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
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
|
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
VPU VPU '"[[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hy' non-polymer 53 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VPU
#
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
VPU OAR O O 0.000 0.000 0.000 0.000
VPU CAP C C 0.000 -0.411 -1.103 -0.305
VPU NAO N NH1 0.000 0.459 -2.102 -0.550
VPU HNAO H H 0.000 0.117 -3.035 -0.734
VPU CAS C CR6 0.000 1.835 -1.849 -0.549
VPU CAX C CR16 0.000 2.668 -2.530 -1.427
VPU HAX H H 0.000 2.255 -3.261 -2.110
VPU CAW C CR16 0.000 4.026 -2.274 -1.427
VPU HAW H H 0.000 4.675 -2.798 -2.117
VPU CAV C CR16 0.000 4.557 -1.348 -0.547
VPU HAV H H 0.000 5.622 -1.152 -0.545
VPU CAU C CR16 0.000 3.729 -0.672 0.332
VPU HAU H H 0.000 4.147 0.052 1.020
VPU CAT C CR16 0.000 2.371 -0.920 0.333
VPU HAT H H 0.000 1.724 -0.391 1.022
VPU OAQ O O2 0.000 -1.736 -1.325 -0.397
VPU NAY N N 0.000 -2.471 -0.382 -0.163
VPU CAA C C 0.000 -3.751 -0.532 -0.235
VPU OAL O O2 0.000 -4.298 -1.729 -0.567
VPU CAE C CH1 0.000 -5.317 -2.214 0.315
VPU HAE H H 0.000 -4.876 -2.441 1.295
VPU CAF C CH2 0.000 -5.941 -3.481 -0.271
VPU HAF H H 0.000 -6.299 -3.276 -1.282
VPU HAFA H H 0.000 -6.779 -3.796 0.354
VPU OAM O OH1 0.000 -4.960 -4.519 -0.313
VPU HOAM H H 0.000 -5.355 -5.320 -0.684
VPU CAD C CH1 0.000 -6.397 -1.140 0.477
VPU HAD H H 0.000 -6.855 -0.930 -0.500
VPU OAK O OH1 0.000 -7.400 -1.605 1.383
VPU HOAK H H 0.000 -7.800 -2.413 1.033
VPU CAC C CH1 0.000 -5.764 0.141 1.029
VPU HAC H H 0.000 -5.307 -0.066 2.007
VPU OAJ O OH1 0.000 -6.767 1.147 1.172
VPU HOAJ H H 0.000 -7.444 0.841 1.790
VPU CAB C CH1 0.000 -4.686 0.624 0.050
VPU HAB H H 0.000 -5.157 0.958 -0.885
VPU NAI N NH1 0.000 -3.935 1.730 0.648
VPU HNAI H H 0.000 -3.882 1.820 1.653
VPU CAG C C 0.000 -3.316 2.629 -0.142
VPU OAN O O 0.000 -3.378 2.521 -1.348
VPU CAH C CH2 0.000 -2.544 3.768 0.474
VPU HAH H H 0.000 -1.744 3.367 1.100
VPU HAHA H H 0.000 -3.216 4.373 1.086
VPU C1 C CH2 0.000 -1.942 4.634 -0.634
VPU H1 H H 0.000 -2.744 5.032 -1.260
VPU H1A H H 0.000 -1.271 4.027 -1.246
VPU C2 C CH2 0.000 -1.159 5.791 -0.009
VPU H2 H H 0.000 -0.358 5.391 0.617
VPU H2A H H 0.000 -1.831 6.395 0.603
VPU C3 C CH3 0.000 -0.558 6.657 -1.117
VPU H3B H H 0.000 -1.334 7.047 -1.726
VPU H3A H H 0.000 -0.014 7.460 -0.687
VPU H3 H H 0.000 0.094 6.072 -1.714
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
VPU OAR n/a CAP START
VPU CAP OAR OAQ .
VPU NAO CAP CAS .
VPU HNAO NAO . .
VPU CAS NAO CAX .
VPU CAX CAS CAW .
VPU HAX CAX . .
VPU CAW CAX CAV .
VPU HAW CAW . .
VPU CAV CAW CAU .
VPU HAV CAV . .
VPU CAU CAV CAT .
VPU HAU CAU . .
