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
|
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
AHD AHD '4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPH' non-polymer 23 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AHD
#
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
AHD O17 O OP 0.000 0.000 0.000 0.000
AHD P14 P P 0.000 -1.460 0.521 0.226
AHD O15 O OP -1.000 -1.665 0.861 1.741
AHD O16 O OP -1.000 -1.692 1.810 -0.634
AHD C8 C CT 0.000 -2.650 -0.765 -0.275
AHD P9 P P 0.000 -4.348 -0.158 -0.014
AHD O11 O OP 0.000 -4.594 0.059 1.519
AHD O10 O OP -1.000 -4.541 1.199 -0.771
AHD O12 O OP -1.000 -5.370 -1.212 -0.561
AHD O13 O OH1 0.000 -2.463 -1.075 -1.659
AHD H13 H H 0.000 -3.093 -1.758 -1.924
AHD C7 C CH2 0.000 -2.423 -2.024 0.564
AHD H71 H H 0.000 -3.136 -2.794 0.264
AHD H72 H H 0.000 -2.567 -1.788 1.620
AHD C2 C CH2 0.000 -0.997 -2.534 0.343
AHD H21 H H 0.000 -0.285 -1.762 0.642
AHD H22 H H 0.000 -0.854 -2.770 -0.714
AHD C3 C CH2 0.000 -0.770 -3.793 1.183
AHD H31 H H 0.000 -1.484 -4.563 0.884
AHD H32 H H 0.000 -0.914 -3.556 2.239
AHD N4 N NH2 0.000 0.600 -4.282 0.971
AHD HN42 H H 0.000 0.760 -5.171 0.512
AHD HN41 H H 0.000 1.393 -3.734 1.283
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
AHD O17 n/a P14 START
AHD P14 O17 C8 .
AHD O15 P14 . .
AHD O16 P14 . .
AHD C8 P14 C7 .
AHD P9 C8 O12 .
AHD O11 P9 . .
AHD O10 P9 . .
AHD O12 P9 . .
AHD O13 C8 H13 .
AHD H13 O13 . .
AHD C7 C8 C2 .
AHD H71 C7 . .
AHD H72 C7 . .
AHD C2 C7 C3 .
AHD H21 C2 . .
AHD H22 C2 . .
AHD C3 C2 N4 .
AHD H31 C3 . .
AHD H32 C3 . .
AHD N4 C3 HN41 .
AHD HN42 N4 . .
AHD HN41 N4 . 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
AHD C3 C2 single 1.524 0.020
AHD C2 C7 single 1.524 0.020
AHD H21 C2 single 1.092 0.020
AHD H22 C2 single 1.092 0.020
AHD N4 C3 single 1.450 0.020
AHD H31 C3 single 1.092 0.020
AHD H32 C3 single 1.092 0.020
AHD C7 C8 single 1.524 0.020
AHD H71 C7 single 1.092 0.020
AHD H72 C7 single 1.092 0.020
AHD P9 C8 single 1.812 0.020
AHD C8 P14 single 1.812 0.020
AHD O13 C8 single 1.432 0.020
AHD O12 P9 deloc 1.510 0.020
AHD O10 P9 deloc 1.510 0.020
AHD O11 P9 deloc 1.510 0.020
AHD O15 P14 deloc 1.510 0.020
AHD O16 P14 deloc 1.510 0.020
AHD P14 O17 deloc 1.510 0.020
AHD H13 O13 single 0.967 0.020
AHD HN41 N4 single 1.010 0.020
AHD HN42 N4 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
AHD O17 P14 O15 119.900 3.000
AHD O17 P14 O16 119.900 3.000
AHD O17 P14 C8 109.500 3.000
AHD O15 P14 O16 119.900 3.000
AHD O15 P14 C8 109.500 3.000
AHD O16 P14 C8 109.500 3.000
AHD P14 C8 P9 109.500 3.000
AHD P14 C8 O13 109.500 3.000
AHD P14 C8 C7 109.500 3.000
AHD P9 C8 O13 109.500 3.000
AHD P9 C8 C7 109.500 3.000
AHD O13 C8 C7 109.470 3.000
AHD C8 P9 O11 109.500 3.000
AHD C8 P9 O10 109.500 3.000
AHD C8 P9 O12 109.500 3.000
AHD O11 P9 O10 119.900 3.000
AHD O11 P9 O12 119.900 3.000
AHD O10 P9 O12 119.900 3.000
AHD C8 O13 H13 109.470 3.000
AHD C8 C7 H71 109.470 3.000
AHD C8 C7 H72 109.470 3.000
AHD C8 C7 C2 111.000 3.000
AHD H71 C7 H72 107.900 3.000
AHD H71 C7 C2 109.470 3.000
AHD H72 C7 C2 109.470 3.000
AHD C7 C2 H21 109.470 3.000
AHD C7 C2 H22 109.470 3.000
AHD C7 C2 C3 111.000 3.000
AHD H21 C2 H22 107.900 3.000
AHD H21 C2 C3 109.470 3.000
AHD H22 C2 C3 109.470 3.000
AHD C2 C3 H31 109.470 3.000
AHD C2 C3 H32 109.470 3.000
AHD C2 C3 N4 109.470 3.000
AHD H31 C3 H32 107.900 3.000
AHD H31 C3 N4 109.470 3.000
AHD H32 C3 N4 109.470 3.000
AHD C3 N4 HN42 120.000 3.000
AHD C3 N4 HN41 120.000 3.000
AHD HN42 N4 HN41 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
AHD var_1 O17 P14 C8 C7 60.012 20.000 1
AHD var_2 P14 C8 P9 O12 175.026 20.000 1
AHD var_3 P14 C8 O13 H13 179.951 20.000 1
AHD var_4 P14 C8 C7 C2 -60.005 20.000 1
AHD var_5 C8 C7 C2 C3 179.969 20.000 3
AHD var_6 C7 C2 C3 N4 -179.999 20.000 3
AHD var_7 C2 C3 N4 HN41 66.235 20.000 1
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
AHD chir_01 C8 C7 P9 P14 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
AHD plan-1 N4 0.020
AHD plan-1 C3 0.000
AHD plan-1 HN41 0.000
AHD plan-1 HN42 0.000
# ------------------------------------------------------
|
