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
|
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
SAI SAI 'S-ADENOSYL-L-HOMOSELENOCYSTEINE ' non-polymer 45 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SAI
#
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
SAI OXT O OC -0.500 0.000 0.000 0.000
SAI C C C 0.000 -0.321 -0.204 -1.192
SAI O O OC -0.500 0.366 -0.970 -1.903
SAI CA C CH1 0.000 -1.534 0.477 -1.773
SAI HA H H 0.000 -1.685 1.444 -1.273
SAI N N NH2 0.000 -1.331 0.695 -3.210
SAI HN2 H H 0.000 -1.346 1.633 -3.592
SAI HN1 H H 0.000 -1.176 -0.092 -3.830
SAI CB C CH2 0.000 -2.765 -0.404 -1.559
SAI HB1 H H 0.000 -2.913 -0.567 -0.489
SAI HB2 H H 0.000 -2.613 -1.366 -2.054
SAI CG C CH2 0.000 -3.996 0.285 -2.146
SAI HG1 H H 0.000 -3.844 0.448 -3.215
SAI HG2 H H 0.000 -4.144 1.246 -1.650
SAI SE SE SE 0.000 -5.574 -0.845 -1.872
SAI "C5'" C CH2 0.000 -6.822 0.389 -2.742
SAI "H5'1" H H 0.000 -6.515 0.546 -3.778
SAI "H5'2" H H 0.000 -6.815 1.345 -2.213
SAI "C4'" C CH1 0.000 -8.231 -0.203 -2.710
SAI "H4'" H H 0.000 -8.241 -1.171 -3.230
SAI "C3'" C CH1 0.000 -9.223 0.763 -3.386
SAI "H3'" H H 0.000 -8.711 1.685 -3.695
SAI "O3'" O OH1 0.000 -9.853 0.141 -4.506
SAI "HO3'" H H 0.000 -10.512 0.742 -4.879
SAI "C2'" C CH1 0.000 -10.265 1.068 -2.277
SAI "H2'" H H 0.000 -10.030 2.014 -1.768
SAI "O2'" O OH1 0.000 -11.588 1.094 -2.816
SAI "HO2'" H H 0.000 -11.679 1.851 -3.410
SAI "C1'" C CH1 0.000 -10.082 -0.136 -1.318
SAI "H1'" H H 0.000 -10.629 -1.013 -1.690
SAI "O4'" O O2 0.000 -8.658 -0.375 -1.348
SAI N9 N NR5 0.000 -10.519 0.208 0.036
SAI C4 C CR56 0.000 -11.761 -0.021 0.570
SAI C5 C CR56 0.000 -11.714 0.470 1.886
SAI N7 N NRD5 0.000 -10.471 0.973 2.079
SAI C8 C CR15 0.000 -9.768 0.819 0.995
SAI H8 H H 0.000 -8.738 1.131 0.873
SAI N3 N NRD6 0.000 -12.884 -0.578 0.131
SAI C2 C CR16 0.000 -13.943 -0.660 0.908
SAI H2 H H 0.000 -14.844 -1.116 0.515
SAI N1 N NRD6 0.000 -13.947 -0.208 2.149
SAI C6 C CR6 0.000 -12.869 0.359 2.678
SAI N6 N NH2 0.000 -12.883 0.831 3.979
SAI HN62 H H 0.000 -12.057 1.266 4.379
SAI HN61 H H 0.000 -13.720 0.749 4.548
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
SAI OXT n/a C START
SAI C OXT CA .
SAI O C . .
SAI CA C CB .
SAI HA CA . .
SAI N CA HN1 .
SAI HN2 N . .
SAI HN1 N . .
SAI CB CA CG .
SAI HB1 CB . .
SAI HB2 CB . .
SAI CG CB SE .
SAI HG1 CG . .
SAI HG2 CG . .
SAI SE CG "C5'" .
SAI "C5'" SE "C4'" .
SAI "H5'1" "C5'" . .
SAI "H5'2" "C5'" . .
SAI "C4'" "C5'" "C3'" .
SAI "H4'" "C4'" . .
SAI "C3'" "C4'" "C2'" .
SAI "H3'" "C3'" . .
SAI "O3'" "C3'" "HO3'" .
SAI "HO3'" "O3'" . .
SAI "C2'" "C3'" "C1'" .
SAI "H2'" "C2'" . .
SAI "O2'" "C2'" "HO2'" .
SAI "HO2'" "O2'" . .
SAI "C1'" "C2'" N9 .
SAI "H1'" "C1'" . .
SAI "O4'" "C1'" . .
SAI N9 "C1'" C4 .
SAI C4 N9 N3 .
SAI C5 C4 N7 .
SAI N7 C5 C8 .
SAI C8 N7 H8 .
SAI H8 C8 . .
SAI N3 C4 C2 .
SAI C2 N3 N1 .
SAI H2 C2 . .
SAI N1 C2 C6 .
SAI C6 N1 N6 .
SAI N6 C6 HN61 .
SAI HN62 N6 . .