VPU CAT CAU HAT .
VPU HAT CAT . .
VPU OAQ CAP NAY .
VPU NAY OAQ CAA .
VPU CAA NAY CAB .
VPU OAL CAA CAE .
VPU CAE OAL CAD .
VPU HAE CAE . .
VPU CAF CAE OAM .
VPU HAF CAF . .
VPU HAFA CAF . .
VPU OAM CAF HOAM .
VPU HOAM OAM . .
VPU CAD CAE CAC .
VPU HAD CAD . .
VPU OAK CAD HOAK .
VPU HOAK OAK . .
VPU CAC CAD OAJ .
VPU HAC CAC . .
VPU OAJ CAC HOAJ .
VPU HOAJ OAJ . .
VPU CAB CAA NAI .
VPU HAB CAB . .
VPU NAI CAB CAG .
VPU HNAI NAI . .
VPU CAG NAI CAH .
VPU OAN CAG . .
VPU CAH CAG C1 .
VPU HAH CAH . .
VPU HAHA CAH . .
VPU C1 CAH C2 .
VPU H1 C1 . .
VPU H1A C1 . .
VPU C2 C1 C3 .
VPU H2 C2 . .
VPU H2A C2 . .
VPU C3 C2 H3 .
VPU H3B C3 . .
VPU H3A C3 . .
VPU H3 C3 . END
VPU CAB CAC . ADD
VPU CAS CAT . 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
VPU C3 C2 single 1.513 0.020
VPU C2 C1 single 1.524 0.020
VPU C1 CAH single 1.524 0.020
VPU CAH CAG single 1.510 0.020
VPU OAN CAG double 1.220 0.020
VPU CAG NAI single 1.330 0.020
VPU NAI CAB single 1.450 0.020
VPU CAB CAC single 1.524 0.020
VPU CAB CAA single 1.500 0.020
VPU OAJ CAC single 1.432 0.020
VPU CAC CAD single 1.524 0.020
VPU OAK CAD single 1.432 0.020
VPU CAD CAE single 1.524 0.020
VPU CAF CAE single 1.524 0.020
VPU CAE OAL single 1.426 0.020
VPU OAM CAF single 1.432 0.020
VPU OAL CAA single 1.454 0.020
VPU CAA NAY double 1.260 0.020
VPU NAY OAQ single 1.255 0.020
VPU OAQ CAP single 1.454 0.020
VPU CAP OAR double 1.220 0.020
VPU NAO CAP single 1.330 0.020
VPU CAS NAO single 1.350 0.020
VPU CAS CAT double 1.390 0.020
VPU CAX CAS single 1.390 0.020
VPU CAT CAU single 1.390 0.020
VPU CAU CAV double 1.390 0.020
VPU CAV CAW single 1.390 0.020
VPU CAW CAX double 1.390 0.020
VPU H3 C3 single 1.059 0.020
VPU H3A C3 single 1.059 0.020
VPU H3B C3 single 1.059 0.020
VPU H2 C2 single 1.092 0.020
VPU H2A C2 single 1.092 0.020
VPU H1 C1 single 1.092 0.020
VPU H1A C1 single 1.092 0.020
VPU HAH CAH single 1.092 0.020
VPU HAHA CAH single 1.092 0.020
VPU HNAI NAI single 1.010 0.020
VPU HAB CAB single 1.099 0.020
VPU HAC CAC single 1.099 0.020
VPU HOAJ OAJ single 0.967 0.020
VPU HAD CAD single 1.099 0.020
VPU HOAK OAK single 0.967 0.020
VPU HAE CAE single 1.099 0.020
VPU HAF CAF single 1.092 0.020
VPU HAFA CAF single 1.092 0.020
VPU HOAM OAM single 0.967 0.020
VPU HNAO NAO single 1.010 0.020
VPU HAT CAT single 1.083 0.020
VPU HAU CAU single 1.083 0.020
VPU HAV CAV single 1.083 0.020
VPU HAW CAW single 1.083 0.020
VPU HAX CAX single 1.083 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
VPU OAR CAP NAO 123.000 3.000
