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
|
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
CR3 CR3 '2-{5-[AMINO(IMINIO)METHYL]-1H-INDOL-' non-polymer 46 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CR3
#
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
CR3 "O6'" O O -1.000 0.000 0.000 0.000
CR3 "C6'" C CR6 0.000 -0.422 -1.242 0.359
CR3 "C5'" C CR6 0.000 0.503 -2.247 0.614
CR3 "O5'" O O2 0.000 1.834 -1.991 0.501
CR3 C2B C CH1 0.000 2.510 -3.240 0.663
CR3 H2A H H 0.000 1.928 -4.047 0.195
CR3 C3B C CH2 0.000 2.718 -3.538 2.162
CR3 H3A H H 0.000 1.962 -4.224 2.552
CR3 H3B H H 0.000 2.725 -2.627 2.764
CR3 C4B C CH2 0.000 4.110 -4.212 2.226
CR3 H4A H H 0.000 4.080 -5.268 1.949
CR3 H4B H H 0.000 4.584 -4.107 3.204
CR3 C5B C CH2 0.000 4.921 -3.422 1.169
CR3 H5A H H 0.000 5.765 -3.999 0.785
CR3 H5B H H 0.000 5.282 -2.468 1.558
CR3 C1B C CH2 0.000 3.911 -3.166 0.031
CR3 H1B H H 0.000 4.001 -3.926 -0.747
CR3 H1A H H 0.000 4.062 -2.178 -0.408
CR3 "C4'" C CR16 0.000 0.070 -3.512 0.980
CR3 "HC4'" H H 0.000 0.793 -4.294 1.175
CR3 "C3'" C CR16 0.000 -1.284 -3.779 1.096
CR3 "HC3'" H H 0.000 -1.615 -4.770 1.380
CR3 "C2'" C CR16 0.000 -2.213 -2.789 0.851
CR3 "HC2'" H H 0.000 -3.270 -3.003 0.945
CR3 "C1'" C CR6 0.000 -1.789 -1.510 0.483
CR3 C8 C CR5 0.000 -2.782 -0.447 0.220
CR3 N3 N NR15 0.000 -2.654 0.870 0.600
CR3 HN3 H H 0.000 -1.843 1.266 1.117
CR3 C4 C CR56 0.000 -3.758 1.583 0.195
CR3 C3 C CR16 0.000 -4.124 2.920 0.323
CR3 HC3 H H 0.000 -3.466 3.614 0.831
CR3 C2 C CR16 0.000 -5.309 3.361 -0.189
CR3 HC2 H H 0.000 -5.584 4.403 -0.084
CR3 CN4 C CR15 0.000 -3.957 -0.619 -0.435
CR3 HCN4 H H 0.000 -4.333 -1.545 -0.853
CR3 C5 C CR56 0.000 -4.619 0.685 -0.468
CR3 C6 C CR16 0.000 -5.831 1.137 -0.987
CR3 HC6 H H 0.000 -6.501 0.451 -1.492
CR3 C1 C CR6 0.000 -6.173 2.479 -0.851
CR3 C7 C C 0.000 -7.453 2.974 -1.400
CR3 N2 N NH2 1.000 -7.784 4.257 -1.266
CR3 HH22 H H 0.000 -8.659 4.595 -1.642
CR3 HH21 H H 0.000 -7.161 4.892 -0.789
CR3 N1 N NH2 0.000 -8.277 2.136 -2.030
CR3 HH12 H H 0.000 -8.026 1.163 -2.132
CR3 HH11 H H 0.000 -9.151 2.474 -2.406
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
CR3 "O6'" n/a "C6'" START
CR3 "C6'" "O6'" "C1'" .
CR3 "C5'" "C6'" "C4'" .
CR3 "O5'" "C5'" C2B .
CR3 C2B "O5'" C3B .
CR3 H2A C2B . .
CR3 C3B C2B C4B .
CR3 H3A C3B . .
CR3 H3B C3B . .
CR3 C4B C3B C5B .
CR3 H4A C4B . .
CR3 H4B C4B . .
CR3 C5B C4B C1B .
CR3 H5A C5B . .
CR3 H5B C5B . .
CR3 C1B C5B H1A .
CR3 H1B C1B . .
CR3 H1A C1B . .
CR3 "C4'" "C5'" "C3'" .
CR3 "HC4'" "C4'" . .
