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
222
223
224
225
226
227
228
229
230
231
232
233
234
|
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
LEP LEP 'N~2~-phosphono-L-leucinamide ' non-polymer 28 13 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_LEP
#
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
LEP O3 O O 0.000 0.000 0.000 0.000
LEP P P P 0.000 -1.427 0.213 0.327
LEP O1 O OH1 0.000 -1.615 1.669 0.987
LEP HO1 H H 0.000 -1.151 1.893 1.806
LEP O2 O OH1 0.000 -1.912 -0.914 1.371
LEP HO2 H H 0.000 -2.826 -0.917 1.689
LEP N1 N NH1 0.000 -2.347 0.110 -1.077
LEP HN1 H H 0.000 -1.969 -0.071 -1.997
LEP CA C CH1 0.000 -3.773 0.317 -0.790
LEP HA H H 0.000 -3.879 0.899 0.136
LEP C C C 0.000 -4.451 -1.019 -0.625
LEP O O O 0.000 -3.809 -2.042 -0.735
LEP N N NH2 0.000 -5.771 -1.076 -0.360
LEP HNA H H 0.000 -6.311 -0.224 -0.270
LEP HN H H 0.000 -6.232 -1.971 -0.248
LEP CB C CH2 0.000 -4.422 1.078 -1.949
LEP HB H H 0.000 -5.500 1.141 -1.784
LEP HBA H H 0.000 -4.227 0.550 -2.885
LEP CG C CH1 0.000 -3.833 2.488 -2.024
LEP HG H H 0.000 -2.737 2.426 -2.083
LEP CD2 C CH3 0.000 -4.234 3.275 -0.775
LEP HD2B H H 0.000 -3.829 4.253 -0.827
LEP HD2A H H 0.000 -5.291 3.335 -0.718
LEP HD2 H H 0.000 -3.862 2.785 0.087
LEP CD1 C CH3 0.000 -4.371 3.198 -3.269
LEP HD1B H H 0.000 -4.024 2.702 -4.138
LEP HD1A H H 0.000 -5.431 3.183 -3.255
LEP HD1 H H 0.000 -4.034 4.202 -3.279
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
LEP O3 n/a P START
LEP P O3 N1 .
LEP O1 P HO1 .
LEP HO1 O1 . .
LEP O2 P HO2 .
LEP HO2 O2 . .
LEP N1 P CA .
LEP HN1 N1 . .
LEP CA N1 CB .
LEP HA CA . .
LEP C CA N .
LEP O C . .
LEP N C HN .
LEP HNA N . .
LEP HN N . .
LEP CB CA CG .
LEP HB CB . .
LEP HBA CB . .
LEP CG CB CD1 .
LEP HG CG . .
LEP CD2 CG HD2 .
LEP HD2B CD2 . .
LEP HD2A CD2 . .
LEP HD2 CD2 . .
LEP CD1 CG HD1 .
LEP HD1B CD1 . .
LEP HD1A CD1 . .
