# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 08:09:18 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: benzene-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(O)c1O
#
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
 PYG  PYG  'benzene-1,2,3-triol      '  ligand  15  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PYG
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
 PYG  C1   C  CR6   0   0.175  -0.0127  -0.0450   1.2773
 PYG  C2   C  CR6   0   0.201  -0.7202  -0.3088   0.1032
 PYG  C3   C  CR6   0   0.239  -0.0323  -0.3253  -1.1110
 PYG  C4   C  CR16  0  -0.341   1.3300  -0.0703  -1.1637
 PYG  C5   C  CR16  0  -0.311   2.0224   0.1984   0.0096
 PYG  C6   C  CR16  0  -0.218   1.3579   0.1920   1.2293
 PYG  O1   O  OH1   0  -0.638  -0.6873  -0.0715   2.4569
 PYG  O2   O  OH1   0  -0.641  -2.0505  -0.5464   0.1871
 PYG  O3   O  OH1   0  -0.622  -0.7587  -0.5997  -2.2331
 PYG  H4   H  HCR6  0   0.264   1.8694  -0.0651  -2.1025
 PYG  H5   H  HCR6  0   0.213   3.0910   0.3675  -0.0290
 PYG  H6   H  HCR6  0   0.262   1.8757   0.4022   2.1602
 PYG  HO1  H  HOH1  0   0.475  -0.4068   0.6565   3.0212
 PYG  HO2  H  HOH1  0   0.469  -2.4969  -0.2179  -0.6021
 PYG  HO3  H  HOH1  0   0.471  -0.5787   0.0382  -2.9296

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
 PYG  C1  C2   aromatic  1.396  0.020  1.396
 PYG  C1  C6   aromatic  1.392  0.020  1.392
 PYG  C1  O1   single    1.359  0.020  1.359
 PYG  C2  C3   aromatic  1.396  0.020  1.396
 PYG  C2  O2   single    1.354  0.020  1.354
 PYG  C3  C4   aromatic  1.387  0.020  1.387
 PYG  C3  O3   single    1.365  0.020  1.365
 PYG  C4  C5   aromatic  1.389  0.020  1.389
 PYG  C4  H4   single    0.930  0.020  1.080
 PYG  C5  C6   aromatic  1.389  0.020  1.389
 PYG  C5  H5   single    0.930  0.020  1.080
 PYG  C6  H6   single    0.930  0.020  1.080
 PYG  O1  HO1  single    0.850  0.020  0.980
 PYG  O2  HO2  single    0.850  0.020  0.980
 PYG  O3  HO3  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
 PYG  O1   C1  C6  121.47  3.000
 PYG  O1   C1  C2  118.34  3.000
 PYG  C6   C1  C2  120.15  3.000
 PYG  O2   C2  C3  122.42  3.000
 PYG  O2   C2  C1  118.63  3.000
 PYG  C3   C2  C1  118.95  3.000
 PYG  O3   C3  C4  121.91  3.000
 PYG  O3   C3  C2  117.09  3.000
 PYG  C4   C3  C2  121.00  3.000
 PYG  H4   C4  C5  118.90  3.000
 PYG  H4   C4  C3  121.55  3.000
 PYG  C5   C4  C3  119.55  3.000
 PYG  H5   C5  C6  120.28  3.000
 PYG  H5   C5  C4  119.49  3.000
 PYG  C6   C5  C4  120.17  3.000
 PYG  H6   C6  C5  121.59  3.000
 PYG  H6   C6  C1  118.23  3.000
 PYG  C5   C6  C1  120.15  3.000
 PYG  HO1  O1  C1  110.45  3.000
 PYG  HO2  O2  C2  110.14  3.000
 PYG  HO3  O3  C3  111.26  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
 PYG  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 PYG  CONST_02  C4  C5  C6  C1    0.00  0.0  0
 PYG  CONST_03  C5  C6  C1  C2    0.00  0.0  0
 PYG  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 PYG  CONST_05  C6  C1  C2  C3    0.00  0.0  0
 PYG  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 PYG  CONST_07  O3  C3  C2  C1  180.00  0.0  0
 PYG  CONST_08  O1  C1  C2  C3  180.00  0.0  0
 PYG  CONST_09  O2  C2  C3  C4  180.00  0.0  0
 PYG  CONST_10  O3  C3  C4  C5  180.00  0.0  0
 PYG  CONST_11  O1  C1  C6  C5  180.00  0.0  0
 PYG  CONST_12  O2  C2  C1  C6  180.00  0.0  0
 PYG  CONST_13  H5  C5  C6  C1  180.00  0.0  0
 PYG  CONST_14  H6  C6  C1  C2  180.00  0.0  0
 PYG  CONST_15  H4  C4  C3  C2  180.00  0.0  0

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
 PYG  plan-1  C1  0.020
 PYG  plan-1  C2  0.020
 PYG  plan-1  C3  0.020
 PYG  plan-1  C4  0.020
 PYG  plan-1  C5  0.020
 PYG  plan-1  C6  0.020
 PYG  plan-1  O1  0.020
 PYG  plan-1  O2  0.020
 PYG  plan-1  O3  0.020
 PYG  plan-1  H4  0.020
 PYG  plan-1  H5  0.020
 PYG  plan-1  H6  0.020

