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
|
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
NGS NGS '2-(acetylamino)-2-deoxy-6-O-sulfo-be' pyranose 34 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_NGS
#
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
NGS C1 C CH1 0.000 0.000 0.000 0.000
NGS H1 H H 0.000 0.185 -0.163 -1.071
NGS O1 O OH1 0.000 0.806 1.086 0.463
NGS H14 H H 0.000 0.582 1.887 -0.029
NGS O5 O O2 0.000 -1.379 0.311 0.203
NGS C5 C CH1 0.000 -2.279 -0.703 -0.252
NGS H5 H H 0.000 -2.123 -0.875 -1.326
NGS C6 C CH2 0.000 -3.721 -0.252 -0.011
NGS H6 H H 0.000 -3.851 0.004 1.042
NGS H6A H H 0.000 -4.404 -1.062 -0.275
NGS O6 O O2 0.000 -4.003 0.892 -0.819
NGS S S ST 0.000 -5.418 1.430 -0.659
NGS O7 O OS 0.000 -6.265 0.296 -0.534
NGS O8 O OH1 0.000 -5.475 2.158 0.675
NGS H15 H H 0.000 -6.297 2.559 0.935
NGS O9 O OS 0.000 -5.587 2.420 -1.665
NGS C4 C CH1 0.000 -2.015 -2.000 0.517
NGS H4 H H 0.000 -2.210 -1.839 1.587
NGS O4 O OH1 0.000 -2.872 -3.030 0.025
NGS HO4 H H 0.000 -3.794 -2.769 0.150
NGS C3 C CH1 0.000 -0.552 -2.412 0.320
NGS H3 H H 0.000 -0.370 -2.623 -0.743
NGS O3 O OH1 0.000 -0.278 -3.582 1.094
NGS HO3 H H 0.000 -0.852 -4.303 0.803
NGS C2 C CH1 0.000 0.357 -1.269 0.780
NGS H2 H H 0.000 0.210 -1.092 1.854
NGS N N NH1 0.000 1.755 -1.622 0.527
NGS HN H H 0.000 1.985 -2.291 -0.193
NGS C C C 0.000 2.736 -1.055 1.257
NGS O O O 0.000 2.462 -0.252 2.122
NGS CH3 C CH3 0.000 4.176 -1.420 0.996
NGS HH3B H H 0.000 4.717 -0.552 0.719
NGS HH3A H H 0.000 4.601 -1.835 1.873
NGS HH3 H H 0.000 4.225 -2.130 0.211
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
NGS C1 n/a O5 START
NGS H1 C1 . .
NGS O1 C1 H14 .
NGS H14 O1 . .
NGS O5 C1 . END
NGS C5 O5 C4 .
NGS H5 C5 . .
NGS C6 C5 O6 .
NGS H6 C6 . .
NGS H6A C6 . .
NGS O6 C6 S .
NGS S O6 O9 .
NGS O7 S . .
NGS O8 S H15 .
NGS H15 O8 . .
NGS O9 S . .
NGS C4 C5 C3 .
NGS H4 C4 . .
NGS O4 C4 HO4 .
NGS HO4 O4 . .
NGS C3 C4 C2 .
NGS H3 C3 . .
NGS O3 C3 HO3 .
NGS HO3 O3 . .
NGS C2 C3 N .
NGS H2 C2 . .
NGS N C2 C .
NGS HN N . .
NGS C N CH3 .
NGS O C . .
NGS CH3 C HH3 .
NGS HH3B CH3 . .
NGS HH3A CH3 . .
NGS HH3 CH3 . .
