moorhen 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (106) hide show
  1. package/baby-gru/CootWorker.js +1071 -0
  2. package/baby-gru/darkly.css +12 -0
  3. package/baby-gru/flatly.css +12 -0
  4. package/baby-gru/keyboard-blank.svg +3126 -0
  5. package/baby-gru/monomers/a/A.cif +271 -0
  6. package/baby-gru/monomers/a/ALA.cif +164 -0
  7. package/baby-gru/monomers/a/ARG.cif +252 -0
  8. package/baby-gru/monomers/a/ASN.cif +192 -0
  9. package/baby-gru/monomers/a/ASP.cif +178 -0
  10. package/baby-gru/monomers/c/C.cif +255 -0
  11. package/baby-gru/monomers/c/CIT.cif +167 -0
  12. package/baby-gru/monomers/c/CYS.cif +169 -0
  13. package/baby-gru/monomers/d/DA.cif +266 -0
  14. package/baby-gru/monomers/d/DC.cif +250 -0
  15. package/baby-gru/monomers/d/DG.cif +271 -0
  16. package/baby-gru/monomers/d/DT.cif +256 -0
  17. package/baby-gru/monomers/e/EDO.cif +108 -0
  18. package/baby-gru/monomers/g/G.cif +276 -0
  19. package/baby-gru/monomers/g/GLN.cif +208 -0
  20. package/baby-gru/monomers/g/GLU.cif +194 -0
  21. package/baby-gru/monomers/g/GLY.cif +138 -0
  22. package/baby-gru/monomers/g/GOL.cif +134 -0
  23. package/baby-gru/monomers/h/HIS.cif +215 -0
  24. package/baby-gru/monomers/h/HOH.cif +55 -0
  25. package/baby-gru/monomers/i/ILE.cif +213 -0
  26. package/baby-gru/monomers/l/LEU.cif +213 -0
  27. package/baby-gru/monomers/l/LYS.cif +228 -0
  28. package/baby-gru/monomers/m/MET.cif +201 -0
  29. package/baby-gru/monomers/m/MSE.cif +201 -0
  30. package/baby-gru/monomers/n/NA.cif +30 -0
  31. package/baby-gru/monomers/p/PHE.cif +233 -0
  32. package/baby-gru/monomers/p/PO4.cif +86 -0
  33. package/baby-gru/monomers/p/PRO.cif +188 -0
  34. package/baby-gru/monomers/s/SER.cif +169 -0
  35. package/baby-gru/monomers/s/SO4.cif +86 -0
  36. package/baby-gru/monomers/t/THR.cif +186 -0
  37. package/baby-gru/monomers/t/TRP.cif +263 -0
  38. package/baby-gru/monomers/t/TYR.cif +238 -0
  39. package/baby-gru/monomers/u/U.cif +248 -0
  40. package/baby-gru/monomers/v/VAL.cif +197 -0
  41. package/baby-gru/pixmaps/MoorhenLogo.png +0 -0
  42. package/baby-gru/pixmaps/add-alt-conf.svg +127 -0
  43. package/baby-gru/pixmaps/add-peptide-1.svg +257 -0
  44. package/baby-gru/pixmaps/atom-at-pointer.svg +91 -0
  45. package/baby-gru/pixmaps/auto-fit-rotamer.svg +118 -0
  46. package/baby-gru/pixmaps/cis-trans.svg +392 -0
  47. package/baby-gru/pixmaps/delete.svg +94 -0
  48. package/baby-gru/pixmaps/diff-map.png +0 -0
  49. package/baby-gru/pixmaps/drag.svg +253 -0
  50. package/baby-gru/pixmaps/edit-chi.svg +303 -0
  51. package/baby-gru/pixmaps/flip-peptide.svg +169 -0
  52. package/baby-gru/pixmaps/jed-flip-reverse.svg +286 -0
  53. package/baby-gru/pixmaps/map.svg +114 -0
  54. package/baby-gru/pixmaps/mutate.svg +111 -0
  55. package/baby-gru/pixmaps/rama-plot-gly-normal.png +0 -0
  56. package/baby-gru/pixmaps/rama-plot-gly-outlier.png +0 -0
  57. package/baby-gru/pixmaps/rama-plot-other-normal.png +0 -0
  58. package/baby-gru/pixmaps/rama-plot-other-outlier.png +0 -0
  59. package/baby-gru/pixmaps/rama-plot-pro-normal.png +0 -0
