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
|
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
X04 X04 '(2-AMINO-4-FORMYL-5-HYDROXY-6-METHYL' non-polymer 26 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_X04
#
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
X04 O1 O O 0.000 0.000 0.000 0.000
X04 C4A C C1 0.000 -1.191 0.229 -0.020
X04 H4A H H 0.000 -1.705 0.487 0.890
X04 C4 C CR6 0.000 -1.933 0.154 -1.288
X04 C5 C CR6 0.000 -3.307 0.414 -1.334
X04 C5A C CH2 0.000 -4.059 0.779 -0.082
X04 H5A1 H H 0.000 -4.896 1.431 -0.338
X04 H5A2 H H 0.000 -3.389 1.301 0.605
X04 OP4 O O2 0.000 -4.551 -0.409 0.541
X04 P P P 0.000 -5.341 0.054 1.865
X04 OP3 O OP -0.666 -4.392 0.788 2.787
X04 OP2 O OP -0.666 -5.890 -1.164 2.576
X04 OP1 O OP -0.666 -6.482 0.970 1.480
X04 C3 C CR6 0.000 -1.282 -0.188 -2.489
X04 O3 O OH1 0.000 0.050 -0.451 -2.500
X04 HO3 H H 0.000 0.192 -1.395 -2.345
X04 C2 C CR6 0.000 -2.020 -0.242 -3.661
X04 C2A C CH3 0.000 -1.335 -0.602 -4.954
X04 H2A3 H H 0.000 -0.516 -1.243 -4.754
X04 H2A2 H H 0.000 -2.022 -1.095 -5.592
X04 H2A1 H H 0.000 -0.985 0.280 -5.426
X04 N1 N NRD6 0.000 -3.313 0.011 -3.659
X04 C6 C CR6 0.000 -3.966 0.331 -2.554
X04 N2 N NH2 0.000 -5.334 0.588 -2.614
X04 HN22 H H 0.000 -5.853 0.835 -1.775
X04 HN21 H H 0.000 -5.834 0.532 -3.498
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
X04 O1 n/a C4A START
X04 C4A O1 C4 .
X04 H4A C4A . .
X04 C4 C4A C3 .
X04 C5 C4 C5A .
X04 C5A C5 OP4 .
X04 H5A1 C5A . .
X04 H5A2 C5A . .
X04 OP4 C5A P .
X04 P OP4 OP1 .
X04 OP3 P . .
X04 OP2 P . .
X04 OP1 P . .
X04 C3 C4 C2 .
X04 O3 C3 HO3 .
X04 HO3 O3 . .
X04 C2 C3 N1 .
X04 C2A C2 H2A1 .
X04 H2A3 C2A . .
X04 H2A2 C2A . .
X04 H2A1 C2A . .
X04 N1 C2 C6 .
X04 C6 N1 N2 .
X04 N2 C6 HN21 .
X04 HN22 N2 . .
X04 HN21 N2 . END
X04 C5 C6 . ADD
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
X04 OP1 P deloc 1.510 0.020
X04 OP2 P deloc 1.510 0.020
X04 OP3 P deloc 1.510 0.020
X04 P OP4 single 1.610 0.020
X04 OP4 C5A single 1.426 0.020
X04 C5A C5 single 1.511 0.020
X04 H5A1 C5A single 1.092 0.020
X04 H5A2 C5A single 1.092 0.020
X04 C5 C6 double 1.487 0.020
X04 C5 C4 single 1.487 0.020
X04 N2 C6 single 1.355 0.020
X04 C6 N1 single 1.350 0.020
X04 HN21 N2 single 1.010 0.020
X04 HN22 N2 single 1.010 0.020
X04 N1 C2 double 1.350 0.020
X04 C2A C2 single 1.506 0.020
X04 C2 C3 single 1.487 0.020
X04 H2A1 C2A single 1.059 0.020
X04 H2A2 C2A single 1.059 0.020
X04 H2A3 C2A single 1.059 0.020
X04 O3 C3 single 1.362 0.020
X04 C3 C4 double 1.487 0.020
