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
|
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
HS2 HS2 '2-deoxy-4-O-(4-deoxy-alpha-L-threo-h' non-polymer 48 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_HS2
#
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
HS2 O34 O OC -0.500 0.000 0.000 0.000
HS2 C27 C C 0.000 -1.233 -0.189 0.094
HS2 O35 O OC -0.500 -1.725 -1.288 -0.246
HS2 C19 C C 0.000 -2.106 0.881 0.608
HS2 O13 O O2 0.000 -3.437 0.644 0.692
HS2 C13 C CH1 0.000 -4.304 1.771 0.841
HS2 H13 H H 0.000 -4.352 2.327 -0.105
HS2 C12 C CH1 0.000 -3.737 2.677 1.942
HS2 H12 H H 0.000 -3.630 2.105 2.875
HS2 O18 O OH1 0.000 -4.614 3.785 2.153
HS2 HO18 H H 0.000 -4.244 4.363 2.834
HS2 C17 C CH1 0.000 -2.365 3.185 1.487
HS2 H17 H H 0.000 -2.496 3.933 0.693
HS2 O25 O OH1 0.000 -1.685 3.779 2.595
HS2 HO25 H H 0.000 -0.819 4.098 2.307
HS2 C24 C C1 0.000 -1.553 2.032 0.961
HS2 H24 H H 0.000 -0.486 2.146 0.868
HS2 O3 O O2 0.000 -5.613 1.331 1.206
HS2 C1 C CH1 0.000 -6.320 0.673 0.153
HS2 H1 H H 0.000 -5.607 0.328 -0.609
HS2 C2 C CH1 0.000 -7.315 1.647 -0.481
HS2 H2 H H 0.000 -8.001 2.023 0.290
HS2 C6 C CH2 0.000 -6.557 2.821 -1.104
HS2 H6 H H 0.000 -5.944 2.459 -1.932
HS2 H6A H H 0.000 -5.914 3.280 -0.350
HS2 O11 O OH1 0.000 -7.491 3.788 -1.588
HS2 HO11 H H 0.000 -7.011 4.530 -1.982
HS2 O5 O O2 0.000 -8.062 0.971 -1.494
HS2 C10 C CH1 0.000 -8.833 -0.133 -1.014
HS2 H10 H H 0.000 -9.389 -0.582 -1.849
HS2 O15 O OH1 0.000 -9.751 0.324 -0.020
HS2 HO15 H H 0.000 -10.342 0.984 -0.407
HS2 C3 C CH1 0.000 -7.897 -1.178 -0.402
HS2 H3 H H 0.000 -7.216 -1.560 -1.176
HS2 C4 C CH1 0.000 -7.082 -0.529 0.720
HS2 H4 H H 0.000 -7.758 -0.193 1.519
HS2 O9 O OH1 0.000 -6.153 -1.478 1.248
HS2 HO9 H H 0.000 -6.636 -2.236 1.606
HS2 N14 N NH1 0.000 -8.689 -2.287 0.145
HS2 HN14 H H 0.000 -8.982 -2.360 1.109
HS2 C7 C CH1 0.000 -9.001 -3.277 -0.896
HS2 H7 H H 0.000 -8.243 -3.223 -1.690
HS2 O7 O OH1 0.000 -10.289 -3.000 -1.447
HS2 HO7 H H 0.000 -10.492 -3.651 -2.132
HS2 C8 C CH3 0.000 -8.998 -4.679 -0.284
HS2 H8B H H 0.000 -9.222 -5.393 -1.033
HS2 H8A H H 0.000 -8.043 -4.886 0.126
HS2 H8 H H 0.000 -9.728 -4.732 0.482
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
HS2 O34 n/a C27 START
HS2 C27 O34 C19 .
HS2 O35 C27 . .
HS2 C19 C27 O13 .
HS2 O13 C19 C13 .
HS2 C13 O13 O3 .
HS2 H13 C13 . .
HS2 C12 C13 C17 .