  60. package/baby-gru/pixmaps/rama-plot-pro-outlier.png +0 -0
  61. package/baby-gru/pixmaps/rama2_all.png +0 -0
  62. package/baby-gru/pixmaps/rama2_gly.png +0 -0
  63. package/baby-gru/pixmaps/rama2_ileval.png +0 -0
  64. package/baby-gru/pixmaps/rama2_non_gly_pro.png +0 -0
  65. package/baby-gru/pixmaps/rama2_non_gly_pro_pre_pro_ileval.png +0 -0
  66. package/baby-gru/pixmaps/rama2_pre_pro.png +0 -0
  67. package/baby-gru/pixmaps/rama2_pro.png +0 -0
  68. package/baby-gru/pixmaps/refine-1.svg +140 -0
  69. package/baby-gru/pixmaps/rigid-body.svg +124 -0
  70. package/baby-gru/pixmaps/rotamers.svg +78 -0
  71. package/baby-gru/pixmaps/rtz.svg +281 -0
  72. package/baby-gru/pixmaps/side-chain-180.svg +129 -0
  73. package/baby-gru/pixmaps/spin-view.svg +104 -0
  74. package/baby-gru/pixmaps/temperature.svg +92 -0
  75. package/baby-gru/tutorials/NUT.cif +453 -0
  76. package/baby-gru/tutorials/legend.html +3 -0
  77. package/baby-gru/tutorials/moorhen-tutorial-map-number-1.mtz +0 -0
  78. package/baby-gru/tutorials/moorhen-tutorial-map-number-2.mtz +0 -0
  79. package/baby-gru/tutorials/moorhen-tutorial-map-number-3.mtz +0 -0
  80. package/baby-gru/tutorials/moorhen-tutorial-map-number-4.mtz +0 -0
  81. package/baby-gru/tutorials/moorhen-tutorial-structure-number-1.pdb +2211 -0
  82. package/baby-gru/tutorials/moorhen-tutorial-structure-number-2.pdb +2018 -0
  83. package/baby-gru/tutorials/moorhen-tutorial-structure-number-3.pdb +1090 -0
  84. package/baby-gru/tutorials/moorhen-tutorial-structure-number-4.pdb +2801 -0
  85. package/baby-gru/wasm/RDKit_minimal.js +21 -0
  86. package/baby-gru/wasm/RDKit_minimal.wasm +0 -0
  87. package/baby-gru/wasm/cif_pdb_worker.js +33 -0
  88. package/baby-gru/wasm/coot_env_web.js +5 -0
  89. package/baby-gru/wasm/crystallography_worker.js +610 -0
  90. package/baby-gru/wasm/mini_rsr_worker.js +72 -0
  91. package/baby-gru/wasm/monid_to_pdb_worker.js +253 -0
  92. package/baby-gru/wasm/moorhen.data +246292 -0
  93. package/baby-gru/wasm/moorhen.js +21 -0
  94. package/baby-gru/wasm/moorhen.wasm +0 -0
  95. package/baby-gru/wasm/moorhen.worker.js +1 -0
  96. package/baby-gru/wasm/mtz_arraybuffer_worker.js +59 -0
  97. package/baby-gru/wasm/mtz_worker.js +45 -0
  98. package/baby-gru/wasm/nma_worker.js +103 -0
  99. package/baby-gru/wasm/papaparse.min.js +7 -0
  100. package/baby-gru/wasm/pdb_worker.js +282 -0
  101. package/baby-gru/wasm/smiles_to_pdb_worker.js +252 -0
  102. package/baby-gru/wasm/superpose_worker.js +144 -0
  103. package/baby-gru/wasm/web_example.js +21 -0
  104. package/baby-gru/wasm/web_example.wasm +0 -0
  105. package/moorhen.css +418 -0
  106. package/package.json +176 -0
package/baby-gru/monomers/d/DC.cif ADDED
@@ -0,0 +1,250 @@
1
+ #
2
+ data_comp_list
3
+ loop_
4
+ _chem_comp.id
5
+ _chem_comp.three_letter_code
6
+ _chem_comp.name
7
+ _chem_comp.group
8
+ _chem_comp.number_atoms_all
9
+ _chem_comp.number_atoms_nh
10
+ _chem_comp.desc_level
11
+ DC DC "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" DNA 32 20 .
