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
|
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
PR8 PR8 '5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2' non-polymer 50 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PR8
#
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
PR8 O2P O OP -0.500 0.000 0.000 0.000
PR8 P P P 0.000 -1.155 -0.931 0.004
PR8 O1P O OP -0.500 -1.317 -1.512 1.359
PR8 O10 O O2 -0.500 -0.819 -2.160 -1.051
PR8 C C C 0.000 0.240 -2.814 -0.926
PR8 O O O -0.500 1.041 -2.538 -0.005
PR8 CA C CH1 0.000 0.547 -3.939 -1.880
PR8 HA H H 0.000 0.246 -3.668 -2.902
PR8 CB C CH2 0.000 -0.166 -5.233 -1.434
PR8 HB H H 0.000 -1.091 -5.396 -1.991
PR8 HBA H H 0.000 -0.383 -5.224 -0.364
PR8 CG C CH2 0.000 0.832 -6.368 -1.748
PR8 HG H H 0.000 0.421 -7.076 -2.472
PR8 HGA H H 0.000 1.129 -6.904 -0.845
PR8 CD C CH2 0.000 2.062 -5.663 -2.358
PR8 HD H H 0.000 2.021 -5.647 -3.449
PR8 HDA H H 0.000 2.997 -6.128 -2.036
PR8 N N NH1 0.000 1.994 -4.274 -1.838
PR8 HN H H 0.000 2.757 -3.690 -1.526
PR8 "O5'" O O2 0.000 -2.492 -0.129 -0.399
PR8 "C5'" C CH2 0.000 -2.934 1.042 0.289
PR8 "H5'" H H 0.000 -2.167 1.816 0.220
PR8 "H5'A" H H 0.000 -3.113 0.801 1.339
PR8 "C4'" C CH1 0.000 -4.230 1.549 -0.348
PR8 "H4'" H H 0.000 -4.101 1.673 -1.432
PR8 "C3'" C CH1 0.000 -4.661 2.884 0.299
PR8 "H3'" H H 0.000 -4.240 2.976 1.310
PR8 "O3'" O OH1 0.000 -4.256 3.987 -0.515
PR8 "HO3'" H H 0.000 -4.585 4.810 -0.128
PR8 "C2'" C CH1 0.000 -6.202 2.793 0.359
PR8 "H2'" H H 0.000 -6.551 2.839 1.400
PR8 "O2'" O OH1 0.000 -6.796 3.836 -0.415
PR8 "HO2'" H H 0.000 -6.587 4.692 -0.016
PR8 "O4'" O O2 0.000 -5.317 0.638 -0.070
PR8 "C1'" C CH1 0.000 -6.520 1.413 -0.258
PR8 "H1'" H H 0.000 -6.746 1.515 -1.329
PR8 N9 N NR5 0.000 -7.644 0.787 0.443
PR8 C4 C CR56 0.000 -8.974 0.947 0.150
PR8 N3 N NRD6 0.000 -9.659 1.634 -0.759
PR8 C2 C CR16 0.000 -10.974 1.582 -0.788
PR8 H2 H H 0.000 -11.502 2.154 -1.542
PR8 C8 C CR15 0.000 -7.559 -0.060 1.508
PR8 H8 H H 0.000 -6.636 -0.381 1.974
PR8 N7 N NRD5 0.000 -8.751 -0.426 1.881
PR8 C5 C CR56 0.000 -9.674 0.161 1.081
PR8 C6 C CR6 0.000 -11.077 0.138 1.009
PR8 N1 N NRD6 0.000 -11.675 0.858 0.066
PR8 N6 N NH2 0.000 -11.819 -0.617 1.901
PR8 HN6A H H 0.000 -11.359 -1.165 2.620
PR8 HN6 H H 0.000 -12.833 -0.630 1.846
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
PR8 O2P n/a P START
PR8 P O2P "O5'" .
PR8 O1P P . .
PR8 O10 P C .
PR8 C O10 CA .
PR8 O C . .
PR8 CA C CB .
PR8 HA CA . .
PR8 CB CA CG .
PR8 HB CB . .
PR8 HBA CB . .
PR8 CG CB CD .
PR8 HG CG . .
PR8 HGA CG . .
PR8 CD CG N .
PR8 HD CD . .
PR8 HDA CD . .
PR8 N CD HN .
PR8 HN N . .
PR8 "O5'" P "C5'" .
PR8 "C5'" "O5'" "C4'" .
