C4 O4
C5M H51

N3

C5

C4

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

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

C3S H32S
C6S H61S

C5M C4

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

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

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

C6

C5

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

PATCH FIRST NONE LAST NONE


RESI CNT1

0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


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

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

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

CG2R62
HGR62

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2S
C1S
H11S
H41S
H62S
C2
N3
C5M
H52

C1S
C5S
C1S
C4S
C6S
N1
C2
C5
C5M

CG2R63
OG2D4
NG2R61
HGP1
CG2R63
OG2D4
CG2R62
CG331
HGA3
HGA3
HGA3

IMPR O2

N1

DONO H3
ACCE O2
ACCE O4

N3
C2
C4

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

N3

C2

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

C3S
C6S
H21S
H42S
N1
C6
H3
C6
H53
O4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C2
N3
C6

O2
C4
H6

C4 C5
C4 O4
C5M H51

N3

C5

C3S H32S
C6S H61S

C4

C5M C4

C6

C5

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

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

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

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

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

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

PATCH FIRST NONE LAST NONE


RESI CNT2

0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


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

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

ATOM H62S
GROUP
ATOM C1S
ATOM H11S
GROUP
ATOM N1

HGA2

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

CG2R62
HGR62

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2S
C1S
H11S
H41S
H62S
C2
N3
C5M
H52

C1S
C5S
C1S
C4S
C6S
N1
C2
C5
C5M

0.09 !

CG3RC1
HGA1
NG2R61

CG2R63
OG2D4
NG2R61
HGP1
CG2R63
OG2D4
CG2R62
CG331
HGA3
HGA3
HGA3

IMPR O2

N1

DONO H3
ACCE O2
ACCE O4

N3
C2
C4

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

N3

H51

C2

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

O4

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

C3S
C6S
H21S
H42S
N1
C6
H3
C6
H53
O4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C2
N3
C6

O2
C4
H6

C4 C5
C4 O4
C5M H51

N3

C5

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

C3S H32S
C6S H61S

C4

C5M C4

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

0.0 -160.00
0.0 -180.00
0.0
-0.02

0.0
0.0
0.0

C6

C5

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

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C6
N1
N1
C5
C2
C4
N1
C6
C5
H51

N1
N3
C2
N3
C4
C6
C5
C5
H51
H52

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

N3
O2
C4
O4
H3
C5M
H6
H51
H52
H53

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

PATCH FIRST NONE LAST NONE


RESI CNT3

0.00 ! C11H14N2O2 carbocyclic sugar with thymine base, north


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

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

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

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

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

ATOM H53 HGA3

0.07

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2S
C5S
C2S
C4S
C2S
N1
N3
C5
C5M

C1S
C5S
C1S
C4S
C6S
N1
C2
C5
C5M

C2S
C1S
H11S
H41S
H62S
C2
N3
C5M
H52

IMPR O2

N1

DONO H3
ACCE O2
ACCE O4

N3
C2
C4

N3

C3S
C6S
H21S
H42S
N1
C6
H3
C6
H53

C2

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

O4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C4S C5S

C2
N3
C6

O2
C4
H6

C4 C5
C4 O4
C5M H51

N3

C5

C4

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

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

C3S H32S
C6S H61S

C5M C4

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

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

C6

C5

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

PATCH FIRST NONE LAST NONE


RESI CNCY

0.00 ! C10H13N3O carbocyclic sugar with cytosine base, north


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

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

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

CG3RC1
HGA1

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

CG3C31
HGA2
HGA2

-0.18 !
0.09 !
0.09 !

CG3RC1
HGA1

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

CG3C52
HGA2
HGA2
CG3C51
HGA1

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

C1S
C5S
C1S
C4S
C6S
N1
C2
C4

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

IMPR O2 N1
IMPR H42 C4
DONO
DONO
ACCE
ACCE

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

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

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

C3S
C6S
H21S
H42S
N1
C6
C4
C6
N4

C3S
C6S
C3S
C5S

C4S
C1S
H31S
H51S

C2
C4
C5

O2
N4
H5

N3

C5

C4S C5S
C3S H32S
C6S H61S
N4
C6

H41
H6

N4

0.00
0.00

0.0000
0.0000

C4

H42 N4
H41 N4
O2 C2
N3

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

0.0000
0.0000

0.00
0.00

0.0
0.0

H42

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

C3S C4S C5S


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

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

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

C2
C6
C5
N3
O2
C4
N4
H41
H42
H5
H6

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

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

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

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

PATCH FIRST NONE LAST NONE


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

CG3RC1

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

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

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

C8H14O5P carbocyclic sugar with 5' OPOCH3


north conformation
used to parameterize gamma
Note : C1 charge changed from -0.09 to 0.00 to
accomodate the CH2-OPOCH3

H31'
H61 H62
/
\ / H51'
O1P C3'-H32'
C6
|
| / \
/ \ C5'-O5'-P-O3' H33'
/
\ / \
|
H51-C5-----C1 H52' O2P
|
|
H41-C4
C2--H21
/ \
/ \
H42 \ / O3T-H3T
C3
/ \
H31 H32

! changed from -0.18 to accomodate O3'-H


!
!
!

GROUP
ATOM C5
ATOM H51
GROUP
ATOM C6
ATOM H61
ATOM H62
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C1
C5
C2
C4
C6
P
C3'
O3T

CG3RC1
HGA1

-0.09 !
0.09 !

CG3C31
HGA2
HGA2

-0.18 !
0.09 !
0.09 !

C2
C1
H21
H41
H62
O2P
H32'
H3T

C2
C5
C4
C6
C5'
P
C3'

C3
C6
H42
H61
O5'
O3'
H33'

! internal coordinates from


IC C1 C2 C3
C4
IC C2 C3 C4
C5
IC C3 C4 C5
C1
IC C5 C2 *C1 C5'
IC C1 O5' *C5' H51'
IC C1 O5' *C5' H52'
IC C3 C5 *C2 H21
IC C3 C5 *C2 O3T
IC C1 C2 O3T H3T
IC C2 C4 *C3 H31
IC C2 C4 *C3 H32
IC C3 C5 *C4 H41
IC C3 C5 *C4 H42
IC C1 C4 *C5 H51
IC C4 C1 *C5 C6
IC C1 C5 *C6 H61
IC C1 C5 *C6 H62
IC C5' C1 C2
O3T
IC O5' C5' C1
C2
IC P
O5' C5' C1
IC C5' O5' P
O3'
IC O5' O3' *P
O1P
IC O5' O3' *P
O2P
IC O5' P O3' C3'
IC H31' C3' O3' P
IC H32' C3' O3' P
IC H33' C3' O3' P

C3
C6
C3
C1
O5'
O3'
C5'

parameter
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

C4
C1
H31
C5'
P
C3'
H51'

C4
C5
C3
C2
P
C3'
C5'

C5
H51
H32
O3T
O1P
H31'
H52'

file, note initial planar geometry


0.00
0.0
0.00 0.0000
0.00
0.0
0.00 0.0000
0.00
0.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 -60.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 120.0
0.00 0.0000
0.00 240.0
0.00 0.0000
0.00 70.0
0.00 0.0000
0.00 50.0
0.00 0.0000
0.0 -105.0
0.0
0.0
0.0 140.0
0.0
0.0
0.0 120.0
0.0
0.0
0.0 240.0
0.0
0.0
0.0 180.0
0.0
0.0
0.0
60.0
0.0
0.0
0.0 -60.0
0.0
0.0
0.0 180.0
0.0
0.0

PATC FIRS NONE LAST NONE


RESI B5SP
GROUP
ATOM C1
ATOM H11
GROUP
ATOM C3
ATOM H31
ATOM O3T
ATOM H3T
GROUP
ATOM C6

-1.00 ! C8H14O5P south carbcyclic sugar with C5'-OPOCH3


CG3RC1
HGA1
CG3C51
HGA1
OG311
HGP1
CG3C31

!
-0.09 !
0.09 !
!
0.14 !
0.09 !
-0.65 !
0.42 !
!
-0.18 !

H61 H62
\ /
C6
/ \
H51-C5------C1-H11 H51' O1P
H31'
|
|
/
|
/
H41-C4
C2-----C5'-O5'-P-O3'-C3'-H32'
/ \
/ \
\
|
\

ATOM H61
ATOM H62
GROUP
ATOM C4
ATOM H41
ATOM H42
GROUP
ATOM C5
ATOM H51
GROUP
ATOM C2
ATOM H21
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3'
ATOM C3'
ATOM H31'
ATOM H32'
ATOM H33'

HGA2
HGA2

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2
C1
H41
H52'
H51
P
O1P
H31'

C1
C5
C4
C5'
C5
O5'
P
C3'

CG3RC1
HGA1

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

CG3C51
HGA1
CG321
HGA2
HGA2
OG303
PG1
OG2P1
OG2P1
OG303
CG331
HGA3
HGA3
HGA3

-0.09
0.09
-0.08
0.09
0.09
-0.57
1.50
-0.78
-0.78
-0.57
-0.17
0.09
0.09
0.09

CG3C52
HGA2
HGA2

C2
C5
C4
C6
C3
O3T
P
C3'

! internal coordinates
IC C1 C2 C3
C4
IC C2 C3 C4
C5
IC C3 C4 C5
C1
IC C4 C5 C1
C6
IC C5 C2 *C1 H11
IC C5 C3 *C4 H41
IC C3 C5 *C4 H42
IC C4 C3 O3T H3T
IC C2 C4 *C3 H31
IC C2 C4 *C3 O3T
IC C3 C1 *C2 C5'
IC C2 O5' *C5' H51'
IC C2 O5' *C5' H52'
IC C5 C3 *C2 H21
IC C4 C1 *C5 H51
IC C1 C4 *C5 C6
IC C1 C5 *C6 H61
IC C1 C5 *C6 H62
IC C5' C2 C3
O3T
IC O5' C5' C2
C3
IC P
O5' C5' C2
IC O1P P O5' C5'
IC O2P P O5' C5'
IC C5' O5' P
O3'
IC O5' P O3' C3'

H42 \ / H21
C3-H31
|
O3T
\
H3T

H52' O2P

H33'

! This charge changed from -0.18 to make it


! compatible with C5'-OPOCH3
!
!
!
!
!
!
!
!
!
!
!
!
C3
C6
H42
H61
H31
H3T
O2P
H32'
0.0000
0.0000
0.0000
1.5000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
1.5000
0.0000
0.0000
0.0000
0.0000
0.0
0.0
0.0
0.0
0.0

C3
C6
C5'
C6
C3

C4
C1
H51'
H62
O3T

C4
C2
C1
C2
C5'

P
O3'
C3' H33'
0.00
0.00
0.00
60.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
60.00
60.00
0.00
0.00
0.0
0.0
0.0
0.0
0.0

C5
C5'
H11
H21
O5'

O3' C3'

0.0
0.0
0.0
120.0
120.0
120.0
120.0
270.0
240.0
120.0
120.0
120.0
240.0
120.0
120.0
120.0
120.0
240.0
150.0
60.0
180.00
-60.0
60.0
180.0
180.0

0.00
0.00
0.00
60.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
60.00
0.00
0.00
0.00
0.00
0.0
0.0
0.0
0.0
0.0

0.0000
0.0000
0.0000
1.5000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
1.5000
0.0000
0.0000
0.0000
0.0000
0.0
0.0
0.0
0.0
0.0

IC
IC
IC
PATC

H31' C3' O3' P


H32' C3' O3' P
H33' C3' O3' P
FIRS NONE LAST NONE

0.0
0.0
0.0

0.0
0.0
0.0

60.0
-60.0
180.0

0.0
0.0
0.0

0.0
0.0
0.0

!toppar_all27_na_model.str
RESI DMPA
GROUP
ATOM P1
ATOM O3
ATOM O4
ATOM O1
ATOM O2
ATOM C1
ATOM H11
ATOM H12
ATOM H13
ATOM C2
ATOM H21
ATOM H22
ATOM H23

PG1
OG2P1
OG2P1
OG303
OG303
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3

-1.00 ! C2H6O4P Dimethylphosphate


!
1.50 !
H11!
-0.78 !
|
-0.78 !
H13- C1-H12
-0.57 !
\
-0.57 !
O3 O1
-0.17 !
\\ /
0.09 !
(-) P1
0.09 !
// \
0.09 !
O4 O2
-0.17 !
/
0.09 !
H23-C2-H22
0.09 !
|
0.09 !
H21
!
P1 O2
P1 O3
P1 O4
O1 C1
O2 C2
C1 H12 C1 H13 C2 H21 C2 H22 C2 H23
conformation (3-21G* opt. structure)
C1 1.4723
107.31
000.0
117.79
1.4356
C2 1.4722
000.0
000.0
117.79
1.4357
C2 1.6343
000.0
73.8
117.79
1.4357
C1 1.6344
000.0
73.7
117.79
1.4356
P1 1.0827
107.8
174.8
117.79
1.6343
P1 1.0800
110.4
54.1
117.79
1.6343
P1 1.0848
110.7
294.3
117.79
1.6343
P1 1.0827
107.9
174.7
117.79
1.6344
P1 1.0800
110.4
54.1
117.79
1.6344
P1 1.0848
110.7
294.2
117.79
1.6344

BOND P1 O1
BOND C1 H11
! IC FOR THE g,g
IC O3 P1 O1
IC O4 P1 O2
IC O1 P1 O2
IC O2 P1 O1
IC H11 C1 O1
IC H12 C1 O1
IC H13 C1 O1
IC H21 C2 O2
IC H22 C2 O2
IC H23 C2 O2

RESI MP_0
0.00
GROUP
! atom order for molvib
ATOM C1 CG331
-0.17
ATOM O1 OG303
-0.56
ATOM P1 PG1
1.50
ATOM O2 OG311
-0.62
ATOM O3 OG311
-0.62
ATOM O4 OG2P1
-0.64
ATOM H11 HGA3
0.09
ATOM H12 HGA3
0.09
ATOM H13 HGA3
0.09
ATOM H2 HGP1
0.42
ATOM H3 HGP1
0.42
BOND P1
BOND C1
IC
IC
IC
IC

H11
C1
H11
H11

O1
H11
C1
O1
O1
O1

P1
C1
O1
P1
*C1
*C1

O2
H12
P1
O2
H12
H13

! CH5O4P Methylphosphate, neutral


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

H11
|
H13--C1--H12
|
O1
|
O4==P1--O3
|
\
O2
H3
\
H2
P1
C1

0.0000
0.0000
0.0000
0.0000

O3
H13

P1
O2
0.00
0.00
0.00
0.00

O4
H2
180.00
180.00
120.00
-120.00

O1
O3

C1
H3
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC

O2
O2
O1
O1

O1
O1
P1
P1

*P1
*P1
O2
O3

O3
O4
H2
H3

RESI MP_1
-1.00
GROUP
! atom order for molvib
ATOM C1 CG331
-0.170
ATOM O1 OG303
-0.620
ATOM P1 PG1
1.500
ATOM O2 OG311
-0.670
ATOM O3 OG2P1
-0.820
ATOM O4 OG2P1
-0.820
ATOM H11 HGA3
0.090
ATOM H12 HGA3
0.090
ATOM H13 HGA3
0.090
ATOM H2 HGP1
0.330

0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00

-2.00
PG1
OG303
OG2P1
OG2P1
OG2P1

1.100
-0.400
-0.900
-0.900
-0.900

CG331
HGA3
HGA3
HGA3

-0.270
0.090
0.090
0.090

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

! CH4O4P Methylphosphate, anionic


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

H11
|
H13--C1--H12
|
O1
|
O4==P1==O3 (-)
|
O2
\
H2

BOND P1 O1
P1 O2
P1 O3
P1
BOND C1 H11
C1 H12 C1 H13 O2
! IC
IC O3 P1 O1 C1 0.0000
000.00
IC O4 P1 O1 C1 0.0000
000.00
IC O2 P1 O1 C1 0.0000
000.00
IC H11 C1 O1 P1 0.0000
000.00
IC H12 C1 O1 P1 0.0000
000.00
IC H13 C1 O1 P1 0.0000
000.00
IC H2 O2 P1 O1 0.0000
000.00
! dummies to analyze cetain angles
IC O3 P1 O4 O1 0.0
0.0
RESI MP_2
GROUP
ATOM P1
ATOM O1
ATOM O2
ATOM O3
ATOM O4
GROUP
ATOM C1
ATOM H11
ATOM H12
ATOM H13

120.00
-120.00
180.00
180.00

O4
H2

O1

000.0
000.0
000.0
000.0
000.0
000.0
000.0

C1
000.00
000.00
000.00
000.00
000.00
000.00
000.00

0.0

0.0

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0

! CH3O4P Methylphosphate, dianionic


!
!
!
H11
!
|
!
H13--C1--H12
!
|
!
O1
!
|
!
(-) O4==P1==O3 (-)
!
||
!
O2

!
BOND P1 O1
P1 O2
P1 O3
P1
BOND C1 H11
C1 H12 C1 H13
! IC
IC O3 P1 O1 C1 0.0000
000.00
IC O4 P1 O1 C1 0.0000
000.00
IC O2 P1 O1 C1 0.0000
000.00
IC H11 C1 O1 P1 0.0000
000.00
IC H12 C1 O1 P1 0.0000
000.00
IC H13 C1 O1 P1 0.0000
000.00
! dummies to analyze cetain angles
IC O3 P1 O4 O1 0.0
0.0

O4
000.0
000.0
000.0
000.0
000.0
000.0
0.0

O1

C1
000.00
000.00
000.00
000.00
000.00
000.00
0.0

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0

! below are residues and patches added for the 97/98 optimization

! and extension of the na all-atom parameters


RESI THF
!
GROUP
ATOM O4'
ATOM C4'
ATOM C3'
ATOM C2'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM H21'
ATOM H22'
ATOM H31'
ATOM H32'
ATOM H41'
ATOM H42'

0.00 ! C4H8O tetrahydrofuran, for MOLVIB


OG3C51
CG3C52
CG3C52
CG3C52
CG3C52
HGA2
HGA2
HGA2
HGA2
HGA2
HGA2
HGA2
HGA2

-0.40
0.02
-0.18
-0.18
0.02
0.09
0.09
0.09
0.09
0.09
0.09
0.09
0.09

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

H41' O4' H11'


\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
H32'
H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
BOND C4' H41' C4' H42'
IC C1' O4' C4' C3'
IC C3' O4' *C4' H41'
IC C3' O4' *C4' H42'
IC C4' O4' C1' C2'
IC C2' O4' *C1' H11'
IC C2' O4' *C1' H12'
IC C3' C1' *C2' H21'
IC C3' C1' *C2' H22'
IC C2' C4' *C3' H31'
IC C2' C4' *C3' H32'
PATC FIRS NONE LAST NONE
RESI THFM
GROUP
ATOM O4'
ATOM C1'
ATOM C2'
ATOM C3'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H21'
ATOM H22'
ATOM H31'
ATOM H32'
ATOM H42'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

45.00
120.00
-120.00
-45.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C5H10O Methyl-tetrahydrofuran


OG3C51
CG3C52
CG3C52
CG3C52
CG3C51
HGA2
HGA2
HGA2
HGA2
HGA2
HGA2
HGA1

-0.40
0.02
-0.18
-0.18
0.11
0.09
0.09
0.09
0.09
0.09
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
!
H52' H53'
!
\ /
! H51'-C5' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
H32'
H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
BOND C4' H42' C5' H51' C5' H52' C5' H53'
IC C4' O4'

C1'

C2'

0.0000

0.00

45.00

0.00

0.0000

IC C2' O4' *C1' H11'


IC C2' O4' *C1' H12'
IC O4' C1' C2' C3'
IC C3' C1' *C2' H21'
IC C3' C1' *C2' H22'
IC C4' C2' *C3' H31'
IC C4' C2' *C3' H32'
IC C3' O4' *C4' C5'
IC C3' O4' *C4' H42'
IC O4' C4' C5' H51'
IC H51' C4' *C5' H52'
IC H51' C4' *C5' H53'
PATC FIRS NONE LAST NONE
RESI THFO
e
GROUP
ATOM O4'
ATOM C1'
ATOM C2'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H21'
ATOM H22'
ATOM H41'
ATOM H42'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM H32'

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

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

120.00
-120.00
-25.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C4H8O2 3'-hydroxyl-tetrahydrofuran


! Atom types for aliphatic hydrogens based on nucleotid
OG3C51
CG3C52
CG3C52
CG3C52
HGA2
HGA2
HGA2
HGA2
HGA2
HGA2
CG3C51
HGA1
OG311
HGP1

-0.40
0.02
-0.18
0.02
0.09
0.09
0.09
0.09
0.09
0.09

!
!
!
!
!
!
!
!
0.14 !
0.09
-0.65
0.42

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
H32'

BOND C1' O4' C1' C2' C2' C3'


BOND C1' H11' C1' H12' C2' H21'
BOND C4' H42' O3' H32'
!Nicolas: the following IC are for
s
IC C4'
O4'
C1'
C2'
IC O4'
C1'
C2'
C3'
IC C1'
C2'
C3'
C4'
IC C2'
C3'
C4'
O4'
IC C3'
C4'
O4'
C1'
IC H11'
C1'
C2'
C3'
IC H12'
C1'
C2'
C3'
IC H21'
C2'
C3'
C4'
IC H22'
C2'
C3'
C4'
IC H31'
C3'
C4'
O4'
IC H41'
C4'
O4'
C1'
IC H42'
C4'
O4'
C1'
IC O3'
C3'
C4'
O4'
IC H32'
O3'
C3'
C4'
PATC FIRS NONE LAST NONE

C3' C4' C4' O4' C3' O3'


C2' H22' C3' H31' C4' H41'
thf-oh as optimized via ab initio calculation
1.4055
1.4127
1.5457
1.5346
1.5211
1.0856
1.0818
1.0846
1.0822
1.0806
1.0891
1.0808
1.4028
0.9492

108.09
106.18
103.11
100.86
103.15
111.62
113.32
110.65
110.88
113.53
110.89
108.72
110.98
108.72

23.45
3.96
-26.93
41.73
-41.62
123.53
-114.11
91.68
-148.45
162.89
77.76
-162.12
-77.39
44.80

106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
110.98

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
1.5211

RESI THFI
0.00 ! C7H10N2O imidazole analog with THF ring
! Sugar: transferred from thf; used for optimization of chi, therefore
! the sugar carbon atom types are not rigorously correct
! Atom types for aliphatic hydrogens based on nucleotide

GROUP
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'
GROUP !
ATOM CG
ATOM HG
ATOM CD2
ATOM HD2
ATOM ND1
ATOM CE1
ATOM HE1
ATOM NE2

OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.11
0.09
0.02
0.09
0.09

!
!
!
!
-0.18 !
0.09 !
0.09 !

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
H41' O4' Imidazole
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
H32'
H22'

CG3C52 -0.18
HGA2
0.09
HGA2
0.09
Imidazole: transferred from isolated imidazole (IMIA)
CG2R51 -0.05 !
C1'
HE1
HGR52
0.09 !
\
/
CG2R51 0.22 !
ND1---CE1
HGR52
0.10 !
/
|
NG2R51 -0.04 ! HG-CG
|
CG2R53 0.25 !
\
|
HGR52
0.13 !
CD2---NE2
NG2R50 -0.70 !
|
!
HD2

BOND C1' O4' C1' C2' C2' C3' C3'


BOND C1' H12' C2' H21' C2' H22' C3'
BOND C4' H41' C4' H42'
BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2
BOND CE1 HE1 CD2 HD2 CG HG
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1 CG CE1 C1'
ND1 CE1
IMPR CD2 CG NE2 HD2
CD2 NE2
IMPR CE1 ND1 NE2 HE1
CE1 NE2
IMPR CG CD2 ND1 HG
CG ND1
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
IC
C2'
C3'
C4'
O4'
IC
H12'
C1'
C2'
C3'
IC
H21'
C2'
C3'
C4'
IC
H22'
C2'
C3'
C4'
IC
H31'
C3'
C4'
O4'
IC
H32'
C3'
C4'
O4'
IC
H41'
C4'
O4'
C1'
IC
H42'
C4'
O4'
C1'
IC
C4'
O4'
C1'
ND1
IC
O4'
C1'
ND1
CE1
IC
C1'
ND1
CE1
NE2
IC
ND1
CE1
NE2
CD2
IC
CE1
NE2
CD2
CG
IC
HE1
CE1
NE2
CD2
IC
CE1
NE2
CD2
HD2
IC
NE2
CD2
CG
HG
PATC FIRS NONE LAST NONE

C4' C4' O4' C1' ND1


H31' C3' H32'
CG CG ND1
CG
CG
ND1
CD2
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

C1'
HD2
HE1
HG
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

324.92
33.390
268.35
82.530
204.06
155.99
276.70
132.30
220.70
256.98
180.00
181.56
0.34
0.00
180.40
179.83
178.45

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

RESI THMI
0.00 ! C8H12N2O thf-ch3-imidazole
! C5' has been declared as CN8, and C3' as CN7, for compatibility
! with DNA, but these carbons are rigorously CG331 and CG321 respectively

! Atom types for aliphatic hydrogens based on nucleotide


GROUP
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
GROUP !
ATOM CG
ATOM HG
ATOM CD2
ATOM HD2
ATOM ND1
ATOM CE1
ATOM HE1
ATOM NE2

! Sugar:
OG3C51
CG3C51
HGA1
CG3C51
HGA1

BOND C1'
BOND C1'
BOND C4'
BOND ND1
BOND CE1
DOUBLE CG

O4'
H12'
H42'
CE1
HE1
CD2

IMPR
IMPR
IMPR
IMPR
! ic
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

transferred from thf


-0.40 ! Note: has 2 asymmetric carbons.
0.11 ! Abs. config is arbitrary.
0.09
0.11 !
H52' H53'
0.09 !
\ /
! H51'-C5' O4' Imidazole
-0.18 !
\ / \ /
0.09 ! H42'--C4' C1'--H12'
0.09 !
|
|
! H31'--C3'--C2'--H21'
-0.18 !
/
\
0.09 !
H32'
H22'
0.09

CG331
-0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
Imidazole: transferred from isolated imidazole (IMIA)
CG2R51 -0.05 !
C1'
HE1
HGR52
0.09 !
\
/
CG2R51
0.22 !
ND1---CE1
HGR52
0.10 !
/
||
NG2R51 -0.04 ! HG-CG
||
CG2R53
0.25 !
\\
||
HGR52
0.13 !
CD2---NE2
NG2R50 -0.70 !
|
!
HD2
C1' C2' C2'
C2' H21' C2'
C4' C5' C5'
NE2 CD2 CG
CD2 HD2 CG
CE1 NE2

C3' C3' C4' C4' O4' C1' ND1


H22' C3' H31' C3' H32'
H51' C5' H52' C5' H53'
ND1
HG

ND1 CG CE1 C1'


ND1 CE1
CD2 CG NE2 HD2
CD2 NE2
CE1 ND1 NE2 HE1
CE1 NE2
CG CD2 ND1 HG
CG ND1
table for thfim, from Nicolas:
C1'
C2'
C3'
C4'
C2'
C3'
C4'
O4'
H12'
C1'
C2'
C3'
H21'
C2'
C3'
C4'
H22'
C2'
C3'
C4'
H31'
C3'
C4'
O4'
H32'
C3'
C4'
O4'
C5'
C4'
O4'
C1'
H51'
C5'
C4'
O4'
H52'
C5'
C4'
O4'
H53'
C5'
C4'
O4'
H42'
C4'
O4'
C1'
C4'
O4'
C1'
ND1
O4'
C1'
ND1
CE1
C1'
ND1
CE1
NE2
ND1
CE1
NE2
CD2

CG
CG
ND1
CD2
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

C1'
HD2
HE1
HG
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

324.92 0.0 0.0


33.390 0.0 0.0
268.35 0.0 0.0
82.530 0.0 0.0
204.06 0.0 0.0
155.99 0.0 0.0
276.70 0.0 0.0
132.30 0.0 0.0
-179.98 0.0 0.0
-59.66 0.0 0.0
59.68 0.0 0.0
220.70 0.0 0.0
256.98 0.0 0.0
180.00 0.0 0.0
181.56 0.0 0.0
0.34 0.0 0.0

IC
CE1
IC
HE1
IC
CE1
IC
NE2
PATC FIRS NONE

NE2
CD2
CE1
NE2
NE2
CD2
CD2
CG
LAST NONE

RESI THFC

CG
CD2
HD2
HG

0.0
0.0
0.0
0.0

0.0 0.00 0.0 0.0


0.0 180.40 0.0 0.0
0.0 179.83 0.0 0.0
0.0 178.45 0.0 0.0

0.00 ! C5H10O2 THF-3'-OH-4'-CH3

! Atom types for aliphatic hydrogens based on nucleotide


GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
BOND C1'
BOND C3'
BOND C1'
BOND C2'
BOND C3'
BOND C4'
BOND C5'
BOND O3'

OG3C51
CG3C52
HGA2
HGA2
CG3C51
HGA1

-0.40
0.02
0.09
0.09
0.11
0.09

! Note: has 2 asymmetric carbons.


! Abs. config is arbitrary.

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

HGA1
CG3C51
OG311
HGP1

0.09
0.14
-0.65
0.42

CG331
HGA3
HGA3
HGA3
O4' C1'
O3'
H11'
H21'
H31'
H42'
H51'
H32'

-0.27
0.09
0.09
0.09
C2' C2' C3' C3' C4' C4' O4' C4' C5'

!
H52' H53'
!
\ /
! H51'-C5' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
!
H32'

C1' H12'
C2' H22'
C5' H52'

IC C4' O4' C1' C2'


IC C2' O4' *C1' H11'
IC C2' O4' *C1' H12'
IC C1' O4' C4' C3'
IC C3' O4' *C4' C5'
IC C3' O4' *C4' H42'
IC C3' C1' *C2' H21'
IC C3' C1' *C2' H22'
IC C2' C4' *C3' O3'
IC C2' C4' *C3' H31'
IC C4' C3' O3' H32'
IC O4' C4' C5' H51'
IC H51' C4' *C5' H52'
IC H51' C4' *C5' H53'
PATC FIRS NONE LAST NONE
RESI TH5P
e -2)

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5' H53'
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
120.00
-120.00
180.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
180.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

-2.00 ! C5H9O5P 5'-phosphate-methyl-tetrahydrofuran (phosphat


! Atom types for aliphatic hydrogens based on nucleotid

GROUP
ATOM O4'
ATOM C1'
ATOM H1'
ATOM H1''
ATOM C4'
ATOM H4''
GROUP
ATOM C2'
ATOM H2'
ATOM H2''
GROUP
ATOM C3'
ATOM H3'
ATOM H3''
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM O5'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

OG3C51
CG3C52
HGA2
HGA2
CG3C51
HGA1

-0.40
0.02
0.09
0.09
0.11
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
!
O1P (-2)
!
||
! O2P==P==O2P
!
|
! H5'' O5'
!
\ |
! H5'--C5' O4' H1'
!
\ / \ /
!
H4'--C4' C1'--H1''
!
|
|
!
H3'--C3'--C2'--H2'
!
/
\
!
H3''
H2''

C1' O4' C1' C2' C2'


C1' H1' C1' H1'' C2'
C4' H4'' C5' H5' C5'
P
O2P P
O3P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H1'
C1'
C2'
H1''
C1'
C2'
H2'
C2'
C3'
H2''
C2'
C3'
H3'
C3'
C4'
H3''
C3'
C4'
H4''
C4'
O4'
C5'
C4'
O4'
H51'
C5'
C4'
H52'
C5'
C4'
O4'
C4'
C5'
C4'
C5'
O5'
C5'
O5'
P
C5'
O5'
P
C5'
O5'
P
FIRS NONE LAST NONE

RESI TH5H
-2)

C3' C3' C4' C4' O4' C4' C5'


H2' C2' H2'' C3' H3' C3' H3''
H5'' C5' O5' O5' P
P
O1P
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
O4'
C1'
C1'
O4'
O4'
O5'
P
O1P
O2P
O3P

1.4416
1.4471
1.5328
1.5200
1.5321
1.1099
1.1111
1.1135
1.1076
1.1127
1.1069
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0

109.61
106.74
103.38
102.18
105.43
113.03
111.16
109.13
113.49
108.68
112.41
106.71
108.43
110.48
110.01
0.0
0.0
0.0
0.0
0.0

0.45
-21.92
33.49
-34.11
21.23
-141.96
93.50
-81.76
155.97
81.68
-156.66
-95.75
144.82
180.00
-60.00
60.00
180.0
-60.0
180.0
60.0

106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
105.43
105.43
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0

1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
1.4416
1.4416
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0

0.00 ! C5H10O2 5'-hydroxy-methyl-tetrahydrofuran (phosphate


! Atom types for aliphatic hydrogens based on nucleotid

e
GROUP
ATOM O4' OG3C51
ATOM C1' CG3C52

-0.40 ! Note: has 1 asymmetric carbon.


0.02 ! Abs. config is arbitrary.

ATOM H1'
ATOM H1''
ATOM C4'
ATOM H4''
GROUP
ATOM C2'
ATOM H2'
ATOM H2''
GROUP
ATOM C3'
ATOM H3'
ATOM H3''
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM O5'
ATOM H5T

HGA2
HGA2
CG3C51
HGA1

CG3C52
HGA2
HGA2

0.09
0.09 !
H5T
0.11 !
/
0.09 ! H5'' O5'
!
\ |
-0.18 ! H5'--C5' O4' H1'
0.09 !
\ / \ /
0.09 !
H4'--C4' C1'--H1''
!
|
|
-0.18 !
H3'--C3'--C2'--H2'
0.09 !
/
\
0.09 !
H3''
H2''

CG321
HGA2
HGA2
OG311
HGP1

0.05
0.09
0.09
-0.65
0.42

CG3C52
HGA2
HGA2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3''
BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

C4'
O4'
O4'
C1'
C1'
C2'
C2'
C3'
C3'
C4'
H1'
C1'
H1''
C1'
H2'
C2'
H2''
C2'
H3'
C3'
H3''
C3'
H4''
C4'
C5'
C4'
H5'
C5'
H5''
C5'
O4'
C4'
C4'
C5'
FIRS NONE LAST

RESI T5PH
te -1)

C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C3'
C4'
C4'
O4'
O4'
C4'
C4'
C5'
O5'
NONE

C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
O4'
C1'
C1'
O4'
O4'
O5'
H5T

1.4416
1.4471
1.5328
1.5200
1.5321
1.1099
1.1111
1.1135
1.1076
1.1127
1.1069
1.1127
1.5325
1.1092
1.1104
0.0
0.0

109.61
106.74
103.38
102.18
105.43
113.03
111.16
109.13
113.49
108.68
112.41
106.71
108.43
110.48
110.01
0.0
0.0

0.45
-21.92
33.49
-34.11
21.23
-141.96
93.50
-81.76
155.97
81.68
-156.66
-95.75
144.82
180.00
-60.00
60.00
180.0

1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
1.4416
1.4416
1.4471
1.4471
1.4416
1.4416
0.0
0.0

-1.00 ! C5H10O5P 5'-phosphate-methyl-tetrahydrofuran (phospha

! Atom types for aliphatic hydrogens based on nucleotide


GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM O5'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
ATOM H5T
GROUP
ATOM O4'
ATOM C1'

106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
105.43
105.43
109.61
109.61
108.43
108.43
0.0
0.0

CG321
HGA2
HGA2
OG303
PG1
OG2P1
OG2P1
OG311
HGP1
OG3C51
CG3C52

-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.

!
O1P
H5T
!
||
/
! O2P==P==O3P
!
|
!
O5'
!
|
! H5'' |
-0.40 !
\ |
0.02 ! H5'--C5' O4' H1'

ATOM H1'
ATOM H1''
ATOM C4'
ATOM H4''
GROUP
ATOM C2'
ATOM H2'
ATOM H2''
GROUP
ATOM C3'
ATOM H3'
ATOM H3''
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

HGA2
HGA2
CG3C51
HGA1

0.09
0.09
0.11
0.09

CG3C52
HGA2
HGA2

!
!
!
!
!
-0.18 !
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

\ / \ /
H4'--C4' C1'--H1''
|
|
H3'--C3'--C2'--H2'
/
\
H3''
H2''

C1' O4' C1' C2' C2'


C1' H1' C1' H1'' C2'
C4' H4'' C5' H5' C5'
P
O2P P
O3P O3P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H1'
C1'
C2'
H1''
C1'
C2'
H2'
C2'
C3'
H2''
C2'
C3'
H3'
C3'
C4'
H3''
C3'
C4'
H4''
C4'
O4'
C5'
C4'
O4'
H51'
C5'
C4'
H52'
C5'
C4'
O4'
C4'
C5'
O4'
C4'
C5'
O4'
C4'
C5'
C4'
C5'
O5'
C5'
O5'
P
C5'
O5'
P
C5'
O5'
P
O5'
P
O3P
FIRS NONE LAST NONE

RESI TH3P
ate -2)

C3'
H2'
H5''
H5T
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
O4'
C1'
C1'
O4'
O4'
O5'
H5'
H5''
P
O1P
O2P
O3P
H5T

C3' C4' C4' O4' C4' C5'


C2' H2'' C3' H3' C3' H3''
C5' O5' O5' P
P
O1P
1.4416
1.4471
1.5328
1.5200
1.5321
1.1099
1.1111
1.1135
1.1076
1.1127
1.1069
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

109.61
106.74
103.38
102.18
105.43
113.03
111.16
109.13
113.49
108.68
112.41
106.71
108.43
110.48
110.01
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.45
-21.92
33.49
-34.11
21.23
-141.96
93.50
-81.76
155.97
81.68
-156.66
-95.75
144.82
180.00
-60.00
60.0
180.0
-60.0
180.0
-60.0
180.0
60.0
180.0

1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
1.4416
1.4416
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

-2.00 ! C4H7O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosph


! used to fit epsilon

! Atom types for aliphatic hydrogens based on nucleotide


GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'

106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
105.43
105.43
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

!
!
!
!
!
-0.18 !
0.09 !
0.09 !

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|

GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

CG3C51
HGA1

! O1P==P==O2P
-0.09 !
||
0.09 !
O3P (-2)

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

C1' O4' C1' C2' C2'


C1' H11' C1' H12' C2'
C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3P
P
O3'
FIRS NONE LAST NONE

RESI T3PH

C3'
H21'
O1P
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C3'
C3'
C3'

C3' C4' C4' O4' C3'


C2' H22' C3' H31' C4'
P
O2P P
O3P
1.4055 108.09 23.45
1.4127 106.18
3.96
1.5457 103.11 -26.93
1.5346 100.86 41.73
1.5211 103.15 -41.62
1.0856 111.62 123.53
1.0818 113.32 -114.11
1.0846 110.65 91.68
1.0822 110.88 -148.45
1.0806 113.53 162.89
1.0891 110.89 77.76
1.0808 108.72 -162.12
1.4028 110.98 -77.39
0.0
0.0 180.00
0.0
0.0 -60.0
0.0
0.0 180.0
0.0
0.0
60.0

O3'
H41'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0

-1.00 ! C4H8O5P monoanionic 3'phosphate-tetrahydrofuran


! used to fit epsilon

! Atom types for aliphatic hydrogens based on nucleotide


GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3T
ATOM H3T

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0

OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG311
HGP1

0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
! O1P==P==O2P
!
|
!
O3T (-1)
!
\
!
H3T

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'

BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1' H11' C1' H12' C2'


C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3T
P
O3'
H3T
O3T
P

H21'
O1P
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C3'
C3'
C3'
O3'

C2' H22' C3' H31' C4'


P
O2P P
O3T O3T
1.4055 108.09 23.45
1.4127 106.18
3.96
1.5457 103.11 -26.93
1.5346 100.86 41.73
1.5211 103.15 -41.62
1.0856 111.62 123.53
1.0818 113.32 -114.11
1.0846 110.65 91.68
1.0822 110.88 -148.45
1.0806 113.53 162.89
1.0891 110.89 77.76
1.0808 108.72 -162.12
1.4028 110.98 -77.39
0.0
0.0 180.00
0.0
0.0 -60.0
0.0
0.0
60.0
0.0
0.0 180.0
0.0
0.0 180.0

H41'
H3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0

PATC FIRS NONE LAST NONE


RESI R3PH

-1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran


! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA

! Atom types for aliphatic hydrogens based on RNA nucleotide


GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM O2'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3T
ATOM H3T
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC

OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG311
HGP1

0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2'
!
|
|
! O1P==P==O2P H22'
!
|
!
O3T (-1)
!
\
!
H3T

C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4'
C4' H42' O3' P
P
O1P P
O2P P
O3T O3T H3T
C4'
O4'
C1'
C2'
1.4055 108.09 23.45 106.18
O4'
C1'
C2'
C3'
1.4127 106.18
3.96 103.11
C1'
C2'
C3'
C4'
1.5457 103.11 -26.93 100.86
C2'
C3'
C4'
O4'
1.5346 100.86 41.73 103.15
C3'
C4'
O4'
C1'
1.5211 103.15 -41.62 108.09
H11'
C1'
C2'
C3'
1.0856 111.62 123.53 103.11

H41'
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H12'
H21'
O2'
H22'
H31'
H41'
H42'
O3'
P
O1P
O2P
O3T
H3T

C1'
C2'
C2'
O2'
C3'
C4'
C4'
C3'
O3'
P
P
P
O3T

C2'
C3'
C3'
C2'
C4'
O4'
O4'
C4'
C3'
O3'
O3'
O3'
P

C3'
C4'
C4'
C3'
O4'
C1'
C1'
O4'
C4'
C3'
C3'
C3'
O3'

1.0818
1.0846
1.0822
1.0822
1.0806
1.0891
1.0808
1.4028
0.0
0.0
0.0
0.0
0.0

113.32
110.65
110.88
110.88
113.53
110.89
108.72
110.98
0.0
0.0
0.0
0.0
0.0

-114.11
91.68
283.41
0.00
162.89
77.76
-162.12
-77.39
180.00
-60.0
60.0
180.0
180.0

103.11
100.86
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0
0.0

1.5346
1.5211
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0

PATC FIRS NONE LAST NONE


RESI A3PH

-1.00 ! C4H8O6P monoanionic 3'phosphate-tetrahydrofuran


! with O2' hydroxyl in an arabinose (beta) conformation

.
! The furanose ring contains atom type CG311 , specific of arabinose
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H22'
ATOM O2'
ATOM H21'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3T
ATOM H3T
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG311
HGP1

0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

!
!
!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2' O2' is beta
!
|
|
! O1P==P==O2P H22'
!
|
!
O3T (-1)
!
\
!
H3T

C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4'
C4' H42' O3' P
P
O1P P
O2P P
O3T O3T H3T
C4'
O4'
C1'
C2'
1.4055 108.09 23.45 106.18
O4'
C1'
C2'
C3'
1.4127 106.18
3.96 103.11
C1'
C2'
C3'
C4'
1.5457 103.11 -26.93 100.86
C2'
C3'
C4'
O4'
1.5346 100.86 41.73 103.15
C3'
C4'
O4'
C1'
1.5211 103.15 -41.62 108.09
H11'
C1'
C2'
C3'
1.0856 111.62 123.53 103.11
H12'
C1'
C2'
C3'
1.0818 113.32 -114.11 103.11
H22'
C2'
C3'
C4'
1.0822 110.88 283.41 100.86
O2'
C2'
C3'
C4'
1.0846 110.65 120.00 100.86
H21'
O2'
C2'
C3'
1.0822 110.88 120.00 100.86
H31'
C3'
C4'
O4'
1.0806 113.53 162.89 103.15
H41'
C4'
O4'
C1'
1.0891 110.89 77.76 108.09

H41'
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.5211
1.4055
1.4127

IC
IC
IC
IC
IC
IC
IC
PATC

H42'
C4'
O3'
C3'
P
O3'
O1P
P
O2P
P
O3T
P
H3T
O3T
FIRS NONE LAST

RESI T3PM
ate -1)

O4'
C4'
C3'
O3'
O3'
O3'
P
NONE

C1'
O4'
C4'
C3'
C3'
C3'
O3'

1.0808 108.72 -162.12 108.09


1.4028 110.98 -77.39 103.15
0.0
0.0 180.00
0.0
0.0
0.0 -60.0
0.0
0.0
0.0
60.0
0.0
0.0
0.0 180.0
0.0
0.0
0.0 180.0
0.0

1.4127
1.4055
0.0
0.0
0.0
0.0
0.0

-1.00 ! C5H10O5P 3'phosphate-hydroxyl-tetrahydrofuran (phosph


! capped with a methyl group. This is to investigate th

e differences
! between BI and BII forms of DNA
! C3T is defined as CG321 to miminck DNA
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3T
ATOM C3T
ATOM H3T1
ATOM H3T2
ATOM H3T3
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1'
C1'
C4'
C3T
C4'
O4'
C1'
C2'
C3'
H11'
H12'
H21'
H22'
H31'
H41'
H42'
O3'
P
C3'

OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1

0.01
0.09

OG303
PG1
OG2P1
OG2P1
OG303
CG331
HGA3
HGA3
HGA3

-0.57
1.50
-0.78
-0.78
-0.57
-0.17
0.09
0.09
0.09

! Note: has 1 asymmetric carbon.


! Abs. config is arbitrary.
!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
! O1P==P==O2P
!
|
!
O3T (-1)
!
\
!
C3T--H3T3
!
/ \
!
H3T1 H3T2

O4' C1' C2' C2' C3' C3' C4' C4' O4' C3'
H11' C1' H12' C2' H21' C2' H22' C3' H31' C4'
H42' O3' P
P
O1P P
O2P P
O3T O3T
H3T1 C3T H3T2 C3T H3T3
O4'
C1'
C2'
1.4055 108.09 23.45
C1'
C2'
C3'
1.4127 106.18
3.96
C2'
C3'
C4'
1.5457 103.11 -26.93
C3'
C4'
O4'
1.5346 100.86 41.73
C4'
O4'
C1'
1.5211 103.15 -41.62
C1'
C2'
C3'
1.0856 111.62 123.53
C1'
C2'
C3'
1.0818 113.32 -114.11
C2'
C3'
C4'
1.0846 110.65 91.68
C2'
C3'
C4'
1.0822 110.88 -148.45
C3'
C4'
O4'
1.0806 113.53 162.89
C4'
O4'
C1'
1.0891 110.89 77.76
C4'
O4'
C1'
1.0808 108.72 -162.12
C3'
C4'
O4'
1.4028 110.98 -77.39
O3'
C3'
C4'
0.0000 000.00 180.00
O3'
P
O3T
0.0000 000.00 -95.22

O3'
H41'
C3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
000.00
000.00

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0000
0.0000

IC
IC
IC
IC
IC
IC
PATC

O3T
O3'
O3T
O3'
C3T
O3T
H3T1
C3T
H3T2
C3T
H3T3
C3T
FIRS NONE LAST

RESI TM3P
hate -2)

*P
*P
P
O3T
O3T
O3T
NONE

O1P
O2P
O3'
P
P
P

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

000.00
000.00
000.00
000.00
000.00
000.00

-115.82
115.90
-46.90
180.00
60.00
-60.00

000.00
000.00
000.00
000.00
000.00
000.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

-2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosp

! This is the DNA version (the RNA version is RM3P, see below)
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1'
C1'
O3'
C4'
C4'
O4'
C1'
C2'
C3'
H11'
H12'
H21'
H22'
H31'
C5'
H51'
H52'
H53'
H42'
O3'
P

OG3C51
CG3C52
HGA2
HGA2
CG3C51
HGA1

-0.40
0.02
0.09
0.09
0.11
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1

-0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

O4' C1'
H11' C1'
P
P
C5' C5'
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C3'
C4'
C5'
C5'
C5'
C4'
C3'
O3'

C2'
H12'
O1P
H51'
C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C3'
C4'
O4'
C4'
C4'
C4'
O4'
C4'
C3'

! Note: has 2 asymmetric carbons.


! Abs. config is arbitrary.
!
H52' H53'
!
\ /
! H51'-C5' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
! O1P==P==O2P
!
||
!
O3P (-2)

C2'
C2'
P
C5'

C3'
H21'
O2P
H52'
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
O4'
O4'
O4'
C1'
O4'
C4'

C3' C4' C4' O4' C3'


C2' H22' C3' H31' C4'
P
O3P
C5' H53'
1.4055 108.09 23.45
1.4127 106.18
3.96
1.5457 103.11 -26.93
1.5346 100.86 41.73
1.5211 103.15 -41.62
1.0856 111.62 123.53
1.0818 113.32 -114.11
1.0846 110.65 91.68
1.0822 110.88 -148.45
1.0806 113.53 162.89
0.0000 000.00 77.76
0.0
0.0 180.0
0.0
0.0 -60.0
0.0
0.0
60.0
1.0808 108.72 -162.12
1.4028 110.98 -77.39
0.0
0.0 180.00

O3'
H42'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
0.0
0.0
0.0
108.09
103.15
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
0.0
0.0
0.0
1.4127
1.4055
0.0

IC
IC
IC
PATC

O1P
P
O2P
P
O3P
P
FIRS NONE LAST

RESI RM3P
hate -2)

O3'
O3'
O3'
NONE

C3'
C3'
C3'

0.0
0.0
0.0

0.0
0.0
0.0

-60.0
180.0
60.0

0.0
0.0
0.0

0.0
0.0
0.0

-2.00 ! C5H9O5P 4'-methyl,3'-phosphate tetrahydrofuran (phosp

! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to
! allow for the determination of the influence of the ring dihedrals on the
! sugar puckering energetics in the absence of the 2' hydroxyl
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1'
C1'
O3'
C4'
C4'
O4'
C1'
C2'
C3'
H11'
H12'
H21'
H22'
H31'
C5'
H51'
H52'
H53'
H42'
O3'
P
O1P

OG3C51
CG3C52
HGA2
HGA2
CG3C51
HGA1

-0.40 ! Note: has 2 asymmetric carbons.


0.02 ! Abs. config is arbitrary.
0.09
0.09
0.11
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1

-0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

O4' C1'
H11' C1'
P
P
C5' C5'
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C3'
C4'
C5'
C5'
C5'
C4'
C3'
O3'
P

C2'
H12'
O1P
H51'
C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C3'
C4'
O4'
C4'
C4'
C4'
O4'
C4'
C3'
O3'

C2'
C2'
P
C5'

C3'
H21'
O2P
H52'
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
O4'
O4'
O4'
C1'
O4'
C4'
C3'

C3' C4' C4' O4' C3'


C2' H22' C3' H31' C4'
P
O3P
C5' H53'
1.4055 108.09 23.45
1.4127 106.18
3.96
1.5457 103.11 -26.93
1.5346 100.86 41.73
1.5211 103.15 -41.62
1.0856 111.62 123.53
1.0818 113.32 -114.11
1.0846 110.65 91.68
1.0822 110.88 -148.45
1.0806 113.53 162.89
0.0000 000.00 77.76
0.0
0.0
180.0
0.0
0.0
-60.0
0.0
0.0
60.0
1.0808 108.72 -162.12
1.4028 110.98 -77.39
0.0
0.0 180.00
0.0
0.0 -60.0

O3'
H42'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
0.0
0.0
0.0
108.09
103.15
0.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
0.0
0.0
0.0
1.4127
1.4055
0.0
0.0

IC O2P
P
O3'
IC O3P
P
O3'
PATC FIRS NONE LAST NONE
RESI T2FU
GROUP
ATOM O4'
ATOM C1'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H22'
ATOM F2'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

C3'
C3'

0.0
0.0

0.0
0.0

180.0
60.0

0.0
0.0

0.0
0.0

-2.00 ! C4H6FO5P THF with PO3 on c3, F (beta, up) on c2


! Charge distribution is preliminary
OG3C51
CG3C52
CG3C52
HGA2
HGA2
HGA2
HGA2

-0.40
0.02
0.02
0.09
0.09
0.09
0.09

CG3C51
HGA1
FGA1

0.14
0.09
-0.23

CG3C51
HGA1

-0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

! Note: has 2 asymmetric carbons.


