# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 15:38:28 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1C=O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 B7J  B7J  '2'-deoxy-5-formylcytidine 5'-(tetrahydrogen triphosphate)'  ligand  46  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B7J
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 B7J  C10  C  CH1   0  -0.002   3.8697   6.3476  11.6617
 B7J  C26  C  CR6   0   0.608   7.7544   7.7618   9.5483
 B7J  C01  C  C1    0   0.120   9.0426   7.1949  13.5253
 B7J  O02  O  O     0  -0.422  10.1807   7.2742  13.9504
 B7J  C03  C  CR6   0  -0.246   8.6413   7.4087  12.1529
 B7J  C04  C  CR16  0   0.095   7.3129   7.2980  11.8454
 B7J  N05  N  NR6   0  -0.549   6.8585   7.4692  10.6097
 B7J  C06  C  CH1   0   0.196   5.4215   7.3611  10.2678
 B7J  C07  C  CH2   0  -0.534   5.0657   5.9993   9.6759
 B7J  C08  C  CH1   0   0.010   4.5787   5.2280  10.8929
 B7J  O09  O  OH1   0  -0.684   3.7430   4.1636  10.5554
 B7J  C11  C  CH2   0  -0.223   3.6541   6.1366  13.1368
 B7J  O12  O  O2    0  -0.594   4.9099   5.8171  13.7521
 B7J  P13  P  P     0   1.523   5.1313   5.2798  15.2267
 B7J  O14  O  O     0  -0.650   6.4592   5.6177  15.7510
 B7J  O15  O  OH1   0  -0.726   3.8457   5.6527  16.0729
 B7J  O16  O  O2    0  -0.684   4.9465   3.6704  15.1353
 B7J  P17  P  P     0   1.532   3.9681   2.6681  14.3641
 B7J  O18  O  OH1   0  -0.725   2.5718   3.0441  14.9991
 B7J  O19  O  O     0  -0.659   4.0839   2.6645  12.8976
 B7J  O20  O  O2    0  -0.668   4.4248   1.2722  14.9887
 B7J  P21  P  P     0   1.464   3.9678   0.5219  16.3681
 B7J  O22  O  OH1   0  -0.726   4.3832   1.6229  17.4261
 B7J  O23  O  O     0  -0.675   2.5772   0.0492  16.3527
 B7J  O24  O  OH1   0  -0.711   5.1120  -0.5641  16.4982
 B7J  O25  O  O2    0  -0.497   4.6674   7.5050  11.4369
 B7J  O27  O  O     0  -0.498   7.2904   7.8803   8.4262
 B7J  N28  N  N     0  -0.530   9.0580   7.9045   9.8345
 B7J  C29  C  CR6   0   0.520   9.5189   7.7439  11.0602
 B7J  N30  N  NH2   0  -0.802  10.8177   7.9008  11.2692
 B7J  H1   H  HCH1  0   0.259   2.8719   6.4948  11.2259
 B7J  H2   H  H     0   0.208   8.2121   6.9328  14.2030
 B7J  H3   H  HCR6  0   0.332   6.5903   7.0758  12.6179
 B7J  H4   H  HCH1  0   0.282   5.2108   8.1825   9.5840
 B7J  H5   H  HCH2  0   0.268   4.2490   6.1207   8.9605
 B7J  H6   H  HCH2  0   0.284   5.8991   5.5251   9.1615
 B7J  H7   H  HCH1  0   0.229   5.4470   4.8795  11.4673
 B7J  H8   H  HOH1  0   0.460   3.7220   3.5606  11.3141
 B7J  H9   H  HCH2  0   0.286   3.2400   7.0344  13.5985
 B7J  H10  H  HCH2  0   0.249   2.9273   5.3317  13.2617
 B7J  H11  H  HOH1  0   0.515   3.8607   6.5336  16.4749
 B7J  H12  H  HOH1  0   0.518   1.7912   2.7558  14.5029
 B7J  H13  H  HOH1  0   0.513   3.8958   1.5843  18.2611
 B7J  H14  H  HOH1  0   0.512   4.8935  -1.4266  16.1172
 B7J  H15  H  HNH2  0   0.406  11.4211   8.1384  10.4993
 B7J  H16  H  HNH2  0   0.417  11.2097   7.7885  12.1900

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
_chem_comp_bond.value_dist_neutron
 B7J  O27  C26  double  1.220  0.020  1.220
 B7J  C26  N28  single  1.342  0.020  1.342
