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
|
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
TQD TQD '(2R,6S)-6-{[methyl(3,4,5-trimethoxyp' non-polymer 56 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TQD
#
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
TQD "N4'" N NH2 0.000 0.000 0.000 0.000
TQD "H4'1" H H 0.000 -0.944 -0.025 0.372
TQD "H4'2" H H 0.000 0.676 0.633 0.414
TQD C4D C CR6 0.000 0.359 -0.816 -1.055
TQD "N3'" N NRD6 0.000 1.578 -0.773 -1.524
TQD C2D C CH1 0.000 1.971 -1.626 -2.649
TQD "H2'" H H 0.000 3.034 -1.887 -2.558
TQD "N2'" N NH2 0.000 1.745 -0.908 -3.910
TQD H2A2 H H 0.000 1.107 -1.281 -4.604
TQD H2A1 H H 0.000 2.226 -0.036 -4.096
TQD C4A C CR6 0.000 -0.634 -1.728 -1.645
TQD C8A C CR6 0.000 -0.201 -2.734 -2.416
TQD "N1'" N NR16 0.000 1.161 -2.850 -2.627
TQD H1D H H 0.000 1.601 -3.782 -2.767
TQD C8 C CH2 0.000 -1.116 -3.736 -3.061
TQD H81 H H 0.000 -1.076 -4.668 -2.493
TQD H82 H H 0.000 -0.777 -3.919 -4.082
TQD "C7'" C CH2 0.000 -2.552 -3.213 -3.084
TQD "H7'1" H H 0.000 -3.235 -4.010 -3.387
TQD "H7'2" H H 0.000 -2.634 -2.379 -3.785
TQD C6D C CH1 0.000 -2.914 -2.734 -1.673
TQD "H6'" H H 0.000 -2.681 -3.523 -0.943
TQD C5D C CH2 0.000 -2.091 -1.485 -1.362
TQD "H5'2" H H 0.000 -2.221 -1.230 -0.308
TQD "H5'1" H H 0.000 -2.451 -0.661 -1.982
TQD "C8'" C CH2 0.000 -4.406 -2.398 -1.610
TQD "H8'1" H H 0.000 -4.988 -3.268 -1.920
TQD "H8'2" H H 0.000 -4.619 -1.562 -2.279
TQD "N9'" N N 0.000 -4.765 -2.032 -0.238
TQD "C9'" C CH3 0.000 -5.209 -3.064 0.703
TQD "H9'3" H H 0.000 -5.884 -2.641 1.402
TQD "H9'2" H H 0.000 -5.694 -3.842 0.173
TQD "H9'1" H H 0.000 -4.372 -3.459 1.219
TQD "C1'" C CR6 0.000 -4.686 -0.697 0.174
TQD "C6'" C CR16 0.000 -4.261 0.279 -0.716
TQD "H6'1" H H 0.000 -3.995 0.008 -1.731
TQD "C5'" C CR6 0.000 -4.176 1.602 -0.308
TQD "O5'" O O2 0.000 -3.760 2.558 -1.180
TQD C5B C CH3 0.000 -3.425 2.129 -2.502
TQD H5B3 H H 0.000 -2.636 1.423 -2.455
TQD H5B2 H H 0.000 -4.272 1.681 -2.954
TQD H5B1 H H 0.000 -3.117 2.963 -3.078
TQD "C4'" C CR6 0.000 -4.518 1.949 0.993
TQD "O4'" O O2 0.000 -4.436 3.248 1.396
TQD C4B C CH3 0.000 -3.193 3.677 1.955
TQD H4B3 H H 0.000 -3.261 4.699 2.225
TQD H4B2 H H 0.000 -2.974 3.098 2.815
TQD H4B1 H H 0.000 -2.422 3.551 1.240
TQD "C3'" C CR6 0.000 -4.944 0.972 1.884
TQD "C2'" C CR16 0.000 -5.027 -0.350 1.474
TQD "H2'1" H H 0.000 -5.359 -1.113 2.168
TQD "O3'" O O2 0.000 -5.279 1.311 3.158
TQD C3B C CH3 0.000 -5.709 0.254 4.019
TQD H3B3 H H 0.000 -6.572 -0.205 3.611
TQD H3B2 H H 0.000 -4.937 -0.465 4.110
TQD H3B1 H H 0.000 -5.938 0.648 4.975
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
TQD "N4'" n/a C4D START
TQD "H4'1" "N4'" . .