! Abs. config is arbitrary.
!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--F2' (beta)
!
/
\
!
O3'
H22'
!
|
! O1P==P==O2P
!
||
!
O3P (-2)

C1' O4' C1' C2' C2'


C1' H11' C1' H12' C2'
C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
F2'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3P
P
O3'
FIRS NONE LAST NONE

RESI TMFU
p) on c2'

C3' C3' C4' C4' O4' C3'


F2' C2' H22' C3' H31' C4'
O1P P
O2P P
O3P
C2'
1.4055 108.09 23.45
C3'
1.4127 106.18
3.96
C4'
1.5457 103.11 -26.93
O4'
1.5346 100.86 41.73
C1'
1.5211 103.15 -41.62
C3'
1.0856 111.62 123.53
C3'
1.0818 113.32 -114.11
C4'
1.0846 110.65 91.68
C4'
1.0822 110.88 -148.45
O4'
1.0806 113.53 162.89
C1'
1.0891 110.89 77.76
C1'
1.0808 108.72 -162.12
O4'
1.4028 110.98 -77.39
C4'
0.0
0.0 180.00
C3'
0.0
0.0 -60.0
C3'
0.0
0.0 180.0
C3'
0.0
0.0
60.0

O3'
H41'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0

-2.00 ! C5H8FO5P THF with ch3 on c4', opo3 on c3', F (beta, u


! Caution: Charges are preliminary. Charge on fluorine wa

s
! taken from Daxu Yin's thesis (monofluoroethane).
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'

OG3C51
CG3C52
HGA2
HGA2

-0.40 ! Note: has 3 asymmetric carbons.


0.02 ! Abs. config is arbitrary.
0.09
0.09 !
H52' H53'

ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H22'
ATOM F2'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'

CG3C51
HGA1

OG303
PG1
OG2P1
OG2P1
OG2P1

0.11 !
\ /
0.09 ! H51'-C5' O4' H11'
!
\ / \ /
0.19 ! H42'--C4' C1'--H12'
0.09 !
|
|
-0.28 ! H31'--C3'--C2'--F2' (beta)
!
/
\
-0.09 !
O3'
H22'
0.09 !
|
! O1P==P==O2P
-0.40 !
||
1.10 !
O3P (-2)
-0.90
-0.90
-0.90

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG3C51
HGA1
FGA1
CG3C51
HGA1

BOND C1' O4' C1' C2' C2'


BOND C1' H11' C1' H12'
BOND C2' H22' C2' F2'
BOND C3' O3' C3' H31'
BOND O3' P
P
O1P P
BOND C4' C5' C5' H51' C5'
! The following IC table is a
IC
C1'
C2'
C3'
IC
C2'
C3'
C4'
IC
H11'
C1'
C2'
IC
H12'
C1'
C2'
IC
F2'
C2'
C3'
IC
H22'
C2'
C3'
IC
H31'
C3'
C4'
IC
O3'
C3'
C4'
IC
P
O3'
C3'
IC
O1P
P
O3'
IC
O2P
P
O3'
IC
O3P
P
O3'
IC
C5'
C4'
O4'
IC
H51'
C5'
C4'
IC
H52'
C5'
C4'
IC
H53'
C5'
C4'
IC
H42'
C4'
O4'

C3' C3' C4' C4' O4'

O2P P O3P
H52' C5' H53' C4' H42'
guess from thfohch3 (Nicolas):
C4'
0.0 0.0 330.81 0.0 0.0
O4'
0.0 0.0 39.77 0.0 0.0
C3'
0.0 0.0 129.38 0.0 0.0
C3'
0.0 0.0 251.29 0.0 0.0
C4'
0.0 0.0 89.74 0.0 0.0
C4'
0.0 0.0 209.60 0.0 0.0
O4'
0.0 0.0 161.48 0.0 0.0
O4'
0.0 0.0 280.72 0.0 0.0
C4'
0.0 0.0 180.00 0.0 0.0
C3'
0.0 0.0 180.00 0.0 0.0
C3'
0.0 0.0 60.00 0.0 0.0
C3'
0.0 0.0 -60.00 0.0 0.0
C1'
0.0 0.0 87.60 0.0 0.0
O4'
0.0 0.0 176.37 0.0 0.0
O4'
0.0 0.0 56.84 0.0 0.0
O4'
0.0 0.0 297.06 0.0 0.0
C1'
0.0 0.0 207.55 0.0 0.0

PATC FIRS NONE LAST NONE


RESI T2FD
GROUP
ATOM O4'
ATOM C1'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'

-2.00 ! C4H6FO5P THF with PO3 on c3, F (alpha, down) on c2


! Charge distribution is preliminary
OG3C51
CG3C52
CG3C52
HGA2
HGA2
HGA2
HGA2
CG3C51

-0.40
0.02
0.02
0.09
0.09
0.09
0.09

!
!
!
!
!
0.14 !

! Note: has 2 asymmetric carbons.


! Abs. config is arbitrary.
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--F2' (alpha)
/
\

ATOM H21'
ATOM F2'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

HGA1
FGA1
CG3C51
HGA1

0.09 !
O3'
H22'
-0.23 !
|
! O1P==P==O2P
-0.09 !
||
0.09 !
O3P (-2)

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

C1' O4' C1' C2' C2'


C1' H11' C1' H12' C2'
C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
F2'
C2'
C3'
H21'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3P
P
O3'
FIRS NONE LAST NONE

C3' C3' C4' C4' O4' C3'


F2' C2' H21' C3' H31' C4'
O1P P
O2P P
O3P
C2'
1.4055 108.09 23.45
C3'
1.4127 106.18
3.96
C4'
1.5457 103.11 -26.93
O4'
1.5346 100.86 41.73
C1'
1.5211 103.15 -41.62
C3'
1.0856 111.62 123.53
C3'
1.0818 113.32 -114.11
C4'
1.0846 110.65 -148.45
C4'
1.0822 110.88 91.68
O4'
1.0806 113.53 162.89
C1'
1.0891 110.89 77.76
C1'
1.0808 108.72 -162.12
O4'
1.4028 110.98 -77.39
C4'
0.0
0.0 180.00
C3'
0.0
0.0 -60.0
C3'
0.0
0.0 180.0
C3'
0.0
0.0
60.0

O3'
H41'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0

RESI TMFD
-2.00 ! C5H8FO5P Flourine on C2' (alpha, down) with ch3 on c4
', opo3 on c3', oh on c2'
! Charge distribution is preliminary
GROUP
ATOM O4' OG3C51 -0.40 ! Note: has 3 asymmetric carbons.
ATOM C1' CG3C52
0.02 ! Abs. config is arbitrary.
ATOM H11' HGA2
0.09
ATOM H12' HGA2
0.09 !
H52' H53'
ATOM C4' CG3C51
0.11 !
\ /
ATOM H42' HGA1
0.09 ! H51'-C5' O4' H11'
GROUP
!
\ / \ /
ATOM C2' CG3C51
0.19 ! H42'--C4' C1'--H12'
ATOM H21' HGA1
0.09 !
|
|
ATOM F2' FGA1
-0.28 ! H31'--C3'--C2'--F2' (alpha)
GROUP
!
/
\
ATOM C3' CG3C51 -0.09 !
O3'
H22'
ATOM H31' HGA1
0.09 !
|
GROUP
! O1P==P==O2P
ATOM O3' OG303
-0.40 !
||
ATOM P
PG1
1.10 !
O3P (-2)
ATOM O1P OG2P1
-0.90
ATOM O2P OG2P1
-0.90
ATOM O3P OG2P1
-0.90
GROUP
ATOM C5' CG331
-0.27
ATOM H51' HGA3
0.09

ATOM H52' HGA3


ATOM H53' HGA3

0.09
0.09

BOND C1' O4' C1' C2' C2'


BOND C1' H11' C1' H12'
BOND C2' F2' C2' H21'
BOND C3' O3' C3' H31'
BOND O3' P
P
O1P P
BOND C4' C5' C5' H51' C5'
! The following IC table is a
IC
C1'
C2'
C3'
IC
C2'
C3'
C4'
IC
H11'
C1'
C2'
IC
H12'
C1'
C2'
IC
H21'
C2'
C3'
IC
F2'
C2'
C3'
IC
H31'
C3'
C4'
IC
O3'
C3'
C4'
IC
P
O3'
C3'
IC
O1P
P
O3'
IC
O2P
P
O3'
IC
O3P
P
O3'
IC
C5'
C4'
O4'
IC
H51'
C5'
C4'
IC
H52'
C5'
C4'
IC
H53'
C5'
C4'
IC
H42'
C4'
O4'
PATC FIRS NONE LAST NONE

C3' C3' C4' C4' O4'

O2P P O3P
H52' C5' H53' C4' H42'
guess from thfohch3 (Nicolas):
C4'
0.0 0.0 330.81 0.0 0.0
O4'
0.0 0.0 39.77 0.0 0.0
C3'
0.0 0.0 129.38 0.0 0.0
C3'
0.0 0.0 251.29 0.0 0.0
C4'
0.0 0.0 89.74 0.0 0.0
C4'
0.0 0.0 209.60 0.0 0.0
O4'
0.0 0.0 161.48 0.0 0.0
O4'
0.0 0.0 280.72 0.0 0.0
C4'
0.0 0.0 180.00 0.0 0.0
C3'
0.0 0.0 180.00 0.0 0.0
C3'
0.0 0.0 60.00 0.0 0.0
C3'
0.0 0.0 -60.00 0.0 0.0
C1'
0.0 0.0 87.60 0.0 0.0
O4'
0.0 0.0 176.37 0.0 0.0
O4'
0.0 0.0 56.84 0.0 0.0
O4'
0.0 0.0 297.06 0.0 0.0
C1'
0.0 0.0 207.55 0.0 0.0

RESI ARMO
0.00
the beta configuration
GROUP
ATOM O4' OG3C51 -0.40
ATOM C1' CG3C52
0.02
ATOM H11' HGA2
0.09
ATOM H12' HGA2
0.09
ATOM C4' CG3C51
0.11
ATOM H42' HGA1
0.09
GROUP
ATOM C2' CG3C51
0.14
ATOM H22' HGA1
0.09
ATOM O2' OG311
-0.65
ATOM H21' HGP1
0.42
GROUP
ATOM C3' CG3C51
0.14
ATOM H31' HGA1
0.09
ATOM O3' OG311
-0.65
ATOM H32' HGP1
0.42
GROUP
ATOM C5' CG331
-0.27
ATOM H51' HGA3
0.09
ATOM H52' HGA3
0.09
ATOM H53' HGA3
0.09

! C5H10O3 ribose, thfch3ohoh, with the c2' hydroxyl in

BOND
BOND
BOND
BOND
BOND

C2' C3' C3' C4' C4' O4'

C1'
C1'
C2'
C3'
C4'

O4'
H11'
O2'
O3'
C5'

C1'
C1'
C2'
O3'
C5'

C2'
H12'
H22'
H32'
H51'

!
H52' H53'
!
\ /
! H51'-C5' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2'
!
|
|
(beta)
!
H32'
H22'
!

O2' H21'
C3' H31'
C5' H52' C5' H53' C4' H42'

! The following IC table is a guess from thfohch3 (Nicolas):


IC
C1'
C2'
C3'
C4'
0.0 0.0 330.81 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 39.77 0.0 0.0
IC
H11'
C1'
C2'
C3'
0.0 0.0 129.38 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 251.29 0.0 0.0
IC
O2'
C2'
C3'
C4'
0.0 0.0 89.74 0.0 0.0
IC
H21'
O2'
C2'
C3'
0.0 0.0 90.00 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 209.60 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 161.48 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 280.72 0.0 0.0
IC
H32'
O3'
C3'
C4'
0.0 0.0 44.72 0.0 0.0
IC
C5'
C4'
O4'
C1'
0.0 0.0 87.60 0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0 176.37 0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0 56.84 0.0 0.0
IC
H53'
C5'
C4'
O4'
0.0 0.0 297.06 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 207.55 0.0 0.0
PATC FIRS NONE LAST NONE
RESI THFA
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
GROUP !
ATOM CG
ATOM HG
ATOM CD2
ATOM HD2
ATOM ND1
ATOM CE1
ATOM HE1
ATOM NE2

OG3C51
CG3C51
HGA1
CG3C51
HGA1
CG3C52
HGA2
HGA2
HGA1
CG3C51
OG311
HGP1

0.00 !
!
-0.40 !
0.11
0.09 !
0.11 !
0.09 !
!
-0.18 !
0.09 !
0.09 !
!
0.09 !
0.14 !
-0.65 !
0.42

C8H12N2O2 THF-OH-CH3-IM
Note: has 3 asymmetric carbons.
Abs. config is arbitrary.
H52' H53'
\ /
H51'-C5' O4' Imidazole
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
H32'

CG331
-0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
Imidazole: transferred from isolated imidazole (IMIA)
CG2R51 -0.05 !
C1'
HE1
HGR52
0.09 !
\
/
CG2R51
0.22 !
ND1---CE1
HGR52
0.10 !
/
||
NG2R51 -0.04 ! HG-CG
||
CG2R53
0.25 !
\\
||
HGR52
0.13 !
CD2---NE2
NG2R50 -0.70 !
|
!
HD2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31'
BOND C5' H51' C5' H52' C5' H53'
BOND O3' H32'
BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1
BOND CE1 HE1 CD2 HD2 CG HG
DOUBLE CG CD2 CE1 NE2
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390

C4' C5'
C4' H42'

0.0 0.0
0.0 0.0

IC
H12'
IC
H21'
IC
H22'
IC
O3'
IC
H32'
IC
H31'
IC
H41'
IC
H42'
IC
C4'
IC
O4'
IC
C1'
IC
ND1
IC
CE1
IC
HE1
IC
CE1
IC
NE2
IC
C5'
IC
H51'
IC
H52'
IC
H53'
PATC FIRS NONE
RESI ARAO
2'
GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H22'
ATOM O2'
ATOM H21'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM H32'
BOND C1'
BOND C1'
BOND C4'
!Nicolas:
s
IC C4'
IC O4'
IC C1'
IC C2'
IC C3'
IC H11'
IC H12'
IC O2'
IC H21'
IC H22'
IC H31'
IC H41'

C1'
C2'
C2'
C3'
C2'
C3'
C3'
C4'
O3'
C3'
C3'
C4'
C4'
O4'
C4'
O4'
O4'
C1'
C1'
ND1
ND1
CE1
CE1
NE2
NE2
CD2
CE1
NE2
NE2
CD2
CD2
CG
C4'
O4'
C5'
C4'
C5'
C4'
C5'
C4'
LAST NONE

C3'
C4'
C4'
O4'
C2'
O4'
C1'
C1'
ND1
CE1
NE2
CD2
CG
CD2
HD2
HG
C1'
O4'
O4'
O4'

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

268.35 0.0 0.0


82.530 0.0 0.0
204.06 0.0 0.0
-93.14 0.0 0.0
-60.00 0.0 0.0
147.80 0.0 0.0
132.30 0.0 0.0
220.70 0.0 0.0
256.98 0.0 0.0
180.00 0.0 0.0
181.56 0.0 0.0
0.34 0.0 0.0
0.00 0.0 0.0
180.40 0.0 0.0
179.83 0.0 0.0
178.45 0.0 0.0
144.82 0.0 0.0
-179.98 0.0 0.0
-59.66 0.0 0.0
59.68 0.0 0.0

0.00 ! C4H8O3 arabinose sugar, oh alpha on c3', oh beta on c


OG3C51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.02
0.09
0.09
0.02
0.09
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

!
!
!
!
!
!
!
!
!
!
!
!

H41' O4' H11'


\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
O2'
|
|
(beta)
H32'
H22'

O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41'
H42' O2' H21' O3' H32'
the following IC are for thf-oh as optimized via ab initio calculation
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
O2'
C2'
C3'
C4'

C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C2'
C3'
C4'
O4'

C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C3'
C4'
O4'
C1'

1.4055
1.4127
1.5457
1.5346
1.5211
1.0856
1.0818
0.0000
0.0
1.0822
1.0806
1.0891

108.09
106.18
103.11
100.86
103.15
111.62
113.32
0.00
0.0
110.88
113.53
110.89

23.45
3.96
-26.93
41.73
-41.62
123.53
-114.11
91.68
-60.0
-148.45
162.89
77.76

106.18
103.11
100.86
103.15
108.09
103.11
103.11
0.0000
0.0
100.86
103.15
108.09

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
0.0000
0.0
1.5211
1.4055
1.4127

IC
IC
IC
PATC

H42'
C4'
O3'
C3'
H32'
O3'
FIRS NONE LAST

RESI ARIM
GROUP
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'
GROUP
ATOM C2'
ATOM H22'
ATOM O2'
ATOM H21'
GROUP !
ATOM CG
ATOM HG
ATOM CD2
ATOM HD2
ATOM ND1
ATOM CE1
ATOM HE1
ATOM NE2

O4'
C4'
C3'
NONE

C1'
O4'
C4'

1.0808 108.72 -162.12 108.09


1.4028 110.98 -77.39 103.15
0.9492 108.72 44.80 110.98

0.00 ! C7H10N2O2 arabinose sugar with imidazole


! transferred from thf
OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

-0.40
0.11
0.09
0.02
0.09
0.09

!
!
!
!
!
!
!
-0.18 !
0.09 !
0.09 !

H41' O4' Imidazole


\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
H32'
O2'
|
(beta)
H22'

CG3C51
0.14
HGA1
0.09
OG311
-0.65
HGP1
0.42
Imidazole: transferred from isolated imidazole (IMIA)
CG2R51 -0.05 !
C1'
HE1
HGR52
0.09 !
\
/
CG2R51
0.22 !
ND1---CE1
HGR52
0.10 !
/
||
NG2R51 -0.04 ! HG-CG
||
CG2R53
0.25 !
\\
||
HGR52
0.13 !
CD2---NE2
NG2R50 -0.70 !
|
!
HD2

BOND C1' O4' C1' C2' C2' C3' C3'


BOND C2' O2' C1' H12' C2' H22' C3'
BOND C4' H41' C4' H42'
BOND ND1 CE1 NE2 CD2 CG ND1
BOND CE1 HE1 CD2 HD2 CG HG
DOUBLE CG CD2 CE1 NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1 CG CE1 C1'
ND1 CE1
IMPR CD2 CG NE2 HD2
CD2 NE2
IMPR CE1 ND1 NE2 HE1
CE1 NE2
IMPR CG CD2 ND1 HG
CG ND1
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
IC
C2'
C3'
C4'
O4'
IC
H12'
C1'
C2'
C3'
IC
O2'
C2'
C3'
C4'
IC
H21'
O2'
C2'
C3'
IC
H22'
C2'
C3'
C4'
IC
H31'
C3'
C4'
O4'
IC
H32'
C3'
C4'
O4'
IC
H41'
C4'
O4'
C1'
IC
H42'
C4'
O4'
C1'
IC
C4'
O4'
C1'
ND1
IC
O4'
C1'
ND1
CE1
IC
C1'
ND1
CE1
NE2
IC
ND1
CE1
NE2
CD2

C4' C4' O4' C1' ND1


H31' C3' H32' O2' H21'

CG
CG
ND1
CD2

C1'
HD2
HE1
HG

1.532 101.886 324.92 0.0 0.0


0.0 0.0 33.390 0.0 0.0
0.0 0.0 268.35 0.0 0.0
0.0 0.0 82.530 0.0 0.0
0.0 0.0 -60.0 0.0 0.0
0.0 0.0 204.06 0.0 0.0
0.0 0.0 155.99 0.0 0.0
0.0 0.0 276.70 0.0 0.0
0.0 0.0 132.30 0.0 0.0
0.0 0.0 220.70 0.0 0.0
0.0 0.0 256.98 0.0 0.0
0.0 0.0 180.00 0.0 0.0
0.0 0.0 181.56 0.0 0.0
0.0 0.0 0.34 0.0 0.0

1.4127
1.4055
1.5211

IC
CE1
IC
HE1
IC
CE1
IC
NE2
PATC FIRS NONE
RESI AR3P
te -2)
GROUP
ATOM O4'
ATOM C1'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H22'
ATOM O2'
ATOM H21'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

NE2
CD2
CE1
NE2
NE2
CD2
CD2
CG
LAST NONE

0.0
0.0
0.0
0.0

0.0 0.00 0.0 0.0


0.0 180.40 0.0 0.0
0.0 179.83 0.0 0.0
0.0 178.45 0.0 0.0

-2.00 ! C4H7O6P arabinose sugar with phosphate on 3' (phospha


OG3C51
CG3C52
CG3C52
HGA2
HGA2
HGA2
HGA2

-0.40
0.02
0.02
0.09
0.09
0.09
0.09

CG3C51
HGA1
OG311
HGP1

!
H41' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H22' (alpha)
!
/
\
!
O3'
O2'
!
|
|
0.14 ! O1P==P==O2P H21'
0.09 !
||
-0.65 !
O3P (-2)
0.42

CG3C51
HGA1

-0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

C1' O4' C1' C2' C2'


C1' H11' C1' H12' C2'
C4' H42' O2' H21' O3'
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
O2'
C2'
C3'
H21'
O2'
C2'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3P
P
O3'
FIRS NONE LAST NONE

RESI RIBO
GROUP
ATOM O4'
ATOM C1'
ATOM C4'
ATOM H11'

CG
CD2
HD2
HG

C3' C3' C4' C4' O4' C3' O3'


O2' C2' H22' C3' H31' C4' H41'
P
P
O1P P
O2P P
O3P
C2'
1.4055 108.09
6.07 106.18
C3'
1.4127 106.18 -25.13 103.11
C4'
1.5457 103.11 33.40 100.86
O4'
1.5346 100.86 -30.20 103.15
C1'
1.5211 103.15 14.98 108.09
C3'
1.0856 111.62 91.77 103.11
C3'
1.0818 113.32 -144.31 103.11
C4'
1.0846 110.65 152.51 100.86
C3'
0.0
0.0
60.0
0.0
C4'
1.0822 110.88 -84.13 100.86
O4'
1.0806 113.53 87.99 103.15
C1'
1.0891 110.89 136.35 108.09
C1'
1.0808 108.72 -102.74 108.09
O4'
1.4028 110.98 -151.73 103.15
C4'
0.0
0.0 180.00
0.0
C3'
0.0
0.0 -60.0
0.0
C3'
0.0
0.0 180.0
0.0
C3'
0.0
0.0
60.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
0.0
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0

0.00 ! C4H8O3 ribose, both c2' and c3' hydroxyls are alpha
OG3C51
CG3C52
CG3C52
HGA2

-0.40
0.02
0.02
0.09

!
!
!
!

H41' O4' H11'


\ / \ /
H42'--C4' C1'--H12'
|
|

ATOM H12'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM O2'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM H32'

HGA2
HGA2
HGA2
CG3C51
HGA1
OG311
HGP1

0.09 !
0.09 !
0.09 !
!
0.14 !
0.09 !
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

H31'--C3'--C2'--H22'
/
\
O3'
O2'
|
|
H32'
H21'

BOND C1' O4' C1' C2' C2' C3'


BOND C1' H11' C1' H12' C2' O2'
BOND C4' H42' O2' H22' O3' H32'
!Nicolas: the following IC are for
s
IC C4'
O4'
C1'
C2'
IC O4'
C1'
C2'
C3'
IC C1'
C2'
C3'
C4'
IC C2'
C3'
C4'
O4'
IC C3'
C4'
O4'
C1'
IC H11'
C1'
C2'
C3'
IC H12'
C1'
C2'
C3'
IC H21'
C2'
C3'
C4'
IC O2'
C2'
C3'
C4'
IC H22'
O2'
C2'
C3'
IC H31'
C3'
C4'
O4'
IC H41'
C4'
O4'
C1'
IC H42'
C4'
O4'
C1'
IC O3'
C3'
C4'
O4'
IC H32'
O3'
C3'
C4'
PATC FIRS NONE LAST NONE
RESI TMPM
(phosphate -1)

C3' C4' C4' O4' C3' O3'


C2' H21' C3' H31' C4' H41'
thf-oh as optimized via ab initio calculation
1.4055
1.4127
1.5457
1.5346
1.5211
1.0856
1.0818
1.0846
1.0822
0.0
1.0806
1.0891
1.0808
1.4028
0.9492

108.09
106.18
103.11
100.86
103.15
111.62
113.32
110.65
110.88
0.0
113.53
110.89
108.72
110.98
108.72

23.45
3.96
-26.93
41.73
-41.62
123.53
-114.11
91.68
-148.45
-60.0
162.89
77.76
-162.12
-77.39
44.80

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
0.0
1.4055
1.4127
1.4127
1.4055
1.5211

-1.00 ! C6H12O5P 4'-methyl,3'-methylphosphate tetrahydrofuran


!charges corrected by adm jr. 9/98

GROUP
ATOM O4'
ATOM C1'
ATOM H11'
ATOM H12'
ATOM C4'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
GROUP
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
ATOM C3T

106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
0.0
103.15
108.09
108.09
103.15
110.98

OG3C51
CG3C52
HGA2
HGA2
CG3C51
HGA1

-0.40
0.02
0.09
0.09
0.11
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1

0.01
0.09

OG303
PG1
OG2P1
OG2P1
OG303
CG331

-0.57
1.50
-0.78
-0.78
-0.57
-0.17

!
H52' H53'
!
\ /
! H51'-C5' O4' H11'
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
! O1P==P==O2P
!
|
!
O3P (-1)
!
\
!
C3T--H3T3
!
/ \
!
H3T1 H3T2
!

ATOM H3T1
ATOM H3T2
ATOM H3T3
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H53'
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

HGA3
HGA3
HGA3

0.09
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

C1' O4' C1' C2' C2'


C1' H11' C1' H12' C2'
O3' P
P
O1P P
O3P C3T C3T H3T1 C3T
C4' C5' C5' H51' C5'
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
C5'
C4'
O4'
H51'
C5'
C4'
H52'
C5'
C4'
H53'
C5'
C4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3P
P
O3'
C3T
O3P
P
H3T1
C3T
O3P
H3T2
C3T
O3P
H3T3
C3T
O3P
FIRS NONE LAST NONE

RESI TADE
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
ATOM O4'
ATOM C1'

C3'
H21'
O2P
H3T2
H52'
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
O4'
O4'
O4'
C1'
O4'
C4'
C3'
C3'
C3'
O3'
P
P
P

C3' C4' C4' O4' C3'


C2' H22' C3' H31' C4'
P
O3P
C3T H3T3
C5' H53'
1.4055 108.09 23.45
1.4127 106.18
3.96
1.5457 103.11 -26.93
1.5346 100.86 41.73
1.5211 103.15 -41.62
1.0856 111.62 123.53
1.0818 113.32 -114.11
1.0846 110.65 91.68
1.0822 110.88 -148.45
1.0806 113.53 162.89
0.0000 000.00 77.76
0.0
0.0
180.0
0.0
0.0
-60.0
0.0
0.0
60.0
1.0808 108.72 -162.12
1.4028 110.98 -77.39
0.0
0.0 180.00
0.0
0.0 -60.0
0.0
0.0
60.0
0.0
0.0 180.0
0.0
0.0 180.0
0.0
0.0
60.0
0.0
0.0 -60.0
0.0
0.0 180.0

O3'
H42'

106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
0.0
0.0
0.0
108.09
103.15
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
0.0
0.0
0.0
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.00 ! C9H11N5O thf with adenine


! Atom types for aliphatic atoms based on nucleotide
! atom order consistent with 9-m-ade
CG2RC0
NG2R50
CG2R53
HGR52
NG2R51
NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64
NG2S3
HGP4
HGP4
OG3C51
CG3C51

0.28
-0.71
0.34
0.12
-0.05
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38
-0.40
0.11

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

H61 H62!
\ /
N6
|
C6
// \
N1 C5--N7\\
|
||
C8-H8
C2 C4--N9/
/ \\ /
\
H2 N3
\
\
\
\
H42' O4' \
\ / \ \

ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'

HGA1
CG3C52
HGA2
HGA2

0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

!
!
!
!
!
-0.18 !
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32' H21' H22'

BOND C1' O4' C1' C2' C2' C3' C3'


BOND C1' H12' C2' H21' C2' H22' C3'
BOND C4' H41' C4' H42'
BOND C1' N9
BOND N9 C4
N9 C8 C4 N3
C2
BOND N6 H61 N6 H62 C6 C5
C5
DOUBLE N1 C6
C2 N3
C4 C5
IMPR N6 C6 H61 H62
C6 N1
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
IC
C2'
C3'
C4'
O4'
IC
H12'
C1'
C2'
C3'
IC
H21'
C2'
C3'
C4'
IC
H22'
C2'
C3'
C4'
IC
H31'
C3'
C4'
O4'
IC
H32'
C3'
C4'
O4'
IC
H41'
C4'
O4'
C1'
IC
H42'
C4'
O4'
C1'
IC C3' C2' C1' N9
1.5284 101.97
IC O4' C1' N9 C4
1.5251 113.71
IC C1' C4 *N9 C8
1.4896 125.97
IC C4 N9 C8 N7
1.376 106.0
IC C8 N9 C4 C5
1.367 106.0
IC C8 N7 C5 C6
0.0
0.0
IC N7 C5 C6 N1
0.0
0.0
IC C5 C6 N1 C2
0.0
0.0
IC N9 C5 *C4 N3
1.376 105.6
IC C5 N1 *C6 N6
1.409 117.6
IC N1 C6 N6 H61
1.337 121.2
IC H61 C6 *N6 H62
1.01
119.0
IC C5 N1 *C6 N6
1.409 117.6
IC N1 C6 N6 H61
1.337 119.0
IC H61 C6 *N6 H62
1.01
119.0
IC N9 N7 *C8 H8
0.0
0.0
IC N1 N3 *C2 H2
0.0
0.0
PATC FIRS NONE LAST NONE
RESI TCYT
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3

C4' C4' O4'


H31' C3' H32'
N1
N7
N7
C5

C6
C8
C8

N6
H8

C2

H2

N6

0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
147.80
180.2
-180.00
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0

324.92 0.0 0.0


33.390 0.0 0.0
268.35 0.0 0.0
82.530 0.0 0.0
204.06 0.0 0.0
155.99 0.0 0.0
276.70 0.0 0.0
132.30 0.0 0.0
220.70 0.0 0.0
113.71 1.4896
125.59 1.3783 !chi
106.0
1.367
113.6
1.312
105.6
1.382
0.0
0.0
0.0
0.0
0.0
0.0
126.9
1.342
121.2
1.337
119.0
1.01
119.00 1.01
119.0
1.337
119.0
1.01
121.00 1.01
0.0
0.0
0.0
0.0

0.00 ! C8H11N3O2 THF with cytosine


! Atom types for aliphatic atoms based on nucleotide
!atom order to be consistent with 1-m-cyt
NG2R61
CG2R62
HGR62
CG2R63
OG2D4
NG2R62

-0.13
0.05
0.17
0.52
-0.49
-0.66

!
!
!
!
!

H42 H41
\ /
N4
|
C4

ATOM C4
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H5
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'

CG2R64
NG2S3
HGP4
HGP4
CG2R62
HGR62
OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2

0.65
-0.75
0.37
0.33
-0.13
0.07
-0.40
0.11
0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

!
!
!
!
!
!
!
!
!
!
!
!
!
-0.18 !
0.09 !
0.09 !

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

/ \\
H5-C5 N3
|| |
H6-C6 C2
\ / \\
N1 O2
\
\
\
H42' O4' \
\ / \ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32' H21' H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
BOND C4' H41' C4' H42'
BOND C1' N1
BOND N1 C2
N1 C6
C4 N4
N4 H41 N4 H42
BOND C2 N3
C4 C5
C5 H5
C6 H6
DOUBLE C2 O2
C5 C6
N3 C4
IMPR C2 N1 N3 O2
C4 N3 C5 N4
IMPR N4 C4 H41 H42
BILD C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
BILD O4' C1' N1 C2
1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C2 *N1 C6
1.4896 117.79 -180.00 120.6
1.364
BILD C2 N1 C6 C5
1.399 120.6
0.0 121.0
1.337
BILD C6 N1 C2 N3
1.364 120.6
0.0 118.9
1.356
BILD N1 N3 *C2 O2
1.399 118.9 180.0 121.9
1.237
BILD N1 C2 N3 C4
1.399 118.9
0.0 120.0
1.334
BILD C5 N3 *C4 N4
1.426 121.8 180.00 118.9
1.337
BILD N3 C4 N4 H41
1.337 117.9
0.00 118.9
1.01
BILD H41 C4 *N4 H42
1.01
118.9 180.00 120.7
1.01
BILD C6 C4 *C5 H5
0.0
0.0 180.0
0.0
0.0
BILD N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
IC
H32'
C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.79 -180.00 120.6
1.364
IC C2 N1 C6 C5
1.399 120.6
0.0 121.0
1.337
IC C6 N1 C2 N3
1.364 120.6
0.0 118.9
1.356
IC N1 N3 *C2 O2
1.399 118.9 180.0 121.9
1.237
IC N1 C2 N3 C4
1.399 118.9
0.0 120.0
1.334
IC C5 N3 *C4 N4
1.426 121.8 180.00 118.9
1.337

IC N3 C4 N4 H41
1.337
IC H41 C4 *N4 H42
1.01
IC C6 C4 *C5 H5
0.0
IC N1 C5 *C6 H6
0.0
PATC FIRS NONE LAST NONE
RESI TGUA
GROUP
ATOM N9
ATOM C4
ATOM N3
ATOM C2
ATOM N1
ATOM H1
ATOM N2
ATOM H21
ATOM H22
ATOM C6
ATOM O6
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'

117.9
118.9
0.0
0.0

0.00 118.9
180.00 120.7
180.0
0.0
180.0
0.0

1.01
1.01
0.0
0.0

0.00 ! C9H11N5O2 thf with guanine


! Atom types for aliphatic atoms based on nucleotide
! atom order consistent with 9-m-gua
NG2R51
CG2RC0
NG2R62
CG2R64
NG2R61
HGP1
NG2S3
HGP4
HGP4
CG2R63
OG2D4
CG2RC0
NG2R50
CG2R53
HGR52
OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2

-0.02
0.26
-0.74
0.75
-0.34
0.26
-0.68
0.32
0.35
0.54
-0.51
0.00
-0.60
0.25
0.16
-0.40
0.11
0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

O6
||
C6
/ \
H1-N1 C5--N7\\
|
||
C8-H8
C2 C4--N9/
/ \\ /
\
H21-N2 N3
\
|
\
H22
\
\
H42' O4' \
\ / \ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32' H21' H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
BOND C4' H41' C4' H42'
BOND C1' N9
BOND N9 C4
N9 C8
C4 N3
C2 N2 C2 N1
N2
BOND N2 H22
N1 H1
N1 C6
C6 C5 C5 N7
C8
DOUBLE C2 N3
C4 C5
N7 C8 C6 O6
IMPR C2 N3 N1 N2
C6 N1 C5 O6
N2 H21
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
IC
H32'
C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N9
1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4
1.5251 113.71 -97.2 125.59 1.3783

H21
H8
C2

!chi

H22

IC C1' C4 *N9 C8
1.4896
IC C4 N9 C8 N7
1.377
IC C8 N9 C4 C5
1.374
IC N9 C5 *C4 N3
1.377
IC C5 C4 N3 C2
1.377
IC C4 N3 C2 N1
1.355
IC N1 N3 *C2 N2
1.375
IC N3 C2 N2 H21
1.327
IC H21 C2 *N2 H22
1.01
IC N3 C2 N1 C6
1.327
IC C6 C2 *N1 H1
1.393
IC C5 N1 *C6 O6
1.415
IC N9 N7 *C8 H8
0.0
PATC FIRS NONE LAST NONE
RESI TTHY

GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM C5M
ATOM H51
ATOM H52
ATOM H53
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'

125.59
106.0
106.0
105.6
128.4
111.8
124.0
119.7
127.0
124.0
124.9
111.7
0.0

-179.99
0.0
0.0
180.0
0.0
0.0
180.0
180.0
-180.0
0.0
180.00
180.0
180.0

106.0
113.5
105.6
128.4
111.8
124.0
119.7
127.0
116.5
124.9
117.4
120.0
0.0

1.374
1.304
1.377
1.355
1.327
1.375
1.341
1.01
1.01
1.393
1.03
1.239
0.0

0.00 ! C9H12N2O3 THF with thymine on C1'


! Atom type for N1 changed from NN2 to NN2B, to adjust
! chi in thymine independantly of cytosine.
! Atom types for aliphatic atoms based on nucleotide
! atom order consistent with 1-m-thy
NG2R61

-0.34 !

CG2R62
HGR62
CG2R63
OG2D4
NG2R61
HGP1
CG2R63
OG2D4
CG2R62
CG331
HGA3
HGA3
HGA3
OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2

0.17
0.17
0.51
-0.41
-0.46
0.36
0.50
-0.45
-0.15
-0.11
0.07
0.07
0.07
-0.40
0.11
0.09
0.02
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

H51

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

BOND C1' O4' C1' C2' C2' C3' C3'


BOND C1' H12' C2' H21' C2' H22' C3'
BOND C4' H41' C4' H42'
BOND C1' N1
BOND N1 C2 N1 C6 C2 N3 N3
BOND C5 C5M C6 H6 C5M H51 C5M
DOUBLE C2 O2
C4 O4
C5 C6
IMPR C2 N1 N3 O2
C4 N3
! ic table for thfim, from Nicolas:

O4

|
||
H52-C5M C4
H3
| \ / \ /
H53 C5 N3
|| |
H6-C6 C2
\ / \\
N1 O2
\
\
\
H42' O4' \
\ / \ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32' H21' H22'

C4' C4' O4'


H31' C3' H32'
H3 N3 C4 C4
H52 C5M H53

C5

C5

C4

O4

C5

C6

C5M

IC
C1'
C2'
C3'
IC
C2'
C3'
C4'
IC
H12'
C1'
C2'
IC
H21'
C2'
C3'
IC
H22'
C2'
C3'
IC
H31'
C3'
C4'
IC
H32'
C3'
C4'
IC
H41'
C4'
O4'
IC
H42'
C4'
O4'
IC C3' C2' C1' N1
1.5284
IC C3' C2' C1' N1
1.5284
IC O4' C1' N1 C2
1.5251
IC C1' C2 *N1 C6
1.4896
IC C2 N1 C6 C5
1.3746
IC C6 N1 C2 N3
1.3704
IC N1 N3 *C2 O2
1.3746
IC N1 C2 N3 C4
1.3746
IC C5 N3 *C4 O4
1.4439
IC C2 C4 *N3 H3
1.3813
IC C4 C6 *C5 C5M
1.4439
IC N1 C5 *C6 H6
0.0
IC C6 C5 C5M H51
0.0
IC C5 H51 *C5M H52
0.0
IC H51 H52 *C5M H53
0.0
PATC FIRS NONE LAST NONE
RESI TURA

C4'
O4'
C3'
C4'
C4'
O4'
O4'
C1'
C1'
101.97
101.97
113.71
117.06
122.08
122.08
115.38
115.38
114.07
126.46
120.78
0.0
0.0
0.0
0.0

0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
147.89
147.89
180.0
-179.96
-0.02
0.06
-179.95
-0.07
179.98
180.00
-179.94
180.0
0.0
115.0
-115.0

324.92 0.0 0.0


33.390 0.0 0.0
268.35 0.0 0.0
82.530 0.0 0.0
204.06 0.0 0.0
155.99 0.0 0.0
276.70 0.0 0.0
132.30 0.0 0.0
220.70 0.0 0.0
113.71 1.4896
113.71 1.4896
125.59 1.3783 !chi
122.08 1.3704
121.23 1.3432
115.38 1.3813
121.70 1.2191
126.46 1.3795
120.59 1.2327
116.77 1.0900
121.63 1.5000
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.00 ! C8H10N2O3 THF with uracil on C1'


! Atom type for N1 changed from NN2 to NN2B, in order

to adjust
! chi in uracil/thymine independantly of cytosine.
! Atom types for aliphatic atoms based on nucleotide
! atom order consistent with 1-m-thy
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM H5
ATOM O4'
ATOM C1'
ATOM H12'
ATOM C4'
ATOM H41'
ATOM H42'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM H32'

NG2R61

-0.34 !

O4

CG2R62
HGR62
CG2R63
OG2D4
NG2R61
HGP1
CG2R63
OG2D4
CG2R62
HGR62
OG3C51
CG3C51
HGA1
CG3C52
HGA2
HGA2

0.20
0.14
0.55
-0.45
-0.46
0.36
0.53
-0.48
-0.15
0.10
-0.40
0.11
0.09
0.02
0.09
0.09

||
C4

CG3C52
HGA2
HGA2

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-0.18 !
0.09
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

H3
/ \ /
H5-C5 N3
|| |
H6-C6 C2
\ / \\
N1 O2
\
\
\
H42' O4' \
\ / \ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32' H21' H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
BOND C4' H41' C4' H42'
BOND C1' N1
BOND N1 C2 N1 C6
BOND C2 N3 N3 H3 N3 C4
C4 C5
BOND C5 H5 C6 H6
DOUBLE C2 O2
C4 O4
C5 C6
IMPR C2 N1 N3 O2
C4 N3 C5 O4
! ic table for thfim, from Nicolas:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
IC
H32'
C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 180.0 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5
1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3
1.3704 122.08
0.06 115.38 1.3813
IC N1 N3 *C2 O2
1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4
1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4
1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3
1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M
1.4439 120.78 -179.94 121.63 1.5000
IC C4 C6 *C5 H5
0.0
0.0 180.0
0.0
0.0
IC N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0
IC C6 C5 C5M H51
0.0
0.0
0.0
0.0
0.0
IC C5 H51 *C5M H52
0.0
0.0 115.0
0.0
0.0
IC H51 H52 *C5M H53
0.0
0.0 -115.0
0.0
0.0
PATC FIRS NONE LAST NONE
RESI THAO
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T
GROUP !

0.00 ! C8H12N2O3 Nucleoside analogue with imidazole


OG3C51
CG3C51
HGA1
CG3C51
HGA1

-0.40
0.11
0.09
0.11
0.09

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

HGA1
CG3C51
OG311
HGP1

0.09
0.14
-0.65
0.42

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Imidazole
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
!
H32'
!

CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42
Imidazole: transferred from isolated imidazole (IMIA)

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

CG
HG
CD2
HD2
ND1
CE1
HE1
NE2

CG2R51
HGR52
CG2R51
HGR52
NG2R51
CG2R53
HGR52
NG2R50

-0.05
0.09
0.22
0.10
-0.04
0.25
0.13
-0.70

!
C1'
HE1
!
\
/
!
ND1---CE1
!
/
||
! HG-CG
||
!
\\
||
!
CD2---NE2
!
|
!
HD2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O3' H32'
BOND C1' ND1
BOND ND1 CE1 NE2 CD2 CG ND1
BOND CE1 HE1 CD2 HD2 CG HG
DOUBLE CG CD2 CE1 NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1 CG CE1 C1'
ND1 CE1 CG C1'
IMPR CD2 CG NE2 HD2
CD2 NE2 CG HD2
IMPR CE1 ND1 NE2 HE1
CE1 NE2 ND1 HE1
IMPR CG CD2 ND1 HG
CG ND1 CD2 HG
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 -93.14 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC
C4'
O4'
C1'
ND1
0.0 0.0 256.98 0.0 0.0
IC
O4'
C1'
ND1
CG
0.0 0.0 90.00 0.0 0.0
IC
C1'
ND1
CE1
NE2
0.0 0.0 181.56 0.0 0.0
IC
ND1
CE1
NE2
CD2
0.0 0.0 0.34 0.0 0.0
IC
CE1
NE2
CD2
CG
0.0 0.0 0.00 0.0 0.0
IC
HE1
CE1
NE2
CD2
0.0 0.0 180.40 0.0 0.0
IC
CE1
NE2
CD2
HD2
0.0 0.0 179.83 0.0 0.0
IC
NE2
CD2
CG
HG
0.0 0.0 178.45 0.0 0.0
IC
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
IC
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
IC
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0
PATC FIRS NONE LAST NONE
RESI NUSA
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM C2'
ATOM H21'
ATOM H22'

0.00 ! C10H13N5O3 deoxy-nucleoside with adenine


OG3C51
CG3C51
HGA1
CG3C51
HGA1
CG3C52
HGA2
HGA2

-0.40
0.11
0.09
0.11
0.09

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Adenine
!
\ / \ /
-0.18 ! H42'--C4' C1'--H12'
0.09 !
|
|
0.09 ! H31'--C3'--C2'--H21'

! Adenine
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
GROUP !
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP !
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T

atoms

!
/
!
O3'
CG2RC0
0.28 !
|
NG2R50 -0.71 !
H32'
CG2R53
0.34
HGR52
0.12
NG2R51 -0.05
NG2R62 -0.74
CG2R64
0.50
HGR62
0.13
NG2R62 -0.75
CG2RC0
0.43
CG2R64
0.46
NG2S3
-0.77
HGP4
0.38
HGP4
0.38
Hydroxyl group on C3'
HGA1
0.09
CG3C51
0.14
OG311
-0.65
HGP1
0.42
Methyl group on C4'
CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42

\
H22'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O3' H32'
BOND C1' N9
BOND N9 C4
N9 C8 C4 N3
C2 N1
C6 N6
BOND N6 H61 N6 H62 C6 C5
C5 N7
C8 H8
C2 H2
DOUBLE N1 C6
C2 N3
C4 C5
N7 C8
IMPR N6 C6 H61 H62
C6 N1 C5 N6
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 -93.14 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N9
1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4
1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8
1.4896 125.97 -179.94 106.0
1.367
IC C4 N9 C8 N7
1.376 106.0
0.0 113.6
1.312
IC C8 N9 C4 C5
1.367 106.0
0.0 105.6
1.382
IC C8 N7 C5 C6
0.0
0.0 180.0
0.0
0.0
IC N7 C5 C6 N1
0.0
0.0 180.0
0.0
0.0
IC C5 C6 N1 C2
0.0
0.0
0.0
0.0
0.0
IC N9 C5 *C4 N3
1.376 105.6 -180.0 126.9
1.342
IC C5 N1 *C6 N6
1.409 117.6 -180.0 121.2
1.337
IC N1 C6 N6 H61
1.337 121.2
0.0 119.0
1.01
IC H61 C6 *N6 H62
1.01
119.0 180.0 119.00 1.01

IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC N9 N7 *C8 H8
0.0
IC N1 N3 *C2 H2
0.0
IC
C5'
C4'
O4'
IC
H51'
C5'
C4'
IC
H52'
C5'
C4'
IC
O5'
C5'
C4'
IC
H5T
O5'
C5'
PATC FIRS NONE LAST NONE
RESI NUSG
0.00
GROUP
ATOM O4' OG3C51 -0.40
ATOM C4' CG3C51
0.11
ATOM H42' HGA1
0.09
ATOM C1' CG3C51
0.11
ATOM H12' HGA1
0.09
GROUP
ATOM C2' CG3C52 -0.18
ATOM H21' HGA2
0.09
ATOM H22' HGA2
0.09
!Guanine atoms
GROUP
ATOM N9 NG2R51 -0.02
ATOM C4 CG2RC0
0.26
ATOM N3 NG2R62 -0.74
ATOM C2 CG2R64
0.75
ATOM N1 NG2R61 -0.34
ATOM H1 HGP1
0.26
ATOM N2 NG2S3
-0.68
ATOM H21 HGP4
0.32
ATOM H22 HGP4
0.35
ATOM C6 CG2R63
0.54
ATOM O6 OG2D4
-0.51
ATOM C5 CG2RC0
0.00
ATOM N7 NG2R50 -0.60
ATOM C8 CG2R53
0.25
ATOM H8 HGR52
0.16
GROUP ! Hydroxyl group
ATOM H31' HGA1
0.09
ATOM C3' CG3C51
0.14
ATOM O3' OG311
-0.65
ATOM H32' HGP1
0.42
GROUP ! C5' hydroxyl
ATOM C5' CG321
0.05
ATOM H51' HGA2
0.09
ATOM H52' HGA2
0.09
ATOM O5' OG311
-0.65
ATOM H5T HGP1
0.42

117.6
119.0
119.0
0.0
0.0
C1'
O4'
O4'
O4'
C4'

-180.0
0.0
180.0
180.0
180.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0
0.0 0.0

119.0
1.337
119.0
1.01
121.00 1.01
0.0
0.0
0.0
0.0
144.82 0.0 0.0
-179.98 0.0 0.0
59.66 0.0 0.0
-59.68 0.0 0.0
180.0 0.0 0.0

! C10H13N5O4 nucleoside with guanine


!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Guanine
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
!
H32'

on C3'

BOND C1' O4' C1' C2' C2' C3' C3'


BOND C3' O3' C1' H12' C2' H21' C2'
BOND C5' H51' C5' H52' C5' O5' O5'
BOND O3' H32'
BOND C1' N9
BOND N9 C4
N9 C8
C4 N3
BOND N2 H22
N1 H1
N1 C6
DOUBLE C2 N3
C4 C5
N7 C8

C4' C4' O4' C4' C5'


H22' C3' H31' C4' H42'
H5T
C2 N2 C2
C6 C5 C5
C6 O6

N1
N7

N2
C8

H21
H8

IMPR C2 N3 N1 N2
C6 N1 C5 O6
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0
IC C3' C2' C1' N9
1.5284 101.97 147.80
IC O4' C1' N9 C4
1.5251 113.71 -97.2
IC C1' C4 *N9 C8
1.4896 125.59 -179.99
IC C4 N9 C8 N7
1.377 106.0
0.0
IC C8 N9 C4 C5
1.374 106.0
0.0
IC N9 C5 *C4 N3
1.377 105.6 180.0
IC C5 C4 N3 C2
1.377 128.4
0.0
IC C4 N3 C2 N1
1.355 111.8
0.0
IC N1 N3 *C2 N2
1.375 124.0 180.0
IC N3 C2 N2 H21
1.327 119.7 180.0
IC H21 C2 *N2 H22
1.01
127.0 -180.0
IC N3 C2 N1 C6
1.327 124.0
0.0
IC C6 C2 *N1 H1
1.393 124.9 180.00
IC C5 N1 *C6 O6
1.415 111.7 180.0
IC N9 N7 *C8 H8
0.0
0.0 180.0
IC
C5'
C4'
O4'
C1'
0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0
IC
O5'
C5'
C4'
O4'
0.0 0.0
IC
H5T
O5'
C5'
C4'
0.0 0.0
PATC FIRS NONE LAST NONE
RESI NUSC
GROUP
ATOM O4' OG3C51
ATOM C4' CG3C51
ATOM H42' HGA1
ATOM C1' CG3C51
ATOM H12' HGA1
GROUP
ATOM C2' CG3C52
ATOM H21' HGA2
ATOM H22' HGA2
! Cytosine atoms
GROUP
ATOM N1 NG2R61
ATOM C6 CG2R62
ATOM H6 HGR62
ATOM C2 CG2R63
ATOM O2 OG2D4
ATOM N3 NG2R62
ATOM C4 CG2R64
ATOM N4 NG2S3
ATOM H41 HGP4
ATOM H42 HGP4
ATOM C5 CG2R62
ATOM H5 HGR62
GROUP ! Hydroxyl

N2 H21 C2
324.92 0.0 0.0
33.390 0.0 0.0
268.35 0.0 0.0
82.530 0.0 0.0
204.06 0.0 0.0
-93.14 0.0 0.0
-60.00 0.0 0.0
147.80 0.0 0.0
132.30 0.0 0.0
220.70 0.0 0.0
113.71 1.4896
125.59 1.3783 !chi
106.0
1.374
113.5
1.304
105.6
1.377
128.4
1.355
111.8
1.327
124.0
1.375
119.7
1.341
127.0
1.01
116.5
1.01
124.9
1.393
117.4
1.03
120.0
1.239
0.0
0.0
144.82 0.0 0.0
-179.98 0.0 0.0
59.66 0.0 0.0
-59.68 0.0 0.0
180.0 0.0 0.0

0.00 ! C9H13N3O4 nucleoside with cytosine


-0.40
0.11
0.09
0.11
0.09
-0.18
0.09
0.09

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Cytosine
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
!
H32'

-0.13
0.05
0.17
0.52
-0.49
-0.66
0.65
-0.75
0.37
0.33
-0.13
0.07
group on C3'

H22

ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP !
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T

HGA1
0.09
CG3C51
0.14
OG311
-0.65
HGP1
0.42
C5' hydroxyl
CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O3' H32'
BOND C1' N1
BOND N1 C2
N1 C6
C4 N4
N4 H41 N4 H42
BOND C2 N3
C4 C5
C5 H5
C6 H6
DOUBLE C2 O2
C5 C6
N3 C4
IMPR N4 C4 H41 H42
C2 N1 N3 O2
C4 N3 C5 N4
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 -93.14 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.79 -180.00 120.6
1.364
IC C2 N1 C6 C5
1.399 120.6
0.0 121.0
1.337
IC C6 N1 C2 N3
1.364 120.6
0.0 118.9
1.356
IC N1 N3 *C2 O2
1.399 118.9 180.0 121.9
1.237
IC N1 C2 N3 C4
1.399 118.9
0.0 120.0
1.334
IC C5 N3 *C4 N4
1.426 121.8 180.00 118.9
1.337
IC N3 C4 N4 H41
1.337 117.9
0.00 118.9
1.01
IC H41 C4 *N4 H42
1.01
118.9 180.00 120.7
1.01
IC C6 C4 *C5 H5
0.0
0.0 180.0
0.0
0.0
IC N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0
IC
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
IC
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
IC
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0
PATC FIRS NONE LAST NONE
RESI NUST
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM C2'
ATOM H21'

