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
|
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
SSS SSS '"N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D' non-polymer 45 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SSS
#
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
SSS O68 O OC -0.500 0.000 0.000 0.000
SSS C64 C C 0.000 -0.725 0.985 0.260
SSS O67 O OC -0.500 -1.271 1.155 1.373
SSS C63 C CH2 0.000 -0.842 1.915 -0.929
SSS H631 H H 0.000 -0.714 1.316 -1.833
SSS H632 H H 0.000 -0.032 2.645 -0.861
SSS C61 C CH1 0.000 -2.187 2.645 -0.985
SSS H61 H H 0.000 -2.286 3.247 -0.070
SSS C62 C C 0.000 -2.221 3.589 -2.175
SSS O66 O OC -0.500 -3.124 3.318 -2.998
SSS O65 O OC -0.500 -1.433 4.548 -2.325
SSS N6 N NH1 0.000 -3.286 1.707 -1.026
SSS H6 H H 0.000 -3.119 0.804 -1.447
SSS C6 C C 0.000 -4.574 1.970 -0.517
SSS O6 O O 0.000 -4.843 3.072 0.019
SSS C5 C CR5 0.000 -5.553 0.929 -0.611
SSS C4 C CR5 0.000 -6.856 0.988 -0.177
SSS N3 N NH2 0.000 -7.584 1.950 0.427
SSS H3N2 H H 0.000 -7.153 2.828 0.672
SSS H3N1 H H 0.000 -8.559 1.788 0.632
SSS N7 N NRD5 0.000 -5.273 -0.292 -1.174
SSS C8 C CR15 0.000 -6.397 -0.968 -1.082
SSS H8 H H 0.000 -6.522 -1.984 -1.438
SSS N9 N NR5 0.000 -7.392 -0.237 -0.484
SSS "C1'" C CH1 0.000 -8.757 -0.698 -0.238
SSS "H1'" H H 0.000 -9.140 -0.176 0.649
SSS "O4'" O O2 0.000 -8.731 -2.113 0.049
SSS "C2'" C CH1 0.000 -9.754 -0.494 -1.381
SSS "H2'" H H 0.000 -10.742 -0.259 -0.961
SSS "O2'" O OH1 0.000 -9.387 0.516 -2.299
SSS HA H H 0.000 -10.181 0.971 -2.606
SSS "C3'" C CH1 0.000 -9.804 -1.856 -2.038
SSS "H3'" H H 0.000 -8.962 -1.984 -2.733
SSS "O3'" O OH1 0.000 -11.038 -2.054 -2.702
SSS HB H H 0.000 -11.057 -1.519 -3.506
SSS "C4'" C CH1 0.000 -9.654 -2.773 -0.835
SSS "H4'" H H 0.000 -10.626 -2.873 -0.333
SSS "C5'" C CH2 0.000 -9.127 -4.153 -1.185
SSS "H5'1" H H 0.000 -8.145 -4.066 -1.655
SSS "H5'2" H H 0.000 -9.815 -4.648 -1.873
SSS "O5'" O O2 0.000 -9.017 -4.913 0.005
SSS PA P P 0.000 -8.474 -6.435 -0.097
SSS O1A O OP -0.666 -9.401 -7.057 -1.118
SSS O2A O OP -0.666 -7.168 -6.300 -0.849
SSS O3A O OP -0.666 -8.389 -7.173 1.221
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
SSS O68 n/a C64 START
SSS C64 O68 C63 .
SSS O67 C64 . .
SSS C63 C64 C61 .
SSS H631 C63 . .
SSS H632 C63 . .
SSS C61 C63 N6 .
SSS H61 C61 . .
SSS C62 C61 O65 .
SSS O66 C62 . .
SSS O65 C62 . .
SSS N6 C61 C6 .
SSS H6 N6 . .
SSS C6 N6 C5 .
SSS O6 C6 . .
SSS C5 C6 N7 .
SSS C4 C5 N3 .
SSS N3 C4 H3N1 .
SSS H3N2 N3 . .
SSS H3N1 N3 . .
SSS N7 C5 C8 .
SSS C8 N7 N9 .
SSS H8 C8 . .
SSS N9 C8 "C1'" .
SSS "C1'" N9 "C2'" .
SSS "H1'" "C1'" . .
SSS "O4'" "C1'" . .
SSS "C2'" "C1'" "C3'" .
SSS "H2'" "C2'" . .
SSS "O2'" "C2'" HA .
SSS HA "O2'" . .
SSS "C3'" "C2'" "C4'" .
SSS "H3'" "C3'" . .
SSS "O3'" "C3'" HB .
SSS HB "O3'" . .
SSS "C4'" "C3'" "C5'" .
SSS "H4'" "C4'" . .
SSS "C5'" "C4'" "O5'" .
SSS "H5'1" "C5'" . .
SSS "H5'2" "C5'" . .
SSS "O5'" "C5'" PA .
SSS PA "O5'" O3A .
SSS O1A PA . .
SSS O2A PA . .
