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
|
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
CXM CXM 'N-CARBOXYMETHIONINE ' M-peptide 22 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CXM
#
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
CXM OXT O OC -0.500 0.000 0.000 0.000
CXM C C C 0.000 -0.974 -0.779 -0.098
CXM O O OC -0.500 -0.897 -1.786 -0.836
CXM CA C CH1 0.000 -2.240 -0.503 0.672
CXM HA H H 0.000 -2.737 -1.454 0.911
CXM N N NH1 0.000 -1.913 0.202 1.913
CXM H H H 0.000 -1.885 1.211 1.928
CXM CN C C 0.000 -1.648 -0.496 3.035
CXM ON2 O OH1 0.000 -1.347 0.152 4.176
CXM HO2 H H 0.000 -1.186 -0.490 4.882
CXM ON1 O O 0.000 -1.682 -1.710 3.017
CXM CB C CH2 0.000 -3.174 0.361 -0.175
CXM HB2 H H 0.000 -3.417 -0.165 -1.100
CXM HB3 H H 0.000 -2.679 1.305 -0.414
CXM CG C CH2 0.000 -4.458 0.641 0.606
CXM HG2 H H 0.000 -4.213 1.166 1.532
CXM HG3 H H 0.000 -4.951 -0.304 0.845
CXM SD S S2 0.000 -5.567 1.667 -0.397
CXM CE C CH3 0.000 -6.965 1.835 0.746
CXM HE3 H H 0.000 -7.362 0.877 0.978
CXM HE2 H H 0.000 -6.646 2.303 1.644
CXM HE1 H H 0.000 -7.729 2.425 0.302
#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
# CXM OXT n/a C START
# CXM C OXT CA .
# CXM O C . .
# CXM CA C CB .
# CXM HA CA . .
# CXM N CA CN .
# CXM H N . .
# CXM CN N ON1 .
# CXM ON2 CN HO2 .
## CXM HO2 ON2 . .
# CXM ON1 CN . .
# CXM CB CA CG .
# CXM HB2 CB . .
# CXM HB3 CB . .
# CXM CG CB SD .
# CXM HG2 CG . .
# CXM HG3 CG . .
# CXM SD CG CE .
# CXM CE SD HE1 .
# CXM HE3 CE . .
# CXM HE2 CE . .
# CXM HE1 CE . 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
CXM N CA single 1.450 0.020
CXM CN N single 1.330 0.020
CXM H N single 1.010 0.020
CXM CB CA single 1.524 0.020
CXM CA C single 1.500 0.020
CXM HA CA single 1.099 0.020
CXM CG CB single 1.524 0.020
CXM HB2 CB single 1.092 0.020
CXM HB3 CB single 1.092 0.020
CXM SD CG single 1.762 0.020
CXM HG2 CG single 1.092 0.020
CXM HG3 CG single 1.092 0.020
CXM CE SD single 1.762 0.020
CXM HE1 CE single 1.059 0.020
CXM HE2 CE single 1.059 0.020
CXM HE3 CE single 1.059 0.020
CXM O C deloc 1.250 0.020
CXM C OXT deloc 1.250 0.020
CXM ON1 CN double 1.220 0.020
CXM ON2 CN single 1.330 0.020
CXM HO2 ON2 single 0.967 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
CXM OXT C O 123.000 3.000
CXM OXT C CA 118.500 3.000
CXM O C CA 118.500 3.000
CXM C CA HA 108.810 3.000
CXM C CA N 111.600 3.000
CXM C CA CB 109.470 3.000
CXM HA CA N 108.550 3.000
CXM HA CA CB 108.340 3.000
CXM N CA CB 110.000 3.000
CXM CA N H 118.500 3.000
CXM CA N CN 121.500 3.000
CXM H N CN 120.000 3.000
CXM N CN ON2 120.000 3.000
CXM N CN ON1 123.000 3.000
CXM ON2 CN ON1 119.000 3.000
CXM CN ON2 HO2 109.470 3.000
CXM CA CB HB2 109.470 3.000
CXM CA CB HB3 109.470 3.000
CXM CA CB CG 111.000 3.000
CXM HB2 CB HB3 107.900 3.000
CXM HB2 CB CG 109.470 3.000
CXM HB3 CB CG 109.470 3.000
CXM CB CG HG2 109.470 3.000
CXM CB CG HG3 109.470 3.000
CXM CB CG SD 109.500 3.000
CXM HG2 CG HG3 107.900 3.000
CXM HG2 CG SD 109.500 3.000
CXM HG3 CG SD 109.500 3.000
CXM CG SD CE 100.087 3.000
CXM SD CE HE3 109.500 3.000
CXM SD CE HE2 109.500 3.000
CXM SD CE HE1 109.500 3.000
CXM HE3 CE HE2 109.470 3.000
CXM HE3 CE HE1 109.470 3.000
CXM HE2 CE HE1 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
CXM var_1 OXT C CA CB 90.029 20.000 3
CXM var_2 C CA N CN -89.947 20.000 3
CXM CONST_1 CA N CN ON1 0.000 0.000 0
CXM var_3 N CN ON2 HO2 179.964 20.000 1
CXM var_4 C CA CB CG -179.994 20.000 3
CXM var_5 CA CB CG SD 179.976 20.000 3
CXM var_6 CB CG SD CE 179.995 20.000 1
CXM var_7 CG SD CE HE1 -179.976 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
CXM chir_01 CA N CB C 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
CXM plan-1 N 0.020
CXM plan-1 CA 0.020
CXM plan-1 CN 0.020
CXM plan-1 H 0.020
CXM plan-2 C 0.020
CXM plan-2 CA 0.020
CXM plan-2 O 0.020
CXM plan-2 OXT 0.020
CXM plan-3 CN 0.020
CXM plan-3 N 0.020
CXM plan-3 ON1 0.020
CXM plan-3 ON2 0.020
CXM plan-3 H 0.020
# ------------------------------------------------------
|