0.00 ! C10H14N2O5 nucleoside with thymine


OG3C51
CG3C51
HGA1
CG3C51
HGA1
CG3C52
HGA2

-0.40
0.11
0.09
0.11
0.09

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Thymine
!
\ / \ /
-0.18 ! H42'--C4' C1'--H12'
0.09 !
|
|

ATOM H22' HGA2


0.09 ! H31'--C3'--C2'--H21'
! Atoms for thymine
!
/
\
GROUP
!
O3'
H22'
ATOM N1 NG2R61 -0.34 !
|
ATOM C6 CG2R62
0.17 !
H32'
ATOM H6 HGR62
0.17
ATOM C2 CG2R63
0.51
ATOM O2 OG2D4
-0.41
ATOM N3 NG2R61 -0.46
ATOM H3 HGP1
0.36
ATOM C4 CG2R63
0.50
ATOM O4 OG2D4
-0.45
ATOM C5 CG2R62 -0.15
ATOM C5M CG331
-0.11
ATOM H51 HGA3
0.07
ATOM H52 HGA3
0.07
ATOM H53 HGA3
0.07
GROUP ! Hydroxyl group on C3'
ATOM H31' HGA1
0.09
ATOM C3' CG3C51
0.14
ATOM O3' OG311
-0.65
ATOM H32' HGP1
0.42
GROUP ! C5' hydroxyl
ATOM C5' CG321
0.05
ATOM H51' HGA2
0.09
ATOM H52' HGA2
0.09
ATOM O5' OG311
-0.65
ATOM H5T HGP1
0.42
BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O3' H32'
BOND C1' N1
BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5
BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53
DOUBLE C2 O2
C4 O4
C5 C6
IMPR C2 N1 N3 O2
C4 N3 C5 O4
C5 C4 C6 C5M
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 -93.14 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5
1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3
1.3704 122.08
0.06 115.38 1.3813
IC N1 N3 *C2 O2
1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4
1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4
1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3
1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M
1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0

IC C6 C5 C5M H51
0.0
IC C5 H51 *C5M H52
0.0
IC H51 H52 *C5M H53
0.0
IC
C5'
C4'
O4'
IC
H51'
C5'
C4'
IC
H52'
C5'
C4'
IC
O5'
C5'
C4'
IC
H5T
O5'
C5'
PATC FIRS NONE LAST NONE
RESI NUSU
0.00
GROUP
ATOM O4' OG3C51 -0.40
ATOM C4' CG3C51
0.11
ATOM H42' HGA1
0.09
ATOM C1' CG3C51
0.11
ATOM H12' HGA1
0.09
GROUP
ATOM C2' CG3C52 -0.18
ATOM H21' HGA2
0.09
ATOM H22' HGA2
0.09
! Atoms for uracil
GROUP
ATOM N1 NG2R61 -0.34
ATOM C6 CG2R62
0.20
ATOM H6 HGR62
0.14
ATOM C2 CG2R63
0.55
ATOM O2 OG2D4
-0.45
ATOM N3 NG2R61 -0.46
ATOM H3 HGP1
0.36
ATOM C4 CG2R63
0.53
ATOM O4 OG2D4
-0.48
ATOM C5 CG2R62 -0.15
ATOM H5 HGR62
0.10
GROUP ! Hydroxyl group
ATOM H31' HGA1
0.09
ATOM C3' CG3C51
0.14
ATOM O3' OG311
-0.65
ATOM H32' HGP1
0.42
GROUP ! C5' hydroxyl
ATOM C5' CG321
0.05
ATOM H51' HGA2
0.09
ATOM H52' HGA2
0.09
ATOM O5' OG311
-0.65
ATOM H5T HGP1
0.42

0.0
0.0
0.0 115.0
0.0 -115.0
C1'
0.0 0.0
O4'
0.0 0.0
O4'
0.0 0.0
O4'
0.0 0.0
C4'
0.0 0.0

0.0
0.0
0.0
0.0
0.0
0.0
144.82 0.0 0.0
-179.98 0.0 0.0
59.66 0.0 0.0
-59.68 0.0 0.0
180.0 0.0 0.0

! C9H12N2O5 nucleoside with uracil


!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Uracil
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
H22'
!
|
!
H32'

on C3'

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O3' H32'
BOND C1' N1
N1 C2
N1 C6
C2
BOND C2 N3
N3 H3
N3 C4
C4
BOND C5 C6
C5 H5
C6 H6
IMPR C2 N1 N3 O2
C4 N3 C5 O4
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530
IC
H22'
C2'
C3'
C4'
0.0 0.0 204.06

C4' C5'
C4' H42'
O2
O4

0.0
0.0
0.0
0.0
0.0

C4

0.0
0.0
0.0
0.0
0.0

C5

IC
IC
IC
IC
IC
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
IC
IC
IC
IC
IC
PATC

O3'
C3'
C4'
O4'
0.0 0.0 -93.14 0.0 0.0
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
C3' C2' C1' N1
1.5284 101.97 144.39 113.71 1.4896
O4' C1' N1 C2
1.5251 113.71 -96.0 117.06 1.3746
C1' C2 *N1 C6
1.4896 117.06 -180.0 121.3
1.379
C2 N1 C6 C5
1.379 121.3
0.0 122.8
1.338
C6 N1 C2 N3
1.380 121.3
0.0 114.8
1.373
N1 N3 *C2 O2
1.379 114.8 -180.0 122.0
1.218
N1 C2 N3 C4
1.379 114.8
0.0 127.0
1.383
C5 N3 *C4 O4
1.440 114.7 180.0 119.8
1.227
C2 C4 *N3 H3
1.373 127.0 180.0 116.5
1.03
C6 C4 *C5 H5
0.0
0.0 180.0
0.0
0.0
N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0
FIRS NONE LAST NONE

RESI RNUS
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM C2'
ATOM H21'
ATOM O2'
ATOM H22'
GROUP
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T
GROUP !
ATOM CG
ATOM HG
ATOM CD2
ATOM HD2
ATOM ND1
ATOM CE1
ATOM HE1
ATOM NE2

0.00 ! C8H12N2O4 Ribonucleoside analogue with imidazole


OG3C51
CG3C51
HGA1
CG3C51
HGA1

-0.40
0.11
0.09
0.11
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

HGA1
CG3C51
OG311
HGP1

0.09
0.14
-0.65
0.42

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Imidazole
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2'
!
|
|
!
H32'
H22'

CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42
Imidazole: transferred from isolated imidazole (IMIA)
CG2R51 -0.05 !
C1'
HE1
HGR52
0.09 !
\
/
CG2R51
0.22 !
ND1---CE1
HGR52
0.10 !
/
||
NG2R51 -0.04 ! HG-CG
||
CG2R53
0.25 !
\\
||
HGR52
0.13 !
CD2---NE2
NG2R50 -0.70 !
|
!
HD2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31'
BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T

BOND O3' H32'


BOND C1' ND1
BOND ND1 CE1 NE2 CD2 CG ND1
BOND CE1 HE1 CD2 HD2 CG HG
DOUBLE CG CD2 CE1 NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1 CG CE1 C1'
ND1 CE1 CG
IMPR CD2 CG NE2 HD2
CD2 NE2 CG
IMPR CE1 ND1 NE2 HE1
CE1 NE2 ND1
IMPR CG CD2 ND1 HG
CG ND1 CD2
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0
IC
C2'
C3'
C4'
O4'
0.0
IC
H12'
C1'
C2'
C3'
0.0
IC
H21'
C2'
C3'
C4'
0.0
IC
O2'
C2'
C3'
C4'
0.0
IC
H22'
O2'
C2'
C3'
0.0
IC
O3'
C3'
C4'
O4'
0.0
IC
H32'
O3'
C3'
C2'
0.0
IC
H31'
C3'
C4'
O4'
0.0
IC
H41'
C4'
O4'
C1'
0.0
IC
H42'
C4'
O4'
C1'
0.0
IC
C4'
O4'
C1'
ND1
0.0
IC
O4'
C1'
ND1
CE1
0.0
IC
C1'
ND1
CE1
NE2
0.0
IC
ND1
CE1
NE2
CD2
0.0
IC
CE1
NE2
CD2
CG
0.0
IC
HE1
CE1
NE2
CD2
0.0
IC
CE1
NE2
CD2
HD2
0.0
IC
NE2
CD2
CG
HG
0.0
IC
C5'
C4'
O4'
C1'
0.0
IC
H51'
C5'
C4'
O4'
0.0
IC
H52'
C5'
C4'
O4'
0.0
IC
O5'
C5'
C4'
O4'
0.0
IC
H5T
O5'
C5'
C4'
0.0
PATC FIRS NONE LAST NONE
RESI RNUA
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM H21'
ATOM C2'
ATOM O2'
ATOM H22'
! Adenine
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM N1
ATOM C2
ATOM H2
ATOM N3

C1'
HD2
HE1
HG
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

324.92 0.0 0.0


33.390 0.0 0.0
268.35 0.0 0.0
82.530 0.0 0.0
204.06 0.0 0.0
-60.00 0.0 0.0
-93.14 0.0 0.0
-60.00 0.0 0.0
147.80 0.0 0.0
132.30 0.0 0.0
220.70 0.0 0.0
256.98 0.0 0.0
180.00 0.0 0.0
181.56 0.0 0.0
0.34 0.0 0.0
0.00 0.0 0.0
180.40 0.0 0.0
179.83 0.0 0.0
178.45 0.0 0.0
144.82 0.0 0.0
-179.98 0.0 0.0
59.66 0.0 0.0
-59.68 0.0 0.0
180.0 0.0 0.0

0.00 ! C10H13N5O4 ribo-nucleoside with adenine


OG3C51
CG3C51
HGA1
CG3C51
HGA1

-0.40
0.11
0.09
0.11
0.09

HGA1
CG3C51
OG311
HGP1
atoms

0.09
0.14
-0.65
0.42

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51
NG2R62
CG2R64
HGR62
NG2R62

0.28
-0.71
0.34
0.12
-0.05
-0.74
0.50
0.13
-0.75

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Adenine
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2'
!
|
|
!
H32'
H22'

ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
GROUP !
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP !
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T

CG2RC0
0.43
CG2R64
0.46
NG2S3
-0.77
HGP4
0.38
HGP4
0.38
Hydroxyl group on C3'
HGA1
0.09
CG3C51
0.14
OG311
-0.65
HGP1
0.42
C5' hydroxyl
CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O2' H22' O3' H32'
BOND C1' N9
BOND N9 C4
N9 C8 C4 N3
C2 N1
C6 N6
BOND N6 H61 N6 H62 C6 C5
C5 N7
C8 H8
C2 H2
DOUBLE N1 C6
C2 N3
C4 C5
N7 C8
IMPR N6 C6 H61 H62
C6 N1 C5 N6
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
O2'
C2'
C3'
C4'
1.42 109.06 283.42 0.0 0.0
IC
H22'
O2'
C2'
C3'
0.98 109.05 283.42 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 324.95 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N9
1.5284 101.97 150.8 113.71 1.4896
IC O4' C1' N9 C4
1.5251 108.6 229.5 125.5
1.3783 !chi
IC C1' C4 *N9 C8
1.4896 125.97 -179.94 106.0
1.367
IC C4 N9 C8 N7
1.376 106.0
0.0 113.6
1.312
IC C8 N9 C4 C5
1.367 106.0
0.0 105.6
1.382
IC C8 N7 C5 C6
0.0
0.0 180.0
0.0
0.0
IC N7 C5 C6 N1
0.0
0.0 180.0
0.0
0.0
IC C5 C6 N1 C2
0.0
0.0
0.0
0.0
0.0
IC N9 C5 *C4 N3
1.376 105.6 -180.0 126.9
1.342
IC C5 N1 *C6 N6
1.409 117.6 -180.0 121.2
1.337
IC N1 C6 N6 H61
1.337 121.2
0.0 119.0
1.01
IC H61 C6 *N6 H62
1.01
119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6
1.409 117.6 -180.0 119.0
1.337
IC N1 C6 N6 H61
1.337 119.0
0.0 119.0
1.01
IC H61 C6 *N6 H62
1.01
119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8
0.0
0.0 180.0
0.0
0.0
IC N1 N3 *C2 H2
0.0
0.0 180.0
0.0
0.0
IC
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
IC
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
IC
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0

PATC FIRS NONE LAST NONE


RESI RNUG
GROUP
ATOM O4'
ATOM C4'
ATOM H42'
ATOM C1'
ATOM H12'
GROUP
ATOM H21'
ATOM C2'
ATOM O2'
ATOM H22'
! Guanine
GROUP
ATOM N9
ATOM C4
ATOM N3
ATOM C2
ATOM N1
ATOM H1
ATOM N2
ATOM H21
ATOM H22
ATOM C6
ATOM O6
ATOM C5
ATOM N7
ATOM C8
ATOM H8
GROUP !
ATOM H31'
ATOM C3'
ATOM O3'
ATOM H32'
GROUP !
ATOM C5'
ATOM H51'
ATOM H52'
ATOM O5'
ATOM H5T

0.00 ! C10H13N5O5 ribo-nucleoside with guanine


OG3C51
CG3C51
HGA1
CG3C51
HGA1

-0.40
0.11
0.09
0.11
0.09

HGA1
CG3C51
OG311
HGP1
atoms

0.09
0.14
-0.65
0.42

!
H5T
!
/
! H51' O5'
!
\ |
!H52'--C5' O4' Guanine
!
\ / \ /
! H42'--C4' C1'--H12'
!
|
|
! H31'--C3'--C2'--H21'
!
/
\
!
O3'
O2'
!
|
|
!
H32'
H22'

NG2R51 -0.02
CG2RC0
0.26
NG2R62 -0.74
CG2R64
0.75
NG2R61 -0.34
HGP1
0.26
NG2S3
-0.68
HGP4
0.32
HGP4
0.35
CG2R63
0.54
OG2D4
-0.51
CG2RC0
0.00
NG2R50 -0.60
CG2R53
0.25
HGR52
0.16
Hydroxyl group on C3'
HGA1
0.09
CG3C51
0.14
OG311
-0.65
HGP1
0.42
C5' hydroxyl
CG321
0.05
HGA2
0.09
HGA2
0.09
OG311
-0.65
HGP1
0.42

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4'
BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O2' H22' O3' H32'
BOND C1' N9
BOND N9 C4
N9 C8
C4 N3
C2 N2 C2 N1
BOND N2 H22
N1 H1
N1 C6
C6 C5 C5 N7
DOUBLE C2 N3
C4 C5
N7 C8 C6 O6
IMPR C2 N3 N1 N2
C6 N1 C5 O6
N2
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0
IC
O2'
C2'
C3'
C4'
1.42 109.06 283.42
IC
H22'
O2'
C2'
C3'
0.98 109.05 283.42
IC
O3'
C3'
C4'
O4'
0.0 0.0 324.95 0.0

C5'
H42'

N2
C8

H21
H8

H21 C2
0.0
0.0
0.0
0.0
0.0 0.0
0.0 0.0
0.0

H22

IC
IC
IC
IC
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
IC
IC
IC
IC
IC
PATC

H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
C3' C2' C1' N9
1.5284 101.97 147.80 113.71 1.4896
O4' C1' N9 C4
1.5251 113.71 -97.2 125.59 1.3783 !chi
C1' C4 *N9 C8
1.4896 125.59 -179.99 106.0
1.374
C4 N9 C8 N7
1.377 106.0
0.0 113.5
1.304
C8 N9 C4 C5
1.374 106.0
0.0 105.6
1.377
N9 C5 *C4 N3
1.377 105.6 180.0 128.4
1.355
C5 C4 N3 C2
1.377 128.4
0.0 111.8
1.327
C4 N3 C2 N1
1.355 111.8
0.0 124.0
1.375
N1 N3 *C2 N2
1.375 124.0 180.0 119.7
1.341
N3 C2 N2 H21
1.327 119.7 180.0 127.0
1.01
H21 C2 *N2 H22
1.01
127.0 -180.0 116.5
1.01
N3 C2 N1 C6
1.327 124.0
0.0 124.9
1.393
C6 C2 *N1 H1
1.393 124.9 180.0 117.4
1.03
C5 N1 *C6 O6
1.415 111.7 180.0 120.0
1.239
N9 N7 *C8 H8
0.0
0.0 180.0
0.0
0.0
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0
FIRS NONE LAST NONE

RESI RNUC
0.00 ! C9H13N3O5 ribo-nucleoside with cytosine
GROUP
ATOM O4' OG3C51 -0.40 !
H5T
ATOM C4' CG3C51
0.11 !
/
ATOM H42' HGA1
0.09 ! H51' O5'
ATOM C1' CG3C51
0.11 !
\ |
ATOM H12' HGA1
0.09 !H52'--C5' O4' Cytosine
GROUP
!
\ / \ /
ATOM H21' HGA1
0.09 ! H42'--C4' C1'--H12'
ATOM C2' CG3C51
0.14 !
|
|
ATOM O2' OG311
-0.65 ! H31'--C3'--C2'--H21'
ATOM H22' HGP1
0.42 !
/
\
! Cytosine atoms
!
O3'
O2'
GROUP
!
|
|
ATOM N1 NG2R61 -0.13 !
H32'
H22'
ATOM C6 CG2R62
0.05
ATOM H6 HGR62
0.17
ATOM C2 CG2R63
0.52
ATOM O2 OG2D4
-0.49
ATOM N3 NG2R62 -0.66
ATOM C4 CG2R64
0.65
ATOM N4 NG2S3
-0.75
ATOM H41 HGP4
0.37
ATOM H42 HGP4
0.33
ATOM C5 CG2R62 -0.13
ATOM H5 HGR62
0.07
GROUP ! Hydroxyl group on C3'
ATOM H31' HGA1
0.09
ATOM C3' CG3C51
0.14
ATOM O3' OG311
-0.65
ATOM H32' HGP1
0.42
GROUP ! Methyl group on C4'
ATOM C5' CG321
0.05
ATOM H51' HGA2
0.09

ATOM H52' HGA2


ATOM O5' OG311
ATOM H5T HGP1

0.09
-0.65
0.42

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5'
BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42'
BOND C5' H51' C5' H52' C5' O5' O5' H5T
BOND O2' H22' O3' H32'
BOND C1' N1
BOND N1 C2
N1 C6
BOND C2 N3
C4 N4
N4 H41
N4 H42
BOND C4 C5
C5 H5
C6 H6
DOUBLE C2 O2
C5 C6
N3 C4
IMPR N4 C4 H41 H42
C2 N1 N3 O2
C4 N3 C5 N4
! This IC table is only an initial guess:
IC
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
IC
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
IC
H12'
C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
IC
H21'
C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
IC
O2'
C2'
C3'
C4'
1.42 109.06 283.42 0.0 0.0
IC
H22'
O2'
C2'
C3'
0.98 109.05 283.42 0.0 0.0
IC
O3'
C3'
C4'
O4'
0.0 0.0 324.95 0.0 0.0
IC
H32'
O3'
C3'
C2'
0.0 0.0 -60.00 0.0 0.0
IC
H31'
C3'
C4'
O4'
0.0 0.0 147.80 0.0 0.0
IC
H41'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
IC
H42'
C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.79 -180.00 120.6
1.364
IC C2 N1 C6 C5
1.399 120.6
0.0 121.0
1.337
IC C6 N1 C2 N3
1.364 120.6
0.0 118.9
1.356
IC N1 N3 *C2 O2
1.399 118.9 180.0 121.9
1.237
IC N1 C2 N3 C4
1.399 118.9
0.0 120.0
1.334
IC C5 N3 *C4 N4
1.426 121.8 180.00 118.9
1.337
IC N3 C4 N4 H41
1.337 117.9
0.00 118.9
1.01
IC H41 C4 *N4 H42
1.01
118.9 180.00 120.7
1.01
IC C6 C4 *C5 H5
0.0
0.0 180.0
0.0
0.0
IC N1 C5 *C6 H6
0.0
0.0 180.0
0.0
0.0
IC
C5'
C4'
O4'
C1'
0.0 0.0 144.82 0.0 0.0
IC
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0 0.0
IC
H52'
C5'
C4'
O4'
0.0 0.0 59.66 0.0 0.0
IC
O5'
C5'
C4'
O4'
0.0 0.0 -59.68 0.0 0.0
IC
H5T
O5'
C5'
C4'
0.0 0.0 180.0 0.0 0.0
PATC FIRS NONE LAST NONE
RESI NUCL
-1.00 ! C9H14N2O6P
!WARNING: - The charge distribution on the imidazole is identical
! to the charge distribution on the imidazole in THFI, which is
! different from the charge distribution on the equivalent moiety
! in adenine.
!
- The charge distribution on the sugar is identical to what
! it is in the DNA.
!
- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
!
- The charges on the 5' extremity of the backbone is as in the
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is in non-terminal residues in DNA.
GROUP
ATOM O4' OG3C51 -0.40

ATOM C1' CG3C51


0.11
ATOM H12' HGA1
0.09
ATOM C4' CG3C51
0.11
ATOM H42' HGA1
0.09
GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
! The following atom types use the parameters specifically developed
! for the imidazole
! Atom types for aliphatic atoms based on nucleotide
ATOM CG CG2R51 -0.05 !
C1'
HE1
ATOM HG HGR52
0.09 !
\
/
ATOM CD2 CG2R51
0.22 !
ND1---CE1
ATOM HD2 HGR52
0.10 !
/
||
ATOM ND1 NG2R51 -0.04 ! HG-CG
||
ATOM CE1 CG2R53
0.25 !
\\
||
ATOM HE1 HGR52
0.13 !
CD2---NE2
ATOM NE2 NG2R50 -0.70 !
|
!
HD2
GROUP
!
ATOM C2' CG3C52 -0.18 !
ATOM H21' HGA2
0.09 !
H5T
ATOM H22' HGA2
0.09 !
|
GROUP
!
H52' O5'
ATOM C3' CG3C51
0.01 !
\ /
ATOM H31' HGA1
0.09 ! H51'-C5' O4' Imidazole
ATOM O3' OG303
-0.57 !
\ / \ /
ATOM P
PG1
1.50 ! H42'--C4' C1'--H12'
ATOM O1P OG2P1
-0.78 !
|
|
ATOM O2P OG2P1
-0.78 ! H31'--C3'--C2'--H21'
ATOM O3P OG303
-0.57 !
/
\
ATOM C3T CG331
-0.17 !
O3'
H22'
ATOM H3T1 HGA3
0.09 !
|
ATOM H3T2 HGA3
0.09 ! O1P==P==O2P
ATOM H3T3 HGA3
0.09 !
|
GROUP
!
O3P (-1)
ATOM C5' CG321
0.05 !
\
ATOM H51' HGA2
0.09 !
C3T--H3T3
ATOM H52' HGA2
0.09 !
/ \
ATOM H5T HGP1
0.42 !
H3T1 H3T2
ATOM O5' OG311
-0.65
BOND C1' O4' C1' C2' C2' C3'
BOND C1' H12' C2' H21' C2' H22'
BOND O3' P
P
O1P P
O2P
BOND O3P C3T C3T H3T1 C3T H3T2
BOND C4' C5' C5' H51' C5' H52'
BOND C5' O5' O5' H5T
BOND C1' ND1
BOND ND1 CE1 NE2 CD2 CG ND1
BOND CE1 HE1 CD2 HD2 CG HG
DOUBLE CG CD2 CE1 NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1 CG CE1 C1'
ND1
IMPR CD2 CG NE2 HD2
CD2
IMPR CE1 ND1 NE2 HE1
CE1
IMPR CG CD2 ND1 HG
CG
IC C4'
O4'
C1'
C2'
IC O4'
C1'
C2'
C3'
IC C1'
C2'
C3'
C4'
IC C2'
C3'
C4'
O4'
IC C3'
C4'
O4'
C1'

C3'
C3'
P
C3T

C4' C4' O4' C3' O3'


H31' C4' H42'
O3P
H3T3

CE1 CG
NE2 CG
NE2 ND1
ND1 CD2
1.4055
1.4127
1.5457
1.5346
1.5211

C1'
HD2
HE1
HG
108.09 23.45 106.18
106.18
3.96 103.11
103.11 -26.93 100.86
100.86 41.73 103.15
103.15 -41.62 108.09

1.5457
1.5346
1.5211
1.4055
1.4127

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC

H12'
C1'
H21'
C2'
H22'
C2'
H31'
C3'
C5'
C4'
H51'
C5'
H52'
C5'
H42'
C4'
O3'
C3'
P
O3'
O1P
P
O2P
P
O3P
P
C3T
O3P
H3T1
C3T
H3T2
C3T
H3T3
C3T
C4'
O4'
O4'
C1'
C1'
ND1
ND1
CE1
CE1
NE2
HE1
CE1
CE1
NE2
NE2
CD2
C3'
C4'
H5T
O5'
FIRS NONE LAST

C2'
C3'
C3'
C4'
O4'
C4'
C4'
O4'
C4'
C3'
O3'
O3'
O3'
P
O3P
O3P
O3P
C1'
ND1
CE1
NE2
CD2
NE2
CD2
CG
C5'
C5'
NONE

C3'
C4'
C4'
O4'
C1'
O4'
O4'
C1'
O4'
C4'
C3'
C3'
C3'
O3'
P
P
P
ND1
CE1
NE2
CD2
CG
CD2
HD2
HG
O5'
C4'

1.0818 113.32 -114.11 103.11


1.0846 110.65 91.68 100.86
1.0822 110.88 -148.45 100.86
1.0806 113.53 162.89 103.15
0.0000 000.00 77.76 108.09
0.0
0.0
180.0
0.0
0.0
0.0
-60.0
0.0
1.0808 108.72 -162.12 108.09
1.4028 110.98 -77.39 103.15
0.0
0.0 180.00
0.0
0.0
0.0 -60.0
0.0
0.0
0.0
60.0
0.0
0.0
0.0 180.0
0.0
0.0
0.0 180.0
0.0
0.0
0.0
60.0
0.0
0.0
0.0 -60.0
0.0
0.0
0.0 180.0
0.0
0.0 0.0 256.98 0.0 0.0
0.0 0.0 90.00 0.0 0.0
0.0 0.0 181.56 0.0 0.0
0.0 0.0 0.34 0.0 0.0
0.0 0.0 0.00 0.0 0.0
0.0 0.0 180.40 0.0 0.0
0.0 0.0 179.83 0.0 0.0
0.0 0.0 178.45 0.0 0.0
0.0 0.0 60.0 0.0 0.0
0.0000
0.00 180.00
0.00

1.5346
1.5211
1.5211
1.4055
1.4127
0.0
0.0
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0000

RESI NADE
-1.00 ! C11H15N5O6P
! NADE is a nucleotide analogue similar to NUCL, except that the imidazole
! has been replaced by an adenine
!
- The charge distribution on the sugar is identical to what
! it is in the DNA.
!
- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
!
- The charges on the 5' extremity of the backbone is as in the
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is actuallly in non-terminal residues in the
! DNA.
GROUP
ATOM O4' OG3C51 -0.40 !
H5T
ATOM C1' CG3C51
0.11 !
|
ATOM H12' HGA1
0.09 !
H52' O5'
ATOM C4' CG3C51
0.11 !
\ /
ATOM H42' HGA1
0.09 ! H51'-C5' O4' Adenine
GROUP
!
\ / \ /
ATOM C5 CG2RC0
0.30 ! H42'--C4' C1'--H12'
ATOM N7 NG2R50 -0.69 !
|
|
ATOM C8 CG2R53
0.34 ! H31'--C3'--C2'--H21'
ATOM H8 HGR52
0.10 !
/
\
ATOM N9 NG2R51 -0.06 !
O3'
H22'
ATOM N1 NG2R62 -0.74 !
|
ATOM C2 CG2R64
0.50 ! O1P==P==O2P
ATOM H2 HGR62
0.13 !
|
ATOM N3 NG2R62 -0.75 !
O3P (-1)
ATOM C4 CG2RC0
0.43 !
\
ATOM C6 CG2R64
0.44 !
C3T--H3T3
ATOM N6 NG2S3
-0.75 !
/ \

ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H21'
ATOM H22'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM P
ATOM O1P
ATOM O2P
ATOM O3P
ATOM C3T
ATOM H3T1
ATOM H3T2
ATOM H3T3
GROUP
ATOM C5'
ATOM H51'
ATOM H52'
ATOM H5T
ATOM O5'

HGP4
HGP4

0.38 !
0.37

CG3C52
HGA2
HGA2

-0.18
0.09
0.09

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG303
CG331
HGA3
HGA3
HGA3

0.01
0.09
-0.57
1.50
-0.78
-0.78
-0.57
-0.17
0.09
0.09
0.09

CG321
HGA2
HGA2
HGP1
OG311

0.05
0.09
0.09
0.42
-0.65

H3T1 H3T2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND O3' P
P
O1P P
O2P P
O3P
BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3
BOND C4' C5' C5' H51' C5' H52'
BOND C5' O5' O5' H5T
BOND C1' N9
BOND N9 C4
N9 C8 C4 N3
C2 N1
C6 N6
BOND N6 H61 N6 H62 C6 C5
C5 N7
C8 H8
C2 H2
DOUBLE N1 C6
C2 N3
C4 C5
N7 C8
IMPR N6 C6 H61 H62
C6 N1 C5 N6
IC C4'
O4'
C1'
C2'
1.4055 108.09 23.45 106.18 1.5457
IC O4'
C1'
C2'
C3'
1.4127 106.18
3.96 103.11 1.5346
IC C1'
C2'
C3'
C4'
1.5457 103.11 -26.93 100.86 1.5211
IC C2'
C3'
C4'
O4'
1.5346 100.86 41.73 103.15 1.4055
IC C3'
C4'
O4'
C1'
1.5211 103.15 -41.62 108.09 1.4127
IC H12'
C1'
C2'
C3'
1.0818 113.32 -114.11 103.11 1.5346
IC H21'
C2'
C3'
C4'
1.0846 110.65 91.68 100.86 1.5211
IC H22'
C2'
C3'
C4'
1.0822 110.88 -148.45 100.86 1.5211
IC H31'
C3'
C4'
O4'
1.0806 113.53 162.89 103.15 1.4055
IC C5'
C4'
O4'
C1'
0.0000 000.00 77.76 108.09 1.4127
IC H51'
C5'
C4'
O4'
0.0
0.0
180.0
0.0
0.0
IC H52'
C5'
C4'
O4'
0.0
0.0
-60.0
0.0
0.0
IC H42'
C4'
O4'
C1'
1.0808 108.72 -162.12 108.09 1.4127
IC O3'
C3'
C4'
O4'
1.4028 110.98 -77.39 103.15 1.4055
IC P
O3'
C3'
C4'
0.0
0.0 180.00
0.0
0.0
IC O1P
P
O3'
C3'
0.0
0.0 -60.0
0.0
0.0
IC O2P
P
O3'
C3'
0.0
0.0
60.0
0.0
0.0
IC O3P
P
O3'
C3'
0.0
0.0 180.0
0.0
0.0
IC C3T
O3P
P
O3'
0.0
0.0 180.0
0.0
0.0
IC H3T1
C3T
O3P
P
0.0
0.0
60.0
0.0
0.0
IC H3T2
C3T
O3P
P
0.0
0.0 -60.0
0.0
0.0
IC H3T3
C3T
O3P
P
0.0
0.0 180.0
0.0
0.0
IC C3' C2' C1' N9
1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4
1.5251 113.71 180.2 125.59 1.3783 !chi

IC C1' C4 *N9 C8
1.4896
IC C4 N9 C8 N7
1.376
IC C8 N9 C4 C5
1.367
IC C8 N7 C5 C6
0.0
IC N7 C5 C6 N1
0.0
IC C5 C6 N1 C2
0.0
IC N9 C5 *C4 N3
1.376
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC N9 N7 *C8 H8
0.0
IC N1 N3 *C2 H2
0.0
IC C3' C4' C5' O5'
0.0
IC H5T O5' C5' C4'
0.0
PATC FIRS NONE LAST NONE

125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
0.0
0.0

-180.00
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
60.0
180.0

106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
0.0
0.0

1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
0.0
0.0

RESI NTHY
-1.00 ! C11H16N2O8P
! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole
! has been replaced by a thymine
!
- The charge distribution on the sugar is identical to what
! it is in the DNA.
!
- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
!
- The charges on the 5' extremity of the backbone is as in the
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is actuallly in non-terminal residues in the
! DNA.
GROUP
ATOM O4' OG3C51 -0.40 !
H5T
ATOM C1' CG3C51
0.11 !
|
ATOM H12' HGA1
0.09 !
H52' O5'
ATOM C4' CG3C51
0.11 !
\ /
ATOM H42' HGA1
0.09 ! H51'-C5' O4' Thymine
GROUP
!
\ / \ /
ATOM N1 NG2R61 -0.34 ! H42'--C4' C1'--H12'
ATOM C6 CG2R62
0.17 !
|
|
ATOM H6 HGR62
0.17 ! H31'--C3'--C2'--H21'
ATOM C2 CG2R63
0.51 !
/
\
ATOM O2 OG2D4
-0.41 !
O3'
H22'
ATOM N3 NG2R61 -0.46 !
|
ATOM H3 HGP1
0.36 ! O1P==P==O2P
ATOM C4 CG2R63
0.50 !
|
ATOM O4 OG2D4
-0.45 !
O3P (-1)
ATOM C5 CG2R62 -0.15 !
\
ATOM C5M CG331
-0.11 !
C3T--H3T3
ATOM H51 HGA3
0.07 !
/ \
ATOM H52 HGA3
0.07 !
H3T1 H3T2
ATOM H53 HGA3
0.07
GROUP
ATOM C2' CG3C52 -0.18
ATOM H21' HGA2
0.09
ATOM H22' HGA2
0.09
GROUP
ATOM C3' CG3C51
0.01
ATOM H31' HGA1
0.09
ATOM O3' OG303
-0.57

ATOM P
PG1
1.50
ATOM O1P OG2P1
-0.78
ATOM O2P OG2P1
-0.78
ATOM O3P OG303
-0.57
ATOM C3T CG331
-0.17
ATOM H3T1 HGA3
0.09
ATOM H3T2 HGA3
0.09
ATOM H3T3 HGA3
0.09
GROUP
ATOM C5' CG321
0.05
ATOM H51' HGA2
0.09
ATOM H52' HGA2
0.09
ATOM H5T HGP1
0.42
ATOM O5' OG311
-0.65
BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42'
BOND O3' P
P
O1P P
O2P P
O3P
BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3
BOND C4' C5' C5' H51' C5' H52'
BOND C5' O5' O5' H5T
BOND C1' N1
BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5
BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53
DOUBLE C2 O2
C4 O4
C5 C6
IMPR C2 N1 N3 O2
C4 N3 C5 O4
C5 C4 C6 C5M
IC C4'
O4'
C1'
C2'
1.4055 108.09 23.45 106.18 1.5457
IC O4'
C1'
C2'
C3'
1.4127 106.18
3.96 103.11 1.5346
IC C1'
C2'
C3'
C4'
1.5457 103.11 -26.93 100.86 1.5211
IC C2'
C3'
C4'
O4'
1.5346 100.86 41.73 103.15 1.4055
IC C3'
C4'
O4'
C1'
1.5211 103.15 -41.62 108.09 1.4127
IC H12'
C1'
C2'
C3'
1.0818 113.32 -114.11 103.11 1.5346
IC H21'
C2'
C3'
C4'
1.0846 110.65 91.68 100.86 1.5211
IC H22'
C2'
C3'
C4'
1.0822 110.88 -148.45 100.86 1.5211
IC H31'
C3'
C4'
O4'
1.0806 113.53 162.89 103.15 1.4055
IC C5'
C4'
O4'
C1'
0.0000 000.00 77.76 108.09 1.4127
IC H51'
C5'
C4'
O4'
0.0
0.0
180.0
0.0
0.0
IC H52'
C5'
C4'
O4'
0.0
0.0
-60.0
0.0
0.0
IC H42'
C4'
O4'
C1'
1.0808 108.72 -162.12 108.09 1.4127
IC O3'
C3'
C4'
O4'
1.4028 110.98 -77.39 103.15 1.4055
IC P
O3'
C3'
C4'
0.0
0.0 180.00
0.0
0.0
IC O1P
P
O3'
C3'
0.0
0.0 -60.0
0.0
0.0
IC O2P
P
O3'
C3'
0.0
0.0
60.0
0.0
0.0
IC O3P
P
O3'
C3'
0.0
0.0 180.0
0.0
0.0
IC C3T
O3P
P
O3'
0.0
0.0 180.0
0.0
0.0
IC H3T1
C3T
O3P
P
0.0
0.0
60.0
0.0
0.0
IC H3T2
C3T
O3P
P
0.0
0.0 -60.0
0.0
0.0
IC H3T3
C3T
O3P
P
0.0
0.0 180.0
0.0
0.0
IC
C3'
C4'
C5'
O5'
0.0 0.0 60.0 0.0 0.0
IC
H5T
O5'
C5'
C4' 0.0000
0.00 180.00
0.00 0.0000
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC C3' C2' C1' N1
1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2
1.5251 113.71 180.0 125.59 1.3783 !chi
IC C1' C2 *N1 C6
1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5
1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3
1.3704 122.08
0.06 115.38 1.3813
IC N1 N3 *C2 O2
1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4
1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4
1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3
1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M
1.4439 120.78 -179.94 121.63 1.5000

IC N1 C5 *C6 H6
0.0
IC C6 C5 C5M H51
0.0
IC C5 H51 *C5M H52
0.0
IC H51 H52 *C5M H53
0.0
PATC FIRS NONE LAST NONE

0.0 180.0
0.0
0.0
0.0 115.0
0.0 -115.0

0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0

!toppar_all27_na_nad_ppi.str
RESI NIC
1.00 ! C6H7N2O oxidized nicotinamide (protonated), jjp1/adm
jr.
! checked for consistency with new NA params, adm jr.,
9/98
! note that differences with respect to published resul
ts exist
! due to new NA params
!
!
H15
GROUP
!
\
ATOM H1 HGP2
0.45 !
H16-N14
H8
ATOM N2 NG2R61 -0.52 !
\
|
ATOM C3 CG2R62
0.16 !
C12 C7
ATOM H4 HGR63
0.19 !
// \ / \\
ATOM C5 CG2R62 -0.10 !
O13 C9 C5-H6
ATOM H6 HGR63
0.16 !
|| |
ATOM C7 CG2R62 -0.05 !
H11-C10 C3-H4
ATOM H8 HGR63
0.16 !
\+ //
ATOM C9 CG2R62
0.05 !
N2
ATOM C10 CG2R62
0.18 !
|
ATOM H11 HGR63
0.16 !
H1
ATOM C12 CG2O1
0.68 !
ATOM O13 OG2D1
-0.40 !
ATOM N14 NG2S2
-0.82 !
ATOM H15 HGP1
0.34 ! trans to O13
ATOM H16 HGP1
0.36 ! cis to O13
BOND N2 H1 C3 H4 C3 C5 C5 H6
BOND C7 H8 C7 C9 N2 C10
BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16
DOUBLE C12 O13 C9 C10 C5 C7 N2 C3
! amide impropers
IMPR C12 N14 C9 O13 C12 C9 N14 O13
IMPR N14 C12 H16 H15 N14 C12 H15 H16
! ring hydrogen impropers
IMPR N2 C10 C3 H1
C3 N2 C5 H4
C5 C3 C7 H6
IMPR C7 C5 C9 H8
C10 C9 N2 H11
! ic table for analysis
IC N2 C3 C5 C7
0.0000 000.00 000.00 000.00 0.000
IC C3 C5 C7 C9
0.0000 000.00 000.00 000.00 0.000
IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000
IC C7 C9 C10 N2
0.0000 000.00 000.00 000.00 0.000
IC C9 C10 N2 C3
0.0000 000.00 000.00 000.00 0.000
IC C10 N2 C3 C5
0.0000 000.00 000.00 000.00 0.000
IC C9 C10 N2 H1
0.0000 000.00 000.00 000.00 0.000
IC C10 N2 C3 H4
0.0000 000.00 000.00 000.00 0.000
IC N2 C3 C5 H6
0.0000 000.00 000.00 000.00 0.000
IC C3 C5 C7 H8
0.0000 000.00 000.00 000.00 0.000
IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000
IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000
IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000
IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000
IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000
IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000

PATCH FIRST NONE LAST NONE


RESI NICH

0.00 ! C6H8N2O reduced nicotinamide, jjp1/adm jr.


! checked for consistency with new NA params, adm jr.,

9/98
! note that differences with respect to published resul
ts exist
! due to new NA params
! HN3 to HN6 atom type switch to maintain proper vdw pa
rams, 9/98
GROUP
ATOM H1
ATOM N2
ATOM C3
ATOM H4
ATOM C5
ATOM H6
ATOM C7
ATOM H8
ATOM H17
ATOM C10
ATOM H11
ATOM C9
ATOM C12
ATOM O13
ATOM N14
ATOM H15
ATOM H16

HGPAM1
NG311
CG2D1O
HGA4
CG2D1
HGA4
CG321
HGA2
HGA2
CG2D1O
HGA4
CG2DC1
CG2O1
OG2D1
NG2S2
HGP1
HGP1

0.42
-0.69
-0.06
0.17
-0.18
0.14
-0.28
0.09
0.09
-0.10
0.14
0.36
0.55
-0.51
-0.72
0.26
0.32

!
!
H15
!
\
!
H16-N14 H8 H17
!
\
\ /
!
C12 C7
!
/ \ / \
!
O13 C9 C5-H6
!
|| ||
!
H11-C10 C3-H4
!
\ /
!
N2
!
|
!
H1
!
!
!
!
! trans to O13
! cis to O13

BOND N2 H1 N2 C3 C3 H4 C5 H6
BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10
BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16
DOUBLE C12 O13 C9 C10 C3 C5
! amide impropers
IMPR C12 N14 C9 O13 C12 C9 N14 O13
IMPR N14 C12 H16 H15 N14 C12 H15 H16
! ring hydrogen impropers
! IMPR N2 C10 C3 H1 ! Unlikely; removed by kevo
IMPR C3 N2 C5 H4 C5 C3 C7 H6
IMPR C10 C9 N2 H11
! new IC table by kevo. Deliberately slightly distorted.
IC C10 C9
C7
C5
0.0000
0.00 10.00
IC C7
C9
C10 N2
0.0000
0.00
0.00
IC C10 C7
*C9 C12
0.0000
0.00 180.00
IC C9
C7
C5
C3
0.0000
0.00 -10.00
IC C10 C9
C12 N14
0.0000
0.00 180.00
IC C9
N14 *C12 O13
0.0000
0.00 180.00
IC C9
C12 N14 H15
0.0000
0.00
0.00
IC C12 H15 *N14 H16
0.0000
0.00 180.00
IC C9
N2
*C10 H11
0.0000
0.00 180.00
IC C10 C3
*N2 H1
0.0000
0.00 175.00
IC N2
C5
*C3 H4
0.0000
0.00 180.00
IC C3
C7
*C5 H6
0.0000
0.00 180.00
IC C5
C9
*C7 H8
0.0000
0.00 120.00
IC C5
C9
*C7 H17
0.0000
0.00 -120.00
PATCH FIRST NONE LAST NONE
RESI PPI1

-3.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

! CH3O7P2 Inorganic phosphate, jjp1/adm jr.

GROUP
ATOM C1
ATOM O11
ATOM P1
ATOM O12
ATOM O13
ATOM O14

CG331
OG303
PG2
OG303
OG2P1
OG2P1

-0.17
-0.62
1.50
-0.74
-0.82
-0.82

ATOM
ATOM
ATOM
ATOM

PG2
OG2P1
OG2P1
OG2P1

1.10
-0.90
-0.90
-0.90

P2
O22
O23
O24

ATOM H11 HGA3


ATOM H12 HGA3
ATOM H13 HGA3

0.09
0.09
0.09

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

BOND P1 O11 P1 O12 P1 O13


BOND C1 H11 C1 H12 C1 H13
BOND O12 P2
P2 O22 P2 O23
! IC Table
IC C1 O11 P1 O12 0.0000
IC O11 P1 O12 P2 0.0000
IC P1 O12 P2 O22 0.0000
IC C1 O11 P1 O13 0.0000
IC C1 O11 P1 O14 0.0000
IC P1 O12 P2 O23 0.0000
IC P1 O12 P2 O24 0.0000
IC P1 O11 C1 H11 0.0000
IC P1 O11 C1 H12 0.0000
IC P1 O11 C1 H13 0.0000
PATC FIRS NONE LAST NONE
RESI PPI2

-2.00

GROUP
ATOM C1
ATOM O11
ATOM P1
ATOM O12
ATOM O13
ATOM O14

CG331
OG303
PG2
OG303
OG2P1
OG2P1

-0.17
-0.62
1.46
-0.63
-0.83
-0.83

ATOM
ATOM
ATOM
ATOM
ATOM

PG3
OG311
HGP1
OG2P1
OG2P1

1.34
-0.71
0.44
-0.86
-0.86

P2
O22
H22
O23
O24

ATOM H11 HGA3


ATOM H12 HGA3
ATOM H13 HGA3

BOND P1 O11 P1
BOND C1 H11 C1
BOND O12 P2
P2
! IC Table
IC C1 O11 P1

0.09
0.09
0.09

O12
H12
O22

H11
|
H13--C1--H12
|
O11
|
O14==P1==O13 (-)
|
O12
|
(-) O24==P2==O23 (-)
||
O22
P1 O14

O11 C1

P2 O24
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

180.0
180.0
180.0
60.0
-60.0
60.0
-60.0
180.0
60.0
-60.0

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

! CH4O7P2 Inorganic phosphate, protonated, adm jr.


! terminal P charges based on neutral
! methylphosphate
!
!
!
H11
!
|
!
H13--C1--H12
!
|
!
O11
!
|
!
O14==P1==O13 (-)
!
|
!
|
!
O12
!
|
!
(-) O24==P2==O23 (-)
!
|
!
O22
!
\
!
H22
P1 O13
C1 H13
P2 O23

O12 0.0000

P1 O14

O11 C1

P2 O24

O22 H22

000.00

180.0

000.00

0.0000

IC O11 P1 O12 P2 0.0000


IC P1 O12 P2 O22 0.0000
IC C1 O11 P1 O13 0.0000
IC C1 O11 P1 O14 0.0000
IC P1 O12 P2 O23 0.0000
IC P1 O12 P2 O24 0.0000
IC P1 O11 C1 H11 0.0000
IC P1 O11 C1 H12 0.0000
IC P1 O11 C1 H13 0.0000
IC O12 P2 O22 H22 0.0000
PATC FIRS NONE LAST NONE
RESI AMP
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

N1
C2
H2
N3
C4
C6

ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM O5'
ATOM PA
ATOM O1A
ATOM O2A
ATOM O3A

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

180.0
180.0
60.0
-60.0
60.0
-60.0
180.0
60.0
-60.0
180.0

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

-2.00 ! C10H12N5O7P adenosine monophosphate, jjp1/adm jr.


! atom names correspond to pdb nomenclature
CG3C51
HGA1
OG3C51
CG3C51
HGA1

0.11
0.09
-0.40
0.11
0.09

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.28
-0.71
0.34
0.12
-0.05

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321
HGA2
HGA2

-0.18
0.09
0.09

OG303
PG1
OG2P1
OG2P1
OG2P1

-0.40
1.10
-0.90
-0.90
-0.90

BOND PA O1A
BOND O5' C5'

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

PA O2A
C5' C4'

H61 H62
\ /
N6
|
C6
// \
N1 C5--N7\\
|
||
C8-H8
C2 C4--N9/
/ \\ /
\
H2 N3
\
\
\
\
O1A
H5' H4' O4' \
|
|
\ / \ \
O3A=PA-O5'-C5'---C4'
C1'
|
|
\
/ \
O2A
H5'' C3'--C2' H1'
/ \ / \
O3' H3' O2' H2''
|
|
H3T
H2'

PA O3A
C4' O4'

PA
O5'
C4' C3'

O3' H3T
O4' C1'

BOND C1' N9
C1' C2'
BOND C2 N1
C6 N6
BOND N6 H61
N6 H62
BOND C2' C3'
C2' O2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8 H8
DOUBLE N1 C6
N3 C2
C4
IMPR N6 C6 H61 H62
C6
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A PA
ACCE O2A PA
ACCE O3A PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC O5' O3A *PA O1A
0.0000
IC O5' O3A *PA O2A
0.0000
IC O3A PA O5' C5'
0.0000
!IC PA O5' C5' C4'
1.5996
minimum
IC PA O5' C5' C4'
0.0000
!IC O5' C5' C4' C3'
1.4401
minimum
IC O5' C5' C4' C3'
0.0000
IC C5' C4' C3' O3'
1.5160
IC H3T O3' C3' C4'
0.9650
IC O4' C3' *C4' C5'
1.4572
IC C2' C4' *C3' O3'
1.5284
IC C4' C3' C2' C1'
1.5284
!IC C3' C2' C1' N9
1.5284
be right
IC O4' C2' *C1' N9
0.0
!IC O4' C1' N9 C4
1.5251
ixing N9
IC O4' C1' N9 C4
0.0
IC C1' C4 *N9 C8
1.4896
IC C4 N9 C8 N7
1.376
IC C8 N9 C4 C5
1.367
IC C8 N7 C5 C6
0.0
IC N7 C5 C6 N1
0.0
IC C5 C6 N1 C2
0.0
IC N9 C5 *C4 N3
1.376
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC N9 N7 *C8 H8
0.0
IC N1 N3 *C2 H2
0.0
IC C1' C3' *C2' O2'
1.5284
IC H2' O2' C2' C3'
0.9600
IC O4' C2' *C1' H1'
0.0
IC C1' C3' *C2' H2'' 0.0

N9

C4

N9

C6
O2'
C3'
C2
C5
N1

C5
H2'
H3'
H2

C5 N7
C3' O3'
C4' H4'

C5

C8

C4

N3

C5' H5'

N7 C8
N6

000.00 120.0
000.00 -120.0
000.00 -30.0
119.00 -151.39

000.00 0.0000
000.00 0.0000
000.00 0.0000
110.04 1.5160 !Not-so-stable

000.00 -110.0 000.00 0.0000


108.83 -179.85 116.10 1.5284 !Not-so-stable
000.00 70.0
116.10 76.70
105.47 38.18
104.06 -120.04
100.16 -124.08
100.16 39.58
101.97 144.39

000.00
115.12
111.98
116.10
115.12
102.04
113.71

0.0000
1.4212
1.5386
1.5160
1.4212
1.5251
1.4896 !144.39 can't

0.0 120.0
0.0
0.0
113.71 -96.00 125.97 1.3703 !clash after f
0.0
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
102.04
114.97
0.0
0.0

-150.0
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0

0.0
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
110.81
111.92
0.0
0.0

0.0
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
0.0
0.0

IC C2' C4' *C3' H3'


0.0
IC C3' O4' *C4' H4'
0.0
IC C4' O5' *C5' H5'
0.0
IC C4' O5' *C5' H5'' 0.0
PATC FIRS NONE LAST NONE
RESI ADP
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9

0.11
0.09
-0.40
0.11
0.09

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.28
-0.71
0.34
0.12
-0.05

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM O5'
ATOM PA
ATOM O1A
ATOM O2A
ATOM O3A
ATOM PB
ATOM O1B
ATOM O2B
ATOM O3B

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321
HGA2
HGA2
OG303
PG2
OG2P1
OG2P1
OG303
PG2
OG2P1
OG2P1
OG2P1

-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.74
1.10
-0.90
-0.90
-0.90

BOND
BOND
BOND
BOND

O3A
O1A
C5'
N9

N1
C2
H2
N3
C4
C6

PB
PA
O5'
C1'

0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0

-3.00 ! C10H12N5O10P2 adenosine diphosphate, jjp1/adm jr.


