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
|
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
DON DON '6-DIAZENYL-5-OXO-L-NORLEUCINE ' peptide 22 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DON
#
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
DON N N NH2 0.000 0.000 0.000 0.000
DON HN1 H H 0.000 0.456 0.322 -0.845
DON HN2 H H 0.000 -0.559 -0.844 -0.027
DON CA C CH1 0.000 0.149 0.748 1.251
DON HA H H 0.000 -0.820 1.171 1.551
DON CB C CH2 0.000 0.667 -0.193 2.347
DON HB2 H H 0.000 0.853 0.420 3.232
DON HB3 H H 0.000 1.611 -0.609 1.989
DON C1E C CH2 0.000 -0.290 -1.330 2.704
DON H1E1 H H 0.000 -0.436 -1.932 1.805
DON H1E2 H H 0.000 -1.240 -0.880 2.998
DON C1D C C 0.000 0.224 -2.212 3.827
DON C1C C CH2 0.000 -0.617 -3.416 4.191
DON H1C1 H H 0.000 -0.707 -4.082 3.330
DON H1C2 H H 0.000 -1.611 -3.095 4.508
DON N1B N N 0.000 0.043 -4.122 5.288
DON N1A N N 0.000 -0.604 -5.125 5.644
DON HN1A H H 0.000 -0.282 -5.676 6.354
DON O1J O O 0.000 1.282 -1.946 4.398
DON C C C 0.000 1.136 1.867 0.974
DON O O OC -0.500 1.741 2.039 -0.107
DON OXT O OC -0.500 1.270 2.636 1.951
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
DON N n/a CA START
DON HN1 N . .
DON HN2 N . .
DON CA N C .
DON HA CA . .
DON CB CA C1E .
DON HB2 CB . .
DON HB3 CB . .
DON C1E CB C1D .
DON H1E1 C1E . .
DON H1E2 C1E . .
DON C1D C1E O1J .
DON C1C C1D N1B .
DON H1C1 C1C . .
DON H1C2 C1C . .
DON N1B C1C N1A .
DON N1A N1B HN1A .
DON HN1A N1A . .
DON O1J C1D . .
DON C CA . END
DON O C . .
DON OXT C . .
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
DON O C deloc 1.250 0.020
DON OXT C deloc 1.250 0.020
DON C CA single 1.500 0.020
DON CA N single 1.450 0.020
DON CB CA single 1.524 0.020
DON HA CA single 1.099 0.020
DON C1E CB single 1.524 0.020
DON HB2 CB single 1.092 0.020
DON HB3 CB single 1.092 0.020
DON C1D C1E single 1.510 0.020
DON H1E1 C1E single 1.092 0.020
DON H1E2 C1E single 1.092 0.020
DON O1J C1D double 1.220 0.020
DON C1C C1D single 1.510 0.020
DON N1B C1C single 1.455 0.020
DON H1C1 C1C single 1.092 0.020
DON H1C2 C1C single 1.092 0.020
DON N1A N1B double 1.240 0.020
DON HN1 N single 1.010 0.020
DON HN2 N single 1.010 0.020
DON HN1A N1A single 0.954 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
DON HN1 N HN2 120.000 3.000
DON HN1 N CA 120.000 3.000
DON HN2 N CA 120.000 3.000
DON N CA HA 109.470 3.000
DON N CA CB 109.470 3.000
DON N CA C 109.470 3.000
DON HA CA CB 108.340 3.000
DON HA CA C 108.810 3.000
DON CB CA C 109.470 3.000
DON CA CB HB2 109.470 3.000
DON CA CB HB3 109.470 3.000
DON CA CB C1E 111.000 3.000
DON HB2 CB HB3 107.900 3.000
DON HB2 CB C1E 109.470 3.000
DON HB3 CB C1E 109.470 3.000
DON CB C1E H1E1 109.470 3.000
DON CB C1E H1E2 109.470 3.000
DON CB C1E C1D 109.470 3.000
DON H1E1 C1E H1E2 107.900 3.000
DON H1E1 C1E C1D 109.470 3.000
DON H1E2 C1E C1D 109.470 3.000
DON C1E C1D C1C 120.000 3.000
DON C1E C1D O1J 120.500 3.000
DON C1C C1D O1J 120.500 3.000
DON C1D C1C H1C1 109.470 3.000
DON C1D C1C H1C2 109.470 3.000
DON C1D C1C N1B 109.500 3.000
DON H1C1 C1C H1C2 107.900 3.000
DON H1C1 C1C N1B 109.470 3.000
DON H1C2 C1C N1B 109.470 3.000
DON C1C N1B N1A 120.000 3.000
DON N1B N1A HN1A 120.000 3.000
DON CA C O 118.500 3.000
DON CA C OXT 118.500 3.000
DON O C OXT 123.000 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
DON var_1 HN2 N CA C 175.000 20.000 1
DON var_2 N CA CB C1E -63.773 20.000 3
DON var_3 CA CB C1E C1D -177.729 20.000 3
DON var_4 CB C1E C1D O1J 3.355 20.000 3
DON var_5 C1E C1D C1C N1B -179.720 20.000 3
DON var_6 C1D C1C N1B N1A 179.611 20.000 1
DON CONST_1 C1C N1B N1A HN1A 180.000 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
DON chir_01 CA C N CB 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
DON plan-1 C 0.020
DON plan-1 O 0.020
DON plan-1 OXT 0.020
DON plan-1 CA 0.020
DON plan-2 N 0.020
DON plan-2 CA 0.020
DON plan-2 HN1 0.020
DON plan-2 HN2 0.020
DON plan-3 C1D 0.020
DON plan-3 C1E 0.020
DON plan-3 O1J 0.020
DON plan-3 C1C 0.020
DON plan-4 N1B 0.020
DON plan-4 C1C 0.020
DON plan-4 N1A 0.020
DON plan-4 HN1A 0.020
# ------------------------------------------------------
|