SSS O3A PA . END
SSS "C4'" "O4'" . ADD
SSS N9 C4 . 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
SSS O1A PA deloc 1.510 0.020
SSS O2A PA deloc 1.510 0.020
SSS O3A PA deloc 1.510 0.020
SSS PA "O5'" single 1.610 0.020
SSS "O5'" "C5'" single 1.426 0.020
SSS "C5'" "C4'" single 1.524 0.020
SSS "H5'1" "C5'" single 1.092 0.020
SSS "H5'2" "C5'" single 1.092 0.020
SSS "C4'" "O4'" single 1.426 0.020
SSS "C4'" "C3'" single 1.524 0.020
SSS "H4'" "C4'" single 1.099 0.020
SSS "O4'" "C1'" single 1.426 0.020
SSS "C1'" N9 single 1.485 0.020
SSS "C2'" "C1'" single 1.524 0.020
SSS "H1'" "C1'" single 1.099 0.020
SSS N9 C4 single 1.337 0.020
SSS N9 C8 single 1.337 0.020
SSS N3 C4 single 1.355 0.020
SSS C4 C5 double 1.490 0.020
SSS O6 C6 double 1.220 0.020
SSS H3N1 N3 single 1.010 0.020
SSS H3N2 N3 single 1.010 0.020
SSS C6 N6 single 1.330 0.020
SSS C5 C6 single 1.490 0.020
SSS N6 C61 single 1.450 0.020
SSS H6 N6 single 1.010 0.020
SSS C62 C61 single 1.500 0.020
SSS C61 C63 single 1.524 0.020
SSS H61 C61 single 1.099 0.020
SSS O65 C62 deloc 1.250 0.020
SSS O66 C62 deloc 1.250 0.020
SSS C63 C64 single 1.510 0.020
SSS H631 C63 single 1.092 0.020
SSS H632 C63 single 1.092 0.020
SSS O67 C64 deloc 1.250 0.020
SSS C64 O68 deloc 1.250 0.020
SSS N7 C5 single 1.350 0.020
SSS C8 N7 double 1.350 0.020
SSS H8 C8 single 1.083 0.020
SSS "O2'" "C2'" single 1.432 0.020
SSS "C3'" "C2'" single 1.524 0.020
SSS "H2'" "C2'" single 1.099 0.020
SSS HA "O2'" single 0.967 0.020
SSS "O3'" "C3'" single 1.432 0.020
SSS "H3'" "C3'" single 1.099 0.020
SSS HB "O3'" single 0.967 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
SSS O68 C64 O67 123.000 3.000
SSS O68 C64 C63 118.500 3.000
SSS O67 C64 C63 118.500 3.000
SSS C64 C63 H631 109.470 3.000
SSS C64 C63 H632 109.470 3.000
SSS C64 C63 C61 109.470 3.000
SSS H631 C63 H632 107.900 3.000
SSS H631 C63 C61 109.470 3.000
SSS H632 C63 C61 109.470 3.000
SSS C63 C61 H61 108.340 3.000
SSS C63 C61 C62 109.470 3.000
SSS C63 C61 N6 110.000 3.000
SSS H61 C61 C62 108.810 3.000
SSS H61 C61 N6 108.550 3.000
SSS C62 C61 N6 111.600 3.000
SSS C61 C62 O66 118.500 3.000
SSS C61 C62 O65 118.500 3.000
SSS O66 C62 O65 123.000 3.000
SSS C61 N6 H6 118.500 3.000
SSS C61 N6 C6 121.500 3.000
SSS H6 N6 C6 120.000 3.000
SSS N6 C6 O6 123.000 3.000
SSS N6 C6 C5 120.000 3.000
SSS O6 C6 C5 120.500 3.000
SSS C6 C5 C4 117.000 3.000
SSS C6 C5 N7 126.000 3.000
SSS C4 C5 N7 108.000 3.000
SSS C5 C4 N3 108.000 3.000
SSS C5 C4 N9 108.000 3.000
SSS N3 C4 N9 108.000 3.000
SSS C4 N3 H3N2 120.000 3.000
SSS C4 N3 H3N1 120.000 3.000
SSS H3N2 N3 H3N1 120.000 3.000
SSS C5 N7 C8 108.000 3.000
SSS N7 C8 H8 126.000 3.000
SSS N7 C8 N9 108.000 3.000
SSS H8 C8 N9 126.000 3.000
SSS C8 N9 "C1'" 126.000 3.000
SSS C8 N9 C4 108.000 3.000
SSS "C1'" N9 C4 126.000 3.000
SSS N9 "C1'" "H1'" 109.470 3.000
SSS N9 "C1'" "O4'" 109.470 3.000
SSS N9 "C1'" "C2'" 109.470 3.000
SSS "H1'" "C1'" "O4'" 109.470 3.000
SSS "H1'" "C1'" "C2'" 108.340 3.000
SSS "O4'" "C1'" "C2'" 109.470 3.000
SSS "C1'" "O4'" "C4'" 111.800 3.000
SSS "C1'" "C2'" "H2'" 108.340 3.000
SSS "C1'" "C2'" "O2'" 109.470 3.000
SSS "C1'" "C2'" "C3'" 111.000 3.000