! atom names correspond to pdb nomenclature
CG3C51
HGA1
OG3C51
CG3C51
HGA1

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

0.0 115.0
0.0 -115.0
0.0 -115.0
0.0 115.0

PB
PA
C5'
C1'

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

O1B
O2A
C4'
C2'

H61 H62
\ /
N6
|
C6
// \
N1 C5--N7\\
|
||
C8-H8
C2 C4--N9/
/ \\ /
\
H2 N3
\
\
\
\
O3B
O1A
H5' H4' O4' \
|
|
|
\ / \ \
O1B=PB-O3A--PA-O5'-C5'---C4'
C1'
|
|
|
\
/ \
O2B
O2A
H5'' C3'--C2' H1'
/ \ / \
O3' H3' O2' H2''
|
|
H3T
H2'

PB
O2B
PA
O5'
C4' O4'
N9 C4

PB
O3'
C4'
N9

O3B
H3T
C3'
C8

O3A PA
O4' C1'
C4 N3

BOND C2 N1
C6 N6
BOND N6 H61
N6 H62
BOND C2' C3'
C2' O2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8 H8
DOUBLE N1 C6
N3 C2
C4
IMPR N6 C6 H61 H62
C6
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A PA
ACCE O2A PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B
IC PA O3A PB O3B
0.0000
IC PB O3A PA O5'
0.0000
IC O5' O3A *PA O1A
0.0000
IC O5' O3A *PA O2A
0.0000
IC O3A O3B *PB O1B
0.0000
IC O3A O3B *PB O2B
0.0000
IC O3A PA O5' C5'
0.0000
!IC PA O5' C5' C4'
1.5996
minimum
IC PA O5' C5' C4'
0.0000
!IC O5' C5' C4' C3'
1.4401
minimum
IC O5' C5' C4' C3'
0.0000
IC C5' C4' C3' O3'
1.5160
IC H3T O3' C3' C4'
0.9650
IC O4' C3' *C4' C5'
1.4572
IC C2' C4' *C3' O3'
1.5284
IC C4' C3' C2' C1'
1.5284
!IC C3' C2' C1' N9
1.5284
be right
IC O4' C2' *C1' N9
0.0
!IC O4' C1' N9 C4
1.5251
ixing N9
IC O4' C1' N9 C4
0.0
IC C1' C4 *N9 C8
1.4896
IC C4 N9 C8 N7
1.376
IC C8 N9 C4 C5
1.367
IC C8 N7 C5 C6
0.0
IC N7 C5 C6 N1
0.0
IC C5 C6 N1 C2
0.0
IC N9 C5 *C4 N3
1.376
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01

C6
O2'
C3'
C2
C5
N1

C5
H2'
H3'
H2
C5

C5 N7
C3' O3'
C4' H4'

C5' H5'

N7 C8
N6

000.00 180.0
000.00 120.0
000.00 120.0
000.00 -120.0
000.00 120.0
000.00 -120.0
000.00 -30.0
119.00 -151.39

000.00
000.00
000.00
000.00
000.00
000.00
000.00
110.04

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
1.5160 !Not-so-stable

000.00 -110.0 000.00 0.0000


108.83 -179.85 116.10 1.5284 !Not-so-stable
000.00 70.0
116.10 76.70
105.47 38.18
104.06 -120.04
100.16 -124.08
100.16 39.58
101.97 144.39

000.00
115.12
111.98
116.10
115.12
102.04
113.71

0.0000
1.4212
1.5386
1.5160
1.4212
1.5251
1.4896 !144.39 can't

0.0 120.0
0.0
0.0
113.71 -96.00 125.97 1.3703 !clash after f
0.0
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0

-150.0
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0

0.0
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00

0.0
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01

IC N9 N7 *C8 H8
0.0
0.0 180.0
0.0
IC N1 N3 *C2 H2
0.0
0.0 180.0
0.0
IC C1' C3' *C2' O2'
1.5284 102.04 -114.67 110.81
IC H2' O2' C2' C3'
0.9600 114.97 148.63 111.92
IC O4' C2' *C1' H1'
0.0
0.0 -115.0
0.0
IC C1' C3' *C2' H2'' 0.0
0.0 115.0
0.0
IC C2' C4' *C3' H3'
0.0
0.0 115.0
0.0
IC C3' O4' *C4' H4'
0.0
0.0 -115.0
0.0
IC C4' O5' *C5' H5'
0.0
0.0 -115.0
0.0
IC C4' O5' *C5' H5'' 0.0
0.0 115.0
0.0
PATC FIRS NONE LAST NONE
RESI ATP
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

N1
C2
H2
N3
C4
C6

ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM O5'
ATOM PA
ATOM O1A
ATOM O2A
ATOM O3A
ATOM PB
ATOM O1B
ATOM O2B

0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0

-4.00 ! C10H12N5O13P3 adenosine triphosphate , jjp1/adm jr.


!atom names correspond to pdb nomenclature
!
CG3C51
HGA1
OG3C51
CG3C51
HGA1

0.11
0.09
-0.40
0.11
0.09

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.28
-0.71
0.34
0.12
-0.05

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321
HGA2
HGA2
OG303
PG2
OG2P1
OG2P1
OG303
PG2
OG2P1
OG2P1

-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.74
1.50
-0.82
-0.82

!
H61 H62
!
\ /
!
N6
!
|
!
C6
!
// \
!
N1 C5--N7\\
!
|
||
C8-H8
!
C2 C4--N9/
!
/ \\ /
\
!
H2 N3
\
!
\
!
\
!
\
! (-)O3G O2B
O1A
H5' H4' O4' \
!
|
|
|
|
\ / \ \
!O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4'
C1'
!
|
|
|
|
\
/ \
! (-)O2G (-)O1B (-)O2A
H5'' C3'--C2' H1'
!
/ \ / \
!
O3' H3' O2' H2''
!
|
|
!
H3T
H2'
!

ATOM
ATOM
ATOM
ATOM
ATOM

O3B
PG
O1G
O2G
O3G

OG303
PG2
OG2P1
OG2P1
OG2P1

-0.86 ! charge adjusted to yield total triP of -4.0


1.10
-0.90
-0.90
-0.90

BOND O5' C5'


O5' PA
BOND O3A PB
PB O1B
BOND PG O1G
PG O2G
BOND C5' C4'
C4' O4'
BOND C1' N9
C1' C2'
BOND C2 N1
C6 N6
BOND N6 H61
N6 H62
BOND C2' C3'
C2' O2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8 H8
DOUBLE N1 C6
N3 C2
C4
IMPR N6 C6 H61 H62
C6
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A PA
ACCE O2A PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G
IC PA O3A PB O3B
0.0000
IC PB O3A PA O5'
0.0000
IC O5' O3A *PA O1A
0.0000
IC O5' O3A *PA O2A
0.0000
IC O3A O3B *PB O1B
0.0000
IC O3A O3B *PB O2B
0.0000
IC O3A PB O3B PG
0.0000
IC PB O3B PG O1G
0.0000
IC O3B O1G *PG O2G
0.0000
IC O3B O1G *PG O3G
0.0000
IC O3A PA O5' C5'
0.0000
!IC PA O5' C5' C4'
1.5996
minimum
IC PA O5' C5' C4'
0.0000
!IC O5' C5' C4' C3'
1.4401
minimum
IC O5' C5' C4' C3'
0.0000
IC C5' C4' C3' O3'
1.5160
IC H3T O3' C3' C4'
0.9650
IC O4' C3' *C4' C5'
1.4572
IC C2' C4' *C3' O3'
1.5284
IC C4' C3' C2' C1'
1.5284
!IC C3' C2' C1' N9
1.5284

PA
PB
PG
C4'
N9

O1A
O2B
O3G
C3'
C4

PA
PB

O4' C1'
N9 C8

C4

C6
O2'
C3'
C2
C5
N1

C5
H2'
H3'
H2

C5 N7
C3' O3'
C4' H4'

O3' H3T
C5' H5'

C5

O2A
O3B

PA O3A
O3B PG
N3

N7 C8
N6

000.00 180.0
000.00 120.0
000.00 120.0
000.00 -120.0
000.00 120.0
000.00 -120.0
000.00 150.0
000.00 150.0
000.00 120.0
000.00 -120.0
000.00 -30.0
119.00 -151.39

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
110.04

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
1.5160 !Not-so-stable

000.00 -110.0 000.00 0.0000


108.83 -179.85 116.10 1.5284 !Not-so-stable
000.00 70.0
116.10 76.70
105.47 38.18
104.06 -120.04
100.16 -124.08
100.16 39.58
101.97 144.39

000.00
115.12
111.98
116.10
115.12
102.04
113.71

0.0000
1.4212
1.5386
1.5160
1.4212
1.5251
1.4896 !144.39 can't

be right
IC O4' C2' *C1' N9
0.0
!IC O4' C1' N9 C4
1.5251
ixing N9
IC O4' C1' N9 C4
0.0
IC C1' C4 *N9 C8
1.4896
IC C4 N9 C8 N7
1.376
IC C8 N9 C4 C5
1.367
IC C8 N7 C5 C6
0.0
IC N7 C5 C6 N1
0.0
IC C5 C6 N1 C2
0.0
IC N9 C5 *C4 N3
1.376
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC C5 N1 *C6 N6
1.409
IC N1 C6 N6 H61
1.337
IC H61 C6 *N6 H62
1.01
IC N9 N7 *C8 H8
0.0
IC N1 N3 *C2 H2
0.0
IC C1' C3' *C2' O2'
1.5284
IC H2' O2' C2' C3'
0.9600
IC O4' C2' *C1' H1'
0.0
IC C1' C3' *C2' H2'' 0.0
IC C2' C4' *C3' H3'
0.0
IC C3' O4' *C4' H4'
0.0
IC C4' O5' *C5' H5'
0.0
IC C4' O5' *C5' H5'' 0.0
PATC FIRS NONE LAST NONE
PRES 5DP
jjp1/adm jr.

0.0 120.0
0.0
0.0
113.71 -96.00 125.97 1.3703 !clash after f
0.0
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0

-150.0
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0

0.0
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0

0.0
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0

-3.00 ! CH2O7P2 patch to create 5' diphosphate on nucleotides,


! as in ADP, use in generate statement

GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM O5'
ATOM P
ATOM O1P
ATOM O2P
ATOM O13
ATOM P2
ATOM O21
ATOM O22
ATOM O23

CG321
HGA2
HGA2
OG303
PG2
OG2P1
OG2P1
OG303
PG2
OG2P1
OG2P1
OG2P1

-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.74
1.10
-0.90
-0.90
-0.90

BOND P
O13
O13 P2
BOND P2
O21
P2
O22
ACCE O13
ACCE O21
ACCE O22
ACCE O23
IC C5' O5' P
O13
0.0000
IC O5' P
O13 P2
0.0000
IC P
O13 P2
O21
0.0000
IC P
O13 P2
O22
0.0000
IC P
O13 P2
O23
0.0000
PATC FIRS NONE LAST NONE

P2

000.00
000.00
000.00
000.00
000.00

O23

180.0 000.00 0.0000


180.0 000.00 0.0000
180.0 000.00 0.0000
60.0 000.00 0.0000
-60.0 000.00 0.0000

RESI NAD
-1.00 !
tide, jjp1/adm jr.
!
!
9/98
!
lts exist
!
GROUP
!
ATOM AC4' CG3C51
0.11 !
ATOM AH4' HGA1
0.09 !
ATOM AO4' OG3C51 -0.40 !
ATOM AC1' CG3C51
0.11 !
ATOM AH1' HGA1
0.09 !
GROUP
!
ATOM AC5 CG2RC0
0.28 !
ATOM AN7 NG2R50 -0.71 !
ATOM AC8 CG2R53
0.34 !
ATOM AH8 HGR52
0.12 !
ATOM AN9 NG2R51 -0.05 !
!
ATOM AN1 NG2R62 -0.74 !
ATOM AC2 CG2R64
0.50 !
ATOM AH2 HGR62
0.13 !
ATOM AN3 NG2R62 -0.75 !
ATOM AC4 CG2RC0
0.43 !
ATOM AC6 CG2R64
0.46 !
!
ATOM AN6 NG2S3
-0.77 !
ATOM AH61 HGP4
0.38 !
ATOM AH62 HGP4
0.38 !
GROUP
!
ATOM AC2' CG3C51
0.14 !
ATOM AH2' HGA1
0.09 !
ATOM AO2' OG311
-0.65 !
ATOM AH2T HGP1
0.42 !
GROUP
!
ATOM AC3' CG3C51
0.14 !
ATOM AH3' HGA1
0.09 !
ATOM AO3' OG311
-0.65 !
ATOM AH3T HGP1
0.42 !
GROUP
!
ATOM AC5' CG321
-0.08 !
ATOM AH5' HGA2
0.09 !
ATOM AH5S HGA2
0.09 !
ATOM AP PG2
1.50 !
ATOM AO1 OG2P1
-0.82 !
ATOM AO2 OG2P1
-0.82 !
ATOM AO5' OG303
-0.62 !
ATOM O3 OG303
-0.68
ATOM NP PG2
1.50
ATOM NO1 OG2P1
-0.82
ATOM NO2 OG2P1
-0.82
ATOM NO5' OG303
-0.62
ATOM NC5' CG321
-0.08
ATOM NH5S HGA2
0.09
ATOM NH5' HGA2
0.09
GROUP
ATOM NC2' CG3C51
0.14
ATOM NH2' HGA1
0.09

C21H26N7O14P2 oxidized nicotinamide adenine dinucleo


atom names correspond to pdb nomenclature
checked for consistency with new NA params, adm jr.,
note that differences with respect to published resu
due to new NA params
AH61 AH62
\ /
AN6
|
AC6
// \
AN1 AC5--AN7\\
|
||
AC8-AH8
AC2 AC4--AN9/
/ \\ /
\
AH2 AN3
\
\
\
\
NO1
AO1
AH5sAH4' AO4' \
|
|
|
\ / \ \
NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
\ |
|
|
\
/ \
\ NO2
AO2
AH5' AC3'-AC2' AH1'
\
/ \ / \
\
AO3' AH3'AO2'AH2'
\
|
|
\
AH3T
AH2T
\
NH71
\
\
\
NH72-NN7
NH4
\
\
|
\
NC7 NC4
\
// \ / \\
\
NO7 NC3 NC5-NH5
\
||
|
\ NH5s NH4'NO4'
NH2-NC2 NC6-NH6
\ |
\ / \
\+//
NC5'--NC4' NC1'---------NN1
|
\
/ \
NH5' NC3'-NC2'NH1'
/ \ / \
NO3' NH3'NO2'NH2'
|
|
NH3T
NH2T

ATOM NO2'
ATOM NH2T
GROUP
ATOM NC3'
ATOM NH3'
ATOM NO3'
ATOM NH3T
GROUP
ATOM NC1'
ATOM NH1'
ATOM NC4'
ATOM NH4'
ATOM NO4'
GROUP
ATOM NN1
ATOM NC6
ATOM NH6
ATOM NC5
ATOM NH5
ATOM NC4
ATOM NH4
ATOM NC3
ATOM NC2
ATOM NH2
ATOM NC7
ATOM NO7
ATOM NN7
ATOM NH71
ATOM NH72

OG311
HGP1

-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C53
HGA1
CG3C51
HGA1
OG3C51

0.11
0.09
0.11
0.09
-0.40

NG2R61
CG2R62
HGR63
CG2R62
HGR63
CG2R62
HGR63
CG2R62
CG2R62
HGR63
CG2O1
OG2D1
NG2S2
HGP1
HGP1

-0.07
0.16
0.19
-0.10
0.16
-0.05
0.16
0.05
0.18
0.16
0.68
-0.40
-0.82
0.34 ! trans to amide O
0.36 ! cis to amide O

BOND AN1 AC2


AN3 AC4
BOND AC6 AN6
AC5 AN7
BOND AN9 AC4
AC2 AH2
DOUBLE AC6 AN1
AC2 AN3
BOND AN9 AC1'
AC1' AC2'
BOND AO4' AC1'
AC1' AH1'
BOND AC3' AH3'
AC3' AO3'
BOND AC5' AH5S
AC5' AH5'
BOND AP AO2
AP O3
BOND NP NO5'
NO5' NC5'
BOND NC4' NO4'
NO4' NC1'
BOND NC1' NH1'
NC2' NH2'
BOND NC3' NO3'
NO3' NH3T
BOND NC3 NC4
NC5 NC6
BOND NC2 NH2
NC3 NC7
BOND NN7 NH72
NC4 NH4
DOUBLE NC2 NC3
NC4 NC5
! adenine impropers
IMPR AN6 AC6 AH61 AH62
AC6
! amide impropers
IMPR NC7 NN7 NC3 NO7
NC7
IMPR NN7 NC7 NH71 NH72 NN7
! ring hydrogen impropers
IMPR NC6 NN1 NC5 NH6
NC5
IMPR NC4 NC5 NC3 NH4
NC2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1

AC5 AC6
AC8 AN9
AN6 AH61
AC4 AC5
AC2' AC3'
AC2' AO2'
AO3' AH3T
AC5' AO5'
O3 NP
NC5' NH5S
NC1' NC2'
NC2' NO2'
NC4' NH4'

AN6
AN7
AC3'
AO2'
AC4'
AO5'
NP
NC5'
NC2'
NO2'
NC1'

NC7 NO7
NC5 NH5
NC6 NN1

AH62
AC8
AC4'
AH2T
AH4'
AP
NO1
NH5'
NC3'
NH2T
NN1

NC7 NN7
NC6 NH6

AN1

AC5 AN6

NC3
NC7

NN7 NO7
NH72 NH71

NC6
NC3

NC4
NN1

NH5
NH2

AC8 AH8
AC4'
AC2'
AC4'
AP
NP
NC5'
NC3'
NC3'
NN1

AO4'
AH2'
AC5'
AO1
NO2
NC4'
NC4'
NH3'
NC2

NN7 NH71

ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1
ACCE AO2
ACCE O3
ACCE NO1
ACCE NO2
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T
DONO NH3T
DONO NH71
DONO NH72
IC AP
IC AC5'
IC AC5'
IC AH5S
IC AP
IC AP
IC AP
IC AO1
IC AO5'
IC AC5'
IC AH3T
IC AO4'
IC AC2'
IC AC4'
IC AC3'
IC AO4'
IC AC1'
IC AC4
IC AC8
IC AC8
IC AN7
IC AC5
IC AN9
IC AC5
IC AN1
IC AH61
IC AC5
IC AN1
IC AH61
IC AN9
IC AN1
IC AC1'
IC AH2'
IC AH2T
IC AO4'
IC AC1'
IC AC2'
IC AC3'
IC AC4'
IC AC4'

AP
AP
NP
NP

NO2'
NO3'
NN7
NN7
O3
AO5'
AO5'
AC5'
O3
O3
AO5'
AP
AC5'
AC4'
AO3'
AC3'
AC4'
AC3'
AC2'
AC1'
AC4
AN9
AN9
AN7
AC5
AC6
AC5
AN1
AC6
AC6
AN1
AC6
AC6
AN7
AN3
AC3'
AO2'
AO2'
AC2'
AC3'
AC4'
AO4'
AO5'
AO5'

NP
AP
AP
AC4'
NP
NP
AC5'
AO5'
AC4'
AC3'
AC3'
*AC4
*AC3'
AC2'
AC1'
AN9
*AN9
AC8
AC4
AC5
AC6
AN1
*AC4
*AC6
AN6
*AN6
*AC6
AN6
*AN6
*AC8
*AC2
*AC2
AC2'
AC2'
*AC1'
*AC2
*AC3'
*AC4
*AC5
*AC5

NO5'
O3
AO2
AC3'
NO1
NO2
AC4'
AC5'
AC3'
AO3'
AC4'
AC5'
AO3'
AC1'
AN9
AC4
AC8
AN7
AC5
AC6
AN1
AC2
AN3
AN6
AH61
AH62
AN6
AH61
AH62
AH8
AH2
AO2'
AC3'
AC3'
AH1'
AH2'
AH3'
AH4'
AH5'
AH5'

1.4863
1.4232
1.4232
0.9935
1.4863
1.4863
1.5901
1.5901
1.4232
1.5491
0.9671
1.8868
1.5097
1.6942
1.5097
1.3646
1.4847
1.4013
1.3777
1.3282
1.3814
1.4146
1.4013
1.4146
1.3482
0.9912
1.4146
1.3482
0.9912
1.3777
1.3300
1.5415
2.0386
0.9953
1.3646
1.5415
1.5097
1.6942
1.5491
1.5491

65.28
127.31
127.31
120.00
65.28
65.28
127.31
127.31
111.63
111.58
98.77
112.95
93.22
93.22
117.82
95.44
125.96
105.34
105.34
103.21
130.78
117.85
105.06
117.85
119.69
116.60
117.85
119.69
116.60
114.01
129.42
117.82
31.12
99.36
120.77
117.82
93.22
112.95
111.63
111.63

-169.00
-165.10
73.33
-58.20
78.51
-54.29
121.29
121.29
-58.20
128.42
147.40
-118.10
-117.72
-12.93
135.56
-90.72
-176.52
-0.07
0.11
-179.92
-179.94
-0.14
-179.67
179.89
-0.39
-179.02
179.89
-0.39
-179.02
-179.37
179.97
-145.06
-93.63
-93.63
-114.99
108.23
117.28
-140.26
-123.75
-123.75

98.59
103.27
111.48
111.58
108.97
112.88
111.63
127.31
111.58
114.19
114.19
111.58
114.19
117.82
115.01
125.96
105.34
114.01
105.06
130.78
117.85
118.87
126.14
119.69
116.60
116.94
119.69
116.60
116.94
126.34
114.82
114.13
114.13
114.13
109.65
86.44
111.94
57.99
111.23
111.23

1.5977
1.4863
1.4836
1.6942
1.4756
1.4636
1.5491
1.4232
1.6942
1.4337
1.6942
1.5491
1.4337
1.5415
1.4847
1.4013
1.3777
1.3282
1.3782
1.4146
1.3482
1.3300
1.3648
1.3419
0.9912
0.9978
1.3419
0.9912
0.9978
1.0962
1.0928
1.4294
1.5097
1.5097
1.1105
1.0999
1.1110
1.0000
1.1111
1.1111

IC NC5' NO5'
IC NH5S NC5'
IC NH5' NC5'
IC NP
NO5'
IC NO5' NC5'
IC NC5' NC4'
IC NC4' NC3'
IC NC3' NC2'
IC NC2' NC1'
IC NO2' NC2'
IC NH2T NO2'
IC NO4' NC2'
IC NC1' NC3'
IC NC2' NC4'
IC NC3' NO4'
IC NC4' NO5'
IC NC4' NO5'
IC NC3' NC2'
IC NO3' NC3'
IC NH3T NO3'
IC NC2' NC1'
IC NC1' NN1
IC NN1
NC2
IC NC2
NC3
IC NC3
NC4
IC NC4
NC5
IC NC5
NC6
IC NN1
NC2
IC NC2
NC3
IC NC2
NC3
IC NO7
NC7
IC NO7
NC7
IC NC2
NC3
IC NC3
NC4
IC NC4
NC5
IC NC6
NN1
PATCH FIRST NONE

NP
NO2
NO5' NP
NO5' NP
NC5' NC4'
NC4' NC3'
NC3' NC2'
NC2' NC1'
NC1' NO4'
NO4' NC4'
NC1' NO4'
NC2' NC1'
*NC1' NH1'
*NC2 NH2'
*NC3 NH3'
*NC4 NH4'
*NC5 NH5'
*NC5 NH5S
NC1' NN1
NC2' NC1'
NC3' NC2'
NN1
NC2
NC2
NC3
NC3
NC4
NC4
NC5
NC5
NC6
NC6
NN1
NN1
NC2
NC3
NC7
NC7
NO7
NC7
NN7
NN7
NH71
NN7
NH72
NC4
NH4
NC5
NH5
NC6
NH6
NC2
NH2
LAST NONE

RESI NADH
-2.00 !
ide, jjp1/adm jr.
!
!
9/98
!
lts exist
!
!
GROUP
!
ATOM AC4' CG3C51
0.11 !
ATOM AH4' HGA1
0.09 !
ATOM AO4' OG3C51 -0.40 !
ATOM AC1' CG3C51
0.11 !
ATOM AH1' HGA1
0.09 !
GROUP
!
ATOM AC5 CG2RC0
0.28 !
ATOM AN7 NG2R50 -0.71 !
ATOM AC8 CG2R53
0.34 !
ATOM AH8 HGR52
0.12 !
ATOM AN9 NG2R51 -0.05 !
!

1.4451
1.1110
1.1110
1.5977
1.4451
1.5160
1.5160
1.5160
1.5270
1.4200
0.9600
1.4100
1.5270
1.5160
1.5160
1.5160
1.5160
1.5160
1.4200
0.9600
1.5270
1.4800
1.3150
1.3500
1.3600
1.3600
1.3500
1.3150
1.3500
1.3500
1.2300
1.2300
1.3500
1.3600
1.3600
1.2199

128.40
109.50
109.50
128.40
110.10
108.50
111.00
105.50
105.00
110.10
106.00
105.00
105.50
111.00
100.64
110.10
110.10
105.50
110.10
106.00
113.70
121.70
122.00
118.00
118.00
118.00
124.51
122.00
131.80
131.80
120.00
120.00
118.00
118.00
118.00
119.49

-49.72
115.00
-115.00
0.00
0.00
0.00
0.00
0.00
0.00
180.00
180.00
-115.00
115.00
115.00
-115.00
-115.00
115.00
0.00
180.00
180.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
180.00
0.00
0.00
0.00
0.00
0.00

108.83
128.40
128.40
110.10
108.50
111.00
105.50
105.00
117.86
105.00
110.10
110.10
110.10
110.10
107.24
109.50
109.50
113.70
105.50
110.10
121.70
122.00
118.00
118.00
118.00
124.51
119.49
131.80
118.50
113.00
120.00
120.00
121.00
119.00
120.50
117.50

1.4636
1.5977
1.5977
1.5160
1.5160
1.5160
1.5270
1.4100
1.4712
1.4100
1.5270
1.1110
1.1110
1.1110
1.1110
1.1110
1.1110
1.4800
1.5270
1.5160
1.3150
1.3500
1.3600
1.3600
1.3500
1.2199
1.3150
1.4800
1.2300
1.3600
1.0000
1.0000
1.0900
1.0900
1.0900
1.0900

C21H27N7O14P2 reduced nicotinamide adenine dinucleot


atom names correspond to pdb nomenclature
checked for consistency with new NA params, adm jr.,
note that differences with respect to published resu
due to new NA params
AH61 AH62
\ /
AN6
|
AC6
// \
AN1 AC5--AN7\\
|
||
AC8-AH8
AC2 AC4--AN9/
/ \\ /
\
AH2 AN3
\
\

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

AN1
AC2
AH2
AN3
AC4
AC6

ATOM AN6
ATOM AH61
ATOM AH62
GROUP
ATOM AC2'
ATOM AH2'
ATOM AO2'
ATOM AH2T
GROUP
ATOM AC3'
ATOM AH3'
ATOM AO3'
ATOM AH3T
GROUP
ATOM AC5'
ATOM AH5'
ATOM AH5S
ATOM AP
ATOM AO1
ATOM AO2
ATOM AO5'
ATOM O3
ATOM NP
ATOM NO1
ATOM NO2
ATOM NO5'
ATOM NC5'
ATOM NH5S
ATOM NH5'
GROUP
ATOM NC2'
ATOM NH2'
ATOM NO2'
ATOM NH2T
GROUP
ATOM NC3'
ATOM NH3'
ATOM NO3'
ATOM NH3T
GROUP
ATOM NC1'
ATOM NH1'
ATOM NC4'
ATOM NH4'
ATOM NO4'
GROUP
ATOM NN1
ATOM NC6
ATOM NH6
ATOM NC5
ATOM NH5
ATOM NC4
ATOM NH4

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321
HGA2
HGA2
PG2
OG2P1
OG2P1
OG303
OG303
PG2
OG2P1
OG2P1
OG303
CG321
HGA2
HGA2

-0.08
0.09
0.09
1.50
-0.82
-0.82
-0.62
-0.68
1.50
-0.82
-0.82
-0.62
-0.08
0.09
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
CG3C51
HGA1
OG3C51

0.11
0.09
0.11
0.09
-0.40

NG301
CG2D1O
HGA4
CG2D1
HGA4
CG321
HGA2

-0.27
-0.06
0.17
-0.18
0.14
-0.28
0.09

!
\
!
\
!
NO1
AO1
AH5sAH4' AO4' \
!
|
|
|
\ / \ \
! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
! \ |
|
|
\
/ \
! \ NO2
AO2
AH5' AC3'-AC2' AH1'
! \
/ \ / \
!
\
AO3' AH3'AO2'AH2'
!
\
|
|
!
\
AH3T
AH2T
!
\
NH71
!
\
\
!
\
NH72-NN7 NH4 NH42
!
\
\
\ /
!
\
NC7 NC4
!
\
/ \ / \
!
\
NO7 NC3 NC5-NH5
!
\
|| ||
!
\ NH5s NH4'NO4'
NH2-NC2 NC6-NH6
!
\ |
\ / \
\ /
!
NC5'--NC4' NC1'---------NN1
!
|
\
/ \
!
NH5' NC3'-NC2'NH1'
!
/ \ / \
!
NO3' NH3'NO2'NH2'
!
|
|
!
NH3T
NH2T

!N2
!C3
!H4
!C5
!H6
!C7
!H8

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

NH42
NC3
NC2
NH2
NC7
NO7
NN7
NH71
NH72

HGA2
CG2DC1
CG2D1O
HGA4
CG2O1
OG2D1
NG2S2
HGP1
HGP1

0.09
0.36
-0.10
0.14
0.55
-0.51
-0.72
0.26
0.32

!H17
!C9
!C10
!H11
!C12
!O13
!N14
!H15 ! trans to amide O
!H16 ! cis to amide O

BOND AN1 AC2


AN3 AC4
AC5 AC6
BOND AC6 AN6
AC5 AN7
AC8 AN9
BOND AN9 AC4
AC2 AH2
AN6 AH61
AN6
DOUBLE AC6 AN1
AC2 AN3
AC4 AC5
AN7
BOND AN9 AC1'
AC1' AC2'
AC2' AC3'
AC3'
BOND AO4' AC1'
AC1' AH1'
AC2' AO2'
AO2'
BOND AC3' AH3'
AC3' AO3'
AO3' AH3T
AC4'
BOND AC5' AH5S
AC5' AH5'
AC5' AO5'
AO5'
BOND AP AO2
AP O3
O3 NP
NP
BOND NP NO5'
NO5' NC5'
NC5' NH5S
NC5'
BOND NC4' NO4'
NO4' NC1'
NC1' NC2'
NC2'
BOND NC1' NH1'
NC2' NH2'
NC2' NO2'
NO2'
BOND NC3' NO3'
NO3' NH3T
NC4' NH4'
NC1'
BOND NC3 NC4
NC4 NC5
NC6 NN1
BOND NC2 NH2
NC3 NC7
NC7 NO7
NC7
BOND NN7 NH72
NC4 NH4
NC4 NH42
NC5
DOUBLE NC2 NC3
NC5 NC6
! adenine impropers
IMPR AN6 AC6 AH61 AH62
AC6 AN1 AC5 AN6
! amide impropers
IMPR NC7 NN7 NC3 NO7
NC7 NC3 NN7 NO7
IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71
! ring hydrogen impropers
IMPR NC6 NN1 NC5 NH6
NC5 NC6 NC4 NH5
IMPR NC2 NC3 NN1 NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1 AP
ACCE AO2 AP
ACCE O3
ACCE NO1 NP
ACCE NO2 NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7

AH62
AC8
AC4'
AH2T
AH4'
AP
NO1
NH5'
NC3'
NH2T
NN1

AC8 AH8

NN7
NH5

NN7 NH71
NC6 NH6

AC4'
AC2'
AC4'
AP
NP
NC5'
NC3'
NC3'
NN1

AO4'
AH2'
AC5'
AO1
NO2
NC4'
NC4'
NH3'
NC2

! IC table was beyond repair ==> replaced (kevo)


IC AP
O3
NP
NO5' 1.6011 92.88 167.64
IC AP
O3
NP
NO1
1.6011 92.88 62.12
IC AP
O3
NP
NO2
1.6011 92.88 -85.34
IC NP
O3
AP
AO5' 1.6074 92.88 169.27
IC O3
AO5' *AP
AO1
1.6011 93.16 -115.15
IC O3
AO5' *AP
AO2
1.6011 93.16 120.82
IC O3
AP
AO5' AC5' 1.6011 93.16 -65.25
IC AP
AO5' AC5' AC4' 1.6636 117.89 -111.08
IC AC4' AO5' *AC5' AH5' 1.5437 111.72 121.91
IC AC4' AO5' *AC5' AH5S 1.5437 111.72 -120.24
IC AO5' AC5' AC4' AC3' 1.4434 111.72 32.23
IC AC5' AC4' AC3' AO3' 1.5437 115.30 82.44
IC AH3T AO3' AC3' AC4' 0.9956 102.19 -78.33
IC AO4' AC3' *AC4' AC5' 1.4436 105.34 -122.02
IC AC2' AC4' *AC3' AO3' 1.5312 103.02 -124.10
IC AC4' AC3' AC2' AC1' 1.5403 103.02 34.98
IC AC3' AC2' AC1' AN9
1.5312 101.18 88.32
IC AO4' AC1' AN9
AC4
1.4336 105.95 -149.10
IC AC1' AC4
*AN9 AC8
1.4609 127.35 179.89
IC AC4
AN9
AC8
AN7
1.3682 106.85
0.34
IC AC8
AN9
AC4
AC5
1.3818 106.85 -0.12
IC AC8
AN7
AC5
AC6
1.3338 103.64 -179.39
IC AN7
AC5
AC6
AN1
1.3924 132.41 179.90
IC AC5
AC6
AN1
AC2
1.4083 118.87 -0.29
IC AN9
AC5
*AC4 AN3
1.3682 105.55 -179.81
IC AC5
AN1
*AC6 AN6
1.4083 118.87 179.60
IC AN1
AC6
AN6
AH61 1.3616 117.11 -176.96
IC AH61 AC6
*AN6 AH62 0.9980 119.87 174.83
IC AN9
AN7
*AC8 AH8
1.3818 112.92 -179.84
IC AN1
AN3
*AC2 AH2
1.3626 125.37 -179.78
IC AO4' AC2' *AC1' AH1' 1.4336 107.49 -118.51
IC AC1' AC3' *AC2' AH2' 1.5414 101.18 120.60
IC AC2' AC4' *AC3' AH3' 1.5312 103.02 114.75
IC AC3' AO4' *AC4' AH4' 1.5403 105.34 -116.63
IC NC5' NO5' NP
NO2
1.4353 125.45 -110.33
IC NP
NO5' NC5' NC4' 1.6600 125.45 -100.01
IC NO5' NC5' NC4' NC3' 1.4353 114.36 42.03
IC NC5' NC4' NC3' NC2' 1.5573 115.36 -91.03
IC NC4' NC3' NC2' NC1' 1.5403 101.62 -39.21
IC NC3' NC2' NC1' NO4' 1.5376 100.72 35.40
IC NO2' NC2' NC1' NO4' 1.4392 115.62 158.69
IC NH2T NO2' NC2' NC1' 0.9686 102.30 157.15
IC NO4' NC2' *NC1' NH1' 1.4395 105.65 -114.11
IC NC1' NC3' *NC2 NH2' 2.4605
9.08 131.65
IC NC2' NC4' *NC3 NH3' 4.7247 22.53 -7.48
IC NC3' NO4' *NC4 NH4' 6.4634 19.31 -56.73
IC NC4' NO5' *NC5 NH5' 5.1412 29.29 35.30
IC NC4' NO5' *NC5 NH5S 5.1412 29.29 55.33
IC NC3' NC2' NC1' NN1
1.5376 100.72 153.61
IC NO3' NC3' NC2' NC1' 1.4390 111.69 79.56
IC NH3T NO3' NC3' NC2' 0.9633 102.31 55.04
IC NC2' NC1' NN1
NC2
1.5399 113.06 115.33
IC NC1' NN1
NC2
NC3
1.4871 119.55 179.60
IC NN1
NC2
NC3
NC4
1.3595 123.83
5.03
IC NC2
NC3
NC4
NC5
1.3763 118.94 -6.70
IC NC3
NC4
NC5
NC6
1.5428 111.53
5.08
IC NN1
NC2
NC3
NC7
1.3595 123.83 -158.70
IC NC2
NC3
NC7
NO7
1.3763 118.33 -160.59
IC NC2
NC3
NC7
NN7
1.3763 118.33 20.47

96.12
118.93
112.47
93.16
102.32
100.53
117.89
111.72
113.03
108.95
115.30
113.07
113.07
115.30
113.07
101.18
111.78
127.35
106.85
112.92
105.55
132.41
118.87
119.53
125.91
117.11
119.87
117.95
125.33
117.21
111.70
111.56
109.97
105.95
103.18
114.36
115.36
101.62
100.72
105.65
105.65
115.62
109.56
26.20
17.99
2.93
14.10
24.87
113.06
100.72
111.69
119.55
123.83
118.94
111.53
122.32
118.33
120.47
119.04

1.6600
1.5360
1.5263
1.6636
1.5255
1.5378
1.4434
1.5437
1.1186
1.1118
1.5403
1.4340
1.5403
1.5437
1.4340
1.5414
1.4609
1.3682
1.3818
1.3338
1.3970
1.4083
1.3616
1.3626
1.3450
1.3448
0.9980
0.9930
1.0978
1.0932
1.1012
1.0994
1.1020
1.1009
1.5263
1.5573
1.5403
1.5376
1.5399
1.4395
1.4395
1.5399
1.1015
3.7695
6.8615
7.0769
6.2151
4.9161
1.4871
1.5399
1.5376
1.3595
1.3763
1.5428
1.5189
1.3550
1.5212
1.2354
1.3683

IC NO7
NC7
IC NO7
NC7
IC NC2
NC3
IC NC2
NC3
IC NC3
NC4
IC NC4
NC5
IC NC6
NN1
IC AC1' AC3'
IC AC3' AC2'
PATCH FIRST NONE
RESI NADP
tide,

NN7
NH71
NN7
NH72
NC4
NH4
NC4
NH42
NC5
NH5
NC6
NH6
NC2
NH2
*AC2' AO2'
AO2' AH2T
LAST NONE

1.2354
1.2354
1.3763
1.3763
1.5428
1.5189
1.3589
1.5414
1.5312

120.48
120.48
118.94
118.94
111.53
122.32
121.05
101.18
110.89

-176.29
0.52
-136.51
108.33
-149.76
179.97
177.95
-118.90
-28.83

120.56
116.91
113.66
105.96
116.93
119.29
116.69
110.89
100.98

0.9982
0.9963
1.1068
1.1115
1.0907
1.0969
1.0900
1.4319
0.9715

-2.00 ! C21H26N7O17P3 oxidized nicotinamide adenine dinucleo


! NADP+, adm jr.
! atom names correspond to pdb nomenclature
! checked for consistency with new NA params, adm jr.,

9/98
! note that differences with respect to published resu
lts exist
GROUP
ATOM AC4'
ATOM AH4'
ATOM AO4'
ATOM AC1'
ATOM AH1'
GROUP
ATOM AC5
ATOM AN7
ATOM AC8
ATOM AH8
ATOM AN9
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

AN1
AC2
AH2
AN3
AC4
AC6

ATOM AN6
ATOM AH61
ATOM AH62
GROUP
ATOM AC2'
ATOM AH2'
ATOM AO2'
ATOM AP2
ATOM AO1P
ATOM AO2P
ATOM AO2T
ATOM AH2T
GROUP
ATOM AC3'
ATOM AH3'
ATOM AO3'
ATOM AH3T
GROUP
ATOM AC5'

CG3C51
HGA1
OG3C51
CG3C51
HGA1

0.11
0.09
-0.40
0.11
0.09

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.28
-0.71
0.34
0.12
-0.05

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG311
HGP1

0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321

-0.08

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

due to new NA params


AH61 AH62
\ /
AN6
|
AC6
// \
AN1 AC5--AN7\\
|
||
AC8-AH8
AC2 AC4--AN9/
/ \\ /
\
AH2 AN3
\
\
\
\
NO1
AO1
AH5sAH4' AO4' \
|
|
|
\ / \ \
NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
\ |
|
|
\
/ \
\ NO2
AO2
AH5' AC3'-AC2' AH1'
\
/ \ / \
\
AO3' AH3'AO2'AH2'
\
|
|
\
AH3T AO1P=AP2==AO2P (-)
\
|
NH71
\
AH2T-AO2T /
\
NH72-NN7
NH4
\
\
|
\
NC7 NC4
\
/ \ / \\
\
NO7 NC3 NC5-NH5
\
|| |
\ NH5s NH4'NO4'
NH2-NC2 NC6-NH6
\ |
\ / \
\+ //
NC5'--NC4' NC1'---------NN1
|
\
/ \
NH5' NC3'-NC2'NH1'
/ \ / \
NO3' NH3'NO2'NH2'

ATOM AH5'
ATOM AH5S
ATOM AP
ATOM AO1
ATOM AO2
ATOM AO5'
ATOM O3
ATOM NP
ATOM NO1
ATOM NO2
ATOM NO5'
ATOM NC5'
ATOM NH5S
ATOM NH5'
GROUP
ATOM NC2'
ATOM NH2'
ATOM NO2'
ATOM NH2T
GROUP
ATOM NC3'
ATOM NH3'
ATOM NO3'
ATOM NH3T
GROUP
ATOM NC1'
ATOM NH1'
ATOM NC4'
ATOM NH4'
ATOM NO4'
GROUP
ATOM NN1
ATOM NC6
ATOM NH6
ATOM NC5
ATOM NH5
ATOM NC4
ATOM NH4
ATOM NC3
ATOM NC2
ATOM NH2
ATOM NC7
ATOM NO7
ATOM NN7
ATOM NH71
ATOM NH72

HGA2
HGA2
PG2
OG2P1
OG2P1
OG303
OG303
PG2
OG2P1
OG2P1
OG303
CG321
HGA2
HGA2

0.09 !
0.09 !
1.50
-0.82
-0.82
-0.62
-0.68
1.50
-0.82
-0.82
-0.62
-0.08
0.09
0.09

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C53
HGA1
CG3C51
HGA1
OG3C51

0.11
0.09
0.11
0.09
-0.40

NG2R61
CG2R62
HGR63
CG2R62
HGR63
CG2R62
HGR63
CG2R62
CG2R62
HGR63
CG2O1
OG2D1
NG2S2
HGP1
HGP1

-0.07
0.16
0.19
-0.10
0.16
-0.05
0.16
0.05
0.18
0.16
0.68
-0.40
-0.82
0.34 ! trans to amide O
0.36 ! cis to amide O

BOND AN1 AC2


BOND AC6 AN6
BOND AN9 AC4
DOUBLE AC6 AN1
BOND AN9 AC1'
BOND AO4' AC1'
BOND AC3' AH3'
BOND AC5' AH5S
BOND AP AO2
BOND NP NO5'
BOND NC4' NO4'
BOND NC1' NH1'
BOND NC3' NO3'

AN3 AC4
AC5 AN7
AC2 AH2
AC2 AN3
AC1' AC2'
AC1' AH1'
AC3' AO3'
AC5' AH5'
AP O3
NO5' NC5'
NO4' NC1'
NC2' NH2'
NO3' NH3T

|
NH3T

AC5 AC6
AC8 AN9
AN6 AH61
AC4 AC5
AC2' AC3'
AC2' AO2'
AO3' AH3T
AC5' AO5'
O3 NP
NC5' NH5S
NC1' NC2'
NC2' NO2'
NC4' NH4'

|
NH2T

AN6
AN7
AC3'
AO2'
AC4'
AO5'
NP
NC5'
NC2'
NO2'
NC1'

AH62
AC8
AC4'
AP2
AH4'
AP
NO1
NH5'
NC3'
NH2T
NN1

AC8 AH8
AC4' AO4'
AC2' AH2'
AC4' AC5'
AP AO1
NP NO2
NC5' NC4'
NC3' NC4'
NC3' NH3'
NN1 NC2

BOND NC3 NC4


NC5 NC6
BOND NC2 NH2
NC3 NC7
NC7 NO7
NC7
BOND NN7 NH72
NC4 NH4
NC5 NH5
NC6
BOND AP2 AO1P
AP2 AO2P
AP2 AO2T
AO2T
DOUBLE NC2 NC3
NC4 NC5
NC6 NN1
! adenine impropers
IMPR AN6 AC6 AH61 AH62
AC6 AN1 AC5 AN6
! amide impropers
IMPR NC7 NN7 NC3 NO7
NC7 NC3 NN7 NO7
IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71
! ring hydrogen impropers
IMPR NC6 NN1 NC5 NH6
NC5 NC6 NC4 NH5
IMPR NC4 NC5 NC3 NH4
NC2 NC3 NN1 NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1 AP
ACCE AO2 AP
ACCE O3
ACCE NO1 NP
ACCE NO2 NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2'
IC AP
O3
NP
NO5' 1.4863 65.28 -169.00
IC AC5' AO5' AP
O3
1.4232 127.31 -165.10
IC AC5' AO5' AP
AO2
1.4232 127.31 73.33
IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20
IC AP
O3
NP
NO1
1.4863 65.28 78.51
IC AP
O3
NP
NO2
1.4863 65.28 -54.29
IC AP
AO5' AC5' AC4' 1.5901 127.31 121.29
IC AO1
AP
AO5' AC5' 1.5901 127.31 121.29
IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20
IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42
IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40
IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10
IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72
IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93
IC AC3' AC2' AC1' AN9
1.5097 117.82 135.56
IC AO4' AC1' AN9
AC4
1.3646 95.44 -90.72
IC AC1' AC4
*AN9 AC8
1.4847 125.96 -176.52
IC AC4
AN9
AC8
AN7
1.4013 105.34 -0.07

NN7
NH6
AH2T

98.59
103.27
111.48
111.58
108.97
112.88
111.63
127.31
111.58
114.19
114.19
111.58
114.19
117.82
115.01
125.96
105.34
114.01

NN7 NH71

1.5977
1.4863
1.4836
1.6942
1.4756
1.4636
1.5491
1.4232
1.6942
1.4337
1.6942
1.5491
1.4337
1.5415
1.4847
1.4013
1.3777
1.3282

IC AC8
IC AC8
IC AN7
IC AC5
IC AN9
IC AC5
IC AN1
IC AH61
IC AC5
IC AN1
IC AH61
IC AN9
IC AN1
IC AC1'
IC AH2'
!IC AH2T
IC AO4'
IC AC1'
IC AC2'
IC AC3'
IC AC4'
IC AC4'
IC NC5'
IC NH5S
IC NH5'
IC NP
IC NO5'
IC NC5'
IC NC4'
IC NC3'
IC NC2'
IC NO2'
IC NH2T
IC NO4'
IC NC1'
IC NC2'
IC NC3'
IC NC4'
IC NC4'
IC NC3'
IC NO3'
IC NH3T
IC NC2'
IC NC1'
IC NN1
IC NC2
IC NC3
IC NC4
IC NC5
IC NN1
IC NC2
IC NC2
IC NO7
IC NO7
IC NC2
IC NC3
IC NC4
IC NC6
IC AC3'
IC AC2'

AN9
AN7
AC5
AC6
AC5
AN1
AC6
AC6
AN1
AC6
AC6
AN7
AN3
AC3'
AO2'
AO2'
AC2'
AC3'
AC4'
AO4'
AO5'
AO5'
NO5'
NC5'
NC5'
NO5'
NC5'
NC4'
NC3'
NC2'
NC1'
NC2'
NO2'
NC2'
NC3'
NC4'
NO4'
NO5'
NO5'
NC2'
NC3'
NO3'
NC1'
NN1
NC2
NC3
NC4
NC5
NC6
NC2
NC3
NC3
NC7
NC7
NC3
NC4
NC5
NN1
AC2'
AO2'

AC4
AC5
AC6
AN1
*AC4
*AC6
AN6
*AN6
*AC6
AN6
*AN6
*AC8
*AC2
*AC2
AC2'
AC2'
*AC1'
*AC2
*AC3'
*AC4
*AC5
*AC5
NP
NO5'
NO5'
NC5'
NC4'
NC3'
NC2'
NC1'
NO4'
NC1'
NC2'
*NC1'
*NC2
*NC3
*NC4
*NC5
*NC5
NC1'
NC2'
NC3'
NN1
NC2
NC3
NC4
NC5
NC6
NN1
NC3
NC7
NC7
NN7
NN7
NC4
NC5
NC6
NC2
AO2'
AP2

AC5
AC6
AN1
AC2
AN3
AN6
AH61
AH62
AN6
AH61
AH62
AH8
AH2
AO2'
AC3'
AC3'
AH1'
AH2'
AH3'
AH4'
AH5'
AH5'
NO2
NP
NP
NC4'
NC3'
NC2'
NC1'
NO4'
NC4'
NO4'
NC1'
NH1'
NH2'
NH3'
NH4'
NH5'
NH5S
NN1
NC1'
NC2'
NC2
NC3
NC4
NC5
NC6
NN1
NC2
NC7
NO7
NN7
NH71
NH72
NH4
NH5
NH6
NH2
AP2
AO2T

1.3777
1.3282
1.3814
1.4146
1.4013
1.4146
1.3482
0.9912
1.4146
1.3482
0.9912
1.3777
1.3300
1.5415
2.0386
0.9953
1.3646
1.5415
1.5097
1.6942
1.5491
1.5491
1.4451
1.1110
1.1110
1.5977
1.4451
1.5160
1.5160
1.5160
1.5270
1.4200
0.9600
1.4100
1.5270
1.5160
1.5160
1.5160
1.5160
1.5160
1.4200
0.9600
1.5270
1.4800
1.3150
1.3500
1.3600
1.3600
1.3500
1.3150
1.3500
1.3500
1.2300
1.2300
1.3500
1.3600
1.3600
1.2199
0.0000
0.0000

105.34
0.11
103.21 -179.92
130.78 -179.94
117.85 -0.14
105.06 -179.67
117.85 179.89
119.69 -0.39
116.60 -179.02
117.85 179.89
119.69 -0.39
116.60 -179.02
114.01 -179.37
129.42 179.97
117.82 -145.06
31.12 -93.63
99.36 -93.63
120.77 -114.99
117.82 108.23
93.22 117.28
112.95 -140.26
111.63 -123.75
111.63 -123.75
128.40 -49.72
109.50 115.00
109.50 -115.00
128.40
0.00
110.10
0.00
108.50
0.00
111.00
0.00
105.50
0.00
105.00
0.00
110.10 180.00
106.00 180.00
105.00 -115.00
105.50 115.00
111.00 115.00
100.64 -115.00
110.10 -115.00
110.10 115.00
105.50
0.00
110.10 180.00
106.00 180.00
113.70
0.00
121.70
0.00
122.00
0.00
118.00
0.00
118.00
0.00
118.00
0.00
124.51
0.00
122.00
0.00
131.80
0.00
131.80
0.00
0.00 180.00
0.00
0.00
118.00
0.00
118.00
0.00
118.00
0.00
119.49
0.00
000.00 180.00
000.00 -39.52

105.06
130.78
117.85
118.87
126.14
119.69
116.60
116.94
119.69
116.60
116.94
126.34
114.82
114.13
114.13
114.13
109.65
86.44
111.94
57.99
111.23
111.23
108.83
128.40
128.40
110.10
108.50
111.00
105.50
105.00
117.86
105.00
110.10
110.10
110.10
110.10
107.24
109.50
109.50
113.70
105.50
110.10
121.70
122.00
118.00
118.00
118.00
124.51
119.49
131.80
118.50
113.00
120.00
120.00
121.00
119.00
120.50
117.50
000.00
000.00

1.3782
1.4146
1.3482
1.3300
1.3648
1.3419
0.9912
0.9978
1.3419
0.9912
0.9978
1.0962
1.0928
1.4294
1.5097
1.5097
1.1105
1.0999
1.1110
1.0000
1.1111
1.1111
1.4636
1.5977
1.5977
1.5160
1.5160
1.5160
1.5270
1.4100
1.4712
1.4100
1.5270
1.1110
1.1110
1.1110
1.1110
1.1110
1.1110
1.4800
1.5270
1.5160
1.3150
1.3500
1.3600
1.3600
1.3500
1.2199
1.3150
1.4800
1.2300
1.3600
1.0000
1.0000
1.0900
1.0900
1.0900
1.0900
0.0000
0.0000