X04 HO3 O3 single 0.967 0.020
X04 C4 C4A single 1.480 0.020
X04 C4A O1 double 1.220 0.020
X04 H4A C4A single 1.077 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
X04 O1 C4A H4A 123.000 3.000
X04 O1 C4A C4 120.000 3.000
X04 H4A C4A C4 120.000 3.000
X04 C4A C4 C5 120.000 3.000
X04 C4A C4 C3 120.000 3.000
X04 C5 C4 C3 120.000 3.000
X04 C4 C5 C5A 120.000 3.000
X04 C4 C5 C6 120.000 3.000
X04 C5A C5 C6 120.000 3.000
X04 C5 C5A H5A1 109.470 3.000
X04 C5 C5A H5A2 109.470 3.000
X04 C5 C5A OP4 109.470 3.000
X04 H5A1 C5A H5A2 107.900 3.000
X04 H5A1 C5A OP4 109.470 3.000
X04 H5A2 C5A OP4 109.470 3.000
X04 C5A OP4 P 120.500 3.000
X04 OP4 P OP3 108.200 3.000
X04 OP4 P OP2 108.200 3.000
X04 OP4 P OP1 108.200 3.000
X04 OP3 P OP2 119.900 3.000
X04 OP3 P OP1 119.900 3.000
X04 OP2 P OP1 119.900 3.000
X04 C4 C3 O3 120.000 3.000
X04 C4 C3 C2 120.000 3.000
X04 O3 C3 C2 120.000 3.000
X04 C3 O3 HO3 109.470 3.000
X04 C3 C2 C2A 120.000 3.000
X04 C3 C2 N1 120.000 3.000
X04 C2A C2 N1 120.000 3.000
X04 C2 C2A H2A3 109.470 3.000
X04 C2 C2A H2A2 109.470 3.000
X04 C2 C2A H2A1 109.470 3.000
X04 H2A3 C2A H2A2 109.470 3.000
X04 H2A3 C2A H2A1 109.470 3.000
X04 H2A2 C2A H2A1 109.470 3.000
X04 C2 N1 C6 120.000 3.000
X04 N1 C6 N2 120.000 3.000
X04 N1 C6 C5 120.000 3.000
X04 N2 C6 C5 120.000 3.000
X04 C6 N2 HN22 120.000 3.000
X04 C6 N2 HN21 120.000 3.000
X04 HN22 N2 HN21 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
X04 var_1 O1 C4A C4 C3 0.298 20.000 1
X04 CONST_1 C4A C4 C5 C5A 0.000 0.000 0
X04 CONST_2 C4 C5 C6 N1 0.000 0.000 0
X04 var_2 C4 C5 C5A OP4 -90.024 20.000 2
X04 var_3 C5 C5A OP4 P -179.955 20.000 1
X04 var_4 C5A OP4 P OP1 60.004 20.000 1
X04 CONST_3 C4A C4 C3 C2 180.000 0.000 0
X04 var_5 C4 C3 O3 HO3 89.960 20.000 1
X04 CONST_4 C4 C3 C2 N1 0.000 0.000 0
X04 var_6 C3 C2 C2A H2A1 -90.279 20.000 1
X04 CONST_5 C3 C2 N1 C6 0.000 0.000 0
X04 CONST_6 C2 N1 C6 N2 180.000 0.000 0
X04 CONST_7 N1 C6 N2 HN21 -0.050 0.000 0
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
X04 plan-1 C5 0.020
X04 plan-1 C5A 0.020
X04 plan-1 C6 0.020
X04 plan-1 C4 0.020
X04 plan-1 N1 0.020
X04 plan-1 C2 0.020
X04 plan-1 C3 0.020
X04 plan-1 N2 0.020
X04 plan-1 C2A 0.020
X04 plan-1 O3 0.020
X04 plan-1 C4A 0.020
X04 plan-1 HN22 0.020
X04 plan-1 HN21 0.020
X04 plan-1 H4A 0.020
X04 plan-2 N2 0.020
X04 plan-2 C6 0.020
X04 plan-2 HN21 0.020
X04 plan-2 HN22 0.020
X04 plan-3 C4A 0.020
X04 plan-3 C4 0.020
X04 plan-3 O1 0.020
X04 plan-3 H4A 0.020
# ------------------------------------------------------
|
