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
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
|
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
s_m_entry_name
r_mmod_Potential_Energy-OPLS-2005
b_mmod_Minimization_Converged-OPLS-2005
r_mmod_RMS_Derivative-OPLS-2005
i_mmod_Times_Found-OPLS-2005
r_mmod_Relative_Potential_Energy-OPLS-2005
b_mmod_Chiralities_Consistent-OPLS-2005
i_mmod_Conformation-OPLS-2005
i_mmod_Serial_Number-OPLS-2005
i_sd_Mol\_ID
s_sd_Formula
r_sd_MolWeight
i_sd_SchIID
s_sd_Source
i_sd_Source\_ID
s_sd_Chemical_Name
r_sd_pKa\_1
i_sd_Temp\_1
s_sd_Assessment\_1
s_sd_Identifier\_1
s_user_Data_Set
r_sd_pKa\_1a
r_sd_pKa\_1b
r_sd_pKa\_1c
s_m_entry_id
:::
"Title with \p \\ \" space"
ligprep-out.1
11.5775423049927
1
0.000241500383708626
1
0
1
1
1
1
CH2O2
46.02538
1
SB79
2002
"Methanoic Acid"
3.749
25
Rel.
carboxylicAcid_aliphatic
Acids
3.737
3.739
3.772
1
m_depend[8] {
# First column is dependency index #
i_m_depend_dependency
s_m_depend_property
:::
1 20 r_mmod_Potential_Energy-OPLS-2005
2 20 b_mmod_Minimization_Converged-OPLS-2005
3 20 r_mmod_RMS_Derivative-OPLS-2005
4 20 i_mmod_Times_Found-OPLS-2005
5 20 r_mmod_Relative_Potential_Energy-OPLS-2005
6 20 b_mmod_Chiralities_Consistent-OPLS-2005
7 20 i_mmod_Conformation-OPLS-2005
8 10 i_mmod_Serial_Number-OPLS-2005
:::
}
m_atom[5] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_insertion_code
s_m_mmod_res
s_m_chain_name
i_m_color
r_m_charge1
r_m_charge2
s_m_pdb_residue_name
s_m_pdb_atom_name
s_m_grow_name
i_m_atomic_number
i_m_formal_charge
i_m_representation
i_m_visibility
s_m_atom_name
i_m_template_index
:::
1 2 1.322943 0.665651 0.033620 900 " " X " " 2 0.52000 0.52000 "UNK " " " " " 6 0 0 1 "Does \p \" \\this work" 0
2 15 2.383264 0.045183 0.036722 900 " " X " " 70 -0.44000 -0.44000 "UNK " " " " " 8 0 0 1 "" 0
3 16 0.088569 0.086898 0.011423 900 " " X " " 70 -0.53000 -0.53000 "UNK " " " " " 8 0 0 1 "" 0
4 41 1.200391 1.759715 0.047865 900 " " X " " 21 0.00000 0.00000 "UNK " " " " " 1 0 0 1 "" 0
5 42 -0.612341 0.720066 0.012557 900 " " X " " 21 0.45000 0.45000 "UNK " " " " " 1 0 0 1 "" <>
:::
}
m_bond[8] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 2 1 1
2 1 3 1 1 1
3 1 4 1 1 1
4 2 1 2 1 1
5 3 1 1 1 1
6 3 5 1 1 1
7 4 1 1 1 1
8 5 3 1 1 1
:::
}
}
f_m_ct {
s_m_title
s_m_entry_name
r_mmod_Potential_Energy-OPLS-2005
b_mmod_Minimization_Converged-OPLS-2005
r_mmod_RMS_Derivative-OPLS-2005
i_mmod_Times_Found-OPLS-2005
r_mmod_Relative_Potential_Energy-OPLS-2005
b_mmod_Chiralities_Consistent-OPLS-2005
i_mmod_Conformation-OPLS-2005
i_mmod_Serial_Number-OPLS-2005
i_sd_Mol\_ID
s_sd_Formula
r_sd_MolWeight
i_sd_SchIID
s_sd_Source
i_sd_Source\_ID
s_sd_Chemical_Name
r_sd_pKa\_1
i_sd_Temp\_1
s_sd_Assessment\_1
s_sd_Identifier\_1
s_user_Data_Set
s_m_entry_id
:::
2:Acids
ligprep-out.2
1.90448498725891
0
10.1268978118896
1
0
1
1
2
2
CH2N2O4
106.03758
2
SB79
2008
"Methane, dinitro-"
3.57
25
Approx.
