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
|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
VNP VNP '3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)M' non-polymer 46 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VNP
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
VNP O2B O O 0.000 0.000 0.000 0.000
VNP PB P P 0.000 -0.639 1.025 -0.856
VNP O1B O OH1 0.000 0.311 1.337 -2.118
VNP H1B H H 0.000 0.039 1.989 -2.779
VNP N3B N NH1 0.000 -0.872 2.434 0.034
VNP H3B H H 0.000 -1.771 2.860 0.207
VNP PG P P 0.000 0.594 3.039 0.599
VNP O3G O O 0.000 1.243 2.031 1.467
VNP O1G O OH1 0.000 0.330 4.383 1.444
VNP H1G H H 0.000 1.073 4.859 1.840
VNP O2G O OH1 0.000 1.555 3.371 -0.650
VNP H2G H H 0.000 1.277 4.014 -1.316
VNP O1 O O2 0.000 -2.061 0.478 -1.377
VNP C7 C CH2 0.000 -3.045 -0.083 -0.507
VNP H71 H H 0.000 -3.337 0.660 0.238
VNP H72 H H 0.000 -2.628 -0.957 -0.003
VNP C12 C CH2 0.000 -4.271 -0.499 -1.323
VNP H121 H H 0.000 -3.977 -1.241 -2.068
VNP H122 H H 0.000 -4.686 0.377 -1.827
VNP C11 C CR5 0.000 -5.309 -1.090 -0.405
VNP S1 S S2 0.000 -5.461 -2.792 0.029
VNP C9 C CR15 0.000 -6.811 -2.429 1.012
VNP H9 H H 0.000 -7.372 -3.155 1.588
VNP N5 N NR5 1.000 -7.066 -1.164 0.970
VNP C10 C CR5 0.000 -6.281 -0.418 0.219
VNP CM4 C CH3 0.000 -6.465 1.070 0.075
VNP HM43 H H 0.000 -6.886 1.461 0.965
VNP HM42 H H 0.000 -5.525 1.526 -0.101
VNP HM41 H H 0.000 -7.112 1.269 -0.739
VNP C7A C CH2 0.000 -8.180 -0.584 1.723
VNP H7A1 H H 0.000 -7.902 0.412 2.074
VNP H7A2 H H 0.000 -8.410 -1.220 2.580
VNP C5A C CR6 0.000 -9.392 -0.484 0.831
VNP C4A C CR6 0.000 -10.248 -1.574 0.664
VNP N4A N NH2 0.000 -10.002 -2.770 1.317
VNP H4A2 H H 0.000 -10.625 -3.562 1.196
VNP H4A1 H H 0.000 -9.195 -2.869 1.926
VNP N3A N NRD6 0.000 -11.308 -1.443 -0.129
VNP C2A C CR6 0.000 -11.543 -0.308 -0.756
VNP CM2 C CH3 0.000 -12.751 -0.201 -1.650
VNP HM23 H H 0.000 -13.517 -0.836 -1.287
VNP HM22 H H 0.000 -13.097 0.800 -1.658
VNP HM21 H H 0.000 -12.489 -0.491 -2.634
VNP N1A N NRD6 0.000 -10.751 0.736 -0.623
VNP C6A C CR16 0.000 -9.678 0.685 0.154
VNP H6A H H 0.000 -9.034 1.550 0.256
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
VNP O2B n/a PB START
VNP PB O2B O1 .
VNP O1B PB H1B .
VNP H1B O1B . .
VNP N3B PB PG .
VNP H3B N3B . .
VNP PG N3B O2G .
VNP O3G PG . .
VNP O1G PG H1G .
VNP H1G O1G . .
VNP O2G PG H2G .
VNP H2G O2G . .
VNP O1 PB C7 .
VNP C7 O1 C12 .
VNP H71 C7 . .
VNP H72 C7 . .
VNP C12 C7 C11 .
VNP H121 C12 . .
VNP H122 C12 . .
VNP C11 C12 S1 .
VNP S1 C11 C9 .
VNP C9 S1 N5 .
VNP H9 C9 . .
VNP N5 C9 C7A .
VNP C10 N5 CM4 .
VNP CM4 C10 HM41 .
VNP HM43 CM4 . .
VNP HM42 CM4 . .
VNP HM41 CM4 . .
VNP C7A N5 C5A .
VNP H7A1 C7A . .
VNP H7A2 C7A . .
VNP C5A C7A C4A .
VNP C4A C5A N3A .
VNP N4A C4A H4A1 .
VNP H4A2 N4A . .
VNP H4A1 N4A . .
VNP N3A C4A C2A .
VNP C2A N3A N1A .
VNP CM2 C2A HM21 .
VNP HM23 CM2 . .
VNP HM22 CM2 . .
VNP HM21 CM2 . .
VNP N1A C2A C6A .