SSS "H2'" "C2'" "O2'" 109.470 3.000
SSS "H2'" "C2'" "C3'" 108.340 3.000
SSS "O2'" "C2'" "C3'" 109.470 3.000
SSS "C2'" "O2'" HA 109.470 3.000
SSS "C2'" "C3'" "H3'" 108.340 3.000
SSS "C2'" "C3'" "O3'" 109.470 3.000
SSS "C2'" "C3'" "C4'" 111.000 3.000
SSS "H3'" "C3'" "O3'" 109.470 3.000
SSS "H3'" "C3'" "C4'" 108.340 3.000
SSS "O3'" "C3'" "C4'" 109.470 3.000
SSS "C3'" "O3'" HB 109.470 3.000
SSS "C3'" "C4'" "H4'" 108.340 3.000
SSS "C3'" "C4'" "C5'" 111.000 3.000
SSS "C3'" "C4'" "O4'" 109.470 3.000
SSS "H4'" "C4'" "C5'" 108.340 3.000
SSS "H4'" "C4'" "O4'" 109.470 3.000
SSS "C5'" "C4'" "O4'" 109.470 3.000
SSS "C4'" "C5'" "H5'1" 109.470 3.000
SSS "C4'" "C5'" "H5'2" 109.470 3.000
SSS "C4'" "C5'" "O5'" 109.470 3.000
SSS "H5'1" "C5'" "H5'2" 107.900 3.000
SSS "H5'1" "C5'" "O5'" 109.470 3.000
SSS "H5'2" "C5'" "O5'" 109.470 3.000
SSS "C5'" "O5'" PA 120.500 3.000
SSS "O5'" PA O1A 108.200 3.000
SSS "O5'" PA O2A 108.200 3.000
SSS "O5'" PA O3A 108.200 3.000
SSS O1A PA O2A 119.900 3.000
SSS O1A PA O3A 119.900 3.000
SSS O2A PA O3A 119.900 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
SSS var_1 O68 C64 C63 C61 149.021 20.000 3
SSS var_2 C64 C63 C61 N6 -57.871 20.000 3
SSS var_3 C63 C61 C62 O65 -61.295 20.000 3
SSS var_4 C63 C61 N6 C6 151.252 20.000 3
SSS CONST_1 C61 N6 C6 C5 180.000 0.000 0
SSS var_5 N6 C6 C5 N7 -0.035 20.000 1
SSS CONST_2 C6 C5 C4 N3 0.000 0.000 0
SSS CONST_3 C5 C4 N3 H3N1 177.619 0.000 0
SSS CONST_4 C6 C5 N7 C8 180.000 0.000 0
SSS CONST_5 C5 N7 C8 N9 0.000 0.000 0
SSS CONST_6 N7 C8 N9 "C1'" 180.000 0.000 0
SSS CONST_7 C8 N9 C4 C5 0.000 0.000 0
SSS var_6 C8 N9 "C1'" "C2'" -86.987 20.000 1
SSS var_7 N9 "C1'" "O4'" "C4'" -120.000 20.000 1
SSS var_8 N9 "C1'" "C2'" "C3'" 90.000 20.000 3
SSS var_9 "C1'" "C2'" "O2'" HA -144.568 20.000 1
SSS var_10 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
SSS var_11 "C2'" "C3'" "O3'" HB 73.219 20.000 1
SSS var_12 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
SSS var_13 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
SSS var_14 "C3'" "C4'" "C5'" "O5'" 179.524 20.000 3
SSS var_15 "C4'" "C5'" "O5'" PA 179.977 20.000 1
SSS var_16 "C5'" "O5'" PA O3A -179.990 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
SSS chir_01 "C4'" "C5'" "O4'" "C3'" negativ
SSS chir_02 "C1'" "O4'" N9 "C2'" negativ
SSS chir_03 C61 N6 C62 C63 positiv
SSS chir_04 "C2'" "C1'" "O2'" "C3'" negativ
SSS 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
SSS plan-1 N9 0.020
SSS plan-1 "C1'" 0.020
SSS plan-1 C4 0.020
SSS plan-1 C8 0.020
SSS plan-1 C5 0.020
SSS plan-1 N7 0.020
SSS plan-1 N3 0.020
SSS plan-1 C6 0.020
SSS plan-1 H8 0.020
SSS plan-1 H3N2 0.020
SSS plan-1 H3N1 0.020
SSS plan-2 N3 0.020
SSS plan-2 C4 0.020
SSS plan-2 H3N1 0.020
SSS plan-2 H3N2 0.020
SSS plan-3 C6 0.020
SSS plan-3 O6 0.020
SSS plan-3 N6 0.020
SSS plan-3 C5 0.020
SSS plan-3 H6 0.020
SSS plan-4 N6 0.020
SSS plan-4 C6 0.020
SSS plan-4 C61 0.020
SSS plan-4 H6 0.020
SSS plan-5 C62 0.020
SSS plan-5 C61 0.020
SSS plan-5 O65 0.020
SSS plan-5 O66 0.020
SSS plan-6 C64 0.020
SSS plan-6 C63 0.020
SSS plan-6 O67 0.020
SSS plan-6 O68 0.020
# ------------------------------------------------------
|
