# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:50:07 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: methanediyldibenzene-4,1-diyl bis[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc(Cc2ccc(O[P](O)(O)=O)cc2)cc1
#
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
 BPM  BPM  'methanediyldibenzene-4,1-diyl bis[dihydrogen (phosphate)]'  ligand  33  23  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BPM
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
 BPM  C0    C  CH2    0  -0.618   0.0007   0.0400  -2.1527
 BPM  C1A   C  CR6    0   0.138  -1.2477   0.0303  -1.3045
 BPM  C2A   C  CR16   0  -0.310  -1.8233   1.2167  -0.8571
 BPM  C3A   C  CR16   0  -0.335  -2.9386   1.2129  -0.0316
 BPM  C5A   C  CR16   0  -0.334  -2.9487  -1.1818  -0.0732
 BPM  C6A   C  CR16   0  -0.312  -1.8337  -1.1659  -0.8990
 BPM  C4A   C  CR6    0   0.378  -3.5061   0.0101   0.3932
 BPM  O1A   O  O2     0  -0.673  -4.5345   0.0004   1.2524
 BPM  PA    P  P      0   1.203  -6.1621  -0.0014   0.6123
 BPM  O2A   O  O      0  -0.878  -6.2342   1.2809  -0.1998
 BPM  O3A   O  OP    -1  -0.878  -6.2320  -1.2824  -0.2023
 BPM  O4A   O  OP    -1  -0.884  -6.9468  -0.0038   1.9127
 BPM  C1B   C  CR6    0   0.138   1.2526   0.0344  -1.3097
 BPM  C2B   C  CR16   0  -0.310   1.8112  -1.1600  -0.8613
 BPM  C3B   C  CR16   0  -0.331   2.9279  -1.1720  -0.0385
 BPM  C5B   C  CR16   0  -0.337   2.9767   1.2221  -0.0871
 BPM  C6B   C  CR16   0  -0.313   1.8585   1.2219  -0.9096
 BPM  C4B   C  CR6    0   0.378   3.5156   0.0231   0.3818
 BPM  O1B   O  O2     0  -0.674   4.5454   0.0210   1.2395
 BPM  PB    P  P      0   1.203   6.1692  -0.0998   0.6007
 BPM  O2B   O  O      0  -0.877   6.1668  -1.4143  -0.1618
 BPM  O3B   O  OP    -1  -0.879   6.3116   1.1427  -0.2620
 BPM  O4B   O  OP    -1  -0.884   6.9552  -0.0926   1.9005
 BPM  HC01  H  HCH2   0   0.255  -0.0001  -0.8309  -2.8127
 BPM  HC02  H  HCH2   0   0.255  -0.0016   0.9213  -2.7987
 BPM  H2A   H  HCR6   0   0.233  -1.3942   2.1658  -1.1603
 BPM  H3A   H  HCR6   0   0.236  -3.3703   2.1483   0.3005
 BPM  H5A   H  HCR6   0   0.236  -3.3877  -2.1246   0.2268
 BPM  H6A   H  HCR6   0   0.234  -1.4123  -2.1074  -1.2349
 BPM  H2B   H  HCR6   0   0.233   1.3672  -2.1031  -1.1616
 BPM  H3B   H  HCR6   0   0.236   3.3457  -2.1128   0.2953
 BPM  H5B   H  HCR6   0   0.236   3.4309   2.1592   0.2091
 BPM  H6B   H  HCR6   0   0.234   1.4506   2.1688  -1.2468

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
 BPM  C0   C1A   single    1.509  0.020  1.509
 BPM  C0   C1B   single    1.509  0.020  1.509
 BPM  C0   HC01  single    0.970  0.020  1.090
 BPM  C0   HC02  single    0.970  0.020  1.090
 BPM  C1A  C2A   aromatic  1.393  0.020  1.393
 BPM  C1A  C6A   aromatic  1.392  0.020  1.392
 BPM  C2A  C3A   aromatic  1.388  0.020  1.388
 BPM  C2A  H2A   single    0.930  0.020  1.080
