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
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
|
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
APR APR 'ADENOSINE-5-DIPHOSPHORIBOSE ' non-polymer 57 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APR
#
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
APR O2B O OP -0.500 0.000 0.000 0.000
APR PB P P 0.000 -0.702 0.104 1.302
APR O1B O OP -0.500 -0.827 1.532 1.682
APR O5D O O2 0.000 0.137 -0.680 2.428
APR C5D C CH2 0.000 1.422 -0.060 2.494
APR H5R1 H H 0.000 1.304 0.993 2.759
APR H5R2 H H 0.000 1.912 -0.137 1.521
APR C4D C CH1 0.000 2.275 -0.762 3.553
APR "HR'4" H H 0.000 1.780 -0.701 4.532
APR C3D C CH1 0.000 3.666 -0.105 3.627
APR "HR'3" H H 0.000 3.757 0.687 2.871
APR O3D O OH1 0.000 3.909 0.421 4.932
APR HOR3 H H 0.000 4.808 0.775 4.974
APR C2D C CH1 0.000 4.647 -1.264 3.317
APR "HR'2" H H 0.000 4.942 -1.255 2.258
APR O2D O OH1 0.000 5.795 -1.202 4.166
APR HOR2 H H 0.000 6.346 -1.983 4.020
APR C1D C CH1 0.000 3.788 -2.513 3.640
APR "HR'1" H H 0.000 3.784 -2.710 4.721
APR O1D O OH1 0.000 4.260 -3.655 2.923
APR HOR1 H H 0.000 3.670 -4.403 3.084
APR O4D O O2 0.000 2.469 -2.139 3.189
APR O3A O O2 0.000 -2.169 -0.546 1.174
APR PA P P 0.000 -2.949 0.284 0.035
APR O1A O OP -0.500 -3.038 1.708 0.436
APR O2A O OP -0.500 -2.211 0.176 -1.247
APR "O5'" O O2 0.000 -4.430 -0.317 -0.146
APR "C5'" C CH2 0.000 -5.068 0.457 -1.164
APR "H5'1" H H 0.000 -4.499 0.375 -2.093
APR "H5'2" H H 0.000 -5.107 1.503 -0.854
APR "C4'" C CH1 0.000 -6.489 -0.064 -1.387
APR "H'4" H H 0.000 -6.464 -1.113 -1.714
APR "C3'" C CH1 0.000 -7.227 0.806 -2.429
APR "H'3" H H 0.000 -6.789 1.813 -2.469
APR "O3'" O OH1 0.000 -7.183 0.190 -3.717
APR "HO'3" H H 0.000 -7.649 0.747 -4.356
APR "C2'" C CH1 0.000 -8.681 0.867 -1.906
APR "H'2" H H 0.000 -8.967 1.905 -1.685
APR "O2'" O OH1 0.000 -9.580 0.294 -2.856
APR "HO'2" H H 0.000 -9.540 0.797 -3.680
APR "O4'" O O2 0.000 -7.268 0.067 -0.178
APR "C1'" C CH1 0.000 -8.646 0.030 -0.608
APR "H'1" H H 0.000 -8.955 -1.005 -0.813
APR N9 N NR5 0.000 -9.514 0.629 0.408
APR C4 C CR56 0.000 -10.837 0.334 0.622
APR N3 N NRD6 0.000 -11.715 -0.494 0.067
APR C2 C CR16 0.000 -12.954 -0.553 0.509
APR H2 H H 0.000 -13.645 -1.238 0.034
APR C8 C CR15 0.000 -9.156 1.581 1.315
APR H8 H H 0.000 -8.170 2.020 1.398
APR N7 N NRD5 0.000 -10.174 1.883 2.066
APR C5 C CR56 0.000 -11.248 1.152 1.688
APR C6 C CR6 0.000 -12.579 1.048 2.127
APR N1 N NRD6 0.000 -13.386 0.193 1.510
APR N6 N NH2 0.000 -13.041 1.826 3.176
APR H62 H H 0.000 -12.421 2.480 3.645
APR H61 H H 0.000 -14.004 1.751 3.489
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
APR O2B n/a PB START
APR PB O2B O3A .
APR O1B PB . .
APR O5D PB C5D .
APR C5D O5D C4D .
APR H5R1 C5D . .
APR H5R2 C5D . .
APR C4D C5D O4D .
APR "HR'4" C4D . .
APR C3D C4D C2D .
APR "HR'3" C3D . .
APR O3D C3D HOR3 .
APR HOR3 O3D . .
APR C2D C3D C1D .
APR "HR'2" C2D . .
APR O2D C2D HOR2 .
APR HOR2 O2D . .
APR C1D C2D O1D .
