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comparison CADDSuite/data/OpenBabel/torlib.txt @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
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1 ##############################################################################
2 # #
3 # Open Babel file: torlib.txt #
4 # #
5 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
6 # Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison #
7 # Part of the Open Babel package, under the GNU General Public License (GPL)#
8 # #
9 # First three lines represent: (used by rotor.cpp::OBRotorRules #
10 # Hybridization pair (atom types around a rotatable bond) #
11 # followed by a list of default bond rotation angles (in degrees) #
12 # #
13 # Later lines should specify: #
14 # * A SMARTS pattern for the rotor rule #
15 # * A set of 4 "reference atoms" (as integers, numbered from 1 #
16 # in the specified SMARTS pattern #
17 # * At least one torsion value (in degrees) #
18 # * Optionally ending with "Delta" and a delta value #
19 # (i.e., the resolution of a dihedral step #
20 # #
21 # SMARTS rules will be attempted first, then hybridization #
22 # #
23 ##############################################################################
24
25 SP3-SP3 60.0 -60.0 180.0
26 SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0
27 SP3-SP2 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0
28
29 # Many of these rules came from the Supporting Information
30 # from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801
31
32 #polysaccaride bridges
33 O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0
34 O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0
35
36 #acids
37 [OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0
38 [a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0
39 [OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0
40
41 #sulfonamides
42 NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0
43 c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0
44 O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0
45 O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0
46 [c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0
47 *=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0
48 O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0
49 [aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0
50 [aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0
51 [aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0
52 [aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0
53 [a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0
54 aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0
55 aaNS(=O)(=O) 1 2 3 4 90.0 -90.0
56
57 #sulfone
58 O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0
59
60 #hydrazides
61 [O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0
62 [O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0
63
64 #cyclopropyl-ketones
65 O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0
66 O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0
67 O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0
68
69 #epoxy-ketone
70 O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0
71
72 #opposite end of tert amide
73 O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0
74 O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0
75 O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0
76
77 #misc
78 [CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0
79 [cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0
80 c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0
81
82 #carbonyls
83 O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0
84 C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0
85 O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0
86 O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0
87 O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0
88 O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0
89 O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0
90 O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0
91 O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
92 O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
93 O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0
94 O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0
95 #O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0
96
97 #amidene and guanidine
98 [aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
99 [a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
100 *[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
101 [CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0
102
103 #ether
104 aCO[CD2] 1 2 3 4 180.0 100.0 -100.0
105
106 #isoprene
107 C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0
108 C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0
109
110 #aryl secondary amines
111 [aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0
112 [aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0
113 [aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0
114 ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0
115
116 #aromatic subtituents
117 [aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
118 [aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0
119 [aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0
120 a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0
121 an[CD2X4][CD1] 1 2 3 4 90.0 -90.0
122 [aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0
123 [aD3]c([aD2])O[CD2] 1 2 3 4 180.0
124 a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0
125 [ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0
126 [aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0
127 [a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0
128 [a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0
129 [a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
130 [a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
131
132 #borderline low-res
133 [CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0
134
135 #conjugated substituents
136 a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0
137 C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0
138 cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0
139 C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0
140 c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0
141 C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0
142
143 #ureas
144 [ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0
145 [ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0
146
147 #carbamates
148 C[ND2]C(=O)O 1 2 3 4 0.0 180.0
149 [ND2]C(=O)OC 3 2 4 5 0.0
150 OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0
151
152 #piperidine amide
153 O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0
154
155 #amides and esters
156 [*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0
157 [OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0
158 [O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0
159 [O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0
160 [O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0
161 [O,SD1]=C(C)cn 1 2 4 5 0.0 180.0
162 [O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0
163 [O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180
164 O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0
165 O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0
166 O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0
167 O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0
168 O=C([CD1])O[CD1] 1 2 4 5 0.0
169 [O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0
170 O=CO[CD2][CD1] 2 3 4 5 180.0
171 O=CO[CD2]* 2 3 4 5 180.0 60.0 -60.0 90.0 -90.0
172 O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0
173 O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0
174 O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
175 O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
176 O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0
177 O=C[ND3]* 1 2 3 4 0.0 180.0
178 CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0
179 [a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0
180 [ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
181 [CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0
182
183 #t-butyl
184 C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0
185 **C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0
186
187 #propyl
188 [CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0
189
190 #highly substituted alkane
191 #[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6
192 *[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0
193 c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0
194 [CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0
195 [*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0
196 [*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0
197 *[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0
198 [CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0
199
200 #long unsubstituted alkanes
201 [CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0
202 [CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0
203 [CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0
204 [*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0
205
206 #nitro
207 [aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0
208 [a]cN(~[OD1])~[OD1] 1 2 3 4 0.0
209
210 #trifluoromethyl
211 **C(F)(F)F 1 2 3 4 0.0
212
213 #trichloromethyl
214 [a]cC(Cl)(Cl)Cl 1 2 3 4 0.0
215
216 #CSD SPECIFIC RULES
217 a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0
218 PPcc 1 2 3 4 60.0 -60.0
219
220 #phosphorus containing groups
221 #[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0
222 #[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0
223 #S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0
224 #[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0