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
APS APS '9-HYDROXYPROPYLADENINE, S-ISOMER ' non-polymer 25 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APS
#
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
APS O1 O OH1 0.000 0.000 0.000 0.000
APS H1 H H 0.000 -0.239 -0.545 0.762
APS C8 C CH1 0.000 0.250 -0.842 -1.126
APS H8 H H 0.000 0.521 -0.222 -1.993
APS C9 C CH3 0.000 1.398 -1.799 -0.805
APS H91 H H 0.000 1.138 -2.397 0.030
APS H92 H H 0.000 1.584 -2.423 -1.640
APS H93 H H 0.000 2.271 -1.242 -0.580
APS C7 C CH2 0.000 -1.010 -1.646 -1.450
APS H72 H H 0.000 -1.279 -2.262 -0.589
APS H71 H H 0.000 -0.819 -2.290 -2.311
APS N4 N NR5 0.000 -2.110 -0.729 -1.759
APS C6 C CR15 0.000 -2.432 -0.243 -2.991
APS H6 H H 0.000 -1.907 -0.477 -3.908
APS N3 N NRD5 0.000 -3.465 0.543 -2.902
APS C3 C CR56 0.000 -3.869 0.612 -1.611
APS C4 C CR56 0.000 -3.008 -0.209 -0.864
APS N1 N NRD6 0.000 -3.190 -0.310 0.449
APS C1 C CR16 0.000 -4.170 0.339 1.042
APS H1C1 H H 0.000 -4.295 0.231 2.113
APS N2 N NRD6 0.000 -5.007 1.118 0.381
APS C2 C CR6 0.000 -4.899 1.284 -0.934
APS N5 N NH2 0.000 -5.782 2.102 -1.617
APS H51 H H 0.000 -5.697 2.228 -2.621
APS H52 H H 0.000 -6.524 2.586 -1.122
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
APS O1 n/a C8 START
APS H1 O1 . .
APS C8 O1 C7 .
APS H8 C8 . .
APS C9 C8 H93 .
APS H91 C9 . .
APS H92 C9 . .
APS H93 C9 . .
APS C7 C8 N4 .
APS H72 C7 . .
APS H71 C7 . .
APS N4 C7 C4 .
APS C6 N4 N3 .
APS H6 C6 . .
APS N3 C6 C3 .
APS C3 N3 . .
APS C4 N4 N1 .
APS N1 C4 C1 .
APS C1 N1 N2 .
APS H1C1 C1 . .
APS N2 C1 C2 .
APS C2 N2 N5 .
APS N5 C2 H52 .
APS H51 N5 . .
APS H52 N5 . END
APS C4 C3 . ADD
APS C3 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
APS C7 C8 single 1.524 0.020
APS N4 C7 single 1.462 0.020
APS H72 C7 single 1.092 0.020
APS H71 C7 single 1.092 0.020
APS C8 O1 single 1.432 0.020
APS C9 C8 single 1.524 0.020
APS H8 C8 single 1.099 0.020
APS H1 O1 single 0.967 0.020
APS H93 C9 single 1.059 0.020
APS H92 C9 single 1.059 0.020
APS H91 C9 single 1.059 0.020
APS C4 C3 double 1.490 0.020
APS C4 N4 single 1.337 0.020
APS N1 C4 single 1.355 0.020
APS C3 C2 single 1.490 0.020
APS C3 N3 single 1.350 0.020
APS C2 N2 double 1.350 0.020
APS N5 C2 single 1.355 0.020
APS N2 C1 single 1.337 0.020
APS C1 N1 double 1.337 0.020
APS H1C1 C1 single 1.083 0.020
APS H52 N5 single 1.010 0.020
APS H51 N5 single 1.010 0.020
APS C6 N4 single 1.337 0.020
APS N3 C6 double 1.350 0.020
