# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 08:23:12 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3OC(=C(O[P](O)(=O)O[P](O)(O)=O)C3=O)CO[P](O)(=O)O[P](O)(O)=O
#
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
 ECJ  ECJ  '(5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate'  ligand  48  35  .  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_ECJ
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
 ECJ  C10  C  CH2   0  -0.234   4.6000  -75.9088  -6.0949
 ECJ  C11  C  CR5   0   0.379   4.0228  -76.9056  -5.1542
 ECJ  C13  C  CR5   0   0.101   4.6024  -77.5156  -4.0897
 ECJ  C15  C  CR5   0   0.353   3.6437  -78.4030  -3.5144
 ECJ  C17  C  CR15  0   0.059   2.3782  -78.1803  -4.3358
 ECJ  C19  C  CR15  0   0.117   2.4873  -80.4560  -5.3833
 ECJ  C21  C  CR56  0  -0.010   0.4234  -80.8622  -5.6182
 ECJ  C22  C  CR6   0   0.468  -0.8667  -81.3638  -5.8755
 ECJ  C25  C  CR16  0   0.051  -1.6972  -79.4227  -4.9564
 ECJ  C28  C  CR56  0   0.514   0.4824  -79.6192  -5.0186
 ECJ  N18  N  NR5   0  -0.547   1.8219  -79.3654  -4.8641
 ECJ  N20  N  N     0  -0.441   1.6845  -81.3637  -5.8366
 ECJ  N23  N  NH2   0  -0.813  -1.0803  -82.5465  -6.4478
 ECJ  N24  N  N     0  -0.470  -1.9118  -80.6034  -5.5263
 ECJ  N27  N  N     0  -0.456  -0.5389  -78.8510  -4.6652
 ECJ  O02  O  OH1   0  -0.716   0.4688  -74.7512  -6.7322
 ECJ  O03  O  O     0  -0.676   0.0462  -72.2434  -7.3888
 ECJ  O04  O  OH1   0  -0.729   1.4021  -73.0732  -5.2984
 ECJ  O05  O  O2    0  -0.685   2.3254  -73.2825  -7.6827
 ECJ  O07  O  O     0  -0.672   4.6165  -73.9302  -8.5947
 ECJ  O08  O  OH1   0  -0.726   4.3935  -72.7263  -6.2940
 ECJ  O09  O  O2    0  -0.586   3.5479  -75.0407  -6.4779
 ECJ  O12  O  O     0  -0.419   2.7737  -77.2873  -5.3821
 ECJ  O14  O  O2    0  -0.593   5.8432  -77.3097  -3.5781
 ECJ  O16  O  O     0  -0.437   3.7219  -79.1765  -2.5776
 ECJ  O30  O  OH1   0  -0.694   8.2777  -76.7980  -3.6996
 ECJ  O31  O  O     0  -0.658   7.0503  -77.7722  -5.8171
 ECJ  O32  O  O2    0  -0.678   7.6302  -79.1062  -3.6281
 ECJ  O34  O  OH1   0  -0.745   6.0648  -80.3569  -2.0704
 ECJ  O35  O  OH1   0  -0.702   7.7917  -81.5712  -3.2405
 ECJ  O36  O  O     0  -0.682   5.8024  -80.5695  -4.6628
 ECJ  P01  P  P     0   1.477   0.9488  -73.2469  -6.8061
 ECJ  P06  P  P     0   1.499   3.8285  -73.7493  -7.3678
 ECJ  P29  P  P     0   1.474   7.2054  -77.7457  -4.3572
 ECJ  P33  P  P     0   1.462   6.7055  -80.4594  -3.5024
 ECJ  H1   H  HCH2  0   0.306   5.0097  -76.4364  -6.9609
 ECJ  H2   H  HCH2  0   0.285   5.4155  -75.3702  -5.6073
 ECJ  H6   H  HCR5  0   0.356   1.6252  -77.6669  -3.7308
 ECJ  H7   H  HCR5  0   0.319   3.5670  -80.5177  -5.3815
 ECJ  H8   H  HCR6  0   0.258  -2.5867  -78.8585  -4.6987
