# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:36:03 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: benzene-1,2,4,5-tetracarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(C(O)=O)c(cc1C(O)=O)C(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
 PMA  PMA  'benzene-1,2,4,5-tetracarboxylic acid'  ligand  20  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PMA
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
 PMA  C1   C  CR6    0  -0.047   0.6900  -0.0326   1.2241
 PMA  C2   C  CR6    0  -0.095  -0.7060   0.0505   1.2302
 PMA  C3   C  CR16   0  -0.340   1.3525  -0.0491   0.0014
 PMA  C4   C  CR6    0  -0.141  -0.7144   0.0470  -1.2170
 PMA  C5   C  CR6    0  -0.039   0.6819  -0.0215  -1.2216
 PMA  C6   C  CR16   0  -0.334  -1.3734   0.0734   0.0115
 PMA  C7   C  C      0   0.377  -1.5259   0.1295  -2.4979
 PMA  C8   C  C      0   0.359   1.5395  -0.1267  -2.4693
 PMA  C9   C  C      0   0.354   1.5134  -0.2126   2.4851
 PMA  C10  C  C      0   0.360  -1.4983   0.1921   2.5150
 PMA  O1   O  O      0  -0.616   1.2726  -1.2386   3.1496
 PMA  O2   O  OC    -1  -0.620   2.4071   0.6294   2.7023
 PMA  O3   O  O      0  -0.603  -0.9570   0.8308   3.4386
 PMA  O4   O  OC    -1  -0.613  -2.6436  -0.3073   2.5330
 PMA  O5   O  O      0  -0.591  -0.9100   0.4284  -3.5392
 PMA  O6   O  OC    -1  -0.608  -2.7527  -0.0939  -2.4087
 PMA  O7   O  O      0  -0.621   1.6106  -1.2547  -2.9919
 PMA  O8   O  OC    -1  -0.625   2.1799   0.8928  -2.7904
 PMA  H3   H  HCR6   0   0.224   2.4368  -0.1089   0.0007
 PMA  H6   H  HCR6   0   0.219  -2.4544   0.1293   0.0123

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
 PMA  C1   C2   aromatic  1.399  0.020  1.399
 PMA  C1   C3   aromatic  1.391  0.020  1.391
 PMA  C1   C9   single    1.517  0.020  1.517
 PMA  C2   C6   aromatic  1.390  0.020  1.390
 PMA  C2   C10  single    1.516  0.020  1.516
 PMA  C3   C5   aromatic  1.395  0.020  1.395
 PMA  C3   H3   single    0.930  0.020  1.080
 PMA  C4   C5   aromatic  1.398  0.020  1.398
 PMA  C4   C6   aromatic  1.394  0.020  1.394
 PMA  C4   C7   single    1.519  0.020  1.519
 PMA  C5   C8   single    1.518  0.020  1.518
 PMA  C6   H6   single    0.930  0.020  1.080
 PMA  C7   O5   deloc     1.246  0.020  1.246
 PMA  C7   O6   deloc     1.250  0.020  1.250
 PMA  C8   O7   deloc     1.245  0.020  1.245
 PMA  C8   O8   deloc     1.246  0.020  1.246
 PMA  C9   O1   deloc     1.246  0.020  1.246
 PMA  C9   O2   deloc     1.247  0.020  1.247
 PMA  C10  O3   deloc     1.247  0.020  1.247
 PMA  C10  O4   deloc     1.250  0.020  1.250

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
 PMA  C9   C1   C3  118.09  3.000
 PMA  C9   C1   C2  123.05  3.000
 PMA  C3   C1   C2  118.68  3.000
