forked from openbabel/openbabel
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathUFF.prm
278 lines (276 loc) · 12.3 KB
/
UFF.prm
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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
#
# Open Babel file: UFF.prm
#
# Force field parameters for UFF, the Universal Force Field
# Used by OBForceField and OBUFFForceField
#
# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
# The parameters in this file are taken from the UFF implementation in RDKit
# http://rdkit.org/
#
# Atom typing rules are based on UFF published atom descriptions
# atom [SMARTS] [atomtype] [description]
# These must be sorted according to the element and complexity
# of the type rule (i.e., generic rules first, more specific rules later)
#
# Parameters follow later
# param Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
#atom [#0] Du Dummy atom (e.g., ligand attachment point)
atom [#1] H_ Generic hydrogen
atom [#1D2] H_b Bridging hydrogen
atom [#2] He4+4 Helium
atom [#3] Li Lithium
atom [#4] Be3+2 Generic Be
atom [#5] B_2 Trigonal planar boron
atom [#5D4] B_3 Tetrahedral boron
atom [#6] C_3 Generic sp3 C
atom [C^2] C_2 sp2 non-aromatic C
atom [C^1] C_1 sp hybridized C
atom [c] C_R aromatic C
atom [#6H1D3r5] C_R aromatic C (cyclopentadienyl ring)
atom [#7] N_3 Generic sp3 N
atom [N^2] N_2 sp2 non-aromatic N
atom [N^1] N_1 sp hybridized N
atom [n] N_R aromatic N
atom [#8] O_3 generic, sp3 hybridized O
atom [#8][#14] O_3_z sp3 hybridized O for zeolites
atom [O^2] O_2 sp2 hybridized O
atom [O^1] O_1 sp hybridized O
atom [o] O_R aromatic O
atom [#9] F_ generic F
atom [#10] Ne4+4
atom [#11] Na
atom [#12] Mg3+2
atom [#13] Al3
atom [#14] Si3
#atom [#15] P_3+q Organometallic phosphine ligands
atom [#15] P_3+3 generic phosphorus
atom [#15D5] P_3+5 formal charge +5
atom [#16] S_3+2 generic S
atom [#16+4] S_3+4 S+4 ( SO2 )
atom [#16+6] S_3+6 S+6 ( SO3 / H2SO4 )
atom [S^2] S_2 non-aromatic sp2 S
atom [s] S_R aromatic S
atom [#17] Cl
atom [#18] Ar4+4
atom [#19] K_
atom [#20] Ca6+2
atom [#21] Sc3+3
atom [#22] Ti6+4 generic Ti (6-valent)
atom [#22D3] Ti3+4
atom [#23] V_3+5
atom [#24] Cr6+3
atom [#25] Mn6+2
atom [#26] Fe6+2 generic Fe (6-valent)
atom [#26D3] Fe3+2
atom [#27] Co6+3
atom [#28] Ni4+2
atom [#29] Cu3+1
atom [#30] Zn3+2
atom [#31] Ga3+3
atom [#32] Ge3
atom [#33] As3+3
atom [#34] Se3+2
atom [#35] Br
atom [#36] Kr4+4
atom [#37] Rb
atom [#38] Sr6+2
atom [#39] Y_3+3
atom [#40] Zr3+4
atom [#41] Nb3+5
atom [#42] Mo6+6 generic Mo (6-valent)
atom [#42D3] Mo3+6 trivalent Mo
atom [#43] Tc6+5
atom [#44] Ru6+2
atom [#45] Rh6+3
atom [#46] Pd4+2
atom [#47] Ag1+1
atom [#48] Cd3+2
atom [#49] In3+3
atom [#50] Sn3
atom [#51] Sb3+3
atom [#52] Te3+2
atom [#53] I_
atom [#54] Xe4+4
atom [#55] Cs
atom [#56] Ba6+2
atom [#57] La3+3
atom [#58] Ce6+3
atom [#59] Pr6+3
atom [#60] Nd6+3
atom [#61] Pm6+3
atom [#62] Sm6+3
atom [#63] Eu6+3
atom [#64] Gd6+3
atom [#65] Tb6+3
atom [#66] Dy6+3
atom [#67] Ho6+3
atom [#68] Er6+3
atom [#69] Tm6+3
atom [#70] Yb6+3
atom [#71] Lu6+3
atom [#72] Hf3+4
atom [#73] Ta3+5
atom [#74] W_6+6 generic W (6-valent)
