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
|
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
SN5 SN5 '2-deoxy-2-(ethanethioylamino)-beta-D' non-polymer 30 15 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SN5
#
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
SN5 S7 S S1 0.000 0.000 0.000 0.000
SN5 C7 C C 0.000 -0.890 0.724 1.114
SN5 C8 C CH3 0.000 -0.231 1.348 2.317
SN5 H83C H H 0.000 -0.892 1.309 3.144
SN5 H82C H H 0.000 0.656 0.816 2.551
SN5 H81C H H 0.000 0.010 2.358 2.106
SN5 N2 N NH1 0.000 -2.230 0.779 0.975
SN5 H2 H H 0.000 -2.792 1.237 1.678
SN5 C2 C CH1 0.000 -2.870 0.174 -0.195
SN5 HA H H 0.000 -2.222 0.297 -1.074
SN5 C3 C CH1 0.000 -4.217 0.858 -0.452
SN5 H3 H H 0.000 -4.847 0.780 0.445
SN5 O3 O OH1 0.000 -4.001 2.234 -0.768
SN5 HC H H 0.000 -4.852 2.664 -0.930
SN5 C4 C CH1 0.000 -4.912 0.165 -1.628
SN5 H4 H H 0.000 -4.306 0.288 -2.537
SN5 O4 O OH1 0.000 -6.200 0.748 -1.832
SN5 HD H H 0.000 -6.638 0.310 -2.575
SN5 C5 C CH1 0.000 -5.067 -1.325 -1.314
SN5 H5 H H 0.000 -5.707 -1.448 -0.429
SN5 C6 C CH2 0.000 -5.707 -2.035 -2.508
SN5 H61C H H 0.000 -5.029 -1.988 -3.363
SN5 H62C H H 0.000 -6.647 -1.541 -2.763
SN5 O6 O OH1 0.000 -5.959 -3.400 -2.173
SN5 H6 H H 0.000 -6.363 -3.848 -2.929
SN5 O5 O O2 0.000 -3.783 -1.892 -1.055
SN5 C1 C CH1 0.000 -3.105 -1.317 0.065
SN5 H1 H H 0.000 -3.719 -1.439 0.967
SN5 O1 O OH1 0.000 -1.849 -1.972 0.251
SN5 HB H H 0.000 -1.999 -2.913 0.414
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
SN5 S7 n/a C7 START
SN5 C7 S7 N2 .
SN5 C8 C7 H81C .
SN5 H83C C8 . .
SN5 H82C C8 . .
SN5 H81C C8 . .
SN5 N2 C7 C2 .
SN5 H2 N2 . .
SN5 C2 N2 C3 .
SN5 HA C2 . .
SN5 C3 C2 C4 .
SN5 H3 C3 . .
SN5 O3 C3 HC .
SN5 HC O3 . .
SN5 C4 C3 C5 .
SN5 H4 C4 . .
SN5 O4 C4 HD .
SN5 HD O4 . .
SN5 C5 C4 O5 .
SN5 H5 C5 . .
SN5 C6 C5 O6 .
SN5 H61C C6 . .
SN5 H62C C6 . .
SN5 O6 C6 H6 .
SN5 H6 O6 . .
SN5 O5 C5 C1 .
SN5 C1 O5 O1 .
SN5 H1 C1 . .
SN5 O1 C1 HB .