methane_nitro_nitro
Acids
2
m_depend[8] {
# First column is dependency index #
i_m_depend_dependency
s_m_depend_property
:::
1 20 r_mmod_Potential_Energy-OPLS-2005
2 20 b_mmod_Minimization_Converged-OPLS-2005
3 20 r_mmod_RMS_Derivative-OPLS-2005
4 20 i_mmod_Times_Found-OPLS-2005
5 20 r_mmod_Relative_Potential_Energy-OPLS-2005
6 20 b_mmod_Chiralities_Consistent-OPLS-2005
7 20 i_mmod_Conformation-OPLS-2005
8 10 i_mmod_Serial_Number-OPLS-2005
:::
}
m_atom[9] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_insertion_code
s_m_mmod_res
s_m_chain_name
i_m_color
r_m_charge1
r_m_charge2
s_m_pdb_residue_name
s_m_pdb_atom_name
s_m_grow_name
i_m_atomic_number
i_m_formal_charge
i_m_representation
i_m_visibility
s_m_atom_name
i_m_template_index
:::
1 3 2.454867 -0.068087 0.028385 900 " " X " " 2 0.28000 0.28000 "UNK " " " " " 6 0 0 1 "" 0
2 31 3.682039 0.774771 -0.121640 900 " " X " " 43 0.54000 0.54000 "UNK " " " " " 7 1 0 1 "" 0
3 15 3.664435 1.669564 -0.966160 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 0 0 1 "" 0
4 18 4.640647 0.508696 0.600789 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 -1 0 1 "" 0
5 31 1.220234 0.767491 0.155745 900 " " X " " 43 0.54000 0.54000 "UNK " " " " " 7 1 0 1 "" 0
6 15 1.203396 1.634407 1.028171 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 0 0 1 "" 0
7 18 0.292550 0.524092 -0.612877 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 -1 0 1 "" 0
8 41 2.368701 -0.700720 -0.855635 900 " " X " " 21 0.06000 0.06000 "UNK " " " " " 1 0 0 1 "" 0
9 41 2.546380 -0.674243 0.930770 900 " " X " " 21 0.06000 0.06000 "UNK " " " " " 1 0 0 1 "" 0
:::
}
m_bond[16] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 1 1
2 1 5 1 1 1
3 1 8 1 1 1
4 1 9 1 1 1
5 2 1 1 1 1
6 2 3 2 1 1
7 2 4 1 1 1
8 3 2 2 1 1
9 4 2 1 1 1
10 5 1 1 1 1
11 5 6 2 1 1
12 5 7 1 1 1
13 6 5 2 1 1
14 7 5 1 1 1
15 8 1 1 1 1
16 9 1 1 1 1
:::
}
}
f_m_ct {
s_m_title
s_m_entry_name
r_mmod_Potential_Energy-OPLS-2005
b_mmod_Minimization_Converged-OPLS-2005
r_mmod_RMS_Derivative-OPLS-2005
i_mmod_Times_Found-OPLS-2005
r_mmod_Relative_Potential_Energy-OPLS-2005
b_mmod_Chiralities_Consistent-OPLS-2005
i_mmod_Conformation-OPLS-2005
i_mmod_Serial_Number-OPLS-2005
i_sd_Mol\_ID
s_sd_Formula
r_sd_MolWeight
i_sd_SchIID
s_sd_Source
i_sd_Source\_ID
s_sd_Chemical_Name
r_sd_pKa\_1
i_sd_Temp\_1
s_sd_Assessment\_1
s_sd_Identifier\_1
s_user_Data_Set
s_m_entry_id
:::
3:Acids
ligprep-out.3
0.36353063583374
0
0.394437789916992
1
0
1
1
3
3
CH3NO2
61.04002
3
SB79
2009
"Methane, nitro-"
10.24
25
Approx.
methane_nitro
Acids
3
m_depend[8] {
# First column is dependency index #
i_m_depend_dependency
s_m_depend_property
:::
1 20 r_mmod_Potential_Energy-OPLS-2005
2 20 b_mmod_Minimization_Converged-OPLS-2005
3 20 r_mmod_RMS_Derivative-OPLS-2005
4 20 i_mmod_Times_Found-OPLS-2005
5 20 r_mmod_Relative_Potential_Energy-OPLS-2005
6 20 b_mmod_Chiralities_Consistent-OPLS-2005
7 20 i_mmod_Conformation-OPLS-2005
8 10 i_mmod_Serial_Number-OPLS-2005
:::
}
m_atom[7] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_insertion_code
s_m_mmod_res
s_m_chain_name
i_m_color
r_m_charge1
r_m_charge2
s_m_pdb_residue_name
s_m_pdb_atom_name
s_m_grow_name
i_m_atomic_number
i_m_formal_charge
i_m_representation
i_m_visibility
s_m_atom_name
i_m_template_index
:::
1 3 2.130632 2.462572 0.019139 900 " " X " " 2 0.02000 0.02000 "UNK " " " " " 6 0 0 1 "" 0
2 31 1.375937 1.174885 0.028298 900 " " X " " 43 0.54000 0.54000 "UNK " " " " " 7 1 0 1 "" 0
3 15 2.019597 0.136895 -0.075313 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 0 0 1 "" 0
4 18 0.156828 1.237457 0.136330 900 " " X " " 70 -0.37000 -0.37000 "UNK " " " " " 8 -1 0 1 "" 0
5 41 3.196829 2.244744 0.089627 900 " " X " " 21 0.06000 0.06000 "UNK " " " " " 1 0 0 1 "" 0
6 41 1.902515 2.975416 -0.915329 900 " " X " " 21 0.06000 0.06000 "UNK " " " " " 1 0 0 1 "" 0
7 41 1.801453 3.051384 0.875647 900 " " X " " 21 0.06000 0.06000 "UNK " " " " " 1 0 0 1 "" 0
:::
}
m_bond[12] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 1 1
2 1 5 1 1 1
3 1 6 1 1 1
4 1 7 1 1 1
5 2 1 1 1 1
6 2 3 2 1 1
7 2 4 1 1 1
8 3 2 2 1 1
9 4 2 1 1 1
10 5 1 1 1 1
11 6 1 1 1 1
12 7 1 1 1 1
:::
}
}
|