APR "HR'1" C1D . .
APR O1D C1D HOR1 .
APR HOR1 O1D . .
APR O4D C4D . .
APR O3A PB PA .
APR PA O3A "O5'" .
APR O1A PA . .
APR O2A PA . .
APR "O5'" PA "C5'" .
APR "C5'" "O5'" "C4'" .
APR "H5'1" "C5'" . .
APR "H5'2" "C5'" . .
APR "C4'" "C5'" "O4'" .
APR "H'4" "C4'" . .
APR "C3'" "C4'" "C2'" .
APR "H'3" "C3'" . .
APR "O3'" "C3'" "HO'3" .
APR "HO'3" "O3'" . .
APR "C2'" "C3'" "O2'" .
APR "H'2" "C2'" . .
APR "O2'" "C2'" "HO'2" .
APR "HO'2" "O2'" . .
APR "O4'" "C4'" "C1'" .
APR "C1'" "O4'" N9 .
APR "H'1" "C1'" . .
APR N9 "C1'" C8 .
APR C4 N9 N3 .
APR N3 C4 C2 .
APR C2 N3 H2 .
APR H2 C2 . .
APR C8 N9 N7 .
APR H8 C8 . .
APR N7 C8 C5 .
APR C5 N7 C6 .
APR C6 C5 N6 .
APR N1 C6 . .
APR N6 C6 H61 .
APR H62 N6 . .
APR H61 N6 . END
APR N1 C2 . ADD
APR C4 C5 . ADD
APR "C1'" "C2'" . ADD
APR O4D C1D . 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
APR N1 C2 single 1.337 0.020
APR N1 C6 double 1.350 0.020
APR C2 N3 double 1.337 0.020
APR H2 C2 single 1.083 0.020
APR N3 C4 single 1.355 0.020
APR C4 C5 double 1.490 0.020
APR C4 N9 single 1.337 0.020
APR C6 C5 single 1.490 0.020
APR C5 N7 single 1.350 0.020
APR N6 C6 single 1.355 0.020
APR H61 N6 single 1.010 0.020
APR H62 N6 single 1.010 0.020
APR N7 C8 double 1.350 0.020
APR C8 N9 single 1.337 0.020
APR H8 C8 single 1.083 0.020
APR N9 "C1'" single 1.485 0.020
APR "C1'" "C2'" single 1.524 0.020
APR "C1'" "O4'" single 1.426 0.020
APR "H'1" "C1'" single 1.099 0.020
APR "O2'" "C2'" single 1.432 0.020
APR "C2'" "C3'" single 1.524 0.020
APR "H'2" "C2'" single 1.099 0.020
APR "HO'2" "O2'" single 0.967 0.020
APR "O3'" "C3'" single 1.432 0.020
APR "C3'" "C4'" single 1.524 0.020
APR "H'3" "C3'" single 1.099 0.020
APR "HO'3" "O3'" single 0.967 0.020
APR "O4'" "C4'" single 1.426 0.020
APR "C4'" "C5'" single 1.524 0.020
APR "H'4" "C4'" single 1.099 0.020
APR "C5'" "O5'" single 1.426 0.020
APR "H5'1" "C5'" single 1.092 0.020
APR "H5'2" "C5'" single 1.092 0.020
APR "O5'" PA single 1.610 0.020
APR O1A PA deloc 1.510 0.020
APR O2A PA deloc 1.510 0.020
APR PA O3A single 1.610 0.020
APR O3A PB single 1.610 0.020
APR O1B PB deloc 1.510 0.020
APR PB O2B deloc 1.510 0.020
APR O5D PB single 1.610 0.020
APR C5D O5D single 1.426 0.020
APR C4D C5D single 1.524 0.020
APR H5R1 C5D single 1.092 0.020
APR H5R2 C5D single 1.092 0.020
APR O4D C1D single 1.426 0.020
APR O4D C4D single 1.426 0.020
APR O1D C1D single 1.432 0.020
APR HOR1 O1D single 0.967 0.020
APR C1D C2D single 1.524 0.020
APR "HR'1" C1D single 1.099 0.020
APR O2D C2D single 1.432 0.020
APR HOR2 O2D single 0.967 0.020
APR C2D C3D single 1.524 0.020
APR "HR'2" C2D single 1.099 0.020
APR O3D C3D single 1.432 0.020
APR HOR3 O3D single 0.967 0.020
APR C3D C4D single 1.524 0.020
APR "HR'3" C3D single 1.099 0.020
APR "HR'4" C4D single 1.099 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
APR O2B PB O1B 119.900 3.000
APR O2B PB O5D 108.200 3.000
APR O2B PB O3A 108.200 3.000