 BPM  C3A  C4A   aromatic  1.396  0.020  1.396
 BPM  C3A  H3A   single    0.930  0.020  1.080
 BPM  C5A  C6A   aromatic  1.388  0.020  1.388
 BPM  C5A  C4A   aromatic  1.396  0.020  1.396
 BPM  C5A  H5A   single    0.930  0.020  1.080
 BPM  C6A  H6A   single    0.930  0.020  1.080
 BPM  C4A  O1A   single    1.340  0.020  1.340
 BPM  O1A  PA    single    1.749  0.020  1.749
 BPM  PA   O2A   deloc     1.520  0.020  1.520
 BPM  PA   O3A   deloc     1.520  0.020  1.520
 BPM  PA   O4A   deloc     1.519  0.020  1.519
 BPM  C1B  C2B   aromatic  1.393  0.020  1.393
 BPM  C1B  C6B   aromatic  1.392  0.020  1.392
 BPM  C2B  C3B   aromatic  1.387  0.020  1.387
 BPM  C2B  H2B   single    0.930  0.020  1.080
 BPM  C3B  C4B   aromatic  1.397  0.020  1.397
 BPM  C3B  H3B   single    0.930  0.020  1.080
 BPM  C5B  C6B   aromatic  1.388  0.020  1.388
 BPM  C5B  C4B   aromatic  1.396  0.020  1.396
 BPM  C5B  H5B   single    0.930  0.020  1.080
 BPM  C6B  H6B   single    0.930  0.020  1.080
 BPM  C4B  O1B   single    1.340  0.020  1.340
 BPM  O1B  PB    single    1.749  0.020  1.749
 BPM  PB   O2B   deloc     1.520  0.020  1.520
 BPM  PB   O3B   deloc     1.519  0.020  1.519
 BPM  PB   O4B   deloc     1.519  0.020  1.519

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
 BPM  HC02  C0   HC01  106.60  3.000
 BPM  HC02  C0   C1B   109.57  3.000
 BPM  HC01  C0   C1B   109.57  3.000
 BPM  HC02  C0   C1A   109.61  3.000
 BPM  HC01  C0   C1A   109.49  3.000
 BPM  C1B   C0   C1A   111.85  3.000
 BPM  C6A   C1A  C2A   117.68  3.000
 BPM  C6A   C1A  C0    121.15  3.000
 BPM  C2A   C1A  C0    121.13  3.000
 BPM  H2A   C2A  C3A   119.12  3.000
 BPM  H2A   C2A  C1A   119.48  3.000
 BPM  C3A   C2A  C1A   121.40  3.000
 BPM  H3A   C3A  C4A   119.28  3.000
 BPM  H3A   C3A  C2A   120.05  3.000
 BPM  C4A   C3A  C2A   120.67  3.000
 BPM  H5A   C5A  C4A   119.28  3.000
 BPM  H5A   C5A  C6A   120.06  3.000
 BPM  C4A   C5A  C6A   120.66  3.000
 BPM  H6A   C6A  C5A   119.11  3.000
 BPM  H6A   C6A  C1A   119.47  3.000
 BPM  C5A   C6A  C1A   121.42  3.000
 BPM  O1A   C4A  C5A   120.96  3.000
 BPM  O1A   C4A  C3A   120.88  3.000
 BPM  C5A   C4A  C3A   118.14  3.000
 BPM  PA    O1A  C4A   118.65  3.000
 BPM  O4A   PA   O3A   115.71  3.000
 BPM  O4A   PA   O2A   115.75  3.000
 BPM  O3A   PA   O2A   115.01  3.000
 BPM  O4A   PA   O1A    99.64  3.000
 BPM  O3A   PA   O1A   103.88  3.000
 BPM  O2A   PA   O1A   103.82  3.000
 BPM  C6B   C1B  C2B   117.68  3.000
 BPM  C6B   C1B  C0    121.23  3.000
 BPM  C2B   C1B  C0    121.04  3.000
 BPM  H2B   C2B  C3B   119.09  3.000
 BPM  H2B   C2B  C1B   119.49  3.000
 BPM  C3B   C2B  C1B   121.42  3.000
 BPM  H3B   C3B  C4B   119.25  3.000
 BPM  H3B   C3B  C2B   120.09  3.000
 BPM  C4B   C3B  C2B   120.66  3.000
 BPM  H5B   C5B  C4B   119.32  3.000
 BPM  H5B   C5B  C6B   120.01  3.000
 BPM  C4B   C5B  C6B   120.66  3.000
