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
|
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
M8E M8E '5'-{[4-(aminooxy)butyl](methyl)amino' non-polymer 55 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_M8E
#
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
M8E "O3'" O OH1 0.000 0.000 0.000 0.000
M8E "HO3'" H H 0.000 0.717 0.320 0.564
M8E "C3'" C CH1 0.000 -1.247 0.151 0.682
M8E "H3'" H H 0.000 -1.230 -0.386 1.641
M8E "C4'" C CH1 0.000 -2.408 -0.351 -0.198
M8E "H4'" H H 0.000 -2.020 -0.696 -1.167
M8E "C5'" C CH2 0.000 -3.138 -1.495 0.508
M8E "H5'" H H 0.000 -3.600 -1.121 1.424
M8E "H5'A" H H 0.000 -2.424 -2.283 0.757
M8E N2 N NT 0.000 -4.176 -2.035 -0.381
M8E C8 C CH3 0.000 -3.578 -2.678 -1.558
M8E H8B H H 0.000 -2.953 -1.985 -2.058
M8E H8A H H 0.000 -3.005 -3.513 -1.251
M8E H8 H H 0.000 -4.346 -2.998 -2.214
M8E C7 C CH2 0.000 -5.051 -2.970 0.340
M8E H7 H H 0.000 -5.395 -2.505 1.267
M8E H7A H H 0.000 -4.496 -3.880 0.575
M8E C6 C CH2 0.000 -6.257 -3.317 -0.536
M8E H6 H H 0.000 -5.912 -3.782 -1.462
M8E H6A H H 0.000 -6.810 -2.406 -0.772
M8E C5 C CH2 0.000 -7.170 -4.289 0.215
M8E H5 H H 0.000 -7.513 -3.824 1.141
M8E H5A H H 0.000 -6.615 -5.200 0.452
M8E C4 C CH2 0.000 -8.375 -4.637 -0.661
M8E H4 H H 0.000 -8.029 -5.102 -1.586
M8E H4A H H 0.000 -8.928 -3.726 -0.897
M8E O1 O O2 0.000 -9.226 -5.545 0.041
M8E N1 N NH2 0.000 -10.416 -5.946 -0.711
M8E HN1A H H 0.000 -11.375 -5.818 -0.340
M8E HN1 H H 0.000 -10.359 -6.377 -1.651
M8E "C2'" C CH1 0.000 -1.564 1.651 0.907
M8E "H2'" H H 0.000 -2.067 1.805 1.872
M8E "O2'" O OH1 0.000 -0.376 2.440 0.820
M8E "HO2'" H H 0.000 0.205 2.231 1.564
M8E "C1'" C CH1 0.000 -2.521 1.960 -0.272
M8E "H1'" H H 0.000 -1.953 2.149 -1.194
M8E "O4'" O O2 0.000 -3.304 0.754 -0.396
M8E N6 N NR5 0.000 -3.380 3.103 0.048
M8E C12 C CR5 0.000 -4.409 3.119 0.958
M8E C14 C C1 0.000 -4.831 1.973 1.780
M8E H14 H H 0.000 -4.320 1.029 1.692
M8E C15 C C2 0.000 -5.844 2.104 2.631
M8E H15A H H 0.000 -6.157 1.267 3.235
M8E H15 H H 0.000 -6.358 3.048 2.721
M8E N5 N NRD5 0.000 -4.954 4.312 0.984
M8E C11 C CR56 0.000 -4.324 5.115 0.100
M8E C13 C CR56 0.000 -3.309 4.355 -0.511
M8E C10 C CR6 0.000 -4.475 6.458 -0.295
M8E N7 N NH2 0.000 -5.454 7.255 0.270
M8E HN7A H H 0.000 -6.079 6.882 0.979
M8E HN7 H H 0.000 -5.560 8.224 -0.017
M8E N4 N NRD6 0.000 -3.656 6.940 -1.223
M8E C9 C CR16 0.000 -2.719 6.186 -1.767
M8E H9 H H 0.000 -2.073 6.621 -2.520
M8E N3 N NRD6 0.000 -2.539 4.926 -1.430
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
M8E "O3'" n/a "C3'" START
M8E "HO3'" "O3'" . .
M8E "C3'" "O3'" "C2'" .
M8E "H3'" "C3'" . .
M8E "C4'" "C3'" "C5'" .
M8E "H4'" "C4'" . .
M8E "C5'" "C4'" N2 .
M8E "H5'" "C5'" . .
M8E "H5'A" "C5'" . .
M8E N2 "C5'" C7 .
M8E C8 N2 H8 .
M8E H8B C8 . .
M8E H8A C8 . .
M8E H8 C8 . .