12
+ #
13
+ data_comp_DC
14
+ #
15
+ loop_
16
+ _chem_comp_atom.comp_id
17
+ _chem_comp_atom.atom_id
18
+ _chem_comp_atom.type_symbol
19
+ _chem_comp_atom.type_energy
20
+ _chem_comp_atom.charge
21
+ _chem_comp_atom.x
22
+ _chem_comp_atom.y
23
+ _chem_comp_atom.z
24
+ DC OP3 O OP -1 4.759 -6.216 1.740
25
+ DC P P P 0 5.427 -6.783 0.501
26
+ DC OP1 O O 0 5.450 -8.300 0.487
27
+ DC OP2 O OP -1 6.788 -6.171 0.232
28
+ DC "O5'" O O2 0 4.494 -6.346 -0.742
29
+ DC "C5'" C CH2 0 3.097 -6.734 -0.736
30
+ DC "C4'" C CH1 0 2.438 -6.261 -2.009
31
+ DC "O4'" O O2 0 2.537 -4.821 -2.097
32
+ DC "C3'" C CH1 0 3.044 -6.825 -3.297
33
+ DC "O3'" O OH1 0 2.035 -7.363 -4.147
34
+ DC "C2'" C CH2 0 3.705 -5.618 -3.951
35
+ DC "C1'" C CH1 0 2.890 -4.454 -3.414
36
+ DC N1 N NR6 0 3.622 -3.158 -3.358
37
+ DC C2 C CR6 0 3.233 -2.087 -4.185
38
+ DC O2 O O 0 2.273 -2.221 -4.961
39
+ DC N3 N NRD6 0 3.923 -0.917 -4.114
40
+ DC C4 C CR6 0 4.961 -0.779 -3.274
41
+ DC N4 N NH2 0 5.596 0.387 -3.250
42
+ DC C5 C CR16 0 5.371 -1.854 -2.432
43
+ DC C6 C CR16 0 4.683 -3.007 -2.507
44
+ DC "H5'" H H 0 2.640 -6.331 0.044
45
+ DC "H5''" H H 0 3.022 -7.718 -0.669
46
+ DC "H4'" H H 0 1.482 -6.507 -1.967
47
+ DC "H3'" H H 0 3.719 -7.516 -3.087
48
+ DC "HO3'" H H 0 1.460 -6.765 -4.330
49
+ DC "H2'" H H 0 3.647 -5.668 -4.930
50
+ DC "H2''" H H 0 4.648 -5.546 -3.691
51
+ DC "H1'" H H 0 2.063 -4.358 -3.951
52
+ DC H41 H H 0 5.385 1.014 -3.827
53
+ DC H42 H H 0 6.226 0.528 -2.656
54
+ DC H5 H H 0 6.097 -1.763 -1.841
55
+ DC H6 H H 0 4.929 -3.731 -1.969
56
+ loop_
57
+ _chem_comp_bond.comp_id
58
+ _chem_comp_bond.atom_id_1
59
+ _chem_comp_bond.atom_id_2
60
+ _chem_comp_bond.type
61
+ _chem_comp_bond.aromatic
62
+ _chem_comp_bond.value_dist_nucleus
63
+ _chem_comp_bond.value_dist_nucleus_esd
64
+ _chem_comp_bond.value_dist
65
+ _chem_comp_bond.value_dist_esd
66
+ DC OP3 P SINGLE n 1.517 0.0192 1.517 0.0192
67
+ DC P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
68
+ DC P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
69
+ DC P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178
70
+ DC "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
71
+ DC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
72
+ DC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100
73
+ DC "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115
74
+ DC "O4'" "C1'" SINGLE n 1.413 0.0100 1.413 0.0100
75
+ DC "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100
76
+ DC "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100
77
+ DC "C2'" "C1'" SINGLE n 1.520 0.0100 1.520 0.0100
78
+ DC "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115
79
+ DC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100
80
+ DC N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118
81
+ DC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100
82
+ DC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119
83
+ DC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110
84
+ DC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109
85
+ DC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123
86
+ DC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100
87
+ DC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
88
+ DC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
89
+ DC "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170
90
+ DC "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189
91
