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
|
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
ADK ADK '3-METHYL-3H-PURIN-6-YLAMINE ' non-polymer 18 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ADK
#
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
ADK N6 N NH2 0.000 0.000 0.000 0.000
ADK HN61 H H 0.000 0.890 0.000 0.485
ADK HN62 H H 0.000 -0.014 0.000 -1.013
ADK C6 C CR6 0.000 -1.175 0.000 0.709
ADK C5 C CR56 0.000 -2.410 0.000 0.040
ADK C4 C CR56 0.000 -3.592 -0.004 0.813
ADK N7 N NRD5 0.000 -2.798 0.000 -1.246
ADK C8 C CR15 0.000 -4.113 0.000 -1.279
ADK H8 H H 0.000 -4.711 0.000 -2.182
ADK N9 N NRD5 0.000 -4.602 0.000 -0.043
ADK N1 N NRD6 0.000 -1.159 0.000 2.046
ADK C2 C CR16 0.000 -2.260 0.000 2.750
ADK HC2 H H 0.000 -2.188 0.000 3.831
ADK N3 N NR6 0.000 -3.477 0.000 2.183
ADK C3A C CH3 0.000 -4.680 0.000 3.021
ADK H3A3 H H 0.000 -5.255 0.865 2.814
ADK H3A2 H H 0.000 -5.255 -0.865 2.814
ADK H3A1 H H 0.000 -4.398 0.000 4.042
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
ADK N6 n/a C6 START
ADK HN61 N6 . .
ADK HN62 N6 . .
ADK C6 N6 N1 .
ADK C5 C6 N7 .
ADK C4 C5 . .
ADK N7 C5 C8 .
ADK C8 N7 N9 .
ADK H8 C8 . .
ADK N9 C8 . .
ADK N1 C6 C2 .
ADK C2 N1 N3 .
ADK HC2 C2 . .
ADK N3 C2 C3A .
ADK C3A N3 H3A1 .
ADK H3A3 C3A . .
ADK H3A2 C3A . .
ADK H3A1 C3A . END
ADK N9 C4 . ADD
ADK 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
ADK N9 C4 double 1.350 0.020
ADK N9 C8 single 1.350 0.020
ADK C4 N3 single 1.337 0.020
ADK C4 C5 single 1.490 0.020
ADK N3 C2 single 1.337 0.020
ADK C3A N3 single 1.465 0.020
ADK C2 N1 double 1.337 0.020
ADK HC2 C2 single 1.083 0.020
ADK N1 C6 single 1.350 0.020
ADK C6 N6 single 1.355 0.020
ADK C5 C6 double 1.490 0.020
ADK HN61 N6 single 1.010 0.020
ADK HN62 N6 single 1.010 0.020
ADK N7 C5 single 1.350 0.020
ADK C8 N7 double 1.350 0.020
ADK H8 C8 single 1.083 0.020
ADK H3A1 C3A single 1.059 0.020
ADK H3A2 C3A single 1.059 0.020
ADK H3A3 C3A 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
ADK HN61 N6 HN62 120.000 3.000
ADK HN61 N6 C6 120.000 3.000
ADK HN62 N6 C6 120.000 3.000
ADK N6 C6 C5 120.000 3.000
ADK N6 C6 N1 120.000 3.000
ADK C5 C6 N1 120.000 3.000
ADK C6 C5 C4 120.000 3.000
ADK C6 C5 N7 132.000 3.000
ADK C4 C5 N7 108.000 3.000
ADK C5 C4 N9 108.000 3.000
ADK C5 C4 N3 120.000 3.000
ADK N9 C4 N3 120.000 3.000
ADK C5 N7 C8 108.000 3.000
ADK N7 C8 H8 126.000 3.000
ADK N7 C8 N9 108.000 3.000
ADK H8 C8 N9 126.000 3.000
ADK C8 N9 C4 108.000 3.000
ADK C6 N1 C2 120.000 3.000
ADK N1 C2 HC2 120.000 3.000
ADK N1 C2 N3 120.000 3.000
ADK HC2 C2 N3 120.000 3.000
ADK C2 N3 C3A 120.000 3.000
ADK C2 N3 C4 120.000 3.000
ADK C3A N3 C4 120.000 3.000
ADK N3 C3A H3A3 109.470 3.000
ADK N3 C3A H3A2 109.470 3.000
ADK N3 C3A H3A1 109.470 3.000
ADK H3A3 C3A H3A2 109.470 3.000
ADK H3A3 C3A H3A1 109.470 3.000
ADK H3A2 C3A H3A1 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
ADK CONST_1 HN62 N6 C6 N1 180.000 0.000 0
ADK CONST_2 N6 C6 C5 N7 0.000 0.000 0
ADK CONST_3 C6 C5 C4 N9 180.000 0.000 0
ADK CONST_4 C5 C4 N3 C2 0.000 0.000 0
ADK CONST_5 C6 C5 N7 C8 180.000 0.000 0
ADK CONST_6 C5 N7 C8 N9 0.000 0.000 0
ADK CONST_7 N7 C8 N9 C4 0.000 0.000 0
ADK CONST_8 C8 N9 C4 C5 0.000 0.000 0
ADK CONST_9 N6 C6 N1 C2 180.000 0.000 0
ADK CONST_10 C6 N1 C2 N3 0.000 0.000 0
ADK CONST_11 N1 C2 N3 C3A 180.000 0.000 0
ADK var_1 C2 N3 C3A H3A1 0.000 20.000 1
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
ADK plan-1 N9 0.020
ADK plan-1 C4 0.020
ADK plan-1 C8 0.020
ADK plan-1 N7 0.020
ADK plan-1 N3 0.020
ADK plan-1 C5 0.020
ADK plan-1 C2 0.020
ADK plan-1 N1 0.020
ADK plan-1 C6 0.020
ADK plan-1 C3A 0.020
ADK plan-1 HC2 0.020
ADK plan-1 N6 0.020
ADK plan-1 H8 0.020
ADK plan-1 HN61 0.020
ADK plan-1 HN62 0.020
ADK plan-2 N6 0.020
ADK plan-2 C6 0.020
ADK plan-2 HN61 0.020
ADK plan-2 HN62 0.020
# ------------------------------------------------------
|
