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
|
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
SOX SOX 'N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-' non-polymer 43 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SOX
#
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
SOX O16 O O 0.000 0.000 0.000 0.000
SOX C15 C C 0.000 -0.634 -0.398 0.974
SOX C17 C CH2 0.000 -0.056 -1.322 2.028
SOX H171 H H 0.000 -0.831 -1.489 2.779
SOX H172 H H 0.000 0.790 -0.807 2.489
SOX C18 C CR6 0.000 0.402 -2.647 1.473
SOX C23 C CR16 0.000 1.708 -2.784 1.026
SOX H23 H H 0.000 2.393 -1.947 1.074
SOX C22 C CR16 0.000 2.132 -4.010 0.512
SOX H22 H H 0.000 3.149 -4.128 0.161
SOX C21 C CR16 0.000 1.245 -5.085 0.452
SOX H21 H H 0.000 1.574 -6.037 0.053
SOX C20 C CR16 0.000 -0.066 -4.934 0.906
SOX H20 H H 0.000 -0.755 -5.769 0.860
SOX C19 C CR16 0.000 -0.490 -3.708 1.419
SOX H19 H H 0.000 -1.506 -3.586 1.773
SOX N14 N NH1 0.000 -1.944 -0.069 1.265
SOX H14 H H 0.000 -2.369 -0.453 2.097
SOX C6 C CH1 0.000 -2.740 0.819 0.406
SOX H6 H H 0.000 -2.278 1.811 0.304
SOX C7 C C 0.000 -4.234 0.916 0.770
SOX O8 O O 0.000 -4.869 1.174 1.767
SOX C5 C CH1 0.000 -3.209 0.267 -0.942
SOX H5 H H 0.000 -2.949 0.899 -1.803
SOX N4 N NT 0.000 -4.590 0.445 -0.458
SOX S1 S ST 0.000 -3.287 -1.448 -1.309
SOX HS H H 0.000 -2.512 -1.870 -2.170
SOX O5 O OH1 0.000 -3.179 -2.113 0.165
SOX HO5 H H 0.000 -3.928 -2.603 0.526
SOX C2 C CT 0.000 -5.052 -1.592 -1.657
SOX C10 C CH3 0.000 -5.248 -1.315 -3.156
SOX H103 H H 0.000 -4.560 -1.894 -3.718
SOX H102 H H 0.000 -6.236 -1.573 -3.440
SOX H101 H H 0.000 -5.083 -0.287 -3.353
SOX C9 C CH3 0.000 -5.577 -2.988 -1.325
SOX H9C3 H H 0.000 -6.209 -2.936 -0.477
SOX H9C2 H H 0.000 -6.124 -3.366 -2.150
SOX H9C1 H H 0.000 -4.762 -3.632 -1.118
SOX C3 C CH1 0.000 -5.654 -0.508 -0.737
SOX H3 H H 0.000 -5.966 -0.977 0.206
SOX C11 C C 0.000 -6.805 0.263 -1.297
SOX O13 O OC -0.500 -6.793 1.488 -1.551
SOX O12 O OC -0.500 -7.792 -0.484 -1.477
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
SOX O16 n/a C15 START
SOX C15 O16 N14 .
SOX C17 C15 C18 .
SOX H171 C17 . .
SOX H172 C17 . .
SOX C18 C17 C23 .
SOX C23 C18 C22 .
SOX H23 C23 . .
SOX C22 C23 C21 .
SOX H22 C22 . .
SOX C21 C22 C20 .
SOX H21 C21 . .
SOX C20 C21 C19 .
SOX H20 C20 . .
SOX C19 C20 H19 .
SOX H19 C19 . .
SOX N14 C15 C6 .
SOX H14 N14 . .
SOX C6 N14 C5 .
SOX H6 C6 . .
SOX C7 C6 O8 .
SOX O8 C7 . .
SOX C5 C6 S1 .
SOX H5 C5 . .
SOX N4 C5 . .
SOX S1 C5 C2 .
SOX HS S1 . .
SOX O5 S1 HO5 .
SOX HO5 O5 . .
SOX C2 S1 C3 .
SOX C10 C2 H101 .
SOX H103 C10 . .
SOX H102 C10 . .
SOX H101 C10 . .
SOX C9 C2 H9C1 .
SOX H9C3 C9 . .
SOX H9C2 C9 . .
SOX H9C1 C9 . .
SOX C3 C2 C11 .
SOX H3 C3 . .
SOX C11 C3 O12 .
SOX O13 C11 . .