 B7J  C26  N05  single  1.419  0.020  1.419
 B7J  N28  C29  double  1.319  0.020  1.319
 B7J  C07  C06  single  1.527  0.020  1.527
 B7J  C07  C08  single  1.521  0.020  1.521
 B7J  C06  N05  single  1.481  0.020  1.481
 B7J  C06  O25  single  1.399  0.020  1.399
 B7J  N05  C04  single  1.328  0.020  1.328
 B7J  C29  N30  single  1.325  0.020  1.325
 B7J  C29  C03  single  1.441  0.020  1.441
 B7J  O09  C08  single  1.395  0.020  1.395
 B7J  C08  C10  single  1.532  0.020  1.532
 B7J  O25  C10  single  1.424  0.020  1.424
 B7J  C04  C03  double  1.368  0.020  1.368
 B7J  C10  C11  single  1.506  0.020  1.506
 B7J  C03  C01  single  1.446  0.020  1.446
 B7J  O19  P17  double  1.471  0.020  1.471
 B7J  C11  O12  single  1.435  0.020  1.435
 B7J  C01  O02  double  1.217  0.020  1.217
 B7J  O12  P13  single  1.585  0.020  1.585
 B7J  P17  O16  single  1.599  0.020  1.599
 B7J  P17  O18  single  1.579  0.020  1.579
 B7J  P17  O20  single  1.596  0.020  1.596
 B7J  O16  P13  single  1.623  0.020  1.623
 B7J  O20  P21  single  1.635  0.020  1.635
 B7J  P13  O14  double  1.467  0.020  1.467
 B7J  P13  O15  single  1.584  0.020  1.584
 B7J  O23  P21  double  1.469  0.020  1.469
 B7J  P21  O22  single  1.582  0.020  1.582
 B7J  P21  O24  single  1.583  0.020  1.583
 B7J  C10  H1   single  0.970  0.020  1.090
 B7J  C01  H2   single  0.930  0.020  1.080
 B7J  C04  H3   single  0.930  0.020  1.080
 B7J  C06  H4   single  0.970  0.020  1.090
 B7J  C07  H5   single  0.970  0.020  1.090
 B7J  C07  H6   single  0.970  0.020  1.090
 B7J  C08  H7   single  0.970  0.020  1.090
 B7J  O09  H8   single  0.850  0.020  0.980
 B7J  C11  H9   single  0.970  0.020  1.090
 B7J  C11  H10  single  0.970  0.020  1.090
 B7J  O15  H11  single  0.850  0.020  0.980
 B7J  O18  H12  single  0.850  0.020  0.980
 B7J  O22  H13  single  0.850  0.020  0.980
 B7J  O24  H14  single  0.850  0.020  0.980
 B7J  N30  H15  single  0.860  0.020  1.020
 B7J  N30  H16  single  0.860  0.020  1.020

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
 B7J  H1   C10  O25  109.71  3.000
 B7J  H1   C10  C11  106.10  3.000
 B7J  O25  C10  C11  110.42  3.000
 B7J  H1   C10  C08  108.61  3.000
 B7J  C11  C10  C08  117.10  3.000
 B7J  O25  C10  C08  104.80  3.000
 B7J  N28  C26  O27  123.72  3.000
 B7J  N28  C26  N05  118.39  3.000
 B7J  O27  C26  N05  117.89  3.000
 B7J  H2   C01  C03  114.16  3.000
 B7J  H2   C01  O02  120.30  3.000
 B7J  C03  C01  O02  125.54  3.000
 B7J  C29  C03  C04  116.09  3.000
 B7J  C04  C03  C01  118.09  3.000
 B7J  C29  C03  C01  125.81  3.000
 B7J  H3   C04  N05  117.58  3.000
 B7J  H3   C04  C03  120.34  3.000
 B7J  N05  C04  C03  122.08  3.000
 B7J  C06  N05  C04  122.52  3.000
 B7J  C04  N05  C26  120.43  3.000
 B7J  C06  N05  C26  117.05  3.000
 B7J  H4   C06  O25  110.05  3.000
 B7J  H4   C06  C07  112.59  3.000
 B7J  O25  C06  C07  106.86  3.000
 B7J  H4   C06  N05  106.12  3.000
 B7J  O25  C06  N05  108.82  3.000
 B7J  C07  C06  N05  112.38  3.000
 B7J  H6   C07  H5   108.14  3.000
 B7J  H6   C07  C08  113.74  3.000
 B7J  H5   C07  C08  109.94  3.000
 B7J  H6   C07  C06  113.17  3.000
 B7J  H5   C07  C06  109.21  3.000
 B7J  C08  C07  C06  102.52  3.000
