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
|
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
DNE DNE 'D-NORLEUCINE ' peptide 21 9 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DNE
#
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
DNE N N NH2 0.000 0.000 0.000 0.000
DNE HN1 H H 0.000 0.155 -0.012 0.997
DNE HN2 H H 0.000 0.572 -0.564 -0.610
DNE CA C CH1 0.000 -1.045 0.827 -0.555
DNE HA H H 0.000 -1.740 0.200 -1.131
DNE CB C CH2 0.000 -0.456 1.903 -1.467
DNE HB2 H H 0.000 0.081 1.399 -2.274
DNE HB3 H H 0.000 0.247 2.493 -0.876
DNE CG C CH2 0.000 -1.526 2.823 -2.061
DNE HG2 H H 0.000 -2.045 3.326 -1.241
DNE HG3 H H 0.000 -2.238 2.213 -2.620
DNE CD C CH2 0.000 -0.906 3.868 -2.990
DNE HD2 H H 0.000 -0.406 3.347 -3.809
DNE HD3 H H 0.000 -0.171 4.441 -2.422
DNE CE C CH3 0.000 -1.959 4.808 -3.553
DNE HE3 H H 0.000 -2.448 5.310 -2.758
DNE HE2 H H 0.000 -1.497 5.520 -4.187
DNE HE1 H H 0.000 -2.671 4.253 -4.108
DNE C C C 0.000 -1.771 1.425 0.633
DNE O O OC -0.500 -1.226 1.778 1.703
DNE OXT O OC -0.500 -3.006 1.502 0.446
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
DNE N n/a CA START
DNE HN1 N . .
DNE HN2 N . .
DNE CA N C .
DNE HA CA . .
DNE CB CA CG .
DNE HB2 CB . .
DNE HB3 CB . .
DNE CG CB CD .
DNE HG2 CG . .
DNE HG3 CG . .
DNE CD CG CE .
DNE HD2 CD . .
DNE HD3 CD . .
DNE CE CD HE1 .
DNE HE3 CE . .
DNE HE2 CE . .
DNE HE1 CE . .
DNE C CA . END
DNE O C . .
DNE 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
DNE CA N single 1.450 0.020
DNE C CA single 1.500 0.020
DNE CB CA single 1.524 0.020
DNE HA CA single 1.099 0.020
DNE O C deloc 1.250 0.020
DNE OXT C deloc 1.250 0.020
DNE CG CB single 1.524 0.020
DNE HB2 CB single 1.092 0.020
DNE HB3 CB single 1.092 0.020
DNE CD CG single 1.524 0.020
DNE HG2 CG single 1.092 0.020
DNE HG3 CG single 1.092 0.020
DNE CE CD single 1.513 0.020
DNE HD2 CD single 1.092 0.020
DNE HD3 CD single 1.092 0.020
DNE HE1 CE single 1.059 0.020
DNE HE2 CE single 1.059 0.020
DNE HE3 CE single 1.059 0.020
DNE HN1 N single 1.010 0.020
DNE HN2 N 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
DNE HN1 N HN2 120.000 3.000
DNE HN1 N CA 120.000 3.000
DNE HN2 N CA 120.000 3.000
DNE N CA HA 109.470 3.000
DNE N CA CB 109.470 3.000
DNE N CA C 109.470 3.000
DNE HA CA CB 108.340 3.000
DNE HA CA C 108.810 3.000
DNE CB CA C 109.470 3.000
DNE CA CB HB2 109.470 3.000
DNE CA CB HB3 109.470 3.000
DNE CA CB CG 111.000 3.000
DNE HB2 CB HB3 107.900 3.000
DNE HB2 CB CG 109.470 3.000
DNE HB3 CB CG 109.470 3.000
DNE CB CG HG2 109.470 3.000
DNE CB CG HG3 109.470 3.000
DNE CB CG CD 111.000 3.000
DNE HG2 CG HG3 107.900 3.000
DNE HG2 CG CD 109.470 3.000
DNE HG3 CG CD 109.470 3.000
DNE CG CD HD2 109.470 3.000
DNE CG CD HD3 109.470 3.000
DNE CG CD CE 111.000 3.000
DNE HD2 CD HD3 107.900 3.000
DNE HD2 CD CE 109.470 3.000
DNE HD3 CD CE 109.470 3.000
DNE CD CE HE3 109.470 3.000
DNE CD CE HE2 109.470 3.000
DNE CD CE HE1 109.470 3.000
DNE HE3 CE HE2 109.470 3.000
DNE HE3 CE HE1 109.470 3.000
DNE HE2 CE HE1 109.470 3.000
DNE CA C O 118.500 3.000
DNE CA C OXT 118.500 3.000
DNE 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
DNE var_1 HN2 N CA C 175.000 20.000 1
DNE var_2 N CA CB CG -178.921 20.000 3
DNE var_3 CA CB CG CD -178.791 20.000 3
DNE var_4 CB CG CD CE -178.476 20.000 3
DNE var_5 CG CD CE HE1 -60.300 20.000 3
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
DNE chir_01 CA N C 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
DNE plan-1 N 0.020
DNE plan-1 CA 0.020
DNE plan-1 HN1 0.020
DNE plan-1 HN2 0.020
DNE plan-2 C 0.020
DNE plan-2 CA 0.020
DNE plan-2 O 0.020
DNE plan-2 OXT 0.020
# ------------------------------------------------------
|