M8E C7 N2 C6 .
M8E H7 C7 . .
M8E H7A C7 . .
M8E C6 C7 C5 .
M8E H6 C6 . .
M8E H6A C6 . .
M8E C5 C6 C4 .
M8E H5 C5 . .
M8E H5A C5 . .
M8E C4 C5 O1 .
M8E H4 C4 . .
M8E H4A C4 . .
M8E O1 C4 N1 .
M8E N1 O1 HN1 .
M8E HN1A N1 . .
M8E HN1 N1 . .
M8E "C2'" "C3'" "C1'" .
M8E "H2'" "C2'" . .
M8E "O2'" "C2'" "HO2'" .
M8E "HO2'" "O2'" . .
M8E "C1'" "C2'" N6 .
M8E "H1'" "C1'" . .
M8E "O4'" "C1'" . .
M8E N6 "C1'" C12 .
M8E C12 N6 N5 .
M8E C14 C12 C15 .
M8E H14 C14 . .
M8E C15 C14 H15 .
M8E H15A C15 . .
M8E H15 C15 . .
M8E N5 C12 C11 .
M8E C11 N5 C10 .
M8E C13 C11 . .
M8E C10 C11 N4 .
M8E N7 C10 HN7 .
M8E HN7A N7 . .
M8E HN7 N7 . .
M8E N4 C10 C9 .
M8E C9 N4 N3 .
M8E H9 C9 . .
M8E N3 C9 . END
M8E "C4'" "O4'" . ADD
M8E N6 C13 . ADD
M8E C13 N3 . 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
M8E N1 O1 single 1.335 0.020
M8E O1 C4 single 1.426 0.020
M8E C6 C7 single 1.524 0.020
M8E C5 C6 single 1.524 0.020
M8E C7 N2 single 1.469 0.020
M8E C8 N2 single 1.469 0.020
M8E N2 "C5'" single 1.469 0.020
M8E "C5'" "C4'" single 1.524 0.020
M8E "C4'" "O4'" single 1.426 0.020
M8E "C4'" "C3'" single 1.524 0.020
M8E "O4'" "C1'" single 1.426 0.020
M8E N6 "C1'" single 1.485 0.020
M8E "C1'" "C2'" single 1.524 0.020
M8E N6 C13 single 1.337 0.020
M8E C12 N6 single 1.337 0.020
M8E C13 N3 double 1.355 0.020
M8E C13 C11 single 1.490 0.020
M8E N3 C9 single 1.337 0.020
M8E C9 N4 double 1.337 0.020
M8E N4 C10 single 1.350 0.020
M8E N7 C10 single 1.355 0.020
M8E C10 C11 double 1.490 0.020
M8E C11 N5 single 1.350 0.020
M8E N5 C12 double 1.350 0.020
M8E C14 C12 single 1.483 0.020
M8E "O2'" "C2'" single 1.432 0.020
M8E "C2'" "C3'" single 1.524 0.020
M8E "C3'" "O3'" single 1.432 0.020
M8E C4 C5 single 1.524 0.020
M8E C15 C14 double 1.320 0.020
M8E HN1 N1 single 1.010 0.020
M8E HN1A N1 single 1.010 0.020
M8E H6 C6 single 1.092 0.020
M8E H6A C6 single 1.092 0.020
M8E H7 C7 single 1.092 0.020
M8E H7A C7 single 1.092 0.020
M8E H8 C8 single 1.059 0.020
M8E H8A C8 single 1.059 0.020
M8E H8B C8 single 1.059 0.020
M8E "H5'" "C5'" single 1.092 0.020
M8E "H5'A" "C5'" single 1.092 0.020
M8E "H4'" "C4'" single 1.099 0.020
M8E "H1'" "C1'" single 1.099 0.020
M8E H9 C9 single 1.083 0.020
M8E HN7 N7 single 1.010 0.020
M8E HN7A N7 single 1.010 0.020
M8E "H2'" "C2'" single 1.099 0.020
M8E "HO2'" "O2'" single 0.967 0.020
M8E "H3'" "C3'" single 1.099 0.020
M8E "HO3'" "O3'" single 0.967 0.020
M8E H5 C5 single 1.092 0.020
M8E H5A C5 single 1.092 0.020
M8E H4 C4 single 1.092 0.020
M8E H4A C4 single 1.092 0.020
M8E H15 C15 single 1.077 0.020
M8E H15A C15 single 1.077 0.020
M8E H14 C14 single 1.077 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
M8E "HO3'" "O3'" "C3'" 109.470 3.000
M8E "O3'" "C3'" "H3'" 109.470 3.000
