# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 08:14:20 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: [2,3-diphosphonooxy-5-(3,4,5-triphosphonooxyphenyl)phenyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc(cc(O[P](O)(O)=O)c1O[P](O)(O)=O)c2cc(O[P](O)(O)=O)c(O[P](O)(O)=O)c(O[P](O)(O)=O)c2
#
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
 B6K  B6K  '[2,3-diphosphonooxy-5-(3,4,5-triphosphonooxyphenyl)phenyl] dihydrogen phosphate'  ligand  46  42  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B6K
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
 B6K  C1   C  CR6    0   0.112   0.7033   0.0076  -0.0460
 B6K  C2   C  CR16   0  -0.507   1.3899  -1.0954  -0.5519
 B6K  C3   C  CR6    0   0.291   2.7862  -1.1079  -0.6107
 B6K  O3   O  O2     0  -0.642   3.4875  -2.1278  -1.1272
 B6K  P3   P  P      0   1.225   3.0263  -3.7901  -0.9733
 B6K  C4   C  CR6    0   0.183   3.5174  -0.0072  -0.1323
 B6K  O4   O  O2     0  -0.661   4.8618  -0.0434  -0.1183
 B6K  P4   P  P      0   1.211   5.8085   0.6300  -1.3980
 B6K  C5   C  CR6    0   0.319   2.8293   1.1103   0.3673
 B6K  O5   O  O2     0  -0.644   3.5635   2.1536   0.7825
 B6K  P5   P  P      0   1.213   3.2658   2.9956   2.2605
 B6K  C6   C  CR16   0  -0.516   1.4339   1.1030   0.4151
 B6K  C14  C  CR6    0   0.111  -0.7780   0.0116   0.0176
 B6K  C15  C  CR16   0  -0.530  -1.4759  -1.1697   0.2614
 B6K  C16  C  CR6    0   0.316  -2.8689  -1.1710   0.3653
 B6K  O16  O  O2     0  -0.644  -3.5746  -2.2873   0.6054
 B6K  P16  P  P      0   1.216  -3.0811  -3.4708   1.7652
 B6K  C17  C  CR6    0   0.187  -3.5832   0.0280   0.2211
 B6K  O17  O  O2     0  -0.663  -4.9158   0.0526   0.4005
 B6K  P17  P  P      0   1.215  -6.0290  -0.2951  -0.8737
 B6K  C18  C  CR6    0   0.310  -2.8863   1.2213  -0.0500
 B6K  O18  O  O2     0  -0.636  -3.6218   2.3328  -0.1596
 B6K  P18  P  P      0   1.229  -3.1200   3.8057  -0.9074
 B6K  C19  C  CR16   0  -0.525  -1.4912   1.2006  -0.1396
 B6K  O31  O  OP    -1  -0.890   4.3029  -4.4570  -1.4653
 B6K  O32  O  O      0  -0.894   2.7356  -3.9647   0.5076
 B6K  O33  O  OP    -1  -0.888   1.8332  -3.9650  -1.9045
 B6K  O41  O  O      0  -0.903   4.8128   1.3628  -2.2847
 B6K  O42  O  OP    -1  -0.903   6.7941   1.5144  -0.6432
 B6K  O43  O  OP    -1  -0.897   6.4605  -0.5867  -2.0443
 B6K  O51  O  OP    -1  -0.890   4.5248   3.8466   2.3356
 B6K  O52  O  OP    -1  -0.885   1.9852   3.7918   2.0318
 B6K  O53  O  O      0  -0.898   3.1578   1.8975   3.3070
 B6K  O61  O  OP    -1  -0.883  -1.9237  -4.2188   1.1136
 B6K  O62  O  O      0  -0.901  -2.7065  -2.6605   2.9975
 B6K  O63  O  OP    -1  -0.888  -4.3646  -4.2785   1.8845
 B6K  O71  O  OP    -1  -0.904  -6.8825  -1.4085  -0.2762
 B6K  O72  O  OP    -1  -0.898  -6.7902   1.0139  -1.0466
 B6K  O73  O  O      0  -0.904  -5.1663  -0.7006  -2.0593