+ DC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
92
+ DC "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200
93
+ DC "C2'" "H2''" SINGLE n 1.089 0.0100 0.982 0.0200
94
+ DC "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103
95
+ DC N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200
96
+ DC N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200
97
+ DC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174
98
+ DC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143
99
+ loop_
100
+ _chem_comp_angle.comp_id
101
+ _chem_comp_angle.atom_id_1
102
+ _chem_comp_angle.atom_id_2
103
+ _chem_comp_angle.atom_id_3
104
+ _chem_comp_angle.value_angle
105
+ _chem_comp_angle.value_angle_esd
106
+ DC OP3 P OP1 112.864 1.69
107
+ DC OP3 P OP2 112.864 1.69
108
+ DC OP3 P "O5'" 105.808 2.07
109
+ DC OP1 P OP2 112.864 1.69
110
+ DC OP1 P "O5'" 105.808 2.07
111
+ DC OP2 P "O5'" 105.808 2.07
112
+ DC P "O5'" "C5'" 118.783 1.50
113
+ DC "O5'" "C5'" "C4'" 109.342 1.50
114
+ DC "O5'" "C5'" "H5'" 109.845 1.50
115
+ DC "O5'" "C5'" "H5''" 109.845 1.50
116
+ DC "C4'" "C5'" "H5'" 109.624 1.50
117
+ DC "C4'" "C5'" "H5''" 109.624 1.50
118
+ DC "H5'" "C5'" "H5''" 108.472 1.50
119
+ DC "C5'" "C4'" "O4'" 109.615 1.50
120
+ DC "C5'" "C4'" "C3'" 114.866 1.63
121
+ DC "C5'" "C4'" "H4'" 108.268 1.50
122
+ DC "O4'" "C4'" "C3'" 105.770 1.50
123
+ DC "O4'" "C4'" "H4'" 108.698 1.50
124
+ DC "C3'" "C4'" "H4'" 109.069 1.50
125
+ DC "C4'" "O4'" "C1'" 109.692 1.50
126
+ DC "C4'" "C3'" "O3'" 110.527 2.37
127
+ DC "C4'" "C3'" "C2'" 102.800 1.50
128
+ DC "C4'" "C3'" "H3'" 110.775 1.50
129
+ DC "O3'" "C3'" "C2'" 110.636 2.59
130
+ DC "O3'" "C3'" "H3'" 110.713 1.50
131
+ DC "C2'" "C3'" "H3'" 110.862 1.50
132
+ DC "C3'" "O3'" "HO3'" 109.026 2.38
133
+ DC "C3'" "C2'" "C1'" 102.834 1.50
134
+ DC "C3'" "C2'" "H2'" 111.310 1.50
135
+ DC "C3'" "C2'" "H2''" 111.310 1.50
136
+ DC "C1'" "C2'" "H2'" 111.187 1.50
137
+ DC "C1'" "C2'" "H2''" 111.187 1.50
138
+ DC "H2'" "C2'" "H2''" 108.952 1.50
139
+ DC "O4'" "C1'" "C2'" 106.308 1.50
140
+ DC "O4'" "C1'" N1 107.584 1.50
141
+ DC "O4'" "C1'" "H1'" 109.550 1.50
142
+ DC "C2'" "C1'" N1 114.268 1.50
143
+ DC "C2'" "C1'" "H1'" 109.741 1.50
144
+ DC N1 "C1'" "H1'" 109.342 1.50
145
+ DC "C1'" N1 C2 118.777 1.50
146
+ DC "C1'" N1 C6 120.713 1.50
147
+ DC C2 N1 C6 120.510 1.50
148
+ DC N1 C2 O2 118.710 1.50
149
+ DC N1 C2 N3 118.927 1.50
150
+ DC O2 C2 N3 122.370 1.50
151
+ DC C2 N3 C4 120.266 1.50
152
+ DC N3 C4 N4 117.855 1.50
153
+ DC N3 C4 C5 121.269 1.50
154
+ DC N4 C4 C5 120.876 1.50
155
+ DC C4 N4 H41 119.818 1.59
156
+ DC C4 N4 H42 119.818 1.59
157
+ DC H41 N4 H42 120.363 1.85
158
+ DC C4 C5 C6 117.808 1.50
159
+ DC C4 C5 H5 121.350 1.50
160
+ DC C6 C5 H5 120.848 1.50
161
+ DC N1 C6 C5 121.215 1.50
162
+ DC N1 C6 H6 118.510 1.50
163
+ DC C5 C6 H6 120.275 1.75
164
+ loop_
165
+ _chem_comp_tor.comp_id
166
+ _chem_comp_tor.id
167
+ _chem_comp_tor.atom_id_1
168
+ _chem_comp_tor.atom_id_2
169
+ _chem_comp_tor.atom_id_3
170
+ _chem_comp_tor.atom_id_4
171
+ _chem_comp_tor.value_angle
172
+ _chem_comp_tor.value_angle_esd
173
+ _chem_comp_tor.period
174
+ DC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
175
+ DC C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
176
+ DC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
177
+ DC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
178
+ DC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
179
