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
|
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
S4A S4A '. ' non-polymer 34 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_S4A
#
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
S4A O2P O OP -0.666 0.000 0.000 0.000
S4A P P P 0.000 -0.823 -0.206 -1.253
S4A O3P O OP -0.666 -1.174 1.138 -1.854
S4A O1P O OP -0.666 -0.026 -1.013 -2.253
S4A "O5'" O O2 0.000 -2.176 -0.998 -0.882
S4A "C5'" C CH2 0.000 -2.180 -2.254 -0.202
S4A "H15'" H H 0.000 -1.700 -2.142 0.772
S4A "H25'" H H 0.000 -1.633 -2.990 -0.794
S4A "C4'" C CH1 0.000 -3.625 -2.723 -0.009
S4A "H4'" H H 0.000 -3.652 -3.743 0.399
S4A "C3'" C CH1 0.000 -4.406 -2.643 -1.336
S4A "H3'" H H 0.000 -3.907 -1.923 -1.999
S4A "O3'" O OH1 0.000 -4.394 -3.929 -1.959
S4A "HO3'" H H 0.000 -4.882 -3.886 -2.793
S4A "C2'" C CH2 0.000 -5.853 -2.208 -1.138
S4A "H22'" H H 0.000 -6.497 -2.999 -1.528
S4A "H12'" H H 0.000 -6.011 -1.294 -1.714
S4A "S4'" S S2 0.000 -4.548 -1.563 1.071
S4A "C1'" C CH1 0.000 -6.193 -1.949 0.345
S4A "H1'" H H 0.000 -6.623 -2.848 0.809
S4A N9 N NR5 0.000 -7.101 -0.808 0.479
S4A C8 C CR15 0.000 -8.450 -0.869 0.665
S4A H8 H H 0.000 -9.026 -1.783 0.742
S4A N7 N NRD5 0.000 -8.943 0.334 0.735
S4A C5 C CR56 0.000 -7.945 1.239 0.599
S4A C4 C CR56 0.000 -6.751 0.518 0.433
S4A C6 C CR6 0.000 -7.879 2.643 0.594
S4A N6 N NH2 0.000 -9.021 3.406 0.754
S4A H2N6 H H 0.000 -8.969 4.420 0.750
S4A H1N6 H H 0.000 -9.925 2.961 0.879
S4A N1 N NRD6 0.000 -6.692 3.220 0.431
S4A C2 C CR16 0.000 -5.597 2.498 0.278
S4A H2 H H 0.000 -4.651 3.009 0.147
S4A N3 N NRD6 0.000 -5.611 1.183 0.277
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
S4A O2P n/a P START
S4A P O2P "O5'" .
S4A O3P P . .
S4A O1P P . .
S4A "O5'" P "C5'" .
S4A "C5'" "O5'" "C4'" .
S4A "H15'" "C5'" . .
S4A "H25'" "C5'" . .
S4A "C4'" "C5'" "S4'" .
S4A "H4'" "C4'" . .
S4A "C3'" "C4'" "C2'" .
S4A "H3'" "C3'" . .
S4A "O3'" "C3'" "HO3'" .
S4A "HO3'" "O3'" . .
S4A "C2'" "C3'" "H12'" .
S4A "H22'" "C2'" . .
S4A "H12'" "C2'" . .
S4A "S4'" "C4'" "C1'" .
S4A "C1'" "S4'" N9 .
S4A "H1'" "C1'" . .
S4A N9 "C1'" C8 .
S4A C8 N9 N7 .
S4A H8 C8 . .
S4A N7 C8 C5 .
S4A C5 N7 C6 .
S4A C4 C5 . .
S4A C6 C5 N1 .
S4A N6 C6 H1N6 .
S4A H2N6 N6 . .
S4A H1N6 N6 . .
S4A N1 C6 C2 .
S4A C2 N1 N3 .
S4A H2 C2 . .