 B6K  O81  O  OP    -1  -0.891  -1.9781   4.3311  -0.0435
 B6K  O82  O  O      0  -0.900  -2.7185   3.4099  -2.3189
 B6K  O83  O  OP    -1  -0.889  -4.4100   4.6031  -0.7927
 B6K  H2   H  HCR6   0   0.233   0.8493  -1.9459  -0.9455
 B6K  H6   H  HCR6   0   0.234   0.9301   1.9672   0.8268
 B6K  H15  H  HCR6   0   0.242  -0.9447  -2.1035   0.3926
 B6K  H19  H  HCR6   0   0.234  -0.9647   2.1281  -0.3137

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
 B6K  C2   C1   aromatic  1.394  0.020  1.394
 B6K  C1   C14  single    1.483  0.020  1.483
 B6K  C1   C6   aromatic  1.395  0.020  1.395
 B6K  C3   C2   aromatic  1.398  0.020  1.398
 B6K  C2   H2   single    0.930  0.020  1.080
 B6K  O3   C3   single    1.341  0.020  1.341
 B6K  C3   C4   aromatic  1.405  0.020  1.405
 B6K  P3   O3   single    1.732  0.020  1.732
 B6K  O32  P3   deloc     1.519  0.020  1.519
 B6K  P3   O33  deloc     1.524  0.020  1.524
 B6K  P3   O31  deloc     1.522  0.020  1.522
 B6K  O4   C4   single    1.345  0.020  1.345
 B6K  C4   C5   aromatic  1.404  0.020  1.404
 B6K  O4   P4   single    1.728  0.020  1.728
 B6K  O41  P4   deloc     1.521  0.020  1.521
 B6K  P4   O43  deloc     1.524  0.020  1.524
 B6K  P4   O42  deloc     1.524  0.020  1.524
 B6K  C5   C6   aromatic  1.396  0.020  1.396
 B6K  C5   O5   single    1.342  0.020  1.342
 B6K  O5   P5   single    1.727  0.020  1.727
 B6K  O53  P5   deloc     1.521  0.020  1.521
 B6K  P5   O51  deloc     1.521  0.020  1.521
 B6K  P5   O52  deloc     1.525  0.020  1.525
 B6K  C6   H6   single    0.930  0.020  1.080
 B6K  C19  C14  aromatic  1.395  0.020  1.395
 B6K  C14  C15  aromatic  1.394  0.020  1.394
 B6K  C15  C16  aromatic  1.397  0.020  1.397
 B6K  C15  H15  single    0.930  0.020  1.080
 B6K  C17  C16  aromatic  1.403  0.020  1.403
 B6K  C16  O16  single    1.342  0.020  1.342
 B6K  O16  P16  single    1.729  0.020  1.729
 B6K  O62  P16  deloc     1.522  0.020  1.522
 B6K  P16  O63  deloc     1.521  0.020  1.521
 B6K  P16  O61  deloc     1.524  0.020  1.524
 B6K  C18  C17  aromatic  1.408  0.020  1.408
 B6K  C17  O17  single    1.345  0.020  1.345
 B6K  O17  P17  single    1.727  0.020  1.727
 B6K  O73  P17  deloc     1.521  0.020  1.521
 B6K  P17  O71  deloc     1.525  0.020  1.525
 B6K  P17  O72  deloc     1.524  0.020  1.524
 B6K  O18  C18  single    1.337  0.020  1.337
 B6K  C19  C18  aromatic  1.398  0.020  1.398
 B6K  P18  O18  single    1.726  0.020  1.726
 B6K  O82  P18  deloc     1.520  0.020  1.520
 B6K  O81  P18  deloc     1.525  0.020  1.525
 B6K  P18  O83  deloc     1.521  0.020  1.521
 B6K  C19  H19  single    0.930  0.020  1.080

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
 B6K  C14  C1   C6   120.46  3.000
 B6K  C6   C1   C2   118.89  3.000
 B6K  C14  C1   C2   120.64  3.000
 B6K  H2   C2   C3   118.48  3.000