IC AO2T AO2'
IC AO2T AO2'
IC AH2T AO2T
PATCH FIRST NONE
RESI NDPH
ide

*AP2 AO1P
*AP2 AO2P
AP2
AO2'
LAST NONE

0.0000 000.00 -115.82 000.00


0.0000 000.00 115.90 000.00
0.0000 000.00 180.00 000.00

0.0000
0.0000
0.0000

-3.00 ! C21H27N7O17P3 reduced nicotinamide adenine dinucleot


! NADPH, VARNAI/adm jr.
! from RESI NADH and 3PHO
! checked for consistency with new NA params, adm jr.,

9/98
! note that differences with respect to published resu
lts exist
GROUP
ATOM AC4'
ATOM AH4'
ATOM AO4'
ATOM AC1'
ATOM AH1'
GROUP
ATOM AC5
ATOM AN7
ATOM AC8
ATOM AH8
ATOM AN9
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

AN1
AC2
AH2
AN3
AC4
AC6

ATOM AN6
ATOM AH61
ATOM AH62
GROUP
ATOM AC2'
ATOM AH2'
ATOM AO2'
ATOM AP2
ATOM AO1P
ATOM AO2P
ATOM AO2T
ATOM AH2T
GROUP
ATOM AC3'
ATOM AH3'
ATOM AO3'
ATOM AH3T
GROUP
ATOM AC5'
ATOM AH5'
ATOM AH5S
ATOM AP
ATOM AO1
ATOM AO2
ATOM AO5'

CG3C51
HGA1
OG3C51
CG3C51
HGA1

0.11
0.09
-0.40
0.11
0.09

CG2RC0
NG2R50
CG2R53
HGR52
NG2R51

0.28
-0.71
0.34
0.12
-0.05

NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64

-0.74
0.50
0.13
-0.75
0.43
0.46

NG2S3
HGP4
HGP4

-0.77
0.38
0.38

CG3C51
HGA1
OG303
PG1
OG2P1
OG2P1
OG311
HGP1

0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.67
0.33

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG321
HGA2
HGA2
PG2
OG2P1
OG2P1
OG303

-0.08
0.09
0.09
1.50
-0.82
-0.82
-0.62

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

due to new NA params


AH61 AH62
\ /
AN6
|
AC6
// \
AN1 AC5--AN7\\
|
||
AC8-AH8
AC2 AC4--AN9/
/ \\ /
\
AH2 AN3
\
\
\
\
NO1
AO1
AH5sAH4' AO4' \
|
|
|
\ / \ \
NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
\ |
|
|
\
/ \
\ NO2
AO2
AH5' AC3'-AC2' AH1'
\
/ \ / \
\
AO3' AH3'AO2'AH2'
\
|
|
\
AH3T AO1P=AP2==AO2P (-)
\
|
NH71
\
AH2T-AO2T /
\
NH72-NN7 NH4 NH42
\
\
\ /
\
NC7 NC4
\
/ \ / \
\
NO7 NC3 NC5-NH5
\
||
||
\ NH5s NH4'NO4'
NH2-NC2 NC6-NH6
\ |
\ / \
\ /
NC5'--NC4' NC1'---------NN1
|
\
/ \
NH5' NC3'-NC2'NH1'
/ \ / \
NO3' NH3'NO2'NH2'
|
|
NH3T
NH2T

ATOM O3 OG303
-0.68
ATOM NP PG2
1.50
ATOM NO1 OG2P1
-0.82
ATOM NO2 OG2P1
-0.82
ATOM NO5' OG303
-0.62
ATOM NC5' CG321
-0.08
ATOM NH5S HGA2
0.09
ATOM NH5' HGA2
0.09
GROUP
ATOM NC2' CG3C51
0.14
ATOM NH2' HGA1
0.09
ATOM NO2' OG311
-0.65
ATOM NH2T HGP1
0.42
GROUP
ATOM NC3' CG3C51
0.14
ATOM NH3' HGA1
0.09
ATOM NO3' OG311
-0.65
ATOM NH3T HGP1
0.42
GROUP
ATOM NC1' CG3C51
0.11
ATOM NH1' HGA1
0.09
ATOM NC4' CG3C51
0.11
ATOM NH4' HGA1
0.09
ATOM NO4' OG3C51 -0.40
GROUP
ATOM NN1 NG301
-0.27 !N2
ATOM NC6 CG2D1O -0.06 !C3
ATOM NH6 HGA4
0.17 !H4
ATOM NC5 CG2D1
-0.18 !C5
ATOM NH5 HGA4
0.14 !H6
ATOM NC4 CG321
-0.28 !C7
ATOM NH4 HGA2
0.09 !H8
ATOM NH42 HGA2
0.09 !H17
ATOM NC3 CG2DC1
0.36 !C9
ATOM NC2 CG2D1O -0.10 !C10
ATOM NH2 HGA4
0.14 !H11
ATOM NC7 CG2O1
0.55 !C12
ATOM NO7 OG2D1
-0.51 !O13
ATOM NN7 NG2S2
-0.72 !N14
ATOM NH71 HGP1
0.26 !H15 ! trans to amide O
ATOM NH72 HGP1
0.32 !H16 ! cis to amide O
BOND AN1 AC2
AN3 AC4
AC5 AC6
BOND AC6 AN6
AC5 AN7
AC8 AN9
BOND AN9 AC4
AC2 AH2
AN6 AH61
AN6 AH62
DOUBLE AC6 AN1
AC2 AN3
AC4 AC5
AN7 AC8
BOND AN9 AC1'
AC1' AC2'
AC2' AC3'
AC3' AC4'
BOND AO4' AC1'
AC1' AH1'
AC2' AO2'
AO2' AP2
BOND AC3' AH3'
AC3' AO3'
AO3' AH3T
AC4' AH4'
BOND AC5' AH5S
AC5' AH5'
AC5' AO5'
AO5' AP
BOND AP AO2
AP O3
O3 NP
NP NO1
BOND NP NO5'
NO5' NC5'
NC5' NH5S
NC5' NH5'
BOND NC4' NO4'
NO4' NC1'
NC1' NC2'
NC2' NC3'
BOND NC1' NH1'
NC2' NH2'
NC2' NO2'
NO2' NH2T
BOND NC3' NO3'
NO3' NH3T
NC4' NH4'
NC1' NN1
BOND NC3 NC4
NC5 NC6
BOND NC2 NH2
NC3 NC7
NC7 NO7
NC7 NN7
BOND NN7 NH72
NC4 NH4
NC4 NH42
NC5 NH5
BOND AP2 AO1P
AP2 AO2P
AP2 AO2T
AO2T AH2T
DOUBLE NC2 NC3
NC4 NC5
NC6 NN1
! adenine impropers

AC8 AH8
AC4'
AC2'
AC4'
AP
NP
NC5'
NC3'
NC3'
NN1

AO4'
AH2'
AC5'
AO1
NO2
NC4'
NC4'
NH3'
NC2

NN7 NH71
NC6 NH6

IMPR AN6 AC6


AH61 AH62
! amide impropers
IMPR NC7 NN7 NC3 NO7
IMPR NN7 NC7 NH71 NH72
! ring hydrogen impropers
IMPR NC6 NN1 NC5 NH6
IMPR NC2 NC3 NN1 NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO3'
ACCE AO5'
ACCE AO1 AP
ACCE AO2 AP
ACCE O3
ACCE NO1 NP
ACCE NO2 NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2'
! IC table was beyond repair
IC AP
O3
NP
NO5'
IC AP
O3
NP
NO1
IC AP
O3
NP
NO2
IC NP
O3
AP
AO5'
IC O3
AO5' *AP
AO1
IC O3
AO5' *AP
AO2
IC O3
AP
AO5' AC5'
IC AP
AO5' AC5' AC4'
IC AC4' AO5' *AC5' AH5'
IC AC4' AO5' *AC5' AH5S
IC AO5' AC5' AC4' AC3'
IC AC5' AC4' AC3' AO3'
IC AH3T AO3' AC3' AC4'
IC AO4' AC3' *AC4' AC5'
IC AC2' AC4' *AC3' AO3'
IC AC4' AC3' AC2' AC1'
IC AC3' AC2' AC1' AN9
IC AO4' AC1' AN9
AC4
IC AC1' AC4
*AN9 AC8
IC AC4
AN9
AC8
AN7
IC AC8
AN9
AC4
AC5
IC AC8
AN7
AC5
AC6
IC AN7
AC5
AC6
AN1
IC AC5
AC6
AN1
AC2

AC6

AN1

AC5

AN6

NC7
NN7

NC3
NC7

NN7 NO7
NH72 NH71

NC5

NC6

NC4

NH5

==> replaced (kevo)


1.5954 101.60 146.76
1.5954 101.60 37.78
1.5954 101.60 -103.74
1.6061 101.60 164.74
1.5954 96.46 -112.08
1.5954 96.46 120.37
1.5954 96.46 -55.54
1.6655 115.61 -176.43
1.5479 112.56 120.22
1.5479 112.56 -120.20
1.4409 112.56 51.86
1.5479 114.73 138.72
0.9769 98.08 131.19
1.4383 107.54 -123.87
1.5457 105.32 -117.01
1.5409 105.32 -20.11
1.5457 102.83 133.28
1.4312 106.95 -116.73
1.4587 127.46 -179.84
1.3677 106.79
0.68
1.3782 106.79 -0.37
1.3348 103.19 179.17
1.3939 132.19 -179.58
1.4074 119.12 -0.76

97.71
120.83
108.35
96.46
103.67
104.32
115.61
112.56
110.27
110.70
114.73
111.81
111.81
114.73
111.81
102.83
112.16
127.46
106.79
113.34
105.46
132.19
119.12
119.15

1.6612
1.5331
1.5264
1.6655
1.5327
1.5300
1.4409
1.5479
1.1161
1.1158
1.5409
1.4297
1.5409
1.5479
1.4297
1.5465
1.4587
1.3677
1.3782
1.3348
1.3976
1.4074
1.3630
1.3635

IC AN9
AC5
IC AC5
AN1
IC AN1
AC6
IC AH61 AC6
IC AN9
AN7
IC AN1
AN3
IC AO4' AC2'
IC AC1' AC3'
IC AC2' AC4'
IC AC3' AO4'
IC NC5' NO5'
IC NP
NO5'
IC NO5' NC5'
IC NC5' NC4'
IC NC4' NC3'
IC NC3' NC2'
IC NO2' NC2'
IC NH2T NO2'
IC NO4' NC2'
IC NC1' NC3'
IC NC2' NC4'
IC NC3' NO4'
IC NC4' NO5'
IC NC4' NO5'
IC NC3' NC2'
IC NO3' NC3'
IC NH3T NO3'
IC NC2' NC1'
IC NC1' NN1
IC NN1
NC2
IC NC2
NC3
IC NC3
NC4
IC NN1
NC2
IC NC2
NC3
IC NC2
NC3
IC NO7
NC7
IC NO7
NC7
IC NC2
NC3
IC NC2
NC3
IC NC3
NC4
IC NC4
NC5
IC NC6
NN1
IC AC1' AC3'
IC AC3' AC2'
IC AC2' AO2'
IC AO2T AO2'
IC AO2T AO2'
IC AO2' AP2
PATCH FIRST NONE

*AC4 AN3
*AC6 AN6
AN6
AH61
*AN6 AH62
*AC8 AH8
*AC2 AH2
*AC1' AH1'
*AC2' AH2'
*AC3' AH3'
*AC4' AH4'
NP
NO2
NC5' NC4'
NC4' NC3'
NC3' NC2'
NC2' NC1'
NC1' NO4'
NC1' NO4'
NC2' NC1'
*NC1' NH1'
*NC2 NH2'
*NC3 NH3'
*NC4 NH4'
*NC5 NH5'
*NC5 NH5S
NC1' NN1
NC2' NC1'
NC3' NC2'
NN1
NC2
NC2
NC3
NC3
NC4
NC4
NC5
NC5
NC6
NC3
NC7
NC7
NO7
NC7
NN7
NN7
NH71
NN7
NH72
NC4
NH4
NC4
NH42
NC5
NH5
NC6
NH6
NC2
NH2
*AC2' AO2'
AO2' AP2
AP2
AO2T
*AP2 AO1P
*AP2 AO2P
AO2T AH2T
LAST NONE

1.3677
1.4074
1.3630
0.9983
1.3782
1.3635
1.4312
1.5465
1.5457
1.5409
1.4347
1.6612
1.4347
1.5645
1.5406
1.5383
1.4360
0.9842
1.4444
2.4561
4.7358
6.4975
5.2257
5.2257
1.5383
1.4402
0.9765
1.5383
1.4868
1.3589
1.3767
1.5415
1.3589
1.3767
1.3767
1.2364
1.2364
1.3767
1.3767
1.5415
1.5185
1.3587
1.5465
1.5457
1.4465
1.5606
1.5606
1.5853

105.46
119.12
117.19
119.41
113.34
125.66
109.65
102.83
105.32
107.54
124.65
124.65
115.34
114.08
100.78
100.30
117.19
100.86
104.62
9.02
22.19
19.19
29.02
29.02
100.30
112.92
102.62
113.54
119.27
123.90
118.97
111.44
123.90
117.98
117.98
120.30
120.30
118.97
118.97
111.44
122.41
120.94
102.83
111.15
121.36
103.37
103.37
103.37

179.47
-178.70
175.38
-173.82
-179.89
-177.12
-115.54
118.17
120.87
-117.93
-95.76
-102.77
72.35
-96.03
-41.51
39.58
163.91
159.27
-113.82
118.36
-3.45
-28.86
-4.03
51.20
157.86
77.43
77.94
116.11
179.46
5.63
-6.62
4.92
-157.15
-162.23
18.92
-176.87
1.04
-136.44
108.13
-151.27
178.77
176.28
-119.62
-174.33
-92.28
-113.56
109.47
81.16

!toppar_amines.str
RESI AMM1
0.00 ! NH3 Ammonia
GROUP
ATOM N1 NG331 -1.125
ATOM H11 HGPAM3 0.375
ATOM H12 HGPAM3 0.375
ATOM H13 HGPAM3 0.375
BOND N1 H11 N1 H12 N1 H13
IC H11 H12 *N1 H13
0.0 0.0 120.

0.0 0.0

125.74
117.19
119.41
118.04
124.72
116.89
110.14
107.40
111.10
106.34
105.77
115.34
114.08
100.78
100.30
104.62
104.62
117.19
109.33
26.48
17.84
1.80
10.68
19.04
113.54
100.30
112.92
119.27
123.90
118.97
111.44
122.41
117.98
120.57
119.12
120.26
117.08
113.82
105.93
117.50
119.10
116.55
111.15
121.36
103.37
111.24
111.16
108.83

1.3491
1.3459
0.9983
0.9911
1.0924
1.0924
1.1011
1.1056
1.0996
1.1019
1.5264
1.5645
1.5406
1.5383
1.5383
1.4444
1.4444
1.5383
1.1012
3.8155
6.8914
7.1052
6.4109
5.7156
1.4868
1.5383
1.5383
1.3589
1.3767
1.5415
1.5185
1.3553
1.5220
1.2364
1.3682
0.9992
0.9956
1.1070
1.1113
1.0907
1.0963
1.0900
1.4465
1.5853
1.5606
1.4737
1.4708
0.9674

IC H13 H11 *N1 H12


to enable seeding.

0.0

0.0

120.

0.0 0.0 !redundant definition needed

RESI MAM1
0.00 !
GROUP
ATOM N1 NG321 -0.99 !
ATOM C1 CG3AM2 -0.06 !
ATOM HN1 HGPAM2 0.39 !
ATOM HN2 HGPAM2 0.39 !
ATOM HC1 HGAAM2 0.09 !
ATOM HC2 HGAAM2 0.09 !
ATOM HC3 HGAAM2 0.09 !
BOND N1 C1 N1 HN1 N1
BOND C1 HC1 C1 HC2 C1
IC N1 HC1 *C1 HC2 0.00
IC N1 HC1 *C1 HC3 0.00
IC HC1 C1 N1 HN1 0.00
IC C1 HN1 *N1 HN2 0.00

CH5N methylamine

RESI DMAM
0.00 !
GROUP
ATOM N1 NG311 -0.82 !
ATOM HN1 HGPAM1 0.40 !
ATOM C1 CG3AM1 -0.06 !
ATOM C2 CG3AM1 -0.06 !
ATOM H11 HGAAM1 0.09 !
ATOM H12 HGAAM1 0.09 !
ATOM H13 HGAAM1 0.09 !
ATOM H21 HGAAM1 0.09 !
ATOM H22 HGAAM1 0.09 !
ATOM H23 HGAAM1 0.09 !
BOND N1 HN1 N1 C1 N1
BOND C1 H11 C1 H12 C1
BOND C2 H21 C2 H22 C2
IC C1 N1 C2 H21 0.00
IC N1 H21 *C2 H22 0.00
IC N1 H21 *C2 H23 0.00
IC C1 C2 *N1 HN1 0.00
IC C2 N1 C1 H11 0.00
IC N1 H11 *C1 H12 0.00
IC N1 H11 *C1 H13 0.00

C2H7N dimethylamine

RESI TMAM
GROUP
ATOM N1 NG301
ATOM C1 CG3AM0
ATOM C2 CG3AM0
ATOM C3 CG3AM0
ATOM H11 HGAAM0
ATOM H12 HGAAM0
ATOM H13 HGAAM0
ATOM H21 HGAAM0
ATOM H22 HGAAM0
ATOM H23 HGAAM0
ATOM H31 HGAAM0
ATOM H32 HGAAM0
ATOM H33 HGAAM0
BOND N1 C1 N1
BOND C1 H11 C1
BOND C2 H21 C2

C3H9N trimethylamine, adm jr.


H31 H32
\ /
H11
C3-H33
\
/
H12-C1---N1
/
\
H13
C2-H23
/ \
H21 H22

0.00 !
!
-0.63 !
-0.06 !
-0.06 !
-0.06 !
0.09 !
0.09 !
0.09 !
0.09 !
0.09 !
0.09 !
0.09 !
0.09 !
0.09 !
C2 N1
H12 C1
H22 C2

HC1

HN1
\
/
HC2-C1---N1
/
\
HC3
HN2
HN2
HC3
0.00
0.00
0.00
0.00

120.0
-120.0
180.0
120.0

0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0

H11

HN1
\
/
H12-C1---N1
/
\
H13
C2-H23
/ \
H21 H22
C2
H13
H23
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C3
H13
H23

180.0
120.0
-120.0
120.0
180.0
120.0
-120.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0

BOND C3
IC C1
IC C2
IC N1
IC N1
IC C1
IC N1
IC N1
IC C1
IC N1
IC N1

H31
C2
N1
H11
H11
N1
H21
H21
N1
H31
H31

C3
*N1
C1
*C1
*C1
C2
*C2
*C2
C3
*C3
*C3

H32
C3
H11
H12
H13
H21
H22
H23
H31
H32
H33

C3
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H33
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

120.0
180.0
120.0
-120.0
180.0
120.0
-120.0
180.0
120.0
-120.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

!toppar_prot_na_all.str
RESI PPH1
-1.00 ! C6H6O4P phenol-phosphate residue
GROUP
ATOM CG CG2R61 -0.115 !
ATOM HG HGR61
0.115 !
HD1 HE1
GROUP
!
|
|
ATOM CD1 CG2R61 -0.115 !
CD1--CE1
ATOM HD1 HGR61
0.115 !
//
\\
GROUP
!
HG--CG
CZ--OH
O2-H2
ATOM CD2 CG2R61 -0.115 !
\ __ /
\ /
ATOM HD2 HGR61
0.115 !
CD2--CE2
P1 (-)
GROUP
!
|
|
// \\
ATOM CE1 CG2R61 -0.21 !
HD2 HE2 O4
O3
ATOM HE1 HGR61
0.21 !
GROUP
ATOM CE2 CG2R61 -0.21
ATOM HE2 HGR61
0.21
GROUP
ATOM CZ CG2R61 -0.16
ATOM OH OG303 -0.36
ATOM P1 PG1
1.40
ATOM O2 OG311 -0.75
ATOM H2 HGP1
0.39
ATOM O3 OG2P1 -0.76
ATOM O4 OG2P1 -0.76
BOND
BOND
BOND
BOND
BOND

CG
CE1
CG
P1
O2

CD1
CZ
HG
OH
H2

! IC table
IC CD2 CG
IC CD1 CG
IC CG CD1
IC CD1 CD2
IC CE1 CG
IC CE2 CG
IC CZ CD1
IC CZ CD2
IC CE2 CE1
IC CE1 CZ
IC CZ OH
IC O2 OH
IC O2 OH
IC OH P1

CG
CE2
CD1
P1

CD1
CD2
CE1
*CG
*CD1
*CD2
*CE1
*CE2
*CZ
OH
P1
*P1
*P1
O2

CE1
CE2
CZ
HG
HD1
HD2
HE1
HE2
OH
P1
O2
O3
O4
H2

CD2
CZ
HD1
O2

CD1
CZ
CD2
P1

1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3800
1.5800
1.5800
1.6100

CE1
OH
HD2
O3

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
108.00
108.00
108.00

CD2 CE2
CE1 HE1 CE2 HE2
P1 O4

0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
90.00
300.00
120.00
-120.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
108.00
103.00
103.00
115.00

1.3750
1.3750
1.3750
1.0800
1.0800
1.0800
1.0800
1.0800
1.3800
1.6100
1.5800
1.4800
1.4800
0.9600

RESI BMPH
-1.00 ! C7H8O3P Benz.methylene phosphate
GROUP
ATOM CG CG2R61 -0.115 !
HD1 HE1
ATOM HG HGR61
0.115 !
|
|
GROUP
!
CD1--CE1 HH1
O2-H2
ATOM CD1 CG2R61 -0.115 !
//
\\
\
/
ATOM HD1 HGR61
0.115 ! HG--CG
CZ---CH---P1 (-)
GROUP
!
\ __ /
/ //\\
ATOM CD2 CG2R61 -0.115 !
CD2--CE2 HH2 O4 O3
ATOM HD2 HGR61
0.115 !
|
|
GROUP
!
HD2 HE2
ATOM CE1 CG2R61 -0.21
ATOM HE1 HGR61
0.24
ATOM CE2 CG2R61 -0.21
ATOM HE2 HGR61
0.24
ATOM CZ CG2R61 -0.44
ATOM CH CG321 -0.18
ATOM HH1 HGA2
0.09
ATOM HH2 HGA2
0.09
ATOM P1 PG1
1.53
ATOM O2 OG311 -0.79
ATOM H2 HGP1
0.36
ATOM O3 OG2P1 -0.86
ATOM O4 OG2P1 -0.86
! NA ATOM TYPE
BOND CG CD1
CG CD2 CD1 CE1 CD2 CE2
BOND CE1 CZ
CE2 CZ
CZ CH
BOND CG HG
CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2
BOND CH HH1
CH HH2 CH P1
P1 O2 P1 O3
BOND P1 O4
O2 H2
! IC table
IC CD2 CG CD1 CE1
1.3750 120.00
0.00 120.00 1.3750
IC CD1 CG CD2 CE2
1.3750 120.00
0.00 120.00 1.3750
IC CG CD1 CE1 CZ
1.3750 120.00
0.00 120.00 1.3750
IC CE2 CE1 *CZ CH
1.3750 120.00 180.00 122.30 1.4900
IC CD1 CD2 *CG HG
1.3750 120.00 180.00 120.00 1.0800
IC CE1 CG *CD1 HD1
1.3750 120.00 180.00 120.00 1.0800
IC CE2 CG *CD2 HD2
1.3750 120.00 180.00 120.00 1.0800
IC CZ CD1 *CE1 HE1
1.3750 120.00 180.00 120.00 1.0800
IC CZ CD2 *CE2 HE2
1.3750 120.00 180.00 120.00 1.0800
IC CE1 CZ CH P1
1.3750 122.30 270.00 111.00 1.8800
IC P1 CZ *CH HH1
1.8800 111.00 120.00 107.50 1.1110
IC HH1 CZ *CH HH2
1.1110 107.50 -120.00 107.50 1.1110
IC CZ CH P1 O2
1.4900 111.00 180.00 93.00 1.5800
IC O2 CH *P1 O3
1.5800 93.00 120.00 103.00 1.4800
IC O2 CH *P1 O4
1.5800 93.00 -120.00 103.00 1.4800
IC CH P1 O2 H2
1.8800 93.00 120.00 115.00 0.9600
RESI BMPD
GROUP
ATOM CG
ATOM HG
GROUP
ATOM CD1
ATOM HD1
GROUP
ATOM CD2
ATOM HD2
GROUP
ATOM CE1

-2.00 ! C7H7O3P Benz.methyl phosphate dianionic


CG2R61 -0.115 !
HD1 HE1
HGR61
0.115 !
|
|
!
CD1--CE1 HH1
O2
CG2R61 -0.115 !
//
\\
\
/
HGR61
0.115 ! HG--CG
CZ---CH---P1 (-2)
!
\ __ /
/ //\\
CG2R61 -0.115 !
CD2--CE2 HH2 O4 O3
HGR61
0.115 !
|
|
HD2 HE2
CG2R61 -0.24

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
BOND
BOND
BOND
BOND
BOND
! IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

HE1 HGR61
CE2 CG2R61
HE2 HGR61
CZ CG2R61
CH CG321
HH1 HGA2
HH2 HGA2
P1 PG1
O2 OG2P1
O3 OG2P1
O4 OG2P1
CG CD1
CE1 CZ
CG HG
CH HH1
P1 O4
table

CE1
CZ
O2
O2
O2
CD1
HD1
CG
HG
CD2
HD2
CE2
HH1
HH2
HE1
HE2

RESI BDFP
GROUP
ATOM CG
ATOM HG
GROUP
ATOM CD1
ATOM HD1
GROUP
ATOM CD2
ATOM HD2
GROUP
ATOM CE1
ATOM HE1
ATOM CE2
ATOM HE2
ATOM CZ
ATOM CF
ATOM F1
ATOM F2
ATOM P1
ATOM O2
ATOM H2
ATOM O3
ATOM O4

CZ
CH
CH
CH
CH
CE1
CD1
CD1
CG
CG
CD2
CD2
CH
CH
CE1
CE2

CH
P1
*P1
*P1
*P1
CZ
CG
CE1
CD1
CD1
CG
CG
P1
P1
CD1
CD2

0.26
-0.24
0.26
-0.45
-0.28
0.09
0.09
1.90
-1.13
-1.13
-1.13
CG CD2
CE2 CZ
CD1 HD1
CH HH2

P1
O2
O3
O3
O4
CH
CD2
CZ
CE1
CE1
HG
CD1
O3
O3
HD1
HD2

CD1
CZ
CD2
CH

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

CE1
CH
HD2
P1

CD2 CE2

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

CE1 HE1 CE2 HE2


P1 O2 P1 O3

90.00
180.00
-115.82
-115.82
115.90
180.00
180.00
0.00
180.00
0.00
0.00
0.00
180.00
0.00
0.00
0.00

000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

-1.00 ! C7H6F2O3P Benz.difluor.phosphate


CG2R61 -0.115 !
HGR61
0.115 !
CG2R61 -0.115 !
HGR61
0.115 !
CG2R61 -0.115 !
HGR61
0.115 !
CG2R61
HGR61
CG2R61
HGR61
CG2R61
CG312
FGA2
FGA2
PG1
OG311
HGP1
OG2P1
OG2P1

-0.21
0.24
-0.21
0.24
-0.40
0.21
-0.17
-0.17
1.43
-0.72
0.36
-0.80
-0.80

HD1 HE1
|
|
CD1--CE1
F1
O2-H2
//
\\
\
/
HG--CG
CZ---CF---P1 (-)
\ __ /
/ //\\
CD2--CE2
F2 O4 O3
|
|
HD2 HE2

BOND CG CD1 CG CD2


BOND CE1 CZ
CE2 CZ
BOND CG HG
CD1 HD1
BOND CF F1
CF F2
BOND P1 O4
O2 H2
! IC table
IC CD2 CG CD1 CE1
IC CD1 CG CD2 CE2
IC CG CD1 CE1 CZ
IC CE2 CE1 *CZ CF
IC CD1 CD2 *CG HG
IC CE1 CG *CD1 HD1
IC CE2 CG *CD2 HD2
IC CZ CD1 *CE1 HE1
IC CZ CD2 *CE2 HE2
IC CE1 CZ CF P1
IC P1 CZ *CF F1
IC F1 CZ *CF F2
IC CZ CF P1 O2
IC O2 CF *P1 O3
IC O2 CF *P1 O4
IC CF P1 O2 H2
RESI BDFD
GROUP
ATOM CG
ATOM HG
GROUP
ATOM CD1
ATOM HD1
GROUP
ATOM CD2
ATOM HD2
GROUP
ATOM CE1
ATOM HE1
ATOM CE2
ATOM HE2
ATOM CZ
ATOM CF
ATOM F1
ATOM F2
ATOM P1
ATOM O2
ATOM O3
ATOM O4
BOND
BOND
BOND
BOND
BOND

CG
CE1
CG
CF
P1

CD1
CZ
CD2
CF
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.3750
1.8800
1.3530
1.4500
1.5800
1.5800
1.8800

CE1 CD2 CE2


CF
HD2 CE1 HE1 CE2 HE2
P1 P1 O2 P1 O3
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
115.00
118.00
115.00
86.00
86.00
86.00

0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
270.00
120.00
-120.00
180.00
120.00
-120.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
115.00
118.00
118.00
86.00
95.00
95.00
115.00

1.3750
1.3750
1.3750
1.4500
1.0800
1.0800
1.0800
1.0800
1.0800
1.8800
1.3530
1.3530
1.5800
1.4800
1.4800
0.9600

-2.00 ! C7H5F2O3P Benz.difluor.phosphate dianionic, chris


CG2R61 -0.115 !
HGR61
0.115 !
CG2R61 -0.115 !
HGR61
0.115 !

HD1 HE1
|
|
CD1--CE1
F1
O2
//
\\
\
/
HG--CG
CZ---CF---P1
(-2)
\ __ /
/ //\\
CD2--CE2
F2 O4 O3
|
|
HD2 HE2

CG2R61 -0.115 !
HGR61
0.115 !
CG2R61
HGR61
CG2R61
HGR61
CG2R61
CG312
FGA2
FGA2
PG1
OG2P1
OG2P1
OG2P1
CD1
CZ
HG
F1
O4

! IC table
IC CD2 CG
IC CD1 CG
IC CG CD1
IC CE2 CE1
IC CD1 CD2
IC CE1 CG

-0.24
0.26
-0.24
0.26
-0.36
0.24
-0.28
-0.28
2.00
-1.12
-1.12
-1.12
CG
CE2
CD1
CF

CD1
CD2
CE1
*CZ
*CG
*CD1

CE1
CE2
CZ
CF
HG
HD1

CD2
CZ
HD1
F2

CD1
CZ
CD2
CF

CE1 CD2 CE2


CF
HD2 CE1 HE1 CE2 HE2
P1 P1 O2 P1 O3

1.3750
1.3750
1.3750
1.3750
1.3750
1.3750

120.00
0.00 120.00
120.00
0.00 120.00
120.00
0.00 120.00
120.00 180.00 120.00
120.00 180.00 120.00
120.00 180.00 120.00

1.3750
1.3750
1.3750
1.4500
1.0800
1.0800

IC
IC
IC
IC
IC
IC
IC
IC
IC

CE2
CZ
CZ
CE1
P1
F1
CZ
O2
O2

CG
CD1
CD2
CZ
CZ
CZ
CF
CF
CF

*CD2
*CE1
*CE2
CF
*CF
*CF
P1
*P1
*P1

HD2
HE1
HE2
P1
F1
F2
O2
O3
O4

1.3750
1.3750
1.3750
1.3750
1.8800
1.3530
1.4500
1.4800
1.4800

120.00
120.00
120.00
120.00
115.00
118.00
115.00
95.00
95.00

180.00
180.00
180.00
90.00
120.00
-120.00
180.00
120.00
-120.00

120.00
120.00
120.00
115.00
118.00
118.00
95.00
95.00
95.00

1.0800
1.0800
1.0800
1.8800
1.3530
1.3530
1.4800
1.4800
1.4800

RESI EP_2
-2.00 ! C2H5O4P Ethylphosphate, dianionic
!test CT3-CT2-ON2-P dihedral without complications from phosphate proton
GROUP
!
H21
ATOM P1 PG1
1.10 !
|
ATOM O1 OG303 -0.40 !
H23--C2--H22
ATOM O2 OG2P1 -0.90 !
|
ATOM O3 OG2P1 -0.90 !
H11--C1--H12
ATOM O4 OG2P1 -0.90 !
|
GROUP
!
O1
ATOM C1 CG321 -0.18 !
|
ATOM H11 HGA2
0.09 !
(-) O4==P1==O3 (-)
ATOM H12 HGA2
0.09 !
||
GROUP
!
O2
ATOM C2 CG331 -0.27 !
ATOM H21 HGA3
0.09 !
ATOM H22 HGA3
0.09 !
ATOM H23 HGA3
0.09 !
BOND P1
BOND C1
BOND C2
!
IC C1 O1
IC O2 O1
IC O2 O1
IC O2 P1
IC P1 O1
IC C2 O1
IC H11 O1
IC O1 C1
IC H21 C1
IC H21 C1

O1
H11
H21
P1
*P1
*P1
O1
C1
*C1
*C1
C2
*C2
*C2

P1
C1
C2
O2
O3
O4
C1
C2
H11
H12
H21
H22
H23

O2
H12
H22

P1
C1
C2

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

O3
C2
H23
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

P1

O4

180.00
120.00
-120.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00

O1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI IP_2
-2.00 ! C3H7O4P isopropylphosphate, dianionic
!test CT3-CT1-ON2-P dihedral without complications from phosphate proton
GROUP
!
H21
ATOM P1 PG1
1.10 !
|
ATOM O1 OG303 -0.40 !
H23--C2--H22 H31
ATOM O2 OG2P1 -0.90 !
|
/
ATOM O3 OG2P1 -0.90 !
H11--C1----C3--H32
ATOM O4 OG2P1 -0.90 !
|
\
GROUP
!
O1
H33
ATOM C1 CG311 -0.09 !
|
ATOM H11 HGA1
0.09 !
(-) O4==P1==O3 (-)
!
||
GROUP
!
O2
ATOM C2 CG331 -0.27 !
ATOM H21 HGA3
0.09 !
ATOM H22 HGA3
0.09 !
ATOM H23 HGA3
0.09 !

GROUP
ATOM C3
ATOM H31
ATOM H32
ATOM H33
BOND P1
BOND C1
BOND C2
BOND C3
!
IC C1 O1
IC O2 O1
IC O2 O1
IC O2 P1
IC P1 O1
IC C2 O1
IC C3 O1
IC O1 C1
IC H21 C1
IC H21 C1
IC O1 C1
IC H31 C1
IC H31 C1
RESI SAHC
GROUP
ATOM N
ATOM HT1
ATOM HT2
ATOM HT3
ATOM CA
ATOM HA
GROUP
ATOM CB
ATOM HB1
ATOM HB2
GROUP
ATOM CG
ATOM HG1
ATOM HG2
ATOM SD
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C
ATOM OT1
ATOM OT2
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N9
ATOM C5
ATOM N7
ATOM C8

CG331
HGA3
HGA3
HGA3
O1
H11
H21
H31
P1
*P1
*P1
O1
C1
*C1
*C1
C2
*C2
*C2
C3
*C3
*C3

!
!
!
!
!

-0.27
0.09
0.09
0.09
P1
C1
C2
C3

O2
C2
H22
H32

O2
O3
O4
C1
C2
C3
H11
H21
H22
H23
H31
H32
H33

P1
C1
C2
C3

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

O3
C3
H23
H33
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

P1

O4

60.00
120.00
-120.00
60.00
220.00
-120.00
-120.00
-60.00
120.00
-120.00
180.00
120.00
-120.00

O1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C14H20N6O5S S-adenosyl-homocysteine


NG3P3
HGP2
HGP2
HGP2
CG314
HGA1

-0.30
0.33
0.33
0.33
0.21
0.10

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2
SG311
CG321
HGA2
HGA2

-0.13
0.09
0.09
-0.10
-0.13
0.09
0.09

CG2O3
OG2D2
OG2D2

0.34
-0.67
-0.67

CG3C51
HGA1
OG3C51
CG3C51
HGA1

0.16
0.09
-0.50
0.16
0.09

NG2R51
CG2RC0
NG2R50
CG2R53

-0.05
0.28
-0.71
0.34

!
!
(2)
HT1
!
|
/
!(1)--CA--N--HT2 (+)
!
|
\
!
HA
HT3
!
!
!
!
HB1 HG1
H5' H4' O4' Adenine
!
| |
|
\ / \ /
!
(1)--CB--CG--SD--C5'----C4' C1'-H1'
!
| |
|
|
|
!
HB2 HG2
H5'' H3'-C3'--C2'-H21'
! kevo: symmetrized
|
|
!
H3T--O3' O2'-H2'
!
!
OT2(-)
!
/
!(2)-C
!
\\
!
OT1

ATOM H8
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T

HGR52
NG2R62
CG2R64
HGR62
NG2R62
CG2RC0
CG2R64
NG2S3
HGP4
HGP4

0.12
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

CG3C51
HGA1
OG311
HGP1

0.14
0.09
-0.65
0.42

BOND C5' C4'


C4' O4'
BOND C1' N9
C1' C2'
BOND C2 N1
C6 N6
BOND N6 H61
N6 H62
BOND C2' C3'
C2' O2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8 H8
BOND N CA O3' H3T
BOND CB CA CG CB SD CG
BOND CA HA CB HB1 CB HB2
BOND HT1 N
HT2 N
HT3 N
DOUBLE N1 C6
C2 N3
DOUBLE C OT1
IMPR N6 C6 H61 H62
IMPR OT1 CA OT2 C
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C5'
O4'
C2'
C4'
C3'
O4'
C1'
C4
C8
C8
N7
C5
N9
C5
N1
H61
C5
N1
H61
N9
N1
C1'
H2'

C4'
C3'
C4'
C3'
C2'
C1'
C4
N9
N9
N7
C5
C6
C5
N1
C6
C6
N1
C6
C6
N7
N3
C3'
O2'

C3'
*C4'
*C3'
C2'
C1'
N9
*N9
C8
C4
C5
C6
N1
*C4
*C6
N6
*N6
*C6
N6
*N6
*C8
*C2
*C2'
C2'

O3'
C5'
O3'
C1'
N9
C4
C8
N7
C5
C6
N1
C2
N3
N6
H61
H62
N6
H61
H62
H8
H2
O2'
C3'

C4' C3'
N9 C4

O4' C1'
N9 C8

C4

C6
O2'
C3'
C2

C5 N7
C3' O3'
C4' H4'

C5' H5'

C5
H2'
H3'
H2

C5' SD C CA
CG HG1 CG HG2
OT2 C
C4 C5

1.5160
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.376
1.367
0.0
0.0
0.0
1.376
1.409
1.337
1.01
1.409
1.337
1.01
0.0
0.0
1.5284
0.9600

C6

N1
116.10
104.06
100.16
100.16
101.97
113.71
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
102.04
114.97

C5

N7

N3

C8

N6

140.00
-120.04
-124.08
-30.00
147.80
-97.2
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63

115.12
116.10
115.12
102.04
113.71
125.59
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
110.81
111.92

1.4212 !delta
1.5160
1.4212
1.5251 !puck
1.4896
1.3783 !chi
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

O4'
C1'
C2'
C3'
N
CA
HT1
HT1
HT1
CB
CB
CG
CG
SD
SD
CB
CG
C4'
C4'
N
OT1
SD
O4'
O4'
C5'
C4'
N9
N9
C4
C1'
C5
N9
C6
N7
C4
N1
N3
C5
C3'
C3'
C1'
C4'

C2'
C3'
C4'
O4'
CA
CB
CA
CA
N
N
N
CA
CA
CB
CB
CG
SD
SD
SD
CA
CA
C5'
C5'
C5'
C4'
O4'
O4'
O4'
C1'
N9
N9
C4
C4
N9
C5
C5
N1
C6
C1'
C1'
C2'
C3'

RESI INDO
GROUP
ATOM HG
ATOM CG
ATOM CD2
ATOM CD1
ATOM HD1
ATOM NE1
ATOM HE1
ATOM CE2
ATOM CE3
ATOM HE3
ATOM CZ2
ATOM HZ2
ATOM CZ3
ATOM HZ3
ATOM CH2

*C1' H1'
0.0
*C2' H2'' 0.0
*C3' H3'
0.0
*C4' H4'
0.0
CB
CG
1.4863
CG
SD
1.5495
*N
HT2
1.0633
*N
HT3
1.0633
CA
CB
1.0633
*CA C
1.5495
*CA HA
1.5495
*CB HB1
1.5438
*CB HB2
1.5438
*CG HG1
1.8249
*CG HG2
1.8249
SD
C5'
1.5438
C5' C4'
1.8249
*C5' H5'
1.5403
*C5' H5'' 1.5403
C
OT1
1.4863
*C
OT2
1.2492
C4' O4'
1.8303
*C4' C3'
1.4591
*C4' H4'
1.4591
O4' C1'
1.5403
C1' N9
1.4591
*C1' C2'
1.4614
*C1' H1'
1.4614
*N9 C8
1.3837
C4
C5
1.4614
*C4 N3
1.3831
C5
C6
1.3837
*C5 N7
1.4115
*C8 H8
1.3073
C6
N1
1.3831
*C6 N6
1.3524
*C2 H2
1.3403
N6
H61
1.4115
*C2' O2'
1.5132
*C2' H2'' 1.5132
O2' H2'
1.5135
O3' H3T
1.5499

0.0 -115.0
0.0 115.0
0.0 115.0
0.0 -115.0
111.52 -68.05
114.80 -169.85
98.00 113.14
98.00 -117.28
98.00 -136.27
111.52 123.39
111.52 -122.64
114.80 125.78
114.80 -119.31
111.97 120.25
111.97 -122.78
111.97 149.65
104.32 -59.34
117.91 122.31
117.91 -122.71
106.34 -166.34
117.88 -178.37
117.91 169.12
108.69 118.83
108.69 -116.07
108.69 133.30
108.22 -159.13
111.15 124.24
111.15 -119.53
126.86 175.00
126.86 176.84
105.37 179.25
105.37 179.94
116.97 179.52
113.91 -179.74
116.97 -0.21
118.01 -179.35
129.44 -179.97
123.62 179.97
95.49 115.41
95.49 -116.10
113.17 177.31
116.35 167.44

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
114.80 1.5438
111.97 1.8249
109.99 1.0338
113.48 1.0305
111.52 1.5495
106.34 1.5395
109.49 1.0806
110.22 1.1112
106.97 1.1179
107.22 1.1112
110.68 1.1101
104.32 1.8303
117.91 1.5403
108.22 1.1127
108.62 1.1118
117.88 1.2492
117.42 1.2654
108.69 1.4591
122.55 1.5499
109.38 1.1099
108.22 1.4240
111.15 1.4614
102.39 1.5135
107.46 1.1156
127.05 1.3697
105.37 1.3831
128.02 1.3472
116.97 1.4115
110.80 1.3914
121.60 1.0918
118.01 1.3524
123.62 1.3438
115.20 1.0945
117.15 0.9949
113.17 1.4151
112.79 1.1120
109.89 0.9633
110.25 0.9629

0.00 ! C8H7N indole, adm jr., atm


HGR51
CG2R51
CG2RC0
CG2R51
HGR52
NG2R51
HGP1
CG2RC0
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61

0.14
-0.17
0.11
-0.15
0.22
-0.51
0.37
0.24
-0.25
0.17
-0.27
0.16
-0.20
0.14
-0.14

!
!
!
!
!
!
!
!
!
!
!

HE3
|
HG
CE3
\
/ \\
CG-----CD2 CZ3-HZ3
||
||
|
CD1
CE2 CH2-HH2
/ \ / \ //
HD1
NE1 CZ2
|
|
HE1 HZ2

ATOM HH2 HGR61


0.14
BOND CG HG CD2 CG NE1 CD1
BOND CZ2 CE2
BOND CZ3 CH2 CD2 CE3 NE1 CE2
BOND CD1 HD1 NE1 HE1 CE3 HE3
BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
DONOR HE1 NE1
IC CG CD1 NE1 CE2 1.3650 110.50
IC CD1 CG CD2 CE2 1.3650 106.40
IC CD2 CG CD1 NE1 1.4300 106.40
IC CE2 CG *CD2 CE3 1.3850 108.00
IC CE2 CD2 CE3 CZ3 1.3850 110.00
IC CD2 CE3 CZ3 CH2 1.3600 113.20
IC CE3 CZ3 CH2 CZ2 1.3750 120.00
IC CZ3 CD2 *CE3 HE3 1.3750 113.20
IC CH2 CE3 *CZ3 HZ3 1.3750 120.00
IC CZ2 CZ3 *CH2 HH2 1.3750 120.00
IC CE2 CH2 *CZ2 HZ2 1.3600 113.20
IC CD1 CE2 *NE1 HE1 1.3700 112.00
IC CG NE1 *CD1 HD1 1.3650 110.50
IC CD1 CD2 *CG HG
1.3650 106.40
PATCH FIRST NONE LAST NONE

0.00
0.00
0.00
180.00
0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

RESI MIND
0.00 ! C9H9N 3-methylindole,
GROUP
ATOM CB CG331 -0.27
ATOM HB1 HGA3
0.09
ATOM HB2 HGA3
0.09
ATOM HB3 HGA3
0.09
GROUP
ATOM CG CG2R51 -0.03
ATOM CD2 CG2RC0 0.11
ATOM CD1 CG2R51 -0.15
ATOM HD1 HGR52
0.22
ATOM NE1 NG2R51 -0.51
ATOM HE1 HGP1
0.37
ATOM CE2 CG2RC0 0.24
ATOM CE3 CG2R61 -0.25
ATOM HE3 HGR61
0.17
ATOM CZ2 CG2R61 -0.27
ATOM HZ2 HGR61
0.16
ATOM CZ3 CG2R61 -0.20
ATOM HZ3 HGR61
0.14
ATOM CH2 CG2R61 -0.14
ATOM HH2 HGR61
0.14
BOND CB HB1 CB HB2 CB HB3
BOND CG CB CD2 CG NE1 CD1
BOND CZ2 CE2
BOND CZ3 CH2 CD2 CE3 NE1 CE2
BOND CD1 HD1 NE1 HE1 CE3 HE3
BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
DONOR HE1 NE1
IC CB CG CD1 NE1
1.4920 127.00 180.00
IC CG CD1 NE1 CE2
1.3650 110.50
0.00
IC CD1 CG CD2 CE2
1.3650 106.40
0.00
IC CD2 CB *CG CD1
1.4300 126.70 180.00
IC HB1 CB CG CD1
1.1110 109.50
0.00
IC HB2 CB CG CD1
1.1110 109.50 120.00

112.00
108.00
110.50
133.50
113.20
120.00
120.00
122.00
120.00
120.00
120.00
126.00
125.00
126.40

1.3700
1.3850
1.3700
1.3600
1.3750
1.3750
1.3750
1.0800
1.0800
1.0800
1.0800
0.9760
1.0800
1.0800

adm jr., atm

110.50
112.00
108.00
127.00
127.00
127.00

1.3700
1.3700
1.3850
1.3650
1.3650
1.3650

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

HB3
CD2
CE2
CE2
CD2
CE3
CZ3
CH2
CZ2
CE2
CD1
CG

CB
CG
CG
CD2
CE3
CZ3
CD2
CE3
CZ3
CH2
CE2
NE1

CG
CD1
*CD2
CE3
CZ3
CH2
*CE3
*CZ3
*CH2
*CZ2
*NE1
*CD1

CD1
NE1
CE3
CZ3
CH2
CZ2
HE3
HZ3
HH2
HZ2
HE1
HD1

1.1110
1.4300
1.3850
1.3850
1.3600
1.3750
1.3750
1.3750
1.3750
1.3600
1.3700
1.3650

109.50
106.40
108.00
110.00
113.20
120.00
113.20
120.00
120.00
113.20
112.00
110.50

240.00
0.00
180.00
0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00

127.00
110.50
133.50
113.20
120.00
120.00
122.00
120.00
120.00
120.00
126.00
125.00

RESI EIND
0.00 ! C10H11N ethylindole, adm jr.,
GROUP
ATOM CA CG331 -0.27 !
HA2
ATOM HA1 HGA3
0.09 !
|
ATOM HA2 HGA3
0.09 ! HA1-CA-HA3
HE3
ATOM HA3 HGA3
0.09 !
|
|
GROUP
! HB1-CB-HB2
CE3
ATOM CB CG321 -0.18 !
\
/ \\
ATOM HB1 HGA2
0.09 !
CG-----CD2 CZ3-HZ3
ATOM HB2 HGA2
0.09 !
||
||
|
GROUP
!
CD1
CE2 CH2-HH2
ATOM CG CG2R51 -0.03 !
/ \ / \ //
ATOM CD2 CG2RC0 0.11 !
HD1
NE1 CZ2
ATOM CD1 CG2R51 -0.15 !
|
|
ATOM HD1 HGR52
0.22 !
HE1 HZ2
ATOM NE1 NG2R51 -0.51
ATOM HE1 HGP1
0.37
ATOM CE2 CG2RC0 0.24
ATOM CE3 CG2R61 -0.25
ATOM HE3 HGR61
0.17
ATOM CZ2 CG2R61 -0.27
ATOM HZ2 HGR61
0.16
ATOM CZ3 CG2R61 -0.20
ATOM HZ3 HGR61
0.14
ATOM CH2 CG2R61 -0.14
ATOM HH2 HGR61
0.14
BOND CA HA1 CA HA2 CA HA3
BOND CA CB CB HB1 CB HB2
BOND CG CB CD2 CG NE1 CD1
BOND CZ2 CE2
BOND CZ3 CH2 CD2 CE3 NE1 CE2
BOND CD1 HD1 NE1 HE1 CE3 HE3
BOND CZ3 HZ3 CH2 HH2 CZ2 HZ2
DOUBLE CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
DONOR HE1 NE1
IC CA CB CG CD1 0.0000 0.0000 180.0000 0.0000
IC CB CG CD1 NE1 0.0000 0.0000 180.0000 0.0000
IC CG CB CA HA1 0.0000 0.0000 180.0000 0.0000
IC HA1 CB *CA HA2 0.0000 0.0000 120.0000 0.0000
IC HA1 CB *CA HA3 0.0000 0.0000 240.0000 0.0000
IC CA CG *CB HB1 0.0000 0.0000 120.0000 0.0000
IC CA CG *CB HB2 0.0000 0.0000 240.0000 0.0000
IC CG CD1 NE1 CE2 0.0000 0.0000 0.0000 0.0000
IC CD2 CB *CG CD1 0.0000 0.0000 180.0000 0.0000
IC CD1 CG CD2 CE2 0.0000 0.0000 0.0000 0.0000
IC CD2 CG CD1 NE1 0.0000 0.0000 0.0000 0.0000

1.3650
1.3700
1.3600
1.3750
1.3750
1.3750
1.0800
1.0800
1.0800
1.0800
0.9760
1.0800
atm

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC CE2 CG *CD2 CE3 0.0000


IC CE2 CD2 CE3 CZ3 0.0000
IC CD2 CE3 CZ3 CH2 0.0000
IC CE3 CZ3 CH2 CZ2 0.0000
IC CZ3 CD2 *CE3 HE3 0.0000
IC CH2 CE3 *CZ3 HZ3 0.0000
IC CZ2 CZ3 *CH2 HH2 0.0000
IC CE2 CH2 *CZ2 HZ2 0.0000
IC CD1 CE2 *NE1 HE1 0.0000
IC CG NE1 *CD1 HD1 0.0000
!IC CD1 CD2 *CG HG
0.0000
!reset default patches
DEFA FIRS NONE LAST NONE
RESI BFL
GROUP
ATOM CG1
ATOM CG2
ATOM CD1
ATOM HD1
ATOM CD2
ATOM HD2
ATOM CE1
ATOM HE1
ATOM CE2
ATOM HE2
ATOM CZ1
ATOM HZ1
ATOM CD3
ATOM HD3
ATOM CD4
ATOM HD4
ATOM CE3
ATOM HE3
ATOM CE4
ATOM HE4
ATOM CZ2
ATOM HZ2
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

0.00 ! C12H10 biphenyl, peml.


