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
|
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
250 250 '(2R)-2-hydroxy-3-[4-(2-hydroxyethyl)' non-polymer 37 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_250
#
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
250 O2 O OS 0.000 0.000 0.000 0.000
250 S1 S ST 0.000 -0.273 -1.394 -0.046
250 O1 O OS 0.000 -0.198 -2.194 1.126
250 O3 O OH1 0.000 0.809 -1.958 -0.956
250 HO3 H H 0.000 1.714 -1.894 -0.672
250 C1 C CH2 0.000 -1.822 -1.710 -0.936
250 H11 H H 0.000 -1.938 -2.784 -1.092
250 H12 H H 0.000 -1.796 -1.203 -1.903
250 C2 C CH1 0.000 -2.999 -1.182 -0.114
250 H2 H H 0.000 -2.880 -0.101 0.043
250 O4 O OH1 0.000 -3.032 -1.846 1.151
250 HO4 H H 0.000 -3.136 -2.797 1.013
250 C3 C CH2 0.000 -4.305 -1.449 -0.864
250 H31 H H 0.000 -4.465 -2.526 -0.943
250 H32 H H 0.000 -4.244 -1.017 -1.865
250 N1 N NT 0.000 -5.423 -0.838 -0.133
250 C4 C CH2 0.000 -6.715 -1.269 -0.688
250 H41 H H 0.000 -6.776 -2.359 -0.665
250 H42 H H 0.000 -6.801 -0.922 -1.720
250 C5 C CH2 0.000 -7.850 -0.674 0.148
250 H51 H H 0.000 -7.780 -1.044 1.173
250 H52 H H 0.000 -8.811 -0.971 -0.279
250 N2 N NT 0.000 -7.742 0.792 0.145
250 C6 C CH2 0.000 -6.452 1.223 0.700
250 H61 H H 0.000 -6.365 0.877 1.732
250 H62 H H 0.000 -6.391 2.313 0.677
250 C7 C CH2 0.000 -5.316 0.629 -0.136
250 H72 H H 0.000 -4.356 0.926 0.291
250 H71 H H 0.000 -5.387 0.998 -1.161
250 C8 C CH2 0.000 -8.860 1.403 0.875
250 H81 H H 0.000 -8.668 1.345 1.949
250 H82 H H 0.000 -9.783 0.867 0.643
250 C9 C CH2 0.000 -9.001 2.868 0.459
250 H91 H H 0.000 -8.051 3.383 0.615
250 H92 H H 0.000 -9.776 3.345 1.062
250 O5 O OH1 0.000 -9.360 2.938 -0.922
250 HO5 H H 0.000 -9.449 3.864 -1.185
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
250 O2 n/a S1 START
250 S1 O2 C1 .
250 O1 S1 . .
250 O3 S1 HO3 .
250 HO3 O3 . .
250 C1 S1 C2 .
250 H11 C1 . .
250 H12 C1 . .
250 C2 C1 C3 .
250 H2 C2 . .
250 O4 C2 HO4 .
250 HO4 O4 . .
250 C3 C2 N1 .
250 H31 C3 . .
250 H32 C3 . .
250 N1 C3 C4 .
250 C4 N1 C5 .
250 H41 C4 . .
250 H42 C4 . .
250 C5 C4 N2 .
250 H51 C5 . .
250 H52 C5 . .
250 N2 C5 C8 .
250 C6 N2 C7 .
250 H61 C6 . .
250 H62 C6 . .
250 C7 C6 H71 .
250 H72 C7 . .
250 H71 C7 . .
250 C8 N2 C9 .
250 H81 C8 . .
250 H82 C8 . .
250 C9 C8 O5 .
250 H91 C9 . .
250 H92 C9 . .
250 O5 C9 HO5 .
250 HO5 O5 . END
250 N1 C7 . 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
250 S1 O2 double 1.436 0.020
250 O1 S1 double 1.436 0.020
250 O3 S1 single 1.635 0.020
250 C1 S1 single 1.662 0.020
250 C2 C1 single 1.524 0.020
250 O4 C2 single 1.432 0.020
250 C3 C2 single 1.524 0.020
250 N1 C3 single 1.469 0.020
250 C4 N1 single 1.469 0.020
250 N1 C7 single 1.469 0.020
250 C5 C4 single 1.524 0.020
250 C7 C6 single 1.524 0.020
250 N2 C5 single 1.469 0.020
250 C6 N2 single 1.469 0.020
250 C8 N2 single 1.469 0.020
250 C9 C8 single 1.524 0.020
250 O5 C9 single 1.432 0.020
250 HO3 O3 single 0.967 0.020
250 H11 C1 single 1.092 0.020
250 H12 C1 single 1.092 0.020
250 H2 C2 single 1.099 0.020
250 HO4 O4 single 0.967 0.020
250 H31 C3 single 1.092 0.020
250 H32 C3 single 1.092 0.020
250 H71 C7 single 1.092 0.020
250 H72 C7 single 1.092 0.020