 B6K  H2   C2   C1   120.52  3.000
 B6K  C3   C2   C1   120.95  3.000
 B6K  C4   C3   O3   117.04  3.000
 B6K  C4   C3   C2   119.90  3.000
 B6K  O3   C3   C2   123.05  3.000
 B6K  P3   O3   C3   123.81  3.000
 B6K  O33  P3   O32  115.64  3.000
 B6K  O33  P3   O31  114.14  3.000
 B6K  O32  P3   O31  115.17  3.000
 B6K  O31  P3   O3    99.70  3.000
 B6K  O33  P3   O3   105.33  3.000
 B6K  O32  P3   O3   104.35  3.000
 B6K  C5   C4   O4   120.50  3.000
 B6K  C5   C4   C3   119.30  3.000
 B6K  O4   C4   C3   120.17  3.000
 B6K  P4   O4   C4   121.96  3.000
 B6K  O43  P4   O42  113.36  3.000
 B6K  O42  P4   O41  115.62  3.000
 B6K  O43  P4   O41  114.67  3.000
 B6K  O42  P4   O4   102.33  3.000
 B6K  O43  P4   O4   103.72  3.000
 B6K  O41  P4   O4   105.11  3.000
 B6K  C6   C5   O5   122.71  3.000
 B6K  O5   C5   C4   117.44  3.000
 B6K  C6   C5   C4   119.86  3.000
 B6K  P5   O5   C5   123.34  3.000
 B6K  O53  P5   O52  114.87  3.000
 B6K  O52  P5   O51  114.22  3.000
 B6K  O53  P5   O51  115.39  3.000
 B6K  O52  P5   O5   105.72  3.000
 B6K  O51  P5   O5    99.92  3.000
 B6K  O53  P5   O5   104.43  3.000
 B6K  H6   C6   C5   118.32  3.000
 B6K  H6   C6   C1   120.60  3.000
 B6K  C5   C6   C1   121.08  3.000
 B6K  C19  C14  C15  119.08  3.000
 B6K  C15  C14  C1   120.37  3.000
 B6K  C19  C14  C1   120.54  3.000
 B6K  H15  C15  C16  118.66  3.000
 B6K  H15  C15  C14  120.45  3.000
 B6K  C16  C15  C14  120.88  3.000
 B6K  C17  C16  O16  117.48  3.000
 B6K  O16  C16  C15  122.57  3.000
 B6K  C17  C16  C15  119.95  3.000
 B6K  P16  O16  C16  122.63  3.000
 B6K  O63  P16  O62  115.28  3.000
 B6K  O63  P16  O61  114.44  3.000
 B6K  O62  P16  O61  114.87  3.000
 B6K  O61  P16  O16  105.42  3.000
 B6K  O63  P16  O16  100.09  3.000
 B6K  O62  P16  O16  104.42  3.000
 B6K  C18  C17  O17  120.04  3.000
 B6K  O17  C17  C16  120.42  3.000
 B6K  C18  C17  C16  119.47  3.000
 B6K  P17  O17  C17  122.45  3.000
 B6K  O73  P17  O72  115.07  3.000
 B6K  O72  P17  O71  113.08  3.000
 B6K  O73  P17  O71  115.35  3.000
 B6K  O72  P17  O17  103.46  3.000
 B6K  O71  P17  O17  102.63  3.000
 B6K  O73  P17  O17  105.26  3.000
 B6K  C19  C18  O18  123.77  3.000
 B6K  C19  C18  C17  119.57  3.000
 B6K  O18  C18  C17  116.61  3.000
 B6K  P18  O18  C18  125.78  3.000
 B6K  O83  P18  O82  115.51  3.000
 B6K  O83  P18  O81  114.31  3.000
 B6K  O82  P18  O81  114.71  3.000
 B6K  O83  P18  O18   99.67  3.000
 B6K  O81  P18  O18  105.43  3.000
 B6K  O82  P18  O18  104.88  3.000
 B6K  H19  C19  C18  118.93  3.000
 B6K  H19  C19  C14  120.04  3.000
 B6K  C18  C19  C14  121.02  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
 B6K  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 B6K  CONST_02  C18  C19  C14  C1    180.00   0.0  0
 B6K  CONST_03  C16  C15  C14  C1    180.00   0.0  0
