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
|
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
ST4 ST4 '4-(ACETYLAMINO)-3-GUANIDINOBENZOIC A' non-polymer 30 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ST4
#
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
ST4 O4 O O 0.000 0.000 0.000 0.000
ST4 "C4'" C C 0.000 -0.538 -0.530 0.950
ST4 CM4 C CH3 0.000 0.272 -0.889 2.169
ST4 HM43 H H 0.000 -0.113 -0.379 3.014
ST4 HM42 H H 0.000 0.219 -1.934 2.336
ST4 HM41 H H 0.000 1.283 -0.608 2.019
ST4 N4 N NH1 0.000 -1.857 -0.797 0.914
ST4 HN4 H H 0.000 -2.323 -1.154 1.737
ST4 C4 C CR6 0.000 -2.582 -0.580 -0.259
ST4 C3 C CR6 0.000 -3.937 -0.246 -0.191
ST4 N3 N NH1 0.000 -4.565 -0.125 1.053
ST4 HN3 H H 0.000 -4.041 -0.286 1.901
ST4 "C3'" C CH1 0.000 -5.982 0.237 1.125
ST4 "H3'" H H 0.000 -6.501 -0.136 0.231
ST4 N2 N NH2 0.000 -6.112 1.698 1.192
ST4 HN22 H H 0.000 -6.622 2.200 0.475
ST4 HN21 H H 0.000 -5.692 2.215 1.956
ST4 N1 N NH2 0.000 -6.581 -0.362 2.325
ST4 HN12 H H 0.000 -6.018 -0.928 2.950
ST4 HN11 H H 0.000 -7.561 -0.215 2.535
ST4 C2 C CR16 0.000 -4.653 -0.026 -1.352
ST4 H2 H H 0.000 -5.701 0.241 -1.301
ST4 C5 C CR16 0.000 -1.956 -0.702 -1.494
ST4 H5 H H 0.000 -0.907 -0.967 -1.543
ST4 C6 C CR16 0.000 -2.666 -0.488 -2.654
ST4 H6 H H 0.000 -2.175 -0.584 -3.614
ST4 C1 C CR6 0.000 -4.021 -0.148 -2.593
ST4 "C'" C C 0.000 -4.781 0.081 -3.835
ST4 "O1'" O OC -0.500 -5.994 0.385 -3.779
ST4 "O2'" O OC -0.500 -4.215 -0.028 -4.944
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
ST4 O4 n/a "C4'" START
ST4 "C4'" O4 N4 .
ST4 CM4 "C4'" HM41 .
ST4 HM43 CM4 . .
ST4 HM42 CM4 . .
ST4 HM41 CM4 . .
ST4 N4 "C4'" C4 .
ST4 HN4 N4 . .
ST4 C4 N4 C5 .
ST4 C3 C4 C2 .
ST4 N3 C3 "C3'" .
ST4 HN3 N3 . .
ST4 "C3'" N3 N1 .
ST4 "H3'" "C3'" . .
ST4 N2 "C3'" HN21 .
ST4 HN22 N2 . .
ST4 HN21 N2 . .
ST4 N1 "C3'" HN11 .
ST4 HN12 N1 . .
ST4 HN11 N1 . .
ST4 C2 C3 H2 .
ST4 H2 C2 . .
ST4 C5 C4 C6 .
ST4 H5 C5 . .
ST4 C6 C5 C1 .
ST4 H6 C6 . .
ST4 C1 C6 "C'" .
ST4 "C'" C1 "O2'" .
ST4 "O1'" "C'" . .
ST4 "O2'" "C'" . END
ST4 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
ST4 "O1'" "C'" deloc 1.250 0.020
ST4 "O2'" "C'" deloc 1.250 0.020
ST4 "C'" C1 single 1.500 0.020
ST4 C1 C2 double 1.390 0.020
ST4 C1 C6 single 1.390 0.020
ST4 C2 C3 single 1.390 0.020
ST4 H2 C2 single 1.083 0.020
ST4 N3 C3 single 1.350 0.020
ST4 C3 C4 double 1.487 0.020
ST4 "C3'" N3 single 1.450 0.020
ST4 HN3 N3 single 1.010 0.020
ST4 N1 "C3'" single 1.450 0.020
ST4 N2 "C3'" single 1.450 0.020
ST4 "H3'" "C3'" single 1.099 0.020
ST4 HN11 N1 single 1.010 0.020
ST4 HN12 N1 single 1.010 0.020
ST4 HN21 N2 single 1.010 0.020
ST4 HN22 N2 single 1.010 0.020
ST4 C4 N4 single 1.350 0.020
ST4 C5 C4 single 1.390 0.020
ST4 N4 "C4'" single 1.330 0.020
ST4 HN4 N4 single 1.010 0.020
ST4 "C4'" O4 double 1.220 0.020
ST4 CM4 "C4'" single 1.500 0.020
ST4 HM41 CM4 single 1.059 0.020
ST4 HM42 CM4 single 1.059 0.020
ST4 HM43 CM4 single 1.059 0.020
ST4 C6 C5 double 1.390 0.020
ST4 H5 C5 single 1.083 0.020
ST4 H6 C6 single 1.083 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