CG2R67
CG2R67
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1

CG2
CD1
CG2
CE1
CG2
CE2
CG1
CZ1
CZ1
CE2
CD1

0.0000 180.0000 0.0000 0.0000


0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000
0.0000 180.0000 0.0000 0.0000

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4
HZ1
CG1
CG2
CG1
CG1
CG1
CG1
CD1
CD1
CD2
CE1
CG1

CG1
CE2
CG2
CZ2

0.000
0.000
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
CD2
CZ1
CD3
CE4

CG1
CZ1
CD3
CE4

!
HE1
HD1 HD3
HE3
!
\
/
\
/
!
CE1--CD1
CD3--CE3
!
/
\
/
\
! HZ1--CZ1
CG1---CG2
CZ2--HZ2
!
\
/
\
/
!
CE2--CD2
CD4--CE4
!
/
\
/
\
!
HE2
HD2 HD4
HE4

CG2
CE1
CE3
CD4

CD2 HD2 CE1 HE1


CD3 HD3
CE3 HE3 CE4 HE4
CZ2 HZ2
CD1
*CG1
CD1
*CD1
CD2
*CD2
CE1
*CE1
*CE2
*CZ1
CG2

CE1
CD2
CE1
HD1
CE2
HD2
CZ1
HE1
HE2
HZ1
CD4

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC

CD4
CG1
CE3
CG1
CE4
CG2
CZ2
CZ2
CE4

CG1
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE3

*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ2

CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
HZ2

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI BF6
-2.00 ! C16H12O6 biphenyl analog, peml.
!KEVO: charges adjusted to reflect updated acetone L-J.
!Resulting charges are unlikey to be good ==> re-optimize?
GROUP
ATOM CG1 CG2R67 0.000
ATOM CG2 CG2R67 0.000
ATOM CD1 CG2R61 -0.115
ATOM HD1 HGR61
0.115
ATOM CD2 CG2R61 -0.115
ATOM HD2 HGR61
0.115
ATOM CE1 CG2R61 -0.115
!
HE1
HD1 HD3
HE3
ATOM HE1 HGR61
0.115
!
\
/
\
/
ATOM CE2 CG2R61 -0.115
!
CE1--CD1
CD3--CE3
ATOM HE2 HGR61
0.115
!
/
\
/
\
ATOM CZ1 CG2R61 0.000
!
SUBS--CZ1
CG1---CG2
CZ2--SUBS
ATOM CD3 CG2R61 -0.115
!
\
/
\
/
ATOM HD3 HGR61
0.115
!
CE2--CD2
CD4--CE4
ATOM CD4 CG2R61 -0.115
!
/
\
/
\
ATOM HD4 HGR61
0.115
!
HE2
HD2 HD4
HE4
ATOM CE3 CG2R61 -0.115
ATOM HE3 HGR61
0.115
ATOM CE4 CG2R61 -0.115
ATOM HE4 HGR61
0.115
ATOM CZ2 CG2R61 0.000
GROUP
ATOM C1
ATOM O1
ATOM C2
ATOM H2
ATOM O2A
ATOM H2A
ATOM O2B

CG2O5
OG2D3
CG311
HGA1
OG311
HGP1
OG312

0.38
-0.48
0.17
0.09
-0.60
0.32
-0.88

GROUP
ATOM C3
ATOM O3
ATOM C4
ATOM H4
ATOM O4A
ATOM H4A
ATOM O4B

CG2O5
OG2D3
CG311
HGA1
OG311
HGP1
OG312

0.38
-0.48
0.17
0.09
-0.60
0.32
-0.88

BOND
BOND
BOND
BOND
BOND

CD1
CD2
CE1
CE3
CD4

CG1
CE2
CD1
CZ2
CG2

CG1
CE2
CG2
CZ2

CD2
CZ1
CD3
CE4

CG1
CZ1
CD3
CE4

!
O1
!
//
!Ring--C1 H2
!
\ /
!
C2--O2A--H2A
!
\
!
O2B (-)

CG2
CE1
CE3
CD4

BOND CD1 HD1 CD2 HD2 CE1 HE1

BOND CE2 HE2


CD3 HD3
BOND CD4 HD4 CE3 HE3 CE4 HE4
BOND
BOND
BOND
BOND
BOND
BOND

CZ1
C2
C2
CZ2
C4
C4

C1
H2
O2B
C3
H4
O4B

C1 O1 C1 C2
C2 O2A O2A H2A
C3 O3 C3 C4
C4 O4A O4A H4A

IMPR C1 CZ1 C2 O1
IMPR C3 CZ2 C4 O3
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CD1
CG2
CE1
CG2
CE2
CG1
CZ1
CZ1
CD1
CD4
CG1
CE3
CG1
CE4
CG2
CZ2
CZ2
CE2
CE1
C2
CZ1
O2A
O2A
C1
CE4
CE3
C4
CZ2
O4A
O4A
C3

CG2
CG1
CG1
CG1
CG1
CD1
CD1
CD2
CG1
CG1
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE1
CZ1
CZ1
C1
C1
C1
C2
CE3
CZ2
CZ2
C3
C3
C3
C4

*CG1
CD1
*CD1
CD2
*CD2
CE1
*CE1
*CE2
CG2
*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ1
C1
*C1
C2
*C2
*C2
O2A
*CZ2
C3
*C3
C4
*C4
*C4
O4A

CD2
CE1
HD1
CE2
HD2
CZ1
HE1
HE2
CD4
CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
C1
C2
O1
O2A
O2B
H2
H2A
C3
C4
O3
O4A
O4B
H4
H4A

1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
110.00
110.00
110.00
120.00
120.00
120.00
120.00
110.00
110.00
110.00

180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
-60.00
120.00
-120.00
180.00
180.00
180.00
180.00
-60.00
120.00
-120.00
180.00

RESI BF7
-2.00 ! C16H8O6 biphenyl analog, peml.
!KEVO: charges adjusted to reflect updated acetone L-J.
!Resulting charges are probably not that bad.
GROUP
ATOM CG1 CG2R67 0.00 !
ATOM CG2 CG2R67 0.00 !
GROUP
!
ATOM CD1 CG2R61 -0.115 !
ATOM HD1 HGR61
0.115 !
GROUP
!
ATOM CD2 CG2R61 -0.115 !
ATOM HD2 HGR61
0.115 !
GROUP
!
ATOM CE1 CG2R61 -0.115 !
ATOM HE1 HGR61
0.115 !

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
110.00
110.00
110.00
110.00
120.00
120.00
120.00
110.00
110.00
110.00
110.00

1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.2000
1.4000
1.4000
1.1000
0.9000
1.0900
1.4000
1.2000
1.4000
1.4000
1.1000
0.9000

GROUP
ATOM CE2 CG2R61 -0.115
ATOM HE2 HGR61
0.115

HE1

GROUP

0.000 !

CE1--CD1

CD3--CE3

ATOM CD3 CG2R61 -0.115 !

SUBS--CZ1

ATOM HD3 HGR61

0.115 !

!
CG2R61 -0.115 !
HGR61
0.115 !
!
CG2R61 -0.115 !
HGR61
0.115 !

!
!
!

ATOM CZ1 CG2R61


GROUP

GROUP
ATOM CD4
ATOM HD4
GROUP
ATOM CE3
ATOM HE3
GROUP
ATOM CE4
ATOM HE4
GROUP
ATOM CZ2
GROUP
ATOM C1
ATOM O1
ATOM C2
ATOM O2A
ATOM O2B
GROUP
ATOM C3
ATOM O3
ATOM C4
ATOM O4A
ATOM O4B
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IMPR
IMPR
IMPR
IMPR
IC
IC
IC
IC

HD1 HD3

HE3

CG1---CG2
/

CZ2--SUBS
/

CE2--CD2
CD4--CE4
/
\
/
\
HE2
HD2 HD4
HE4

CG2R61 -0.115
HGR61
0.115

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1
C1
C2
C3
C4
C1
C2
C3
C4

CG2R61
CG2O5
OG2D3
CG2O3
OG2D2
OG2D2

0.38
-0.48
0.62
-0.76
-0.76

CG2O5
OG2D3
CG2O3
OG2D2
OG2D2

0.38
-0.48
0.62
-0.76
-0.76

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4
C1
O1
O2B
O3
O4B
CZ1
C1
CZ2
C3

CD1
CG2
CE1
CG2

0.000

CG1
CE2
CG2
CZ2

CD2
CZ1
CD3
CE4

!
O
!
//
! Ring-C
!
\
!
C==O
!
|
!
O (-)
!
!
!
!

CG1
CZ1
CD3
CE4

CG2
CE1
CE3
CD4

CD2 HD2 CE1


CD3
CE3 HE3 CE4
CZ2 C3
C1 C2 C2

HE1
HD3
HE4
O2A

C3 C4 C4 O4A
C2
O2A
C4
O4A
CG2
CG1
CG1
CG1

O1
O2B
O3
O4B
*CG1
CD1
*CD1
CD2

CD2
CE1
HD1
CE2

1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00

180.00
180.00
180.00
180.00

120.00
120.00
120.00
120.00

1.4000
1.4000
1.0900
1.4000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CE2
CG1
CZ1
CZ1
CD1
CD4
CG1
CE3
CG1
CE4
CG2
CZ2
CZ2
CE2
CE1
C2
CZ1
O2A
CE4
CE3
C4
CZ2
O4A

RESI BCA
GROUP
ATOM CG1
ATOM CG2
GROUP
ATOM CD1
ATOM HD1
GROUP
ATOM CD2
ATOM HD2
GROUP
ATOM CE1
ATOM HE1
GROUP
ATOM CE2
ATOM HE2
GROUP
ATOM CD3
ATOM HD3
GROUP
ATOM CD4
ATOM HD4
GROUP
ATOM CE3
ATOM HE3
GROUP
ATOM CE4
ATOM HE4
GROUP
ATOM CZ1
ATOM C1
ATOM O1A
ATOM O1B
GROUP
ATOM CZ2
ATOM C2

CG1
CD1
CD1
CD2
CG1
CG1
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE1
CZ1
CZ1
C1
C1
CE3
CZ2
CZ2
C3
C3

*CD2
CE1
*CE1
*CE2
CG2
*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ1
C1
*C1
C2
*C2
*CZ2
C3
*C3
C4
*C4

HD2
CZ1
HE1
HE2
CD4
CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
C1
C2
O1
O2A
O2B
C3
C4
O3
O4A
O4B

1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
110.00
120.00
120.00
120.00
120.00
110.00

180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
-60.00
120.00
180.00
180.00
180.00
-60.00
120.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
110.00
110.00
120.00
120.00
120.00
110.00
110.00

1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.2000
1.4000
1.4000
1.0900
1.4000
1.2000
1.4000
1.4000

-2.00 ! C14H8O4 biphenyl analog, peml., acid analog


CG2R67
CG2R67

0.000
0.000

CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115

!
!
!
!
!
!
!
!
!

CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.10 !
O
CG2O3
0.62 !
//
OG2D2 -0.76 ! Ring-C (-)
OG2D2 -0.76 !
\
!
O
CG2R61 -0.10 !
CG2O3
0.62

HE1
HD1 HD3
HE3
\
/
\
/
CE1--CD1
CD3--CE3
/
\
/
\
SUBS--CZ1
CG1---CG2
CZ2--SUBS
\
/
\
/
CE2--CD2
CD4--CE4
/
\
/
\
HE2
HD2 HD4
HE4

ATOM O2A OG2D2


ATOM O2B OG2D2
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1
CZ2

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4
C1
C2
CD1
CG2
CE1
CG2
CE2
CG1
CZ1
CZ1
CD1
CD4
CG1
CE3
CG1
CE4
CG2
CZ2
CZ2
CE2
CE1
O1A
CE4
CE3
O2A

-0.76
-0.76

CG1
CE2
CG2
CZ2

CD2
CZ1
CD3
CE4

CG1
CZ1
CD3
CE4

CG2
CE1
CE3
CD4

CD2 HD2 CE1


CD3
CE3 HE3 CE4
C1 O1A C1
C2 O2A C2

HE1
HD3
HE4
O1B
O2B

CG2
CG1
CG1
CG1
CG1
CD1
CD1
CD2
CG1
CG1
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE1
CZ1
CZ1
CE3
CZ2
CZ2

*CG1
CD1
*CD1
CD2
*CD2
CE1
*CE1
*CE2
CG2
*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ1
C1
*C1
*CZ2
C2
*C2

CD2
CE1
HD1
CE2
HD2
CZ1
HE1
HE2
CD4
CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
C1
O1A
O1B
C2
O2A
O2B

1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

RESI C36
-2.00 ! C16H12O7 biphenyl with bridging O analog, peml.
!KEVO: charges adjusted to reflect updated acetone L-J.
!Resulting charges are unlikey to be good ==> re-optimize?
GROUP
! hydrated aldehyde analog (ionized)
ATOM CG1 CG2R61 0.215
ATOM O
OG301 -0.430
ATOM CD1 CG2R61 -0.115
ATOM HD1 HGR61
0.115
!
HE3
ATOM CD2 CG2R61 -0.115
!
\
/
ATOM HD2 HGR61
0.115
!
CD3--CE3
ATOM CE1 CG2R61 -0.115
!
/
\
ATOM HE1 HGR61
0.115
!
HD1
O ---CG2
CZ2--SUBS
ATOM CE2 CG2R61 -0.115
!
\
/
\
/
ATOM HE2 HGR61
0.115
!
CD1--CG1
CD4--CE4
ATOM CZ1 CG2R61 0.000
!
/
\
/
\
ATOM CG2 CG2R61 0.215
! HE1--CE1
CD2--HD2 HD4
HE4
ATOM CD3 CG2R61 -0.115
!
\
/
ATOM HD3 HGR61
0.115
!
CZ1--CE2
ATOM CD4 CG2R61 -0.115
!
/
\
ATOM HD4 HGR61
0.115
!
SUBS
HE2
ATOM CE3 CG2R61 -0.115

ATOM HE3
ATOM CE4
ATOM HE4
ATOM CZ2
GROUP
ATOM C1
ATOM O1
ATOM C2
ATOM H2
ATOM O2A
ATOM H2A
ATOM O2B
GROUP
ATOM C3
ATOM O3
ATOM C4
ATOM H4
ATOM O4A
ATOM H4A
ATOM O4B
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1
C2
C2
CZ2
C4
C4

HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 0.000
CG2O5
OG2D3
CG311
HGA1
OG311
HGP1
OG312

0.38
-0.48
0.17
0.09
-0.60
0.32
-0.88

CG2O5
OG2D3
CG311
HGA1
OG311
HGP1
OG312

0.38
-0.48
0.17
0.09
-0.60
0.32
-0.88

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4
C1
H2
O2B
C3
H4
O4B

CG1
CE2
CG2
CZ2
CG2
CD2

CD2
CZ1
CD3
CE4
O
HD2

!
O1
!
//
!Ring--C1 H2
!
\ /
!
C2--OH
!
\
!
O (-)

CG1
CZ1
CD3
CE4

O
CE1
CE3
CD4

CE1
CD3
CE3 HE3 CE4
C1 O1 C1
C2 O2A O2A

HE1
HD3
HE4
C2
H2A

C3 O3 C3 C4
C4 O4A O4A H4A

IMPR C1 CZ1 C2 O1
IMPR C3 CZ2 C4 O3
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CD1
O
CE1
O
CE2
CG1
CZ1
CZ1
CD1
CG1
CD4
O
CE3
O
CE4
CG2
CZ2
CZ2
CE2
CE1
C2

O
CG1
CG1
CG1
CG1
CD1
CD1
CD2
CG1
O
O
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE1
CZ1
CZ1

*CG1
CD1
*CD1
CD2
*CD2
CE1
*CE1
*CE2
O
CG2
*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ1
C1
*C1

CD2
CE1
HD1
CE2
HD2
CZ1
HE1
HE2
CG2
CD4
CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
C1
C2
O1

1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.3820
1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
-144.00
40.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.3820
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.2000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CZ1
O2A
O2A
C1
CE4
CE3
C4
CZ2
O4A
O4A
C3

C1
C1
C1
C2
CE3
CZ2
CZ2
C3
C3
C3
C4

C2
*C2
*C2
O2A
*CZ2
C3
*C3
C4
*C4
*C4
O4A

O2A
O2B
H2
H2A
C3
C4
O3
O4A
O4B
H4
H4A

1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
110.00
110.00
110.00
120.00
120.00
120.00
120.00
110.00
110.00
110.00

-60.00
120.00
-120.00
180.00
180.00
180.00
180.00
-60.00
120.00
-120.00
180.00

110.00
110.00
110.00
110.00
120.00
120.00
120.00
110.00
110.00
110.00
110.00

RESI C37
-2.00 ! C16H8O7 biphenyl analog, peml.
!KEVO: charges adjusted to reflect updated acetone L-J.
!Resulting charges are probably not that bad.
GROUP
ATOM CG1 CG2R61 0.215
ATOM O
OG301 -0.430
ATOM CD1 CG2R61 -0.115
ATOM HD1 HGR61
0.115
!
ATOM
ATOM
ATOM
ATOM
S
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
GROUP
ATOM
ATOM
ATOM
ATOM
ATOM
GROUP
ATOM
ATOM
ATOM
ATOM
ATOM
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

1.4000
1.4000
1.1000
0.9000
1.0900
1.4000
1.2000
1.4000
1.4000
1.1000
0.9000

HE3

CD2
HD2
CE1
HE1

CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115

!
!
!
!

CE2
HE2
CZ1
CG2
CD3
HD3
CD4
HD4
CE3
HE3
CE4
HE4
CZ2

CG2R61
HGR61
CG2R61
CG2R61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61

!
\
/
\
/
!
CD1--CG1
CD4--CE4
!
/
\
/
\
! HE1--CE1
CD2--HD2 HD4
HE4
!
\
/
!
CZ1--CE2
!
/
\
!
SUBS
HE2

-0.115
0.115
0.000
0.215
-0.115
0.115
-0.115
0.115
-0.115
0.115
-0.115
0.115
0.000

C1
O1
C2
O2A
O2B

CG2O5
OG2D3
CG2O3
OG2D2
OG2D2

0.38
-0.48
0.62
-0.76
-0.76

C3
O3
C4
O4A
O4B

CG2O5
OG2D3
CG2O3
OG2D2
OG2D2

0.38
-0.48
0.62
-0.76
-0.76

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4

CG1
CE2
CG2
CZ2
CG2
CD2

CD2
CZ1
CD3
CE4
O
HD2

CG1
CZ1
CD3
CE4

O
CE1
CE3
CD4

CE1 HE1
CD3 HD3
CE3 HE3 CE4 HE4

\
/
CD3--CE3
/
\
O ---CG2
CZ2--SUB

HD1

!
!
!
!
!
!
!

O
//
Ring--C
\
C--O (-)
//
O

BOND
BOND
BOND
BOND
BOND
BOND
IMPR
IMPR
IMPR
IMPR
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

CZ1 C1 C1
C2
C2 O2B
CZ2 C3 C3
C4
C4 O4B
C1 CZ1 C2
C2 C1 O2A
C3 CZ2 C4
C4 C3 O4A
CD1
O
CE1
O
CE2
CG1
CZ1
CZ1
CD1
CG1
CD4
O
CE3
O
CE4
CG2
CZ2
CZ2
CE2
CE1
C2
CZ1
O2A
CE4
CE3
C4
CZ2
O4A

RESI C3C
GROUP
ATOM CG1
ATOM O
ATOM CD1
ATOM HD1
ATOM CD2
ATOM
ATOM
ATOM
ATOM
S
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

O1 C1 C2
O2A
O3 C3 C4
O4A
O1
O2B
O3
O4B

O
CG1
CG1
CG1
CG1
CD1
CD1
CD2
CG1
O
O
CG2
CG2
CG2
CG2
CD3
CD3
CD4
CE1
CZ1
CZ1
C1
C1
CE3
CZ2
CZ2
C3
C3

*CG1
CD1
*CD1
CD2
*CD2
CE1
*CE1
*CE2
O
CG2
*CG2
CD3
*CD3
CD4
*CD4
CE3
*CE3
*CE4
*CZ1
C1
*C1
C2
*C2
*CZ2
C3
*C3
C4
*C4

CD2
CE1
HD1
CE2
HD2
CZ1
HE1
HE2
CG2
CD4
CD3
CE3
HD3
CE4
HD4
CZ2
HE3
HE4
C1
C2
O1
O2A
O2B
C3
C4
O3
O4A
O4B

1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.3820
1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
-144.00
40.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.3820
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.2000
1.4000
1.4000
1.0900
1.4000
1.2000
1.4000
1.4000

-2.00 ! C14H8O5
CG2R61 0.215
OG301 -0.430
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115

HD2
CE1
HE1
CE2

HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115

!
!
!
!

HE2
CZ1
CG2
CD3
HD3
CD4
HD4

HGR61
0.115
CG2R61 -0.100
CG2R61 0.215
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115

!
\
/
\
/
!
CD1--CG1
CD4--CE4
!
/
\
/
\
! HE1--CE1
CD2--HD2 HD4
HE4
!
\
/
!
CZ1--CE2
!
/
\

HE3

HD1

\
/
CD3--CE3
/
\
O ---CG2
CZ2--SUB

ATOM
ATOM
ATOM
ATOM
ATOM
GROUP
ATOM
ATOM
ATOM
GROUP
ATOM
ATOM
ATOM
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

CE3
HE3
CE4
HE4
CZ2

CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.100

C1
O1A
O1B

CG2O3
OG2D2
OG2D2

0.62
-0.76
-0.76

C2
O2A
O2B

CG2O3
OG2D2
OG2D2

0.62
-0.76
-0.76

CD1
CD2
CE1
CE3
CD4
CD1
CE2
CD4
CZ1
CZ2

CG1
CE2
CD1
CZ2
CG2
HD1
HE2
HD4
C1
C2

CG1
CE2
CG2
CZ2
CG2
CD2

CG1
CZ1
CD3
CE4

O
CE1
CE3
CD4

CE1
CD3
CE3 HE3 CE4
C1 O1A C1
C2 O2A C2

HE1
HD3
HE4
O1B
O2B

IC CD1
IC O
IC CE1
IC O
IC CE2
IC CG1
IC CZ1
IC CZ1
IC CD1
IC CG1
IC CD3
IC O
IC CE3
IC O
IC CE4
IC CG2
IC CZ2
IC CZ2
IC CE2
IC CE1
IC O1A
IC CE4
IC CE3
IC O2A
PATCHING FIRST

CD2
CZ1
CD3
CE4
O
HD2

HE2

!
O
!
//
! Ring-C (-)
!
\
!
O
!

O
*CG1 CD2
CG1
CD1
CE1
CG1
*CD1 HD1
CG1
CD2
CE2
CG1
*CD2 HD2
CD1
CE1
CZ1
CD1
*CE1 HE1
CD2
*CE2 HE2
CG1
O
CG2
O
CG2
CD3
O
*CG2 CD4
CG2
CD3
CE3
CG2
*CD3 HD3
CG2
CD4
CE4
CG2
*CD4 HD4
CD3
CE3
CZ2
CD3
*CE3 HE3
CD4
*CE4 HE4
CE1
*CZ1 C1
CZ1
C1
O1A
CZ1
*C1
O1B
CE3
*CZ2 C2
CZ2
C2
O2A
CZ2
*C2
O2B
NONE LAST NONE

!toppar_retinol_2.str
RESI HEX3
0.00
!
GROUP
ATOM C1 CG2DC3 -0.42
ATOM H11 HGA5
0.21
ATOM H12 HGA5
0.21
ATOM C2 CG2DC2 -0.15

SUBS

1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.3820
1.4000
1.3820
1.4000
1.3820
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

! C6H8 1,3,5-hexatriene
!
! H11
H21
!
\
/
!
C1=C2

H41

180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
-144.00
0.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00
120.00

1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.3820
1.4000
1.4000
1.4000
1.0900
1.4000
1.0900
1.4000
1.0900
1.0900
1.4000
1.4000
1.4000
1.4000
1.4000
1.4000

ATOM H21
GROUP
ATOM C3
ATOM H31
ATOM C4
ATOM H41
GROUP
ATOM C5
ATOM H51
GROUP
ATOM C6
ATOM H61
ATOM H62

HGA4

BOND C1
BOND C1
BOND C4

C2 C2
H11 C1
H41 C5

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

0.15 !
/
! H12
CG2DC1 -0.15 !
HGA4
0.15 !
CG2DC1 -0.15 !
HGA4
0.15 !
!
CG2DC2 -0.15
HGA4
0.15

/
C3=C4
H61
/
\
/
H31
C5=C6
/
\
H51
H62

C1
C2
C3
H11
H11
C3
C4
C5
C6
C4
H61

CG2DC3 -0.42
HGA5
0.21
HGA5
0.21

C2
C3
C4
C2
C1
C1
C2
C3
C4
C5
C5

C3
C4
C5
*C1
C2
*C2
*C3
*C4
*C5
C6
*C6

C3 C3
H12 C2
H51 C6
C4
C5
C6
H12
C3
H21
H31
H41
H51
H61
H62

C4
H21
H61

C4
C3
C6

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5 C5
H31
H62
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

PATCH FIRST NONE LAST NONE


RESI 13DB
!
GROUP
ATOM C1
ATOM H11
ATOM H12
GROUP
ATOM C2
ATOM H21
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM H41
ATOM H42

0.00 ! C4H6 1,3-dibutene


CG2DC3 -0.42 ! H11
H21
HGA5
0.21 ! \
/
HGA5
0.21 !
C1=C2
H41
! /
\
/
CG2DC2 -0.15 ! H12
C3=C4
HGA4
0.15 !
/
\
CG2DC1 -0.15 !
H31
H42
HGA4
0.15 !
!
CG2DC3 -0.42 !
HGA5
0.21 !
HGA5
0.21 !

BOND C1
BOND C1
BOND C4

C2 C2
H11 C1
H41 C4

C3 C3
H12 C2
H42

IC C1 C2 C3 C4 0.00
IC C2 C3 C4 H41 0.00
IC C3 C2 C1 H11 0.00
IC C2 H11 *C1 H12 0.00
IC C3 H41 *C4 H42 0.00
IC C1 C3 *C2 H21 0.00
IC C2 C4 *C3 H31 0.00
PATCH FIRST NONE LAST NONE

C4
H21

C3

H31

0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
180.0
180.0
180.0
180.0
180.0
180.0

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI 13DP
!
GROUP
ATOM C1
ATOM H11
ATOM H12
ATOM C2
ATOM H21
GROUP
ATOM C3
ATOM H31
ATOM C4
ATOM H41
GROUP
ATOM C5
ATOM H51
ATOM H52
ATOM H53
BOND C1
BOND C1
BOND C4

0.00 ! C5H8 1,3-dipentene


CG2DC3
HGA5
HGA5
CG2DC2
HGA4

-0.42
0.21
0.21
-0.15
0.15

CG2DC1
HGA4
CG2DC1
HGA4

-0.15
0.15
-0.15
0.15

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
C2 C2
H11 C1
H41 C5

!
! H11
H21
!
\
/
!
C1=C2
H41
!
/
\
/
! H12
C3=C4 H51
!
/
\ /
!
H31
C5-H52
!
\
!
H53
!
!
!
!
!

C3 C3
H12 C2
H51 C5

IC C1 C2 C3 C4 0.00
IC C2 C3 C4 C5 0.00
IC C3 C4 C5 H51 0.00
IC C3 C2 C1 H11 0.00
IC C2 H11 *C1 H12 0.00
IC C1 C3 *C2 H21 0.00
IC C2 C4 *C3 H31 0.00
IC C3 C5 *C4 H41 0.00
IC C4 H51 *C5 H52 0.00
IC C4 H51 *C5 H53 0.00
PATCH FIRST NONE LAST NONE
RESI DMB1
!
GROUP
ATOM C1
ATOM H11
ATOM H12
GROUP
ATOM C2
ATOM C2M
ATOM H2M1
ATOM H2M2
ATOM H2M3
GROUP
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM H41
ATOM H42

C4
H21
H52

C4
C3
C5

C5
H31
H53

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
180.0
0.0
180.0
180.0
180.0
180.0
180.0
120.0
-120.0

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C5H8 2-methyl-1,3-butadiene


CG2DC3 -0.42 !
HGA5
0.21 !
H2M1 H2M2
HGA5
0.21 !
\ /
! H11
C2M-H2M3
CG2DC2 0.00 !
\
/
CG331 -0.27 !
C1=C2
H41
HGA3
0.09 !
/
\
/
HGA3
0.09 ! H12
C3=C4
HGA3
0.09 !
/
\
!
H31
H42
CG2DC1 -0.15 !
HGA4
0.15 !
!
CG2DC3 -0.42 !
HGA5
0.21 !
HGA5
0.21 !

BOND C1 C2 C2 C3 C3 C4
C2
BOND C1 H11 C1 H12 C3 H31 C4
BOND C2M H2M1 C2M H2M2 C2M H2M3

C2M
H41 C4

H42

IC C1 C2 C3 C4 0.00
IC C2 C3 C4 H41 0.00
IC C3 C2 C1 H11 0.00
IC C2 H11 *C1 H12 0.00
IC C1 C3 *C2 C2M 0.00
IC C2 C4 *C3 H31 0.00
IC C3 H41 *C4 H42 0.00
IC C1 C2 C2M H2M1 0.00
IC C2 H2M1 *C2M H2M2 0.00
IC C2 H2M1 *C2M H2M3 0.00
PATCH FIRST NONE LAST NONE
RESI DMP1
!
GROUP
ATOM C1
ATOM H11
ATOM H12
GROUP
ATOM C2
ATOM H21
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM C4M
ATOM H4M1
ATOM H4M2
ATOM H4M3
GROUP
ATOM C5
ATOM H51
ATOM H52
ATOM H53
BOND
BOND
BOND
BOND

C1
C1
C4M
C5

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
120.0
-120.0

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C6H10 4-methyl-1,3-pentadiene


CG2DC3 -0.42 !
HGA5
0.21 ! H11
H21 H4M1 H4M2
HGA5
0.21 !
\
/
\ /
!
C1=C2
C4M-H4M3
CG2DC2 -0.15 !
/
\
/
HGA4
0.15 ! H12
C3=C4 H51
CG2DC1 -0.15 !
/
\ /
HGA4
0.15 !
H31
C5-H52
!
\
CG2DC1 0.00 !
H53
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
C2
H11
H4M1
H51

C2
C1
C4M
C5

C3
H12
H4M2
H52

C3
C2
C4M
C5

IC C1 C2 C3 C4 0.00
IC C2 C3 C4 C5 0.00
IC C3 C4 C5 H51 0.00
IC C3 C2 C1 H11 0.00
IC C2 H11 *C1 H12 0.00
IC C1 C3 *C2 H21 0.00
IC C2 C4 *C3 H31 0.00
IC C3 C5 *C4 C4M 0.00
IC C3 C4 C4M H4M1 0.00
IC C4 H4M1 *C4M H4M2 0.00
IC C4 H4M1 *C4M H4M3 0.00
IC C4 H51 *C5 H52 0.00
IC C4 H51 *C5 H53 0.00
PATCH FIRST NONE LAST NONE

C4
C4
H21 C3
H4M3
H53
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
120.0
-120.0
120.0
-120.0

C5 C4
H31

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C4M

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

RESI DMP2
0.00 ! C6H10 2-methyl-1,3-pentadiene
!
GROUP
!
H2M1 H2M2
ATOM C1 CG2DC3 -0.42 !
\ /

ATOM H11
ATOM H12
GROUP
ATOM C2
ATOM C2M
ATOM H2M1
ATOM H2M2
ATOM H2M3
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM H41
ATOM C5
ATOM H51
ATOM H52
ATOM H53

HGA5
HGA5

BOND
BOND
BOND
BOND

C2
H11
H2M1
H51

C1
C1
C2M
C5

CG2DC2
CG331
HGA3
HGA3
HGA3
CG2DC1
HGA4
CG2DC1
HGA4
CG331
HGA3
HGA3
HGA3

0.21 ! H11
C2M-H2M3
0.21 !
\
/
!
C1=C2
H41
0.00 !
/
\
/
-0.27 ! H12
C3=C4 H51
0.09 !
/
\ /
0.09 !
H31
C5-H52
0.09 !
\
-0.15 !
H53
0.15 !
!
-0.15 !
0.15 !
-0.27 !
0.09 !
0.09 !
0.09 !

C2
C1
C2M
C5

C3
H12
H2M2
H52

C3
C3
C2M
C5

IC C1 C2 C3 C4 0.00
IC C2 C3 C4 C5 0.00
IC C3 C4 C5 H51 0.00
IC C3 C2 C1 H11 0.00
IC C2 H11 *C1 H12 0.00
IC C1 C3 *C2 C2M 0.00
IC C2 C4 *C3 H31 0.00
IC C3 C5 *C4 H41 0.00
IC C1 C2 C2M H2M1 0.00
IC C2 H2M1 *C2M H2M2 0.00
IC C2 H2M1 *C2M H2M3 0.00
IC C4 H51 *C5 H52 0.00
IC C4 H51 *C5 H53 0.00
PATCH FIRST NONE LAST NONE
RESI CROT

C4
C4
H31 C4
H2M3
H53
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
120.0
-120.0
120.0
-120.0

C5 C2 C2M
H41

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C6H11NO 2-buteneamide,N,3-dimethyl (crotonamide)


! numbering as in fennretinide
! note different atom types for N21 and C15: this is consistent
! with differences in NMA and acetamide
GROUP
ATOM C12 CG331 -0.27 !
ATOM H121 HGA3
0.09 !
H202 H203
ATOM H122 HGA3
0.09 !
\ /
ATOM H123 HGA3
0.09 !
H201-C20
GROUP
!
|
ATOM C13 CG2DC2 0.00 !H121-C12--C13
O29
ATOM C14 CG2DC2 -0.15 !
/ |
\\
||
ATOM H141 HGA4
0.15 !H122 H123
C14--C15
GROUP
!
/
\
ATOM C15 CG2O1 0.51 !
H141
N21-H211 (cis)
ATOM O29 OG2D1 -0.51 !
|
GROUP
!
H132-C16-H131
ATOM N21 NG2S1 -0.47 !
|
ATOM H211 HGP1
0.28 !
H133
ATOM C16 CG331 -0.08
ATOM H131 HGA3
0.09
ATOM H132 HGA3
0.09

ATOM H133
GROUP
ATOM C20
ATOM H201
ATOM H202
ATOM H203

HGA3

BOND
BOND
BOND
BOND
BOND

C13
C20
H131
H121
H201

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

0.09

C12
C13
C16
C12
C20

!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !

C12
C13
C14
H121
H121
H121
C14
C15
N21
C16
C15
H131
H131
C12
H201
H201

C14
O29
H132
H122
H202

C14
C15
N21
*C12
*C12
C13
*C13
*C14
*C15
*N21
C16
*C16
*C16
C20
*C20
*C20

C15
N21
C16
H122
H123
C14
C20
H141
O29
H211
H131
H132
H133
H201
H202
H203

C13
C14
C15
C13
C13
C12
C12
C13
C14
C15
N21
N21
N21
C13
C13
C13

C13
C15
C16
C12
C20

C14
C14
C16
C12
C20

C15 C15 N21 N21 C16


H141 N21 H211
H133
H123
H203

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00

PATCH FIRST NONE LAST NONE


RESI PACP
ATOM C14
ATOM H141
ATOM H142
ATOM H143
GROUP
ATOM C15
ATOM O29
GROUP
ATOM N21
ATOM H211
ATOM C22
GROUP
ATOM C23
ATOM H231
GROUP
ATOM C24
ATOM H241
GROUP
ATOM C26
ATOM H261
GROUP
ATOM C27
ATOM H271
GROUP
ATOM C25

CG331
HGA3
HGA3
HGA3
CG2O1
OG2D1
NG2S1
HGP1
CG2R61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61

0.00 ! C8H9NO2 p-acetamide-phenol


! numbering as in fennretinide
!
-0.27 !
H142
0.09 !
|
0.09 !
H141-C14-H143
0.09 !
|
!
C15=O29
0.52 !
|
-0.52 !
N21-H211
!
|
-0.47 !
C22
0.33 !
// \
0.14 ! H231-C23 C27-H271
!
|
||
-0.115! H241-C24 C26-H261
0.115!
\\ /
!
C25
-0.115!
|
0.115!
O28
!
\
-0.115!
H281
0.115

CG2R61 -0.115
HGR61 0.115
CG2R61 0.11

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM O28 OG311 -0.53


ATOM H281 HGP1
0.42
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C14
C23
C25
C14
C23

C14
C15
N21
C22
C23
H141
H141
H141
N21
C22
C27
C24
C25
O28
C27
C26
C24

C15
C24
O28
H141
H231
C15
N21
C22
C23
C24
C15
C15
C14
C14
C15
N21
C22
C23
C24
C25
C22
C25

C15
C24
O28
C14
C24

N21
C25
H281
H142
H241

N21
C22
C23
C24
C25
*C14
*C14
C15
*C15
*N21
*C22
*C23
*C24
*C25
*C26
*C27
O28

N21
C25
N21
C14
C26

C22
C27
C24
C25
O28
H142
H143
N21
O29
H211
C23
H231
H241
C26
H261
H271
H281

C22 C22 C23 C15 O29


C26 C26 C27 C27 C22
H211
H143
H261 C27 H271
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
0.00
180.00
0.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI MECH
GROUP
ATOM C1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM C6
GROUP
ATOM C7
ATOM H71
ATOM C8
ATOM H81
ATOM H82
GROUP
ATOM C16
ATOM H161
ATOM H162
ATOM H163
GROUP
ATOM C17
ATOM H171
ATOM H172
ATOM H173

0.00 ! C11H18 1,6,6-trimethyl-2-ethenyl-cyclohexene


! using retinol numbering
CG301
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG2DC2
CG2DC2

0.00
-0.18
0.09
0.09
-0.18
0.09
0.09
-0.18
0.09
0.09
0.00
0.00

CG2DC1
HGA4
CG2DC3
HGA5
HGA5

-0.15
0.15
-0.42
0.21
0.21

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09

!H162 H163 H171 H172


!
\ |
| /
!H161-C16
C17-H173 H81
!
\ /
|
! H21
C1
C8-H82
!
\ / \
//
! H22-C2
C6------C7
!
|
||
\
! H31-C3
C5 H181 H71
!
/ \ / \ /
! H32
C4
C18-H18
!
/ \
\
!
H41 H42 H183
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183

!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !

BOND
BOND
BOND
BOND
BOND

C2
C7
H21
H161
H71

C1
C6
C2
C16
C7

C2
C7
C2
C16
C8

C3
C8
H22
H162
H81

C3
C1
C3
C16
C8

C4
C16
H31
H163
H82

!initial ring geometry is planar


IC C1 C2 C3 C4 0.00 0.00
IC C2 C3 C4 C5 0.00 0.00
IC C3 C4 C5 C6 0.00 0.00
IC C1 C3 *C2 H21 0.00 0.00
IC C1 C3 *C2 H22 0.00 0.00
IC C2 C4 *C3 H31 0.00 0.00
IC C2 C4 *C3 H32 0.00 0.00
IC C3 C5 *C4 H41 0.00 0.00
IC C3 C5 *C4 H42 0.00 0.00
IC C1 C5 *C6 C7 0.00 0.00
IC C5 C6 C7 C8 0.00 0.00
IC C6 C8 *C7 H71 0.00 0.00
IC C6 C7 C8 H81 0.00 0.00
IC C7 H81 *C8 H82 0.00 0.00
IC C6 C2 *C1 C16 0.00 0.00
IC C6 C2 *C1 C17 0.00 0.00
IC C2 C1 C16 H161 0.00 0.00
IC C1 H161 *C16 H162 0.00 0.00
IC C1 H161 *C16 H163 0.00 0.00
IC C2 C1 C17 H171 0.00 0.00
IC C1 H171 *C17 H172 0.00 0.00
IC C1 H171 *C17 H173 0.00 0.00
IC C4 C6 *C5 C18 0.00 0.00
IC C4 C5 C18 H181 0.00 0.00
IC C5 H181 *C18 H182 0.00 0.00
IC C5 H181 *C18 H183 0.00 0.00
PATCH FIRST NONE LAST NONE
RESI TMCH
GROUP
ATOM C1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM C6
GROUP
ATOM C7
ATOM H71
ATOM H72

C4
C1
C3
C17
C18
63.0
-46.0
15.0
120.0
-120.0
120.0
-120.0
120.0
-120.0
180.0
60.0
180.0
180.0
180.0
120.0
-120.0
180.0
120.0
-120.0
180.0
120.0
-120.0
180.0
180.0
120.0
-120.0

C5
C17
H32
H171
H181
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5
C5
C4
C17
C18

C6
C18
H41
H172
H182

C6

C1

C4 H42
C17 H173
C18 H183

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C10H18 1,2,6,6-tetramethylcyclohexene


! using retinol numbering
CG301
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG2DC2
CG2DC2

0.00
-0.18
0.09
0.09
-0.18
0.09
0.09
-0.18
0.09
0.09
0.00
0.00

!H162 H163 H171 H172


!
\ |
| /
!H161-C16
C17-H173
!
\ /
! H21
C1
H71 H72
!
\ / \
| /
! H22-C2
C6------C7-H73
!
|
||
! H31-C3
C5 H181
!
/ \ / \ /
! H32
C4
C18-H18
!
/ \
\
!
H41 H42 H183
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !

ATOM H73
GROUP
ATOM C16
ATOM H161
ATOM H162
ATOM H163
GROUP
ATOM C17
ATOM H171
ATOM H172
ATOM H173
GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183

HGA3

BOND
BOND
BOND
BOND
BOND

C2
C7
H21
H161
H71

C1
C6
C2
C16
C7

0.09 !
!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
C2
C1
C2
C16
C7

C3
C16
H22
H162
H72

C3
C1
C3
C16
C7

!initial geometry is planar


IC C1 C2 C3 C4 0.00
IC C2 C3 C4 C5 0.00
IC C3 C4 C5 C6 0.00
IC C1 C3 *C2 H21 0.00
IC C1 C3 *C2 H22 0.00
IC C2 C4 *C3 H31 0.00
IC C2 C4 *C3 H32 0.00
IC C3 C5 *C4 H41 0.00
IC C3 C5 *C4 H42 0.00
IC C1 C5 *C6 C7 0.00
IC C5 C6 C7 H71 0.00
IC C6 H71 *C7 H72 0.00
IC C6 H71 *C7 H73 0.00
IC C6 C2 *C1 C16 0.00
IC C6 C2 *C1 C17 0.00
IC C2 C1 C16 H161 0.00
IC C1 H161 *C16 H162 0.00
IC C1 H161 *C16 H163 0.00
IC C2 C1 C17 H171 0.00
IC C1 H171 *C17 H172 0.00
IC C1 H171 *C17 H173 0.00
IC C4 C6 *C5 C18 0.00
IC C4 C5 C18 H181 0.00
IC C5 H181 *C18 H182 0.00
IC C5 H181 *C18 H183 0.00
PATCH FIRST NONE LAST NONE

C4
C17
H31
H163
H73
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C4
C5
C3
C17
C18
-63.0
46.0
-13.0
120.0
-120.0
120.0
-120.0
120.0
-120.0
180.0
180.0
120.0
-120.0
120.0
-120.0
180.0
120.0
-120.0
180.0
120.0
-120.0
180.0
180.0
120.0
-120.0

C5
C18
H32
H171
H181

C5

C6

C6

C1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C4 H41 C4 H42
C17 H172 C17 H173
C18 H182 C18 H183
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

RESI FRET
0.00 ! C26H33NO2 fennretinide, nomenclature consistent with re
tinol
!
!
!
GROUP
ATOM C1 CG301 0.00
ATOM C2 CG321 -0.18
ATOM H21 HGA2
0.09

ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM C6
GROUP
ATOM C7
ATOM H71
ATOM C8
ATOM H81
ATOM C9
ATOM C10
ATOM H101
GROUP
ATOM C11
ATOM H111
ATOM C12
ATOM H121
ATOM C13
ATOM C14
ATOM H141
GROUP
ATOM C16
ATOM H161
ATOM H162
ATOM H163
GROUP
ATOM C17
ATOM H171
ATOM H172
ATOM H173
GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183
GROUP
ATOM C19
ATOM H191
ATOM H192
ATOM H193
GROUP
ATOM C20
ATOM H201
ATOM H202
ATOM H203
GROUP
ATOM C15
ATOM O29
GROUP
ATOM N21
ATOM H211
ATOM C22
GROUP
ATOM C23
ATOM H231

HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG2DC2
CG2DC2

0.09
-0.18
0.09
0.09
-0.18
0.09
0.09
0.00
0.00

CG2DC1
HGA4
CG2DC1
HGA4
CG2DC2
CG2DC2
HGA4

-0.15
0.15
-0.15
0.15
0.00
-0.15
0.15

CG2DC1
HGA4
CG2DC1
HGA4
CG2DC2
CG2DC2
HGA4

-0.15
0.15
-0.15
0.15
0.00
-0.15
0.15

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09

!H162 H163 H171 H172


!
\ |
| /
!H161-C16
C17-H173
H191 H192
!
\ /
\ /
! H21
C1
H71
H81
C19
!
\ / \
|
|
/ \
! H22-C2
C6------C7=====C8----C9
H193
!
|
||
||
! H31-C3
C5 H181
C10-H101
!
/ \ / \ /
|
! H32
C4
C18-H182
C11-H111
!
/ \
\
||
!
H41 H42 H183
C12-H121 H201
!
|
/
!
C13---C20-H202
!
||
\
!
C14-H141 H203
!
|
!
C15=O29
!
|
!
N21-H211
!
|
!
C22
!
// \
!
H231-C23 C27-H271
!
|
||
!
H241-C24 C26-H261
!
\\ /
!
C25
!
|
!
O28
!
\
!
H281
! charges from CROT
!

CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG2O1 0.51
OG2D1 -0.51

NG2S1 -0.47 !
HGP1
0.33 ! charges from PACP
CG2R61 0.14 !
CG2R61 -0.115
HGR61 0.115

GROUP
ATOM C24
ATOM H241
GROUP
ATOM C26
ATOM H261
GROUP
ATOM C27
ATOM H271
GROUP
ATOM C25
ATOM O28
ATOM H281
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
C6
C12
C23
C1
C25
C2
C7
C16
C18
C20
C23

C1
C2
C6
C1
C6
C7
C2
C2
C3
C3
C4
C4
C5
C5
C5
C8
C9
C10
C8
C11
C9
C12
C10
C13
C11
C14
C12
C15
C6
H161
H161
C6
H171

CG2R61 -0.115
HGR61 0.115
CG2R61 -0.115
HGR61 0.115
CG2R61 -0.115
HGR61 0.115
CG2R61 0.11
OG311 -0.53
HGP1
0.42
C2
C7
C13
C24
C16
O28
H21
H71
H161
H181
H201
H231
C2
C3
C1
C6
C7
C8
C6
C6
C1
C1
C2
C2
C3
C3
C1
C6
C7
C8
C9
C9
C10
C10
C11
C11
C12
C12
C13
C13
C1
C1
C1
C1
C1

C2
C7
C13
C24
C1
O28
C2
C8
C16
C18
C20
C24
C3
C4
C2
C7
C8
C9
*C1
*C1
*C2
*C2
*C3
*C3
*C4
*C4
*C6
*C7
*C8
*C9
C10
*C10
C11
*C11
C12
*C12
C13
*C13
C14
*C14
C16
*C16
*C16
C17
*C17

C3
C8
C14
C25
C17
H281
H22
H81
H162
H182
H202
H241
C4
C5
C3
C8
C9
C10
C16
C17
H21
H22
H31
H32
H41
H42
C7
H71
H81
C19
C11
H101
C12
H111
C13
H121
C14
C20
C15
H141
H161
H162
H163
H171
H172

C3
C8
C14
C25
C5
N21
C3
C10
C16
C18
C20
C26

C4
C9
C15
C26
C18
H211
H31
H101
H163
H183
H203
H261
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
C9
C15
C26
C9

C5
C10
N21
C27
C19

C5
C10
N21
C27
C13

C6
C11
C22
C22
C20

C6 C1
C11 C12
C22 C23

C3
C11
C17
C19

H32
H111
H171
H191

C4
C12
C17
C19

H41
H121
H172
H192

C4
C14
C17
C19

C15 O29
H42
H141
H173
H193

C27 H271
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
180.00
180.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H171
C6
C4
H181
H181
C8
H191
H191
C12
H201
H201
C13
N21
C14
C22
C15
C27
N21
C24
C22
C25
C23
O28
C27
C26
C24

C1
C4
C5
C5
C5
C9
C9
C9
C13
C13
C13
C14
C14
C15
C15
N21
N21
C22
C22
C23
C23
C24
C24
C25
C22
C25

*C17
*C5
C18
*C18
*C18
C19
*C19
*C19
C20
*C20
*C20
C15
*C15
N21
*N21
C22
*C22
C23
*C23
C24
*C24
C25
*C25
*C26
*C27
O28

H173
C18
H181
H182
H183
H191
H192
H193
H201
H202
H203
N21
O29
C22
H211
C27
C23
C24
H231
C25
H241
O28
C26
H261
H271
H281

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-120.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI RTOL
!
GROUP
ATOM C1
ATOM C2
ATOM H21
ATOM H22
GROUP
ATOM C3
ATOM H31
ATOM H32
GROUP
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM C6
GROUP
ATOM C7
ATOM H71
ATOM C8
ATOM H81
GROUP
ATOM C9
ATOM C10
ATOM H101
GROUP
ATOM C11
ATOM H111
GROUP
ATOM C12

0.00 ! C20H30O retinol, nomenclature from PDB


CG301 0.00
CG321 -0.18
HGA2
0.09
HGA2
0.09
CG321 -0.18
HGA2
0.09
HGA2
0.09
CG321
HGA2
HGA2
CG2DC2
CG2DC2

-0.18
0.09
0.09
0.00
0.00

CG2DC1
HGA4
CG2DC1
HGA4

-0.15
0.15
-0.15
0.15

CG2DC2 0.00
CG2DC2 -0.15
HGA4
0.15
CG2DC1 -0.15
HGA4
0.15
CG2DC1 -0.15

ATOM H121
GROUP
ATOM C13
ATOM C14
ATOM H141
GROUP
ATOM C15
ATOM H151
ATOM H152
ATOM OR
ATOM HR
GROUP
ATOM C16
ATOM H161
ATOM H162
ATOM H163
GROUP
ATOM C17
ATOM H171
ATOM H172
ATOM H173
GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183
GROUP
ATOM C19
ATOM H191
ATOM H192
ATOM H193
GROUP
ATOM C20
ATOM H201
ATOM H202
ATOM H203

HGA4

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2
C7
C13
C16
H21
H71
H151
H161
H181
H201

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
C6
C2
C1
C6
C7
C2
C2
C3
C3
C4
C4

C1
C6
C12
C1
C2
C7
C15
C16
C18
C20

0.15

CG2DC2 0.00
CG2DC2 -0.15 !
HGA4
0.15 !H162 H163 H171 H172
!
\ |
| /
CG321 0.05 !H161-C16
C17-H173
H191 H192
HGA2
0.09 !
\ /
\ /
HGA2
0.09 ! H21
C1
H71
H81
C19
OG311 -0.65 !
\ / \
|
|
/ \
HGP1
0.42 ! H22-C2
C6------C7=====C8----C9
H193
!
|
||
||
CG331 -0.27 ! H31-C3
C5 H181
C10-H101
HGA3
0.09 !
/ \ / \ /
|
HGA3
0.09 ! H32
C4
C18-H182
C11-H111
HGA3
0.09 !
/ \
\
||
!
H41 H42 H183
C12-H121 H201
CG331 -0.27 !
|
/
HGA3
0.09 !
C13---C20-H202
HGA3
0.09 !
||
\
HGA3
0.09 !
C14-H141 H203
!
|
CG331 -0.27 !
H151-C15-H152
HGA3
0.09 !
|
HGA3
0.09 !
OR
HGA3
0.09 !
\
!
HR
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !
!
CG331 -0.27 !
HGA3
0.09 !
HGA3
0.09 !
HGA3
0.09 !