HS2 H12 C12 . .
HS2 O18 C12 HO18 .
HS2 HO18 O18 . .
HS2 C17 C12 C24 .
HS2 H17 C17 . .
HS2 O25 C17 HO25 .
HS2 HO25 O25 . .
HS2 C24 C17 H24 .
HS2 H24 C24 . .
HS2 O3 C13 C1 .
HS2 C1 O3 C2 .
HS2 H1 C1 . .
HS2 C2 C1 O5 .
HS2 H2 C2 . .
HS2 C6 C2 O11 .
HS2 H6 C6 . .
HS2 H6A C6 . .
HS2 O11 C6 HO11 .
HS2 HO11 O11 . .
HS2 O5 C2 C10 .
HS2 C10 O5 C3 .
HS2 H10 C10 . .
HS2 O15 C10 HO15 .
HS2 HO15 O15 . .
HS2 C3 C10 N14 .
HS2 H3 C3 . .
HS2 C4 C3 O9 .
HS2 H4 C4 . .
HS2 O9 C4 HO9 .
HS2 HO9 O9 . .
HS2 N14 C3 C7 .
HS2 HN14 N14 . .
HS2 C7 N14 C8 .
HS2 H7 C7 . .
HS2 O7 C7 HO7 .
HS2 HO7 O7 . .
HS2 C8 C7 H8 .
HS2 H8B C8 . .
HS2 H8A C8 . .
HS2 H8 C8 . END
HS2 C19 C24 . ADD
HS2 C1 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
HS2 O35 C27 deloc 1.250 0.020
HS2 C27 O34 deloc 1.250 0.020
HS2 C19 C27 single 1.460 0.020
HS2 O13 C19 single 1.454 0.020
HS2 C19 C24 double 1.340 0.020
HS2 C24 C17 single 1.510 0.020
HS2 H24 C24 single 1.077 0.020
HS2 O25 C17 single 1.432 0.020
HS2 C17 C12 single 1.524 0.020
HS2 H17 C17 single 1.099 0.020
HS2 HO25 O25 single 0.967 0.020
HS2 C12 C13 single 1.524 0.020
HS2 O18 C12 single 1.432 0.020
HS2 H12 C12 single 1.099 0.020
HS2 HO18 O18 single 0.967 0.020
HS2 O3 C13 single 1.426 0.020
HS2 C13 O13 single 1.426 0.020
HS2 H13 C13 single 1.099 0.020
HS2 C1 O3 single 1.426 0.020
HS2 C2 C1 single 1.524 0.020
HS2 C1 C4 single 1.524 0.020
HS2 H1 C1 single 1.099 0.020
HS2 C4 C3 single 1.524 0.020
HS2 O9 C4 single 1.432 0.020
HS2 H4 C4 single 1.099 0.020
HS2 HO9 O9 single 0.967 0.020
HS2 C3 C10 single 1.524 0.020
HS2 N14 C3 single 1.450 0.020
HS2 H3 C3 single 1.099 0.020
HS2 C7 N14 single 1.450 0.020
HS2 HN14 N14 single 1.010 0.020
HS2 C8 C7 single 1.524 0.020
HS2 O7 C7 single 1.432 0.020
HS2 H7 C7 single 1.099 0.020
HS2 H8 C8 single 1.059 0.020
HS2 H8A C8 single 1.059 0.020
HS2 H8B C8 single 1.059 0.020
HS2 HO7 O7 single 0.967 0.020
HS2 O15 C10 single 1.432 0.020
HS2 C10 O5 single 1.426 0.020
HS2 H10 C10 single 1.099 0.020
HS2 HO15 O15 single 0.967 0.020
HS2 O5 C2 single 1.426 0.020
HS2 C6 C2 single 1.524 0.020
HS2 H2 C2 single 1.099 0.020
HS2 O11 C6 single 1.432 0.020
HS2 H6 C6 single 1.092 0.020
HS2 H6A C6 single 1.092 0.020
HS2 HO11 O11 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