ST4 O4 "C4'" CM4 123.000 3.000
ST4 O4 "C4'" N4 123.000 3.000
ST4 CM4 "C4'" N4 116.500 3.000
ST4 "C4'" CM4 HM43 109.470 3.000
ST4 "C4'" CM4 HM42 109.470 3.000
ST4 "C4'" CM4 HM41 109.470 3.000
ST4 HM43 CM4 HM42 109.470 3.000
ST4 HM43 CM4 HM41 109.470 3.000
ST4 HM42 CM4 HM41 109.470 3.000
ST4 "C4'" N4 HN4 120.000 3.000
ST4 "C4'" N4 C4 120.000 3.000
ST4 HN4 N4 C4 120.000 3.000
ST4 N4 C4 C3 120.000 3.000
ST4 N4 C4 C5 120.000 3.000
ST4 C3 C4 C5 120.000 3.000
ST4 C4 C3 N3 120.000 3.000
ST4 C4 C3 C2 120.000 3.000
ST4 N3 C3 C2 120.000 3.000
ST4 C3 N3 HN3 120.000 3.000
ST4 C3 N3 "C3'" 120.000 3.000
ST4 HN3 N3 "C3'" 118.500 3.000
ST4 N3 "C3'" "H3'" 108.550 3.000
ST4 N3 "C3'" N2 109.500 3.000
ST4 N3 "C3'" N1 109.500 3.000
ST4 "H3'" "C3'" N2 109.470 3.000
ST4 "H3'" "C3'" N1 109.470 3.000
ST4 N2 "C3'" N1 109.470 3.000
ST4 "C3'" N2 HN22 120.000 3.000
ST4 "C3'" N2 HN21 120.000 3.000
ST4 HN22 N2 HN21 120.000 3.000
ST4 "C3'" N1 HN12 120.000 3.000
ST4 "C3'" N1 HN11 120.000 3.000
ST4 HN12 N1 HN11 120.000 3.000
ST4 C3 C2 H2 120.000 3.000
ST4 C3 C2 C1 120.000 3.000
ST4 H2 C2 C1 120.000 3.000
ST4 C4 C5 H5 120.000 3.000
ST4 C4 C5 C6 120.000 3.000
ST4 H5 C5 C6 120.000 3.000
ST4 C5 C6 H6 120.000 3.000
ST4 C5 C6 C1 120.000 3.000
ST4 H6 C6 C1 120.000 3.000
ST4 C6 C1 "C'" 120.000 3.000
ST4 C6 C1 C2 120.000 3.000
ST4 "C'" C1 C2 120.000 3.000
ST4 C1 "C'" "O1'" 120.000 3.000
ST4 C1 "C'" "O2'" 120.000 3.000
ST4 "O1'" "C'" "O2'" 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
ST4 var_1 O4 "C4'" CM4 HM41 -0.061 20.000 1
ST4 CONST_1 O4 "C4'" N4 C4 0.000 0.000 0
ST4 var_2 "C4'" N4 C4 C5 29.943 20.000 1
ST4 CONST_2 N4 C4 C3 C2 180.000 0.000 0
ST4 var_3 C4 C3 N3 "C3'" 179.477 20.000 1
ST4 var_4 C3 N3 "C3'" N1 149.991 20.000 3
ST4 var_5 N3 "C3'" N2 HN21 -60.052 20.000 1
ST4 var_6 N3 "C3'" N1 HN11 179.976 20.000 1
ST4 CONST_3 C4 C3 C2 C1 0.000 0.000 0
ST4 CONST_4 N4 C4 C5 C6 180.000 0.000 0
ST4 CONST_5 C4 C5 C6 C1 0.000 0.000 0
ST4 CONST_6 C5 C6 C1 "C'" 180.000 0.000 0
ST4 CONST_7 C6 C1 C2 C3 0.000 0.000 0
ST4 var_7 C6 C1 "C'" "O2'" -0.014 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
ST4 chir_01 "C3'" N3 N1 N2 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
ST4 plan-1 "C'" 0.020
ST4 plan-1 "O1'" 0.020
ST4 plan-1 "O2'" 0.020
ST4 plan-1 C1 0.020
ST4 plan-2 C1 0.020
ST4 plan-2 "C'" 0.020
ST4 plan-2 C2 0.020
ST4 plan-2 C6 0.020
ST4 plan-2 C3 0.020
ST4 plan-2 C4 0.020
ST4 plan-2 C5 0.020
ST4 plan-2 H2 0.020
ST4 plan-2 N3 0.020
ST4 plan-2 N4 0.020
ST4 plan-2 H5 0.020
ST4 plan-2 H6 0.020
ST4 plan-2 HN3 0.020
ST4 plan-2 HN4 0.020
ST4 plan-3 N3 0.020
ST4 plan-3 C3 0.020
ST4 plan-3 "C3'" 0.020
ST4 plan-3 HN3 0.020
ST4 plan-4 N1 0.020
ST4 plan-4 "C3'" 0.020
ST4 plan-4 HN11 0.020
ST4 plan-4 HN12 0.020
ST4 plan-5 N2 0.020
ST4 plan-5 "C3'" 0.020
ST4 plan-5 HN21 0.020
ST4 plan-5 HN22 0.020
ST4 plan-6 N4 0.020
ST4 plan-6 C4 0.020
ST4 plan-6 "C4'" 0.020
ST4 plan-6 HN4 0.020
ST4 plan-7 "C4'" 0.020
ST4 plan-7 N4 0.020
ST4 plan-7 O4 0.020
ST4 plan-7 CM4 0.020
ST4 plan-7 HN4 0.020
# ------------------------------------------------------
|
