-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathvdw.dat
143 lines (143 loc) · 8.9 KB
/
vdw.dat
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
H 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
h3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963
h4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor
h5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor
ha 1.4590 0.0150 Spellmeyer
hc 1.4870 0.0157 OPLS
hn 0.6000 0.0157 !Ferguson base pair geom.
ho 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657
hp 0.6000 0.0157 same to hs (be careful !)
hs 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
hw 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657
hx 1.1000 0.0157 Veenstra et al JCC,8,(1992),963
o 1.6612 0.2100 OPLS
OD 1.6612 0.2100 alias for o
OU 1.6612 0.2100 alias for o
D1 1.6612 0.2100 alias for o
D2 1.6612 0.2100 alias for o
D3 1.6612 0.2100 alias for o
D4 1.6612 0.2100 alias for o
D5 1.6612 0.2100 alias for o
D6 1.6612 0.2100 alias for o
D7 1.6612 0.2100 alias for o
D8 1.6612 0.2100 alias for o
D9 1.6612 0.2100 alias for o
DA 1.6612 0.2100 alias for o
DB 1.6612 0.2100 alias for o
DC 1.6612 0.2100 alias for o
DD 1.6612 0.2100 alias for o
oh 1.7210 0.2104 OPLS
os 1.6837 0.1700 OPLS ether
ow 1.7683 0.1520 TIP3P water model
c 1.9080 0.0860 OPLS
c1 1.9080 0.2100 cp C DLM 11/2007 well depth from OPLS replacing 0.0860
c2 1.9080 0.0860 sp2 atom in the middle of C=CD-CD=C
c3 1.9080 0.1094 OPLS
ca 1.9080 0.0860 OPLS
CB 1.9080 0.0860 OPLS
CC 1.9080 0.0860 OPLS
CD 1.9080 0.0860 OPLS
cc 1.9080 0.0860 OPLS
cd 1.9080 0.0860 OPLS
ce 1.9080 0.0860 OPLS
cf 1.9080 0.0860 OPLS
cg 1.9080 0.2100 DLM 12/2007 as c1
ch 1.9080 0.2100 DLM 12/2007 as c1
cp 1.9080 0.0860 OPLS
cq 1.9080 0.0860 OPLS
cu 1.9080 0.0860 OPLS
cv 1.9080 0.0860 OPLS
cx 1.9080 0.0860 OPLS
cy 1.9080 0.0860 OPLS
cz 1.9080 0.0860 OPLS
n 1.8240 0.1700 OPLS
n1 1.8240 0.1700 OPLS
n2 1.8240 0.1700 OPLS
n3 1.8240 0.1700 OPLS
NT 1.8240 0.1700 OPLS
n4 1.8240 0.1700 OPLS
na 1.8240 0.1700 OPLS
nb 1.8240 0.1700 OPLS
nc 1.8240 0.1700 OPLS
nd 1.8240 0.1700 OPLS
ne 1.8240 0.1700 OPLS
nf 1.8240 0.1700 OPLS
nh 1.8240 0.1700 OPLS
no 1.8240 0.1700 OPLS
s 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
s2 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
s4 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
s6 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
sx 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
sy 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
sh 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
ss 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
p2 2.1000 0.2000 JCC,7,(1986),230;
p3 2.1000 0.2000 JCC,7,(1986),230;
p4 2.1000 0.2000 JCC,7,(1986),230;
p5 2.1000 0.2000 JCC,7,(1986),230;
pb 2.1000 0.2000 JCC,7,(1986),230;
pc 2.1000 0.2000 JCC,7,(1986),230;
pd 2.1000 0.2000 JCC,7,(1986),230;
pe 2.1000 0.2000 JCC,7,(1986),230;
pf 2.1000 0.2000 JCC,7,(1986),230;
px 2.1000 0.2000 JCC,7,(1986),230;
py 2.1000 0.2000 JCC,7,(1986),230;
f 1.75 0.061 Gough et al. JCC 13,(1992),963.
cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3
br 2.02 0.420 Junmei, 2010
i 2.15 0.50 Junmei, 2010
H 0.6000 0.0157 !Ferguson base pair geom.
HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657
HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
HC 1.4870 0.0157 OPLS
H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963
HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963
HA 1.4590 0.0150 Spellmeyer
H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor
H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor
HW 0.0000 0.0000 TIP3P water model
HZ 1.4590 0.0150 H bonded to sp C (Howard et al JCC 16)
O 1.6612 0.2100 OPLS
O2 1.6612 0.2100 OPLS
OW 1.7683 0.1520 TIP3P water model
OH 1.7210 0.2104 OPLS
OS 1.6837 0.1700 OPLS ether
OP 1.8500 0.1700 Steinbrecher/Latzer for 2- phosphate
C* 1.9080 0.0860 Spellmeyer
CI 1.9080 0.1094 parmbsc0
C5 1.9080 0.0860 Spellmeyer
C4 1.9080 0.0860 Spellmeyer
CT 1.9080 0.1094 Spellmeyer
CX 1.9080 0.1094 Spellmeyer (was CT)
C 1.9080 0.0860 OPLS
N 1.8240 0.1700 OPLS
N3 1.8240 0.1700 OPLS
S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
P 2.1000 0.2000 JCC,7,(1986),230;
MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)
F 1.75 0.061 Gough et al. JCC 13,(1992),963.
Cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3
Br 2.22 0.320 Junmei(?)
I 2.35 0.40 JCC,7,(1986),230;
EP 0.00 0.0000 lone pair
B 1.9800 0.0340 Added by HH (temporary) from A. Tafi et al. / European Journal of Medicinal Chemistry 40 (2005) 1134-1142
DU 1.4590 0.0150 Added by HH (temporary) for hydrogen (ha)
Si 2.1350 0.3100 Added by HH (temporary) for Vibert et al Si Chem. Sci., 2014, 5, 4716
Cu 1.409 0.01721000 IOD Cu2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Zn 1.395 0.01491700 IOD Zn2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Zn1 1.395 0.01491700 IOD Zn2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Zn2 1.395 0.01491700 IOD Zn2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Zn3 1.395 0.01491700 IOD Zn2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Zn4 1.395 0.01491700 IOD Zn2+: Li,PF; Merz,Jr; JCTC2013 DOI:10.1021/ct400146w
Al 1.297 0.00471279 Al3+ For TIP3P/IOD: Li,PF; Merz,Jr; JPCB DOI:10.1021/jp505875v Table3
Al1 1.297 0.00471279 Al3+ For TIP3P/IOD: Li,PF; Merz,Jr; JPCB DOI:10.1021/jp505875v Table3
Al2 1.297 0.00471279 Al3+ For TIP3P/IOD: Li,PF; Merz,Jr; JPCB DOI:10.1021/jp505875v Table3
Al3 1.297 0.00471279 Al3+ For TIP3P/IOD: Li,PF; Merz,Jr; JPCB DOI:10.1021/jp505875v Table3
Al4 1.297 0.00471279 Al3+ For TIP3P/IOD: Li,PF; Merz,Jr; JPCB DOI:10.1021/jp505875v Table3