 ECJ  H9   H  HNH2  0   0.407  -2.0179  -82.8821  -6.5862
 ECJ  H10  H  HNH2  0   0.414  -0.3165  -83.1490  -6.6999
 ECJ  H11  H  HOH1  0   0.509   0.1653  -75.1223  -7.5721
 ECJ  H12  H  HOH1  0   0.510   1.4902  -72.1539  -5.0116
 ECJ  H13  H  HOH1  0   0.508   4.9091  -71.9967  -6.6652
 ECJ  H15  H  HOH1  0   0.519   8.4926  -76.0053  -4.2121
 ECJ  H16  H  HOH1  0   0.511   5.1871  -79.8988  -2.0792
 ECJ  H17  H  HOH1  0   0.516   8.2766  -81.8654  -4.0247

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
 ECJ  O07  P06  double    1.469  0.020  1.469
 ECJ  O03  P01  double    1.470  0.020  1.470
 ECJ  O05  P06  single    1.605  0.020  1.605
 ECJ  O05  P01  single    1.632  0.020  1.632
 ECJ  O08  P06  single    1.587  0.020  1.587
 ECJ  P06  O09  single    1.593  0.020  1.593
 ECJ  P01  O04  single    1.584  0.020  1.584
 ECJ  P01  O02  single    1.581  0.020  1.581
 ECJ  N23  C22  single    1.331  0.020  1.331
 ECJ  N20  C19  aromatic  1.294  0.020  1.294
 ECJ  N20  C21  aromatic  1.375  0.020  1.375
 ECJ  O09  C10  single    1.417  0.020  1.417
 ECJ  C10  C11  single    1.487  0.020  1.487
 ECJ  C22  C21  aromatic  1.408  0.020  1.408
 ECJ  C22  N24  aromatic  1.339  0.020  1.339
 ECJ  C19  N18  aromatic  1.379  0.020  1.379
 ECJ  C21  C28  aromatic  1.381  0.020  1.381
 ECJ  N24  C25  aromatic  1.329  0.020  1.329
 ECJ  N18  C28  aromatic  1.372  0.020  1.372
 ECJ  N18  C17  single    1.412  0.020  1.412
 ECJ  O36  P33  double    1.475  0.020  1.475
 ECJ  C28  N27  aromatic  1.326  0.020  1.326
 ECJ  C15  C13  single    1.427  0.020  1.427
 ECJ  C15  C17  single    1.525  0.020  1.525
 ECJ  C15  O16  double    1.217  0.020  1.217
 ECJ  C11  C13  double    1.357  0.020  1.357
 ECJ  C11  O12  single    1.326  0.020  1.326
 ECJ  C13  O14  single    1.358  0.020  1.358
 ECJ  C25  N27  aromatic  1.324  0.020  1.324
 ECJ  C17  O12  single    1.431  0.020  1.431
 ECJ  P33  O35  single    1.576  0.020  1.576
 ECJ  P33  O32  single    1.644  0.020  1.644
 ECJ  P33  O34  single    1.572  0.020  1.572
 ECJ  O14  P29  single    1.629  0.020  1.629
 ECJ  O31  P29  double    1.468  0.020  1.468
 ECJ  O32  P29  single    1.601  0.020  1.601
 ECJ  P29  O30  single    1.575  0.020  1.575
 ECJ  C10  H1   single    0.970  0.020  1.090
 ECJ  C10  H2   single    0.970  0.020  1.090
 ECJ  C17  H6   single    0.970  0.020  1.090
 ECJ  C19  H7   single    0.930  0.020  1.080
 ECJ  C25  H8   single    0.930  0.020  1.080
 ECJ  N23  H9   single    0.860  0.020  1.020
 ECJ  N23  H10  single    0.860  0.020  1.020
 ECJ  O02  H11  single    0.850  0.020  0.980
 ECJ  O04  H12  single    0.850  0.020  0.980
 ECJ  O08  H13  single    0.850  0.020  0.980
 ECJ  O30  H15  single    0.850  0.020  0.980