CR3 "C3'" "C4'" "C2'" .
CR3 "HC3'" "C3'" . .
CR3 "C2'" "C3'" "HC2'" .
CR3 "HC2'" "C2'" . .
CR3 "C1'" "C6'" C8 .
CR3 C8 "C1'" CN4 .
CR3 N3 C8 C4 .
CR3 HN3 N3 . .
CR3 C4 N3 C3 .
CR3 C3 C4 C2 .
CR3 HC3 C3 . .
CR3 C2 C3 HC2 .
CR3 HC2 C2 . .
CR3 CN4 C8 C5 .
CR3 HCN4 CN4 . .
CR3 C5 CN4 C6 .
CR3 C6 C5 C1 .
CR3 HC6 C6 . .
CR3 C1 C6 C7 .
CR3 C7 C1 N1 .
CR3 N2 C7 HH21 .
CR3 HH22 N2 . .
CR3 HH21 N2 . .
CR3 N1 C7 HH11 .
CR3 HH12 N1 . .
CR3 HH11 N1 . END
CR3 C1 C2 . ADD
CR3 C4 C5 . ADD
CR3 "C1'" "C2'" . ADD
CR3 C1B C2B . 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
CR3 C1 C2 double 1.390 0.020
CR3 C1 C6 single 1.390 0.020
CR3 C7 C1 single 1.500 0.020
CR3 C2 C3 single 1.390 0.020
CR3 HC2 C2 single 1.083 0.020
CR3 C3 C4 double 1.390 0.020
CR3 HC3 C3 single 1.083 0.020
CR3 C4 C5 single 1.490 0.020
CR3 C4 N3 single 1.340 0.020
CR3 C6 C5 double 1.390 0.020
CR3 C5 CN4 single 1.440 0.020
CR3 HC6 C6 single 1.083 0.020
CR3 N1 C7 single 1.332 0.020
CR3 N2 C7 double 1.332 0.020
CR3 HH11 N1 single 1.010 0.020
CR3 HH12 N1 single 1.010 0.020
CR3 HH21 N2 single 1.010 0.020
CR3 HH22 N2 single 1.010 0.020
CR3 N3 C8 single 1.340 0.020
CR3 HN3 N3 single 1.040 0.020
CR3 CN4 C8 double 1.387 0.020
CR3 HCN4 CN4 single 1.083 0.020
CR3 C8 "C1'" single 1.490 0.020
CR3 "C1'" "C2'" double 1.390 0.020
CR3 "C1'" "C6'" single 1.487 0.020
CR3 "C2'" "C3'" single 1.390 0.020
CR3 "HC2'" "C2'" single 1.083 0.020
CR3 "C3'" "C4'" double 1.390 0.020
CR3 "HC3'" "C3'" single 1.083 0.020
CR3 "C4'" "C5'" single 1.390 0.020
CR3 "HC4'" "C4'" single 1.083 0.020
CR3 "O5'" "C5'" single 1.370 0.020
CR3 "C5'" "C6'" double 1.487 0.020
CR3 C2B "O5'" single 1.426 0.020
CR3 "C6'" "O6'" single 1.330 0.020
CR3 C1B C2B single 1.524 0.020
CR3 C1B C5B single 1.524 0.020
CR3 H1A C1B single 1.092 0.020
CR3 H1B C1B single 1.092 0.020
CR3 C3B C2B single 1.524 0.020
CR3 H2A C2B single 1.099 0.020
CR3 C4B C3B single 1.524 0.020
CR3 H3A C3B single 1.092 0.020
CR3 H3B C3B single 1.092 0.020
CR3 C5B C4B single 1.524 0.020
CR3 H4A C4B single 1.092 0.020
CR3 H4B C4B single 1.092 0.020
CR3 H5A C5B single 1.092 0.020
CR3 H5B C5B 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
CR3 "O6'" "C6'" "C5'" 120.000 3.000
CR3 "O6'" "C6'" "C1'" 120.000 3.000
CR3 "C5'" "C6'" "C1'" 120.000 3.000
CR3 "C6'" "C5'" "O5'" 120.000 3.000
CR3 "C6'" "C5'" "C4'" 120.000 3.000
