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
UCD UCD '"(4S,5R,6R)-6-((2R,3R,4R,5R,6R)-3-AC' pyranose 46 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_UCD
#
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
UCD C1 C CH1 0.000 0.000 0.000 0.000
UCD H1 H H 0.000 -0.126 -0.197 1.074
UCD O1 O OH1 0.000 1.263 0.628 -0.223
UCD HO1 H H 0.000 1.971 0.045 0.082
UCD O5 O O2 0.000 -0.048 -1.232 -0.717
UCD C5 C CH1 0.000 -1.242 -1.911 -0.329
UCD H5 H H 0.000 -1.284 -1.978 0.767
UCD C6 C CH2 0.000 -1.242 -3.319 -0.927
UCD H61 H H 0.000 -1.108 -3.255 -2.008
UCD H62 H H 0.000 -2.194 -3.807 -0.707
UCD O6 O OH1 0.000 -0.174 -4.079 -0.357
UCD HO6 H H 0.000 -0.174 -4.969 -0.735
UCD C4 C CH1 0.000 -2.463 -1.143 -0.840
UCD H4 H H 0.000 -3.380 -1.679 -0.557
UCD O4 O OH1 0.000 -2.396 -1.029 -2.263
UCD HO4 H H 0.000 -2.384 -1.912 -2.655
UCD C3 C CH1 0.000 -2.473 0.257 -0.214
UCD H3 H H 0.000 -2.632 0.173 0.871
UCD C2 C CH1 0.000 -1.121 0.924 -0.484
UCD H2 H H 0.000 -1.009 1.104 -1.562
UCD N2 N NH1 0.000 -1.050 2.198 0.236
UCD HN2 H H 0.000 -1.613 2.343 1.062
UCD CAP C C 0.000 -0.234 3.176 -0.203
UCD OAB O O 0.000 0.441 3.003 -1.195
UCD CAA C CH3 0.000 -0.162 4.487 0.537
UCD HAA3 H H 0.000 -1.120 4.940 0.551
UCD HAA2 H H 0.000 0.160 4.315 1.532
UCD HAA1 H H 0.000 0.525 5.131 0.052
UCD O3 O O2 0.000 -3.523 1.034 -0.793
UCD CAX C CH1 0.000 -4.687 0.818 0.008
UCD HAX H H 0.000 -4.460 1.056 1.057
UCD CAU C CH1 0.000 -5.824 1.721 -0.488
UCD HAU H H 0.000 -6.167 1.381 -1.475
UCD OAH O OH1 0.000 -5.373 3.074 -0.571
UCD HAH H H 0.000 -6.104 3.640 -0.855
UCD CAS C CH1 0.000 -6.971 1.614 0.527
UCD HAS H H 0.000 -6.734 2.213 1.418
UCD OAF O OH1 0.000 -8.184 2.086 -0.062
UCD HAF H H 0.000 -8.906 1.998 0.575
UCD CAJ C C1 0.000 -7.123 0.166 0.914
UCD HAJ H H 0.000 -7.997 -0.136 1.467
UCD CAR C C 0.000 -6.222 -0.746 0.600
UCD OAM O O2 0.000 -5.089 -0.543 -0.094
UCD CAQ C C 0.000 -6.484 -2.123 1.055
UCD OAE O OC -0.500 -5.669 -3.035 0.791
UCD OAC O OC -0.500 -7.520 -2.379 1.707
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
UCD C1 n/a O5 START
UCD H1 C1 . .
UCD O1 C1 HO1 .
UCD HO1 O1 . .
UCD O5 C1 . END
UCD C5 O5 C4 .
UCD H5 C5 . .
UCD C6 C5 O6 .
UCD H61 C6 . .
UCD H62 C6 . .
UCD O6 C6 HO6 .
UCD HO6 O6 . .
UCD C4 C5 C3 .
UCD H4 C4 . .
UCD O4 C4 HO4 .
UCD HO4 O4 . .
UCD C3 C4 O3 .
UCD H3 C3 . .
UCD C2 C3 N2 .
UCD H2 C2 . .
UCD N2 C2 CAP .
UCD HN2 N2 . .
UCD CAP N2 CAA .
UCD OAB CAP . .
UCD CAA CAP HAA1 .
UCD HAA3 CAA . .
UCD HAA2 CAA . .
UCD HAA1 CAA . .
UCD O3 C3 CAX .
UCD CAX O3 CAU .
UCD HAX CAX . .
UCD CAU CAX CAS .
UCD HAU CAU . .
UCD OAH CAU HAH .
UCD HAH OAH . .
UCD CAS CAU CAJ .
UCD HAS CAS . .
UCD OAF CAS HAF .
UCD HAF OAF . .
UCD CAJ CAS CAR .
UCD HAJ CAJ . .
UCD CAR CAJ CAQ .
UCD OAM CAR . .
UCD CAQ CAR OAC .
UCD OAE CAQ . .
UCD OAC CAQ . .
