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
|
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
2AL 2AL '1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL' non-polymer 15 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2AL
#
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
2AL O2 O O 0.000 0.000 0.000 0.000
2AL C2 C C 0.000 -0.243 -1.192 0.001
2AL N1 N NH2 0.000 0.765 -2.086 0.002
2AL HN12 H H 0.000 0.568 -3.079 0.002
2AL HN11 H H 0.000 1.728 -1.770 0.001
2AL N3 N NH1 0.000 -1.522 -1.618 0.003
2AL HN3 H H 0.000 -1.725 -2.607 0.004
2AL C4 C CR5 0.000 -2.547 -0.709 0.002
2AL N9 N NRD5 0.000 -2.443 0.599 0.000
2AL C8 C CR5 0.000 -3.667 1.149 0.001
2AL O8 O O 0.000 -3.885 2.344 -0.001
2AL N7 N NR15 0.000 -4.622 0.202 0.003
2AL HN7 H H 0.000 -5.648 0.370 0.007
2AL C5 C CR5 0.000 -4.015 -1.006 -0.002
2AL O5 O O 0.000 -4.545 -2.096 -0.002
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
2AL O2 n/a C2 START
2AL C2 O2 N3 .
2AL N1 C2 HN11 .
2AL HN12 N1 . .
2AL HN11 N1 . .
2AL N3 C2 C4 .
2AL HN3 N3 . .
2AL C4 N3 N9 .
2AL N9 C4 C8 .
2AL C8 N9 N7 .
2AL O8 C8 . .
2AL N7 C8 C5 .
2AL HN7 N7 . .
2AL C5 N7 O5 .
2AL O5 C5 . END
2AL C4 C5 . 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
2AL C4 C5 single 1.490 0.020
2AL N9 C4 double 1.350 0.020
2AL C4 N3 single 1.350 0.020
2AL O5 C5 double 1.285 0.020
2AL C5 N7 single 1.340 0.020
2AL N7 C8 single 1.340 0.020
2AL HN7 N7 single 1.040 0.020
2AL O8 C8 double 1.285 0.020
2AL C8 N9 single 1.350 0.020
2AL N3 C2 single 1.330 0.020
2AL HN3 N3 single 1.010 0.020
2AL N1 C2 single 1.332 0.020
2AL C2 O2 double 1.220 0.020
2AL HN11 N1 single 1.010 0.020
2AL HN12 N1 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
2AL O2 C2 N1 123.000 3.000
2AL O2 C2 N3 123.000 3.000
2AL N1 C2 N3 120.000 3.000
2AL C2 N1 HN12 120.000 3.000
2AL C2 N1 HN11 120.000 3.000
2AL HN12 N1 HN11 120.000 3.000
2AL C2 N3 HN3 120.000 3.000
2AL C2 N3 C4 120.000 3.000
2AL HN3 N3 C4 120.000 3.000
2AL N3 C4 N9 108.000 3.000
2AL N3 C4 C5 108.000 3.000
2AL N9 C4 C5 108.000 3.000
2AL C4 N9 C8 108.000 3.000
2AL N9 C8 O8 108.000 3.000
2AL N9 C8 N7 108.000 3.000
2AL O8 C8 N7 108.000 3.000
2AL C8 N7 HN7 126.000 3.000
2AL C8 N7 C5 108.000 3.000
2AL HN7 N7 C5 126.000 3.000
2AL N7 C5 O5 108.000 3.000
2AL N7 C5 C4 108.000 3.000
2AL O5 C5 C4 108.000 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
2AL CONST_1 O2 C2 N1 HN11 0.000 0.000 0
2AL CONST_2 O2 C2 N3 C4 0.000 0.000 0
2AL var_1 C2 N3 C4 N9 0.011 20.000 1
2AL CONST_3 N3 C4 C5 N7 180.000 0.000 0
2AL CONST_4 N3 C4 N9 C8 180.000 0.000 0
2AL CONST_5 C4 N9 C8 N7 0.000 0.000 0
2AL CONST_6 N9 C8 N7 C5 0.000 0.000 0
2AL CONST_7 C8 N7 C5 O5 180.000 0.000 0
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
2AL plan-1 C4 0.020
2AL plan-1 C5 0.020
2AL plan-1 N9 0.020
2AL plan-1 N3 0.020
2AL plan-1 N7 0.020
2AL plan-1 C8 0.020
2AL plan-1 O5 0.020
2AL plan-1 HN7 0.020
2AL plan-1 O8 0.020
2AL plan-1 HN3 0.020
2AL plan-2 N3 0.020
2AL plan-2 C4 0.020
2AL plan-2 C2 0.020
2AL plan-2 HN3 0.020
2AL plan-3 C2 0.020
2AL plan-3 N3 0.020
2AL plan-3 N1 0.020
2AL plan-3 O2 0.020
2AL plan-3 HN3 0.020
2AL plan-3 HN12 0.020
2AL plan-3 HN11 0.020
2AL plan-4 N1 0.020
2AL plan-4 C2 0.020
2AL plan-4 HN11 0.020
2AL plan-4 HN12 0.020
# ------------------------------------------------------
|