 B7J  H7   C08  O09  110.99  3.000
 B7J  H7   C08  C07  109.05  3.000
 B7J  O09  C08  C07  112.66  3.000
 B7J  H7   C08  C10  109.60  3.000
 B7J  O09  C08  C10  113.69  3.000
 B7J  C07  C08  C10  100.32  3.000
 B7J  H8   O09  C08  107.36  3.000
 B7J  H10  C11  H9   107.80  3.000
 B7J  H10  C11  O12  111.69  3.000
 B7J  H9   C11  O12  109.51  3.000
 B7J  H10  C11  C10  108.11  3.000
 B7J  H9   C11  C10  110.71  3.000
 B7J  O12  C11  C10  109.03  3.000
 B7J  P13  O12  C11  126.65  3.000
 B7J  O16  P13  O15   99.86  3.000
 B7J  O15  P13  O14  119.31  3.000
 B7J  O16  P13  O14  110.59  3.000
 B7J  O15  P13  O12  107.69  3.000
 B7J  O14  P13  O12  112.39  3.000
 B7J  O16  P13  O12  105.54  3.000
 B7J  H11  O15  P13  115.05  3.000
 B7J  P17  O16  P13  135.94  3.000
 B7J  O20  P17  O19  111.43  3.000
 B7J  O20  P17  O18  107.69  3.000
 B7J  O19  P17  O18  118.10  3.000
 B7J  O20  P17  O16  100.63  3.000
 B7J  O18  P17  O16  101.41  3.000
 B7J  O19  P17  O16  115.73  3.000
 B7J  H12  O18  P17  115.82  3.000
 B7J  P21  O20  P17  130.64  3.000
 B7J  O24  P21  O23  117.67  3.000
 B7J  O24  P21  O22  103.45  3.000
 B7J  O23  P21  O22  118.65  3.000
 B7J  O24  P21  O20  100.49  3.000
 B7J  O22  P21  O20   99.87  3.000
 B7J  O23  P21  O20  113.79  3.000
 B7J  H13  O22  P21  114.64  3.000
 B7J  H14  O24  P21  114.57  3.000
 B7J  C06  O25  C10  110.52  3.000
 B7J  C29  N28  C26  121.63  3.000
 B7J  N30  C29  N28  118.34  3.000
 B7J  N30  C29  C03  120.33  3.000
 B7J  N28  C29  C03  121.33  3.000
 B7J  H16  N30  H15  119.49  3.000
 B7J  H16  N30  C29  120.84  3.000
 B7J  H15  N30  C29  119.66  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
 B7J  CONST_01  C03  C29  N28  C26    0.00   0.0  0
 B7J  CONST_02  N28  C26  N05  C04    0.00   0.0  0
 B7J  CONST_03  C29  N28  C26  N05    0.00   0.0  0
 B7J  CONST_04  N28  C26  N05  C06  180.00   0.0  0
 B7J  CONST_05  N30  C29  N28  C26  180.00   0.0  0
 B7J  CONST_06  O27  C26  N05  C04  180.00   0.0  0
 B7J  CONST_07  O27  C26  N05  C06    0.00   0.0  0
 B7J  CONST_08  C29  N28  C26  O27  180.00   0.0  0
 B7J  CONST_09  H15  N30  C29  C03  180.00   0.0  0
 B7J  CONST_10  H16  N30  C29  C03    0.00   0.0  0
 B7J  Var_01    C29  C03  C01  O02    0.33  30.0  2
 B7J  Var_02    O16  P13  O12  C11   85.33  30.0  3
 B7J  Var_03    O19  P17  O16  P13   65.24  30.0  1
 B7J  Var_04    O23  P21  O20  P17   68.34  30.0  3
 B7J  Var_05    H9   C11  O12  P13   69.81  30.0  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
 B7J  chir_01  C10  C08  O25  C11  positiv
 B7J  chir_02  C06  O25  N05  C07  negativ
 B7J  chir_03  C08  O09  C10  C07  positiv
 B7J  chir_04  P13  O16  O14  O15  both
 B7J  chir_05  P17  O18  O16  O19  both

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
 B7J  plan-1  C26  0.020
 B7J  plan-1  C01  0.020
 B7J  plan-1  C03  0.020
 B7J  plan-1  C04  0.020
 B7J  plan-1  N05  0.020
 B7J  plan-1  C06  0.020
 B7J  plan-1  O27  0.020
 B7J  plan-1  N28  0.020
 B7J  plan-1  C29  0.020
 B7J  plan-1  N30  0.020
 B7J  plan-1  H3   0.020
 B7J  plan-1  H15  0.020
 B7J  plan-1  H16  0.020
 B7J  plan-2  C01  0.020
 B7J  plan-2  O02  0.020
 B7J  plan-2  C03  0.020
 B7J  plan-2  H2   0.020