atom [#74D3+4] W_3+4
atom [#74D3+6] W_3+6
atom [#75] Re6+5 generic Re (6-valent)
atom [#75D3] Re3+7 trivalent Re
atom [#76] Os6+6
atom [#77] Ir6+3
atom [#78] Pt4+2
atom [#79] Au4+3
atom [#80] Hg1+2
atom [#81] Tl3+3
atom [#82] Pb3
atom [#83] Bi3+3
atom [#84] Po3+2
atom [#85] At
atom [#86] Rn4+4
atom [#87] Fr
atom [#88] Ra6+2
atom [#89] Ac6+3
atom [#90] Th6+4
atom [#91] Pa6+4
atom [#92] U_6+4
atom [#93] Np6+4
atom [#94] Pu6+4
atom [#95] Am6+4
atom [#96] Cm6+3
atom [#97] Bk6+3
atom [#98] Cf6+3
atom [#99] Es6+3
atom [#100] Fm6+3
atom [#101] Md6+3
atom [#102] No6+3
atom [#103] Lw6+3
# Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
param Du 0.01 180 0.4 5000 12 10.0 0 0 9.66 14.92 0.7
param H_ 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
param D 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
param H_b 0.46 83.5 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
param He4+4 0.849 90 2.362 0.056 15.24 0.098 0 0 9.66 14.92 1.3
param Li 1.336 180 2.451 0.025 12 1.026 0 2 3.006 2.386 1.557
param Be3+2 1.074 109.47 2.745 0.085 12 1.565 0 2 4.877 4.443 1.24
param B_3 0.838 109.47 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
param B_2 0.828 120 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
param C_3 0.757 109.47 3.851 0.105 12.73 1.912 2.119 2 5.343 5.063 0.759
param C_R 0.729 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
param C_2 0.732 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
param C_1 0.706 180 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
param N_3 0.7 106.7 3.66 0.069 13.407 2.544 0.45 2 6.899 5.88 0.715
param N_R 0.699 120 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
param N_2 0.685 111.2 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
param N_1 0.656 180 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
param O_3 0.658 104.51 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
param O_3_z 0.528 146 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
param O_R 0.68 110 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
param O_2 0.634 120 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
param O_1 0.639 180 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
param F_ 0.668 180 3.364 0.05 14.762 1.735 0 2 10.874 7.474 0.706
param Ne4+4 0.92 90 3.243 0.042 15.44 0.194 0 2 11.04 10.55 1.768
param Na 1.539 180 2.983 0.03 12 1.081 0 1.25 2.843 2.296 2.085
param Mg3+2 1.421 109.47 3.021 0.111 12 1.787 0 1.25 3.951 3.693 1.5
param Al3 1.244 109.47 4.499 0.505 11.278 1.792 0 1.25 4.06 3.59 1.201
param Si3 1.117 109.47 4.295 0.402 12.175 2.323 1.225 1.25 4.168 3.487 1.176
param P_3+3 1.101 93.8 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
param P_3+5 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
param P_3+q 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
param S_3+2 1.064 92.1 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
param S_3+4 1.049 103.2 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
param S_3+6 1.027 109.47 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
param S_R 1.077 92.2 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
