# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 18:53:20 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 3,4,5-trihydroxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(O)c(O)c(O)c1
#
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
 GDE  GDE  '3,4,5-trihydroxybenzoic acid'  ligand  17  12  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GDE
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
 GDE  OAA   O  OC    -1  -0.658   3.2419   1.0494  -0.0862
 GDE  OAB   O  O      0  -0.522   3.1880  -1.1742  -0.0466
 GDE  OAD   O  OH1    0  -0.692  -1.5377   2.4497  -0.0503
 GDE  OAE   O  OH1    0  -0.648  -3.0093   0.1286   0.2870
 GDE  CAF   C  CR16   0  -0.357   0.4159  -1.1838   0.1740
 GDE  CAG   C  CR16   0  -0.334   0.4672   1.2092  -0.0964
 GDE  CAH   C  C      0   0.378   2.6568  -0.0491  -0.1181
 GDE  CAI   C  CR6    0   0.281  -0.9710  -1.1449   0.2552
 GDE  CAJ   C  CR6    0   0.272  -0.9182   1.2524  -0.0073
 GDE  CAK   C  CR6    0  -0.127   1.1346  -0.0078  -0.0104
 GDE  CAL   C  CR6    0   0.206  -1.6411   0.0728   0.1648
 GDE  HOAC  H  HOH1   0   0.411  -2.5626  -2.1012   0.6885
 GDE  HOAD  H  HOH1   0   0.454  -2.4829   2.3290   0.1055
 GDE  HOAE  H  HOH1   0   0.459  -3.4289  -0.1195  -0.5476
 GDE  HAF   H  HCR6   0   0.267   0.9284  -2.1334   0.2550
 GDE  HAG   H  HCR6   0   0.265   1.0251   2.1279  -0.2213
 GDE  OAC   O  OH1    0  -0.654  -1.6502  -2.2958   0.4434

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
 GDE  OAA  CAH   deloc     1.245  0.020  1.245
 GDE  OAB  CAH   deloc     1.246  0.020  1.246
 GDE  OAC  CAI   single    1.350  0.020  1.350
 GDE  OAD  CAJ   single    1.349  0.020  1.349
 GDE  OAE  CAL   single    1.375  0.020  1.375
 GDE  CAF  CAI   aromatic  1.390  0.020  1.390
 GDE  CAF  CAK   aromatic  1.391  0.020  1.391
 GDE  CAG  CAJ   aromatic  1.389  0.020  1.389
 GDE  CAG  CAK   aromatic  1.391  0.020  1.391
 GDE  CAH  CAK   single    1.527  0.020  1.527
 GDE  CAI  CAL   aromatic  1.393  0.020  1.393
 GDE  CAJ  CAL   aromatic  1.394  0.020  1.394
 GDE  OAC  HOAC  single    0.850  0.020  0.980
 GDE  OAD  HOAD  single    0.850  0.020  0.980
 GDE  OAE  HOAE  single    0.850  0.020  0.980
 GDE  CAF  HAF   single    0.930  0.020  1.080
 GDE  CAG  HAG   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
 GDE  HOAD  OAD  CAJ  109.48  3.000
 GDE  HOAE  OAE  CAL  110.18  3.000
 GDE  HAF   CAF  CAK  120.48  3.000
 GDE  HAF   CAF  CAI  119.53  3.000
 GDE  CAK   CAF  CAI  119.99  3.000
 GDE  HAG   CAG  CAK  120.18  3.000
 GDE  HAG   CAG  CAJ  119.69  3.000
 GDE  CAK   CAG  CAJ  120.13  3.000
 GDE  CAK   CAH  OAB  116.45  3.000
 GDE  CAK   CAH  OAA  116.29  3.000
 GDE  OAB   CAH  OAA  126.50  3.000
 GDE  CAL   CAI  CAF  120.05  3.000
 GDE  CAL   CAI  OAC  120.83  3.000
 GDE  CAF   CAI  OAC  119.11  3.000
 GDE  CAL   CAJ  CAG  119.92  3.000
 GDE  CAL   CAJ  OAD  121.12  3.000
 GDE  CAG   CAJ  OAD  118.93  3.000
 GDE  CAH   CAK  CAG  119.86  3.000
 GDE  CAH   CAK  CAF  120.12  3.000
 GDE  CAG   CAK  CAF  120.02  3.000
 GDE  CAJ   CAL  CAI  119.88  3.000
 GDE  CAJ   CAL  OAE  119.52  3.000
 GDE  CAI   CAL  OAE  120.57  3.000
 GDE  HOAC  OAC  CAI  109.84  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
 GDE  CONST_01  CAJ  CAL  CAI  CAF     0.00   0.0  0
 GDE  CONST_02  CAJ  CAG  CAK  CAF     0.00   0.0  0
 GDE  CONST_03  CAI  CAL  CAJ  CAG     0.00   0.0  0
 GDE  CONST_04  CAI  CAF  CAK  CAG     0.00   0.0  0
 GDE  CONST_05  CAL  CAI  CAF  CAK     0.00   0.0  0
 GDE  CONST_06  CAL  CAJ  CAG  CAK     0.00   0.0  0
 GDE  CONST_07  CAK  CAF  CAI  OAC   180.00   0.0  0
 GDE  CONST_08  CAJ  CAL  CAI  OAC   180.00   0.0  0
 GDE  CONST_09  CAK  CAG  CAJ  OAD   180.00   0.0  0
 GDE  CONST_10  CAI  CAL  CAJ  OAD   180.00   0.0  0
 GDE  CONST_11  CAF  CAI  CAL  OAE   180.00   0.0  0
 GDE  CONST_12  CAG  CAJ  CAL  OAE   180.00   0.0  0
 GDE  CONST_13  CAI  CAF  CAK  CAH   180.00   0.0  0
 GDE  CONST_14  CAJ  CAG  CAK  CAH   180.00   0.0  0
 GDE  CONST_15  HAG  CAG  CAK  CAF   180.00   0.0  0
 GDE  CONST_16  HAF  CAF  CAK  CAG   180.00   0.0  0
 GDE  Var_01    CAF  CAK  CAH  OAA  -169.88  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
 GDE  plan-1  OAD  0.020
 GDE  plan-1  OAE  0.020
 GDE  plan-1  CAF  0.020
 GDE  plan-1  CAG  0.020
 GDE  plan-1  CAH  0.020
 GDE  plan-1  CAI  0.020
 GDE  plan-1  CAJ  0.020
 GDE  plan-1  CAK  0.020
 GDE  plan-1  CAL  0.020
 GDE  plan-1  HAF  0.020
 GDE  plan-1  HAG  0.020
 GDE  plan-1  OAC  0.020
 GDE  plan-2  OAA  0.020
 GDE  plan-2  OAB  0.020
 GDE  plan-2  CAH  0.020
 GDE  plan-2  CAK  0.020