 B6K  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 B6K  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 B6K  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 B6K  CONST_09  C14  C1   C2   C3    180.00   0.0  0
 B6K  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 B6K  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 B6K  CONST_12  C14  C1   C6   C5    180.00   0.0  0
 B6K  CONST_15  C17  C18  C19  C14     0.00   0.0  0
 B6K  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 B6K  CONST_17  C18  C19  C14  C15     0.00   0.0  0
 B6K  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 B6K  CONST_19  C19  C14  C15  C16     0.00   0.0  0
 B6K  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 B6K  CONST_21  O3   C3   C2   C1    180.00   0.0  0
 B6K  CONST_22  O5   C5   C6   C1    180.00   0.0  0
 B6K  CONST_23  O4   C4   C3   C2    180.00   0.0  0
 B6K  CONST_24  O5   C5   C4   C3    180.00   0.0  0
 B6K  CONST_25  C5   C4   C3   O3    180.00   0.0  0
 B6K  CONST_26  C6   C5   C4   O4    180.00   0.0  0
 B6K  CONST_27  O18  C18  C19  C14   180.00   0.0  0
 B6K  CONST_28  O16  C16  C15  C14   180.00   0.0  0
 B6K  CONST_29  O17  C17  C16  C15   180.00   0.0  0
 B6K  CONST_30  O18  C18  C17  C16   180.00   0.0  0
 B6K  CONST_31  C18  C17  C16  O16   180.00   0.0  0
 B6K  CONST_32  C19  C18  C17  O17   180.00   0.0  0
 B6K  CONST_33  H19  C19  C14  C1      0.00   0.0  0
 B6K  CONST_34  H15  C15  C14  C1      0.00   0.0  0
 B6K  CONST_35  H6   C6   C1   C2    180.00   0.0  0
 B6K  CONST_36  H2   C2   C3   C4    180.00   0.0  0
 B6K  Var_01    C4   C3   O3   P3    145.11  30.0  2
 B6K  Var_02    C5   C4   O4   P4    -86.32  30.0  2
 B6K  Var_03    C6   C5   O5   P5     45.11  30.0  2
 B6K  Var_04    C17  C16  O16  P16  -137.45  30.0  2
 B6K  Var_05    C18  C17  O17  P17    96.20  30.0  2
 B6K  Var_06    C19  C18  O18  P18    20.85  30.0  2
 B6K  Var_07    O32  P3   O3   C3    -49.20  30.0  2
 B6K  Var_08    O41  P4   O4   C4      7.95  30.0  3
 B6K  Var_09    O53  P5   O5   C5     49.59  30.0  3
 B6K  Var_10    O62  P16  O16  C16    46.48  30.0  3
 B6K  Var_11    O73  P17  O17  C17     4.28  30.0  3
 B6K  Var_12    O82  P18  O18  C18    56.23  30.0  3

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
 B6K  plan-1  C1   0.020
 B6K  plan-1  C2   0.020
 B6K  plan-1  C3   0.020
 B6K  plan-1  O3   0.020
 B6K  plan-1  C4   0.020
 B6K  plan-1  O4   0.020
 B6K  plan-1  C5   0.020
 B6K  plan-1  O5   0.020
 B6K  plan-1  C6   0.020
 B6K  plan-1  C14  0.020
 B6K  plan-1  H2   0.020
 B6K  plan-1  H6   0.020
 B6K  plan-2  C1   0.020
 B6K  plan-2  C14  0.020
 B6K  plan-2  C15  0.020
 B6K  plan-2  C16  0.020
 B6K  plan-2  O16  0.020
 B6K  plan-2  C17  0.020
 B6K  plan-2  O17  0.020
 B6K  plan-2  C18  0.020
 B6K  plan-2  O18  0.020
 B6K  plan-2  C19  0.020
 B6K  plan-2  H15  0.020
 B6K  plan-2  H19  0.020