+ DC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
180
+ DC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
181
+ DC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
182
+ DC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
183
+ DC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
184
+ DC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
185
+ DC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
186
+ DC alpha "C5'" "O5'" P OP3 -60.000 10.00 3
187
+ DC beta P "O5'" "C5'" "C4'" 180.000 10.00 3
188
+ DC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
189
+ DC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
190
+ DC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2
191
+ DC const_18 C5 C6 N1 "C1'" 180.000 10.0 2
192
+ DC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2
193
+ DC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2
194
+ DC sp2_sp2_3 N3 C4 N4 H41 0.000 5.0 2
195
+ DC const_11 N4 C4 C5 C6 180.000 10.0 2
196
+ DC const_13 C4 C5 C6 N1 0.000 10.0 2
197
+ loop_
198
+ _chem_comp_chir.comp_id
199
+ _chem_comp_chir.id
200
+ _chem_comp_chir.atom_id_centre
201
+ _chem_comp_chir.atom_id_1
202
+ _chem_comp_chir.atom_id_2
203
+ _chem_comp_chir.atom_id_3
204
+ _chem_comp_chir.volume_sign
205
+ DC chir_1 P "O5'" OP3 OP2 both
206
+ DC chir_2 "C4'" "O4'" "C3'" "C5'" negative
207
+ DC chir_3 "C3'" "O3'" "C4'" "C2'" positive
208
+ DC chir_4 "C1'" "O4'" N1 "C2'" negative
209
+ loop_
210
+ _chem_comp_plane_atom.comp_id
211
+ _chem_comp_plane_atom.plane_id
212
+ _chem_comp_plane_atom.atom_id
213
+ _chem_comp_plane_atom.dist_esd
214
+ DC plan-1 "C1'" 0.020
215
+ DC plan-1 C2 0.020
216
+ DC plan-1 C4 0.020
217
+ DC plan-1 C5 0.020
218
+ DC plan-1 C6 0.020
219
+ DC plan-1 H5 0.020
220
+ DC plan-1 H6 0.020
221
+ DC plan-1 N1 0.020
222
+ DC plan-1 N3 0.020
223
+ DC plan-1 N4 0.020
224
+ DC plan-1 O2 0.020
225
+ DC plan-2 C4 0.020
226
+ DC plan-2 H41 0.020
227
+ DC plan-2 H42 0.020
228
+ DC plan-2 N4 0.020
229
+ loop_
230
+ _pdbx_chem_comp_descriptor.comp_id
231
+ _pdbx_chem_comp_descriptor.type
232
+ _pdbx_chem_comp_descriptor.program
233
+ _pdbx_chem_comp_descriptor.program_version
234
+ _pdbx_chem_comp_descriptor.descriptor
235
+ DC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
236
+ DC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
237
+ DC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
238
+ DC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
239
+ DC SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
240
+ DC InChI InChI 1.03 InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
241
+ DC InChIKey InChI 1.03 NCMVOABPESMRCP-SHYZEUOFSA-N
242
+ loop_
243
+ _pdbx_chem_comp_description_generator.comp_id
244
+ _pdbx_chem_comp_description_generator.program_name
245
+ _pdbx_chem_comp_description_generator.program_version
246
+ _pdbx_chem_comp_description_generator.descriptor
247
+ DC acedrg 243 "dictionary generator"
248
+ DC acedrg_database 11 "data source"
249
+ DC rdkit 2017.03.2 "Chemoinformatics tool"
250
+ DC refmac5 5.8.0238 "optimization tool"
package/baby-gru/monomers/d/DG.cif ADDED
@@ -0,0 +1,271 @@
1
+ #
2
+ data_comp_list
3
+ loop_
4
+ _chem_comp.id
5
+ _chem_comp.three_letter_code
6
+ _chem_comp.name
7
+ _chem_comp.group
8
+ _chem_comp.number_atoms_all
9
+ _chem_comp.number_atoms_nh
10
+ _chem_comp.desc_level
11
+ DG DG "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" DNA 35 23 .
