Mercurial > repos > marcel > caddsuite_linux_x86_64

comparison CADDSuite/data/OpenBabel/phmodel.txt @ 3:ff6df146c0d5

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
parents bac3c274238f
children
comparison
equal deleted inserted replaced
2:bbc4a2c1d276 3:ff6df146c0d5
1 ##############################################################################
2 # #
3 # Open Babel file: phmodel.txt #
4 # #
5 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
6 # Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison #
7 # Part of the Open Babel package, under the GNU General Public License (GPL)#
8 # #
9 # pH model data (used by phmodel.cpp:OBPhModel) #
10 # #
11 # TRANSFORM: chemical transforms can be used to modify formal charges, bond #
12 # orders, and to delete atoms (i.e hydrogens). Changes are applied#
13 # to vector bound atoms (use the [:#] SMARTS notation) and bonds #
14 # between vector bound atoms. #
15 # SEEDCHARGE: used to seed partial charges. Seed partial charges #
16 # are used as initial values in Gasteiger charge calculation #
17 # #
18 ##############################################################################
19
20 #carboxylic acid # pKa
21 #TRANSFORM O=CO[#1:1] >> O=CO 4.0 # pKa from acid (AH)
22 TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] 4.0 # pKa from acid (AH)
23
24 #uncomment for vinylogous carboxylic acids (e.g. ascorbic acid)
25 TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O-:1][C:2]=[C:3][C:4]=[O:5] 4.0 # pKa from acid (AH)
26
27 #charged amine
28 TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] 10.0 # pKa from conjugated acid (BH+)
29
30 #imidazole: note pKa=7.0
31 #if you uncomment this, also uncomment the seedcharge statement below
32 TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0
33
34 #imine
35 TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] 4.0 # pKa from conjugated acid (BH+)
36
37 #tetrazole
38 TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH)
39 TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 4.89 #pKa from acid (AH)
40 TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH)
41
42 #azide
43 TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A 1E+10 # always apply transformation
44 TRANSFORM [ND2:1]=[ND2:2]=A >> N=[N+:2]=A 1E+10 # always apply this transformation
45
46 #hydroxamic acid
47 #TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] 8.0
48 TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] 8.0
49
50 #sulfinic acid
51 TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] 2.0
52 TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] 2.0
53
54 #sulfonic acid
55 TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6
56 TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6
57 #sulfuric acid (same as sulfonic acid...)
58 #TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]
59 #TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]
60
61 #guanidine or amidine
62 TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5
63
64 #phosphate ester
65 TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0
66 #TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0
67
68 #phosphoric acid
69 #TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] 2.12
70 TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O 2.12
71 TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] 2.12
72 #phosphate
73
74 #
75 # Amino acids
76 # pKa sidechain
77 # aspartic acid
78 #TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O 3.8
79 TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1] 3.8
80 TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1] 3.8
81
82 # glutamic acid
83 #TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O 4.3
84 TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1] 5.0
85 TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1] 5.0
86
87 # arginine
88 TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 12.0
89 TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0
90
91 # lysine
92 TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 10.5
93 TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 10.5
94
95 # histidine
96 TRANSFORM O=C(O)C(N)Cc1nc[n:1]c1 >> O=C(O)C(N)Cc1nc[n+:1]c1 6.08
97 TRANSFORM O=C(NCC=O)C(N)Cc1nc[n:1]c1 >> O=C(NCC=O)C(N)Cc1nc[n+:1]c1 6.08
98
99 # cysteine
100 TRANSFORM O=C(O)C(N)C[S:1] >> O=C(O)C(N)C[S-:1] 8.28
101 TRANSFORM O=C(NCC=O)C(N)C[S:1] >> O=C(NCC=O)C(N)C[S-:1] 8.28
102
103 # tyrosine
104 TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1 >> O=C(O)C(N)Cc1ccc([O-:1])cc1 10.1
105 TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1 >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1 10.1
106
107 # old:
108 # histidine
109 #TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1
110 # uncomment for tryptophan
111 # TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1
112 #, histidine pKa=6.0
113
114
115 #
116 # Seeding partial charges for gasteiger calculation
117 #
118 #default charges
119 SEEDCHARGE [#6+] 1.0
120 SEEDCHARGE [#6-] -1.0
121 SEEDCHARGE [#7+] 1.0
122 SEEDCHARGE [#7-] -1.0
123 SEEDCHARGE [#8+] 1.0
124 SEEDCHARGE [#8-] -1.0
125 SEEDCHARGE [#15+] 1.0
126 SEEDCHARGE [#15-] -1.0
127 SEEDCHARGE [#16+] 1.0
128 SEEDCHARGE [#16-] -1.0
129
130 #charges spread over multiple atoms
131 #carboxylic acid
132 SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5
133
134 #amines
135 SEEDCHARGE [N+] 1.0
136 #tetrazole
137 SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2
138
139 #sulfinic
140 SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5
141 #sulfuric acid
142 SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0
143 #sulfonic acid
144 SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33
145
146 #guanidine
147 SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33
148
149 #amidine
150 SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5
151
152 #phosphoate ester
153 SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5
154 #phosphoric acid
155 SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66
156
157
158 #phosphuric acid
159 SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5
160 #phosphonic acid
161 SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33
162
163 #hydroxamic acid
164 SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5
165 SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 0.0 -0.33
166
167 #imidazole: note pKa=7.0, histidine pKa=6.0
168 #if you uncomment this, also uncomment the transform statement above
169 SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0