param S_2 0.854 120 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
param Cl 1.044 180 3.947 0.227 14.866 2.348 0 1.25 8.564 4.946 0.994
param Ar4+4 1.032 90 3.868 0.185 15.763 0.3 0 1.25 9.465 6.355 2.108
param K_ 1.953 180 3.812 0.035 12 1.165 0 0.7 2.421 1.92 2.586
param Ca6+2 1.761 90 3.399 0.238 12 2.141 0 0.7 3.231 2.88 2
param Sc3+3 1.513 109.47 3.295 0.019 12 2.592 0 0.7 3.395 3.08 1.75
param Ti3+4 1.412 109.47 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
param Ti6+4 1.412 90 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
param V_3+5 1.402 109.47 3.144 0.016 12 2.679 0 0.7 3.65 3.41 1.47
param Cr6+3 1.345 90 3.023 0.015 12 2.463 0 0.7 3.415 3.865 1.402
param Mn6+2 1.382 90 2.961 0.013 12 2.43 0 0.7 3.325 4.105 1.533
param Fe3+2 1.27 109.47 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
param Fe6+2 1.335 90 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
param Co6+3 1.241 90 2.872 0.014 12 2.43 0 0.7 4.105 4.175 1.406
param Ni4+2 1.164 90 2.834 0.015 12 2.43 0 0.7 4.465 4.205 1.398
param Cu3+1 1.302 109.47 3.495 0.005 12 1.756 0 0.7 4.2 4.22 1.434
param Zn3+2 1.193 109.47 2.763 0.124 12 1.308 0 0.7 5.106 4.285 1.4
param Ga3+3 1.26 109.47 4.383 0.415 11 1.821 0 0.7 3.641 3.16 1.211
param Ge3 1.197 109.47 4.28 0.379 12 2.789 0.701 0.7 4.051 3.438 1.189
param As3+3 1.211 92.1 4.23 0.309 13 2.864 1.5 0.7 5.188 3.809 1.204
param Se3+2 1.19 90.6 4.205 0.291 14 2.764 0.335 0.7 6.428 4.131 1.224
param Br 1.192 180 4.189 0.251 15 2.519 0 0.7 7.79 4.425 1.141
param Kr4+4 1.147 90 4.141 0.22 16 0.452 0 0.7 8.505 5.715 2.27
param Rb 2.26 180 4.114 0.04 12 1.592 0 0.2 2.331 1.846 2.77
param Sr6+2 2.052 90 3.641 0.235 12 2.449 0 0.2 3.024 2.44 2.415
param Y_3+3 1.698 109.47 3.345 0.072 12 3.257 0 0.2 3.83 2.81 1.998
param Zr3+4 1.564 109.47 3.124 0.069 12 3.667 0 0.2 3.4 3.55 1.758
param Nb3+5 1.473 109.47 3.165 0.059 12 3.618 0 0.2 3.55 3.38 1.603
param Mo6+6 1.467 90 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
param Mo3+6 1.484 109.47 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
param Tc6+5 1.322 90 2.998 0.048 12 3.4 0 0.2 3.29 3.99 1.5
param Ru6+2 1.478 90 2.963 0.056 12 3.4 0 0.2 3.575 4.015 1.5
param Rh6+3 1.332 90 2.929 0.053 12 3.5 0 0.2 3.975 4.005 1.509
param Pd4+2 1.338 90 2.899 0.048 12 3.21 0 0.2 4.32 4 1.544
param Ag1+1 1.386 180 3.148 0.036 12 1.956 0 0.2 4.436 3.134 1.622
param Cd3+2 1.403 109.47 2.848 0.228 12 1.65 0 0.2 5.034 3.957 1.6
param In3+3 1.459 109.47 4.463 0.599 11 2.07 0 0.2 3.506 2.896 1.404
param Sn3 1.398 109.47 4.392 0.567 12 2.961 0.199 0.2 3.987 3.124 1.354
param Sb3+3 1.407 91.6 4.42 0.449 13 2.704 1.1 0.2 4.899 3.342 1.404
param Te3+2 1.386 90.25 4.47 0.398 14 2.882 0.3 0.2 5.816 3.526 1.38
param I_ 1.382 180 4.5 0.339 15 2.65 0 0.2 6.822 3.762 1.333
param Xe4+4 1.267 90 4.404 0.332 12 0.556 0 0.2 7.595 4.975 2.459
param Cs 2.57 180 4.517 0.045 12 1.573 0 0.1 2.183 1.711 2.984
param Ba6+2 2.277 90 3.703 0.364 12 2.727 0 0.1 2.814 2.396 2.442
param La3+3 1.943 109.47 3.522 0.017 12 3.3 0 0.1 2.8355 2.7415 2.071
