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
|
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
POB POB '2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHI' non-polymer 29 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_POB
#
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
POB O6P O OP -0.666 0.000 0.000 0.000
POB P2 P P 0.000 -0.694 -0.588 -1.209
POB O4P O OP -0.666 -1.077 -2.023 -0.921
POB O5P O OP -0.666 0.242 -0.543 -2.397
POB O3P O O2 0.000 -2.019 0.266 -1.536
POB P1 P P 0.000 -3.122 -0.147 -0.440
POB O1P O O 0.000 -3.400 -1.597 -0.544
POB "C1'" C CH1 0.000 -2.493 0.231 1.229
POB "H1'" H H 0.000 -1.611 -0.390 1.438
POB "C2'" C CH3 0.000 -2.106 1.710 1.303
POB "H2'3" H H 0.000 -1.352 1.915 0.587
POB "H2'2" H H 0.000 -2.956 2.309 1.101
POB "H2'1" H H 0.000 -1.740 1.932 2.272
POB "N1'" N NH2 0.000 -3.538 -0.051 2.222
POB HN12 H H 0.000 -3.377 -0.733 2.954
POB HN11 H H 0.000 -4.427 0.434 2.181
POB O2P O O2 0.000 -4.476 0.679 -0.704
POB C2 C CH1 0.000 -4.918 0.341 -2.020
POB H2 H H 0.000 -4.217 -0.376 -2.468
POB C1 C C 0.000 -6.290 -0.278 -1.946
POB O2 O OC -0.500 -6.865 -0.650 -2.993
POB O1 O OC -0.500 -6.854 -0.419 -0.838
POB C3 C CH2 0.000 -4.974 1.605 -2.879
POB H31 H H 0.000 -5.673 2.316 -2.433
POB H32 H H 0.000 -5.312 1.346 -3.884
POB C4 C CH3 0.000 -3.581 2.234 -2.953
POB H43 H H 0.000 -3.251 2.486 -1.978
POB H42 H H 0.000 -2.901 1.544 -3.386
POB H41 H H 0.000 -3.617 3.110 -3.549
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
POB O6P n/a P2 START
POB P2 O6P O3P .
POB O4P P2 . .
POB O5P P2 . .
POB O3P P2 P1 .
POB P1 O3P O2P .
POB O1P P1 . .
POB "C1'" P1 "N1'" .
POB "H1'" "C1'" . .
POB "C2'" "C1'" "H2'1" .
POB "H2'3" "C2'" . .
POB "H2'2" "C2'" . .
POB "H2'1" "C2'" . .
POB "N1'" "C1'" HN11 .
POB HN12 "N1'" . .
POB HN11 "N1'" . .
POB O2P P1 C2 .
POB C2 O2P C3 .
POB H2 C2 . .
POB C1 C2 O1 .
POB O2 C1 . .
POB O1 C1 . .
POB C3 C2 C4 .
POB H31 C3 . .
POB H32 C3 . .
POB C4 C3 H41 .
POB H43 C4 . .
POB H42 C4 . .