LEP HD1 CD1 . 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
LEP N C single 1.332 0.020
LEP O C double 1.220 0.020
LEP C CA single 1.500 0.020
LEP HN N single 1.010 0.020
LEP HNA N single 1.010 0.020
LEP P O3 double 1.480 0.020
LEP O2 P single 1.610 0.020
LEP O1 P single 1.610 0.020
LEP N1 P single 1.750 0.020
LEP CA N1 single 1.450 0.020
LEP HN1 N1 single 1.010 0.020
LEP HO1 O1 single 0.967 0.020
LEP HO2 O2 single 0.967 0.020
LEP CB CA single 1.524 0.020
LEP HA CA single 1.099 0.020
LEP CG CB single 1.524 0.020
LEP HB CB single 1.092 0.020
LEP HBA CB single 1.092 0.020
LEP CD1 CG single 1.524 0.020
LEP CD2 CG single 1.524 0.020
LEP HG CG single 1.099 0.020
LEP HD1 CD1 single 1.059 0.020
LEP HD1A CD1 single 1.059 0.020
LEP HD1B CD1 single 1.059 0.020
LEP HD2 CD2 single 1.059 0.020
LEP HD2A CD2 single 1.059 0.020
LEP HD2B CD2 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
LEP O3 P O1 109.500 3.000
LEP O3 P O2 109.500 3.000
LEP O3 P N1 109.500 3.000
LEP O1 P O2 109.500 3.000
LEP O1 P N1 109.500 3.000
LEP O2 P N1 109.500 3.000
LEP P O1 HO1 120.000 3.000
LEP P O2 HO2 120.000 3.000
LEP P N1 HN1 120.000 3.000
LEP P N1 CA 120.000 3.000
LEP HN1 N1 CA 118.500 3.000
LEP N1 CA HA 108.550 3.000
LEP N1 CA C 111.600 3.000
LEP N1 CA CB 110.000 3.000
LEP HA CA C 108.810 3.000
LEP HA CA CB 108.340 3.000
LEP C CA CB 109.470 3.000
LEP CA C O 120.500 3.000
LEP CA C N 120.000 3.000
LEP O C N 123.000 3.000
LEP C N HNA 120.000 3.000
LEP C N HN 120.000 3.000
LEP HNA N HN 120.000 3.000
LEP CA CB HB 109.470 3.000
LEP CA CB HBA 109.470 3.000
LEP CA CB CG 111.000 3.000
LEP HB CB HBA 107.900 3.000
LEP HB CB CG 109.470 3.000
LEP HBA CB CG 109.470 3.000
LEP CB CG HG 108.340 3.000
LEP CB CG CD2 111.000 3.000
LEP CB CG CD1 111.000 3.000
LEP HG CG CD2 108.340 3.000
LEP HG CG CD1 108.340 3.000
LEP CD2 CG CD1 111.000 3.000
LEP CG CD2 HD2B 109.470 3.000
LEP CG CD2 HD2A 109.470 3.000
LEP CG CD2 HD2 109.470 3.000
LEP HD2B CD2 HD2A 109.470 3.000
LEP HD2B CD2 HD2 109.470 3.000
LEP HD2A CD2 HD2 109.470 3.000
LEP CG CD1 HD1B 109.470 3.000
LEP CG CD1 HD1A 109.470 3.000
LEP CG CD1 HD1 109.470 3.000
LEP HD1B CD1 HD1A 109.470 3.000
LEP HD1B CD1 HD1 109.470 3.000
LEP HD1A CD1 HD1 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
LEP var_1 O3 P O1 HO1 -59.984 20.000 1
LEP var_2 O3 P O2 HO2 -179.992 20.000 1
LEP var_3 O3 P N1 CA -179.998 20.000 1
LEP var_4 P N1 CA CB 144.204 20.000 3
LEP var_5 N1 CA C N -179.724 20.000 3
LEP CONST_1 CA C N HN 180.000 0.000 0
LEP var_6 N1 CA CB CG -65.823 20.000 3
LEP var_7 CA CB CG CD1 174.068 20.000 3
LEP var_8 CB CG CD2 HD2 60.115 20.000 3
LEP var_9 CB CG CD1 HD1 175.029 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
LEP chir_01 CA C N1 CB negativ
LEP chir_02 CG CB CD1 CD2 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
LEP plan-1 C 0.020
LEP plan-1 N 0.020
LEP plan-1 O 0.020
LEP plan-1 CA 0.020
LEP plan-1 HNA 0.020
LEP plan-1 HN 0.020
LEP plan-2 N 0.020
LEP plan-2 C 0.020
LEP plan-2 HN 0.020
LEP plan-2 HNA 0.020
LEP plan-3 N1 0.020
LEP plan-3 P 0.020
LEP plan-3 CA 0.020
LEP plan-3 HN1 0.020
# ------------------------------------------------------
|
