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
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
|
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
DUN DUN '. ' non-polymer 39 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DUN
#
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
DUN O2B O O 0.000 0.000 0.000 0.000
DUN PB P P 0.000 -1.055 0.275 -1.001
DUN O1B O OH1 0.000 -1.013 -0.854 -2.149
DUN H1B H H 0.000 -0.213 -0.974 -2.679
DUN O3B O OH1 0.000 -0.805 1.721 -1.661
DUN H3B H H 0.000 -1.409 2.053 -2.339
DUN N3A N NH1 0.000 -2.561 0.255 -0.249
DUN H3A H H 0.000 -3.334 -0.359 -0.465
DUN PA P P 0.000 -2.530 1.452 0.930
DUN O2A O O 0.000 -1.451 1.159 1.902
DUN O1A O OH1 0.000 -2.254 2.879 0.238
DUN H1A H H 0.000 -2.868 3.222 -0.425
DUN "O5'" O O2 0.000 -3.945 1.491 1.695
DUN "C5'" C CH2 0.000 -4.132 0.203 2.285
DUN "H5'1" H H 0.000 -3.317 0.003 2.984
DUN "H5'2" H H 0.000 -4.133 -0.558 1.502
DUN "C4'" C CH1 0.000 -5.465 0.171 3.031
DUN "H4'" H H 0.000 -5.473 0.925 3.832
DUN "C3'" C CH1 0.000 -5.731 -1.233 3.615
DUN "H3'" H H 0.000 -5.176 -1.996 3.050
DUN "O3'" O OH1 0.000 -5.373 -1.276 4.998
DUN HA H H 0.000 -5.573 -2.153 5.355
DUN "C2'" C CH2 0.000 -7.253 -1.433 3.443
DUN "H2'2" H H 0.000 -7.760 -1.561 4.402
DUN "H2'1" H H 0.000 -7.485 -2.280 2.794
DUN "O4'" O O2 0.000 -6.561 0.401 2.114
DUN "C1'" C CH1 0.000 -7.731 -0.125 2.777
DUN "H1'" H H 0.000 -8.089 0.583 3.538
DUN N1 N NR6 0.000 -8.789 -0.405 1.803
DUN C6 C CR16 0.000 -10.024 0.161 1.962
DUN H6 H H 0.000 -10.219 0.812 2.804
DUN C5 C CR16 0.000 -10.999 -0.097 1.065
DUN H5 H H 0.000 -11.981 0.345 1.179
DUN C4 C CR6 0.000 -10.720 -0.952 -0.028
DUN O4 O O 0.000 -11.582 -1.199 -0.851
DUN N3 N NR16 0.000 -9.489 -1.489 -0.150
DUN H3 H H 0.000 -9.276 -2.120 -0.948
DUN C2 C CR6 0.000 -8.535 -1.212 0.757
DUN O2 O O 0.000 -7.429 -1.703 0.635
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
DUN O2B n/a PB START
DUN PB O2B N3A .
DUN O1B PB H1B .
DUN H1B O1B . .
DUN O3B PB H3B .
DUN H3B O3B . .
DUN N3A PB PA .
DUN H3A N3A . .
DUN PA N3A "O5'" .
DUN O2A PA . .
DUN O1A PA H1A .
DUN H1A O1A . .
DUN "O5'" PA "C5'" .
DUN "C5'" "O5'" "C4'" .
DUN "H5'1" "C5'" . .
DUN "H5'2" "C5'" . .
DUN "C4'" "C5'" "O4'" .
DUN "H4'" "C4'" . .
DUN "C3'" "C4'" "C2'" .
DUN "H3'" "C3'" . .
DUN "O3'" "C3'" HA .
DUN HA "O3'" . .
DUN "C2'" "C3'" "H2'1" .
DUN "H2'2" "C2'" . .
DUN "H2'1" "C2'" . .
DUN "O4'" "C4'" "C1'" .
DUN "C1'" "O4'" N1 .
DUN "H1'" "C1'" . .
DUN N1 "C1'" C6 .
DUN C6 N1 C5 .
DUN H6 C6 . .
DUN C5 C6 C4 .
DUN H5 C5 . .
DUN C4 C5 N3 .
DUN O4 C4 . .