 ECJ  O34  H16  single    0.850  0.020  0.980
 ECJ  O35  H17  single    0.850  0.020  0.980

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
 ECJ  H2   C10  H1   108.17  3.000
 ECJ  H2   C10  O09  111.90  3.000
 ECJ  H1   C10  O09  111.08  3.000
 ECJ  H2   C10  C11  109.75  3.000
 ECJ  H1   C10  C11  108.84  3.000
 ECJ  O09  C10  C11  107.07  3.000
 ECJ  O12  C11  C13  114.07  3.000
 ECJ  O12  C11  C10  116.73  3.000
 ECJ  C13  C11  C10  129.18  3.000
 ECJ  O14  C13  C15  123.79  3.000
 ECJ  O14  C13  C11  128.15  3.000
 ECJ  C15  C13  C11  107.99  3.000
 ECJ  O16  C15  C17  124.09  3.000
 ECJ  O16  C15  C13  131.46  3.000
 ECJ  C17  C15  C13  104.45  3.000
 ECJ  H6   C17  O12  107.56  3.000
 ECJ  H6   C17  N18  109.25  3.000
 ECJ  O12  C17  N18  111.04  3.000
 ECJ  H6   C17  C15  109.99  3.000
 ECJ  O12  C17  C15  104.81  3.000
 ECJ  N18  C17  C15  113.95  3.000
 ECJ  H7   C19  N20  125.46  3.000
 ECJ  H7   C19  N18  121.75  3.000
 ECJ  N20  C19  N18  112.79  3.000
 ECJ  N20  C21  C28  110.98  3.000
 ECJ  C28  C21  C22  116.04  3.000
 ECJ  N20  C21  C22  132.97  3.000
 ECJ  N24  C22  N23  119.44  3.000
 ECJ  N24  C22  C21  117.73  3.000
 ECJ  N23  C22  C21  122.83  3.000
 ECJ  H8   C25  N27  116.15  3.000
 ECJ  H8   C25  N24  115.59  3.000
 ECJ  N27  C25  N24  128.27  3.000
 ECJ  N27  C28  N18  127.94  3.000
 ECJ  N27  C28  C21  127.17  3.000
 ECJ  N18  C28  C21  104.89  3.000
 ECJ  C28  N18  C19  106.41  3.000
 ECJ  C28  N18  C17  125.60  3.000
 ECJ  C19  N18  C17  127.92  3.000
 ECJ  C21  N20  C19  104.93  3.000
 ECJ  H10  N23  H9   118.30  3.000
 ECJ  H10  N23  C22  121.23  3.000
 ECJ  H9   N23  C22  120.36  3.000
 ECJ  C25  N24  C22  119.38  3.000
 ECJ  C28  N27  C25  111.42  3.000
 ECJ  H11  O02  P01  114.82  3.000
 ECJ  H12  O04  P01  114.37  3.000
 ECJ  P06  O05  P01  133.68  3.000
 ECJ  H13  O08  P06  114.60  3.000
 ECJ  P06  O09  C10  121.12  3.000
 ECJ  C17  O12  C11  108.32  3.000
 ECJ  P29  O14  C13  122.92  3.000
 ECJ  H15  O30  P29  115.01  3.000
 ECJ  P33  O32  P29  125.81  3.000
 ECJ  H16  O34  P33  112.54  3.000
 ECJ  H17  O35  P33  115.15  3.000
 ECJ  O05  P01  O04  105.80  3.000
 ECJ  O04  P01  O03  118.57  3.000
 ECJ  O05  P01  O03  108.65  3.000
 ECJ  O04  P01  O02   98.44  3.000
 ECJ  O05  P01  O02  105.10  3.000
 ECJ  O03  P01  O02  118.79  3.000
 ECJ  O09  P06  O08  101.96  3.000
 ECJ  O09  P06  O07  117.45  3.000
 ECJ  O08  P06  O07  116.96  3.000
 ECJ  O09  P06  O05  100.40  3.000
 ECJ  O08  P06  O05  106.18  3.000
 ECJ  O07  P06  O05  111.97  3.000
 ECJ  O32  P29  O31  117.74  3.000
 ECJ  O32  P29  O30   98.08  3.000
 ECJ  O31  P29  O30  119.86  3.000
 ECJ  O30  P29  O14  102.04  3.000
 ECJ  O32  P29  O14  103.39  3.000
