# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:38:07 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  18  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  OH1   0  -0.597   3.0351   1.0540  -0.1354
 GDE  OAB   O  O     0  -0.446   3.0805  -1.1682   0.0251
 GDE  OAD   O  OH1   0  -0.643  -1.8252   2.2958  -0.0671
 GDE  OAE   O  OH1   0  -0.616  -3.1468  -0.0465   0.1600
 GDE  CAF   C  CR16  0  -0.418   0.2671  -1.2508   0.1290
 GDE  CAG   C  CR16  0  -0.418   0.3027   1.1563  -0.0543
 GDE  CAH   C  C     0   0.536   2.4545  -0.1351  -0.0302
 GDE  CAI   C  CR6   0   0.303  -1.1175  -1.2343   0.1768
 GDE  CAJ   C  CR6   0   0.295  -1.0815   1.1704  -0.0059
 GDE  CAK   C  CR6   0  -0.088   0.9785  -0.0595   0.0138
 GDE  CAL   C  CR6   0   0.229  -1.8042  -0.0194   0.1098
 GDE  HOAA  H  HOH1  0   0.486   3.9973   0.9479  -0.1551
 GDE  HOAC  H  HOH1  0   0.478  -1.3125  -3.1256   0.3209
 GDE  HOAD  H  HOH1  0   0.485  -1.2662   3.0782  -0.1265
 GDE  HOAE  H  HOH1  0   0.477  -3.5030   0.8482   0.0981
 GDE  HAF   H  HCR6  0   0.278   0.7953  -2.1950   0.1838
 GDE  HAG   H  HCR6  0   0.282   0.8392   2.0919  -0.1474
 GDE  OAC   O  OH1   0  -0.625  -1.8737  -2.3431   0.2897

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   single    1.327  0.020  1.327
 GDE  OAB  CAH   double    1.209  0.020  1.209
 GDE  OAC  CAI   single    1.347  0.020  1.347
 GDE  OAD  CAJ   single    1.350  0.020  1.350
 GDE  OAE  CAL   single    1.344  0.020  1.344
 GDE  CAF  CAI   aromatic  1.385  0.020  1.385
 GDE  CAF  CAK   aromatic  1.392  0.020  1.392
 GDE  CAG  CAJ   aromatic  1.385  0.020  1.385
 GDE  CAG  CAK   aromatic  1.393  0.020  1.393
 GDE  CAH  CAK   single    1.479  0.020  1.479
 GDE  CAI  CAL   aromatic  1.397  0.020  1.397
 GDE  CAJ  CAL   aromatic  1.397  0.020  1.397
 GDE  OAA  HOAA  single    0.850  0.020  0.980
 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  HOAA  OAA  CAH  109.76  3.000
 GDE  HOAD  OAD  CAJ  111.10  3.000
 GDE  HOAE  OAE  CAL  110.34  3.000
 GDE  HAF   CAF  CAK  120.05  3.000
 GDE  HAF   CAF  CAI  119.72  3.000
 GDE  CAK   CAF  CAI  120.22  3.000
 GDE  HAG   CAG  CAK  121.21  3.000
 GDE  HAG   CAG  CAJ  119.31  3.000
 GDE  CAK   CAG  CAJ  119.48  3.000
 GDE  CAK   CAH  OAB  123.99  3.000
 GDE  CAK   CAH  OAA  113.15  3.000
 GDE  OAB   CAH  OAA  122.86  3.000
 GDE  CAL   CAI  CAF  119.99  3.000
 GDE  CAL   CAI  OAC  116.35  3.000
 GDE  CAF   CAI  OAC  123.66  3.000
 GDE  CAL   CAJ  CAG  120.75  3.000
 GDE  CAL   CAJ  OAD  115.38  3.000
 GDE  CAG   CAJ  OAD  123.87  3.000
 GDE  CAH   CAK  CAG  121.84  3.000
 GDE  CAH   CAK  CAF  117.96  3.000
 GDE  CAG   CAK  CAF  120.20  3.000
 GDE  CAJ   CAL  CAI  119.36  3.000
 GDE  CAJ   CAL  OAE  122.49  3.000
 GDE  CAI   CAL  OAE  118.14  3.000
 GDE  HOAC  OAC  CAI  110.14  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  CONST_17  HOAA  OAA  CAH  CAK   180.00   0.0  0
 GDE  Var_01    CAF   CAK  CAH  OAA  -179.74  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
 GDE  plan-2  HOAA  0.020