DUN N3 C4 C2 .
DUN H3 N3 . .
DUN C2 N3 O2 .
DUN O2 C2 . END
DUN N1 C2 . ADD
DUN "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
DUN N1 C2 single 1.410 0.020
DUN C6 N1 single 1.337 0.020
DUN N1 "C1'" single 1.465 0.020
DUN C2 N3 single 1.337 0.020
DUN O2 C2 double 1.250 0.020
DUN N3 C4 single 1.337 0.020
DUN H3 N3 single 1.040 0.020
DUN C4 C5 single 1.390 0.020
DUN O4 C4 double 1.250 0.020
DUN C5 C6 double 1.390 0.020
DUN H5 C5 single 1.083 0.020
DUN H6 C6 single 1.083 0.020
DUN "C1'" "C2'" single 1.524 0.020
DUN "C1'" "O4'" single 1.426 0.020
DUN "H1'" "C1'" single 1.099 0.020
DUN "C2'" "C3'" single 1.524 0.020
DUN "H2'1" "C2'" single 1.092 0.020
DUN "H2'2" "C2'" single 1.092 0.020
DUN "C3'" "C4'" single 1.524 0.020
DUN "O3'" "C3'" single 1.432 0.020
DUN "H3'" "C3'" single 1.099 0.020
DUN "O4'" "C4'" single 1.426 0.020
DUN "C4'" "C5'" single 1.524 0.020
DUN "H4'" "C4'" single 1.099 0.020
DUN HA "O3'" single 0.967 0.020
DUN "C5'" "O5'" single 1.426 0.020
DUN "H5'1" "C5'" single 1.092 0.020
DUN "H5'2" "C5'" single 1.092 0.020
DUN "O5'" PA single 1.610 0.020
DUN O1A PA single 1.610 0.020
DUN O2A PA double 1.480 0.020
DUN PA N3A single 1.750 0.020
DUN H1A O1A single 0.967 0.020
DUN O1B PB single 1.610 0.020
DUN PB O2B double 1.480 0.020
DUN O3B PB single 1.610 0.020
DUN N3A PB single 1.750 0.020
DUN H1B O1B single 0.967 0.020
DUN H3B O3B single 0.967 0.020
DUN H3A N3A single 1.010 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
DUN O2B PB O1B 109.500 3.000
DUN O2B PB O3B 109.500 3.000
DUN O2B PB N3A 109.500 3.000
DUN O1B PB O3B 109.500 3.000
DUN O1B PB N3A 109.500 3.000
DUN O3B PB N3A 109.500 3.000
DUN PB O1B H1B 120.000 3.000
DUN PB O3B H3B 120.000 3.000
DUN PB N3A H3A 120.000 3.000
DUN PB N3A PA 120.000 3.000
DUN H3A N3A PA 120.000 3.000
DUN N3A PA O2A 109.500 3.000
DUN N3A PA O1A 109.500 3.000
DUN N3A PA "O5'" 109.500 3.000
DUN O2A PA O1A 109.500 3.000
DUN O2A PA "O5'" 109.500 3.000
DUN O1A PA "O5'" 109.500 3.000
DUN PA O1A H1A 120.000 3.000
DUN PA "O5'" "C5'" 120.500 3.000
DUN "O5'" "C5'" "H5'1" 109.470 3.000
DUN "O5'" "C5'" "H5'2" 109.470 3.000
DUN "O5'" "C5'" "C4'" 109.470 3.000
DUN "H5'1" "C5'" "H5'2" 107.900 3.000
DUN "H5'1" "C5'" "C4'" 109.470 3.000
DUN "H5'2" "C5'" "C4'" 109.470 3.000
DUN "C5'" "C4'" "H4'" 108.340 3.000
DUN "C5'" "C4'" "C3'" 111.000 3.000
DUN "C5'" "C4'" "O4'" 109.470 3.000
DUN "H4'" "C4'" "C3'" 108.340 3.000
DUN "H4'" "C4'" "O4'" 109.470 3.000
DUN "C3'" "C4'" "O4'" 109.470 3.000
DUN "C4'" "C3'" "H3'" 108.340 3.000
DUN "C4'" "C3'" "O3'" 109.470 3.000
DUN "C4'" "C3'" "C2'" 111.000 3.000
DUN "H3'" "C3'" "O3'" 109.470 3.000
DUN "H3'" "C3'" "C2'" 108.340 3.000
DUN "O3'" "C3'" "C2'" 109.470 3.000