S4A N3 C2 . END
S4A N9 C4 . ADD
S4A C4 N3 . ADD
S4A "C2'" "C1'" . 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
S4A O3P P deloc 1.510 0.020
S4A P O2P deloc 1.510 0.020
S4A O1P P deloc 1.510 0.020
S4A "O5'" P single 1.610 0.020
S4A "C5'" "O5'" single 1.426 0.020
S4A C8 N9 single 1.337 0.020
S4A N9 "C1'" single 1.485 0.020
S4A N9 C4 single 1.337 0.020
S4A C4 C5 double 1.490 0.020
S4A C4 N3 single 1.355 0.020
S4A N3 C2 double 1.337 0.020
S4A C2 N1 single 1.337 0.020
S4A H2 C2 single 1.083 0.020
S4A N1 C6 double 1.350 0.020
S4A C6 C5 single 1.490 0.020
S4A N6 C6 single 1.355 0.020
S4A H1N6 N6 single 1.010 0.020
S4A H2N6 N6 single 1.010 0.020
S4A C5 N7 single 1.350 0.020
S4A N7 C8 double 1.350 0.020
S4A H8 C8 single 1.083 0.020
S4A "C2'" "C3'" single 1.524 0.020
S4A "C2'" "C1'" single 1.524 0.020
S4A "H22'" "C2'" single 1.092 0.020
S4A "H12'" "C2'" single 1.092 0.020
S4A "H15'" "C5'" single 1.092 0.020
S4A "H25'" "C5'" single 1.092 0.020
S4A "C4'" "C5'" single 1.524 0.020
S4A "H4'" "C4'" single 1.099 0.020
S4A "S4'" "C4'" single 1.765 0.020
S4A "C3'" "C4'" single 1.524 0.020
S4A "C1'" "S4'" single 1.765 0.020
S4A "H1'" "C1'" single 1.099 0.020
S4A "H3'" "C3'" single 1.099 0.020
S4A "O3'" "C3'" single 1.432 0.020
S4A "HO3'" "O3'" 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
S4A O2P P O3P 119.900 3.000
S4A O2P P O1P 119.900 3.000
S4A O2P P "O5'" 108.200 3.000
S4A O3P P O1P 119.900 3.000
S4A O3P P "O5'" 108.200 3.000
S4A O1P P "O5'" 108.200 3.000
S4A P "O5'" "C5'" 120.500 3.000
S4A "O5'" "C5'" "H15'" 109.470 3.000
S4A "O5'" "C5'" "H25'" 109.470 3.000
S4A "O5'" "C5'" "C4'" 109.470 3.000
S4A "H15'" "C5'" "H25'" 107.900 3.000
S4A "H15'" "C5'" "C4'" 109.470 3.000
S4A "H25'" "C5'" "C4'" 109.470 3.000
S4A "C5'" "C4'" "H4'" 108.340 3.000
S4A "C5'" "C4'" "C3'" 111.000 3.000
S4A "C5'" "C4'" "S4'" 109.500 3.000
S4A "H4'" "C4'" "C3'" 108.340 3.000
S4A "H4'" "C4'" "S4'" 109.500 3.000
S4A "C3'" "C4'" "S4'" 109.500 3.000
S4A "C4'" "C3'" "H3'" 108.340 3.000
S4A "C4'" "C3'" "O3'" 109.470 3.000
S4A "C4'" "C3'" "C2'" 111.000 3.000
S4A "H3'" "C3'" "O3'" 109.470 3.000
S4A "H3'" "C3'" "C2'" 108.340 3.000
S4A "O3'" "C3'" "C2'" 109.470 3.000
S4A "C3'" "O3'" "HO3'" 109.470 3.000
S4A "C3'" "C2'" "H22'" 109.470 3.000
S4A "C3'" "C2'" "H12'" 109.470 3.000
S4A "C3'" "C2'" "C1'" 111.000 3.000
S4A "H22'" "C2'" "H12'" 107.900 3.000
S4A "H22'" "C2'" "C1'" 109.470 3.000
S4A "H12'" "C2'" "C1'" 109.470 3.000
S4A "C4'" "S4'" "C1'" 94.865 3.000
S4A "S4'" "C1'" "H1'" 109.500 3.000
S4A "S4'" "C1'" N9 109.500 3.000