PR8 "H5'" "C5'" . .
PR8 "H5'A" "C5'" . .
PR8 "C4'" "C5'" "O4'" .
PR8 "H4'" "C4'" . .
PR8 "C3'" "C4'" "C2'" .
PR8 "H3'" "C3'" . .
PR8 "O3'" "C3'" "HO3'" .
PR8 "HO3'" "O3'" . .
PR8 "C2'" "C3'" "O2'" .
PR8 "H2'" "C2'" . .
PR8 "O2'" "C2'" "HO2'" .
PR8 "HO2'" "O2'" . .
PR8 "O4'" "C4'" "C1'" .
PR8 "C1'" "O4'" N9 .
PR8 "H1'" "C1'" . .
PR8 N9 "C1'" C8 .
PR8 C4 N9 N3 .
PR8 N3 C4 C2 .
PR8 C2 N3 H2 .
PR8 H2 C2 . .
PR8 C8 N9 N7 .
PR8 H8 C8 . .
PR8 N7 C8 C5 .
PR8 C5 N7 C6 .
PR8 C6 C5 N6 .
PR8 N1 C6 . .
PR8 N6 C6 HN6 .
PR8 HN6A N6 . .
PR8 HN6 N6 . END
PR8 N CA . ADD
PR8 N1 C2 . ADD
PR8 C4 C5 . ADD
PR8 "C1'" "C2'" . 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
PR8 C O10 deloc 1.454 0.020
PR8 O C deloc 1.220 0.020
PR8 CA C single 1.500 0.020
PR8 N CA single 1.450 0.020
PR8 N CD single 1.450 0.020
PR8 HN N single 1.010 0.020
PR8 P O2P deloc 1.510 0.020
PR8 "O5'" P single 1.610 0.020
PR8 O1P P deloc 1.510 0.020
PR8 O10 P single 1.610 0.020
PR8 N1 C2 double 1.337 0.020
PR8 N1 C6 single 1.350 0.020
PR8 C2 N3 single 1.337 0.020
PR8 H2 C2 single 1.083 0.020
PR8 N3 C4 double 1.355 0.020
PR8 C4 N9 single 1.337 0.020
PR8 C4 C5 single 1.490 0.020
PR8 C6 C5 double 1.490 0.020
PR8 C5 N7 single 1.350 0.020
PR8 N6 C6 single 1.355 0.020
PR8 HN6 N6 single 1.010 0.020
PR8 HN6A N6 single 1.010 0.020
PR8 N7 C8 double 1.350 0.020
PR8 C8 N9 single 1.337 0.020
PR8 H8 C8 single 1.083 0.020
PR8 N9 "C1'" single 1.485 0.020
PR8 CB CA single 1.524 0.020
PR8 HA CA single 1.099 0.020
PR8 CG CB single 1.524 0.020
PR8 HB CB single 1.092 0.020
PR8 HBA CB single 1.092 0.020
PR8 CD CG single 1.524 0.020
PR8 HD CD single 1.092 0.020
PR8 HDA CD single 1.092 0.020
PR8 HG CG single 1.092 0.020
PR8 HGA CG single 1.092 0.020
PR8 "C1'" "C2'" single 1.524 0.020
PR8 "C1'" "O4'" single 1.426 0.020
PR8 "H1'" "C1'" single 1.099 0.020
PR8 "O2'" "C2'" single 1.432 0.020
PR8 "C2'" "C3'" single 1.524 0.020
PR8 "H2'" "C2'" single 1.099 0.020
PR8 "HO2'" "O2'" single 0.967 0.020
PR8 "O3'" "C3'" single 1.432 0.020
PR8 "C3'" "C4'" single 1.524 0.020
PR8 "H3'" "C3'" single 1.099 0.020
PR8 "HO3'" "O3'" single 0.967 0.020
PR8 "O4'" "C4'" single 1.426 0.020
PR8 "C4'" "C5'" single 1.524 0.020
PR8 "H4'" "C4'" single 1.099 0.020
PR8 "C5'" "O5'" single 1.426 0.020
PR8 "H5'" "C5'" single 1.092 0.020
PR8 "H5'A" "C5'" single 1.092 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
PR8 O2P P O1P 119.900 3.000
PR8 O2P P O10 108.200 3.000
PR8 O2P P "O5'" 108.200 3.000
PR8 O1P P O10 108.200 3.000
PR8 O1P P "O5'" 108.200 3.000
PR8 O10 P "O5'" 102.600 3.000