param Ce6+3 1.841 90 3.556 0.013 12 3.3 0 0.1 2.774 2.692 1.925
param Pr6+3 1.823 90 3.606 0.01 12 3.3 0 0.1 2.858 2.564 2.007
param Nd6+3 1.816 90 3.575 0.01 12 3.3 0 0.1 2.8685 2.6205 2.007
param Pm6+3 1.801 90 3.547 0.009 12 3.3 0 0.1 2.881 2.673 2
param Sm6+3 1.78 90 3.52 0.008 12 3.3 0 0.1 2.9115 2.7195 1.978
param Eu6+3 1.771 90 3.493 0.008 12 3.3 0 0.1 2.8785 2.7875 2.227
param Gd6+3 1.735 90 3.368 0.009 12 3.3 0 0.1 3.1665 2.9745 1.968
param Tb6+3 1.732 90 3.451 0.007 12 3.3 0 0.1 3.018 2.834 1.954
param Dy6+3 1.71 90 3.428 0.007 12 3.3 0 0.1 3.0555 2.8715 1.934
param Ho6+3 1.696 90 3.409 0.007 12 3.416 0 0.1 3.127 2.891 1.925
param Er6+3 1.673 90 3.391 0.007 12 3.3 0 0.1 3.1865 2.9145 1.915
param Tm6+3 1.66 90 3.374 0.006 12 3.3 0 0.1 3.2514 2.9329 2
param Yb6+3 1.637 90 3.355 0.228 12 2.618 0 0.1 3.2889 2.965 2.158
param Lu6+3 1.671 90 3.64 0.041 12 3.271 0 0.1 2.9629 2.4629 1.896
param Hf3+4 1.611 109.47 3.141 0.072 12 3.921 0 0.1 3.7 3.4 1.759
param Ta3+5 1.511 109.47 3.17 0.081 12 4.075 0 0.1 5.1 2.85 1.605
param W_6+6 1.392 90 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
param W_3+4 1.526 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
param W_3+6 1.38 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
param Re6+5 1.372 90 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
param Re3+7 1.314 109.47 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
param Os6+6 1.372 90 3.12 0.037 12 3.7 0 0.1 5.14 3.63 1.7
param Ir6+3 1.371 90 2.84 0.073 12 3.731 0 0.1 5 4 1.866
param Pt4+2 1.364 90 2.754 0.08 12 3.382 0 0.1 4.79 4.43 1.557
param Au4+3 1.262 90 3.293 0.039 12 2.625 0 0.1 4.894 2.586 1.618
param Hg1+2 1.34 180 2.705 0.385 12 1.75 0 0.1 6.27 4.16 1.6
param Tl3+3 1.518 120 4.347 0.68 11 2.068 0 0.1 3.2 2.9 1.53
param Pb3 1.459 109.47 4.297 0.663 12 2.846 0.1 0.1 3.9 3.53 1.444
param Bi3+3 1.512 90 4.37 0.518 13 2.47 1 0.1 4.69 3.74 1.514
param Po3+2 1.5 90 4.709 0.325 14 2.33 0.3 0.1 4.21 4.21 1.48
param At 1.545 180 4.75 0.284 15 2.24 0 0.1 4.75 4.75 1.47
param Rn4+4 1.42 90 4.765 0.248 16 0.583 0 0.1 5.37 5.37 2.2
param Fr 2.88 180 4.9 0.05 12 1.847 0 0 2 2 2.3
param Ra6+2 2.512 90 3.677 0.404 12 2.92 0 0 2.843 2.434 2.2
param Ac6+3 1.983 90 3.478 0.033 12 3.9 0 0 2.835 2.835 2.108
param Th6+4 1.721 90 3.396 0.026 12 4.202 0 0 3.175 2.905 2.018
param Pa6+4 1.711 90 3.424 0.022 12 3.9 0 0 2.985 2.905 1.8
param U_6+4 1.684 90 3.395 0.022 12 3.9 0 0 3.341 2.853 1.713
param Np6+4 1.666 90 3.424 0.019 12 3.9 0 0 3.549 2.717 1.8
param Pu6+4 1.657 90 3.424 0.016 12 3.9 0 0 3.243 2.819 1.84
param Am6+4 1.66 90 3.381 0.014 12 3.9 0 0 2.9895 3.0035 1.942
param Cm6+3 1.801 90 3.326 0.013 12 3.9 0 0 2.8315 3.1895 1.9
param Bk6+3 1.761 90 3.339 0.013 12 3.9 0 0 3.1935 3.0355 1.9
param Cf6+3 1.75 90 3.313 0.013 12 3.9 0 0 3.197 3.101 1.9
param Es6+3 1.724 90 3.299 0.012 12 3.9 0 0 3.333 3.089 1.9
param Fm6+3 1.712 90 3.286 0.012 12 3.9 0 0 3.4 3.1 1.9
param Md6+3 1.689 90 3.274 0.011 12 3.9 0 0 3.47 3.11 1.9
param No6+3 1.679 90 3.248 0.011 12 3.9 0 0 3.475 3.175 1.9
param Lw6+3 1.698 90 3.236 0.011 12 3.9 0 0 3.5 3.2 1.9