C2
C1
C3
C6
C7
C8
C6
C6
C1
C1
C2
C2

C2
C7
C13
C1
C2
C8
C15
C16
C18
C20

C3
C8
C14
C17
H22
H81
H152
H162
H182
H202

C3
C2
C4
C7
C8
C9
*C1
*C1
*C2
*C2
*C3
*C3

C4
C3
C5
C8
C9
C10
C16
C17
H21
H22
H31
H32

C3
C8
C14
C5
C3
C10
OR
C16
C18
C20

C4
C9
C15
C18
H31
H101
HR
H163
H183
H203
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
C9
C15
C9
C3
C11

C5
C10
OR
C19
H32
H111

C5 C6 C6 C1
C10 C11 C11 C12
C13 C20
C4 H41 C4 H42
C12 H121 C14 H141

C17 H171 C17 H172 C17 H173


C19 H191 C19 H192 C19 H193
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
180.00
180.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C5
C5
C5
C8
C9
C10
C8
C11
C9
C12
C10
C13
C11
C14
C12
C15
C13
OR
OR
C14
C6
H161
H161
C6
H171
H171
C6
C4
H181
H181
C8
H191
H191
C12
H201
H201

C3
C3
C1
C6
C7
C8
C9
C9
C10
C10
C11
C11
C12
C12
C13
C13
C14
C14
C14
C15
C1
C1
C1
C1
C1
C1
C4
C5
C5
C5
C9
C9
C9
C13
C13
C13

*C4
*C4
*C6
*C7
*C8
*C9
C10
*C10
C11
*C11
C12
*C12
C13
*C13
C14
*C14
C15
*C15
*C15
OR
C16
*C16
*C16
C17
*C17
*C17
*C5
C18
*C18
*C18
C19
*C19
*C19
C20
*C20
*C20

H41
H42
C7
H71
H81
C19
C11
H101
C12
H111
C13
H121
C14
C20
C15
H141
OR
H151
H152
HR
H161
H162
H163
H171
H172
H173
C18
H181
H182
H183
H191
H192
H193
H201
H202
H203

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI RTAL
!
GROUP
ATOM C1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM C6
GROUP
ATOM C7
ATOM H71
ATOM C8
ATOM H81
ATOM C9

0.00 ! C20H28O retinal, nomenclature from PDB based on retinol


CG301
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG2DC2
CG2DC2

0.00
-0.18
0.09
0.09
-0.18
0.09
0.09
-0.18
0.09
0.09
0.00
0.00

CG2DC1
HGA4
CG2DC1
HGA4
CG2DC2

-0.15
0.15
-0.15
0.15
0.00

ATOM C10
ATOM H101
GROUP
ATOM C11
ATOM H111
ATOM C12
ATOM H121
ATOM C13
GROUP
ATOM C14
ATOM H141
ATOM C15
ATOM O15
ATOM H15
GROUP
ATOM C16
ATOM H161
ATOM H162
ATOM H163
GROUP
ATOM C17
ATOM H171
ATOM H172
ATOM H173
GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183
GROUP
ATOM C19
ATOM H191
ATOM H192
ATOM H193
GROUP
ATOM C20
ATOM H201
ATOM H202
ATOM H203

CG2DC2 -0.15
HGA4
0.15

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2
C7
C13
C16
H21
H71
H161
H181
H201

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
C2
C6
C1
C6
C7
C8
C2
C2
C3

C1
C6
C12
C1
C2
C7
C16
C18
C20

CG2DC1
HGA4
CG2DC1
HGA4
CG2DC2
CG2DC2
HGA4
CG2O4
OG2D1
HGR52
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3
CG331
HGA3
HGA3
HGA3

C2
C3
C1
C6
C7
C8
C9
C6
C6
C1

-0.15
0.15
-0.15
0.15 !
0.00 !H162 H163 H171 H172
!
\ |
| /
-0.04 !H161-C16
C17-H173
H191 H192
0.15 !
\ /
\ /
0.27 ! H21
C1
H71
H81
C19
-0.51 !
\ / \
|
|
/ \
0.13 ! H22-C2
C6------C7=====C8----C9
H193
!
|
||
||
-0.27 ! H31-C3
C5 H181
C10-H101
0.09 !
/ \ / \ /
|
0.09 ! H32
C4
C18-H182
C11-H111
0.09 !
/ \
\
||
!
H41 H42 H183
C12-H121 H201
-0.27 !
|
/
0.09 !
C13---C20-H202
0.09 !
||
\
0.09 !
C14-H141 H203
!
|
-0.27 !
C15
0.09 !
/ \\
0.09 !
H15 O15
0.09 !
!
-0.27 !
0.09 !
0.09 !
0.09 !
!
-0.27 !
0.09 !
0.09 !
0.09 !

C2
C7
C13
C1
C2
C8
C16
C18
C20

C3
C8
C14
C17
H22
H81
H162
H182
H202

C3
C4
C2
C7
C8
C9
C10
*C1
*C1
*C2

C4
C5
C3
C8
C9
C10
C11
C16
C17
H21

C3
C8
C14
C5
C3
C10
C16
C18
C20

C4
C9
C15
C18
H31
H101
H163
H183
H203
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
C9
C15
C9
C3
C11
C17
C19

C5
C10
O15
C19
H32
H111
H171
H191
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5
C10
C15
C13
C4
C12
C17
C19

0.00
0.00
0.00
180.00
180.00
180.00
180.00
120.00
-120.00
120.00

C6
C11
H15
C20
H41
H121
H172
H192

C6 C1
C11 C12
C4
C14
C17
C19
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H42
H141
H173
H193
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C3
C4
C4
C5
C5
C5
C8
C9
C10
C11
C9
C12
C10
C13
C11
C14
C12
C15
C13
O15
C6
H161
H161
C6
H171
H171
C6
C4
H181
H181
C8
H191
H191
C12
H201
H201

C1
C2
C2
C3
C3
C1
C6
C7
C8
C9
C10
C10
C11
C11
C12
C12
C13
C13
C14
C14
C1
C1
C1
C1
C1
C1
C4
C5
C5
C5
C9
C9
C9
C13
C13
C13

*C2
*C3
*C3
*C4
*C4
*C6
*C7
*C8
*C9
*C10
C11
*C11
C12
*C12
C13
*C13
C14
*C14
C15
*C15
C16
*C16
*C16
C17
*C17
*C17
*C5
C18
*C18
*C18
C19
*C19
*C19
C20
*C20
*C20

H22
H31
H32
H41
H42
C7
H71
H81
C19
H101
C12
H111
C13
H121
C14
C20
C15
H141
O15
H15
H161
H162
H163
H171
H172
H173
C18
H181
H182
H183
H191
H192
H193
H201
H202
H203

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-120.00
120.00
-120.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
180.00
120.00
-120.00
180.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI RTAC
!
GROUP
ATOM C1
ATOM C16
ATOM H161
ATOM H162
ATOM H163
ATOM C17
ATOM H171
ATOM H172
ATOM H173
GROUP
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41

-1.00 ! C20H27O2 all-trans-retinoic acid, nomenclature from PDB


CG301 0.00
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG321 -0.18
HGA2
0.09
HGA2
0.09
CG321 -0.18
HGA2
0.09
HGA2
0.09
CG321 -0.18
HGA2
0.09

ATOM H42
GROUP
ATOM C5
ATOM C6
GROUP
ATOM C18
ATOM H181
ATOM H182
ATOM H183
GROUP
ATOM C7
ATOM H71
ATOM C8
ATOM H81
GROUP
ATOM C9
ATOM C19
ATOM H191
ATOM H192
ATOM H193
ATOM C10
ATOM H101
GROUP
ATOM C11
ATOM H111
ATOM C12
ATOM H121
GROUP
ATOM C13
ATOM C20
ATOM H201
ATOM H202
ATOM H203
GROUP
ATOM C14
ATOM H141
ATOM C15
ATOM O29
ATOM O29B

HGA2

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

C2
C7
C13
C16
H21
H71
H161
H181
H201

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
C6
C12
C1
C2
C7
C16
C18
C20

C1
C2
C6
C1
C6
C7
C2
C2
C6
H161

0.09

CG2DC2 0.00
CG2DC2 0.00
CG331 -0.27
HGA3
0.09
HGA3
0.09
HGA3
0.09
CG2DC1
HGA4
CG2DC1
HGA4

-0.15
0.15
-0.15
0.15

CG2DC2
CG331
HGA3
HGA3
HGA3
CG2DC2
HGA4

0.00
-0.27
0.09
0.09
0.09
-0.15
0.15

CG2DC1
HGA4
CG2DC1
HGA4

-0.15
0.15
-0.15
0.15

CG2DC2
CG331
HGA3
HGA3
HGA3

0.00
-0.27
0.09
0.09
0.09

CG2DC2
HGA4
CG2O3
OG2D2
OG2D2

-0.25
0.15
0.62
-0.76
-0.76

C2
C3
C1
C6
C7
C8
C6
C6
C1
C1

C2
C7
C13
C1
C2
C8
C16
C18
C20
C3
C4
C2
C7
C8
C9
*C1
*C1
C16
*C16

!H162 H163 H171 H172


!
\ |
| /
!H161-C16
C17-H173
H191 H192
!
\ /
\ /
! H21
C1
H71
H81
C19
!
\ / \
|
|
/ \
! H22-C2
C6------C7=====C8----C9
H193
!
|
||
||
! H31-C3
C5 H181
C10-H101
!
/ \ / \ /
|
! H32
C4
C18-H182
C11-H111
!
/ \
\
||
!
H41 H42 H183
C12-H121 H201
!
|
/
!
C13---C20-H202
!
||
\
!
C14-H141 H203
!
|
!
C15=O29
!
| (-)
!
O29B
!

C3
C8
C14
C17
H22
H81
H162
H182
H202
C4
C5
C3
C8
C9
C10
C16
C17
H161
H162

C3
C8
C14
C5
C3
C10
C16
C18
C20

C4
C9
C15
C18
H31
H101
H163
H183
H203
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
C9
C15
C9
C3
C11
C17
C19

C5
C10
O29
C19
H32
H111
H171
H191
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5
C10
C15
C13
C4
C12
C17
C19

0.00
0.00
0.00
180.00
180.00
180.00
120.00
-120.00
180.00
120.00

C6
C11
O29B
C20
H41
H121
H172
H192

C6 C1
C11 C12
C4
C14
C17
C19
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H42
H141
H173
H193
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H161
C6
H171
H171
C3
C3
C4
C4
C5
C5
C6
C4
H181
H181
C5
C8
C9
C10
C8
H191
H191
C8
C11
C9
C12
C10
C13
C11
C14
C12
H201
H201
C12
C15
C13
O29

C1
C1
C1
C1
C1
C1
C2
C2
C3
C3
C4
C5
C5
C5
C1
C6
C7
C8
C9
C9
C9
C9
C9
C10
C10
C11
C11
C12
C12
C13
C13
C13
C13
C13
C14
C14

*C16
C17
*C17
*C17
*C2
*C2
*C3
*C3
*C4
*C4
*C5
C18
*C18
*C18
*C6
*C7
*C8
*C9
C19
*C19
*C19
C10
*C10
C11
*C11
C12
*C12
C13
*C13
C20
*C20
*C20
C14
*C14
C15
*C15

H163
H171
H172
H173
H21
H22
H31
H32
H41
H42
C18
H181
H182
H183
C7
H71
H81
C19
H191
H192
H193
C11
H101
C12
H111
C13
H121
C14
C20
H201
H202
H203
C15
H141
O29
O29B

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-120.00
180.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
180.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

PATCH FIRST NONE LAST NONE


!naming convention changed in following model compounds to
!standard double bond nomenclature, vs. conjugated double
!bond nomenclature. Done due to the double bonds not being
!conjugated with other double bonds.
RESI PRAC
!
GROUP
ATOM C1 CG2D2
ATOM H11 HGA5
ATOM H12 HGA5
GROUP
ATOM C2 CG2D1
ATOM H21 HGA4
ATOM CG CG2O3
ATOM OD1 OG2D2
ATOM OD2 OG2D2

-1.00 ! C3H3O2 2-propenoic acid


-0.42 !
0.21 !
0.21 ! H11
OD1
! \
||
-0.25 !
C1 CG
0.15 ! / \\ / \
0.62 ! H12 C2 OD2 (-)
-0.76 !
|
-0.76 !
H21

BOND C1 H11 C1 H12 C1 C2 C2


BOND C2 CG CG OD1 CG OD2

H21

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC

C1
OD1
H11
H11
CG

C2
C2
C1
C2
C1

CG
*CG
C2
*C1
*C2

OD1
OD2
CG
H12
H21

0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI PROL
0.00
!
GROUP
ATOM C1 CG2D2 -0.42
ATOM H11 HGA5
0.21
ATOM H12 HGA5
0.21
ATOM C2 CG2D1 -0.15
ATOM H21 HGA4
0.15
GROUP
ATOM C3 CG321
0.05
ATOM H31 HGA2
0.09
ATOM H32 HGA2
0.09
ATOM OR OG311 -0.65
ATOM HR HGP1
0.42
BOND C1 C2 C2 C3
BOND H11 C1 H12 C1
BOND H32 C3
IC
IC
IC
IC
IC
IC
IC

C1
C2
H11
H11
C3
OR
OR

C2
C3
C1
C2
C1
C2
C2

C3
OR
C2
*C1
*C2
*C3
*C3

! C3H6O 3-propenol (1-hydroxy-2-propene)


!
! H11
H31
! \
|
! C1
C3-OR
! / \\ / | \
! H12 C2 H32 HR
!
|
!
H21

C3 OR
H21 C2

OR
HR
C3
H12
H21
H31
H32

OR HR
H31 C3

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
60.00
180.00
180.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI PRAL
GROUP
ATOM C1 CG2D2
ATOM H11 HGA5
ATOM H12 HGA5
ATOM C2 CG2D1
ATOM H21 HGA4
ATOM CG CG2O4
ATOM OD1 OG2D1
ATOM H HGR52

0.00 ! C3H4O 2-propenal (acrolein)


-0.42
0.21
0.21
-0.04
0.15
0.27
-0.51
0.13

!
! H11
OD1
! \
||
! C1
CG
! / \\ / \
! H12 C2 H
!
|
!
H21

BOND C1 H11 C1 H12 C1 C2 C2 H21


BOND C2 CG CG OD1 CG H
IMPR CG C2 OD1 H
IC
IC
IC
IC
IC

C1
H11
H11
CG
OD1

C2
C1
C2
C1
C2

RESI SCH1
GROUP
ATOM C1 CG331

CG
C2
*C1
*C2
*CG

OD1
CG
H12
H21
H

0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00

0.00 ! C3H7N Schiff's base model compound 1, deprotonated


-0.05 !

H11

H31

ATOM H11
ATOM H12
ATOM H13
ATOM N2
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM H41
ATOM H42
ATOM H43

HGA3
HGA3
HGA3
NG2D1
CG2D1
HGA4

0.09
0.09
0.09
-0.60
0.23
0.15

!
\
/
! H12--C1-N2=C3
H41
!
/
\ /
! H13
C4--H42
!
\
!
H43

CG331
HGA3
HGA3
HGA3

!
-0.27 !
0.09 !
0.09
0.09

BOND C1 H11 C1 H12 C1 H13


BOND C1 N2 N2 C3 C3 H31
BOND C3 C4 C4 H41 C4 H42 C4 H43
IC
IC
IC
IC
IC
IC
IC
IC

C1
N2
C3
H11
H11
C4
H41
H41

N2
C3
N2
N2
N2
N2
C3
C3

RESI SCH2
GROUP
ATOM C1 CG334
ATOM H11 HGA3
ATOM H12 HGA3
ATOM H13 HGA3
ATOM N2 NG2P1
ATOM H21 HGP2
ATOM C3 CG2D1
ATOM H31 HGR52
GROUP
ATOM C4 CG331
ATOM H41 HGA3
ATOM H42 HGA3
ATOM H43 HGA3

C3
C4
C1
*C1
*C1
*C3
*C4
*C4

C4
H41
H11
H12
H13
H31
H42
H43

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
0.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.00 ! C3H8N Schiff's base model compound 2, protonated


0.18
0.09
0.09
0.09
-0.40
0.38
0.37
0.20

! H11 H21
H31
!
\ |
/
! H12--C1-N2=C3
H41
!
/ (+) \ /
! H13
C4--H42
!
\
!
H43
! hydrogen with intermediate VDW radius

!
-0.27 !
0.09 !
0.09
0.09

BOND C1 H11 C1 H12 C1 H13


BOND C1 N2 N2 H21 N2 C3 C3 H31
BOND C3 C4 C4 H41 C4 H42 C4 H43
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
N2
C1
C3
H11
H11
C4
H41
H41

N2
C3
C3
N2
N2
N2
N2
C3
C3

RESI SCH3
GROUP
ATOM C1 CG334
ATOM H11 HGA3
ATOM H12 HGA3

C3
C4
*N2
C1
*C1
*C1
*C3
*C4
*C4

C4
H41
H21
H11
H12
H13
H31
H42
H43

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
0.00
120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.00 ! C4H8N Schiff's base model compound 3, protonated


0.18 ! H11 H21
H31
0.09 !
\ |
/
0.09 ! H12--C1-N2=C3
H51

ATOM H13
ATOM N2
ATOM H21
ATOM C3
ATOM H31
GROUP
ATOM C4
ATOM H41
ATOM C5
ATOM H51
ATOM H52

HGA3
0.09 !
/ (+) \
/
NG2P1 -0.40 ! H13
C4=C5
HGP2
0.38 !
/
\
CG2DC1 0.37 !
H41
H52
HGR52
0.20 ! hydrogen with intermediate VDW radius

BOND
BOND
BOND
BOND

H11
N2
C4
C5

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
C1
C3
C4

CG2DC2 -0.15
HGA4
0.15
CG2DC3 -0.42
HGA5
0.21
HGA5
0.21

C1
N2
H11
H11
H11
C3
C4
C5
C3
H51

C1
N2
C4
C5

N2
C3
C1
N2
N2
C1
N2
C3
C4
C4

C3
C4
N2
*C1
*C1
*N2
*C3
*C4
C5
*C5

H12 C1 H13
H21 N2 C3 C3 H31
H41
H51 C5 H52
C4
C5
C3
H12
H13
H21
H31
H41
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

!/home/alex/param/general/Cyprus/toppar
!toppar_all22_flavopyridol_apr05.str
!piperidine models only
RESI PIP1
about the
GROUP
ATOM C1
ATOM H1A
ATOM H1B
ATOM H1C
ATOM N1
ATOM HNA
ATOM C12
ATOM H12A
ATOM H12B
ATOM C16
ATOM H16A
ATOM H16B
GROUP
ATOM C13
ATOM H13A
ATOM H13B
GROUP
ATOM C14
ATOM H14A
ATOM H14B
GROUP
ATOM C15
ATOM H15A

1.00 ! C6H14N N-methyl piperidinium


!methyl axial to ring
!Note that PIP1 and 2 only differ by the configuration
N
!
!
!
!
!
!
!
!
!
!
!
!
!

CG334
HGA3
HGA3
HGA3
NG3P1
HGP2
CG324
HGA2
HGA2
CG324
HGA2
HGA2

0.15
0.09
0.09
0.09
-0.40
0.32
0.15
0.09
0.09
0.15
0.09
0.09

CG321
HGA2
HGA2

-0.18 !
0.09
0.09

CG321
HGA2
HGA2

-0.18!
0.09
0.09

CG321
HGA2

-0.18
0.09

C15--C16
/

\
(+) N1--C1
\
/
C13--C12

C14

ATOM
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H15B
C1
N1
N1
C12
C13
C15
C16

C16
N1
C12
C13
C12
H1A
H1A
H1A
C16
C12
C13
H12A
C15
C15
C14
H13A
C15
H14A
C14
C14

HGA2
H1A
HNA
C16
C13
C14
H15A
H16B
N1
C12
C13
C14
C16
N1
N1
C1
C1
C1
N1
N1
N1
N1
C12
C12
C13
C13
C16
C16

C12
C13
C14
C15
*N1
*C1
*C1
N1
*N1
*N1
*C12
*C12
*C16
*C16
*C13
*C13
*C14
*C14
*C15
*C15

0.09
C1 H1B

C1

H1C

C1

N1
C13
C14
C15

C12
C13
C14
C15

H12A
H13B
H14B
C16

C12 H12B

C12
H13A
H14A
H15B

C13
C14
C15
C16
C1
H1B
H1C
C16
C12
HNA
H12A
H12B
H16A
H16B
H13A
H13B
H14A
H14B
H15A
H15B

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-60.00
60.00
-60.00
60.00
-120.00
120.00
-120.00
180.00
-120.00
-120.00
120.00
120.00
120.00
-120.00
120.00
120.00
-120.00
-120.00
120.00
-120.00

N1

C14 C15
C16 H16A
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

PATCH FIRST NONE LAST NONE


RESI PIP2
GROUP
ATOM C1
ATOM H1A
ATOM H1B
ATOM H1C
ATOM N1
ATOM HNA
ATOM C12
ATOM H12A
ATOM H12B
ATOM C16
ATOM H16A
ATOM H16B
GROUP
ATOM C13
ATOM H13A
ATOM H13B
GROUP
ATOM C14
ATOM H14A
ATOM H14B
GROUP
ATOM C15
ATOM H15A
ATOM H15B

1.00 ! C6H14N N-methyl piperidinium


!methyl equitorial to ring
CG334
HGA3
HGA3
HGA3
NG3P1
HGP2
CG324
HGA2
HGA2
CG324
HGA2
HGA2

0.15
0.09
0.09
0.09
-0.40
0.32
0.15
0.09
0.09
0.15
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2

-0.18
0.09
0.09

!
!
!
!
!
!
!
!
!
!
!
!

C15--C16
/

\
(+) N1--C1
\
/
C13--C12

C14

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

BOND
BOND
BOND
BOND
BOND
BOND
BOND

C1
N1
N1
C12
C13
C15
C16

H1A
HNA
C16
C13
C14
H15A
H16B

C1

H1B

C1

H1C

C1

N1
C13
C14
C15

C12
H13A
H14A
H15B

C12
C13
C14
C15

H12A
H13B
H14B
C16

C12 H12B

IC C16 N1
C12 C13
IC N1
C12 C13 C14
IC C12 C13 C14 C15
IC C13 C14 C15 C16
IC C12 C16 *N1 C1
IC H1A N1
*C1 H1B
IC H1A N1
*C1 H1C
IC H1A C1
N1
C16
IC C16 C1
*N1 C12
IC C12 C1
*N1 HNA
IC C13 N1
*C12 H12A
IC H12A N1
*C12 H12B
IC C15 N1
*C16 H16A
IC C15 N1
*C16 H16B
IC C14 C12 *C13 H13A
IC H13A C12 *C13 H13B
IC C15 C13 *C14 H14A
IC H14A C13 *C14 H14B
IC C14 C16 *C15 H15A
IC C14 C16 *C15 H15B
PATCH FIRST NONE LAST NONE
RESI PIP3
GROUP
ATOM C1
ATOM H1A
ATOM H1B
ATOM H1C
ATOM N1
ATOM HNA
ATOM C12
ATOM H12A
ATOM H12B
ATOM C16
ATOM H16A
ATOM H16B
GROUP
ATOM C13
ATOM H13
ATOM O3
ATOM HO3
GROUP
ATOM C14
ATOM H14A
ATOM H14B
GROUP
ATOM C15
ATOM H15A
ATOM H15B
BOND
BOND
BOND

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

N1

C14 C15
C16 H16A

-60.00
60.00
-60.00
60.00
120.00
120.00
-120.00
180.00
-120.00
120.00
120.00
120.00
120.00
-120.00
120.00
120.00
-120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.00 ! C6H14NO 3-hydroxy-N-methyl piperidinium


CG334
HGA3
HGA3
HGA3
NG3P1
HGP2
CG324
HGA2
HGA2
CG324
HGA2
HGA2

0.15
0.09
0.09
0.09
-0.40
0.32
0.15
0.09
0.09
0.15
0.09
0.09

! group charge should be 1.0


!
!
C15--C16
!
/
\
!
----C14
(+) N1--C1
!
\
/
!
C13--C12
!
/
!
H-O3
!
!
!

CG311
HGA1
OG311
HGP1

0.14 !
0.09
-0.65
0.42

CG321
HGA2
HGA2

-0.18
0.09
0.09

CG321
HGA2
HGA2
C1
N1
N1

-0.18
0.09
0.09
H1A
HNA
C16

C1

H1B

C1

H1C

C1

N1

N1

C12

C12

H12A

C12 H12B

BOND
C12 C13
C13 H13
C13 O3
BOND
C13 C14
C14 H14A
C14 H14B
BOND
C15 H15A
C15 H15B
C15 C16
BOND
C16 H16B
IC C14 C15 C16 N1
.0000
.00 -60.00
IC C15 C16 N1
C12
.0000
.00 60.00
IC C16 N1
C12 C13
.0000
.00 -60.00
IC N1
C12 C13 C14
.0000
.00 60.00
IC C12 C16 *N1 C1
.0000
.00 120.00
IC C12 C16 *N1 HNA
.0000
.00 -120.00
IC C16 N1
C1
H1A
.0000
.00 120.00
IC H1A N1
*C1 H1B
.0000
.00 120.00
IC H1A N1
*C1 H1C
.0000
.00 -120.00
IC C13 N1
*C12 H12A
.0000
.00 120.00
IC C13 N1
*C12 H12B
.0000
.00 -120.00
IC C15 N1
*C16 H16A
.0000
.00 120.00
IC C15 N1
*C16 H16B
.0000
.00 -120.00
IC C12 C14 *C13 O3
.0000
.00 120.00
IC C12 C14 *C13 H13
.0000
.00 -120.00
IC C12 C13 O3
HO3
.0000
.00 60.00
IC C15 C13 *C14 H14A
.0000
.00 120.00
IC C15 C13 *C14 H14B
.0000
.00 -120.00
IC C14 C16 *C15 H15A
.0000
.00 120.00
IC C14 C16 *C15 H15B
.0000
.00 -120.00
PATCH FIRST NONE LAST NONE

O3 HO3
C14 C15
C16 H16A
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00
.00

.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.0000

!RESI DUM
0.00 ! DUMMY ATOM
!GROUP
!ATOM DUM DUM 0.00
!PATCHING FIRST NONE LAST NONE
!RESI HE
0.00 ! helium
!GROUP
!ATOM HE HE
0.00
!PATCHING FIRST NONE LAST NONE
!RESI NE
0.00 ! neon
!GROUP
!ATOM NE NE
0.00
!PATCHING FIRST NONE LAST NONE
!adm jr(?), july2006
RESI ALF4
-1.00 ! AlF4 Aluminum tetraflouride, tetrahedral geometry
GROUP
ATOM AL1 ALG1
1.16
ATOM F1 FGP1
-0.54
ATOM F2 FGP1
-0.54
ATOM F3 FGP1
-0.54
ATOM F4 FGP1
-0.54
BOND AL1 F1 AL1 F2 AL1 F3 AL1 F4
IC
IC

F2
F2

F1
F1

*AL1 F3
*AL1 F4

RESI FLUB
0.00
GROUP
ATOM C1 CG2R61 -0.10
ATOM H1 HGR62
0.15 !

0.0000
0.0000

0.00 120.00
0.00 -120.00

0.00
0.00

0.0000
0.0000

! C6H5F fluorobenzene, adm jr.


! atom numbering based on difluorotoluene
H5

H4

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC

C2
H2
C3
H3
C4
H4
C5
H5
C6
F6
C1
C3
C6
C2
C6
C3
C1
C4
C2
C5
C6
C5

RESI BROB
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
ATOM C6
ATOM BR
BOND C1
BOND C3
BOND C6
IC C2
IC C6
IC C3
IC C1
IC C4
IC C2
IC C5
IC C6
IC C5
RESI CHLB
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4

CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.115
HGR61
0.115
CG2R61 -0.10
HGR62
0.15
CG2R66 0.11
FGR1
-0.21
H1 C1 C2
H3 C3 C4
C1 C6 F6
C6 *C1 H1
C1 C2 C3
C1 *C2 H2
C2 C3 C4
C2 *C3 H3
C3 C4 C5
C3 *C4 H4
C4 *C5 H5
C1 *C6 F6

!
\ ___ /
!
C5---C4
!
/
\
! F6--C6
C3--H3
!
\\
//
!
C1---C2
!
/
\
!
H1
H2
C2
C4

H2
H4

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C2
C4
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C3
C5

C5

180.00
0.00
180.00
0.00
180.00
0.00
180.00
180.00
180.00

0.000 ! C6H5Br bromobenzene


!
CG2R61 -0.06 !
HGR62
0.15 !
H5
H4
CG2R61 -0.115 !
\ ___ /
HGR61
0.115 !
C5---C4
CG2R61 -0.115 !
/
\
HGR61
0.115 ! BR--C6
C3--H3
CG2R61 -0.115 !
\\ //
HGR61
0.115 !
C1---C2
CG2R61 -0.06 !
/
\
HGR62
0.15 !
H1
H2
CG2R61 -0.08 !
BRGR1 -0.10 !
H1 C1 C2 C2 H2 C2 C3
H3 C3 C4 C4 H4 C4 C5 C5
C1 C6 BR
C6 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 C4 C5 0.0000
0.00
0.00
C3 *C4 H4 0.0000
0.00 180.00
C4 *C5 H5 0.0000
0.00 180.00
C1 *C6 BR 0.0000
0.00 180.00

CG2R61
HGR62
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61

0.000 ! C6H5Cl compound #


!
-0.10 !
0.15 !
H5
H4
-0.115 !
\ ___ /
0.115 !
C5---C4
-0.115 !
/
\
0.115 ! CL--C6
C3--H3
-0.115 !
\\ //
0.115 !
C1---C2

H5

C5

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

H5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5

C6
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

: chlorobenzene

ATOM
ATOM
ATOM
ATOM
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC

C5
H5
C6
CL
C1
C3
C6
C2
C6
C3
C1
C4
C2
C5
C6
C5

RESI IODB
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
ATOM C6
ATOM I6
BOND C1
BOND C3
BOND C6
IC C2
IC C6
IC C3
IC C1
IC C4
IC C2
IC C5
IC C6
IC C5
RESI UREA
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM O2
ATOM N3
ATOM H31
ATOM H32

CG2R61 -0.10
HGR62
0.15
CG2R61 0.03
CLGR1 -0.13
H1 C1 C2
H3 C3 C4
C1 C6 CL
C6 *C1 H1
C1 C2 C3
C1 *C2 H2
C2 C3 C4
C2 *C3 H3
C3 C4 C5
C3 *C4 H4
C4 *C5 H5
C1 *C6 CL

!
!

/
H1

\
H2

!
!
C2
C4

H2
H4

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C2
C4
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C3
C5

C5

180.00
0.00
180.00
0.00
180.00
0.00
180.00
180.00
180.00

0.000 ! C6H5I iodobenzene


!
CG2R61 -0.06 !
HGR62
0.14 !
H5
H4
CG2R61 -0.115 !
\ ___ /
HGR61
0.115 !
C5---C4
CG2R61 -0.115 !
/
\
HGR61
0.115 ! I--C6
C3--H3
CG2R61 -0.115 !
\\ //
HGR61
0.115 !
C1---C2
CG2R61 -0.06 !
/
\
HGR62
0.14 !
H1
H2
CG2R61 -0.08 !
IGR1
-0.08 !
H1 C1 C2 C2 H2 C2 C3
H3 C3 C4 C4 H4 C4 C5 C5
C1 C6 I6
C6 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 C4 C5 0.0000
0.00
0.00
C3 *C4 H4 0.0000
0.00 180.00
C4 *C5 H5 0.0000
0.00 180.00
C1 *C6 I6 0.0000
0.00 180.00
0.00 ! CH4N2O Urea, adm
NG2S2
HGP1
HGP1
CG2O6
OG2D1
NG2S2
HGP1
HGP1

-0.69
0.34
0.34
0.60
-0.58
-0.69
0.34
0.34

BOND C2 O2 C2 N1 C2 N3
BOND N1 H11 N1 H12
BOND N3 H31 N3 H32
IMPR O2 N1 N3 C2

H5

C5

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

H5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5

C6
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC

O2
H11
H11
N3
N1
H31

C2
C2
N1
N1
C2
C2

N1
*N1
C2
*C2
N3
*N3

H11
H12
N3
O2
H31
H32

RESI PY01
GROUP
ATOM O1
ATOM C2
ATOM H21
ATOM C3
ATOM H31
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM C6
ATOM H61

0.000 !
!
OG3R60 -0.32 !
CG2D1O -0.04 !
HGA4
0.20 !
CG2D1 -0.15 !
HGA4
0.15 !
CG321 -0.18 !
HGA2
0.09 !
HGA2
0.09 !
CG2D1 -0.15 !
HGA4
0.15 !
CG2D1O -0.04 !
HGA4
0.20 !

BOND O1
BOND C3
BOND C5

C2
C4
C6

IC
IC
IC
IC
IC
IC
IC
IC
IC

C6
O1
C2
C3
C4
C5
C5
C6
C5

O1
C2
C3
O1
C2
C3
C3
C4
O1

C2
C4
C6
C2
C3
C4
*C2
*C3
*C4
*C4
*C5
*C6

RESI PY02
GROUP
ATOM O1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM C4
ATOM H41
ATOM C5
ATOM H51
ATOM C6
ATOM H61

OG3R60
CG321
HGA2
HGA2
CG2DC2
HGA4
CG2DC2
HGA4
CG2DC1
HGA4
CG2D1O
HGA4

BOND O1
BOND C3
BOND C5

C2
C4
C6

C2
C4
C6

!mp2/6-31g* ring
IC C6 O1
C2
IC O1 C2
C3
IC C2 C3
C4
IC C3 C4
C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5H6O 4H-Pyran, maybridge list, adm


new atom type!!
new atom type!!
O1
/ \
H21-C2
C6-H61
||
||
H31-C3
C5-H51
\ /
C4
/ \
H41 H42

H21 C2
H41 C4
H61 C6

C3 C3
H42 C4
O1

C3
C4
C5
H21
H31
H41
H42
H51
H61

H31
C5 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 !
!
-0.37 !
0.00 !
0.09 !
0.09 !
-0.15 !
0.15 !
-0.15 !
0.15 !
-0.15 !
0.15 !
0.00 !
0.19 !

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H51

0.00
0.00
0.00
180.00
180.00
120.00
240.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5H6O 2H-Pyran, maybridge list, adm


Note use of conjugated C types

H21

O1
\ / \
H22-C2
C6-H61
|
||
H31-C3
C5-H51
\\ /
C4
|
H41

H21 C2
H41 C4
H61 C6
C3
C4
C5
C6

0.00
0.00
0.00
0.00
0.00
0.00

H22 C2
C5 C5
O1
0.0000
0.0000
0.0000
0.0000

C3 C3
H51

0.00 51.00
0.00 -42.00
0.00
8.00
0.00 18.00

H31

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC

C4
C5
C3
C3
C4
C5
C6
C5

C5
C6
O1
O1
C2
C3
C4
O1

C6
O1
*C2
*C2
*C3
*C4
*C5
*C6

O1
C2
H21
H22
H31
H41
H51
H61

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-8.00
-27.00
120.00
240.00
180.00
180.00
180.00
180.00

RESI NITB
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
ATOM C6
ATOM N6
ATOM O6A
ATOM O6B
BOND C1
BOND C3
BOND C6
IC C2
IC C6
IC C3
IC C1
IC C4
IC C2
IC C5
IC C6
IC C5
IC C1
IC O6A

0.000 ! C6H5NO2 nitrobenzene


!
CG2R61 -0.18 !
HGR61
0.16 !
H5
H4
CG2R61 -0.115 !
\ ___ /
HGR61
0.115 ! O6A
C5---C4
CG2R61 -0.115 !
\ +
/
\
HGR61
0.115 ! - N6--C6
C3--H3
CG2R61 -0.115 !
/
\\
//
HGR61
0.115 ! O6B
C1---C2
CG2R61 -0.18 !
/
\
HGR61
0.16 !
H1
H2
CG2R61 0.32 !
NG2O1
0.40 !
OG2N1 -0.34 !
OG2N1 -0.34 !
H1 C1 C2 C2 H2 C2 C3
H3 C3 C4 C4 H4 C4 C5 C5
C1 C6 N6 N6 O6A N6 O6B
C6 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 C4 C5 0.0000
0.00
0.00
C3 *C4 H4 0.0000
0.00 180.00
C4 *C5 H5 0.0000
0.00 180.00
C1 *C6 N6 0.0000
0.00 180.00
C6 N6 O6A 0.0000
0.00 180.00
C6 *N6 O6B 0.0000
0.00 180.00

RESI PYRL
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM N5
ATOM H5
BOND C1
BOND C3
IC C2
IC N5
IC C3
IC C1
IC C4
IC N5

0.000 ! C4H5N pyrrole


! H2
H1
CG2R51 -0.04 !
\ ____ /
HGR52
0.14 !
C2----C1
CG2R51 -0.25 !
|
\
HGR51
0.15 !
|
N5--H5
CG2R51 -0.25 !
|____ /
HGR51
0.15 !
C3----C4
CG2R51 -0.04 !
/
\
HGR52
0.14 ! H3
H4
NG2R51 -0.35 !
HGP1
0.35 !
H1 C1 C2 C2 H2 C2 C3 C3
C4 C4 H4 C4 N5 N5 H5 N5
N5 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 *C4 H4 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H5

C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C6

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

H3
C1
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC

C4

C1

*N5 H5

0.0000

0.00 180.00

0.00

0.0000

RESI FURA
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM O5
BOND C1
BOND C3
IC C2
IC O5
IC C3
IC C1
IC C4
IC O5

0.00 ! C4H4O furan


! H2
H1
CG2R51 0.10 !
\ ____ /
HGR52
0.14 !
C2----C1
CG2R51 -0.25 !
|
\
HGR51
0.15 !
|
O5
CG2R51 -0.25 !
|____ /
HGR51
0.15 !
C3----C4
CG2R51 0.10 !
/
\
HGR52
0.14 ! H3
H4
OG2R50 -0.28 !
H1 C1 C2 C2 H2 C2 C3
H3 C3 C4 C4 H4 C4 O5 O5
O5 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 *C4 H4 0.0000
0.00 180.00

C1
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI THIP
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM S5
BOND C1
BOND C3
IC C2
IC S5
IC C3
IC C1
IC C4
IC S5
!
RESI OXAZ
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM H4
ATOM O5
BOND C1
BOND N3
IC C2
IC O5
IC N3
IC C1
IC O5
!

0.000 ! C4H4S thiophene


!
CG2R51 -0.06 ! H2
H1
HGR52
0.18 !
\ ____ /
CG2R51 -0.24 !
C2----C1
HGR51
0.17 !
|
\
CG2R51 -0.24 !
|
S5
HGR51
0.17 !
|____ /
CG2R51 -0.06 !
C3----C4
HGR52
0.18 !
/
\
SG2R50 -0.10 ! H3
H4
H1 C1 C2 C2 H2 C2 C3
H3 C3 C4 C4 H4 C4 S5 S5
S5 *C1 H1 0.0000
0.00 180.00
C1 C2 C3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 C3 C4 0.0000
0.00
0.00
C2 *C3 H3 0.0000
0.00 180.00
C3 *C4 H4 0.0000
0.00 180.00

C1
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C3H3NO oxazole


! H2
H1
CG2R51 0.11 !
\ ____ /
HGR52
0.12 !
C2----C1
CG2R51 0.15 !
|
\
HGR52
0.11 !
|
O5
NG2R50 -0.61 !
|____ /
CG2R53 0.22 !
N3----C4
HGR52
0.19 !
\
OG2R50 -0.29 !
H4
H1 C1 C2 C2 H2 C2 N3
C4 C4 H4 C4 O5 O5 C1
O5 *C1 H1 0.0000
0.00 180.00
C1 C2 N3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 N3 C4 0.0000
0.00
0.00
N3 *C4 H4 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

RESI ISOX
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM N4
ATOM O5
BOND C1
BOND C3
IC C1
IC O5
IC C2
IC C3
IC N4
!
RESI THAZ
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM H4
ATOM S5
BOND C1
BOND N3
IC C1
IC S5
IC C2
IC N3
IC S5
!
RESI ISOT
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM N4
ATOM S5
BOND C1
BOND C3
IC S5
IC C1
IC C2
IC C3
IC N4
!
RESI PYRZ
GROUP
ATOM C1
ATOM H1
ATOM C2

CG2R51
HGR52
CG2R51
HGR51
CG2R52
HGR52
NG2R50
OG2R50

0.000 ! C3H3NO isoxazole


! H2
H1
0.28 !
\ ____ /
0.13 !
C2----C1
-0.43 !
|
\
0.18 !
|
O5
0.35 !
|____ /
0.11 !
C3----N4
-0.45 !
/
-0.17 ! H3

H1
N4
C2
C1
O5
C1
C2

C1
C3
C3
C2
*C1
*C2
*C3

C2
H3
N4
C3
H1
H2
H3

C2 H2
N4 O5
0.0000
0.0000
0.0000
0.0000
0.0000

C2
O5
0.00
0.00
0.00
0.00
0.00

C3
C1
0.00
0.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C3H3NS thiazole


! H2
H1
CG2R51 -0.30 !
\ ____ /
HGR52
0.21 !
C2----C1
CG2R51 0.20 !
|
\
HGR52
0.13 !
|
S5
NG2R50 -0.61 !
|____ /
CG2R53 0.22 !
N3----C4
HGR52
0.14 !
\
SG2R50 0.01 !
H4
H1 C1 C2 C2 H2 C2 N3
C4 C4 H4 C4 S5 S5 C1
C2 N3 C4 0.0000
0.00
0.00
C1 C2 N3 0.0000
0.00
0.00
S5 *C1 H1 0.0000
0.00 180.00
C1 *C2 H2 0.0000
0.00 180.00
N3 *C4 H4 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C3H3NS isothiazole


! H2
H1
CG2R51 -0.04 !
\ ____ /
HGR52
0.16 !
C2----C1
CG2R51 -0.20 !
|
\
HGR51
0.13 !
|
S5
CG2R52 0.23 !
|____ /
HGR52
0.11 !
C3----N4
NG2R50 -0.53 !
/
SG2R50 0.14 ! H3
H1 C1 C2 C2 H2 C2 C3
N4 C3 H3 N4 S5 S5 C1
C1 C2 C3 0.0000
0.00
0.00
C2 C3 N4 0.0000
0.00
0.00
S5 *C1 H1 0.0000
0.00 180.00
C1 *C2 H2 0.0000
0.00 180.00
C2 *C3 H3 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C3H4N2 pyrazole


!
CG2R51 -0.03 ! H2
H1
HGR52
0.15 !
\ ____ /
CG2R51 -0.24 !
C2----C1

ATOM H2
ATOM C3
ATOM H3
ATOM N4
ATOM N5
ATOM H5
BOND C1
BOND C3
IC C1
IC N5
IC C2
IC C3
IC N4
IC N4
!
RESI OXAD
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM N4
ATOM O5
BOND C1
BOND N3
IC C1
IC C2
IC N3
IC O5
IC C2
IC N3
!
RESI TRZ3
GROUP
ATOM C1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM N4
ATOM N5
ATOM H5
BOND C1
BOND N3
IC C2
IC N5
IC N3
IC C1
IC N4
!
RESI TRZ4
GROUP
ATOM C1
ATOM H1
ATOM N2
ATOM C3
ATOM H3
ATOM N4
ATOM N5

HGR51
0.14
CG2R52 0.14
HGR52
0.13
NG2R50 -0.57
NG2R51 -0.05
HGP1
0.33
H1 C1 C2
H3 C3 N4
C2 C3 N4
C1 C2 C3
N5 *C1 H1
C1 *C2 H2
C2 *C3 H3
C1 *N5 H5

!
|
\
!
|
N5--H5
!
|____ /
!
C3----N4
!
/
! H3
C2 H2 C2 C3
N4 N5 N5 H5 N5
0.0000
0.00
0.00
0.0000
0.00
0.00
0.0000
0.00 180.00
0.0000
0.00 180.00
0.0000
0.00 180.00
0.0000
0.00 180.00

C1
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C2H2N2O oxadiazole123


! H2
H1
CG2R51 0.17 !
\ ____ /
HGR52
0.14 !
C2----C1
CG2R51 0.19 !
|
\
HGR52
0.10 !
|
O5
NG2R50 -0.32 !
|____ /
NG2R50 -0.10 !
N3----N4
OG2R50 -0.18 !
H1 C1 C2 C2 H2 C2 N3
N4 N4 O5 O5 C1
C2 N3 N4 0.0000
0.00
0.00
N3 N4 O5 0.0000
0.00
0.00
N4 O5 C1 0.0000
0.00
0.00
C1 C2 N3 0.0000
0.00
0.00
O5 *C1 H1 0.0000
0.00 180.00
C1 *C2 H2 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C2H3N3 triazole123


! H2
H1
CG2R51 -0.35 !
\ ____ /
HGR52
0.20 !
C2----C1
CG2R51 0.25 !
|
\
HGR52
0.11 !
|
N5--H5
NG2R50 -0.41 !
|____ /
NG2R50 -0.37 !
N3----N4
NG2R51 0.28 !
HGP1
0.29 !
H1 C1 C2 C2 H2 C2 N3
N4 N4 N5 N5 H5 N5 C1
N5 *C1 H1 0.0000
0.00 180.00
C1 C2 N3 0.0000
0.00
0.00
C1 *C2 H2 0.0000
0.00 180.00
C2 N3 N4 0.0000
0.00
0.00
C1 *N5 H5 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

CG2R52
HGR52
NG2R50
CG2R52
HGR52
NG2R50
NG2R51

0.00 ! C2H3N3 triazole124


!
H1
0.21 !
____ /
0.16 !
N2----C1
-0.68 !
|
\
0.45 !
|
N5--H5
0.12 !
|____ /
-0.62 !
C3----N4
0.03 ! /

ATOM H5

HGP1

BOND C1
BOND C3
IC C1
IC N2
IC N5
IC N2
IC N4
IC N4
!
RESI TEAZ
GROUP
ATOM C1
ATOM H1
ATOM N2
ATOM N3
ATOM N4
ATOM N5
ATOM H5
BOND C1
BOND N3
IC C1
IC N2
IC N5
IC N2
IC N4
!
RESI TDAZ
GROUP
ATOM C1
ATOM H1
ATOM N2
ATOM N3
ATOM C4
ATOM H4
ATOM S5

H1
N4
N2
C3
C1
N5
N2
C1

BOND
BOND
IC
IC
IC
IC
IC
!

H1
H4
N2
N3
C1
S5
N3

C1
C4
C1
N2
S5
N2
S5

RESI PYRD
GROUP
ATOM N1
ATOM N2
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
ATOM C6
ATOM H6

0.33 ! H3
C1
N4
C3
N4
N2
*C1
*C3
*N5

N2
N5
N4
N5
C3
H1
H3
H5

N2 C3
N5 H5
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C3
N5
0.00
0.00
0.00
0.00
0.00
0.00

H3
C1
0.00
0.00
0.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! CH2N4 tetrazole


!
H1
CG2R52 0.24 !
____ /
HGR52
0.14 !
N2----C1
NG2R50 -0.41 !
|
\
NG2R50 -0.14 !
|
N5--H5
NG2R50 -0.34 !
|____ /
NG2R51 0.23 !
N3----N4
HGP1
0.28 !
H1 C1 N2 N2 N3
N4 N4 N5 N5 H5 N5 C1
N2 N3 N4 0.0000
0.00
0.00
N3 N4 N5 0.0000
0.00
0.00
C1 N2 N3 0.0000
0.00
0.00
N5 *C1 H1 0.0000
0.00 180.00
C1 *N5 H5 0.0000
0.00 180.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

CG2R52
HGR52
NG2R50
NG2R50
CG2R52
HGR52
SG2R50

0.000 ! C2H2N2S thiadiazole 1,3,4


!
H1
0.11 !
____ /
0.27 !
N2----C1
-0.37 !
|
\
-0.37 !
|
S5
0.11 !
|____ /
0.27 !
N3----C4
-0.02 !
\
!
H4

C1
C4
N3
C4
N2
*C1
*C4

N2
S5
C4
S5
N3
H1
H4

N2 N3
S5 C1
0.0000
0.0000
0.0000
0.0000
0.0000

N3

C4

0.00
0.00
0.00
0.00
0.00
0.00
0.00 180.00
0.00 180.00

0.000 ! C4H4N2 pyridazine


NG2R62
NG2R62
CG2R61
HGR62
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR62

-0.44
-0.44
0.31
0.11
-0.16
0.18
-0.16
0.18
0.31
0.11

!
!
H5
H6
!
\
/
!
C5----C6
!
/
\
! H4--C4
N1
!
\\
//
!
C3----N2
!
/
!
H3

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

BOND N1 N2
BOND C3 H3
IC
IC
IC
IC
IC
IC
IC

N1
N2
C6
C4
C5
C6
C5

!
RESI PYZN
GROUP
ATOM N1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM N4
ATOM C5
ATOM H5
ATOM C6
ATOM H6
BOND C6
BOND C3
IC N1
IC C2
IC C2
IC C6
IC C3
IC N4
IC C5
IC N4
!
RESI PYRM
GROUP
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
ATOM C6
ATOM H6
!
BOND N1
BOND C2
!
IC
N1
IC
C2
IC
N3
IC
C6
IC
N3
IC
C5
IC
C6

N2 C3
C4 H4

C5 C6

C6 N1

0.00
0.00
0.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C4H4N2 pyrazine


!
NG2R60 -0.56 !
H5
H6
CG2R61 0.18 !
\ ____ /
HGR62
0.10 !
C5----C6
CG2R61 0.18 !
/
\
HGR62
0.10 !
N4
N1
NG2R60 -0.56 !
\\
//
CG2R61 0.18 !
C3----C2
HGR62
0.10 !
/
\
CG2R61 0.18 !
H3
H2
HGR62
0.10 !
H6 C6 C5 C5 H5 C5 N4 N4
H3 C3 C2 C2 H2 C2 N1 N1
C2 C3 N4 0.0000
0.00
0.00
C3 N4 C5 0.0000
0.00
0.00
N1 C6 C5 0.0000
0.00
0.00
N1 C2 C3 0.0000
0.00
0.00
N1 *C2 H2 0.0000
0.00 180.00
C2 *C3 H3 0.0000
0.00 180.00
N1 *C6 H6 0.0000
0.00 180.00
C6 *C5 H5 0.0000
0.00 180.00

C3
C6
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

N2
C3
N1
N2
C3
C4
N1

C3
C4
N2
*C3
*C4
*C5
*C6

C2
N3
C4
N1
N1
N3
C4

C4
C5
C3
H3
H4
H5
H6

C4 C5
C6 H6

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C4H4N2 pyrimidine


!
-0.73 !
H5
H6
0.50 !
\ ___ /
0.14 !
C5---C6
-0.73 !
/
\
0.29 ! H4--C4
N1
0.12 !
\\
//
-0.115 !
N3---C2
0.115 !
\
0.29 !
H2
0.12 !

NG2R62
CG2R64
HGR62
NG2R62
CG2R61
HGR62
CG2R61
HGR61
CG2R61
HGR62
C2
H2

C3 C4
C5 H5

C2
C4
N3
C4
C5
C2
*C2
*C4
*C5

N3
H4
C4
C5
C6
N3
H2
H4
H5

N3
C5

C4
H5

C4
C6
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5
H6

C5 C6 C6 N1
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00 180.00
0.00 180.00
0.00 180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC
C5
!
RESI TRIA
GROUP
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM H4
ATOM N5
ATOM C6
ATOM H6
!
BOND C6
BOND N3
IC N1
IC C2
IC N3
IC C6
IC N3
IC N5
IC N5
!
RESI TRIB
GROUP
ATOM N1
ATOM N2
ATOM C3
ATOM H3
ATOM N4
ATOM C5
ATOM H5
ATOM C6
ATOM H6
!