PR8 P O10 C 120.000 3.000
PR8 O10 C O 119.000 3.000
PR8 O10 C CA 120.000 3.000
PR8 O C CA 120.500 3.000
PR8 C CA HA 108.810 3.000
PR8 C CA CB 109.470 3.000
PR8 C CA N 111.600 3.000
PR8 HA CA CB 108.340 3.000
PR8 HA CA N 108.550 3.000
PR8 CB CA N 110.000 3.000
PR8 CA CB HB 109.470 3.000
PR8 CA CB HBA 109.470 3.000
PR8 CA CB CG 111.000 3.000
PR8 HB CB HBA 107.900 3.000
PR8 HB CB CG 109.470 3.000
PR8 HBA CB CG 109.470 3.000
PR8 CB CG HG 109.470 3.000
PR8 CB CG HGA 109.470 3.000
PR8 CB CG CD 111.000 3.000
PR8 HG CG HGA 107.900 3.000
PR8 HG CG CD 109.470 3.000
PR8 HGA CG CD 109.470 3.000
PR8 CG CD HD 109.470 3.000
PR8 CG CD HDA 109.470 3.000
PR8 CG CD N 112.000 3.000
PR8 HD CD HDA 107.900 3.000
PR8 HD CD N 109.470 3.000
PR8 HDA CD N 109.470 3.000
PR8 CD N HN 118.500 3.000
PR8 CD N CA 120.000 3.000
PR8 HN N CA 118.500 3.000
PR8 P "O5'" "C5'" 120.500 3.000
PR8 "O5'" "C5'" "H5'" 109.470 3.000
PR8 "O5'" "C5'" "H5'A" 109.470 3.000
PR8 "O5'" "C5'" "C4'" 109.470 3.000
PR8 "H5'" "C5'" "H5'A" 107.900 3.000
PR8 "H5'" "C5'" "C4'" 109.470 3.000
PR8 "H5'A" "C5'" "C4'" 109.470 3.000
PR8 "C5'" "C4'" "H4'" 108.340 3.000
PR8 "C5'" "C4'" "C3'" 111.000 3.000
PR8 "C5'" "C4'" "O4'" 109.470 3.000
PR8 "H4'" "C4'" "C3'" 108.340 3.000
PR8 "H4'" "C4'" "O4'" 109.470 3.000
PR8 "C3'" "C4'" "O4'" 109.470 3.000
PR8 "C4'" "C3'" "H3'" 108.340 3.000
PR8 "C4'" "C3'" "O3'" 109.470 3.000
PR8 "C4'" "C3'" "C2'" 111.000 3.000
PR8 "H3'" "C3'" "O3'" 109.470 3.000
PR8 "H3'" "C3'" "C2'" 108.340 3.000
PR8 "O3'" "C3'" "C2'" 109.470 3.000
PR8 "C3'" "O3'" "HO3'" 109.470 3.000
PR8 "C3'" "C2'" "H2'" 108.340 3.000
PR8 "C3'" "C2'" "O2'" 109.470 3.000
PR8 "C3'" "C2'" "C1'" 111.000 3.000
PR8 "H2'" "C2'" "O2'" 109.470 3.000
PR8 "H2'" "C2'" "C1'" 108.340 3.000
PR8 "O2'" "C2'" "C1'" 109.470 3.000
PR8 "C2'" "O2'" "HO2'" 109.470 3.000
PR8 "C4'" "O4'" "C1'" 111.800 3.000
PR8 "O4'" "C1'" "H1'" 109.470 3.000
PR8 "O4'" "C1'" N9 109.470 3.000
PR8 "O4'" "C1'" "C2'" 109.470 3.000
PR8 "H1'" "C1'" N9 109.470 3.000
PR8 "H1'" "C1'" "C2'" 108.340 3.000
PR8 N9 "C1'" "C2'" 109.470 3.000
PR8 "C1'" N9 C4 126.000 3.000
PR8 "C1'" N9 C8 126.000 3.000
PR8 C4 N9 C8 108.000 3.000
PR8 N9 C4 N3 132.000 3.000
PR8 N9 C4 C5 108.000 3.000
PR8 N3 C4 C5 120.000 3.000
PR8 C4 N3 C2 120.000 3.000
PR8 N3 C2 H2 120.000 3.000
PR8 N3 C2 N1 120.000 3.000
PR8 H2 C2 N1 120.000 3.000
PR8 N9 C8 H8 126.000 3.000
PR8 N9 C8 N7 108.000 3.000
PR8 H8 C8 N7 126.000 3.000
PR8 C8 N7 C5 108.000 3.000
PR8 N7 C5 C6 132.000 3.000
PR8 N7 C5 C4 108.000 3.000
PR8 C6 C5 C4 120.000 3.000