12
+ #
13
+ data_comp_DG
14
+ #
15
+ loop_
16
+ _chem_comp_atom.comp_id
17
+ _chem_comp_atom.atom_id
18
+ _chem_comp_atom.type_symbol
19
+ _chem_comp_atom.type_energy
20
+ _chem_comp_atom.charge
21
+ _chem_comp_atom.x
22
+ _chem_comp_atom.y
23
+ _chem_comp_atom.z
24
+ DG OP3 O OP -1 0.424 -8.734 -9.816
25
+ DG P P P 0 0.296 -8.811 -11.326
26
+ DG OP1 O O 0 -0.898 -9.631 -11.775
27
+ DG OP2 O OP -1 1.587 -9.229 -12.005
28
+ DG "O5'" O O2 0 0.007 -7.303 -11.822
29
+ DG "C5'" C CH2 0 -1.170 -6.617 -11.324
30
+ DG "C4'" C CH1 0 -1.206 -5.213 -11.876
31
+ DG "O4'" O O2 0 -0.018 -4.512 -11.450
32
+ DG "C3'" C CH1 0 -1.259 -5.123 -13.404
33
+ DG "O3'" O OH1 0 -2.248 -4.188 -13.827
34
+ DG "C2'" C CH2 0 0.144 -4.654 -13.783
35
+ DG "C1'" C CH1 0 0.565 -3.849 -12.566
36
+ DG N9 N NR5 0 2.012 -3.775 -12.354
37
+ DG C8 C CR15 0 2.857 -4.830 -12.111
38
+ DG N7 N NRD5 0 4.108 -4.471 -11.958
39
+ DG C5 C CR56 0 4.088 -3.091 -12.106
40
+ DG C6 C CR6 0 5.150 -2.149 -12.042
41
+ DG O6 O O 0 6.352 -2.369 -11.834
42
+ DG N1 N NR16 0 4.698 -0.841 -12.249
43
+ DG C2 C CR6 0 3.388 -0.485 -12.487
44
+ DG N2 N NH2 0 3.138 0.820 -12.662
45
+ DG N3 N NRD6 0 2.387 -1.368 -12.548
46
+ DG C4 C CR56 0 2.803 -2.647 -12.350
47
+ DG "H5'" H H 0 -1.147 -6.585 -10.336
48
+ DG "H5''" H H 0 -1.985 -7.104 -11.602
49
+ DG "H4'" H H 0 -1.996 -4.756 -11.498
50
+ DG "H3'" H H 0 -1.441 -6.012 -13.795
51
+ DG "HO3'" H H 0 -2.096 -3.427 -13.481
52
+ DG "H2'" H H 0 0.125 -4.097 -14.586
53
+ DG "H2''" H H 0 0.741 -5.412 -13.932
54
+ DG "H1'" H H 0 0.190 -2.932 -12.632
55
+ DG H8 H H 0 2.565 -5.725 -12.063
56
+ DG H1 H H 0 5.314 -0.188 -12.222
57
+ DG H21 H H 0 2.584 1.078 -13.291
58
+ DG H22 H H 0 3.528 1.412 -12.146
59
+ loop_
60
+ _chem_comp_bond.comp_id
61
+ _chem_comp_bond.atom_id_1
62
+ _chem_comp_bond.atom_id_2
63
+ _chem_comp_bond.type
64
+ _chem_comp_bond.aromatic
65
+ _chem_comp_bond.value_dist_nucleus
66
+ _chem_comp_bond.value_dist_nucleus_esd
67
+ _chem_comp_bond.value_dist
68
+ _chem_comp_bond.value_dist_esd
69
+ DG OP3 P SINGLE n 1.517 0.0192 1.517 0.0192
70
+ DG P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
71
+ DG P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
72
+ DG P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178
73
+ DG "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
74
+ DG "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
75
+ DG "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100
76
+ DG "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115
77
+ DG "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100
78
+ DG "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100
79
+ DG "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101
80
+ DG "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118
81
+ DG "C1'" N9 SINGLE n 1.462 0.0111 1.462 0.0111
82
+ DG N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100
83
+ DG N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100
84
+ DG C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100
85
+ DG N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100
86
+ DG C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103
87
+ DG C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100
88
+ DG C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100
89
+ DG C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107
90
+ DG N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100
91
+ DG C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101
92
+ DG C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104
93
+ DG N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100
