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
|
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
2AD 2AD '2'-AMINO-2'-DEOXYADENOSINE ' non-polymer 33 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2AD
#
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
2AD "O3'" O OH1 0.000 0.000 0.000 0.000
2AD HA H H 0.000 0.673 0.171 -0.673
2AD "C3'" C CH1 0.000 -1.147 -0.590 -0.615
2AD "H3'" H H 0.000 -0.869 -1.515 -1.139
2AD "C4'" C CH1 0.000 -1.811 0.401 -1.588
2AD "H4'" H H 0.000 -1.267 1.356 -1.577
2AD "C5'" C CH2 0.000 -1.811 -0.180 -3.003
2AD "H5'1" H H 0.000 -2.367 -1.120 -3.009
2AD "H5'2" H H 0.000 -0.783 -0.364 -3.320
2AD "O5'" O OH1 0.000 -2.429 0.746 -3.899
2AD "H5'" H H 0.000 -2.430 0.378 -4.793
2AD "C2'" C CH1 0.000 -2.241 -0.875 0.443
2AD "H2'" H H 0.000 -2.776 -1.807 0.211
2AD N N NH2 0.000 -1.666 -0.924 1.793
2AD HN2 H H 0.000 -1.932 -0.237 2.488
2AD HN1 H H 0.000 -0.998 -1.646 2.039
2AD "C1'" C CH1 0.000 -3.174 0.351 0.284
2AD "H1'" H H 0.000 -2.773 1.215 0.832
2AD "O4'" O O2 0.000 -3.161 0.602 -1.138
2AD N9 N NR5 0.000 -4.529 0.037 0.740
2AD C4 C CR56 0.000 -5.040 0.269 1.992
2AD C5 C CR56 0.000 -6.367 -0.190 1.962
2AD N7 N NRD5 0.000 -6.591 -0.678 0.718
2AD C8 C CR15 0.000 -5.515 -0.546 -0.001
2AD H8 H H 0.000 -5.416 -0.853 -1.034
2AD N3 N NRD6 0.000 -4.568 0.807 3.112
2AD C2 C CR16 0.000 -5.328 0.899 4.183
2AD H2 H H 0.000 -4.912 1.338 5.081
2AD N1 N NRD6 0.000 -6.579 0.476 4.203
2AD C6 C CR6 0.000 -7.138 -0.070 3.130
2AD N6 N NH2 0.000 -8.449 -0.511 3.162
2AD H6N2 H H 0.000 -8.872 -0.929 2.339
2AD H6N1 H H 0.000 -9.002 -0.421 4.008
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
2AD "O3'" n/a "C3'" START
2AD HA "O3'" . .
2AD "C3'" "O3'" "C2'" .
2AD "H3'" "C3'" . .
2AD "C4'" "C3'" "C5'" .
2AD "H4'" "C4'" . .
2AD "C5'" "C4'" "O5'" .
2AD "H5'1" "C5'" . .
2AD "H5'2" "C5'" . .
2AD "O5'" "C5'" "H5'" .
2AD "H5'" "O5'" . .
2AD "C2'" "C3'" "C1'" .
2AD "H2'" "C2'" . .
2AD N "C2'" HN1 .
2AD HN2 N . .
2AD HN1 N . .
2AD "C1'" "C2'" N9 .
2AD "H1'" "C1'" . .
2AD "O4'" "C1'" . .
2AD N9 "C1'" C4 .
2AD C4 N9 N3 .
2AD C5 C4 N7 .
2AD N7 C5 C8 .
2AD C8 N7 H8 .
2AD H8 C8 . .
2AD N3 C4 C2 .
2AD C2 N3 N1 .
2AD H2 C2 . .
2AD N1 C2 C6 .
2AD C6 N1 N6 .
2AD N6 C6 H6N1 .
2AD H6N2 N6 . .