NGS C1 C2 . 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
NGS C1 C2 single 1.524 0.020
NGS O1 C1 single 1.432 0.020
NGS O5 C1 single 1.426 0.020
NGS H1 C1 single 1.099 0.020
NGS C2 C3 single 1.524 0.020
NGS N C2 single 1.450 0.020
NGS H2 C2 single 1.099 0.020
NGS C3 C4 single 1.524 0.020
NGS O3 C3 single 1.432 0.020
NGS H3 C3 single 1.099 0.020
NGS C4 C5 single 1.524 0.020
NGS O4 C4 single 1.432 0.020
NGS H4 C4 single 1.099 0.020
NGS C6 C5 single 1.524 0.020
NGS C5 O5 single 1.426 0.020
NGS H5 C5 single 1.099 0.020
NGS O6 C6 single 1.426 0.020
NGS H6 C6 single 1.092 0.020
NGS H6A C6 single 1.092 0.020
NGS HO3 O3 single 0.967 0.020
NGS S O6 single 1.535 0.020
NGS C N single 1.330 0.020
NGS HN N single 1.010 0.020
NGS O C double 1.220 0.020
NGS CH3 C single 1.500 0.020
NGS HH3 CH3 single 1.059 0.020
NGS HH3A CH3 single 1.059 0.020
NGS HH3B CH3 single 1.059 0.020
NGS O7 S double 1.436 0.020
NGS O8 S single 1.635 0.020
NGS O9 S double 1.436 0.020
NGS HO4 O4 single 0.967 0.020
NGS H14 O1 single 0.967 0.020
NGS H15 O8 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
NGS H1 C1 O1 109.470 3.000
NGS H1 C1 O5 109.470 3.000
NGS O1 C1 O5 109.470 3.000
NGS H1 C1 C2 108.340 3.000
NGS O1 C1 C2 109.470 3.000
NGS O5 C1 C2 109.470 3.000
NGS C1 O1 H14 109.470 3.000
NGS C1 O5 C5 111.800 3.000
NGS O5 C5 H5 109.470 3.000
NGS O5 C5 C6 109.470 3.000
NGS O5 C5 C4 109.470 3.000
NGS H5 C5 C6 108.340 3.000
NGS H5 C5 C4 108.340 3.000
NGS C6 C5 C4 111.000 3.000
NGS C5 C6 H6 109.470 3.000
NGS C5 C6 H6A 109.470 3.000
NGS C5 C6 O6 109.470 3.000
NGS H6 C6 H6A 107.900 3.000
NGS H6 C6 O6 109.470 3.000
NGS H6A C6 O6 109.470 3.000
NGS C6 O6 S 120.000 3.000
NGS O6 S O7 109.500 3.000
NGS O6 S O8 109.500 3.000
NGS O6 S O9 109.500 3.000
NGS O7 S O8 109.500 3.000
NGS O7 S O9 109.500 3.000
NGS O8 S O9 109.500 3.000
NGS S O8 H15 120.000 3.000
NGS C5 C4 H4 108.340 3.000
NGS C5 C4 O4 109.470 3.000
NGS C5 C4 C3 111.000 3.000
NGS H4 C4 O4 109.470 3.000
NGS H4 C4 C3 108.340 3.000
NGS O4 C4 C3 109.470 3.000
NGS C4 O4 HO4 109.470 3.000
NGS C4 C3 H3 108.340 3.000
NGS C4 C3 O3 109.470 3.000
NGS C4 C3 C2 111.000 3.000
NGS H3 C3 O3 109.470 3.000
NGS H3 C3 C2 108.340 3.000
NGS O3 C3 C2 109.470 3.000
NGS C3 O3 HO3 109.470 3.000
NGS C3 C2 H2 108.340 3.000
NGS C3 C2 N 110.000 3.000
NGS C3 C2 C1 111.000 3.000
NGS H2 C2 N 108.550 3.000
NGS H2 C2 C1 108.340 3.000
NGS N C2 C1 110.000 3.000
NGS C2 N HN 118.500 3.000
NGS C2 N C 121.500 3.000
NGS HN N C 120.000 3.000
NGS N C O 123.000 3.000
NGS N C CH3 116.500 3.000
NGS O C CH3 123.000 3.000
NGS C CH3 HH3B 109.470 3.000
NGS C CH3 HH3A 109.470 3.000
NGS C CH3 HH3 109.470 3.000
NGS HH3B CH3 HH3A 109.470 3.000
NGS HH3B CH3 HH3 109.470 3.000
NGS HH3A CH3 HH3 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
NGS var_1 O5 C1 O1 H14 -60.096 20.000 1
NGS var_2 C1 O5 C5 C4 60.000 20.000 1
NGS var_3 O5 C5 C6 O6 65.027 20.000 3
NGS var_4 C5 C6 O6 S -179.962 20.000 1
NGS var_5 C6 O6 S O9 -171.418 20.000 1
NGS var_6 O6 S O8 H15 -179.985 20.000 1
NGS var_7 O5 C5 C4 C3 -60.000 20.000 3
NGS var_8 C5 C4 O4 HO4 -60.307 20.000 1
NGS var_9 C5 C4 C3 C2 60.000 20.000 3
NGS var_10 C4 C3 O3 HO3 60.444 20.000 1
NGS var_11 C4 C3 C2 N 180.000 20.000 3
NGS var_12 C3 C2 C1 O5 60.000 20.000 3
NGS var_13 C3 C2 N C -155.330 20.000 3
NGS CONST_1 C2 N C CH3 180.000 0.000 0
NGS var_14 N C CH3 HH3 0.001 20.000 1
NGS var_1 C5 O5 C1 C2 0.000 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
NGS chir_01 C1 C2 O1 O5 positiv
NGS chir_02 C2 C1 C3 N negativ
NGS chir_03 C3 C2 C4 O3 positiv
NGS chir_04 C4 C3 C5 O4 negativ
NGS chir_05 C5 C4 C6 O5 negativ
NGS chir_06 S O6 O7 O8 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
NGS plan-1 N 0.020
NGS plan-1 C2 0.020
NGS plan-1 C 0.020
NGS plan-1 HN 0.020
NGS plan-2 C 0.020
NGS plan-2 N 0.020
NGS plan-2 O 0.020
NGS plan-2 CH3 0.020
NGS plan-2 HN 0.020
# ------------------------------------------------------
|
