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
|
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
3PD 3PD '2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENT' non-polymer 35 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_3PD
#
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
3PD O1 O OP -0.666 0.000 0.000 0.000
3PD P P P 0.000 0.163 1.158 -0.960
3PD O1P O OP -0.666 1.590 1.484 -1.341
3PD O2P O OP -0.666 -0.524 0.983 -2.296
3PD "O3'" O O2 0.000 -0.429 2.568 -0.440
3PD "C3'" C CH1 0.000 -1.808 2.644 -0.142
3PD "H3'" H H 0.000 -2.406 2.460 -1.046
3PD "C4'" C CH1 0.000 -2.192 3.974 0.484
3PD "H4'" H H 0.000 -1.400 4.292 1.176
3PD "C5'" C CH2 0.000 -2.442 5.074 -0.531
3PD "H5'1" H H 0.000 -3.254 4.782 -1.201
3PD "H5'2" H H 0.000 -1.537 5.253 -1.115
3PD "O5'" O OH1 0.000 -2.801 6.257 0.160
3PD "H5'" H H 0.000 -3.177 6.890 -0.465
3PD "C2'" C CH2 0.000 -2.189 1.668 0.949
3PD "H2'1" H H 0.000 -1.401 1.547 1.695
3PD "H2'2" H H 0.000 -2.470 0.689 0.555
3PD "C1'" C CH1 0.000 -3.404 2.325 1.594
3PD "H1'" H H 0.000 -3.305 2.251 2.686
3PD "O4'" O O2 0.000 -3.395 3.716 1.225
3PD N9 N NR5 0.000 -4.680 1.725 1.199
3PD C8 C CR15 0.000 -5.432 2.069 0.101
3PD H8 H H 0.000 -5.149 2.841 -0.605
3PD N7 N NRD5 0.000 -6.536 1.355 0.001
3PD C5 C CR56 0.000 -6.485 0.522 1.080
3PD C4 C CR56 0.000 -5.357 0.724 1.837
3PD C6 C CR6 0.000 -7.430 -0.483 1.484
3PD O6 O O 0.000 -8.462 -0.732 0.873
3PD N1 N NR16 0.000 -7.005 -1.122 2.657
3PD HN1 H H 0.000 -7.616 -1.871 3.041
3PD C2 C CR6 0.000 -5.812 -0.831 3.360
3PD N3 N NRD6 0.000 -4.965 0.094 2.967
3PD N2 N NH2 0.000 -5.597 -1.584 4.485
3PD HN22 H H 0.000 -5.253 -1.149 5.333
3PD HN21 H H 0.000 -5.780 -2.580 4.476
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
3PD O1 n/a P START
3PD P O1 "O3'" .
3PD O1P P . .
3PD O2P P . .
3PD "O3'" P "C3'" .
3PD "C3'" "O3'" "C2'" .
3PD "H3'" "C3'" . .
3PD "C4'" "C3'" "C5'" .
3PD "H4'" "C4'" . .
3PD "C5'" "C4'" "O5'" .
3PD "H5'1" "C5'" . .
3PD "H5'2" "C5'" . .
3PD "O5'" "C5'" "H5'" .
3PD "H5'" "O5'" . .
3PD "C2'" "C3'" "C1'" .
3PD "H2'1" "C2'" . .
3PD "H2'2" "C2'" . .
3PD "C1'" "C2'" N9 .
3PD "H1'" "C1'" . .
3PD "O4'" "C1'" . .
3PD N9 "C1'" C8 .
3PD C8 N9 N7 .
3PD H8 C8 . .
3PD N7 C8 C5 .
3PD C5 N7 C6 .
3PD C4 C5 . .
3PD C6 C5 N1 .
3PD O6 C6 . .
3PD N1 C6 C2 .
3PD HN1 N1 . .
3PD C2 N1 N2 .
3PD N3 C2 . .
3PD N2 C2 HN21 .
3PD HN22 N2 . .