SAI HN61 N6 . END
SAI "C4'" "O4'" . ADD
SAI N9 C8 . ADD
SAI C5 C6 . 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
SAI N CA single 1.450 0.020
SAI HN1 N single 1.010 0.020
SAI HN2 N single 1.010 0.020
SAI CB CA single 1.524 0.020
SAI CA C single 1.500 0.020
SAI HA CA single 1.099 0.020
SAI CG CB single 1.524 0.020
SAI HB1 CB single 1.092 0.020
SAI HB2 CB single 1.092 0.020
SAI SE CG single 1.970 0.020
SAI HG1 CG single 1.092 0.020
SAI HG2 CG single 1.092 0.020
SAI "C5'" SE single 1.970 0.020
SAI O C deloc 1.250 0.020
SAI C OXT deloc 1.250 0.020
SAI "C4'" "C5'" single 1.524 0.020
SAI "H5'1" "C5'" single 1.092 0.020
SAI "H5'2" "C5'" single 1.092 0.020
SAI "C4'" "O4'" single 1.426 0.020
SAI "C3'" "C4'" single 1.524 0.020
SAI "H4'" "C4'" single 1.099 0.020
SAI "O4'" "C1'" single 1.426 0.020
SAI "O3'" "C3'" single 1.432 0.020
SAI "C2'" "C3'" single 1.524 0.020
SAI "H3'" "C3'" single 1.099 0.020
SAI "HO3'" "O3'" single 0.967 0.020
SAI "O2'" "C2'" single 1.432 0.020
SAI "C1'" "C2'" single 1.524 0.020
SAI "H2'" "C2'" single 1.099 0.020
SAI "HO2'" "O2'" single 0.967 0.020
SAI N9 "C1'" single 1.485 0.020
SAI "H1'" "C1'" single 1.099 0.020
SAI N9 C8 single 1.337 0.020
SAI C4 N9 single 1.337 0.020
SAI C8 N7 double 1.350 0.020
SAI H8 C8 single 1.083 0.020
SAI N7 C5 single 1.350 0.020
SAI C5 C6 single 1.490 0.020
SAI C5 C4 double 1.490 0.020
SAI N6 C6 single 1.355 0.020
SAI C6 N1 double 1.350 0.020
SAI HN61 N6 single 1.010 0.020
SAI HN62 N6 single 1.010 0.020
SAI N1 C2 single 1.337 0.020
SAI C2 N3 double 1.337 0.020
SAI H2 C2 single 1.083 0.020
SAI N3 C4 single 1.355 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
SAI OXT C O 123.000 3.000
SAI OXT C CA 118.500 3.000
SAI O C CA 118.500 3.000
SAI C CA HA 108.810 3.000
SAI C CA N 109.470 3.000
SAI C CA CB 109.470 3.000
SAI HA CA N 109.470 3.000
SAI HA CA CB 108.340 3.000
SAI N CA CB 109.470 3.000
SAI CA N HN2 120.000 3.000
SAI CA N HN1 120.000 3.000
SAI HN2 N HN1 120.000 3.000
SAI CA CB HB1 109.470 3.000
SAI CA CB HB2 109.470 3.000
SAI CA CB CG 111.000 3.000
SAI HB1 CB HB2 107.900 3.000
SAI HB1 CB CG 109.470 3.000
SAI HB2 CB CG 109.470 3.000
SAI CB CG HG1 109.470 3.000
SAI CB CG HG2 109.470 3.000
SAI CB CG SE 109.500 3.000
SAI HG1 CG HG2 107.900 3.000
SAI HG1 CG SE 109.500 3.000
SAI HG2 CG SE 109.500 3.000
SAI CG SE "C5'" 98.000 3.000
SAI SE "C5'" "H5'1" 109.500 3.000
SAI SE "C5'" "H5'2" 109.500 3.000
SAI SE "C5'" "C4'" 109.500 3.000
SAI "H5'1" "C5'" "H5'2" 107.900 3.000
SAI "H5'1" "C5'" "C4'" 109.470 3.000
SAI "H5'2" "C5'" "C4'" 109.470 3.000
SAI "C5'" "C4'" "H4'" 108.340 3.000
SAI "C5'" "C4'" "C3'" 111.000 3.000
SAI "C5'" "C4'" "O4'" 109.470 3.000
SAI "H4'" "C4'" "C3'" 108.340 3.000
SAI "H4'" "C4'" "O4'" 109.470 3.000
SAI "C3'" "C4'" "O4'" 109.470 3.000
SAI "C4'" "C3'" "H3'" 108.340 3.000
SAI "C4'" "C3'" "O3'" 109.470 3.000
SAI "C4'" "C3'" "C2'" 111.000 3.000
SAI "H3'" "C3'" "O3'" 109.470 3.000
SAI "H3'" "C3'" "C2'" 108.340 3.000
SAI "O3'" "C3'" "C2'" 109.470 3.000
SAI "C3'" "O3'" "HO3'" 109.470 3.000
SAI "C3'" "C2'" "H2'" 108.340 3.000
SAI "C3'" "C2'" "O2'" 109.470 3.000
SAI "C3'" "C2'" "C1'" 111.000 3.000
SAI "H2'" "C2'" "O2'" 109.470 3.000
