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
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
|
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
LYM LYM 'DEOXY-METHYL-LYSINE ' non-polymer 26 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_LYM
#
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
LYM O O O 0.000 0.000 0.000 0.000
LYM C C C 0.000 -0.654 -0.791 -0.636
LYM CM C CH3 0.000 0.006 -1.629 -1.700
LYM HM3 H H 0.000 -0.107 -2.656 -1.465
LYM HM2 H H 0.000 -0.445 -1.431 -2.638
LYM HM1 H H 0.000 1.038 -1.392 -1.749
LYM CA C CH1 0.000 -2.129 -0.939 -0.368
LYM HA H H 0.000 -2.440 -1.969 -0.589
LYM N N NH2 0.000 -2.402 -0.637 1.044
LYM H2 H H 0.000 -1.638 -0.469 1.689
LYM H H H 0.000 -3.356 -0.595 1.384
LYM CB C CH2 0.000 -2.910 0.031 -1.255
LYM HB2 H H 0.000 -2.706 -0.192 -2.304
LYM HB3 H H 0.000 -2.599 1.055 -1.035
LYM CG C CH2 0.000 -4.407 -0.119 -0.983
LYM HG2 H H 0.000 -4.608 0.104 0.067
LYM HG3 H H 0.000 -4.714 -1.143 -1.202
LYM CD C CH2 0.000 -5.188 0.852 -1.870
LYM HD2 H H 0.000 -4.983 0.628 -2.919
LYM HD3 H H 0.000 -4.877 1.875 -1.650
LYM CE C CH2 0.000 -6.685 0.702 -1.598
LYM HE2 H H 0.000 -6.887 0.924 -0.548
LYM HE3 H H 0.000 -6.993 -0.322 -1.818
LYM NZ N NH2 0.000 -7.435 1.634 -2.449
LYM HZ2 H H 0.000 -6.946 2.247 -3.091
LYM HZ1 H H 0.000 -8.446 1.671 -2.400
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
LYM O n/a C START
LYM C O CA .
LYM CM C HM1 .
LYM HM3 CM . .
LYM HM2 CM . .
LYM HM1 CM . .
LYM CA C CB .
LYM HA CA . .
LYM N CA H .
LYM H2 N . .
LYM H N . .
LYM CB CA CG .
LYM HB2 CB . .
LYM HB3 CB . .
LYM CG CB CD .
LYM HG2 CG . .
LYM HG3 CG . .
LYM CD CG CE .
LYM HD2 CD . .
LYM HD3 CD . .
LYM CE CD NZ .
LYM HE2 CE . .
LYM HE3 CE . .
LYM NZ CE HZ1 .
LYM HZ2 NZ . .
LYM HZ1 NZ . 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
LYM N CA single 1.450 0.020
LYM H N single 1.010 0.020
LYM H2 N single 1.010 0.020
LYM CA C single 1.500 0.020
LYM CB CA single 1.524 0.020
LYM HA CA single 1.099 0.020
LYM C O double 1.220 0.020
LYM CM C single 1.500 0.020
LYM CG CB single 1.524 0.020
LYM HB2 CB single 1.092 0.020
LYM HB3 CB single 1.092 0.020
LYM CD CG single 1.524 0.020
LYM HG2 CG single 1.092 0.020
LYM HG3 CG single 1.092 0.020
LYM CE CD single 1.524 0.020
LYM HD2 CD single 1.092 0.020
LYM HD3 CD single 1.092 0.020
LYM NZ CE single 1.450 0.020
LYM HE2 CE single 1.092 0.020
LYM HE3 CE single 1.092 0.020
LYM HZ1 NZ single 1.010 0.020
LYM HZ2 NZ single 1.010 0.020
LYM HM1 CM single 1.059 0.020
LYM HM2 CM single 1.059 0.020
LYM HM3 CM 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
LYM O C CM 123.000 3.000
LYM O C CA 120.500 3.000
LYM CM C CA 120.000 3.000
LYM C CM HM3 109.470 3.000
LYM C CM HM2 109.470 3.000
LYM C CM HM1 109.470 3.000
LYM HM3 CM HM2 109.470 3.000
LYM HM3 CM HM1 109.470 3.000
LYM HM2 CM HM1 109.470 3.000
LYM C CA HA 108.810 3.000
LYM C CA N 109.470 3.000
LYM C CA CB 109.470 3.000
LYM HA CA N 109.470 3.000
LYM HA CA CB 108.340 3.000
LYM N CA CB 109.470 3.000
LYM CA N H2 120.000 3.000
LYM CA N H 120.000 3.000
LYM H2 N H 120.000 3.000
LYM CA CB HB2 109.470 3.000
LYM CA CB HB3 109.470 3.000
LYM CA CB CG 111.000 3.000
LYM HB2 CB HB3 107.900 3.000
LYM HB2 CB CG 109.470 3.000
LYM HB3 CB CG 109.470 3.000
LYM CB CG HG2 109.470 3.000
LYM CB CG HG3 109.470 3.000
LYM CB CG CD 111.000 3.000
LYM HG2 CG HG3 107.900 3.000
LYM HG2 CG CD 109.470 3.000
LYM HG3 CG CD 109.470 3.000
LYM CG CD HD2 109.470 3.000
LYM CG CD HD3 109.470 3.000
LYM CG CD CE 111.000 3.000
LYM HD2 CD HD3 107.900 3.000
LYM HD2 CD CE 109.470 3.000
LYM HD3 CD CE 109.470 3.000
LYM CD CE HE2 109.470 3.000
LYM CD CE HE3 109.470 3.000
LYM CD CE NZ 109.470 3.000
LYM HE2 CE HE3 107.900 3.000
LYM HE2 CE NZ 109.470 3.000
LYM HE3 CE NZ 109.470 3.000
LYM CE NZ HZ2 120.000 3.000
LYM CE NZ HZ1 120.000 3.000
LYM HZ2 NZ HZ1 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
LYM var_1 O C CM HM1 0.069 20.000 1
LYM var_2 O C CA CB 89.921 20.000 3
LYM var_3 C CA N H 173.854 20.000 1
LYM var_4 C CA CB CG -179.988 20.000 3
LYM var_5 CA CB CG CD 180.000 20.000 3
LYM var_6 CB CG CD CE 180.000 20.000 3
LYM var_7 CG CD CE NZ 179.970 20.000 3
LYM var_8 CD CE NZ HZ1 -179.992 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
LYM chir_01 CA N C CB positiv
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
LYM plan-1 N 0.020
LYM plan-1 CA 0.020
LYM plan-1 H 0.020
LYM plan-1 H2 0.020
LYM plan-2 C 0.020
LYM plan-2 CA 0.020
LYM plan-2 O 0.020
LYM plan-2 CM 0.020
LYM plan-3 NZ 0.020
LYM plan-3 CE 0.020
LYM plan-3 HZ1 0.020
LYM plan-3 HZ2 0.020
# ------------------------------------------------------
|