DUN "C3'" "O3'" HA 109.470 3.000
DUN "C3'" "C2'" "H2'2" 109.470 3.000
DUN "C3'" "C2'" "H2'1" 109.470 3.000
DUN "C3'" "C2'" "C1'" 111.000 3.000
DUN "H2'2" "C2'" "H2'1" 107.900 3.000
DUN "H2'2" "C2'" "C1'" 109.470 3.000
DUN "H2'1" "C2'" "C1'" 109.470 3.000
DUN "C4'" "O4'" "C1'" 111.800 3.000
DUN "O4'" "C1'" "H1'" 109.470 3.000
DUN "O4'" "C1'" N1 109.470 3.000
DUN "O4'" "C1'" "C2'" 109.470 3.000
DUN "H1'" "C1'" N1 109.470 3.000
DUN "H1'" "C1'" "C2'" 108.340 3.000
DUN N1 "C1'" "C2'" 109.470 3.000
DUN "C1'" N1 C6 120.000 3.000
DUN "C1'" N1 C2 120.000 3.000
DUN C6 N1 C2 120.000 3.000
DUN N1 C6 H6 120.000 3.000
DUN N1 C6 C5 120.000 3.000
DUN H6 C6 C5 120.000 3.000
DUN C6 C5 H5 120.000 3.000
DUN C6 C5 C4 120.000 3.000
DUN H5 C5 C4 120.000 3.000
DUN C5 C4 O4 120.000 3.000
DUN C5 C4 N3 120.000 3.000
DUN O4 C4 N3 120.000 3.000
DUN C4 N3 H3 120.000 3.000
DUN C4 N3 C2 120.000 3.000
DUN H3 N3 C2 120.000 3.000
DUN N3 C2 O2 120.000 3.000
DUN N3 C2 N1 120.000 3.000
DUN O2 C2 N1 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
DUN var_1 O2B PB O1B H1B -59.998 20.000 1
DUN var_2 O2B PB O3B H3B 179.954 20.000 1
DUN var_3 O2B PB N3A PA 60.038 20.000 1
DUN var_4 PB N3A PA "O5'" -179.982 20.000 1
DUN var_5 N3A PA O1A H1A 60.037 20.000 1
DUN var_6 N3A PA "O5'" "C5'" 59.969 20.000 1
DUN var_7 PA "O5'" "C5'" "C4'" 179.980 20.000 1
DUN var_8 "O5'" "C5'" "C4'" "O4'" 61.465 20.000 3
DUN var_9 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DUN var_10 "C4'" "C3'" "O3'" HA 178.161 20.000 1
DUN var_11 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
DUN var_12 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DUN var_13 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
DUN var_14 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
DUN var_15 "O4'" "C1'" N1 C6 -124.549 20.000 1
DUN CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DUN CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DUN CONST_3 N1 C6 C5 C4 0.000 0.000 0
DUN CONST_4 C6 C5 C4 N3 0.000 0.000 0
DUN CONST_5 C5 C4 N3 C2 0.000 0.000 0
DUN CONST_6 C4 N3 C2 O2 180.000 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
DUN chir_01 "C1'" N1 "C2'" "O4'" negativ
DUN chir_02 "C3'" "C2'" "C4'" "O3'" negativ
DUN chir_03 "C4'" "C3'" "O4'" "C5'" positiv
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
DUN plan-1 N1 0.020
DUN plan-1 C2 0.020
DUN plan-1 C6 0.020
DUN plan-1 "C1'" 0.020
DUN plan-1 N3 0.020
DUN plan-1 C4 0.020
DUN plan-1 C5 0.020
DUN plan-1 O2 0.020
DUN plan-1 H3 0.020
DUN plan-1 O4 0.020
DUN plan-1 H5 0.020
DUN plan-1 H6 0.020
DUN plan-2 N3A 0.020
DUN plan-2 PA 0.020
DUN plan-2 PB 0.020
DUN plan-2 H3A 0.020
# ------------------------------------------------------
|