SOX O12 C11 . END
SOX C7 N4 . ADD
SOX N4 C3 . ADD
SOX C18 C19 . 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
SOX O8 C7 double 1.220 0.020
SOX C7 N4 single 1.416 0.020
SOX C7 C6 single 1.500 0.020
SOX N4 C3 single 1.469 0.020
SOX N4 C5 single 1.469 0.020
SOX C11 C3 single 1.500 0.020
SOX C3 C2 single 1.524 0.020
SOX H3 C3 single 1.099 0.020
SOX O13 C11 deloc 1.250 0.020
SOX O12 C11 deloc 1.250 0.020
SOX C10 C2 single 1.524 0.020
SOX C9 C2 single 1.524 0.020
SOX C2 S1 single 1.662 0.020
SOX H101 C10 single 1.059 0.020
SOX H102 C10 single 1.059 0.020
SOX H103 C10 single 1.059 0.020
SOX H9C1 C9 single 1.059 0.020
SOX H9C2 C9 single 1.059 0.020
SOX H9C3 C9 single 1.059 0.020
SOX S1 C5 single 1.665 0.020
SOX O5 S1 single 1.635 0.020
SOX HS S1 single 1.234 0.020
SOX C5 C6 single 1.524 0.020
SOX H5 C5 single 1.099 0.020
SOX C6 N14 single 1.450 0.020
SOX H6 C6 single 1.099 0.020
SOX N14 C15 single 1.330 0.020
SOX H14 N14 single 1.010 0.020
SOX C15 O16 double 1.220 0.020
SOX C17 C15 single 1.510 0.020
SOX C18 C17 single 1.511 0.020
SOX H171 C17 single 1.092 0.020
SOX H172 C17 single 1.092 0.020
SOX C18 C19 double 1.390 0.020
SOX C23 C18 single 1.390 0.020
SOX C19 C20 single 1.390 0.020
SOX H19 C19 single 1.083 0.020
SOX C20 C21 double 1.390 0.020
SOX H20 C20 single 1.083 0.020
SOX C21 C22 single 1.390 0.020
SOX H21 C21 single 1.083 0.020
SOX C22 C23 double 1.390 0.020
SOX H22 C22 single 1.083 0.020
SOX H23 C23 single 1.083 0.020
SOX HO5 O5 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
SOX O16 C15 C17 120.500 3.000
SOX O16 C15 N14 123.000 3.000
SOX C17 C15 N14 116.500 3.000
SOX C15 C17 H171 109.470 3.000
SOX C15 C17 H172 109.470 3.000
SOX C15 C17 C18 109.470 3.000
SOX H171 C17 H172 107.900 3.000
SOX H171 C17 C18 109.470 3.000
SOX H172 C17 C18 109.470 3.000
SOX C17 C18 C23 120.000 3.000
SOX C17 C18 C19 120.000 3.000
SOX C23 C18 C19 120.000 3.000
SOX C18 C23 H23 120.000 3.000
SOX C18 C23 C22 120.000 3.000
SOX H23 C23 C22 120.000 3.000
SOX C23 C22 H22 120.000 3.000
SOX C23 C22 C21 120.000 3.000
SOX H22 C22 C21 120.000 3.000
SOX C22 C21 H21 120.000 3.000
SOX C22 C21 C20 120.000 3.000
SOX H21 C21 C20 120.000 3.000
SOX C21 C20 H20 120.000 3.000
SOX C21 C20 C19 120.000 3.000
SOX H20 C20 C19 120.000 3.000
SOX C20 C19 H19 120.000 3.000
SOX C20 C19 C18 120.000 3.000
SOX H19 C19 C18 120.000 3.000
SOX C15 N14 H14 120.000 3.000
SOX C15 N14 C6 121.500 3.000
SOX H14 N14 C6 118.500 3.000
SOX N14 C6 H6 108.550 3.000
SOX N14 C6 C7 111.600 3.000
SOX N14 C6 C5 110.000 3.000
SOX H6 C6 C7 108.810 3.000
SOX H6 C6 C5 108.340 3.000
SOX C7 C6 C5 109.470 3.000
SOX C6 C7 O8 120.500 3.000
SOX C6 C7 N4 120.000 3.000
SOX O8 C7 N4 120.000 3.000
SOX C6 C5 H5 108.340 3.000
SOX C6 C5 N4 109.500 3.000
SOX C6 C5 S1 109.500 3.000
SOX H5 C5 N4 109.500 3.000
SOX H5 C5 S1 109.500 3.000
SOX N4 C5 S1 109.500 3.000
SOX C5 N4 C7 109.470 3.000
SOX C5 N4 C3 109.500 3.000