VNP C6A N1A H6A .
VNP H6A C6A . END
VNP C11 C10 . ADD
VNP C5A C6A . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
VNP O2G PG single 1.610 0.020
VNP H2G O2G single 0.967 0.020
VNP O3G PG double 1.480 0.020
VNP O1G PG single 1.610 0.020
VNP PG N3B single 1.750 0.020
VNP H1G O1G single 0.967 0.020
VNP N3B PB single 1.750 0.020
VNP H3B N3B single 1.010 0.020
VNP PB O2B double 1.480 0.020
VNP O1B PB single 1.610 0.020
VNP O1 PB single 1.610 0.020
VNP H1B O1B single 0.967 0.020
VNP C7 O1 single 1.426 0.020
VNP C12 C7 single 1.524 0.020
VNP H71 C7 single 1.092 0.020
VNP H72 C7 single 1.092 0.020
VNP C11 C12 single 1.510 0.020
VNP H121 C12 single 1.092 0.020
VNP H122 C12 single 1.092 0.020
VNP C11 C10 double 1.490 0.020
VNP S1 C11 single 1.745 0.020
VNP CM4 C10 single 1.506 0.020
VNP C10 N5 single 1.337 0.020
VNP HM41 CM4 single 1.059 0.020
VNP HM42 CM4 single 1.059 0.020
VNP HM43 CM4 single 1.059 0.020
VNP C9 S1 single 1.745 0.020
VNP N5 C9 double 1.337 0.020
VNP H9 C9 single 1.083 0.020
VNP C7A N5 single 1.462 0.020
VNP C5A C7A single 1.511 0.020
VNP H7A1 C7A single 1.092 0.020
VNP H7A2 C7A single 1.092 0.020
VNP C5A C6A double 1.390 0.020
VNP C4A C5A single 1.487 0.020
VNP C6A N1A single 1.337 0.020
VNP H6A C6A single 1.083 0.020
VNP N1A C2A double 1.350 0.020
VNP CM2 C2A single 1.506 0.020
VNP C2A N3A single 1.350 0.020
VNP HM21 CM2 single 1.059 0.020
VNP HM22 CM2 single 1.059 0.020
VNP HM23 CM2 single 1.059 0.020
VNP N3A C4A double 1.350 0.020
VNP N4A C4A single 1.355 0.020
VNP H4A1 N4A single 1.010 0.020
VNP H4A2 N4A single 1.010 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
VNP O2B PB O1B 109.500 3.000
VNP O2B PB N3B 109.500 3.000
VNP O2B PB O1 109.500 3.000
VNP O1B PB N3B 109.500 3.000
VNP O1B PB O1 109.500 3.000
VNP N3B PB O1 109.500 3.000
VNP PB O1B H1B 120.000 3.000
VNP PB N3B H3B 120.000 3.000
VNP PB N3B PG 120.000 3.000
VNP H3B N3B PG 120.000 3.000
VNP N3B PG O3G 109.500 3.000
VNP N3B PG O1G 109.500 3.000
VNP N3B PG O2G 109.500 3.000
VNP O3G PG O1G 109.500 3.000
VNP O3G PG O2G 109.500 3.000
VNP O1G PG O2G 109.500 3.000
VNP PG O1G H1G 120.000 3.000
VNP PG O2G H2G 120.000 3.000
VNP PB O1 C7 120.500 3.000
VNP O1 C7 H71 109.470 3.000
VNP O1 C7 H72 109.470 3.000
VNP O1 C7 C12 109.470 3.000
VNP H71 C7 H72 107.900 3.000
VNP H71 C7 C12 109.470 3.000
VNP H72 C7 C12 109.470 3.000
VNP C7 C12 H121 109.470 3.000
VNP C7 C12 H122 109.470 3.000
VNP C7 C12 C11 109.470 3.000
VNP H121 C12 H122 107.900 3.000
VNP H121 C12 C11 109.470 3.000
VNP H122 C12 C11 109.470 3.000
VNP C12 C11 S1 108.000 3.000
VNP C12 C11 C10 126.000 3.000
VNP S1 C11 C10 108.000 3.000
VNP C11 S1 C9 90.282 3.000
VNP S1 C9 H9 108.000 3.000
VNP S1 C9 N5 108.000 3.000
VNP H9 C9 N5 126.000 3.000
VNP C9 N5 C10 108.000 3.000
VNP C9 N5 C7A 126.000 3.000
VNP C10 N5 C7A 126.000 3.000
VNP N5 C10 CM4 126.000 3.000
VNP N5 C10 C11 108.000 3.000
VNP CM4 C10 C11 126.000 3.000