SN5 HB O1 . END
SN5 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
SN5 C7 S7 double 1.565 0.020
SN5 C8 C7 single 1.500 0.020
SN5 N2 C7 single 1.330 0.020
SN5 C2 N2 single 1.450 0.020
SN5 C1 C2 single 1.524 0.020
SN5 C3 C2 single 1.524 0.020
SN5 O1 C1 single 1.432 0.020
SN5 C1 O5 single 1.426 0.020
SN5 O3 C3 single 1.432 0.020
SN5 C4 C3 single 1.524 0.020
SN5 O4 C4 single 1.432 0.020
SN5 C5 C4 single 1.524 0.020
SN5 O5 C5 single 1.426 0.020
SN5 C6 C5 single 1.524 0.020
SN5 O6 C6 single 1.432 0.020
SN5 H81C C8 single 1.059 0.020
SN5 H82C C8 single 1.059 0.020
SN5 H83C C8 single 1.059 0.020
SN5 H2 N2 single 1.010 0.020
SN5 HA C2 single 1.099 0.020
SN5 H1 C1 single 1.099 0.020
SN5 H3 C3 single 1.099 0.020
SN5 HB O1 single 0.967 0.020
SN5 HC O3 single 0.967 0.020
SN5 H4 C4 single 1.099 0.020
SN5 HD O4 single 0.967 0.020
SN5 H5 C5 single 1.099 0.020
SN5 H61C C6 single 1.092 0.020
SN5 H62C C6 single 1.092 0.020
SN5 H6 O6 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
SN5 S7 C7 C8 120.000 3.000
SN5 S7 C7 N2 120.000 3.000
SN5 C8 C7 N2 116.500 3.000
SN5 C7 C8 H83C 109.470 3.000
SN5 C7 C8 H82C 109.470 3.000
SN5 C7 C8 H81C 109.470 3.000
SN5 H83C C8 H82C 109.470 3.000
SN5 H83C C8 H81C 109.470 3.000
SN5 H82C C8 H81C 109.470 3.000
SN5 C7 N2 H2 120.000 3.000
SN5 C7 N2 C2 121.500 3.000
SN5 H2 N2 C2 118.500 3.000
SN5 N2 C2 HA 108.550 3.000
SN5 N2 C2 C3 110.000 3.000
SN5 N2 C2 C1 110.000 3.000
SN5 HA C2 C3 108.340 3.000
SN5 HA C2 C1 108.340 3.000
SN5 C3 C2 C1 111.000 3.000
SN5 C2 C3 H3 108.340 3.000
SN5 C2 C3 O3 109.470 3.000
SN5 C2 C3 C4 111.000 3.000
SN5 H3 C3 O3 109.470 3.000
SN5 H3 C3 C4 108.340 3.000
SN5 O3 C3 C4 109.470 3.000
SN5 C3 O3 HC 109.470 3.000
SN5 C3 C4 H4 108.340 3.000
SN5 C3 C4 O4 109.470 3.000
SN5 C3 C4 C5 111.000 3.000
SN5 H4 C4 O4 109.470 3.000
SN5 H4 C4 C5 108.340 3.000
SN5 O4 C4 C5 109.470 3.000
SN5 C4 O4 HD 109.470 3.000
SN5 C4 C5 H5 108.340 3.000
SN5 C4 C5 C6 111.000 3.000
SN5 C4 C5 O5 109.470 3.000
SN5 H5 C5 C6 108.340 3.000
SN5 H5 C5 O5 109.470 3.000
SN5 C6 C5 O5 109.470 3.000
SN5 C5 C6 H61C 109.470 3.000
SN5 C5 C6 H62C 109.470 3.000
SN5 C5 C6 O6 109.470 3.000
SN5 H61C C6 H62C 107.900 3.000
SN5 H61C C6 O6 109.470 3.000
SN5 H62C C6 O6 109.470 3.000
SN5 C6 O6 H6 109.470 3.000
SN5 C5 O5 C1 111.800 3.000
SN5 O5 C1 H1 109.470 3.000
SN5 O5 C1 O1 109.470 3.000
SN5 O5 C1 C2 109.470 3.000
SN5 H1 C1 O1 109.470 3.000
SN5 H1 C1 C2 108.340 3.000
SN5 O1 C1 C2 109.470 3.000
SN5 C1 O1 HB 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
SN5 var_1 S7 C7 C8 H81C 89.959 20.000 1
SN5 CONST_1 S7 C7 N2 C2 0.000 0.000 0
SN5 var_2 C7 N2 C2 C3 -155.344 20.000 3
SN5 var_3 N2 C2 C3 C4 180.000 20.000 3
SN5 var_4 C2 C3 O3 HC 179.999 20.000 1
SN5 var_5 C2 C3 C4 C5 60.000 20.000 3
SN5 var_6 C3 C4 O4 HD 179.958 20.000 1
SN5 var_7 C3 C4 C5 O5 -60.000 20.000 3
SN5 var_8 C4 C5 C6 O6 -174.970 20.000 3
SN5 var_9 C5 C6 O6 H6 -179.995 20.000 1
SN5 var_10 C4 C5 O5 C1 60.000 20.000 1
SN5 var_11 C5 O5 C1 O1 180.000 20.000 1
SN5 var_12 O5 C1 C2 N2 180.000 20.000 3
SN5 var_13 O5 C1 O1 HB -60.016 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
SN5 chir_01 C1 C2 O5 O1 negativ
SN5 chir_02 C2 C1 C3 N2 negativ
SN5 chir_03 C3 C2 C4 O3 positiv
SN5 chir_04 C4 C3 C5 O4 negativ
SN5 chir_05 C5 C4 C6 O5 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
SN5 plan-1 C7 0.020
SN5 plan-1 S7 0.020
SN5 plan-1 C8 0.020
SN5 plan-1 N2 0.020
SN5 plan-1 H2 0.020
SN5 plan-2 N2 0.020
SN5 plan-2 C2 0.020
SN5 plan-2 C7 0.020
SN5 plan-2 H2 0.020
# ------------------------------------------------------
|