HS2 O34 C27 O35 123.000 3.000
HS2 O34 C27 C19 120.000 3.000
HS2 O35 C27 C19 120.000 3.000
HS2 C27 C19 O13 120.000 3.000
HS2 C27 C19 C24 120.000 3.000
HS2 O13 C19 C24 120.000 3.000
HS2 C19 O13 C13 111.800 3.000
HS2 O13 C13 H13 109.470 3.000
HS2 O13 C13 C12 109.470 3.000
HS2 O13 C13 O3 109.470 3.000
HS2 H13 C13 C12 108.340 3.000
HS2 H13 C13 O3 109.470 3.000
HS2 C12 C13 O3 109.470 3.000
HS2 C13 C12 H12 108.340 3.000
HS2 C13 C12 O18 109.470 3.000
HS2 C13 C12 C17 111.000 3.000
HS2 H12 C12 O18 109.470 3.000
HS2 H12 C12 C17 108.340 3.000
HS2 O18 C12 C17 109.470 3.000
HS2 C12 O18 HO18 109.470 3.000
HS2 C12 C17 H17 108.340 3.000
HS2 C12 C17 O25 109.470 3.000
HS2 C12 C17 C24 109.470 3.000
HS2 H17 C17 O25 109.470 3.000
HS2 H17 C17 C24 108.810 3.000
HS2 O25 C17 C24 109.470 3.000
HS2 C17 O25 HO25 109.470 3.000
HS2 C17 C24 H24 120.000 3.000
HS2 C17 C24 C19 120.500 3.000
HS2 H24 C24 C19 120.000 3.000
HS2 C13 O3 C1 111.800 3.000
HS2 O3 C1 H1 109.470 3.000
HS2 O3 C1 C2 109.470 3.000
HS2 O3 C1 C4 109.470 3.000
HS2 H1 C1 C2 108.340 3.000
HS2 H1 C1 C4 108.340 3.000
HS2 C2 C1 C4 111.000 3.000
HS2 C1 C2 H2 108.340 3.000
HS2 C1 C2 C6 111.000 3.000
HS2 C1 C2 O5 109.470 3.000
HS2 H2 C2 C6 108.340 3.000
HS2 H2 C2 O5 109.470 3.000
HS2 C6 C2 O5 109.470 3.000
HS2 C2 C6 H6 109.470 3.000
HS2 C2 C6 H6A 109.470 3.000
HS2 C2 C6 O11 109.470 3.000
HS2 H6 C6 H6A 107.900 3.000
HS2 H6 C6 O11 109.470 3.000
HS2 H6A C6 O11 109.470 3.000
HS2 C6 O11 HO11 109.470 3.000
HS2 C2 O5 C10 111.800 3.000
HS2 O5 C10 H10 109.470 3.000
HS2 O5 C10 O15 109.470 3.000
HS2 O5 C10 C3 109.470 3.000
HS2 H10 C10 O15 109.470 3.000
HS2 H10 C10 C3 108.340 3.000
HS2 O15 C10 C3 109.470 3.000
HS2 C10 O15 HO15 109.470 3.000
HS2 C10 C3 H3 108.340 3.000
HS2 C10 C3 C4 111.000 3.000
HS2 C10 C3 N14 110.000 3.000
HS2 H3 C3 C4 108.340 3.000
HS2 H3 C3 N14 108.550 3.000
HS2 C4 C3 N14 110.000 3.000
HS2 C3 C4 H4 108.340 3.000
HS2 C3 C4 O9 109.470 3.000
HS2 C3 C4 C1 111.000 3.000
HS2 H4 C4 O9 109.470 3.000
HS2 H4 C4 C1 108.340 3.000
HS2 O9 C4 C1 109.470 3.000
HS2 C4 O9 HO9 109.470 3.000
HS2 C3 N14 HN14 118.500 3.000
HS2 C3 N14 C7 120.000 3.000
HS2 HN14 N14 C7 118.500 3.000
HS2 N14 C7 H7 108.550 3.000
HS2 N14 C7 O7 109.470 3.000