APS H6 C6 single 1.083 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
APS H1 O1 C8 109.470 3.000
APS O1 C8 H8 109.470 3.000
APS O1 C8 C9 109.470 3.000
APS O1 C8 C7 109.470 3.000
APS H8 C8 C9 108.340 3.000
APS H8 C8 C7 108.340 3.000
APS C9 C8 C7 111.000 3.000
APS C8 C9 H91 109.470 3.000
APS C8 C9 H92 109.470 3.000
APS C8 C9 H93 109.470 3.000
APS H91 C9 H92 109.470 3.000
APS H91 C9 H93 109.470 3.000
APS H92 C9 H93 109.470 3.000
APS C8 C7 H72 109.470 3.000
APS C8 C7 H71 109.470 3.000
APS C8 C7 N4 109.500 3.000
APS H72 C7 H71 107.900 3.000
APS H72 C7 N4 109.500 3.000
APS H71 C7 N4 109.500 3.000
APS C7 N4 C6 126.000 3.000
APS C7 N4 C4 126.000 3.000
APS C6 N4 C4 108.000 3.000
APS N4 C6 H6 126.000 3.000
APS N4 C6 N3 108.000 3.000
APS H6 C6 N3 126.000 3.000
APS C6 N3 C3 108.000 3.000
APS N3 C3 C4 108.000 3.000
APS N3 C3 C2 132.000 3.000
APS C4 C3 C2 120.000 3.000
APS N4 C4 N1 132.000 3.000
APS N4 C4 C3 108.000 3.000
APS N1 C4 C3 120.000 3.000
APS C4 N1 C1 120.000 3.000
APS N1 C1 H1C1 120.000 3.000
APS N1 C1 N2 120.000 3.000
APS H1C1 C1 N2 120.000 3.000
APS C1 N2 C2 120.000 3.000
APS N2 C2 N5 120.000 3.000
APS N2 C2 C3 120.000 3.000
APS N5 C2 C3 120.000 3.000
APS C2 N5 H51 120.000 3.000
APS C2 N5 H52 120.000 3.000
APS H51 N5 H52 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
APS var_1 H1 O1 C8 C7 60.066 20.000 1
APS var_2 O1 C8 C9 H93 -59.957 20.000 3
APS var_3 O1 C8 C7 N4 59.943 20.000 3
APS var_4 C8 C7 N4 C4 -90.308 20.000 1
APS CONST_1 C7 N4 C6 N3 180.000 0.000 0
APS CONST_2 N4 C6 N3 C3 0.000 0.000 0
APS CONST_3 C6 N3 C3 C4 0.000 0.000 0
APS CONST_4 N3 C3 C2 N2 180.000 0.000 0
APS CONST_5 C7 N4 C4 N1 0.000 0.000 0
APS CONST_6 N4 C4 C3 N3 0.000 0.000 0
APS CONST_7 N4 C4 N1 C1 180.000 0.000 0
APS CONST_8 C4 N1 C1 N2 0.000 0.000 0
APS CONST_9 N1 C1 N2 C2 0.000 0.000 0
APS CONST_10 C1 N2 C2 N5 180.000 0.000 0
APS CONST_11 N2 C2 N5 H52 -0.039 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
APS chir_01 C8 C7 O1 C9 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
APS plan-1 C4 0.020
APS plan-1 C3 0.020
APS plan-1 N4 0.020
APS plan-1 N1 0.020
APS plan-1 N3 0.020
APS plan-1 C6 0.020
APS plan-1 C2 0.020
APS plan-1 N2 0.020
APS plan-1 N5 0.020
APS plan-1 C1 0.020
APS plan-1 H1C1 0.020
APS plan-1 C7 0.020
APS plan-1 H6 0.020
APS plan-1 H51 0.020
APS plan-1 H52 0.020
APS plan-2 N5 0.020
APS plan-2 C2 0.020
APS plan-2 H52 0.020
APS plan-2 H51 0.020
# ------------------------------------------------------
|