TQD "H4'2" "N4'" . .
TQD C4D "N4'" C4A .
TQD "N3'" C4D C2D .
TQD C2D "N3'" "N2'" .
TQD "H2'" C2D . .
TQD "N2'" C2D H2A1 .
TQD H2A2 "N2'" . .
TQD H2A1 "N2'" . .
TQD C4A C4D C8A .
TQD C8A C4A C8 .
TQD "N1'" C8A H1D .
TQD H1D "N1'" . .
TQD C8 C8A "C7'" .
TQD H81 C8 . .
TQD H82 C8 . .
TQD "C7'" C8 C6D .
TQD "H7'1" "C7'" . .
TQD "H7'2" "C7'" . .
TQD C6D "C7'" "C8'" .
TQD "H6'" C6D . .
TQD C5D C6D "H5'1" .
TQD "H5'2" C5D . .
TQD "H5'1" C5D . .
TQD "C8'" C6D "N9'" .
TQD "H8'1" "C8'" . .
TQD "H8'2" "C8'" . .
TQD "N9'" "C8'" "C1'" .
TQD "C9'" "N9'" "H9'1" .
TQD "H9'3" "C9'" . .
TQD "H9'2" "C9'" . .
TQD "H9'1" "C9'" . .
TQD "C1'" "N9'" "C6'" .
TQD "C6'" "C1'" "C5'" .
TQD "H6'1" "C6'" . .
TQD "C5'" "C6'" "C4'" .
TQD "O5'" "C5'" C5B .
TQD C5B "O5'" H5B1 .
TQD H5B3 C5B . .
TQD H5B2 C5B . .
TQD H5B1 C5B . .
TQD "C4'" "C5'" "C3'" .
TQD "O4'" "C4'" C4B .
TQD C4B "O4'" H4B1 .
TQD H4B3 C4B . .
TQD H4B2 C4B . .
TQD H4B1 C4B . .
TQD "C3'" "C4'" "O3'" .
TQD "C2'" "C3'" "H2'1" .
TQD "H2'1" "C2'" . .
TQD "O3'" "C3'" C3B .
TQD C3B "O3'" H3B1 .
TQD H3B3 C3B . .
TQD H3B2 C3B . .
TQD H3B1 C3B . END
TQD C2D "N1'" . ADD
TQD C4A C5D . ADD
TQD "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
TQD C2D "N1'" single 1.465 0.020
TQD "N2'" C2D single 1.450 0.020
TQD C2D "N3'" single 1.465 0.020
TQD "H2'" C2D single 1.099 0.020
TQD C4A C4D single 1.487 0.020
TQD "N3'" C4D double 1.350 0.020
TQD C4D "N4'" single 1.355 0.020
TQD C4A C5D single 1.511 0.020
TQD C8A C4A double 1.487 0.020
TQD C5D C6D single 1.524 0.020
TQD "H5'1" C5D single 1.092 0.020
TQD "H5'2" C5D single 1.092 0.020
TQD C6D "C7'" single 1.524 0.020
TQD "C8'" C6D single 1.524 0.020
TQD "H6'" C6D single 1.099 0.020
TQD "C7'" C8 single 1.524 0.020
TQD "H7'1" "C7'" single 1.092 0.020
TQD "H7'2" "C7'" single 1.092 0.020
TQD C8 C8A single 1.511 0.020
TQD H81 C8 single 1.092 0.020
TQD H82 C8 single 1.092 0.020
TQD "N1'" C8A single 1.337 0.020
TQD "N9'" "C8'" single 1.455 0.020
TQD "H8'1" "C8'" single 1.092 0.020
TQD "H8'2" "C8'" single 1.092 0.020
TQD "C1'" "C2'" double 1.390 0.020
TQD "C6'" "C1'" single 1.390 0.020
TQD "C1'" "N9'" single 1.400 0.020
TQD "C2'" "C3'" single 1.390 0.020
TQD "H2'1" "C2'" single 1.083 0.020
TQD "C3'" "C4'" double 1.487 0.020
TQD "O3'" "C3'" single 1.370 0.020
TQD C3B "O3'" single 1.426 0.020