 ECJ  O31  P29  O14  113.09  3.000
 ECJ  O36  P33  O35  120.01  3.000
 ECJ  O35  P33  O34  100.10  3.000
 ECJ  O36  P33  O34  118.17  3.000
 ECJ  O34  P33  O32  104.20  3.000
 ECJ  O35  P33  O32  101.87  3.000
 ECJ  O36  P33  O32  110.23  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
 ECJ  CONST_01  C22  C21  N20  C19   180.00   0.0  0
 ECJ  CONST_02  C28  C21  N20  C19     0.00   0.0  0
 ECJ  CONST_03  C21  C28  N18  C19     0.00   0.0  0
 ECJ  CONST_04  N27  C28  N18  C19   180.00   0.0  0
 ECJ  CONST_05  N18  C19  N20  C21     0.00   0.0  0
 ECJ  CONST_06  C25  N24  C22  C21     0.00   0.0  0
 ECJ  CONST_07  C25  N27  C28  C21     0.00   0.0  0
 ECJ  CONST_08  N18  C28  C21  C22   180.00   0.0  0
 ECJ  CONST_09  N27  C28  C21  C22     0.00   0.0  0
 ECJ  CONST_10  N27  C25  N24  C22     0.00   0.0  0
 ECJ  CONST_11  N18  C28  N27  C25   180.00   0.0  0
 ECJ  CONST_12  N24  C22  C21  C28     0.00   0.0  0
 ECJ  CONST_13  N20  C19  N18  C28     0.00   0.0  0
 ECJ  CONST_14  N24  C25  N27  C28     0.00   0.0  0
 ECJ  CONST_15  N20  C21  C28  N18     0.00   0.0  0
 ECJ  CONST_16  N24  C22  C21  N20   180.00   0.0  0
 ECJ  CONST_17  N27  C28  C21  N20   180.00   0.0  0
 ECJ  CONST_18  N20  C19  N18  C17   180.00   0.0  0
 ECJ  CONST_19  C21  C28  N18  C17   180.00   0.0  0
 ECJ  CONST_20  N27  C28  N18  C17     0.00   0.0  0
 ECJ  CONST_21  N23  C22  N24  C25   180.00   0.0  0
 ECJ  CONST_22  N23  C22  C21  C28   180.00   0.0  0
 ECJ  CONST_23  N23  C22  C21  N20     0.00   0.0  0
 ECJ  CONST_24  H7   C19  N18  C17     0.00   0.0  0
 ECJ  CONST_25  H8   C25  N24  C22   180.00   0.0  0
 ECJ  CONST_26  H9   N23  C22  C21   180.00   0.0  0
 ECJ  CONST_27  H10  N23  C22  C21     0.00   0.0  0
 ECJ  Var_01    C17  C15  C13  C11    -3.16  30.0  1
 ECJ  Var_02    O12  C11  C13  C15    -0.66  30.0  1
 ECJ  Var_03    O09  C10  C11  C13  -146.70  30.0  2
 ECJ  Var_04    O31  P29  O14  C13    27.18  30.0  3
 ECJ  Var_05    O07  P06  O09  C10    50.20  30.0  2

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
 ECJ  chir_01  C17  N18  C15  O12  negativ
 ECJ  chir_02  P06  O05  O08  O09  both
 ECJ  chir_03  P29  O32  O31  O14  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
 ECJ  plan-1  C17  0.020
 ECJ  plan-1  C19  0.020
 ECJ  plan-1  C21  0.020
 ECJ  plan-1  C22  0.020
 ECJ  plan-1  C25  0.020
 ECJ  plan-1  C28  0.020
 ECJ  plan-1  N18  0.020
 ECJ  plan-1  N20  0.020
 ECJ  plan-1  N23  0.020
 ECJ  plan-1  N24  0.020
 ECJ  plan-1  N27  0.020
 ECJ  plan-1  H7   0.020
 ECJ  plan-1  H8   0.020
 ECJ  plan-2  C22  0.020
 ECJ  plan-2  N23  0.020
 ECJ  plan-2  H9   0.020
 ECJ  plan-2  H10  0.020
 ECJ  plan-3  C13  0.020
 ECJ  plan-3  C15  0.020
 ECJ  plan-3  C17  0.020
 ECJ  plan-3  O16  0.020