CR3 "O5'" "C5'" "C4'" 120.000 3.000
CR3 "C5'" "O5'" C2B 120.000 3.000
CR3 "O5'" C2B H2A 109.470 3.000
CR3 "O5'" C2B C3B 109.470 3.000
CR3 "O5'" C2B C1B 109.470 3.000
CR3 H2A C2B C3B 108.340 3.000
CR3 H2A C2B C1B 108.340 3.000
CR3 C3B C2B C1B 109.470 3.000
CR3 C2B C3B H3A 109.470 3.000
CR3 C2B C3B H3B 109.470 3.000
CR3 C2B C3B C4B 111.000 3.000
CR3 H3A C3B H3B 107.900 3.000
CR3 H3A C3B C4B 109.470 3.000
CR3 H3B C3B C4B 109.470 3.000
CR3 C3B C4B H4A 109.470 3.000
CR3 C3B C4B H4B 109.470 3.000
CR3 C3B C4B C5B 111.000 3.000
CR3 H4A C4B H4B 107.900 3.000
CR3 H4A C4B C5B 109.470 3.000
CR3 H4B C4B C5B 109.470 3.000
CR3 C4B C5B H5A 109.470 3.000
CR3 C4B C5B H5B 109.470 3.000
CR3 C4B C5B C1B 111.000 3.000
CR3 H5A C5B H5B 107.900 3.000
CR3 H5A C5B C1B 109.470 3.000
CR3 H5B C5B C1B 109.470 3.000
CR3 C5B C1B H1B 109.470 3.000
CR3 C5B C1B H1A 109.470 3.000
CR3 C5B C1B C2B 111.000 3.000
CR3 H1B C1B H1A 107.900 3.000
CR3 H1B C1B C2B 109.470 3.000
CR3 H1A C1B C2B 109.470 3.000
CR3 "C5'" "C4'" "HC4'" 120.000 3.000
CR3 "C5'" "C4'" "C3'" 120.000 3.000
CR3 "HC4'" "C4'" "C3'" 120.000 3.000
CR3 "C4'" "C3'" "HC3'" 120.000 3.000
CR3 "C4'" "C3'" "C2'" 120.000 3.000
CR3 "HC3'" "C3'" "C2'" 120.000 3.000
CR3 "C3'" "C2'" "HC2'" 120.000 3.000
CR3 "C3'" "C2'" "C1'" 120.000 3.000
CR3 "HC2'" "C2'" "C1'" 120.000 3.000
CR3 "C6'" "C1'" C8 120.000 3.000
CR3 "C6'" "C1'" "C2'" 120.000 3.000
CR3 C8 "C1'" "C2'" 120.000 3.000
CR3 "C1'" C8 N3 108.000 3.000
CR3 "C1'" C8 CN4 126.000 3.000
CR3 N3 C8 CN4 108.000 3.000
CR3 C8 N3 HN3 126.000 3.000
CR3 C8 N3 C4 108.000 3.000
CR3 HN3 N3 C4 126.000 3.000
CR3 N3 C4 C3 132.000 3.000
CR3 N3 C4 C5 108.000 3.000
CR3 C3 C4 C5 120.000 3.000
CR3 C4 C3 HC3 120.000 3.000
CR3 C4 C3 C2 120.000 3.000
CR3 HC3 C3 C2 120.000 3.000
CR3 C3 C2 HC2 120.000 3.000
CR3 C3 C2 C1 120.000 3.000
CR3 HC2 C2 C1 120.000 3.000
CR3 C8 CN4 HCN4 126.000 3.000
CR3 C8 CN4 C5 108.000 3.000
CR3 HCN4 CN4 C5 108.000 3.000
CR3 CN4 C5 C6 126.000 3.000
CR3 CN4 C5 C4 120.000 3.000
CR3 C6 C5 C4 120.000 3.000
CR3 C5 C6 HC6 120.000 3.000
CR3 C5 C6 C1 120.000 3.000
CR3 HC6 C6 C1 120.000 3.000
CR3 C6 C1 C7 120.000 3.000
CR3 C6 C1 C2 120.000 3.000
CR3 C7 C1 C2 120.000 3.000
CR3 C1 C7 N2 120.000 3.000
CR3 C1 C7 N1 120.000 3.000
CR3 N2 C7 N1 120.000 3.000
CR3 C7 N2 HH22 120.000 3.000
CR3 C7 N2 HH21 120.000 3.000
CR3 HH22 N2 HH21 120.000 3.000
CR3 C7 N1 HH12 120.000 3.000