TQD H3B1 C3B single 1.059 0.020
TQD H3B2 C3B single 1.059 0.020
TQD H3B3 C3B single 1.059 0.020
TQD "C4'" "C5'" single 1.487 0.020
TQD "O4'" "C4'" single 1.370 0.020
TQD C4B "O4'" single 1.426 0.020
TQD H4B1 C4B single 1.059 0.020
TQD H4B2 C4B single 1.059 0.020
TQD H4B3 C4B single 1.059 0.020
TQD "C5'" "C6'" double 1.390 0.020
TQD "O5'" "C5'" single 1.370 0.020
TQD C5B "O5'" single 1.426 0.020
TQD H5B1 C5B single 1.059 0.020
TQD H5B2 C5B single 1.059 0.020
TQD H5B3 C5B single 1.059 0.020
TQD "H6'1" "C6'" single 1.083 0.020
TQD H1D "N1'" single 1.040 0.020
TQD H2A1 "N2'" single 1.010 0.020
TQD H2A2 "N2'" single 1.010 0.020
TQD "H4'1" "N4'" single 1.010 0.020
TQD "H4'2" "N4'" single 1.010 0.020
TQD "C9'" "N9'" single 1.455 0.020
TQD "H9'1" "C9'" single 1.059 0.020
TQD "H9'2" "C9'" single 1.059 0.020
TQD "H9'3" "C9'" single 1.059 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
TQD "H4'1" "N4'" "H4'2" 120.000 3.000
TQD "H4'1" "N4'" C4D 120.000 3.000
TQD "H4'2" "N4'" C4D 120.000 3.000
TQD "N4'" C4D "N3'" 120.000 3.000
TQD "N4'" C4D C4A 120.000 3.000
TQD "N3'" C4D C4A 120.000 3.000
TQD C4D "N3'" C2D 120.000 3.000
TQD "N3'" C2D "H2'" 109.500 3.000
TQD "N3'" C2D "N2'" 109.500 3.000
TQD "N3'" C2D "N1'" 109.500 3.000
TQD "H2'" C2D "N2'" 109.470 3.000
TQD "H2'" C2D "N1'" 109.500 3.000
TQD "N2'" C2D "N1'" 109.500 3.000
TQD C2D "N2'" H2A2 120.000 3.000
TQD C2D "N2'" H2A1 120.000 3.000
TQD H2A2 "N2'" H2A1 120.000 3.000
TQD C4D C4A C8A 120.000 3.000
TQD C4D C4A C5D 120.000 3.000
TQD C8A C4A C5D 120.000 3.000
TQD C4A C8A "N1'" 120.000 3.000
TQD C4A C8A C8 120.000 3.000
TQD "N1'" C8A C8 120.000 3.000
TQD C8A "N1'" H1D 120.000 3.000
TQD C8A "N1'" C2D 120.000 3.000
TQD H1D "N1'" C2D 120.000 3.000
TQD C8A C8 H81 109.470 3.000
TQD C8A C8 H82 109.470 3.000
TQD C8A C8 "C7'" 109.470 3.000
TQD H81 C8 H82 107.900 3.000
TQD H81 C8 "C7'" 109.470 3.000
TQD H82 C8 "C7'" 109.470 3.000
TQD C8 "C7'" "H7'1" 109.470 3.000
TQD C8 "C7'" "H7'2" 109.470 3.000
TQD C8 "C7'" C6D 111.000 3.000
TQD "H7'1" "C7'" "H7'2" 107.900 3.000
TQD "H7'1" "C7'" C6D 109.470 3.000
TQD "H7'2" "C7'" C6D 109.470 3.000
TQD "C7'" C6D "H6'" 108.340 3.000
TQD "C7'" C6D C5D 109.470 3.000
TQD "C7'" C6D "C8'" 109.470 3.000
TQD "H6'" C6D C5D 108.340 3.000
TQD "H6'" C6D "C8'" 108.340 3.000
TQD C5D C6D "C8'" 109.470 3.000