2AD H6N1 N6 . END
2AD "C4'" "O4'" . ADD
2AD N9 C8 . ADD
2AD C5 C6 . 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
2AD "O5'" "C5'" single 1.432 0.020
2AD "H5'" "O5'" single 0.967 0.020
2AD "C5'" "C4'" single 1.524 0.020
2AD "H5'1" "C5'" single 1.092 0.020
2AD "H5'2" "C5'" single 1.092 0.020
2AD "C4'" "O4'" single 1.426 0.020
2AD "C4'" "C3'" single 1.524 0.020
2AD "H4'" "C4'" single 1.099 0.020
2AD "O4'" "C1'" single 1.426 0.020
2AD "C3'" "O3'" single 1.432 0.020
2AD "C2'" "C3'" single 1.524 0.020
2AD "H3'" "C3'" single 1.099 0.020
2AD HA "O3'" single 0.967 0.020
2AD "C1'" "C2'" single 1.524 0.020
2AD N "C2'" single 1.450 0.020
2AD "H2'" "C2'" single 1.099 0.020
2AD N9 "C1'" single 1.485 0.020
2AD "H1'" "C1'" single 1.099 0.020
2AD N9 C8 single 1.337 0.020
2AD C4 N9 single 1.337 0.020
2AD C8 N7 double 1.350 0.020
2AD H8 C8 single 1.083 0.020
2AD N7 C5 single 1.350 0.020
2AD C5 C6 double 1.490 0.020
2AD C5 C4 single 1.490 0.020
2AD N6 C6 single 1.355 0.020
2AD C6 N1 single 1.350 0.020
2AD H6N1 N6 single 1.010 0.020
2AD H6N2 N6 single 1.010 0.020
2AD N1 C2 double 1.337 0.020
2AD C2 N3 single 1.337 0.020
2AD H2 C2 single 1.083 0.020
2AD N3 C4 double 1.355 0.020
2AD HN1 N single 1.010 0.020
2AD HN2 N 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
2AD HA "O3'" "C3'" 109.470 3.000
2AD "O3'" "C3'" "H3'" 109.470 3.000
2AD "O3'" "C3'" "C4'" 109.470 3.000
2AD "O3'" "C3'" "C2'" 109.470 3.000
2AD "H3'" "C3'" "C4'" 108.340 3.000
2AD "H3'" "C3'" "C2'" 108.340 3.000
2AD "C4'" "C3'" "C2'" 111.000 3.000
2AD "C3'" "C4'" "H4'" 108.340 3.000
2AD "C3'" "C4'" "C5'" 111.000 3.000
2AD "C3'" "C4'" "O4'" 109.470 3.000
2AD "H4'" "C4'" "C5'" 108.340 3.000
2AD "H4'" "C4'" "O4'" 109.470 3.000
2AD "C5'" "C4'" "O4'" 109.470 3.000
2AD "C4'" "C5'" "H5'1" 109.470 3.000
2AD "C4'" "C5'" "H5'2" 109.470 3.000
2AD "C4'" "C5'" "O5'" 109.470 3.000
2AD "H5'1" "C5'" "H5'2" 107.900 3.000
2AD "H5'1" "C5'" "O5'" 109.470 3.000
2AD "H5'2" "C5'" "O5'" 109.470 3.000
2AD "C5'" "O5'" "H5'" 109.470 3.000
2AD "C3'" "C2'" "H2'" 108.340 3.000
2AD "C3'" "C2'" N 109.470 3.000
2AD "C3'" "C2'" "C1'" 111.000 3.000
2AD "H2'" "C2'" N 109.470 3.000
2AD "H2'" "C2'" "C1'" 108.340 3.000
2AD N "C2'" "C1'" 109.470 3.000
2AD "C2'" N HN2 120.000 3.000
2AD "C2'" N HN1 120.000 3.000
2AD HN2 N HN1 120.000 3.000
2AD "C2'" "C1'" "H1'" 108.340 3.000
2AD "C2'" "C1'" "O4'" 109.470 3.000
2AD "C2'" "C1'" N9 109.470 3.000
2AD "H1'" "C1'" "O4'" 109.470 3.000
2AD "H1'" "C1'" N9 109.470 3.000
2AD "O4'" "C1'" N9 109.470 3.000
2AD "C1'" "O4'" "C4'" 111.800 3.000