CR3 C7 N1 HH11 120.000 3.000
CR3 HH12 N1 HH11 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
CR3 CONST_1 "O6'" "C6'" "C5'" "C4'" 180.000 0.000 0
CR3 var_1 "C6'" "C5'" "O5'" C2B -173.127 20.000 1
CR3 var_2 "C5'" "O5'" C2B C3B -84.572 20.000 1
CR3 var_3 "O5'" C2B C3B C4B -150.000 20.000 3
CR3 var_4 C2B C3B C4B C5B 30.000 20.000 3
CR3 var_5 C3B C4B C5B C1B -30.000 20.000 3
CR3 var_6 C4B C5B C1B C2B 30.000 20.000 3
CR3 var_7 C5B C1B C2B "O5'" 120.000 20.000 3
CR3 CONST_2 "C6'" "C5'" "C4'" "C3'" 0.000 0.000 0
CR3 CONST_3 "C5'" "C4'" "C3'" "C2'" 0.000 0.000 0
CR3 CONST_4 "C4'" "C3'" "C2'" "C1'" 0.000 0.000 0
CR3 CONST_5 "O6'" "C6'" "C1'" C8 0.000 0.000 0
CR3 CONST_6 "C6'" "C1'" "C2'" "C3'" 0.000 0.000 0
CR3 var_8 "C6'" "C1'" C8 CN4 139.680 20.000 1
CR3 CONST_7 "C1'" C8 N3 C4 180.000 0.000 0
CR3 CONST_8 C8 N3 C4 C3 180.000 0.000 0
CR3 CONST_9 N3 C4 C5 CN4 0.000 0.000 0
CR3 CONST_10 N3 C4 C3 C2 180.000 0.000 0
CR3 CONST_11 C4 C3 C2 C1 0.000 0.000 0
CR3 CONST_12 "C1'" C8 CN4 C5 180.000 0.000 0
CR3 CONST_13 C8 CN4 C5 C6 180.000 0.000 0
CR3 CONST_14 CN4 C5 C6 C1 180.000 0.000 0
CR3 CONST_15 C5 C6 C1 C7 180.000 0.000 0
CR3 CONST_16 C6 C1 C2 C3 0.000 0.000 0
CR3 var_9 C6 C1 C7 N1 -0.250 20.000 1
CR3 CONST_17 C1 C7 N2 HH21 0.000 0.000 0
CR3 CONST_18 C1 C7 N1 HH11 180.000 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
CR3 chir_01 C2B "O5'" C1B C3B 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
CR3 plan-1 C1 0.020
CR3 plan-1 C2 0.020
CR3 plan-1 C6 0.020
CR3 plan-1 C7 0.020
CR3 plan-1 C3 0.020
CR3 plan-1 HC2 0.020
CR3 plan-1 C4 0.020
CR3 plan-1 HC3 0.020
CR3 plan-1 C5 0.020
CR3 plan-1 N3 0.020
CR3 plan-1 CN4 0.020
CR3 plan-1 C8 0.020
CR3 plan-1 HC6 0.020
CR3 plan-1 HN3 0.020
CR3 plan-1 HCN4 0.020
CR3 plan-1 "C1'" 0.020
CR3 plan-2 C7 0.020
CR3 plan-2 C1 0.020
CR3 plan-2 N1 0.020
CR3 plan-2 N2 0.020
CR3 plan-2 HH21 0.020
CR3 plan-2 HH22 0.020
CR3 plan-2 HH12 0.020
CR3 plan-2 HH11 0.020
CR3 plan-3 N1 0.020
CR3 plan-3 C7 0.020
CR3 plan-3 HH11 0.020
CR3 plan-3 HH12 0.020
CR3 plan-4 "C1'" 0.020
CR3 plan-4 C8 0.020
CR3 plan-4 "C2'" 0.020
CR3 plan-4 "C6'" 0.020
CR3 plan-4 "C3'" 0.020
CR3 plan-4 "C4'" 0.020
CR3 plan-4 "C5'" 0.020
CR3 plan-4 "HC2'" 0.020
CR3 plan-4 "HC3'" 0.020
CR3 plan-4 "HC4'" 0.020
CR3 plan-4 "O5'" 0.020
CR3 plan-4 "O6'" 0.020
# ------------------------------------------------------
|