UCD C2 C1 . ADD
UCD CAX OAM . 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
UCD CAA CAP single 1.500 0.020
UCD HAA1 CAA single 1.059 0.020
UCD HAA2 CAA single 1.059 0.020
UCD HAA3 CAA single 1.059 0.020
UCD OAB CAP double 1.220 0.020
UCD CAP N2 single 1.330 0.020
UCD N2 C2 single 1.450 0.020
UCD HN2 N2 single 1.010 0.020
UCD C2 C1 single 1.524 0.020
UCD C2 C3 single 1.524 0.020
UCD H2 C2 single 1.099 0.020
UCD O1 C1 single 1.432 0.020
UCD O5 C1 single 1.426 0.020
UCD H1 C1 single 1.099 0.020
UCD HO1 O1 single 0.967 0.020
UCD C5 O5 single 1.426 0.020
UCD C6 C5 single 1.524 0.020
UCD C4 C5 single 1.524 0.020
UCD H5 C5 single 1.099 0.020
UCD O6 C6 single 1.432 0.020
UCD H61 C6 single 1.092 0.020
UCD H62 C6 single 1.092 0.020
UCD HO6 O6 single 0.967 0.020
UCD O4 C4 single 1.432 0.020
UCD C3 C4 single 1.524 0.020
UCD H4 C4 single 1.099 0.020
UCD HO4 O4 single 0.967 0.020
UCD O3 C3 single 1.426 0.020
UCD H3 C3 single 1.099 0.020
UCD CAX O3 single 1.426 0.020
UCD CAX OAM single 1.426 0.020
UCD CAU CAX single 1.524 0.020
UCD HAX CAX single 1.099 0.020
UCD OAM CAR single 1.454 0.020
UCD CAQ CAR single 1.460 0.020
UCD CAR CAJ double 1.340 0.020
UCD OAE CAQ deloc 1.250 0.020
UCD OAC CAQ deloc 1.250 0.020
UCD CAJ CAS single 1.510 0.020
UCD HAJ CAJ single 1.077 0.020
UCD OAF CAS single 1.432 0.020
UCD CAS CAU single 1.524 0.020
UCD HAS CAS single 1.099 0.020
UCD HAF OAF single 0.967 0.020
UCD OAH CAU single 1.432 0.020
UCD HAU CAU single 1.099 0.020
UCD HAH OAH 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
UCD H1 C1 O1 109.470 3.000
UCD H1 C1 O5 109.470 3.000
UCD O1 C1 O5 109.470 3.000
UCD H1 C1 C2 108.340 3.000
UCD O1 C1 C2 109.470 3.000
UCD O5 C1 C2 109.470 3.000
UCD C1 O1 HO1 109.470 3.000
UCD C1 O5 C5 111.800 3.000
UCD O5 C5 H5 109.470 3.000
UCD O5 C5 C6 109.470 3.000
UCD O5 C5 C4 109.470 3.000
UCD H5 C5 C6 108.340 3.000
UCD H5 C5 C4 108.340 3.000
UCD C6 C5 C4 111.000 3.000
UCD C5 C6 H61 109.470 3.000
UCD C5 C6 H62 109.470 3.000
UCD C5 C6 O6 109.470 3.000
UCD H61 C6 H62 107.900 3.000
UCD H61 C6 O6 109.470 3.000
UCD H62 C6 O6 109.470 3.000
UCD C6 O6 HO6 109.470 3.000
UCD C5 C4 H4 108.340 3.000
UCD C5 C4 O4 109.470 3.000
UCD C5 C4 C3 111.000 3.000
UCD H4 C4 O4 109.470 3.000
UCD H4 C4 C3 108.340 3.000
UCD O4 C4 C3 109.470 3.000
UCD C4 O4 HO4 109.470 3.000
UCD C4 C3 H3 108.340 3.000
UCD C4 C3 C2 111.000 3.000
UCD C4 C3 O3 109.470 3.000
UCD H3 C3 C2 108.340 3.000
UCD H3 C3 O3 109.470 3.000
UCD C2 C3 O3 109.470 3.000
UCD C3 C2 H2 108.340 3.000
UCD C3 C2 N2 110.000 3.000
UCD C3 C2 C1 111.000 3.000
UCD H2 C2 N2 108.550 3.000
UCD H2 C2 C1 108.340 3.000
UCD N2 C2 C1 110.000 3.000
UCD C2 N2 HN2 118.500 3.000
UCD C2 N2 CAP 121.500 3.000
UCD HN2 N2 CAP 120.000 3.000
UCD N2 CAP OAB 123.000 3.000
UCD N2 CAP CAA 116.500 3.000
UCD OAB CAP CAA 123.000 3.000
UCD CAP CAA HAA3 109.470 3.000
UCD CAP CAA HAA2 109.470 3.000
UCD CAP CAA HAA1 109.470 3.000
UCD HAA3 CAA HAA2 109.470 3.000