APR O1B PB O5D 108.200 3.000
APR O1B PB O3A 108.200 3.000
APR O5D PB O3A 102.600 3.000
APR PB O5D C5D 120.500 3.000
APR O5D C5D H5R1 109.470 3.000
APR O5D C5D H5R2 109.470 3.000
APR O5D C5D C4D 109.470 3.000
APR H5R1 C5D H5R2 107.900 3.000
APR H5R1 C5D C4D 109.470 3.000
APR H5R2 C5D C4D 109.470 3.000
APR C5D C4D "HR'4" 108.340 3.000
APR C5D C4D C3D 111.000 3.000
APR C5D C4D O4D 109.470 3.000
APR "HR'4" C4D C3D 108.340 3.000
APR "HR'4" C4D O4D 109.470 3.000
APR C3D C4D O4D 109.470 3.000
APR C4D C3D "HR'3" 108.340 3.000
APR C4D C3D O3D 109.470 3.000
APR C4D C3D C2D 111.000 3.000
APR "HR'3" C3D O3D 109.470 3.000
APR "HR'3" C3D C2D 108.340 3.000
APR O3D C3D C2D 109.470 3.000
APR C3D O3D HOR3 109.470 3.000
APR C3D C2D "HR'2" 108.340 3.000
APR C3D C2D O2D 109.470 3.000
APR C3D C2D C1D 111.000 3.000
APR "HR'2" C2D O2D 109.470 3.000
APR "HR'2" C2D C1D 108.340 3.000
APR O2D C2D C1D 109.470 3.000
APR C2D O2D HOR2 109.470 3.000
APR C2D C1D "HR'1" 108.340 3.000
APR C2D C1D O1D 109.470 3.000
APR C2D C1D O4D 109.470 3.000
APR "HR'1" C1D O1D 109.470 3.000
APR "HR'1" C1D O4D 109.470 3.000
APR O1D C1D O4D 109.470 3.000
APR C1D O1D HOR1 109.470 3.000
APR C4D O4D C1D 111.800 3.000
APR PB O3A PA 120.500 3.000
APR O3A PA O1A 108.200 3.000
APR O3A PA O2A 108.200 3.000
APR O3A PA "O5'" 102.600 3.000
APR O1A PA O2A 119.900 3.000
APR O1A PA "O5'" 108.200 3.000
APR O2A PA "O5'" 108.200 3.000
APR PA "O5'" "C5'" 120.500 3.000
APR "O5'" "C5'" "H5'1" 109.470 3.000
APR "O5'" "C5'" "H5'2" 109.470 3.000
APR "O5'" "C5'" "C4'" 109.470 3.000
APR "H5'1" "C5'" "H5'2" 107.900 3.000
APR "H5'1" "C5'" "C4'" 109.470 3.000
APR "H5'2" "C5'" "C4'" 109.470 3.000
APR "C5'" "C4'" "H'4" 108.340 3.000
APR "C5'" "C4'" "C3'" 111.000 3.000
APR "C5'" "C4'" "O4'" 109.470 3.000
APR "H'4" "C4'" "C3'" 108.340 3.000
APR "H'4" "C4'" "O4'" 109.470 3.000
APR "C3'" "C4'" "O4'" 109.470 3.000
APR "C4'" "C3'" "H'3" 108.340 3.000
APR "C4'" "C3'" "O3'" 109.470 3.000
APR "C4'" "C3'" "C2'" 111.000 3.000
APR "H'3" "C3'" "O3'" 109.470 3.000
APR "H'3" "C3'" "C2'" 108.340 3.000
APR "O3'" "C3'" "C2'" 109.470 3.000
APR "C3'" "O3'" "HO'3" 109.470 3.000
APR "C3'" "C2'" "H'2" 108.340 3.000
APR "C3'" "C2'" "O2'" 109.470 3.000
APR "C3'" "C2'" "C1'" 111.000 3.000
APR "H'2" "C2'" "O2'" 109.470 3.000
APR "H'2" "C2'" "C1'" 108.340 3.000
APR "O2'" "C2'" "C1'" 109.470 3.000
APR "C2'" "O2'" "HO'2" 109.470 3.000
APR "C4'" "O4'" "C1'" 111.800 3.000
APR "O4'" "C1'" "H'1" 109.470 3.000
APR "O4'" "C1'" N9 109.470 3.000
APR "O4'" "C1'" "C2'" 109.470 3.000
APR "H'1" "C1'" N9 109.470 3.000
APR "H'1" "C1'" "C2'" 108.340 3.000
APR N9 "C1'" "C2'" 109.470 3.000
APR "C1'" N9 C4 126.000 3.000
APR "C1'" N9 C8 126.000 3.000
APR C4 N9 C8 108.000 3.000
APR N9 C4 N3 132.000 3.000
APR N9 C4 C5 108.000 3.000
APR N3 C4 C5 120.000 3.000
APR C4 N3 C2 120.000 3.000
APR N3 C2 H2 120.000 3.000
APR N3 C2 N1 120.000 3.000
APR H2 C2 N1 120.000 3.000