S4A "S4'" "C1'" "C2'" 109.500 3.000
S4A "H1'" "C1'" N9 109.470 3.000
S4A "H1'" "C1'" "C2'" 108.340 3.000
S4A N9 "C1'" "C2'" 109.470 3.000
S4A "C1'" N9 C8 126.000 3.000
S4A "C1'" N9 C4 126.000 3.000
S4A C8 N9 C4 108.000 3.000
S4A N9 C8 H8 126.000 3.000
S4A N9 C8 N7 108.000 3.000
S4A H8 C8 N7 126.000 3.000
S4A C8 N7 C5 108.000 3.000
S4A N7 C5 C4 108.000 3.000
S4A N7 C5 C6 132.000 3.000
S4A C4 C5 C6 120.000 3.000
S4A C5 C4 N9 108.000 3.000
S4A C5 C4 N3 120.000 3.000
S4A N9 C4 N3 132.000 3.000
S4A C5 C6 N6 120.000 3.000
S4A C5 C6 N1 120.000 3.000
S4A N6 C6 N1 120.000 3.000
S4A C6 N6 H2N6 120.000 3.000
S4A C6 N6 H1N6 120.000 3.000
S4A H2N6 N6 H1N6 120.000 3.000
S4A C6 N1 C2 120.000 3.000
S4A N1 C2 H2 120.000 3.000
S4A N1 C2 N3 120.000 3.000
S4A H2 C2 N3 120.000 3.000
S4A C2 N3 C4 120.000 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
S4A var_1 O2P P "O5'" "C5'" -54.955 20.000 1
S4A var_2 P "O5'" "C5'" "C4'" 179.992 20.000 1
S4A var_3 "O5'" "C5'" "C4'" "S4'" -63.573 20.000 3
S4A var_4 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
S4A var_5 "C4'" "C3'" "O3'" "HO3'" -179.963 20.000 1
S4A var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
S4A var_7 "C3'" "C2'" "C1'" "S4'" 30.000 20.000 3
S4A var_8 "C5'" "C4'" "S4'" "C1'" 150.000 20.000 1
S4A var_9 "C4'" "S4'" "C1'" N9 -150.000 20.000 1
S4A var_10 "S4'" "C1'" N9 C8 -146.767 20.000 1
S4A CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
S4A CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
S4A CONST_3 N9 C8 N7 C5 0.000 0.000 0
S4A CONST_4 C8 N7 C5 C6 180.000 0.000 0
S4A CONST_5 N7 C5 C4 N9 0.000 0.000 0
S4A CONST_6 C5 C4 N3 C2 0.000 0.000 0
S4A CONST_7 N7 C5 C6 N1 180.000 0.000 0
S4A CONST_8 C5 C6 N6 H1N6 0.010 0.000 0
S4A CONST_9 C5 C6 N1 C2 0.000 0.000 0
S4A CONST_10 C6 N1 C2 N3 0.000 0.000 0
S4A CONST_11 N1 C2 N3 C4 0.000 0.000 0
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
S4A chir_01 "C4'" "C5'" "S4'" "C3'" negativ
S4A chir_02 "C1'" N9 "C2'" "S4'" negativ
S4A chir_03 "C3'" "C2'" "C4'" "O3'" 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
S4A plan-1 N9 0.020
S4A plan-1 C4 0.020
S4A plan-1 C8 0.020
S4A plan-1 "C1'" 0.020
S4A plan-1 N7 0.020
S4A plan-1 N3 0.020
S4A plan-1 C5 0.020
S4A plan-1 C2 0.020
S4A plan-1 N1 0.020
S4A plan-1 C6 0.020
S4A plan-1 H2 0.020
S4A plan-1 N6 0.020
S4A plan-1 H8 0.020
S4A plan-1 H2N6 0.020
S4A plan-1 H1N6 0.020
S4A plan-2 N6 0.020
S4A plan-2 C6 0.020
S4A plan-2 H1N6 0.020
S4A plan-2 H2N6 0.020
# ------------------------------------------------------
|