2AD "C1'" N9 C4 126.000 3.000
2AD "C1'" N9 C8 126.000 3.000
2AD C4 N9 C8 108.000 3.000
2AD N9 C4 C5 108.000 3.000
2AD N9 C4 N3 132.000 3.000
2AD C5 C4 N3 120.000 3.000
2AD C4 C5 N7 108.000 3.000
2AD C4 C5 C6 120.000 3.000
2AD N7 C5 C6 132.000 3.000
2AD C5 N7 C8 108.000 3.000
2AD N7 C8 H8 126.000 3.000
2AD N7 C8 N9 108.000 3.000
2AD H8 C8 N9 126.000 3.000
2AD C4 N3 C2 120.000 3.000
2AD N3 C2 H2 120.000 3.000
2AD N3 C2 N1 120.000 3.000
2AD H2 C2 N1 120.000 3.000
2AD C2 N1 C6 120.000 3.000
2AD N1 C6 N6 120.000 3.000
2AD N1 C6 C5 120.000 3.000
2AD N6 C6 C5 120.000 3.000
2AD C6 N6 H6N2 120.000 3.000
2AD C6 N6 H6N1 120.000 3.000
2AD H6N2 N6 H6N1 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
2AD var_1 HA "O3'" "C3'" "C2'" 179.956 20.000 1
2AD var_2 "O3'" "C3'" "C4'" "C5'" 120.000 20.000 3
2AD var_3 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
2AD var_4 "C3'" "C4'" "C5'" "O5'" 179.976 20.000 3
2AD var_5 "C4'" "C5'" "O5'" "H5'" -179.966 20.000 1
2AD var_6 "O3'" "C3'" "C2'" "C1'" 90.000 20.000 3
2AD var_7 "C3'" "C2'" N HN1 -64.345 20.000 1
2AD var_8 "C3'" "C2'" "C1'" N9 150.000 20.000 3
2AD var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
2AD var_10 "C2'" "C1'" N9 C4 94.097 20.000 1
2AD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
2AD CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
2AD CONST_3 N9 C4 C5 N7 0.000 0.000 0
2AD CONST_4 C4 C5 C6 N1 0.000 0.000 0
2AD CONST_5 C4 C5 N7 C8 0.000 0.000 0
2AD CONST_6 C5 N7 C8 N9 0.000 0.000 0
2AD CONST_7 N9 C4 N3 C2 180.000 0.000 0
2AD CONST_8 C4 N3 C2 N1 0.000 0.000 0
2AD CONST_9 N3 C2 N1 C6 0.000 0.000 0
2AD CONST_10 C2 N1 C6 N6 180.000 0.000 0
2AD CONST_11 N1 C6 N6 H6N1 0.072 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
2AD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2AD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
2AD chir_03 "C2'" "C3'" "C1'" N positiv
2AD chir_04 "C1'" "O4'" "C2'" N9 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
2AD plan-1 N9 0.020
2AD plan-1 "C1'" 0.020
2AD plan-1 C8 0.020
2AD plan-1 C4 0.020
2AD plan-1 N7 0.020
2AD plan-1 H8 0.020
2AD plan-1 C5 0.020
2AD plan-1 C6 0.020
2AD plan-1 N1 0.020
2AD plan-1 C2 0.020
2AD plan-1 N3 0.020
2AD plan-1 N6 0.020
2AD plan-1 H2 0.020
2AD plan-1 H6N2 0.020
2AD plan-1 H6N1 0.020
2AD plan-2 N6 0.020
2AD plan-2 C6 0.020
2AD plan-2 H6N1 0.020
2AD plan-2 H6N2 0.020
2AD plan-3 N 0.020
2AD plan-3 "C2'" 0.020
2AD plan-3 HN1 0.020
2AD plan-3 HN2 0.020
# ------------------------------------------------------
|
