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
|
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
XYD XYD '2,5-DIMETHYLANILINE ' non-polymer 20 9 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XYD
#
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
XYD N N NH2 0.000 0.000 0.000 0.000
XYD H1N H H 0.000 0.159 0.001 -1.006
XYD H2N H H 0.000 0.808 0.000 0.619
XYD C1 C CR6 0.000 -1.297 0.000 0.519
XYD C6 C CR16 0.000 -2.389 -0.004 -0.339
XYD H6 H H 0.000 -2.237 -0.010 -1.411
XYD C5 C CR6 0.000 -3.670 0.001 0.177
XYD C8 C CH3 0.000 -4.856 0.003 -0.753
XYD H83 H H 0.000 -4.601 -0.496 -1.652
XYD H82 H H 0.000 -5.668 -0.496 -0.291
XYD H81 H H 0.000 -5.133 1.001 -0.971
XYD C4 C CR16 0.000 -3.866 0.001 1.544
XYD H4 H H 0.000 -4.872 0.002 1.946
XYD C3 C CR16 0.000 -2.782 0.001 2.401
XYD H3 H H 0.000 -2.939 0.001 3.472
XYD C2 C CR6 0.000 -1.497 0.000 1.893
XYD C9 C CH3 0.000 -0.315 -0.001 2.827
XYD H93 H H 0.000 0.498 0.499 2.368
XYD H92 H H 0.000 -0.574 0.498 3.725
XYD H91 H H 0.000 -0.038 -0.999 3.045
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
XYD N n/a C1 START
XYD H1N N . .
XYD H2N N . .
XYD C1 N C6 .
XYD C6 C1 C5 .
XYD H6 C6 . .
XYD C5 C6 C4 .
XYD C8 C5 H81 .
XYD H83 C8 . .
XYD H82 C8 . .
XYD H81 C8 . .
XYD C4 C5 C3 .
XYD H4 C4 . .
XYD C3 C4 C2 .
XYD H3 C3 . .
XYD C2 C3 C9 .
XYD C9 C2 H91 .
XYD H93 C9 . .
XYD H92 C9 . .
XYD H91 C9 . END
XYD C1 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
XYD C1 C2 double 1.487 0.020
XYD C6 C1 single 1.390 0.020
XYD C1 N single 1.355 0.020
XYD C2 C3 single 1.390 0.020
XYD C9 C2 single 1.506 0.020
XYD C3 C4 double 1.390 0.020
XYD H3 C3 single 1.083 0.020
XYD C4 C5 single 1.390 0.020
XYD H4 C4 single 1.083 0.020
XYD C5 C6 double 1.390 0.020
XYD C8 C5 single 1.506 0.020
XYD H6 C6 single 1.083 0.020
XYD H1N N single 1.010 0.020
XYD H2N N single 1.010 0.020
XYD H81 C8 single 1.059 0.020
XYD H82 C8 single 1.059 0.020
XYD H83 C8 single 1.059 0.020
XYD H91 C9 single 1.059 0.020
XYD H92 C9 single 1.059 0.020
XYD H93 C9 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
XYD H1N N H2N 120.000 3.000
XYD H1N N C1 120.000 3.000
XYD H2N N C1 120.000 3.000
XYD N C1 C6 120.000 3.000
XYD N C1 C2 120.000 3.000
XYD C6 C1 C2 120.000 3.000
XYD C1 C6 H6 120.000 3.000
XYD C1 C6 C5 120.000 3.000
XYD H6 C6 C5 120.000 3.000
XYD C6 C5 C8 120.000 3.000
XYD C6 C5 C4 120.000 3.000
XYD C8 C5 C4 120.000 3.000
XYD C5 C8 H83 109.470 3.000
XYD C5 C8 H82 109.470 3.000
XYD C5 C8 H81 109.470 3.000
XYD H83 C8 H82 109.470 3.000
XYD H83 C8 H81 109.470 3.000
XYD H82 C8 H81 109.470 3.000
XYD C5 C4 H4 120.000 3.000
XYD C5 C4 C3 120.000 3.000
XYD H4 C4 C3 120.000 3.000
XYD C4 C3 H3 120.000 3.000
XYD C4 C3 C2 120.000 3.000
XYD H3 C3 C2 120.000 3.000
XYD C3 C2 C9 120.000 3.000
XYD C3 C2 C1 120.000 3.000
XYD C9 C2 C1 120.000 3.000
XYD C2 C9 H93 109.470 3.000
XYD C2 C9 H92 109.470 3.000
XYD C2 C9 H91 109.470 3.000
XYD H93 C9 H92 109.470 3.000
XYD H93 C9 H91 109.470 3.000
XYD H92 C9 H91 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
XYD CONST_1 H2N N C1 C6 -179.809 0.000 0
XYD CONST_2 N C1 C2 C3 180.000 0.000 0
XYD CONST_3 N C1 C6 C5 180.000 0.000 0
XYD CONST_4 C1 C6 C5 C4 0.000 0.000 0
XYD var_1 C6 C5 C8 H81 -90.178 20.000 1
XYD CONST_5 C6 C5 C4 C3 0.000 0.000 0
XYD CONST_6 C5 C4 C3 C2 0.000 0.000 0
XYD CONST_7 C4 C3 C2 C9 180.000 0.000 0
XYD var_2 C3 C2 C9 H91 90.039 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
XYD plan-1 C1 0.020
XYD plan-1 C2 0.020
XYD plan-1 C6 0.020
XYD plan-1 N 0.020
XYD plan-1 C3 0.020
XYD plan-1 C4 0.020
XYD plan-1 C5 0.020
XYD plan-1 C9 0.020
XYD plan-1 H3 0.020
XYD plan-1 H4 0.020
XYD plan-1 C8 0.020
XYD plan-1 H6 0.020
XYD plan-1 H1N 0.020
XYD plan-1 H2N 0.020
XYD plan-2 N 0.020
XYD plan-2 C1 0.020
XYD plan-2 H1N 0.020
XYD plan-2 H2N 0.020
# ------------------------------------------------------
|
