# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:15:54 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (phenylmethanediyl)bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(c1ccccc1)[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
 787  787  '(phenylmethanediyl)bis(phosphonic acid)'  ligand  25  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_787
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
 787  C1   C  CR16  0  -0.261  -3.9825   0.0211   0.2187
 787  C2   C  CR16  0  -0.239  -3.4981   0.1424  -1.0765
 787  C3   C  CR16  0  -0.299  -2.1303   0.1657  -1.3081
 787  C4   C  CR6   0   0.115  -1.2299   0.0702  -0.2504
 787  C5   C  CR16  0  -0.277  -1.7220  -0.0493   1.0485
 787  C6   C  CR16  0  -0.240  -3.0905  -0.0755   1.2782
 787  C7   C  CH1   0  -0.928   0.2523   0.0907  -0.5422
 787  P8   P  P     0   1.385   1.0852  -1.4200   0.0681
 787  P9   P  P     0   1.401   1.0097   1.6084   0.1188
 787  O11  O  OH1   0  -0.752   2.5392   1.3397  -0.2960
 787  O12  O  OH1   0  -0.733   0.4622   2.8004  -0.7994
 787  O13  O  O     0  -0.685   0.7558   1.9185   1.5402
 787  O14  O  OH1   0  -0.733   2.3782  -1.6154  -0.8511
 787  O15  O  O     0  -0.688   1.2894  -1.4162   1.5345
 787  O16  O  OH1   0  -0.731   0.2294  -2.6263  -0.5392
 787  H1   H  HCR6  0   0.261  -5.0491   0.0015   0.4006
 787  H2   H  HCR6  0   0.262  -4.1846   0.2178  -1.9094
 787  H3   H  HCR6  0   0.261  -1.7604   0.2584  -2.3221
 787  H5   H  HCR6  0   0.266  -1.0409  -0.1227   1.8848
 787  H6   H  HCR6  0   0.260  -3.4595  -0.1709   2.2911
 787  H7   H  HCH1  0   0.358   0.3930   0.1007  -1.6286
 787  H11  H  HOH1  0   0.505   3.1822   1.9524   0.0894
 787  H12  H  HOH1  0   0.495   0.6501   2.7365  -1.7450
 787  H14  H  HOH1  0   0.497   3.0653  -0.9499  -0.7080
 787  H16  H  HOH1  0   0.500  -0.4829  -2.9324   0.0371

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
 787  C1   C2   aromatic  1.388  0.020  1.388
 787  C1   C6   aromatic  1.388  0.020  1.388
 787  C1   H1   single    0.930  0.020  1.080
 787  C2   C3   aromatic  1.387  0.020  1.387
 787  C2   H2   single    0.930  0.020  1.080
 787  C3   C4   aromatic  1.392  0.020  1.392
 787  C3   H3   single    0.930  0.020  1.080
 787  C4   C5   aromatic  1.394  0.020  1.394
 787  C4   C7   single    1.511  0.020  1.511
 787  C5   C6   aromatic  1.388  0.020  1.388
 787  C5   H5   single    0.930  0.020  1.080
 787  C6   H6   single    0.930  0.020  1.080
 787  C7   P8   single    1.830  0.020  1.830
 787  C7   P9   single    1.820  0.020  1.820
 787  C7   H7   single    0.970  0.020  1.090
 787  P8   O14  single    1.598  0.020  1.598
 787  P8   O15  double    1.481  0.020  1.481
 787  P8   O16  single    1.599  0.020  1.599
 787  P9   O11  single    1.607  0.020  1.607
 787  P9   O12  single    1.601  0.020  1.601
 787  P9   O13  double    1.477  0.020  1.477
 787  O11  H11  single    0.850  0.020  0.980
 787  O12  H12  single    0.850  0.020  0.980
 787  O14  H14  single    0.850  0.020  0.980
 787  O16  H16  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
 787  H1   C1   C6   120.25  3.000
 787  H1   C1   C2   120.15  3.000
 787  C6   C1   C2   119.60  3.000
 787  H2   C2   C3   119.72  3.000
 787  H2   C2   C1   120.20  3.000
 787  C3   C2   C1   120.08  3.000
 787  H3   C3   C4   119.74  3.000
 787  H3   C3   C2   119.63  3.000
 787  C4   C3   C2   120.63  3.000
 787  C7   C4   C5   121.83  3.000
 787  C7   C4   C3   119.13  3.000
 787  C5   C4   C3   119.04  3.000
 787  H5   C5   C6   119.47  3.000
 787  H5   C5   C4   120.28  3.000
 787  C6   C5   C4   120.25  3.000
 787  H6   C6   C5   119.52  3.000
 787  H6   C6   C1   120.09  3.000
 787  C5   C6   C1   120.40  3.000
 787  H7   C7   P9   107.40  3.000
 787  H7   C7   P8   106.25  3.000
 787  P9   C7   P8   112.20  3.000
 787  H7   C7   C4   108.53  3.000
 787  P9   C7   C4   110.45  3.000
 787  P8   C7   C4   111.77  3.000
 787  O16  P8   O15  116.87  3.000
 787  O16  P8   O14   97.02  3.000
 787  O15  P8   O14  117.28  3.000
 787  O16  P8   C7   104.63  3.000
 787  O15  P8   C7   113.02  3.000
 787  O14  P8   C7   106.10  3.000
 787  O13  P9   O12  109.69  3.000
 787  O13  P9   O11  116.55  3.000
 787  O12  P9   O11  107.57  3.000
 787  O13  P9   C7   116.94  3.000
 787  O12  P9   C7   105.67  3.000
 787  O11  P9   C7    99.37  3.000
 787  H11  O11  P9   115.06  3.000
 787  H12  O12  P9   116.45  3.000
 787  H14  O14  P8   113.92  3.000
 787  H16  O16  P8   114.03  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
 787  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 787  CONST_02  C4   C5  C6  C1     0.00   0.0  0
 787  CONST_03  C5   C6  C1  C2     0.00   0.0  0
 787  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 787  CONST_05  C6   C1  C2  C3     0.00   0.0  0
 787  CONST_06  C6   C5  C4  C3     0.00   0.0  0
 787  CONST_07  C7   C4  C3  C2   180.00   0.0  0
 787  CONST_08  C7   C4  C5  C6   180.00   0.0  0
 787  CONST_09  H3   C3  C2  C1   180.00   0.0  0
 787  CONST_10  H5   C5  C6  C1   180.00   0.0  0
 787  CONST_11  H6   C6  C1  C2   180.00   0.0  0
 787  CONST_12  H1   C1  C2  C3   180.00   0.0  0
 787  CONST_13  H2   C2  C3  C4   180.00   0.0  0
 787  Var_01    P8   C7  C4  C3  -121.50  30.0  2
 787  Var_02    O14  P8  C7  C4   153.74  30.0  3
 787  Var_03    O11  P9  C7  C4   178.68  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
 787  plan-1  C1  0.020
 787  plan-1  C2  0.020
 787  plan-1  C3  0.020
 787  plan-1  C4  0.020
 787  plan-1  C5  0.020
 787  plan-1  C6  0.020
 787  plan-1  C7  0.020
 787  plan-1  H1  0.020
 787  plan-1  H2  0.020
 787  plan-1  H3  0.020
 787  plan-1  H5  0.020
 787  plan-1  H6  0.020