PR8 C5 C6 N1 120.000 3.000
PR8 C5 C6 N6 120.000 3.000
PR8 N1 C6 N6 120.000 3.000
PR8 C6 N1 C2 120.000 3.000
PR8 C6 N6 HN6A 120.000 3.000
PR8 C6 N6 HN6 120.000 3.000
PR8 HN6A N6 HN6 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
PR8 var_1 O2P P O10 C 54.239 20.000 1
PR8 var_2 P O10 C CA 179.724 20.000 1
PR8 var_3 O10 C CA CB -83.096 20.000 3
PR8 var_4 C CA CB CG -150.000 20.000 3
PR8 var_5 CA CB CG CD 0.000 20.000 3
PR8 var_6 CB CG CD N 30.000 20.000 3
PR8 var_7 CG CD N CA -30.000 20.000 3
PR8 var_8 CD N CA C 150.000 20.000 3
PR8 var_9 O2P P "O5'" "C5'" -55.016 20.000 1
PR8 var_10 P "O5'" "C5'" "C4'" 179.981 20.000 1
PR8 var_11 "O5'" "C5'" "C4'" "O4'" 69.646 20.000 3
PR8 var_12 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
PR8 var_13 "C4'" "C3'" "O3'" "HO3'" 176.121 20.000 1
PR8 var_14 "C4'" "C3'" "C2'" "O2'" -120.000 20.000 3
PR8 var_15 "C3'" "C2'" "O2'" "HO2'" -65.360 20.000 1
PR8 var_16 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
PR8 var_17 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
PR8 var_18 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
PR8 var_19 "O4'" "C1'" N9 C8 23.567 20.000 1
PR8 CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
PR8 CONST_2 N9 C4 C5 N7 0.000 0.000 0
PR8 CONST_3 N9 C4 N3 C2 180.000 0.000 0
PR8 CONST_4 C4 N3 C2 N1 0.000 0.000 0
PR8 CONST_5 "C1'" N9 C8 N7 180.000 0.000 0
PR8 CONST_6 N9 C8 N7 C5 0.000 0.000 0
PR8 CONST_7 C8 N7 C5 C6 180.000 0.000 0
PR8 CONST_8 N7 C5 C6 N6 0.000 0.000 0
PR8 CONST_9 C5 C6 N1 C2 0.000 0.000 0
PR8 CONST_10 C6 N1 C2 N3 0.000 0.000 0
PR8 CONST_11 C5 C6 N6 HN6 -179.995 0.000 0
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
PR8 chir_01 CA C N CB negativ
PR8 chir_02 "C1'" N9 "C2'" "O4'" negativ
PR8 chir_03 "C2'" "C1'" "O2'" "C3'" positiv
PR8 chir_04 "C3'" "C2'" "O3'" "C4'" positiv
PR8 chir_05 "C4'" "C3'" "O4'" "C5'" positiv
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
PR8 plan-1 C 0.020
PR8 plan-1 O 0.020
PR8 plan-1 CA 0.020
PR8 plan-1 O10 0.020
PR8 plan-2 N 0.020
PR8 plan-2 CA 0.020
PR8 plan-2 CD 0.020
PR8 plan-2 HN 0.020
PR8 plan-3 N1 0.020
PR8 plan-3 C2 0.020
PR8 plan-3 C6 0.020
PR8 plan-3 N3 0.020
PR8 plan-3 H2 0.020
PR8 plan-3 C4 0.020
PR8 plan-3 C5 0.020
PR8 plan-3 N9 0.020
PR8 plan-3 N7 0.020
PR8 plan-3 C8 0.020
PR8 plan-3 N6 0.020
PR8 plan-3 H8 0.020
PR8 plan-3 "C1'" 0.020
PR8 plan-3 HN6A 0.020
PR8 plan-3 HN6 0.020
PR8 plan-4 N6 0.020
PR8 plan-4 C6 0.020
PR8 plan-4 HN6 0.020
PR8 plan-4 HN6A 0.020
# ------------------------------------------------------
|