POB H41 C4 . END
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
POB O1 C1 deloc 1.250 0.020
POB O2 C1 deloc 1.250 0.020
POB C1 C2 single 1.500 0.020
POB C3 C2 single 1.524 0.020
POB C2 O2P single 1.426 0.020
POB H2 C2 single 1.099 0.020
POB C4 C3 single 1.513 0.020
POB H31 C3 single 1.092 0.020
POB H32 C3 single 1.092 0.020
POB H41 C4 single 1.059 0.020
POB H42 C4 single 1.059 0.020
POB H43 C4 single 1.059 0.020
POB O2P P1 single 1.610 0.020
POB O1P P1 double 1.480 0.020
POB P1 O3P single 1.610 0.020
POB "C1'" P1 single 1.815 0.020
POB O3P P2 single 1.610 0.020
POB O4P P2 deloc 1.510 0.020
POB O5P P2 deloc 1.510 0.020
POB P2 O6P deloc 1.510 0.020
POB "N1'" "C1'" single 1.450 0.020
POB "C2'" "C1'" single 1.524 0.020
POB "H1'" "C1'" single 1.099 0.020
POB HN11 "N1'" single 1.010 0.020
POB HN12 "N1'" single 1.010 0.020
POB "H2'1" "C2'" single 1.059 0.020
POB "H2'2" "C2'" single 1.059 0.020
POB "H2'3" "C2'" single 1.059 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
POB O6P P2 O4P 119.900 3.000
POB O6P P2 O5P 119.900 3.000
POB O6P P2 O3P 108.200 3.000
POB O4P P2 O5P 119.900 3.000
POB O4P P2 O3P 108.200 3.000
POB O5P P2 O3P 108.200 3.000
POB P2 O3P P1 120.500 3.000
POB O3P P1 O1P 109.500 3.000
POB O3P P1 "C1'" 109.500 3.000
POB O3P P1 O2P 102.600 3.000
POB O1P P1 "C1'" 109.500 3.000
POB O1P P1 O2P 109.500 3.000
POB "C1'" P1 O2P 109.500 3.000
POB P1 "C1'" "H1'" 109.500 3.000
POB P1 "C1'" "C2'" 109.500 3.000
POB P1 "C1'" "N1'" 109.500 3.000
POB "H1'" "C1'" "C2'" 108.340 3.000
POB "H1'" "C1'" "N1'" 109.470 3.000
POB "C2'" "C1'" "N1'" 109.470 3.000
POB "C1'" "C2'" "H2'3" 109.470 3.000
POB "C1'" "C2'" "H2'2" 109.470 3.000
POB "C1'" "C2'" "H2'1" 109.470 3.000
POB "H2'3" "C2'" "H2'2" 109.470 3.000
POB "H2'3" "C2'" "H2'1" 109.470 3.000
POB "H2'2" "C2'" "H2'1" 109.470 3.000
POB "C1'" "N1'" HN12 120.000 3.000
POB "C1'" "N1'" HN11 120.000 3.000
POB HN12 "N1'" HN11 120.000 3.000
POB P1 O2P C2 120.500 3.000
POB O2P C2 H2 109.470 3.000
POB O2P C2 C1 109.470 3.000
POB O2P C2 C3 109.470 3.000
POB H2 C2 C1 108.810 3.000
POB H2 C2 C3 108.340 3.000
POB C1 C2 C3 109.470 3.000
POB C2 C1 O2 118.500 3.000
POB C2 C1 O1 118.500 3.000
POB O2 C1 O1 123.000 3.000
POB C2 C3 H31 109.470 3.000
POB C2 C3 H32 109.470 3.000
POB C2 C3 C4 111.000 3.000
POB H31 C3 H32 107.900 3.000
POB H31 C3 C4 109.470 3.000
POB H32 C3 C4 109.470 3.000
POB C3 C4 H43 109.470 3.000
POB C3 C4 H42 109.470 3.000
POB C3 C4 H41 109.470 3.000
POB H43 C4 H42 109.470 3.000
POB H43 C4 H41 109.470 3.000
POB H42 C4 H41 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
POB var_1 O6P P2 O3P P1 -75.454 20.000 1
POB var_2 P2 O3P P1 O2P 179.695 20.000 1
POB var_3 O3P P1 "C1'" "N1'" 175.738 20.000 1
POB var_4 P1 "C1'" "C2'" "H2'1" 179.992 20.000 3
POB var_5 P1 "C1'" "N1'" HN11 -59.906 20.000 1
POB var_6 O3P P1 O2P C2 60.008 20.000 1
POB var_7 P1 O2P C2 C3 -119.984 20.000 1
POB var_8 O2P C2 C1 O1 0.024 20.000 3
POB var_9 O2P C2 C3 C4 59.946 20.000 3
POB var_10 C2 C3 C4 H41 179.981 20.000 3
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
POB chir_01 C2 C1 C3 O2P negativ
POB chir_02 "C1'" P1 "N1'" "C2'" 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
POB plan-1 C1 0.020
POB plan-1 O1 0.020
POB plan-1 O2 0.020
POB plan-1 C2 0.020
POB plan-2 "N1'" 0.020
POB plan-2 "C1'" 0.020
POB plan-2 HN11 0.020
POB plan-2 HN12 0.020
# ------------------------------------------------------
|