3PD HN21 N2 . END
3PD "C4'" "O4'" . ADD
3PD N9 C4 . ADD
3PD C4 N3 . 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
3PD "O5'" "C5'" single 1.432 0.020
3PD "H5'" "O5'" single 0.967 0.020
3PD "C5'" "C4'" single 1.524 0.020
3PD "H5'1" "C5'" single 1.092 0.020
3PD "H5'2" "C5'" single 1.092 0.020
3PD "C4'" "O4'" single 1.426 0.020
3PD "C4'" "C3'" single 1.524 0.020
3PD "H4'" "C4'" single 1.099 0.020
3PD "O4'" "C1'" single 1.426 0.020
3PD "C1'" "C2'" single 1.524 0.020
3PD N9 "C1'" single 1.485 0.020
3PD "H1'" "C1'" single 1.099 0.020
3PD "C2'" "C3'" single 1.524 0.020
3PD "H2'1" "C2'" single 1.092 0.020
3PD "H2'2" "C2'" single 1.092 0.020
3PD "C3'" "O3'" single 1.426 0.020
3PD "H3'" "C3'" single 1.099 0.020
3PD "O3'" P single 1.610 0.020
3PD N9 C4 single 1.337 0.020
3PD C8 N9 single 1.337 0.020
3PD C4 N3 single 1.355 0.020
3PD C4 C5 double 1.490 0.020
3PD N3 C2 double 1.350 0.020
3PD N2 C2 single 1.355 0.020
3PD C2 N1 single 1.337 0.020
3PD HN21 N2 single 1.010 0.020
3PD HN22 N2 single 1.010 0.020
3PD N1 C6 single 1.337 0.020
3PD HN1 N1 single 1.040 0.020
3PD O6 C6 double 1.250 0.020
3PD C6 C5 single 1.490 0.020
3PD C5 N7 single 1.350 0.020
3PD N7 C8 double 1.350 0.020
3PD H8 C8 single 1.083 0.020
3PD O1P P deloc 1.510 0.020
3PD O2P P deloc 1.510 0.020
3PD P O1 deloc 1.510 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
3PD O1 P O1P 119.900 3.000
3PD O1 P O2P 119.900 3.000
3PD O1 P "O3'" 108.200 3.000
3PD O1P P O2P 119.900 3.000
3PD O1P P "O3'" 108.200 3.000
3PD O2P P "O3'" 108.200 3.000
3PD P "O3'" "C3'" 120.500 3.000
3PD "O3'" "C3'" "H3'" 109.470 3.000
3PD "O3'" "C3'" "C4'" 109.470 3.000
3PD "O3'" "C3'" "C2'" 109.470 3.000
3PD "H3'" "C3'" "C4'" 108.340 3.000
3PD "H3'" "C3'" "C2'" 108.340 3.000
3PD "C4'" "C3'" "C2'" 111.000 3.000
3PD "C3'" "C4'" "H4'" 108.340 3.000
3PD "C3'" "C4'" "C5'" 111.000 3.000
3PD "C3'" "C4'" "O4'" 109.470 3.000
3PD "H4'" "C4'" "C5'" 108.340 3.000
3PD "H4'" "C4'" "O4'" 109.470 3.000
3PD "C5'" "C4'" "O4'" 109.470 3.000
3PD "C4'" "C5'" "H5'1" 109.470 3.000
3PD "C4'" "C5'" "H5'2" 109.470 3.000
3PD "C4'" "C5'" "O5'" 109.470 3.000
3PD "H5'1" "C5'" "H5'2" 107.900 3.000
3PD "H5'1" "C5'" "O5'" 109.470 3.000
3PD "H5'2" "C5'" "O5'" 109.470 3.000
3PD "C5'" "O5'" "H5'" 109.470 3.000
3PD "C3'" "C2'" "H2'1" 109.470 3.000
3PD "C3'" "C2'" "H2'2" 109.470 3.000
3PD "C3'" "C2'" "C1'" 111.000 3.000
3PD "H2'1" "C2'" "H2'2" 107.900 3.000
3PD "H2'1" "C2'" "C1'" 109.470 3.000
3PD "H2'2" "C2'" "C1'" 109.470 3.000
3PD "C2'" "C1'" "H1'" 108.340 3.000
3PD "C2'" "C1'" "O4'" 109.470 3.000
3PD "C2'" "C1'" N9 109.470 3.000