M8E "O3'" "C3'" "C4'" 109.470 3.000
M8E "O3'" "C3'" "C2'" 109.470 3.000
M8E "H3'" "C3'" "C4'" 108.340 3.000
M8E "H3'" "C3'" "C2'" 108.340 3.000
M8E "C4'" "C3'" "C2'" 111.000 3.000
M8E "C3'" "C4'" "H4'" 108.340 3.000
M8E "C3'" "C4'" "C5'" 111.000 3.000
M8E "C3'" "C4'" "O4'" 109.470 3.000
M8E "H4'" "C4'" "C5'" 108.340 3.000
M8E "H4'" "C4'" "O4'" 109.470 3.000
M8E "C5'" "C4'" "O4'" 109.470 3.000
M8E "C4'" "C5'" "H5'" 109.470 3.000
M8E "C4'" "C5'" "H5'A" 109.470 3.000
M8E "C4'" "C5'" N2 109.500 3.000
M8E "H5'" "C5'" "H5'A" 107.900 3.000
M8E "H5'" "C5'" N2 109.470 3.000
M8E "H5'A" "C5'" N2 109.470 3.000
M8E "C5'" N2 C8 109.470 3.000
M8E "C5'" N2 C7 109.470 3.000
M8E C8 N2 C7 109.470 3.000
M8E N2 C8 H8B 109.470 3.000
M8E N2 C8 H8A 109.470 3.000
M8E N2 C8 H8 109.470 3.000
M8E H8B C8 H8A 109.470 3.000
M8E H8B C8 H8 109.470 3.000
M8E H8A C8 H8 109.470 3.000
M8E N2 C7 H7 109.470 3.000
M8E N2 C7 H7A 109.470 3.000
M8E N2 C7 C6 109.470 3.000
M8E H7 C7 H7A 107.900 3.000
M8E H7 C7 C6 109.470 3.000
M8E H7A C7 C6 109.470 3.000
M8E C7 C6 H6 109.470 3.000
M8E C7 C6 H6A 109.470 3.000
M8E C7 C6 C5 111.000 3.000
M8E H6 C6 H6A 107.900 3.000
M8E H6 C6 C5 109.470 3.000
M8E H6A C6 C5 109.470 3.000
M8E C6 C5 H5 109.470 3.000
M8E C6 C5 H5A 109.470 3.000
M8E C6 C5 C4 111.000 3.000
M8E H5 C5 H5A 107.900 3.000
M8E H5 C5 C4 109.470 3.000
M8E H5A C5 C4 109.470 3.000
M8E C5 C4 H4 109.470 3.000
M8E C5 C4 H4A 109.470 3.000
M8E C5 C4 O1 109.470 3.000
M8E H4 C4 H4A 107.900 3.000
M8E H4 C4 O1 109.470 3.000
M8E H4A C4 O1 109.470 3.000
M8E C4 O1 N1 120.000 3.000
M8E O1 N1 HN1A 120.000 3.000
M8E O1 N1 HN1 120.000 3.000
M8E HN1A N1 HN1 120.000 3.000
M8E "C3'" "C2'" "H2'" 108.340 3.000
M8E "C3'" "C2'" "O2'" 109.470 3.000
M8E "C3'" "C2'" "C1'" 111.000 3.000
M8E "H2'" "C2'" "O2'" 109.470 3.000
M8E "H2'" "C2'" "C1'" 108.340 3.000
M8E "O2'" "C2'" "C1'" 109.470 3.000
M8E "C2'" "O2'" "HO2'" 109.470 3.000
M8E "C2'" "C1'" "H1'" 108.340 3.000
M8E "C2'" "C1'" "O4'" 109.470 3.000
M8E "C2'" "C1'" N6 109.470 3.000
M8E "H1'" "C1'" "O4'" 109.470 3.000
M8E "H1'" "C1'" N6 109.470 3.000
M8E "O4'" "C1'" N6 109.470 3.000
M8E "C1'" "O4'" "C4'" 111.800 3.000
M8E "C1'" N6 C12 126.000 3.000
M8E "C1'" N6 C13 126.000 3.000
M8E C12 N6 C13 108.000 3.000
M8E N6 C12 C14 108.000 3.000
M8E N6 C12 N5 108.000 3.000
M8E C14 C12 N5 108.000 3.000
M8E C12 C14 H14 120.000 3.000
M8E C12 C14 C15 120.000 3.000
M8E H14 C14 C15 120.000 3.000
M8E C14 C15 H15A 120.000 3.000
M8E C14 C15 H15 120.000 3.000
M8E H15A C15 H15 120.000 3.000
M8E C12 N5 C11 108.000 3.000
M8E N5 C11 C13 108.000 3.000
M8E N5 C11 C10 132.000 3.000
M8E C13 C11 C10 120.000 3.000
M8E C11 C13 N6 108.000 3.000
M8E C11 C13 N3 120.000 3.000
M8E N6 C13 N3 132.000 3.000