TQD C6D C5D "H5'2" 109.470 3.000
TQD C6D C5D "H5'1" 109.470 3.000
TQD C6D C5D C4A 109.470 3.000
TQD "H5'2" C5D "H5'1" 107.900 3.000
TQD "H5'2" C5D C4A 109.470 3.000
TQD "H5'1" C5D C4A 109.470 3.000
TQD C6D "C8'" "H8'1" 109.470 3.000
TQD C6D "C8'" "H8'2" 109.470 3.000
TQD C6D "C8'" "N9'" 105.000 3.000
TQD "H8'1" "C8'" "H8'2" 107.900 3.000
TQD "H8'1" "C8'" "N9'" 109.470 3.000
TQD "H8'2" "C8'" "N9'" 109.470 3.000
TQD "C8'" "N9'" "C9'" 120.000 3.000
TQD "C8'" "N9'" "C1'" 120.000 3.000
TQD "C9'" "N9'" "C1'" 120.000 3.000
TQD "N9'" "C9'" "H9'3" 109.470 3.000
TQD "N9'" "C9'" "H9'2" 109.470 3.000
TQD "N9'" "C9'" "H9'1" 109.470 3.000
TQD "H9'3" "C9'" "H9'2" 109.470 3.000
TQD "H9'3" "C9'" "H9'1" 109.470 3.000
TQD "H9'2" "C9'" "H9'1" 109.470 3.000
TQD "N9'" "C1'" "C6'" 120.000 3.000
TQD "N9'" "C1'" "C2'" 120.000 3.000
TQD "C6'" "C1'" "C2'" 120.000 3.000
TQD "C1'" "C6'" "H6'1" 120.000 3.000
TQD "C1'" "C6'" "C5'" 120.000 3.000
TQD "H6'1" "C6'" "C5'" 120.000 3.000
TQD "C6'" "C5'" "O5'" 120.000 3.000
TQD "C6'" "C5'" "C4'" 120.000 3.000
TQD "O5'" "C5'" "C4'" 120.000 3.000
TQD "C5'" "O5'" C5B 120.000 3.000
TQD "O5'" C5B H5B3 109.470 3.000
TQD "O5'" C5B H5B2 109.470 3.000
TQD "O5'" C5B H5B1 109.470 3.000
TQD H5B3 C5B H5B2 109.470 3.000
TQD H5B3 C5B H5B1 109.470 3.000
TQD H5B2 C5B H5B1 109.470 3.000
TQD "C5'" "C4'" "O4'" 120.000 3.000
TQD "C5'" "C4'" "C3'" 120.000 3.000
TQD "O4'" "C4'" "C3'" 120.000 3.000
TQD "C4'" "O4'" C4B 120.000 3.000
TQD "O4'" C4B H4B3 109.470 3.000
TQD "O4'" C4B H4B2 109.470 3.000
TQD "O4'" C4B H4B1 109.470 3.000
TQD H4B3 C4B H4B2 109.470 3.000
TQD H4B3 C4B H4B1 109.470 3.000
TQD H4B2 C4B H4B1 109.470 3.000
TQD "C4'" "C3'" "C2'" 120.000 3.000
TQD "C4'" "C3'" "O3'" 120.000 3.000
TQD "C2'" "C3'" "O3'" 120.000 3.000
TQD "C3'" "C2'" "H2'1" 120.000 3.000
TQD "C3'" "C2'" "C1'" 120.000 3.000
TQD "H2'1" "C2'" "C1'" 120.000 3.000
TQD "C3'" "O3'" C3B 120.000 3.000
TQD "O3'" C3B H3B3 109.470 3.000
TQD "O3'" C3B H3B2 109.470 3.000
TQD "O3'" C3B H3B1 109.470 3.000
TQD H3B3 C3B H3B2 109.470 3.000
TQD H3B3 C3B H3B1 109.470 3.000
TQD H3B2 C3B H3B1 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
TQD CONST_1 "H4'2" "N4'" C4D C4A -179.980 0.000 0
TQD CONST_2 "N4'" C4D "N3'" C2D 180.000 0.000 0
TQD CONST_3 C4D "N3'" C2D "N2'" 90.000 0.000 0