94
+ DG "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
95
+ DG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
96
+ DG "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170
97
+ DG "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189
98
+ DG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
99
+ DG "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113
100
+ DG "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113
101
+ DG "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101
102
+ DG C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
103
+ DG N1 H1 SINGLE n 1.016 0.0100 0.897 0.0200
104
+ DG N2 H21 SINGLE n 1.016 0.0100 0.877 0.0200
105
+ DG N2 H22 SINGLE n 1.016 0.0100 0.877 0.0200
106
+ loop_
107
+ _chem_comp_angle.comp_id
108
+ _chem_comp_angle.atom_id_1
109
+ _chem_comp_angle.atom_id_2
110
+ _chem_comp_angle.atom_id_3
111
+ _chem_comp_angle.value_angle
112
+ _chem_comp_angle.value_angle_esd
113
+ DG OP3 P OP1 112.864 1.69
114
+ DG OP3 P OP2 112.864 1.69
115
+ DG OP3 P "O5'" 105.808 2.07
116
+ DG OP1 P OP2 112.864 1.69
117
+ DG OP1 P "O5'" 105.808 2.07
118
+ DG OP2 P "O5'" 105.808 2.07
119
+ DG P "O5'" "C5'" 118.783 1.50
120
+ DG "O5'" "C5'" "C4'" 109.342 1.50
121
+ DG "O5'" "C5'" "H5'" 109.845 1.50
122
+ DG "O5'" "C5'" "H5''" 109.845 1.50
123
+ DG "C4'" "C5'" "H5'" 109.624 1.50
124
+ DG "C4'" "C5'" "H5''" 109.624 1.50
125
+ DG "H5'" "C5'" "H5''" 108.472 1.50
126
+ DG "C5'" "C4'" "O4'" 109.123 1.50
127
+ DG "C5'" "C4'" "C3'" 114.866 1.63
128
+ DG "C5'" "C4'" "H4'" 108.268 1.50
129
+ DG "O4'" "C4'" "C3'" 105.506 1.50
130
+ DG "O4'" "C4'" "H4'" 108.947 1.50
131
+ DG "C3'" "C4'" "H4'" 109.069 1.50
132
+ DG "C4'" "O4'" "C1'" 108.795 1.50
133
+ DG "C4'" "C3'" "O3'" 110.527 2.37
134
+ DG "C4'" "C3'" "C2'" 102.433 1.50
135
+ DG "C4'" "C3'" "H3'" 110.775 1.50
136
+ DG "O3'" "C3'" "C2'" 111.424 1.96
137
+ DG "O3'" "C3'" "H3'" 110.713 1.50
138
+ DG "C2'" "C3'" "H3'" 110.846 1.50
139
+ DG "C3'" "O3'" "HO3'" 109.026 2.38
140
+ DG "C3'" "C2'" "C1'" 102.663 1.50
141
+ DG "C3'" "C2'" "H2'" 111.194 1.50
142
+ DG "C3'" "C2'" "H2''" 111.194 1.50
143
+ DG "C1'" "C2'" "H2'" 111.213 1.50
144
+ DG "C1'" "C2'" "H2''" 111.213 1.50
145
+ DG "H2'" "C2'" "H2''" 109.148 1.50
146
+ DG "O4'" "C1'" "C2'" 106.035 1.50
147
+ DG "O4'" "C1'" N9 108.236 1.50
148
+ DG "O4'" "C1'" "H1'" 109.059 1.50
149
+ DG "C2'" "C1'" N9 114.190 1.67
150
+ DG "C2'" "C1'" "H1'" 109.272 1.50
151
+ DG N9 "C1'" "H1'" 109.282 1.50
152
+ DG "C1'" N9 C8 127.617 2.81
153
+ DG "C1'" N9 C4 126.652 2.93
154
+ DG C8 N9 C4 105.731 1.50
155
+ DG N9 C8 N7 113.507 1.50
156
+ DG N9 C8 H8 123.187 1.50
157
+ DG N7 C8 H8 123.307 1.50
158
+ DG C8 N7 C5 104.778 1.50
159
+ DG N7 C5 C6 130.030 1.50
160
+ DG N7 C5 C4 110.574 1.50
161
+ DG C6 C5 C4 119.397 1.50
162
+ DG C5 C6 O6 128.244 1.50
163
+ DG C5 C6 N1 111.367 1.50
164
+ DG O6 C6 N1 120.389 1.50
165
+ DG C6 N1 C2 125.351 1.50
166
+ DG C6 N1 H1 116.978 2.44
167
+ DG C2 N1 H1 117.677 2.71
168
+ DG N1 C2 N2 116.576 1.50
169
+ DG N1 C2 N3 123.602 1.50
170
+ DG N2 C2 N3 119.821 1.50
171
+ DG C2 N2 H21 119.868 1.50
172
+ DG C2 N2 H22 119.868 1.50
173
+ DG H21 N2 H22 120.263 1.96
174
+ DG C2 N3 C4 112.066 1.50
175
+ DG N9 C4 C5 105.411 1.50
176
+ DG N9 C4 N3 126.378 1.50
177
+ DG C5 C4 N3 128.211 1.50
178
+ loop_
179
+ _chem_comp_tor.comp_id
180
+ _chem_comp_tor.id
181
+ _chem_comp_tor.atom_id_1
182
+ _chem_comp_tor.atom_id_2
183
+ _chem_comp_tor.atom_id_3
184
+ _chem_comp_tor.atom_id_4
185
+ _chem_comp_tor.value_angle
186
+ _chem_comp_tor.value_angle_esd
187
+ _chem_comp_tor.period
188
+ DG C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