UCD HAA3 CAA HAA1 109.470 3.000
UCD HAA2 CAA HAA1 109.470 3.000
UCD C3 O3 CAX 111.800 3.000
UCD O3 CAX HAX 109.470 3.000
UCD O3 CAX CAU 109.470 3.000
UCD O3 CAX OAM 109.470 3.000
UCD HAX CAX CAU 108.340 3.000
UCD HAX CAX OAM 109.470 3.000
UCD CAU CAX OAM 109.470 3.000
UCD CAX CAU HAU 108.340 3.000
UCD CAX CAU OAH 109.470 3.000
UCD CAX CAU CAS 111.000 3.000
UCD HAU CAU OAH 109.470 3.000
UCD HAU CAU CAS 108.340 3.000
UCD OAH CAU CAS 109.470 3.000
UCD CAU OAH HAH 109.470 3.000
UCD CAU CAS HAS 108.340 3.000
UCD CAU CAS OAF 109.470 3.000
UCD CAU CAS CAJ 109.470 3.000
UCD HAS CAS OAF 109.470 3.000
UCD HAS CAS CAJ 108.810 3.000
UCD OAF CAS CAJ 109.470 3.000
UCD CAS OAF HAF 109.470 3.000
UCD CAS CAJ HAJ 120.000 3.000
UCD CAS CAJ CAR 120.500 3.000
UCD HAJ CAJ CAR 120.000 3.000
UCD CAJ CAR OAM 120.000 3.000
UCD CAJ CAR CAQ 120.000 3.000
UCD OAM CAR CAQ 120.000 3.000
UCD CAR OAM CAX 111.800 3.000
UCD CAR CAQ OAE 120.000 3.000
UCD CAR CAQ OAC 120.000 3.000
UCD OAE CAQ OAC 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
UCD var_1 O5 C1 O1 HO1 -59.793 20.000 1
UCD var_2 C1 O5 C5 C4 60.000 20.000 1
UCD var_3 O5 C5 C6 O6 65.071 20.000 3
UCD var_4 C5 C6 O6 HO6 -179.993 20.000 1
UCD var_5 O5 C5 C4 C3 -60.000 20.000 3
UCD var_6 C5 C4 O4 HO4 60.021 20.000 1
UCD var_7 C5 C4 C3 O3 180.000 20.000 3
UCD var_8 C4 C3 C2 N2 180.000 20.000 3
UCD var_9 C3 C2 C1 O5 60.000 20.000 3
UCD var_10 C3 C2 N2 CAP -155.204 20.000 3
UCD CONST_1 C2 N2 CAP CAA 180.000 0.000 0
UCD var_11 N2 CAP CAA HAA1 -179.969 20.000 1
UCD var_12 C4 C3 O3 CAX 89.967 20.000 1
UCD var_13 C3 O3 CAX CAU 175.077 20.000 1
UCD var_14 O3 CAX OAM CAR 180.000 20.000 1
UCD var_15 O3 CAX CAU CAS 180.000 20.000 3
UCD var_16 CAX CAU OAH HAH -178.042 20.000 1
UCD var_17 CAX CAU CAS CAJ -30.000 20.000 3
UCD var_18 CAU CAS OAF HAF 178.789 20.000 1
UCD var_19 CAU CAS CAJ CAR 0.000 20.000 1
UCD var_20 CAS CAJ CAR CAQ 180.000 20.000 1
UCD var_21 CAJ CAR OAM CAX 30.000 20.000 1
UCD var_22 CAJ CAR CAQ OAC -0.048 20.000 1
UCD var_1 C2 C1 O5 C5 -60.000 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
UCD chir_01 C2 N2 C1 C3 negativ
UCD chir_02 C1 C2 O1 O5 positiv
UCD chir_03 C5 O5 C6 C4 positiv
UCD chir_04 C4 C5 O4 C3 positiv
UCD chir_05 C3 C2 C4 O3 positiv
UCD chir_06 CAX O3 OAM CAU positiv
UCD chir_07 CAS CAJ OAF CAU positiv
UCD chir_08 CAU CAX CAS OAH negativ
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
UCD plan-1 CAP 0.020
UCD plan-1 CAA 0.020
UCD plan-1 OAB 0.020
UCD plan-1 N2 0.020
UCD plan-1 HN2 0.020
UCD plan-2 N2 0.020
UCD plan-2 CAP 0.020
UCD plan-2 C2 0.020
UCD plan-2 HN2 0.020
UCD plan-3 CAR 0.020
UCD plan-3 OAM 0.020
UCD plan-3 CAQ 0.020
UCD plan-3 CAJ 0.020
UCD plan-3 HAJ 0.020
UCD plan-4 CAQ 0.020
UCD plan-4 CAR 0.020
UCD plan-4 OAE 0.020
UCD plan-4 OAC 0.020
UCD plan-5 CAJ 0.020
UCD plan-5 CAR 0.020
UCD plan-5 CAS 0.020
UCD plan-5 HAJ 0.020
# ------------------------------------------------------
|