SAI "H2'" "C2'" "C1'" 108.340 3.000
SAI "O2'" "C2'" "C1'" 109.470 3.000
SAI "C2'" "O2'" "HO2'" 109.470 3.000
SAI "C2'" "C1'" "H1'" 108.340 3.000
SAI "C2'" "C1'" "O4'" 109.470 3.000
SAI "C2'" "C1'" N9 109.470 3.000
SAI "H1'" "C1'" "O4'" 109.470 3.000
SAI "H1'" "C1'" N9 109.470 3.000
SAI "O4'" "C1'" N9 109.470 3.000
SAI "C1'" "O4'" "C4'" 111.800 3.000
SAI "C1'" N9 C4 126.000 3.000
SAI "C1'" N9 C8 126.000 3.000
SAI C4 N9 C8 108.000 3.000
SAI N9 C4 C5 108.000 3.000
SAI N9 C4 N3 132.000 3.000
SAI C5 C4 N3 120.000 3.000
SAI C4 C5 N7 108.000 3.000
SAI C4 C5 C6 120.000 3.000
SAI N7 C5 C6 132.000 3.000
SAI C5 N7 C8 108.000 3.000
SAI N7 C8 H8 126.000 3.000
SAI N7 C8 N9 108.000 3.000
SAI H8 C8 N9 126.000 3.000
SAI C4 N3 C2 120.000 3.000
SAI N3 C2 H2 120.000 3.000
SAI N3 C2 N1 120.000 3.000
SAI H2 C2 N1 120.000 3.000
SAI C2 N1 C6 120.000 3.000
SAI N1 C6 N6 120.000 3.000
SAI N1 C6 C5 120.000 3.000
SAI N6 C6 C5 120.000 3.000
SAI C6 N6 HN62 120.000 3.000
SAI C6 N6 HN61 120.000 3.000
SAI HN62 N6 HN61 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
SAI var_1 OXT C CA CB -90.014 20.000 3
SAI var_2 C CA N HN1 60.043 20.000 1
SAI var_3 C CA CB CG 179.956 20.000 3
SAI var_4 CA CB CG SE -179.999 20.000 3
SAI var_5 CB CG SE "C5'" -179.967 20.000 1
SAI var_6 CG SE "C5'" "C4'" 179.992 20.000 1
SAI var_7 SE "C5'" "C4'" "C3'" 179.714 20.000 3
SAI var_8 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
SAI var_9 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
SAI var_10 "C4'" "C3'" "O3'" "HO3'" 176.283 20.000 1
SAI var_11 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
SAI var_12 "C3'" "C2'" "O2'" "HO2'" -67.277 20.000 1
SAI var_13 "C3'" "C2'" "C1'" N9 150.000 20.000 3
SAI var_14 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
SAI var_15 "C2'" "C1'" N9 C4 94.112 20.000 1
SAI CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
SAI CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
SAI CONST_3 N9 C4 C5 N7 0.000 0.000 0
SAI CONST_4 C4 C5 C6 N1 0.000 0.000 0
SAI CONST_5 C4 C5 N7 C8 0.000 0.000 0
SAI CONST_6 C5 N7 C8 N9 0.000 0.000 0
SAI CONST_7 N9 C4 N3 C2 180.000 0.000 0
SAI CONST_8 C4 N3 C2 N1 0.000 0.000 0
SAI CONST_9 N3 C2 N1 C6 0.000 0.000 0
SAI CONST_10 C2 N1 C6 N6 180.000 0.000 0
SAI CONST_11 N1 C6 N6 HN61 0.112 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
SAI chir_01 CA N CB C negativ
SAI chir_02 "C4'" "C5'" "O4'" "C3'" negativ
SAI chir_03 "C3'" "C4'" "O3'" "C2'" negativ
SAI chir_04 "C2'" "C3'" "O2'" "C1'" negativ
SAI chir_05 "C1'" "O4'" "C2'" N9 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
SAI plan-1 N 0.020
SAI plan-1 CA 0.020
SAI plan-1 HN1 0.020
SAI plan-1 HN2 0.020
SAI plan-2 C 0.020
SAI plan-2 CA 0.020
SAI plan-2 O 0.020
SAI plan-2 OXT 0.020
SAI plan-3 N9 0.020
SAI plan-3 "C1'" 0.020
SAI plan-3 C8 0.020
SAI plan-3 C4 0.020
SAI plan-3 N7 0.020
SAI plan-3 H8 0.020
SAI plan-3 C5 0.020
SAI plan-3 C6 0.020
SAI plan-3 N1 0.020
SAI plan-3 C2 0.020
SAI plan-3 N3 0.020
SAI plan-3 N6 0.020
SAI plan-3 H2 0.020
SAI plan-3 HN62 0.020
SAI plan-3 HN61 0.020
SAI plan-4 N6 0.020
SAI plan-4 C6 0.020
SAI plan-4 HN61 0.020
SAI plan-4 HN62 0.020
# ------------------------------------------------------
|