VPU OAR CAP OAQ 119.000 3.000
VPU NAO CAP OAQ 118.000 3.000
VPU CAP NAO HNAO 120.000 3.000
VPU CAP NAO CAS 120.000 3.000
VPU HNAO NAO CAS 120.000 3.000
VPU NAO CAS CAX 120.000 3.000
VPU NAO CAS CAT 120.000 3.000
VPU CAX CAS CAT 120.000 3.000
VPU CAS CAX HAX 120.000 3.000
VPU CAS CAX CAW 120.000 3.000
VPU HAX CAX CAW 120.000 3.000
VPU CAX CAW HAW 120.000 3.000
VPU CAX CAW CAV 120.000 3.000
VPU HAW CAW CAV 120.000 3.000
VPU CAW CAV HAV 120.000 3.000
VPU CAW CAV CAU 120.000 3.000
VPU HAV CAV CAU 120.000 3.000
VPU CAV CAU HAU 120.000 3.000
VPU CAV CAU CAT 120.000 3.000
VPU HAU CAU CAT 120.000 3.000
VPU CAU CAT HAT 120.000 3.000
VPU CAU CAT CAS 120.000 3.000
VPU HAT CAT CAS 120.000 3.000
VPU CAP OAQ NAY 120.000 3.000
VPU OAQ NAY CAA 120.000 3.000
VPU NAY CAA OAL 120.000 3.000
VPU NAY CAA CAB 116.500 3.000
VPU OAL CAA CAB 120.000 3.000
VPU CAA OAL CAE 111.800 3.000
VPU OAL CAE HAE 109.470 3.000
VPU OAL CAE CAF 109.470 3.000
VPU OAL CAE CAD 109.470 3.000
VPU HAE CAE CAF 108.340 3.000
VPU HAE CAE CAD 108.340 3.000
VPU CAF CAE CAD 111.000 3.000
VPU CAE CAF HAF 109.470 3.000
VPU CAE CAF HAFA 109.470 3.000
VPU CAE CAF OAM 109.470 3.000
VPU HAF CAF HAFA 107.900 3.000
VPU HAF CAF OAM 109.470 3.000
VPU HAFA CAF OAM 109.470 3.000
VPU CAF OAM HOAM 109.470 3.000
VPU CAE CAD HAD 108.340 3.000
VPU CAE CAD OAK 109.470 3.000
VPU CAE CAD CAC 111.000 3.000
VPU HAD CAD OAK 109.470 3.000
VPU HAD CAD CAC 108.340 3.000
VPU OAK CAD CAC 109.470 3.000
VPU CAD OAK HOAK 109.470 3.000
VPU CAD CAC HAC 108.340 3.000
VPU CAD CAC OAJ 109.470 3.000
VPU CAD CAC CAB 111.000 3.000
VPU HAC CAC OAJ 109.470 3.000
VPU HAC CAC CAB 108.340 3.000
VPU OAJ CAC CAB 109.470 3.000
VPU CAC OAJ HOAJ 109.470 3.000
VPU CAA CAB HAB 108.810 3.000
VPU CAA CAB NAI 111.600 3.000
VPU CAA CAB CAC 109.470 3.000
VPU HAB CAB NAI 108.550 3.000
VPU HAB CAB CAC 108.340 3.000
VPU NAI CAB CAC 110.000 3.000
VPU CAB NAI HNAI 118.500 3.000
VPU CAB NAI CAG 121.500 3.000
VPU HNAI NAI CAG 120.000 3.000
VPU NAI CAG OAN 123.000 3.000
VPU NAI CAG CAH 116.500 3.000
VPU OAN CAG CAH 120.500 3.000
VPU CAG CAH HAH 109.470 3.000
VPU CAG CAH HAHA 109.470 3.000
VPU CAG CAH C1 109.470 3.000
VPU HAH CAH HAHA 107.900 3.000
VPU HAH CAH C1 109.470 3.000
VPU HAHA CAH C1 109.470 3.000
VPU CAH C1 H1 109.470 3.000
VPU CAH C1 H1A 109.470 3.000
VPU CAH C1 C2 111.000 3.000
VPU H1 C1 H1A 107.900 3.000
VPU H1 C1 C2 109.470 3.000
VPU H1A C1 C2 109.470 3.000
VPU C1 C2 H2 109.470 3.000
VPU C1 C2 H2A 109.470 3.000
VPU C1 C2 C3 111.000 3.000
VPU H2 C2 H2A 107.900 3.000