189
+ DG C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
190
+ DG C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
191
+ DG C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
192
+ DG C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
193
+ DG C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
194
+ DG C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
195
+ DG C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
196
+ DG C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
197
+ DG C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
198
+ DG C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
199
+ DG C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
200
+ DG alpha "C5'" "O5'" P OP3 -60.000 10.00 3
201
+ DG beta P "O5'" "C5'" "C4'" 180.000 10.00 3
202
+ DG epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
203
+ DG gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
204
+ DG const_18 N7 C8 N9 "C1'" 180.000 10.0 2
205
+ DG const_30 C5 C4 N9 "C1'" 180.000 10.0 2
206
+ DG const_21 N9 C8 N7 C5 0.000 10.0 2
207
+ DG const_24 C6 C5 N7 C8 180.000 10.0 2
208
+ DG const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2
209
+ DG const_25 N9 C4 C5 N7 0.000 10.0 2
210
+ DG const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2
211
+ DG const_11 N2 C2 N1 C6 180.000 10.0 2
212
+ DG sp2_sp2_1 N1 C2 N2 H21 180.000 5.0 2
213
+ DG const_14 N2 C2 N3 C4 180.000 10.0 2
214
+ DG const_16 N9 C4 N3 C2 180.000 10.0 2
215
+ loop_
216
+ _chem_comp_chir.comp_id
217
+ _chem_comp_chir.id
218
+ _chem_comp_chir.atom_id_centre
219
+ _chem_comp_chir.atom_id_1
220
+ _chem_comp_chir.atom_id_2
221
+ _chem_comp_chir.atom_id_3
222
+ _chem_comp_chir.volume_sign
223
+ DG chir_1 P "O5'" OP3 OP2 both
224
+ DG chir_2 "C4'" "O4'" "C3'" "C5'" negative
225
+ DG chir_3 "C3'" "O3'" "C4'" "C2'" positive
226
+ DG chir_4 "C1'" "O4'" N9 "C2'" negative
227
+ loop_
228
+ _chem_comp_plane_atom.comp_id
229
+ _chem_comp_plane_atom.plane_id
230
+ _chem_comp_plane_atom.atom_id
231
+ _chem_comp_plane_atom.dist_esd
232
+ DG plan-1 "C1'" 0.020
233
+ DG plan-1 C2 0.020
234
+ DG plan-1 C4 0.020
235
+ DG plan-1 C5 0.020
236
+ DG plan-1 C6 0.020
237
+ DG plan-1 C8 0.020
238
+ DG plan-1 H1 0.020
239
+ DG plan-1 H8 0.020
240
+ DG plan-1 N1 0.020
241
+ DG plan-1 N2 0.020
242
+ DG plan-1 N3 0.020
243
+ DG plan-1 N7 0.020
244
+ DG plan-1 N9 0.020
245
+ DG plan-1 O6 0.020
246
+ DG plan-2 C2 0.020
247
+ DG plan-2 H21 0.020
248
+ DG plan-2 H22 0.020
249
+ DG plan-2 N2 0.020
250
+ loop_
251
+ _pdbx_chem_comp_descriptor.comp_id
252
+ _pdbx_chem_comp_descriptor.type
253
+ _pdbx_chem_comp_descriptor.program
254
+ _pdbx_chem_comp_descriptor.program_version
255
+ _pdbx_chem_comp_descriptor.descriptor
256
+ DG SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O
257
+ DG SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
258
+ DG SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
259
+ DG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N
260
+ DG SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
261
+ DG InChI InChI 1.03 InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
262
+ DG InChIKey InChI 1.03 LTFMZDNNPPEQNG-KVQBGUIXSA-N
263
+ loop_
264
+ _pdbx_chem_comp_description_generator.comp_id
265
+ _pdbx_chem_comp_description_generator.program_name
266
+ _pdbx_chem_comp_description_generator.program_version
267
+ _pdbx_chem_comp_description_generator.descriptor
268
+ DG acedrg 243 "dictionary generator"
269
+ DG acedrg_database 11 "data source"
270
+ DG rdkit 2017.03.2 "Chemoinformatics tool"
271
+ DG refmac5 5.8.0238 "optimization tool"