VNP C10 CM4 HM43 109.470 3.000
VNP C10 CM4 HM42 109.470 3.000
VNP C10 CM4 HM41 109.470 3.000
VNP HM43 CM4 HM42 109.470 3.000
VNP HM43 CM4 HM41 109.470 3.000
VNP HM42 CM4 HM41 109.470 3.000
VNP N5 C7A H7A1 109.500 3.000
VNP N5 C7A H7A2 109.500 3.000
VNP N5 C7A C5A 109.500 3.000
VNP H7A1 C7A H7A2 107.900 3.000
VNP H7A1 C7A C5A 109.470 3.000
VNP H7A2 C7A C5A 109.470 3.000
VNP C7A C5A C4A 120.000 3.000
VNP C7A C5A C6A 120.000 3.000
VNP C4A C5A C6A 120.000 3.000
VNP C5A C4A N4A 120.000 3.000
VNP C5A C4A N3A 120.000 3.000
VNP N4A C4A N3A 120.000 3.000
VNP C4A N4A H4A2 120.000 3.000
VNP C4A N4A H4A1 120.000 3.000
VNP H4A2 N4A H4A1 120.000 3.000
VNP C4A N3A C2A 120.000 3.000
VNP N3A C2A CM2 120.000 3.000
VNP N3A C2A N1A 120.000 3.000
VNP CM2 C2A N1A 120.000 3.000
VNP C2A CM2 HM23 109.470 3.000
VNP C2A CM2 HM22 109.470 3.000
VNP C2A CM2 HM21 109.470 3.000
VNP HM23 CM2 HM22 109.470 3.000
VNP HM23 CM2 HM21 109.470 3.000
VNP HM22 CM2 HM21 109.470 3.000
VNP C2A N1A C6A 120.000 3.000
VNP N1A C6A H6A 120.000 3.000
VNP N1A C6A C5A 120.000 3.000
VNP H6A C6A C5A 120.000 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
VNP var_1 O2B PB O1B H1B -179.966 20.000 1
VNP var_2 O2B PB N3B PG 59.966 20.000 1
VNP var_3 PB N3B PG O2G 60.017 20.000 1
VNP var_4 N3B PG O1G H1G 179.985 20.000 1
VNP var_5 N3B PG O2G H2G 59.932 20.000 1
VNP var_6 O2B PB O1 C7 49.972 20.000 1
VNP var_7 PB O1 C7 C12 179.973 20.000 1
VNP var_8 O1 C7 C12 C11 -179.992 20.000 3
VNP var_9 C7 C12 C11 S1 -90.250 20.000 2
VNP CONST_1 C12 C11 C10 N5 180.000 0.000 0
VNP CONST_2 C12 C11 S1 C9 180.000 0.000 0
VNP CONST_3 C11 S1 C9 N5 0.000 0.000 0
VNP CONST_4 S1 C9 N5 C7A 180.000 0.000 0
VNP CONST_5 C9 N5 C10 CM4 180.000 0.000 0
VNP var_10 N5 C10 CM4 HM41 -90.024 20.000 1
VNP var_11 C9 N5 C7A C5A -94.942 20.000 1
VNP var_12 N5 C7A C5A C4A 84.708 20.000 2
VNP CONST_6 C7A C5A C6A N1A 180.000 0.000 0
VNP CONST_7 C7A C5A C4A N3A 180.000 0.000 0
VNP CONST_8 C5A C4A N4A H4A1 -0.038 0.000 0
VNP CONST_9 C5A C4A N3A C2A 0.000 0.000 0
VNP CONST_10 C4A N3A C2A N1A 0.000 0.000 0
VNP var_13 N3A C2A CM2 HM21 -89.945 20.000 1
VNP CONST_11 N3A C2A N1A C6A 0.000 0.000 0
VNP CONST_12 C2A N1A C6A C5A 0.000 0.000 0
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
VNP plan-1 N3B 0.020
VNP plan-1 PG 0.020
VNP plan-1 PB 0.020
VNP plan-1 H3B 0.020
VNP plan-2 C11 0.020
VNP plan-2 C12 0.020
VNP plan-2 C10 0.020
VNP plan-2 S1 0.020
VNP plan-2 C9 0.020
VNP plan-2 N5 0.020
VNP plan-2 CM4 0.020
VNP plan-2 H9 0.020
VNP plan-2 C7A 0.020
VNP plan-3 C5A 0.020
VNP plan-3 C7A 0.020
VNP plan-3 C6A 0.020
VNP plan-3 C4A 0.020
VNP plan-3 N1A 0.020
VNP plan-3 C2A 0.020
VNP plan-3 N3A 0.020
VNP plan-3 H6A 0.020
VNP plan-3 CM2 0.020
VNP plan-3 N4A 0.020
VNP plan-3 H4A2 0.020
VNP plan-3 H4A1 0.020
VNP plan-4 N4A 0.020
VNP plan-4 C4A 0.020
VNP plan-4 H4A1 0.020
VNP plan-4 H4A2 0.020
# ------------------------------------------------------
|