 PMA  C10  C2   C6  119.38  3.000
 PMA  C10  C2   C1  122.06  3.000
 PMA  C6   C2   C1  118.47  3.000
 PMA  H3   C3   C5  118.72  3.000
 PMA  H3   C3   C1  118.48  3.000
 PMA  C5   C3   C1  122.79  3.000
 PMA  C7   C4   C6  119.31  3.000
 PMA  C7   C4   C5  122.25  3.000
 PMA  C6   C4   C5  118.42  3.000
 PMA  C8   C5   C4  124.78  3.000
 PMA  C8   C5   C3  116.60  3.000
 PMA  C4   C5   C3  118.57  3.000
 PMA  H6   C6   C4  118.27  3.000
 PMA  H6   C6   C2  118.68  3.000
 PMA  C4   C6   C2  123.05  3.000
 PMA  O6   C7   O5  125.98  3.000
 PMA  O6   C7   C4  117.03  3.000
 PMA  O5   C7   C4  116.98  3.000
 PMA  O8   C8   O7  127.13  3.000
 PMA  O8   C8   C5  116.46  3.000
 PMA  O7   C8   C5  116.11  3.000
 PMA  O2   C9   O1  126.99  3.000
 PMA  O2   C9   C1  116.99  3.000
 PMA  O1   C9   C1  115.86  3.000
 PMA  O4   C10  O3  126.30  3.000
 PMA  O4   C10  C2  116.99  3.000
 PMA  O3   C10  C2  116.67  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
 PMA  CONST_01  C4   C6   C2  C1    0.00   0.0  0
 PMA  CONST_02  C4   C5   C3  C1    0.00   0.0  0
 PMA  CONST_03  C5   C3   C1  C2    0.00   0.0  0
 PMA  CONST_04  C5   C4   C6  C2    0.00   0.0  0
 PMA  CONST_05  C6   C2   C1  C3    0.00   0.0  0
 PMA  CONST_06  C6   C4   C5  C3    0.00   0.0  0
 PMA  CONST_07  C8   C5   C3  C1  180.00   0.0  0
 PMA  CONST_08  C7   C4   C6  C2  180.00   0.0  0
 PMA  CONST_09  C10  C2   C1  C3  180.00   0.0  0
 PMA  CONST_10  C7   C4   C5  C3  180.00   0.0  0
 PMA  CONST_11  C10  C2   C6  C4  180.00   0.0  0
 PMA  CONST_12  C9   C1   C3  C5  180.00   0.0  0
 PMA  CONST_13  C9   C1   C2  C6  180.00   0.0  0
 PMA  CONST_14  C8   C5   C4  C6  180.00   0.0  0
 PMA  CONST_15  H6   C6   C2  C1  180.00   0.0  0
 PMA  CONST_16  H3   C3   C1  C2  180.00   0.0  0
 PMA  Var_01    O3   C10  C2  C1   32.59  30.0  2
 PMA  Var_02    O1   C9   C1  C2   59.38  30.0  2
 PMA  Var_03    O7   C8   C5  C3   98.99  30.0  2
 PMA  Var_04    O5   C7   C4  C5  -15.36  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
 PMA  plan-1  C1   0.020
 PMA  plan-1  C2   0.020
 PMA  plan-1  C3   0.020
 PMA  plan-1  C4   0.020
 PMA  plan-1  C5   0.020
 PMA  plan-1  C6   0.020
 PMA  plan-1  C7   0.020
 PMA  plan-1  C8   0.020
 PMA  plan-1  C9   0.020
 PMA  plan-1  C10  0.020
 PMA  plan-1  H3   0.020
 PMA  plan-1  H6   0.020
 PMA  plan-2  C4   0.020
 PMA  plan-2  C7   0.020
 PMA  plan-2  O5   0.020
 PMA  plan-2  O6   0.020
 PMA  plan-3  C5   0.020
 PMA  plan-3  C8   0.020
 PMA  plan-3  O7   0.020
 PMA  plan-3  O8   0.020
 PMA  plan-4  C1   0.020
 PMA  plan-4  C9   0.020
 PMA  plan-4  O1   0.020
 PMA  plan-4  O2   0.020
 PMA  plan-5  C2   0.020
 PMA  plan-5  C10  0.020
 PMA  plan-5  O3   0.020
 PMA  plan-5  O4   0.020