M8E C11 C10 N7 120.000 3.000
M8E C11 C10 N4 120.000 3.000
M8E N7 C10 N4 120.000 3.000
M8E C10 N7 HN7A 120.000 3.000
M8E C10 N7 HN7 120.000 3.000
M8E HN7A N7 HN7 120.000 3.000
M8E C10 N4 C9 120.000 3.000
M8E N4 C9 H9 120.000 3.000
M8E N4 C9 N3 120.000 3.000
M8E H9 C9 N3 120.000 3.000
M8E C9 N3 C13 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
M8E var_1 "HO3'" "O3'" "C3'" "C2'" 65.213 20.000 1
M8E var_2 "O3'" "C3'" "C4'" "C5'" 120.000 20.000 3
M8E var_3 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
M8E var_4 "C3'" "C4'" "C5'" N2 -175.686 20.000 3
M8E var_5 "C4'" "C5'" N2 C7 -169.993 20.000 1
M8E var_6 "C5'" N2 C8 H8 -176.053 20.000 1
M8E var_7 "C5'" N2 C7 C6 169.996 20.000 1
M8E var_8 N2 C7 C6 C5 -179.957 20.000 3
M8E var_9 C7 C6 C5 C4 -179.969 20.000 3
M8E var_10 C6 C5 C4 O1 179.999 20.000 3
M8E var_11 C5 C4 O1 N1 -179.997 20.000 1
M8E var_12 C4 O1 N1 HN1 55.986 20.000 1
M8E var_13 "O3'" "C3'" "C2'" "C1'" 90.000 20.000 3
M8E var_14 "C3'" "C2'" "O2'" "HO2'" -67.361 20.000 1
M8E var_15 "C3'" "C2'" "C1'" N6 150.000 20.000 3
M8E var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
M8E var_17 "C2'" "C1'" N6 C12 -70.832 20.000 1
M8E CONST_1 "C1'" N6 C13 C11 180.000 0.000 0
M8E CONST_2 "C1'" N6 C12 N5 180.000 0.000 0
M8E var_18 N6 C12 C14 C15 -179.982 20.000 1
M8E CONST_3 C12 C14 C15 H15 -0.003 0.000 0
M8E CONST_4 N6 C12 N5 C11 0.000 0.000 0
M8E CONST_5 C12 N5 C11 C10 180.000 0.000 0
M8E CONST_6 N5 C11 C13 N6 0.000 0.000 0
M8E CONST_7 C11 C13 N3 C9 0.000 0.000 0
M8E CONST_8 N5 C11 C10 N4 180.000 0.000 0
M8E CONST_9 C11 C10 N7 HN7 179.972 0.000 0
M8E CONST_10 C11 C10 N4 C9 0.000 0.000 0
M8E CONST_11 C10 N4 C9 N3 0.000 0.000 0
M8E CONST_12 N4 C9 N3 C13 0.000 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
M8E chir_01 N2 C7 C8 "C5'" positiv
M8E chir_02 "C4'" "C5'" "O4'" "C3'" negativ
M8E chir_03 "C1'" "O4'" N6 "C2'" negativ
M8E chir_04 "C2'" "C1'" "O2'" "C3'" positiv
M8E chir_05 "C3'" "C4'" "C2'" "O3'" 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
M8E plan-1 N1 0.020
M8E plan-1 O1 0.020
M8E plan-1 HN1 0.020
M8E plan-1 HN1A 0.020
M8E plan-2 N6 0.020
M8E plan-2 "C1'" 0.020
M8E plan-2 C13 0.020
M8E plan-2 C12 0.020
M8E plan-2 N5 0.020
M8E plan-2 N3 0.020
M8E plan-2 C11 0.020
M8E plan-2 C9 0.020
M8E plan-2 N4 0.020
M8E plan-2 C10 0.020
M8E plan-2 H9 0.020
M8E plan-2 N7 0.020
M8E plan-2 C14 0.020
M8E plan-2 HN7A 0.020
M8E plan-2 HN7 0.020
M8E plan-2 H14 0.020
M8E plan-3 N7 0.020
M8E plan-3 C10 0.020
M8E plan-3 HN7 0.020
M8E plan-3 HN7A 0.020
M8E plan-4 C15 0.020
M8E plan-4 C14 0.020
M8E plan-4 H15 0.020
M8E plan-4 H15A 0.020
M8E plan-4 C12 0.020
M8E plan-4 H14 0.020
# ------------------------------------------------------
|