TQD CONST_4 "N3'" C2D "N1'" C8A 60.000 0.000 0
TQD var_1 "N3'" C2D "N2'" H2A1 60.421 20.000 1
TQD CONST_5 "N4'" C4D C4A C8A -150.000 0.000 0
TQD var_2 C4D C4A C5D C6D -150.000 20.000 2
TQD CONST_6 C4D C4A C8A C8 180.000 0.000 0
TQD CONST_7 C4A C8A "N1'" C2D -30.000 0.000 0
TQD var_3 C4A C8A C8 "C7'" 30.000 20.000 2
TQD var_4 C8A C8 "C7'" C6D -60.000 20.000 3
TQD var_5 C8 "C7'" C6D "C8'" 180.000 20.000 3
TQD var_6 "C7'" C6D C5D C4A -60.000 20.000 3
TQD var_7 "C7'" C6D "C8'" "N9'" 176.087 20.000 3
TQD var_8 C6D "C8'" "N9'" "C1'" 90.024 20.000 1
TQD var_9 "C8'" "N9'" "C9'" "H9'1" 90.114 20.000 1
TQD var_10 "C8'" "N9'" "C1'" "C6'" -0.310 20.000 1
TQD CONST_8 "N9'" "C1'" "C2'" "C3'" 180.000 0.000 0
TQD CONST_9 "N9'" "C1'" "C6'" "C5'" 180.000 0.000 0
TQD CONST_10 "C1'" "C6'" "C5'" "C4'" 0.000 0.000 0
TQD var_11 "C6'" "C5'" "O5'" C5B -0.035 20.000 1
TQD var_12 "C5'" "O5'" C5B H5B1 -179.965 20.000 1
TQD CONST_11 "C6'" "C5'" "C4'" "C3'" 0.000 0.000 0
TQD var_13 "C5'" "C4'" "O4'" C4B -90.037 20.000 1
TQD var_14 "C4'" "O4'" C4B H4B1 59.992 20.000 1
TQD CONST_12 "C5'" "C4'" "C3'" "O3'" 180.000 0.000 0
TQD CONST_13 "C4'" "C3'" "C2'" "C1'" 0.000 0.000 0
TQD var_15 "C4'" "C3'" "O3'" C3B 179.965 20.000 1
TQD var_16 "C3'" "O3'" C3B H3B1 179.994 20.000 1
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
TQD chir_01 C2D "N1'" "N2'" "N3'" negativ
TQD chir_02 C6D C5D "C7'" "C8'" 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
TQD plan-1 C4D 0.020
TQD plan-1 C4A 0.020
TQD plan-1 "N3'" 0.020
TQD plan-1 "N4'" 0.020
TQD plan-1 C2D 0.020
TQD plan-1 C8A 0.020
TQD plan-1 "N1'" 0.020
TQD plan-1 C5D 0.020
TQD plan-1 C8 0.020
TQD plan-1 H1D 0.020
TQD plan-1 "H4'1" 0.020
TQD plan-1 "H4'2" 0.020
TQD plan-2 "C1'" 0.020
TQD plan-2 "C2'" 0.020
TQD plan-2 "C6'" 0.020
TQD plan-2 "N9'" 0.020
TQD plan-2 "C3'" 0.020
TQD plan-2 "C4'" 0.020
TQD plan-2 "C5'" 0.020
TQD plan-2 "H2'1" 0.020
TQD plan-2 "O3'" 0.020
TQD plan-2 "O4'" 0.020
TQD plan-2 "O5'" 0.020
TQD plan-2 "H6'1" 0.020
TQD plan-3 "N2'" 0.020
TQD plan-3 C2D 0.020
TQD plan-3 H2A1 0.020
TQD plan-3 H2A2 0.020
TQD plan-4 "N4'" 0.020
TQD plan-4 C4D 0.020
TQD plan-4 "H4'1" 0.020
TQD plan-4 "H4'2" 0.020
TQD plan-5 "N9'" 0.020
TQD plan-5 "C8'" 0.020
TQD plan-5 "C1'" 0.020
TQD plan-5 "C9'" 0.020
# ------------------------------------------------------
|