250 H61 C6 single 1.092 0.020
250 H62 C6 single 1.092 0.020
250 H51 C5 single 1.092 0.020
250 H52 C5 single 1.092 0.020
250 H41 C4 single 1.092 0.020
250 H42 C4 single 1.092 0.020
250 H81 C8 single 1.092 0.020
250 H82 C8 single 1.092 0.020
250 H91 C9 single 1.092 0.020
250 H92 C9 single 1.092 0.020
250 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
250 O2 S1 O1 109.500 3.000
250 O2 S1 O3 109.500 3.000
250 O2 S1 C1 109.500 3.000
250 O1 S1 O3 109.500 3.000
250 O1 S1 C1 109.500 3.000
250 O3 S1 C1 109.500 3.000
250 S1 O3 HO3 120.000 3.000
250 S1 C1 H11 109.500 3.000
250 S1 C1 H12 109.500 3.000
250 S1 C1 C2 109.500 3.000
250 H11 C1 H12 107.900 3.000
250 H11 C1 C2 109.470 3.000
250 H12 C1 C2 109.470 3.000
250 C1 C2 H2 108.340 3.000
250 C1 C2 O4 109.470 3.000
250 C1 C2 C3 109.470 3.000
250 H2 C2 O4 109.470 3.000
250 H2 C2 C3 108.340 3.000
250 O4 C2 C3 109.470 3.000
250 C2 O4 HO4 109.470 3.000
250 C2 C3 H31 109.470 3.000
250 C2 C3 H32 109.470 3.000
250 C2 C3 N1 109.500 3.000
250 H31 C3 H32 107.900 3.000
250 H31 C3 N1 109.470 3.000
250 H32 C3 N1 109.470 3.000
250 C3 N1 C4 109.470 3.000
250 C3 N1 C7 109.470 3.000
250 C4 N1 C7 109.470 3.000
250 N1 C4 H41 109.470 3.000
250 N1 C4 H42 109.470 3.000
250 N1 C4 C5 109.470 3.000
250 H41 C4 H42 107.900 3.000
250 H41 C4 C5 109.470 3.000
250 H42 C4 C5 109.470 3.000
250 C4 C5 H51 109.470 3.000
250 C4 C5 H52 109.470 3.000
250 C4 C5 N2 109.470 3.000
250 H51 C5 H52 107.900 3.000
250 H51 C5 N2 109.470 3.000
250 H52 C5 N2 109.470 3.000
250 C5 N2 C6 109.470 3.000
250 C5 N2 C8 109.470 3.000
250 C6 N2 C8 109.470 3.000
250 N2 C6 H61 109.470 3.000
250 N2 C6 H62 109.470 3.000
250 N2 C6 C7 109.470 3.000
250 H61 C6 H62 107.900 3.000
250 H61 C6 C7 109.470 3.000
250 H62 C6 C7 109.470 3.000
250 C6 C7 H72 109.470 3.000
250 C6 C7 H71 109.470 3.000
250 C6 C7 N1 109.470 3.000
250 H72 C7 H71 107.900 3.000
250 H72 C7 N1 109.470 3.000
250 H71 C7 N1 109.470 3.000
250 N2 C8 H81 109.470 3.000
250 N2 C8 H82 109.470 3.000
250 N2 C8 C9 109.470 3.000
250 H81 C8 H82 107.900 3.000
250 H81 C8 C9 109.470 3.000
250 H82 C8 C9 109.470 3.000
250 C8 C9 H91 109.470 3.000
250 C8 C9 H92 109.470 3.000
250 C8 C9 O5 109.470 3.000
250 H91 C9 H92 107.900 3.000
250 H91 C9 O5 109.470 3.000
250 H92 C9 O5 109.470 3.000
250 C9 O5 HO5 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
250 var_1 O2 S1 O3 HO3 63.924 20.000 1
250 var_2 O2 S1 C1 C2 -68.372 20.000 1
250 var_3 S1 C1 C2 C3 179.996 20.000 3
250 var_4 C1 C2 O4 HO4 -59.985 20.000 1
250 var_5 C1 C2 C3 N1 -175.031 20.000 3
250 var_6 C2 C3 N1 C4 -170.009 20.000 1
250 var_7 C3 N1 C7 C6 180.000 20.000 1
250 var_8 C3 N1 C4 C5 180.000 20.000 1
250 var_9 N1 C4 C5 N2 60.000 20.000 3
250 var_10 C4 C5 N2 C8 180.000 20.000 1
250 var_11 C5 N2 C6 C7 60.000 20.000 1
250 var_12 N2 C6 C7 N1 -60.000 20.000 3
250 var_13 C5 N2 C8 C9 -160.465 20.000 1
250 var_14 N2 C8 C9 O5 64.718 20.000 3
250 var_15 C8 C9 O5 HO5 179.990 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
250 chir_01 S1 O1 O2 O3 negativ
250 chir_02 C2 C1 O4 C3 positiv
250 chir_03 N1 C3 C7 C4 negativ
250 chir_04 N2 C6 C5 C8 negativ
# ------------------------------------------------------
|