SOX C7 N4 C3 109.470 3.000
SOX C5 S1 HS 109.500 3.000
SOX C5 S1 O5 109.500 3.000
SOX C5 S1 C2 109.500 3.000
SOX HS S1 O5 109.500 3.000
SOX HS S1 C2 109.500 3.000
SOX O5 S1 C2 109.500 3.000
SOX S1 O5 HO5 120.000 3.000
SOX S1 C2 C10 109.500 3.000
SOX S1 C2 C9 109.500 3.000
SOX S1 C2 C3 109.500 3.000
SOX C10 C2 C9 111.000 3.000
SOX C10 C2 C3 111.000 3.000
SOX C9 C2 C3 111.000 3.000
SOX C2 C10 H103 109.470 3.000
SOX C2 C10 H102 109.470 3.000
SOX C2 C10 H101 109.470 3.000
SOX H103 C10 H102 109.470 3.000
SOX H103 C10 H101 109.470 3.000
SOX H102 C10 H101 109.470 3.000
SOX C2 C9 H9C3 109.470 3.000
SOX C2 C9 H9C2 109.470 3.000
SOX C2 C9 H9C1 109.470 3.000
SOX H9C3 C9 H9C2 109.470 3.000
SOX H9C3 C9 H9C1 109.470 3.000
SOX H9C2 C9 H9C1 109.470 3.000
SOX C2 C3 H3 108.340 3.000
SOX C2 C3 C11 109.470 3.000
SOX C2 C3 N4 109.500 3.000
SOX H3 C3 C11 108.810 3.000
SOX H3 C3 N4 109.500 3.000
SOX C11 C3 N4 109.500 3.000
SOX C3 C11 O13 118.500 3.000
SOX C3 C11 O12 118.500 3.000
SOX O13 C11 O12 123.000 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
SOX var_1 O16 C15 C17 C18 -60.042 20.000 3
SOX var_2 C15 C17 C18 C23 90.017 20.000 2
SOX CONST_1 C17 C18 C19 C20 180.000 0.000 0
SOX CONST_2 C17 C18 C23 C22 180.000 0.000 0
SOX CONST_3 C18 C23 C22 C21 0.000 0.000 0
SOX CONST_4 C23 C22 C21 C20 0.000 0.000 0
SOX CONST_5 C22 C21 C20 C19 0.000 0.000 0
SOX CONST_6 C21 C20 C19 C18 0.000 0.000 0
SOX CONST_7 O16 C15 N14 C6 0.000 0.000 0
SOX var_3 C15 N14 C6 C5 72.305 20.000 3
SOX var_4 N14 C6 C7 O8 53.727 20.000 3
SOX var_5 C6 C7 N4 C5 1.198 20.000 1
SOX var_6 N14 C6 C5 S1 19.315 20.000 3
SOX var_7 C6 C5 N4 C7 0.000 20.000 1
SOX var_8 C5 N4 C3 C2 0.000 20.000 1
SOX var_9 C6 C5 S1 C2 120.000 20.000 1
SOX var_10 C5 S1 O5 HO5 114.298 20.000 1
SOX var_11 C5 S1 C2 C3 -30.000 20.000 1
SOX var_12 S1 C2 C10 H101 -70.912 20.000 1
SOX var_13 S1 C2 C9 H9C1 -9.796 20.000 1
SOX var_14 S1 C2 C3 C11 150.000 20.000 1
SOX var_15 C2 C3 C11 O12 65.174 20.000 3
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
SOX chir_01 N4 C7 C3 C5 positiv
SOX chir_02 C3 N4 C11 C2 negativ
SOX chir_03 C2 C3 C10 C9 positiv
SOX chir_04 S1 C2 C5 O5 negativ
SOX chir_05 C5 N4 S1 C6 positiv
SOX chir_06 C6 C7 C5 N14 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
SOX plan-1 C7 0.020
SOX plan-1 O8 0.020
SOX plan-1 N4 0.020
SOX plan-1 C6 0.020
SOX plan-2 C11 0.020
SOX plan-2 C3 0.020
SOX plan-2 O13 0.020
SOX plan-2 O12 0.020
SOX plan-3 N14 0.020
SOX plan-3 C6 0.020
SOX plan-3 C15 0.020
SOX plan-3 H14 0.020
SOX plan-4 C15 0.020
SOX plan-4 N14 0.020
SOX plan-4 O16 0.020
SOX plan-4 C17 0.020
SOX plan-4 H14 0.020
SOX plan-5 C18 0.020
SOX plan-5 C17 0.020
SOX plan-5 C19 0.020
SOX plan-5 C23 0.020
SOX plan-5 C20 0.020
SOX plan-5 C21 0.020
SOX plan-5 C22 0.020
SOX plan-5 H19 0.020
SOX plan-5 H20 0.020
SOX plan-5 H21 0.020
SOX plan-5 H22 0.020
SOX plan-5 H23 0.020
# ------------------------------------------------------
|