APR N9 C8 H8 126.000 3.000
APR N9 C8 N7 108.000 3.000
APR H8 C8 N7 126.000 3.000
APR C8 N7 C5 108.000 3.000
APR N7 C5 C6 132.000 3.000
APR N7 C5 C4 108.000 3.000
APR C6 C5 C4 120.000 3.000
APR C5 C6 N1 120.000 3.000
APR C5 C6 N6 120.000 3.000
APR N1 C6 N6 120.000 3.000
APR C6 N1 C2 120.000 3.000
APR C6 N6 H62 120.000 3.000
APR C6 N6 H61 120.000 3.000
APR H62 N6 H61 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
APR var_1 O2B PB O5D C5D 59.924 20.000 1
APR var_2 PB O5D C5D C4D 179.990 20.000 1
APR var_3 O5D C5D C4D O4D 61.786 20.000 3
APR var_4 C5D C4D C3D C2D -120.000 20.000 3
APR var_5 C4D C3D O3D HOR3 176.222 20.000 1
APR var_6 C4D C3D C2D C1D -30.000 20.000 3
APR var_7 C3D C2D O2D HOR2 174.128 20.000 1
APR var_8 C3D C2D C1D O1D 150.000 20.000 3
APR var_9 C2D C1D O1D HOR1 -175.595 20.000 1
APR var_10 C5D C4D O4D C1D 150.000 20.000 1
APR var_11 C4D O4D C1D C2D -30.000 20.000 1
APR var_12 O2B PB O3A PA -59.939 20.000 1
APR var_13 PB O3A PA "O5'" 179.990 20.000 1
APR var_14 O3A PA "O5'" "C5'" 179.982 20.000 1
APR var_15 PA "O5'" "C5'" "C4'" -179.983 20.000 1
APR var_16 "O5'" "C5'" "C4'" "O4'" 61.433 20.000 3
APR var_17 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
APR var_18 "C4'" "C3'" "O3'" "HO'3" 179.966 20.000 1
APR var_19 "C4'" "C3'" "C2'" "O2'" -120.000 20.000 3
APR var_20 "C3'" "C2'" "O2'" "HO'2" -61.399 20.000 1
APR var_21 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
APR var_22 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
APR var_23 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
APR var_24 "O4'" "C1'" N9 C8 26.965 20.000 1
APR CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
APR CONST_2 N9 C4 C5 N7 0.000 0.000 0
APR CONST_3 N9 C4 N3 C2 180.000 0.000 0
APR CONST_4 C4 N3 C2 N1 0.000 0.000 0
APR CONST_5 "C1'" N9 C8 N7 180.000 0.000 0
APR CONST_6 N9 C8 N7 C5 0.000 0.000 0
APR CONST_7 C8 N7 C5 C6 180.000 0.000 0
APR CONST_8 N7 C5 C6 N6 0.000 0.000 0
APR CONST_9 C5 C6 N1 C2 0.000 0.000 0
APR CONST_10 C6 N1 C2 N3 0.000 0.000 0
APR CONST_11 C5 C6 N6 H61 179.782 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
APR chir_01 "C1'" N9 "C2'" "O4'" negativ
APR chir_02 "C2'" "C1'" "O2'" "C3'" positiv
APR chir_03 "C3'" "C2'" "O3'" "C4'" positiv
APR chir_04 "C4'" "C3'" "O4'" "C5'" positiv
APR chir_05 C1D O4D O1D C2D negativ
APR chir_06 C2D C1D O2D C3D positiv
APR chir_07 C3D C2D O3D C4D positiv
APR chir_08 C4D C5D O4D C3D 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
APR plan-1 N1 0.020
APR plan-1 C2 0.020
APR plan-1 C6 0.020
APR plan-1 N3 0.020
APR plan-1 H2 0.020
APR plan-1 C4 0.020
APR plan-1 C5 0.020
APR plan-1 N9 0.020
APR plan-1 N7 0.020
APR plan-1 C8 0.020
APR plan-1 N6 0.020
APR plan-1 H8 0.020
APR plan-1 "C1'" 0.020
APR plan-1 H62 0.020
APR plan-1 H61 0.020
APR plan-2 N6 0.020
APR plan-2 C6 0.020
APR plan-2 H61 0.020
APR plan-2 H62 0.020
# ------------------------------------------------------
|