VPU H2 C2 C3 109.470 3.000
VPU H2A C2 C3 109.470 3.000
VPU C2 C3 H3B 109.470 3.000
VPU C2 C3 H3A 109.470 3.000
VPU C2 C3 H3 109.470 3.000
VPU H3B C3 H3A 109.470 3.000
VPU H3B C3 H3 109.470 3.000
VPU H3A C3 H3 109.470 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
VPU CONST_1 OAR CAP NAO CAS 0.000 0.000 0
VPU var_1 CAP NAO CAS CAX -145.199 20.000 1
VPU CONST_2 NAO CAS CAT CAU 180.000 0.000 0
VPU CONST_3 NAO CAS CAX CAW 180.000 0.000 0
VPU CONST_4 CAS CAX CAW CAV 0.000 0.000 0
VPU CONST_5 CAX CAW CAV CAU 0.000 0.000 0
VPU CONST_6 CAW CAV CAU CAT 0.000 0.000 0
VPU CONST_7 CAV CAU CAT CAS 0.000 0.000 0
VPU var_2 OAR CAP OAQ NAY -0.027 20.000 1
VPU var_3 CAP OAQ NAY CAA -179.995 20.000 1
VPU CONST_8 OAQ NAY CAA CAB 180.000 0.000 0
VPU var_4 NAY CAA OAL CAE 120.000 20.000 1
VPU var_5 CAA OAL CAE CAD 60.000 20.000 1
VPU var_6 OAL CAE CAF OAM 65.206 20.000 3
VPU var_7 CAE CAF OAM HOAM 180.000 20.000 1
VPU var_8 OAL CAE CAD CAC -60.000 20.000 3
VPU var_9 CAE CAD OAK HOAK -60.056 20.000 1
VPU var_10 CAE CAD CAC OAJ 180.000 20.000 3
VPU var_11 CAD CAC OAJ HOAJ 60.668 20.000 1
VPU var_12 NAY CAA CAB NAI 0.000 20.000 3
VPU var_13 CAA CAB CAC CAD -60.000 20.000 3
VPU var_14 CAA CAB NAI CAG 86.251 20.000 3
VPU CONST_9 CAB NAI CAG CAH 180.000 0.000 0
VPU var_15 NAI CAG CAH C1 179.948 20.000 3
VPU var_16 CAG CAH C1 C2 179.970 20.000 3
VPU var_17 CAH C1 C2 C3 -179.967 20.000 3
VPU var_18 C1 C2 C3 H3 -59.975 20.000 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
VPU chir_01 CAB NAI CAC CAA positiv
VPU chir_02 CAC CAB OAJ CAD negativ
VPU chir_03 CAD CAC OAK CAE positiv
VPU chir_04 CAE CAD CAF OAL negativ
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
VPU plan-1 CAG 0.020
VPU plan-1 CAH 0.020
VPU plan-1 OAN 0.020
VPU plan-1 NAI 0.020
VPU plan-1 HNAI 0.020
VPU plan-2 NAI 0.020
VPU plan-2 CAG 0.020
VPU plan-2 CAB 0.020
VPU plan-2 HNAI 0.020
VPU plan-3 CAA 0.020
VPU plan-3 CAB 0.020
VPU plan-3 OAL 0.020
VPU plan-3 NAY 0.020
VPU plan-3 OAQ 0.020
VPU plan-4 CAP 0.020
VPU plan-4 OAQ 0.020
VPU plan-4 OAR 0.020
VPU plan-4 NAO 0.020
VPU plan-4 HNAO 0.020
VPU plan-5 NAO 0.020
VPU plan-5 CAP 0.020
VPU plan-5 CAS 0.020
VPU plan-5 HNAO 0.020
VPU plan-6 CAS 0.020
VPU plan-6 NAO 0.020
VPU plan-6 CAT 0.020
VPU plan-6 CAX 0.020
VPU plan-6 CAU 0.020
VPU plan-6 CAV 0.020
VPU plan-6 CAW 0.020
VPU plan-6 HAT 0.020
VPU plan-6 HAU 0.020
VPU plan-6 HAV 0.020
VPU plan-6 HAW 0.020
VPU plan-6 HAX 0.020
VPU plan-6 HNAO 0.020
# ------------------------------------------------------
|