HS2 N14 C7 C8 110.000 3.000
HS2 H7 C7 O7 109.470 3.000
HS2 H7 C7 C8 108.340 3.000
HS2 O7 C7 C8 109.470 3.000
HS2 C7 O7 HO7 109.470 3.000
HS2 C7 C8 H8B 109.470 3.000
HS2 C7 C8 H8A 109.470 3.000
HS2 C7 C8 H8 109.470 3.000
HS2 H8B C8 H8A 109.470 3.000
HS2 H8B C8 H8 109.470 3.000
HS2 H8A C8 H8 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
HS2 var_1 O34 C27 C19 O13 179.731 20.000 1
HS2 var_2 C27 C19 C24 C17 180.000 20.000 1
HS2 var_3 C27 C19 O13 C13 -150.000 20.000 1
HS2 var_4 C19 O13 C13 O3 180.000 20.000 1
HS2 var_5 O13 C13 C12 C17 60.000 20.000 3
HS2 var_6 C13 C12 O18 HO18 -178.838 20.000 1
HS2 var_7 C13 C12 C17 C24 -60.000 20.000 3
HS2 var_8 C12 C17 O25 HO25 179.922 20.000 1
HS2 var_9 C12 C17 C24 C19 30.000 20.000 1
HS2 var_10 O13 C13 O3 C1 -71.118 20.000 1
HS2 var_11 C13 O3 C1 C2 -100.530 20.000 1
HS2 var_12 O3 C1 C4 C3 180.000 20.000 3
HS2 var_13 O3 C1 C2 O5 180.000 20.000 3
HS2 var_14 C1 C2 C6 O11 -174.776 20.000 3
HS2 var_15 C2 C6 O11 HO11 179.993 20.000 1
HS2 var_16 C1 C2 O5 C10 60.000 20.000 1
HS2 var_17 C2 O5 C10 C3 -60.000 20.000 1
HS2 var_18 O5 C10 O15 HO15 60.126 20.000 1
HS2 var_19 O5 C10 C3 N14 180.000 20.000 3
HS2 var_20 C10 C3 C4 O9 180.000 20.000 3
HS2 var_21 C3 C4 O9 HO9 -60.467 20.000 1
HS2 var_22 C10 C3 N14 C7 85.245 20.000 3
HS2 var_23 C3 N14 C7 C8 144.970 20.000 3
HS2 var_24 N14 C7 O7 HO7 179.949 20.000 1
HS2 var_25 N14 C7 C8 H8 60.025 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
HS2 chir_01 C17 C24 O25 C12 positiv
HS2 chir_02 C12 C17 O18 C13 negativ
HS2 chir_03 C13 C12 O13 O3 negativ
HS2 chir_04 C1 O3 C4 C2 negativ
HS2 chir_05 C4 C1 O9 C3 positiv
HS2 chir_06 C3 C4 N14 C10 negativ
HS2 chir_07 C7 N14 C8 O7 negativ
HS2 chir_08 C10 C3 O15 O5 negativ
HS2 chir_09 C2 C1 O5 C6 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
HS2 plan-1 C27 0.020
HS2 plan-1 O35 0.020
HS2 plan-1 O34 0.020
HS2 plan-1 C19 0.020
HS2 plan-2 C19 0.020
HS2 plan-2 C27 0.020
HS2 plan-2 C24 0.020
HS2 plan-2 O13 0.020
HS2 plan-2 H24 0.020
HS2 plan-3 C24 0.020
HS2 plan-3 C19 0.020
HS2 plan-3 C17 0.020
HS2 plan-3 H24 0.020
HS2 plan-4 N14 0.020
HS2 plan-4 C3 0.020
HS2 plan-4 C7 0.020
HS2 plan-4 HN14 0.020
# ------------------------------------------------------
|