3PD "H1'" "C1'" "O4'" 109.470 3.000
3PD "H1'" "C1'" N9 109.470 3.000
3PD "O4'" "C1'" N9 109.470 3.000
3PD "C1'" "O4'" "C4'" 111.800 3.000
3PD "C1'" N9 C8 126.000 3.000
3PD "C1'" N9 C4 126.000 3.000
3PD C8 N9 C4 108.000 3.000
3PD N9 C8 H8 126.000 3.000
3PD N9 C8 N7 108.000 3.000
3PD H8 C8 N7 126.000 3.000
3PD C8 N7 C5 108.000 3.000
3PD N7 C5 C4 108.000 3.000
3PD N7 C5 C6 132.000 3.000
3PD C4 C5 C6 120.000 3.000
3PD C5 C4 N9 108.000 3.000
3PD C5 C4 N3 120.000 3.000
3PD N9 C4 N3 132.000 3.000
3PD C5 C6 O6 120.000 3.000
3PD C5 C6 N1 120.000 3.000
3PD O6 C6 N1 120.000 3.000
3PD C6 N1 HN1 120.000 3.000
3PD C6 N1 C2 120.000 3.000
3PD HN1 N1 C2 120.000 3.000
3PD N1 C2 N3 120.000 3.000
3PD N1 C2 N2 120.000 3.000
3PD N3 C2 N2 120.000 3.000
3PD C2 N3 C4 120.000 3.000
3PD C2 N2 HN22 120.000 3.000
3PD C2 N2 HN21 120.000 3.000
3PD HN22 N2 HN21 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
3PD var_1 O1 P "O3'" "C3'" -60.018 20.000 1
3PD var_2 P "O3'" "C3'" "C2'" 59.987 20.000 1
3PD var_3 "O3'" "C3'" "C4'" "C5'" 90.000 20.000 3
3PD var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
3PD var_5 "C3'" "C4'" "C5'" "O5'" 179.534 20.000 3
3PD var_6 "C4'" "C5'" "O5'" "H5'" -165.674 20.000 1
3PD var_7 "O3'" "C3'" "C2'" "C1'" 150.000 20.000 3
3PD var_8 "C3'" "C2'" "C1'" N9 90.000 20.000 3
3PD var_9 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
3PD var_10 "C2'" "C1'" N9 C8 -87.505 20.000 1
3PD CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
3PD CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
3PD CONST_3 N9 C8 N7 C5 0.000 0.000 0
3PD CONST_4 C8 N7 C5 C6 180.000 0.000 0
3PD CONST_5 N7 C5 C4 N9 0.000 0.000 0
3PD CONST_6 C5 C4 N3 C2 0.000 0.000 0
3PD CONST_7 N7 C5 C6 N1 180.000 0.000 0
3PD CONST_8 C5 C6 N1 C2 0.000 0.000 0
3PD CONST_9 C6 N1 C2 N2 180.000 0.000 0
3PD CONST_10 N1 C2 N3 C4 0.000 0.000 0
3PD CONST_11 N1 C2 N2 HN21 42.603 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
3PD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
3PD chir_02 "C1'" "O4'" "C2'" N9 positiv
3PD chir_03 "C3'" "C4'" "C2'" "O3'" 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
3PD plan-1 N9 0.020
3PD plan-1 "C1'" 0.020
3PD plan-1 C4 0.020
3PD plan-1 C8 0.020
3PD plan-1 N7 0.020
3PD plan-1 N3 0.020
3PD plan-1 C5 0.020
3PD plan-1 C2 0.020
3PD plan-1 N1 0.020
3PD plan-1 C6 0.020
3PD plan-1 N2 0.020
3PD plan-1 HN1 0.020
3PD plan-1 O6 0.020
3PD plan-1 H8 0.020
3PD plan-1 HN22 0.020
3PD plan-1 HN21 0.020
3PD plan-2 N2 0.020
3PD plan-2 C2 0.020
3PD plan-2 HN21 0.020
3PD plan-2 HN22 0.020
# ------------------------------------------------------
|