N1

*C6 H6

0.0000

0.00 180.00

0.00

0.00 ! C3H3N3 1,3,5-triazine


!
-0.88 !
H6
0.78 !
___ /
0.10 !
N5---C6
-0.88 !
/
\
0.78 ! H4--C4
N1
0.10 !
\\
//
-0.88 !
N3---C2
0.78 !
\
0.10 !
H2

NG2R62
CG2R64
HGR62
NG2R62
CG2R64
HGR62
NG2R62
CG2R64
HGR62
H6
C2

C6
C2

N5
H2

N5
C2

C4
N1

C2
N3
C4
N1
N1
N3
N1

N3
C4
N5
C2
*C2
*C4
*C6

C4
N5
C6
N3
H2
H4
H6

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
N1

H4
C6

C4

N3

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00 180.00
0.00 180.00
0.00 180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C3H3N3 1,2,4-triazine


!
-0.41 !
H5
H6
-0.53 !
\ ___ /
0.72 !
C5---C6
0.09 !
/
\
-0.75 !
N4
N1
0.36 !
\\
//
0.09 !
C3---N2
0.36 !
/
0.07 !
H3

NG2R62
NG2R62
CG2R64
HGR62
NG2R62
CG2R61
HGR62
CG2R61
HGR62

BOND N1 N2 N2 C3 C3 N4 N4 C5 C5 C6 C6 N1
BOND C3 H3 C5 H5 C6 H6
IC
IC
IC
IC
IC
IC

C6
N1
N2
N4
C6
C5

RESI THP
GROUP
ATOM O1
ATOM C2
ATOM H21
ATOM H22
ATOM C6
ATOM H61
ATOM H62
GROUP
ATOM C3
ATOM H31

N1
N2
C3
N2
N4
N1

N2
C3
N4
*C3
*C5
*C6

C3
N4
C5
H3
H5
H6

0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00

! C5H10O tetrahydropyran sng

OG3C61 -0.40
CG321
0.02 !
HGA2
0.09 !
HGA2
0.09 !
CG321
0.02 !
HGA2
0.09 !
HGA2
0.09 !
!
CG321 -0.18 !
HGA2
0.09

O1
/
C6
|
C5
\

\
C2
|
C3
/
C4

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

H32
C4
H41
H42
C5
H51
H52

HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C6
O1
C2
C3
C3
C5
C5
C4
C4
C5
C5
C4
C4

O1
C2
O1
O1
O1
O1
O1
C2
C2
C3
C3
C6
C6

BOND
BOND
BOND
BOND
BOND
BOND

O1
C2
C3
C4
C5
C6

0.09
-0.18
0.09
0.09
-0.18
0.09
0.09

C2
H21
H31
H41
H51
H61

C2
C3
C6
*C2
*C2
*C6
*C6
*C3
*C3
*C4
*C4
*C5
*C5
C2
C2
C3
C4
C5
C6

C3
C4
C5
H21
H22
H61
H62
H31
H32
H41
H42
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-60.00
60.00
60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C3 C3 C4 C4 C5 C5 C6 C6 O1
H22
H32
H42
H52
H62

PATC FIRS NONE LAST NONE


RESI DIOX
GROUP
ATOM O1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM O4
ATOM C5
ATOM H51
ATOM H52
ATOM C6
ATOM H61
ATOM H62

0.00 ! C4H8O2 dioxane14


!
OG3C61 -0.40 !
CG321
0.02 !
HGA2
0.09 ! H52 H61 H62
HGA2
0.09 !
\
\ /
CG321
0.02 ! H51--C5---C6
HGA2
0.09 !
/
\
HGA2
0.09 !
O4
O1
OG3C61 -0.40 !
\
/
CG321
0.02 ! H31--C3---C2
HGA2
0.09 !
/
/ \
HGA2
0.09 ! H32 H21 H22
CG321
0.02 !
HGA2
0.09 !
HGA2
0.09 !

BOND O1
BOND C2
BOND C6

C2 C2
H21 C2
H61 C6

C3 C3
H22 C3
H62 C5

IC
IC
IC
IC
IC
IC
IC
IC

C2
C3
O4
C5
C3
C3
O4
O4

O4
C5
C6
O1
H21
H22
H31
H32

O1
C2
C3
O4
O1
O1
C2
C2

C3
O4
C5
C6
*C2
*C2
*C3
*C3

O4 O4
H31 C3
H51 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5 C5
H32
H52
60.00
-60.00
60.00
-60.00
120.00
-120.00
120.00
-120.00

C6

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6 O1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC O4
IC O4
IC C5
IC C5
!
RESI DIXB
GROUP
ATOM O1
ATOM C2
ATOM H21
ATOM H22
ATOM O3
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52
ATOM C6
ATOM H61
ATOM H62

C6
C6
O1
O1

BOND O1
BOND C2
BOND C6

C2 C2
H21 C2
H61 C6

O3 O3
H22 C4
H62 C5

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

O1
C2
O3
O1
O1
O3
O3
C4
C4
O1
O1

O3
C4
C5
H21
H22
H41
H42
H51
H52
H61
H62

C6
O1
C2
O3
O3
C5
C5
C6
C6
C5
C5

RESI PIP
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM H21
ATOM H22
ATOM C6
ATOM H61
ATOM H62
GROUP
ATOM C3
ATOM H31
ATOM H32
GROUP
ATOM C4
ATOM H41
ATOM H42
GROUP
ATOM C5
ATOM H51

*C5
*C5
*C6
*C6

H51
H52
H61
H62

0.0000
0.0000
0.0000
0.0000

0.00 !
!
OG3C61 -0.40 !
CG321
0.22 !
HGA2
0.09 !
HGA2
0.09 !
OG3C61 -0.40 !
CG321
0.02 !
HGA2
0.09 !
HGA2
0.09 !
CG321 -0.18 !
HGA2
0.09 !
HGA2
0.09 !
CG321
0.02 !
HGA2
0.09 !
HGA2
0.09 !

C2
O3
C4
*C2
*C2
*C4
*C4
*C5
*C5
*C6
*C6

0.00
0.00
0.00
0.00

120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

C4H8O2 1,3-dioxane

H52

H61 H62
\
\ /
H51--C5---C6
/
\
H42-C4
O1
/ \
/
H41 O3---C2
/ \
H21 H22

C4 C4
H41 C4
H51 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5 C5
H42
H52
-60.00
60.00
60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

C6

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6 O1

NG3P2
HGP2
HGP2
CG324
HGA2
HGA2
CG324
HGA2
HGA2

1.00 ! C5H12N piperidine


!
-0.40 !
0.32 !
0.32 !
C5---C6
H11
0.20 !
/
\ /
0.09 !
C4
(+) N1
0.09 !
\
/ \
0.20 !
C3---C2
H12
0.09 !
0.09 !

CG321
HGA2
HGA2

-0.18 !
0.09
0.09

CG321
HGA2
HGA2

-0.18!
0.09
0.09

CG321
HGA2

-0.18
0.09

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM H52 HGA2


BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

N1
N1
C2
C3
C4
C5
C6

C6
N1
C2
C2
C2
C3
C3
C5
C5
C4
C4
C5
C5
C4
C4

C2
H11
H21
H31
H41
H51
H61

C2
N1
C2
C3
C4
C5
C6

N1
C2
N1
C6
C6
N1
N1
N1
N1
C2
C2
C3
C3
C6
C6

RESI PIPZ
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM H21
ATOM H22
ATOM C6
ATOM H61
ATOM H62
GROUP
ATOM C3
ATOM H31
ATOM H32
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IC
IC
IC
IC

0.09

C6
N1
C2
C2

N1
N1
C2
C3
N4
C5
C6

C2
C3
C6
*N1
*N1
*C2
*C2
*C6
*C6
*C3
*C3
*C4
*C4
*C5
*C5

C3 C3
H12
H22
H32
H42
H52
H62
C3
C4
C5
H11
H12
H21
H22
H61
H62
H31
H32
H41
H42
H51
H52

C4

C4 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5 C6 C6 N1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-60.00
60.00
60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

NG3P2
HGP2
HGP2
CG324
HGA2
HGA2
CG324
HGA2
HGA2

2.00 ! C4H12N2 piperazine


!
-0.76 !
0.50 !
0.50 !
H41
C5---C6
H11
0.20 !
\ /
\ /
0.09 !
N4 (+) (+) N1
0.09 !
/ \
/ \
0.20 !
H42
C3---C2
H12
0.09 !
0.09 !

CG324
HGA2
HGA2
NG3P2
HGP2
HGP2
CG324
HGA2
HGA2

0.20 !
0.09
0.09
-0.76
0.50
0.50
0.20
0.09
0.09

C2
H11
H21
H31
H41
H51
H61
N1
C2
N1
C6

C2
N1
C2
C3
N4
C5
C6
C2
C3
C6
*N1

C3 C3
H12
H22
H32
H42
H52
H62
C3
N4
C5
H11

N4

N4 C5

0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5 C6 C6 N1

0.00 -60.00
0.00 60.00
0.00 60.00
0.00 120.00

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C2
C3
C3
C5
C5
N4
N4
C5
C5
N4
N4

C6
N1
N1
N1
N1
C2
C2
C3
C3
C6
C6

*N1
*C2
*C2
*C6
*C6
*C3
*C3
*N4
*N4
*C5
*C5

H12
H21
H22
H61
H62
H31
H32
H41
H42
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

PATCH FIRST NONE LAST NONE


RESI THPS
GROUP
ATOM S1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52
ATOM C6
ATOM H61
ATOM H62

SG311
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2
CG321
HGA2
HGA2

BOND
BOND
BOND
BOND

C2
H21
H41
H61

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

S1
C2
C3
C6
C3
C3
C4
C4
C5
C5
C6
C6
C5
C5

S1
C2
C4
C6
C2
C3
C4
S1
S1
S1
C2
C2
C3
C3
C4
C4
S1
S1

RESI DITH
GROUP
ATOM S1
ATOM C2
ATOM H21
ATOM H22
ATOM C3

0.00 !
!
-0.24 !
-0.06 !
0.09 !
0.09 !
-0.18 !
0.09 !
0.09 !
-0.18 !
0.09 !
0.09 !
-0.18 !
0.09 !
0.09 !
-0.06 !
0.09 !
0.09 !
C2
C2
C4
C6

C3
C4
C5
C2
*C2
*C2
*C3
*C3
*C4
*C4
*C5
*C5
*C6
*C6

SG311
CG321
HGA2
HGA2
CG321

C5H10S tetrahydro-thiopyran (thiane)


from ethylmethylsulfide (-0.09)

H61 H62
\
\ /
H51--C5---C6
H41 /
\
\ /
\
C4
S1
/ \
/
H42 \
/
H31--C3---C2
/
/ \
H32 H21 H22

C3 C3
H22 C3
H42 C5
H62

H52

C4
C5
C6
C3
H21
H22
H31
H32
H41
H42
H51
H52
H61
H62

C4 C4
H31 C3
H51 C5
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5 C5
H32
H52
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-60.00
60.00
-60.00
60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

C6

C6 S1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C4H8S2 1,4-dithiane


!
-0.22 ! from ethylmethylsulfide (-0.09)
-0.07 !
0.09 ! H52 H61 H62
0.09 !
\
\ /
-0.07 ! H51--C5---C6

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

H31
H32
S4
C5
H51
H52
C6
H61
H62

HGA2
HGA2
SG311
CG321
HGA2
HGA2
CG321
HGA2
HGA2

BOND
BOND
BOND
BOND

S1
C2
C5
C6

C2
H21
H51
H61

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

S1
C2
C3
C6
C3
C3
S4
S4
C6
C6
C5
C5

C2
C3
S4
S1
S1
S1
C2
C2
S4
S4
S1
S1

0.09
0.09
-0.22
-0.07
0.09
0.09
-0.07
0.09
0.09
C2
C2
C5
C6

SG311
CG321
HGA2
HGA2
SG311
CG321
HGA2
HGA2
SG311
CG321
HGA2
HGA2

BOND S1
BOND C2
BOND C6

C2 C2
H21 C2
H61 C6

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

S1
C2
S3
C6
S3
S3
S5
S5
S5
S5

C3 C3
H22 C3
H52
H62

C3
S4
C5
C2
*C2
*C2
*C3
*C3
*C5
*C5
*C6
*C6

RESI TRIT
GROUP
ATOM S1
ATOM C2
ATOM H21
ATOM H22
ATOM S3
ATOM C4
ATOM H41
ATOM H42
ATOM S5
ATOM C6
ATOM H61
ATOM H62

C2
S3
C4
S1
S1
S1
S3
S3
S1
S1

!
/
\
!
/
\
!
S4
S1
!
\
/
!
\
/
! H31--C3---C2
!
/
/ \
! H32 H21 H22
!

S4
C5
C6
C3
H21
H22
H31
H32
H51
H52
H61
H62

S4 S4
H31 C3

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5 C5
H32

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

-60.00
60.00
-60.00
60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

C6 S1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C3H6S3 trithiane135


!
-0.18 !
0.00 !
H61 H62
0.09 !
\ /
0.09 ! H41 S5---C6
-0.18 !
\ /
\
0.00 !
C4
S1
0.09 !
/ \
/
0.09 ! H42 S3---C2
-0.18 !
/ \
0.00 !
H21 H22
0.09 !
0.09 !

S3
C4
S5
C2
*C2
*C2
*C4
*C4
*C6
*C6

S3 S3
H22 C4
H62
C4
S5
C6
S3
H21
H22
H41
H42
H61
H62

C4 C4
H41 C4
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

S5 S5
H42
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

RESI MORP
1.00 ! C4H10NO morpholine
ATOM O1 OG3C61 -0.28 !

60.00
-60.00
60.00
-60.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

C6

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

S1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

C2
H21
H22
C3
H31
H32
N4
H41
H42
C5
H51
H52
C6
H61
H62

CG321
HGA2
HGA2
CG324
HGA2
HGA2
NG3P2
HGP2
HGP2
CG324
HGA2
HGA2
CG321
HGA2
HGA2

BOND
BOND
BOND
BOND

O1
C2
N4
C5

C2
H21
H41
H51

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

O1
C2
C3
C6
C3
C3
N4
N4
C5
C5
C6
C6
C5
C5

-0.04
0.09
0.09
0.20
0.09
0.09
-0.46
0.35
0.35
0.20
0.09
0.09
-0.04
0.09
0.09
C2
C2
N4
C5

C3 C3
H22 C3
H42
H52 C6

C2
C3
N4
O1
O1
O1
C2
C2
C3
C3
N4
N4
O1
O1
TMOR
S1
C2
H21
H22
C3
H31
H32
N4
H41
H42
C5
H51
H52
C6
H61
H62

SG311
CG321
HGA2
HGA2
CG324
HGA2
HGA2
NG3P2
HGP2
HGP2
CG324
HGA2
HGA2
CG321
HGA2
HGA2

BOND
BOND
BOND
BOND

S1
C2
N4
C5

C2
H21
H41
H51

C3
N4
C5
C2
*C2
*C2
*C3
*C3
*N4
*N4
*C5
*C5
*C6
*C6

RESI
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

IC S1

C2

!
! H52 H61 H62
!
\
\ /
! H51--C5---C6
!H41 /
\
! \ /
\
!
N4 (+)
O1
! / \
/
!H42 \
/
! H31--C3---C2
!
/
/ \
! H32 H21 H22
!
!
!

N4
C5
C6
C3
H21
H22
H31
H32
H41
H42
H51
H52
H61
H62

1.00
-0.12
-0.12
0.09
0.09
0.20
0.09
0.09
-0.40
0.32
0.32
0.20
0.09
0.09
-0.12
0.09
0.09
C2
C2
N4
C5

C5 C5
H32

H61 C6

H62

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C6

C6

60.00
-30.00
-30.00
-30.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

O1

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

! C4H10NS thiomorpholine
!
!
! H52 H61 H62
!
\
\ /
! H51--C5---C6
!H41 /
\
! \ /
\
!
N4 (+)
S1
! / \
/
!H42 \
/
! H31--C3---C2
!
/
/ \
! H32 H21 H22
!
!
!

C3 C3
H22 C3
H42
H52 C6
C3

N4 N4
H31 C3

N4

N4 N4
H31 C3

C5 C5
H32

H61 C6

H62

0.0000

0.00

C6

60.00

C6

S1

0.00

0.0000

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C2
C3
C6
C3
C3
N4
N4
C5
C5
C6
C6
C5
C5

RESI MGU1
GROUP
ATOM C
ATOM N1
ATOM H11
ATOM H12
ATOM N2
ATOM H21
ATOM H22
ATOM N3
ATOM C4
e
ATOM H41
ATOM H42
ATOM H43
BOND C
BOND N1
BOND C4
IMPR C
IMPR N1

C3
N4
S1
S1
S1
C2
C2
C3
C3
N4
N4
S1
S1

CG2N1
NG321
HGPAM2
HGPAM2
NG321
HGPAM2
HGPAM2
NG2D1
CG331

N4
C5
C2
*C2
*C2
*C3
*C3
*N4
*N4
*C5
*C5
*C6
*C6

C5
C6
C3
H21
H22
H31
H32
H41
H42
H51
H52
H61
H62

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

-60.00
0.00
0.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C2H7N3 deprotonated methyl-guanidinium


! Ne deprotonated
0.66 !
H11 H12
-0.60 !
\ /
0.29 !
N1
0.29 !
|
-0.60 !
C
H41
0.29 !
/ \\
/
0.29 ! H21-N2 N3--C4-H42
-0.86 !
|
\
-0.03 !
H22
H43 !extra charge on C4 to neutraliz

HGA3
0.09
HGA3
0.09
HGA3
0.09
N1 C N2
C N3
N3 C4
H11 N1 H12 N2 H21 N2 H22
H41 C4 H42 C4 H43
N2 N1 N3
H11 H12 C N2 H21 H22 C

IC N3 C
N1 H11
IC H11 C
*N1 H12
IC N1 N3 *C N2
IC N3 C
N2 H21
IC H21 C
*N2 H22
IC N1 C
N3 C4
IC C
N3 C4 H41
IC H41 N3 *C4 H42
IC H41 N3 *C4 H43
PATC FIRS NONE LAST NONE
RESI MGU2
GROUP
ATOM C
ATOM N1
ATOM H11
ATOM N2
ATOM H21
ATOM H22
ATOM N3
ATOM H31
ATOM C4
ATOM H41
ATOM H42
ATOM H43

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

150.00
-120.00
180.00
150.00
-120.00
180.00
-170.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C2H7N3 deprotonated methyl-guanidinium


! NH1-H12 (outer) deprotonated
CG2N1
0.59 !
NG2D1 -0.91 !
H11
HGP1
0.37 !
\
NG321 -0.60 !
N1
HGPAM2 0.33 !
||
HGPAM2 0.33 !
C
H41
NG311 -0.54 !
/ \
/
HGPAM1 0.36 ! H21-N2 N3--C4-H42
CG331 -0.20 !
| |
\
!carbon charge to neutralize
HGA3
0.09 !
H22 H31 H43
HGA3
0.09
HGA3
0.09

BOND
BOND
BOND
IMPR
IMPR

C
N1
C4
C
N3

N1
H11
H41
N2
C4

C N2
C N3 N3 C4
N2 H21 N2 H22 N3 H31
C4 H42 C4 H43
N1 N3
C H31 N2 H21 H22 C

IC N3 C
N1 H11
IC N1 N3 *C N2
IC N3 C
N2 H21
IC H21 C
*N2 H22
IC N1 C
N3 C4
IC C
C4 *N3 H31
IC C
N3 C4 H41
IC H41 N3 *C4 H42
IC H41 N3 *C4 H43
PATC FIRS NONE LAST NONE

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
150.00
-120.00
-120.00
-120.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

!end adm jr(?), jul2006


!start adm jr(?),
RESI HDZ1
GROUP
ATOM C1 CG331
ATOM H11 HGA3
ATOM H12 HGA3
ATOM H13 HGA3
GROUP
ATOM C2 CG2O1
ATOM O2 OG2D1
ATOM N3 NG2S1
ATOM H3 HGP1
ATOM N4 NG2D1
ATOM C5 CG2D1
ATOM H5 HGA4
ATOM C6 CG331
ATOM H61 HGA3
ATOM H62 HGA3
ATOM H63 HGA3

dec2006
0.00 ! C4H8N2O Hydrazone model compound
!
-0.27 !
0.09 ! C1
H3
0.09 !
\
|
0.09 !
C2--N3
H5
!
//
\
/
0.58 !
O2
N4=C5
-0.49 !
\
-0.34 !
C6
0.31
-0.31
-0.24
0.24
-0.02
0.09
0.09
0.09

BOND C1 H11 C1 H12 C1 H13 C1 C2 C2 O2 C2 N3 N3 H3


BOND N3 N4 C5 H5 C5 C6 C6 H61 C6 H62 C6 H63
BOND N4 C5
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C1
H11
H11
H11
N3
N4
C2
N3
C6
N4
H61
H61

C2
C2
C2
C1
C1
C2
N3
N4
N4
C5
C5
C5

RESI HDZ2 0.00


GROUP
ATOM HG HGR51

N3
*C1
*C1
C2
*C2
*N3
N4
C5
*C5
C6
*C6
*C6

N4
H12
H13
N3
O2
H3
C5
C6
H5
H61
H62
H63

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
120.00
-120.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
120.00
-120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

! C16H13N3O2 Hydrazone containing drug-like molecule


0.14 !

HE3

ATOM CG CG2R51
ATOM CD2 CG2RC0
ATOM CD1 CG2R51
ATOM HD1 HGR52
ATOM NE1 NG2R51
ATOM HE1 HGP1
ATOM CE2 CG2RC0
ATOM CE3 CG2R61
ATOM HE3 HGR61
ATOM CZ2 CG2R61
ATOM CZ3 CG2R61
ATOM HZ3 HGR61
ATOM CH2 CG2R61
ATOM HH2 HGR61
GROUP
ATOM C2 CG2O1
ATOM O2 OG2D1
ATOM N3 NG2S1
ATOM H3 HGP1
ATOM N4 NG2D1
ATOM C5 CG2D1
ATOM H5 HGA4
!
!Phenol moiety: P
!
ATOM CPG CG2R61
GROUP
ATOM CPD1 CG2R61
ATOM HPD1 HGR61
GROUP
ATOM CPD2 CG2R61
ATOM HPD2 HGR61
GROUP
ATOM CPE1 CG2R61
ATOM HPE1 HGR61
GROUP
ATOM CPE2 CG2R61
ATOM HPE2 HGR61
GROUP
ATOM CPZ CG2R61
ATOM OPH OG311
ATOM HPH HGP1

-0.17
0.11
-0.15
0.22
-0.51
0.37
0.24
-0.25
0.17
-0.11
-0.20
0.14
-0.14
0.14
0.58
-0.49
-0.34
0.31
-0.31
-0.24
0.24

!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!

added to
0.25 !
!
-0.115 !
0.115 !
!
-0.115 !
0.115 !
!
-0.115 !
0.115

|
CE3
\
/ \\
CG-----CD2 CZ3-HZ3
||
||
|
CD1
CE2 CH2-HH2
/ \ / \ //
HD1
NE1 CZ2
|
/
HE1 /
/
/
/
___________/
\
\
H3
\
|
C2--N3
H5
//
\
/
O2
N4=C5
\
________________\
|
atom names to avoid conflicts with indole
|
| HPD1 HPE1
|
|
|
| CPD1--CPE1
| //
\\
|--CPG
CPZ--OPH
\
/
\
CPD2==CPE2
HPH
|
|
HPD2 HPE2
HG

-0.115
0.115
0.11
-0.53
0.42

!indole section
BOND CG HG CD2 CG NE1 CD1 CZ2 CE2
BOND CZ3 CH2 CD2 CE3 NE1 CE2
BOND CD1 HD1 NE1 HE1 CE3 HE3
BOND CZ3 HZ3 CH2 HH2
BOND CD1 CG CE2 CD2 CH2 CZ2 CZ3 CE3
BOND CZ2 C2
BOND C2 O2 C2 N3 N3 H3 N3 N4 C5 H5
BOND N4 C5 C5 CPG
BOND CPD2 CPG CPE1 CPD1 CPZ CPE2
BOND CPD1 HPD1 CPD2 HPD2 CPE1 HPE1
BOND CPE2 HPE2 CPZ OPH OPH HPH
BOND CPD1 CPG CPE2 CPD2 CPZ CPE1
IC CG
180.0
IC CD2

CD1

NE1

CE2

0.0000

0.00

0.00

0.00

0.0000 !dihe from

HG

*CG

CD1

0.0000

0.00 180.00

0.00

0.0000

IC HG
IC NE1
IC CE2
IC CE2
IC CG
IC CZ3
IC CD2
IC CD2
180.0
IC CH2
IC CZ2
IC CH2
IC CE2
IC N3
IC CZ2
IC N4
IC C2
IC N3
IC CPG
IC N4
IC CPD1
IC C5
IC CPE1
IC C5
IC CPE2
IC CPG
80.0
IC CPZ
IC CPZ
IC CPE2
IC CPE1
!end adm

CG
CG
CD1
CG
CD2
CD2
NE1
CE3

CD1
*CD1
*NE1
*CD2
CE3
*CE3
*CE2
CZ3

NE1
HD1
HE1
CE3
CZ3
HE3
CZ2
CH2

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000 !dihe from

CE3
CZ3
CE2
CZ2
CZ2
C2
C2
N3
N4
N4
C5
C5
CPG
CPG
CPG
CPG
CPD1

*CZ3
*CH2
*CZ2
C2
*C2
N3
*N3
N4
C5
*C5
CPG
*CPG
CPD1
*CPD1
CPD2
*CPD2
CPE1

HZ3
HH2
C2
N3
O2
N4
H3
C5
CPG
H5
CPD1
CPD2
CPE1
HPD1
CPE2
HPD2
CPZ

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
0.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000 !dihe from 1

CPD1 *CPE1 HPE1


CPD2 *CPE2 HPE2
CPE1 *CPZ OPH
CPZ OPH HPH
jr(?), dec2006

0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00

180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

0.00
0.00

0.0000
0.0000

!Continuation of
RESI INDZ
GROUP
ATOM C1 CG2R51
ATOM H1 HGR51
ATOM C2 CG2R51
ATOM H2 HGR51
ATOM C3 CG2R51
ATOM H3 HGR52
ATOM N4 NG2RC0
ATOM C5 CG2R61
ATOM H5 HGR62
ATOM C6 CG2R61
ATOM H6 HGR61
ATOM C7 CG2R61
ATOM H7 HGR61
ATOM C8 CG2R61
ATOM H8 HGR61
ATOM C9 CG2RC0

Maybridge list, kevo, dec2006


0.00 ! C8H7N indolizine, kevo

BOND
BOND
BOND
BOND

C3
C6
H2
H6

IC C9
IC C1

C1
N4
C1
C5

C2
C5
H1
H5
C1
C2

C2
C5
C2
C6

-0.28
0.23
-0.23
0.19
0.07
0.14
-0.28
-0.10
0.24
-0.14
0.17
-0.15
0.18
-0.22
0.24
-0.06

C2
C3

C3
C6
C3
C7
C3
N4

!
!
!
!
!
!
!
!
!
!
!

H5
|
C5

H3
\

/ \\
C3----N4
C6-H6
||
|
|
C2
C9
C7-H7
/ \ // \ //
H2
C1
C8
|
|
H1
H8

N4 N4 C9 C9 C1
C7 C7 C8 C8 C9
H3
H7 C8 H8
0.0000
0.0000

0.00
0.00

0.00
0.00

IC C3
N4
C5
C6
IC N4
C5
C6
C7
IC C5
C6
C7
C8
IC C2
C9
*C1 H1
IC C3
C1
*C2 H2
IC N4
C2
*C3 H3
IC C9
C3
*N4 C5
IC C6
N4
*C5 H5
IC C7
C5
*C6 H6
IC C8
C6
*C7 H7
IC C9
C7
*C8 H8
PATCH FIRST NONE LAST NONE
RESI ISOI
GROUP
ATOM HG
ATOM CG
ATOM CD2
ATOM ND1
ATOM HD1
ATOM CE1
ATOM HE1
ATOM CE2
ATOM CE3
ATOM HE3
ATOM CZ2
ATOM HZ2
ATOM CZ3
ATOM HZ3
ATOM CH2
ATOM HH2

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

180.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00 ! C8H7N isoindole, kevo


HGR52
CG2R51
CG2RC0
NG2R51
HGP1
CG2R51
HGR52
CG2RC0
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61

0.15
-0.16
0.17
-0.29
0.35
-0.16
0.15
0.17
-0.36
0.23
-0.36
0.23
-0.30
0.24
-0.30
0.24

!
!
!
!
!
!
!
!
!
!
!

HE3
|
HG
CE3
\ _____ / \\
CG-----CD2 CZ3-HZ3
|
|
|
ND1
CE2 CH2-HH2
/ \ // \ //
HD1
CE1 CZ2
|
|
HE1 HZ2

BOND CD2 CE2


BOND CE1 ND1 ND1 CG
BOND CD2 CE3 CZ3 CH2 CZ2 CE2
BOND CE1 HE1 ND1 HD1 CG HG
BOND CE3 HE3 CZ3 HZ3 CH2 HH2 CZ2 HZ2
DOUBLE CE2 CE1 CG CD2 CE3 CZ3 CH2 CZ2
DONOR HD1 ND1
IC CG ND1
IC ND1 CG
IC CD2 CG
IC CE2 CG
IC CE2 CD2
IC CD2 CE3
IC CE3 CZ3
IC CZ3 CD2
IC CH2 CE3
IC CZ2 CZ3
IC CE2 CH2
IC ND1 CE2
IC CG CE1
IC ND1 CD2
PATCH FIRST

CE1 CE2 0.0000


CD2 CE2 0.0000
ND1 CE1 0.0000
*CD2 CE3 0.0000
CE3 CZ3 0.0000
CZ3 CH2 0.0000
CH2 CZ2 0.0000
*CE3 HE3 0.0000
*CZ3 HZ3 0.0000
*CH2 HH2 0.0000
*CZ2 HZ2 0.0000
*CE1 HE1 0.0000
*ND1 HD1 0.0000
*CG HG
0.0000
NONE LAST NONE

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00
180.00

RESI INDA
0.00 ! C7H6N2 1H-indazole, kevo
GROUP
ATOM N1 NG2R51 -0.05 !
H5
ATOM H1 HGP1
0.28 !
|

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

N2
C3
H3
C4
C5
H5
C6
H6
C7
H7
C8
H8
C9

NG2R50
CG2R52
HGR52
CG2RC0
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2RC0

-0.60
0.28
0.09
-0.11
-0.43
0.30
-0.38
0.28
-0.26
0.24
-0.20
0.15
0.41

!
!
!
!
!
!
!
!
!

H3

BOND C3 H3 C4 C3 N1 N2
BOND C8 C9
BOND C6 C7 C4 C5 N1 C9
BOND N1 H1 C5 H5 C6 H6
BOND C7 H7 C8 H8
DOUBLE N2 C3 C9 C4 C7 C8 C6
DONOR H1 N1
IC C3 N2 N1 C9
0.0000
IC N1 N2 C3 C4
0.0000
IC N2 C3 C4 C9
0.0000
IC C9 C3 *C4 C5
0.0000
IC C9 C4 C5 C6
0.0000
IC C4 C5 C6 C7
0.0000
IC C5 C6 C7 C8
0.0000
IC C6 C4 *C5 H5
0.0000
IC C7 C5 *C6 H6
0.0000
IC C8 C6 *C7 H7
0.0000
IC C9 C7 *C8 H8
0.0000
IC N2 C9 *N1 H1
0.0000
IC N2 C4 *C3 H3
0.0000
PATCH FIRST NONE LAST NONE
RESI ZIMI
GROUP
ATOM N1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C5
ATOM H5
ATOM C6
ATOM H6
ATOM C7
ATOM H7
ATOM C8
ATOM H8
ATOM C9

C5
/ \\
C3-----C4
C6 -H6
||
||
|
N2
C9
C7 -H7
\ / \ //
N1
C8
|
|
H1
H8

C5
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00 ! C7H6N2 benzimidazole, kevo


NG2R51
HGP1
CG2R53
HGR52
NG2R50
CG2RC0
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2R61
HGR61
CG2RC0

-0.28
0.31
0.24
0.14
-0.72
0.45
-0.35
0.23
-0.19
0.20
-0.34
0.24
-0.32
0.22
0.17

!
!
!
!
!
!
!
!
!
!
!

H5
|
C5
/ \\
N3----C4
C6 -H6
||
||
|
C2
C9
C7 -H7
/ \ / \ //
H2
N1
C8
|
|
H1
H8

BOND N1 H1 C2 H2
BOND C5 H5 C6 H6 C7 H7 C8 H8
BOND C9 N1 N1 C2 N3 C4
BOND C4 C5 C6 C7 C8 C9
DOUBLE C2 N3 C4 C9 C5 C6 C7 C8
DONOR H1 N1

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC N3 C2
IC N1 C2
IC C2 N3
IC C9 N3
IC C9 C4
IC C4 C5
IC C5 C6
IC C6 C4
IC C7 C5
IC C8 C6
IC C9 C7
IC C2 C9
IC N3 N1
PATCH FIRST

N1
N3
C4
*C4
C5
C6
C7
*C5
*C6
*C7
*C8
*N1
*C2
NONE

C9
0.0000
C4
0.0000
C9
0.0000
C5
0.0000
C6
0.0000
C7
0.0000
C8
0.0000
H5
0.0000
H6
0.0000
H7
0.0000
H8
0.0000
H1
0.0000
H2
0.0000
LAST NONE

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
0.00
0.00
180.00
0.00
0.00
0.00
180.00
180.00
180.00
180.00
180.00
180.00

RESI 2HPR
GROUP
ATOM N1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5

NG2R50 -0.72 ! H5
CG3C52 0.45 !
\ ____
HGA2
0.09 !
C5----N1 H21
HGA2
0.09 !
|
\ /
CG2R51 -0.75 !
|
C2
HGR51
0.33 !
|____ / \
CG2R51 0.05 !
C4----C3 H22
HGR51
0.15 !
/
\
CG2R52 0.20 ! H4
H3
HGR52
0.11

BOND C2
BOND N1
DOUBLE C3
IC C2
IC C3
IC C3
IC C3
IC C4
IC C5
IC N1

H21
C2
C4
C3
C4
N1
N1
C2
C3
C4

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C4H5N 2H-pyrrole, kevo

C2
C2
C5
C4
C5
*C2
*C2
*C3
*C4
*C5

H22
C3
N1
C5
N1
H21
H22
H3
H4
H5

RESI 2PRL
GROUP
ATOM N1
ATOM H1
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52

NG3C51
HGP1
CG2R51
HGR52
CG2R51
HGR51
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2

BOND N1
BOND C4
BOND N1
DOUBLE C2
IC N1
IC C2

H1
H41
C2
C3
C2
C3

C3
C4

H3
C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H4

C5

0.00
0.00
120.00
240.00
180.00
180.00
180.00

H5
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00

0.0000
0.0000

0.000 ! C4H7N 2-pyrroline, kevo


-0.60
0.32
-0.01
0.17
-0.36
0.20
-0.10
0.09
0.09
0.02
0.09
0.09

! H3
H41 H42
! \
| /
!
C3----C4
!
||
|
!
C2
C5--H51
! / \ / \
! H2
N1
H52
!
|
!
H1

C2
C4
C3

H2 C3
H42 C5
C4 C4

C3
C4

C4
C5

H3
H51 C5
C5 C5

0.0000
0.0000

0.00
0.00

H52
N1
0.00
20.00

IC
IC
IC
IC
IC
IC
IC

C2
C3
C4
C5
C5
N1
N1

C5
N1
C2
C3
C3
C4
C4

*N1
*C2
*C3
*C4
*C4
*C5
*C5

H1
H2
H3
H41
H42
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00

120.00
180.00
180.00
120.00
240.00
120.00
240.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI 2PRZ
0.000 ! C3H6N2 2-pyrazoline, kevo
GROUP
ATOM N1 NG3C51 -0.46
ATOM H1 HGP1
0.34 ! H3
H41 H42
ATOM N2 NG2R50 -0.49 ! \
| /
ATOM C3 CG2R52 0.32 !
C3----C4
ATOM H3 HGR52
0.06 !
||
|
ATOM C4 CG3C52 -0.15 !
N2
C5--H51
ATOM H41 HGA2
0.09 !
\ / \
ATOM H42 HGA2
0.09 !
N1
H52
ATOM C5 CG3C52 0.02 !
|
ATOM H51 HGA2
0.09 !
H1
ATOM H52 HGA2
0.09
!H[45][12] constrained at +0.09, pre1g
BOND N1
BOND C4
BOND N1
DOUBLE N2
IC N1
IC N2
IC N2
IC C4
IC C5
IC C5
IC N1
IC N1

H1
H41
N2
C3
N2
C3
C5
N2
C3
C3
C4
C4

C3
C4
C3

H3
H42 C5
C4 C4

C3
C4
*N1
*C3
*C4
*C4
*C5
*C5

C4
C5
H1
H3
H41
H42
H51
H52

H51 C5
C5 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H52
N1
0.00
20.00
120.00
180.00
120.00
240.00
120.00
240.00

RESI 2IMI
GROUP
ATOM N1
ATOM H1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52

NG3C51 -0.68
HGP1
0.32 !
H41 H42
CG2R53 0.61 !
| /
HGR52
0.06 !
N3----C4
NG2R50 -0.79 !
||
|
CG3C52 0.12 !
C2
C5--H51
HGA2
0.09 ! / \ / \
HGA2
0.09 ! H2
N1
H52
CG3C52 0.00 !
|
HGA2
0.09 !
H1
HGA2
0.09

BOND N1
BOND C4
BOND N1
DOUBLE C2
IC N1
IC C2
IC C2
IC N3
IC C5
IC C5

H1
H41
C2
N3
C2
N3
C5
N1
N3
N3

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.000 ! C3H6N2 2-imidazoline, kevo

C2
C4
N3

H2
H42 C5
C4 C4

N3
C4
*N1
*C2
*C4
*C4

C4
C5
H1
H2
H41
H42

H51 C5
C5 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00

H52
N1
0.00
20.00
120.00
180.00
120.00
240.00

0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

IC N1 C4 *C5 H51 0.0000


0.00 120.00
0.00
IC N1 C4 *C5 H52 0.0000
0.00 240.00
0.00
!end continuation of Maybridge list, kevo, dec2006
!Continuation of
RESI PRLD
GROUP
ATOM N1 NG3C51
ATOM H1 HGP1
ATOM C2 CG3C52
ATOM H21 HGA2
ATOM H22 HGA2
ATOM C3 CG3C52
ATOM H31 HGA2
ATOM H32 HGA2
ATOM C4 CG3C52
ATOM H41 HGA2
ATOM H42 HGA2
ATOM C5 CG3C52
ATOM H51 HGA2
ATOM H52 HGA2
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

N1
N1
C4
C2
C3
C2
C4
C4
C3
C3
N1
N1
N1
N1

RESI 3PRL
GROUP
ATOM N1
ATOM H1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H51
ATOM H52
BOND N1
BOND C3
BOND N1
DOUBLE C3
IC C2
IC C3
IC C2
IC C4

C2
H1
H41
C3
C4
C5
C2
C2
C5
C5
C3
C3
C4
C4

0.0000
0.0000

Maybridge list, kevo, may2007


0.000 ! C4H9N pyrrolidine, kevo

C2
C2
C4
C4
C5
*N1
*C3
*C3
*C4
*C4
*C2
*C2
*C5
*C5

-0.86
0.36
0.10
0.09
0.09
-0.21
0.09
0.09
-0.21
0.09
0.09
0.10
0.09
0.09
C3
H21
H42
C5
N1
H1
H31
H32
H41
H42
H21
H22
H51
H52

!
!
!
!
!
!
!
!
!

H32

H42
\
/
H31--C3----C4--H41
|
|
H21--C2
C5--H51
/ \ / \
H22
N1
H52
|
H1

C3 C4
C2 H22
C5 H51
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C4
C3
C5
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

C5 C5
H31 C3
H52
10.00
15.00
120.00
-120.00
120.00
120.00
-120.00
120.00
-120.00
-120.00
120.00

N1
H32
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000

0.000 ! C4H7N 3-pyrroline, kevo


NG3C51 -0.89
HGP1
0.37 ! H3
H4
CG3C52 0.17 !
\ ____ /
HGA2
0.09 !
C3----C4
HGA2
0.09 !
|
|
CG2R51 -0.28 ! H21--C2
C5--H52
HGR51
0.19 !
/ \ / \
CG2R51 -0.28 ! H22
N1
H51
HGR51
0.19 !
|
CG3C52 0.17 !
H1
HGA2
0.09
HGA2
0.09
H1
H3
C2

C2
C4
C2

H21 C2
H4 C5
C3 C4

C4
C5
*N1
*C3

C5
N1
H1
H3

H22
H51 C5
C5 C5

H52
N1

C4
C3
C4
C5
C2

0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00 20.00
0.00 120.00
0.00 180.00

IC
IC
IC
IC
IC

C3
N1
N1
N1
N1

C5
C3
C3
C4
C4

*C4
*C2
*C2
*C5
*C5

RESI PRLP
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H31
ATOM H32
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52

NG3P2
HGP2
HGP2
CG3C54
HGA2
HGA2
CG3C52
HGA2
HGA2
CG3C52
HGA2
HGA2
CG3C54
HGA2
HGA2

BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H11
H32
C2
C3
C4
C5
C5
C2
C2
C5
C5
C3
C3
C4
C4

N1
C3
N1
C2
C3
C2
C2
C4
C4
C3
C3
N1
N1
N1
N1

0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00

180.00
120.00
240.00
120.00
240.00

0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000

1.000 ! C4H10N pyrrolidine protonated, kevo


-0.22
0.34
0.34
-0.35
0.28
0.28
-0.12
0.09
0.09
-0.12
0.09
0.09
-0.35
0.28
0.28

N1
C4
C2
C4
C5
*N1
*N1
*C3
*C3
*C4
*C4
*C2
*C2
*C5
*C5

RESI 3PRP
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H51
ATOM H52

NG3P2
HGP2
HGP2
CG3C54
HGA2
HGA2
CG2R51
HGR51
CG2R51
HGR51
CG3C54
HGA2
HGA2

BOND
BOND
BOND
BOND

H11 N1
H3 C4
C2 C2
C4

N1
C3
N1
C3

H4
H21
H22
H51
H52

H12
H41
C3
C5
N1
H11
H12
H31
H32
H41
H42
H21
H22
H51
H52

!
!
!
!
!
!
!
!
!

H32

H42
\
/
H31--C3----C4--H41
|
|
H21--C2
C5--H51
/ \ / \
H22
N1(+) H52
/ \
H11
H12

C2 H21
C4 H42
C3 C4
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C2
C5
C4
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H22 C3
H51 C5
C5 C5
40.00
330.00
120.00
240.00
240.00
120.00
120.00
240.00
120.00
240.00
240.00
120.00

H31
H52
N1
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.000 ! C4H8N 3-pyrroline protonated, kevo


-0.40
0.39
0.39
-0.17
0.28
0.28
-0.33
0.25
-0.33
0.25
-0.17
0.28
0.28

! H3
H4
!
\ ____ /
!
C3----C4
!
|
|
! H21--C2
C5--H51
!
/ \ / \
! H22
N1(+) H52
!
/ \
!
H11
H12

H12 C2
H4 C5
C3 C4

H21 C2
H51 C5
C5 C5

H22
H52
N1

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C2
C3
C5
C5
C4
C3
N1
N1
N1
N1

C3
C4
C2
C2
C2
C5
C3
C3
C4
C4

C4
C5
*N1
*N1
*C3
*C4
*C2
*C2
*C5
*C5

RESI 2PRP
GROUP
ATOM N1
ATOM H11
ATOM H12
ATOM C2
ATOM H2
ATOM C3
ATOM H3
ATOM C4
ATOM H41
ATOM H42
ATOM C5
ATOM H51
ATOM H52

NG3P2
HGP2
HGP2
CG2R51
HGR52
CG2R51
HGR51
CG3C52
HGA2
HGA2
CG3C54
HGA2
HGA2

BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

H11
H41
C2
C3
C2
C3
C5
C5
N1
C2
C3
C3
C4
C4

N1
C4
N1
C2
N1
C2
C2
C2
C3
C4
C5
C5
N1
N1

C5
N1
H11
H12
H3
H4
H21
H22
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
20.00
120.00
240.00
180.00
180.00
120.00
240.00
240.00
120.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.000 ! C4H8N 2-pyrroline protonated, kevo


-0.13
0.33
0.33
-0.18
0.22
-0.06
0.20
-0.12
0.09
0.09
-0.33
0.28
0.28

! H3
H41 H42
! \
| /
!
C3----C4
!
||
|
!
C2
C5--H51
! / \ / \
! H2
N1(+) H52
!
/ \
! H11
H12

N1
C4
C3

H12 C2
H42 C5
C4 C4

C3
C4
*N1
*N1
*C2
*C3
*C4
*C4
*C5
*C5

C4
C5
H11
H12
H2
H3
H41
H42
H51
H52

H2 C3
H51 C5
C5 C5

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

H3
H52
N1
0.00
20.00
120.00
240.00
180.00
180.00
120.00
240.00
120.00
240.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

RESI 2IMP
1.000 ! C3H7N2 2-imidazoline protonated, kevo
GROUP
ATOM N1 NG2R52 -0.35
ATOM H1 HGP2
0.38
ATOM C2 CG2R53 0.52 ! H3
H41 H42
ATOM H2 HGR53
0.12 !
\
| /
ATOM N3 NG2R52 -0.35 ! (+) N3----C4
ATOM H3 HGP2
0.38 !
||
|
ATOM C4 CG3C54 -0.41 !
C2
C5--H51
ATOM H41 HGA2
0.28 !
/ \ / \
ATOM H42 HGA2
0.28 ! H2
N1
H52
ATOM C5 CG3C54 -0.41 !
|
ATOM H51 HGA2
0.28 !
H1
ATOM H52 HGA2
0.28
!H[2-5][12] constrained, pre1g
BOND N1
BOND C4

H1 C2
H41 C4

H2 N3
H42 C5

H3
H51 C5

H52

BOND N1
DOUBLE C2
IC N1
IC C2
IC C2
IC N3
IC C4
IC C5
IC C5
IC N1
IC N1
RESI 2HPP
GROUP
ATOM N1
ATOM H1
ATOM C2
ATOM H21
ATOM H22
ATOM C3
ATOM H3
ATOM C4
ATOM H4
ATOM C5
ATOM H5
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
!End

C2

N3

C4

C4

C5

N3
C4
*N1
*C2
*N3
*C4
*C4
*C5
*C5

C4
C5
H1
H2
H3
H41
H42
H51
H52

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

C5

N1

N3
C2
N3
C5
N1
C2
N3
N3
C4
C4

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.00
-12.00
180.00
180.00
180.00
120.00
240.00
120.00
240.00

0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00

0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

1.000 ! C4H6N 2H-pyrrole protonated, kevo


NG2R52
HGP2
CG3C54
HGA2
HGA2
CG2R51
HGR51
CG2R51
HGR51
CG2R52
HGR52

-0.27
0.39
-0.19
0.28
0.28
-0.08
0.25
-0.27
0.25
0.07
0.29

! H5
H1
!
\ ____ /
!
C5----N1 H21
!
| (+) \ /
!
|
C2
!
|____ / \
!
C4----C3 H22
!
/
\
! H4
H3

N1 H1 C2 H21 C2 H22 C3 H3 C4 H4 C5
N1 C2 C2 C3 C3 C4 C4 C5 C5 N1
C2 C3 C4 C5 0.0000
0.00
0.00
0.00
C3 C4 C5 N1 0.0000
0.00
0.00
0.00
C2 C5 *N1 H1 0.0000
0.00 180.00
0.00
C3 N1 *C2 H21 0.0000
0.00 120.00
0.00
C3 N1 *C2 H22 0.0000
0.00 240.00
0.00
C4 C2 *C3 H3 0.0000
0.00 180.00
0.00
C5 C3 *C4 H4 0.0000
0.00 180.00
0.00
N1 C4 *C5 H5 0.0000
0.00 180.00
0.00
continuation of Maybridge list, kevo, may2007

H5
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000

!Bile acids and related compounds, chayan, jul2006


RESI BAM1
0.00 ! C13H24 Bile Acid Model cmpd 1, chayan (to estimate di
hedral rotational surface energy)
GROUP
ATOM C12
ATOM H12A
ATOM H12B
GROUP
ATOM C11
ATOM H11A
ATOM H11B
GROUP
ATOM C9
ATOM H9A
ATOM H9B
GROUP
ATOM C8
ATOM H8A
ATOM H8B
GROUP
ATOM C14

CG321
HGA2
HGA2
CG321
HGA2
HGA2

-0.18
0.09
0.09

-0.18 !
0.09 !
0.09 !
!
CG321 -0.18 !
HGA2
0.09 !
HGA2
0.09 !
!
CG321 -0.18 !
HGA2
0.09 !
HGA2
0.09 !
!
CG3RC1 -0.09

C21
|
C12 C18 C20--C22
/ \ | |
C11 C13--C17
|
|
|
C9 C14 C16
\ / \ /
C8 C15
Model Compound

ATOM H14
GROUP
ATOM C13
GROUP
ATOM C15
ATOM H15A
ATOM H15B
GROUP
ATOM C16
ATOM H16A
ATOM H16B
GROUP
ATOM C17
ATOM H17
GROUP
ATOM C18
ATOM H18A
ATOM H18B
ATOM H18C
GROUP
ATOM C20
ATOM H20
GROUP
ATOM C21
ATOM H21A
ATOM H21B
ATOM H21C
GROUP
ATOM C22
ATOM H22A
ATOM H22B
ATOM H22C

HGA1

0.09

CG3RC1

0.00

BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND
BOND

H12A
C11
C9
C8
C14
C15
C16
C17
C13
C18
C20
C21
C22

!
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C12
C12
C11
C9
C8
C14
C15
C16
C17
C13
C17
C20
C20

C12
C11
C9
C8
C14
C15
C16
C8
C8
C14
C13

CG3C52 -0.18
HGA2
0.09
HGA2
0.09
CG3C52 -0.18
HGA2
0.09
HGA2
0.09
CG3C51 -0.09
HGA1
0.09
CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG311
HGA1

-0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

CG331
HGA3
HGA3
HGA3

-0.27
0.09
0.09
0.09

C11
C9
C8
C14
C15
C16
C17
C14
C14
C13
C8

C12
C11
C9
C8
C14
C15
C16
C17
C13
C18
C20
C21
C22

C9
C8
C14
C15
C16
C17
C13
C13
C13
C12
*C14

H12B
H11A
H9A
H8A
H14
H15A
H16A
H17
C12
H18A
H20
H21A
H22A
C8
C14
C15
C16
C17
C13
C12
C12
C17
C11
C15

C11
C9
C8
C14
C15
C16

H11B
H9B
H8B
C13
H15B
H16B

C18 H18B C18 H18C


C21 H21B C21 H21C
C22 H22B C22 H22C

R(I(J/K))
1.5465
1.5370
1.5369
1.5301
1.5242
1.5463
1.5545
1.5301
1.5301
1.5400
1.5400

T(I(JK/KJ)) PHI
113.07 53.26
111.97 -54.31
108.19 179.63
117.07 -157.35
103.25 -1.62
106.76 32.90
98.76 -165.58
113.89 -59.62
113.89 -179.99
108.36 54.13
113.89 120.29

T(JKL)
111.97
108.19
117.07
103.25
106.76
98.76
115.64
108.36
97.80
111.30
117.07

R(KL)
1.5369
1.5301
1.5242
1.5463
1.5545
1.5707
1.5392
1.5392
1.5707
1.5465
1.5242

IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC

C17
C14
H8A
C8
H9A
C9
H11A
C14
H12A
C13
C16
H15A
C17
H16A
C13
C12
C14
H18A
H18A
C13
C16
C22
C21
C17
H21A
H21A
C17
H22A
H22A

RESI CA
GROUP
ATOM C3
ATOM O3
ATOM H3'
ATOM H3
GROUP
ATOM C4
ATOM H4A
ATOM H4B
GROUP
ATOM C5
ATOM H5
GROUP
ATOM C6
ATOM H6A
ATOM H6B

C14
C9
C9
C11
C11
C12
C12
C13
C13
C8
C14
C14
C15
C15
C16
C14
C13
C13
C13
C16
C17
C17
C17
C20
C20
C20
C20
C20
C20

*C13
*C8
*C8
*C9
*C9
*C11
*C11
C12
*C12
*C14
*C15
*C15
*C16
*C16
*C17
*C13
C18
*C18
*C18
*C17
C20
*C20
*C20
C21
*C21
*C21
C22
*C22
*C22

C12
H8A
H8B
H9A
H9B
H11A
H11B
H12A
H12B
H14
H15A
H15B
H16A
H16B
H17
C18
H18A
H18B
H18C
C20
C22
C21
H20
H21A
H21B
H21C
H22A
H22B
H22C

1.5707
1.5301
1.1090
1.5369
1.1138
1.5370
1.1127
1.5400
1.1064
1.5400
1.5463
1.0999
1.5545
1.0991
1.5707
1.5392
1.5400
1.1059
1.1059
1.5707
1.5545
1.5428
1.5383