 BPM  H6B   C6B  C5B   119.14  3.000
 BPM  H6B   C6B  C1B   119.45  3.000
 BPM  C5B   C6B  C1B   121.41  3.000
 BPM  O1B   C4B  C5B   120.87  3.000
 BPM  O1B   C4B  C3B   120.97  3.000
 BPM  C5B   C4B  C3B   118.14  3.000
 BPM  PB    O1B  C4B   118.67  3.000
 BPM  O4B   PB   O3B   115.69  3.000
 BPM  O4B   PB   O2B   115.73  3.000
 BPM  O3B   PB   O2B   115.00  3.000
 BPM  O4B   PB   O1B    99.65  3.000
 BPM  O3B   PB   O1B   103.77  3.000
 BPM  O2B   PB   O1B   103.98  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
 BPM  CONST_01  C4A  C3A  C2A  C1A    0.00   0.0  0
 BPM  CONST_02  C4A  C5A  C6A  C1A    0.00   0.0  0
 BPM  CONST_03  C5A  C6A  C1A  C2A    0.00   0.0  0
 BPM  CONST_04  C5A  C4A  C3A  C2A    0.00   0.0  0
 BPM  CONST_05  C6A  C1A  C2A  C3A    0.00   0.0  0
 BPM  CONST_06  C6A  C5A  C4A  C3A    0.00   0.0  0
 BPM  CONST_07  C4B  C3B  C2B  C1B    0.00   0.0  0
 BPM  CONST_08  C4B  C5B  C6B  C1B    0.00   0.0  0
 BPM  CONST_09  C5B  C6B  C1B  C2B    0.00   0.0  0
 BPM  CONST_10  C5B  C4B  C3B  C2B    0.00   0.0  0
 BPM  CONST_11  C6B  C1B  C2B  C3B    0.00   0.0  0
 BPM  CONST_12  C6B  C5B  C4B  C3B    0.00   0.0  0
 BPM  CONST_13  C3A  C2A  C1A  C0   180.00   0.0  0
 BPM  CONST_14  C5A  C6A  C1A  C0   180.00   0.0  0
 BPM  CONST_15  C3B  C2B  C1B  C0   180.00   0.0  0
 BPM  CONST_16  C5B  C6B  C1B  C0   180.00   0.0  0
 BPM  CONST_17  O1A  C4A  C3A  C2A  180.00   0.0  0
 BPM  CONST_18  O1A  C4A  C5A  C6A  180.00   0.0  0
 BPM  CONST_19  O1B  C4B  C3B  C2B  180.00   0.0  0
 BPM  CONST_20  O1B  C4B  C5B  C6B  180.00   0.0  0
 BPM  CONST_21  H3A  C3A  C2A  C1A  180.00   0.0  0
 BPM  CONST_22  H5A  C5A  C6A  C1A  180.00   0.0  0
 BPM  CONST_23  H6A  C6A  C1A  C2A  180.00   0.0  0
 BPM  CONST_24  H2A  C2A  C1A  C6A  180.00   0.0  0
 BPM  CONST_25  H3B  C3B  C2B  C1B  180.00   0.0  0
 BPM  CONST_26  H5B  C5B  C6B  C1B  180.00   0.0  0
 BPM  CONST_27  H6B  C6B  C1B  C2B  180.00   0.0  0
 BPM  CONST_28  H2B  C2B  C1B  C6B  180.00   0.0  0
 BPM  Var_01    C2B  C1B  C0   C1A   86.64  30.0  2
 BPM  Var_02    C1B  C0   C1A  C2A   88.13  30.0  2
 BPM  Var_03    O2A  PA   O1A  C4A  -59.94  30.0  3
 BPM  Var_04    O2B  PB   O1B  C4B  -59.13  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
 BPM  plan-1  C0   0.020
 BPM  plan-1  C1A  0.020
 BPM  plan-1  C2A  0.020
 BPM  plan-1  C3A  0.020
 BPM  plan-1  C5A  0.020
 BPM  plan-1  C6A  0.020
 BPM  plan-1  C4A  0.020
 BPM  plan-1  O1A  0.020
 BPM  plan-1  H2A  0.020
 BPM  plan-1  H3A  0.020
 BPM  plan-1  H5A  0.020
 BPM  plan-1  H6A  0.020
 BPM  plan-2  C0   0.020
 BPM  plan-2  C1B  0.020
 BPM  plan-2  C2B  0.020
 BPM  plan-2  C3B  0.020
 BPM  plan-2  C5B  0.020
 BPM  plan-2  C6B  0.020
 BPM  plan-2  C4B  0.020
 BPM  plan-2  O1B  0.020
 BPM  plan-2  H2B  0.020
 BPM  plan-2  H3B  0.020
 BPM  plan-2  H5B  0.020
 BPM  plan-2  H6B  0.020

