# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 06:03:48 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: benzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1C(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
 PHT  PHT  'benzene-1,2-dicarboxylic acid'  ligand  18  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PHT
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
 PHT  O8   O  O     0  -0.425   1.0120   1.1770   1.9116
 PHT  O9   O  OH1   0  -0.580   1.9946  -0.8108   1.6135
 PHT  O11  O  O     0  -0.433  -1.3127  -0.6499   1.7170
 PHT  O12  O  OH1   0  -0.586  -2.8385   0.1352   0.2889
 PHT  C7   C  C     0   0.466   1.2279   0.2004   1.2430
 PHT  C1   C  CR16  0  -0.256  -1.0310  -0.0451  -1.7976
 PHT  C2   C  CR6   0  -0.065  -0.6266  -0.0326  -0.4659
 PHT  C3   C  CR6   0  -0.004   0.7352   0.0407  -0.1599
 PHT  C4   C  CR16  0  -0.250   1.6707   0.0853  -1.1844
 PHT  C5   C  CR16  0  -0.235   1.2580   0.0729  -2.5099
 PHT  C6   C  CR16  0  -0.239  -0.0921   0.0104  -2.8167
 PHT  H9   H  HOH1  0   0.490   2.3544  -0.6507   2.5001
 PHT  H12  H  HOH1  0   0.492  -3.4547  -0.0535   1.0130
 PHT  H1   H  HCR6  0   0.278  -2.0802  -0.1198  -2.0476
 PHT  H4   H  HCR6  0   0.279   2.7266   0.1460  -0.9549
 PHT  H5   H  HCR6  0   0.277   1.9954   0.1120  -3.3001
 PHT  H6   H  HCR6  0   0.274  -0.4167  -0.0050  -3.8483
 PHT  C10  C  C     0   0.517  -1.6098  -0.2115   0.6325

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
 PHT  O8   C7   double    1.203  0.020  1.203
 PHT  O9   C7   single    1.322  0.020  1.322
 PHT  O9   H9   single    0.850  0.020  0.980
 PHT  C10  O11  double    1.207  0.020  1.207
 PHT  C10  O12  single    1.322  0.020  1.322
 PHT  C10  C2   single    1.485  0.020  1.485
 PHT  O12  H12  single    0.850  0.020  0.980
 PHT  C7   C3   single    1.495  0.020  1.495
 PHT  C1   C2   aromatic  1.392  0.020  1.392
 PHT  C1   C6   aromatic  1.387  0.020  1.387
 PHT  C1   H1   single    0.930  0.020  1.080
 PHT  C2   C3   aromatic  1.398  0.020  1.398
 PHT  C3   C4   aromatic  1.388  0.020  1.388
 PHT  C4   C5   aromatic  1.388  0.020  1.388
 PHT  C4   H4   single    0.930  0.020  1.080
 PHT  C5   C6   aromatic  1.386  0.020  1.386
 PHT  C5   H5   single    0.930  0.020  1.080
 PHT  C6   H6   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
 PHT  H9   O9   C7   110.18  3.000
 PHT  H12  O12  C10  110.22  3.000
 PHT  C3   C7   O9   111.86  3.000
 PHT  C3   C7   O8   123.29  3.000
 PHT  O9   C7   O8   124.70  3.000
 PHT  H1   C1   C6   119.33  3.000
 PHT  H1   C1   C2   120.25  3.000
 PHT  C6   C1   C2   120.41  3.000
 PHT  C3   C2   C1   119.54  3.000
 PHT  C3   C2   C10  119.31  3.000
 PHT  C1   C2   C10  120.95  3.000
 PHT  C4   C3   C2   119.79  3.000
 PHT  C4   C3   C7   117.83  3.000
 PHT  C2   C3   C7   122.14  3.000
 PHT  H4   C4   C5   119.53  3.000
 PHT  H4   C4   C3   120.19  3.000
 PHT  C5   C4   C3   120.27  3.000
 PHT  H5   C5   C6   120.27  3.000
 PHT  H5   C5   C4   119.64  3.000
 PHT  C6   C5   C4   120.09  3.000
 PHT  H6   C6   C5   120.28  3.000
 PHT  H6   C6   C1   119.81  3.000
 PHT  C5   C6   C1   119.91  3.000
 PHT  C2   C10  O12  113.05  3.000
 PHT  C2   C10  O11  123.05  3.000
 PHT  O12  C10  O11  123.89  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
 PHT  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 PHT  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 PHT  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 PHT  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 PHT  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 PHT  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 PHT  CONST_07  C6   C1   C2   C10  180.00   0.0  0
 PHT  CONST_08  C4   C3   C2   C10  180.00   0.0  0
 PHT  CONST_09  C1   C2   C3   C7   180.00   0.0  0
 PHT  CONST_10  C5   C4   C3   C7   180.00   0.0  0
 PHT  CONST_11  H5   C5   C6   C1   180.00   0.0  0
 PHT  CONST_12  H6   C6   C1   C2   180.00   0.0  0
 PHT  CONST_13  H4   C4   C3   C2   180.00   0.0  0
 PHT  CONST_14  H1   C1   C2   C3   180.00   0.0  0
 PHT  CONST_15  H12  O12  C10  C2   180.00   0.0  0
 PHT  CONST_16  H9   O9   C7   C3   180.00   0.0  0
 PHT  Var_01    C2   C3   C7   O8   -64.69  30.0  2
 PHT  Var_02    C1   C2   C10  O11  154.27  30.0  2

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
 PHT  plan-1  C7   0.020
 PHT  plan-1  C1   0.020
 PHT  plan-1  C2   0.020
 PHT  plan-1  C3   0.020
 PHT  plan-1  C4   0.020
 PHT  plan-1  C5   0.020
 PHT  plan-1  C6   0.020
 PHT  plan-1  H1   0.020
 PHT  plan-1  H4   0.020
 PHT  plan-1  H5   0.020
 PHT  plan-1  H6   0.020
 PHT  plan-1  C10  0.020
 PHT  plan-2  O8   0.020
 PHT  plan-2  O9   0.020
 PHT  plan-2  C7   0.020
 PHT  plan-2  C3   0.020
 PHT  plan-2  H9   0.020
 PHT  plan-3  O11  0.020
 PHT  plan-3  O12  0.020
 PHT  plan-3  C2   0.020
 PHT  plan-3  H12  0.020
 PHT  plan-3  C10  0.020

