# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:39:10 2021
#   Inital geometry file: a 54 line input string
#   Ligand name: 2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(F)c(F)cc(C(O)=O)c1F
#
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
 SYA  SYA  '2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid'  ligand  19  14  .  2022-03-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SYA
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
 SYA  C4  C  CR16  0  -0.439  -2.7137  13.8716  -34.3516
 SYA  C5  C  CR6   0   0.423  -2.0462  12.7678  -34.8146
 SYA  C6  C  CR6   0   0.381  -0.9242  12.9086  -35.6158
 SYA  C2  C  CR6   0   0.540  -1.1504  15.2793  -35.4888
 SYA  C3  C  CR6   0  -0.305  -2.2750  15.1559  -34.6824
 SYA  O2  O  OH1   0  -0.582  -2.6137  17.4801  -34.4827
 SYA  O1  O  O     0  -0.428  -4.0362  16.1223  -33.4371
 SYA  F1  F  F     0  -0.299  -2.4600  11.5395  -34.5005
 SYA  F   F  F     0  -0.283  -0.2869  11.8333  -36.0577
 SYA  C1  C  CR6   0   0.067  -0.4617  14.1663  -35.9678
 SYA  O   O  O2    0  -0.479   0.6060  14.3023  -36.7757
 SYA  C   C  CH3   0  -0.416   1.8588  14.4091  -36.0934
 SYA  H1  H  HCR6  0   0.312  -3.5873  13.7425  -33.7276
 SYA  H2  H  HOH1  0   0.491  -3.1772  18.1685  -34.0969
 SYA  H3  H  HCH3  0   0.253   2.6237  14.5076  -36.8590
 SYA  H4  H  HCH3  0   0.236   1.8883  15.2871  -35.4459
 SYA  H5  H  HCH3  0   0.235   2.0638  13.5185  -35.4964
 SYA  C7  C  C     0   0.573  -3.0669  16.2908  -34.1350
 SYA  F2  F  F     0  -0.279  -0.6735  16.4644  -35.8511

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
 SYA  O   C   single    1.431  0.020  1.431
 SYA  O   C1  single    1.346  0.020  1.346
 SYA  F2  C2  single    1.328  0.020  1.328
 SYA  C1  C2  aromatic  1.394  0.020  1.394
 SYA  C1  C6  aromatic  1.385  0.020  1.385
 SYA  F   C6  single    1.326  0.020  1.326
 SYA  C2  C3  aromatic  1.389  0.020  1.389
 SYA  C6  C5  aromatic  1.386  0.020  1.386
 SYA  C3  C4  aromatic  1.397  0.020  1.397
 SYA  C3  C7  single    1.488  0.020  1.488
 SYA  C5  C4  aromatic  1.370  0.020  1.370
 SYA  C5  F1  single    1.334  0.020  1.334
 SYA  C7  O1  double    1.206  0.020  1.206
 SYA  C7  O2  single    1.319  0.020  1.319
 SYA  C4  H1  single    0.930  0.020  1.080
 SYA  O2  H2  single    0.850  0.020  0.980
 SYA  C   H3  single    0.970  0.020  1.090
 SYA  C   H4  single    0.970  0.020  1.090
 SYA  C   H5  single    0.970  0.020  1.090

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
 SYA  H1  C4  C3  120.01  3.000
 SYA  H1  C4  C5  119.49  3.000
 SYA  C3  C4  C5  120.50  3.000
 SYA  F1  C5  C6  118.75  3.000
 SYA  F1  C5  C4  120.74  3.000
 SYA  C6  C5  C4  120.51  3.000
 SYA  C1  C6  F   119.41  3.000
 SYA  F   C6  C5  119.96  3.000
 SYA  C1  C6  C5  120.62  3.000
 SYA  C1  C2  C3  121.91  3.000
 SYA  C3  C2  F2  121.89  3.000
 SYA  C1  C2  F2  116.20  3.000
 SYA  C2  C3  C7  125.21  3.000
 SYA  C7  C3  C4  116.55  3.000
 SYA  C2  C3  C4  118.25  3.000
 SYA  H2  O2  C7  109.60  3.000
 SYA  O   C1  C2  121.17  3.000
 SYA  C2  C1  C6  118.21  3.000
 SYA  O   C1  C6  120.60  3.000
 SYA  C   O   C1  114.58  3.000
 SYA  H5  C   H4  109.08  3.000
 SYA  H5  C   H3  109.09  3.000
 SYA  H4  C   H3  109.03  3.000
 SYA  H5  C   O   111.37  3.000
 SYA  H4  C   O   111.51  3.000
 SYA  H3  C   O   106.68  3.000
 SYA  O1  C7  O2  123.67  3.000
 SYA  O2  C7  C3  114.06  3.000
 SYA  O1  C7  C3  122.27  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
 SYA  CONST_01  C1  C2  C3  C4    0.00   0.0  0
 SYA  CONST_02  C1  C6  C5  C4    0.00   0.0  0
 SYA  CONST_03  C2  C1  C6  C5    0.00   0.0  0
 SYA  CONST_04  C2  C3  C4  C5    0.00   0.0  0
 SYA  CONST_05  C3  C2  C1  C6    0.00   0.0  0
 SYA  CONST_06  C3  C4  C5  C6    0.00   0.0  0
 SYA  CONST_07  F2  C2  C3  C4  180.00   0.0  0
 SYA  CONST_08  F   C6  C5  C4  180.00   0.0  0
 SYA  CONST_09  O   C1  C6  C5  180.00   0.0  0
 SYA  CONST_10  C7  C3  C4  C5  180.00   0.0  0
 SYA  CONST_11  F2  C2  C1  C6  180.00   0.0  0
 SYA  CONST_12  C1  C2  C3  C7  180.00   0.0  0
 SYA  CONST_13  F   C6  C1  C2  180.00   0.0  0
 SYA  CONST_14  O   C1  C2  C3  180.00   0.0  0
 SYA  CONST_15  F1  C5  C4  C3  180.00   0.0  0
 SYA  CONST_16  C1  C6  C5  F1  180.00   0.0  0
 SYA  CONST_17  H1  C4  C5  C6  180.00   0.0  0
 SYA  CONST_18  H2  O2  C7  C3  180.00   0.0  0
 SYA  Var_01    O1  C7  C3  C4    0.25  30.0  2
 SYA  Var_02    H3  C   O   C1  179.73  30.0  3

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
 SYA  plan-1  C4  0.020
 SYA  plan-1  C5  0.020
 SYA  plan-1  C6  0.020
 SYA  plan-1  C2  0.020
 SYA  plan-1  C3  0.020
 SYA  plan-1  F1  0.020
 SYA  plan-1  F   0.020
 SYA  plan-1  C1  0.020
 SYA  plan-1  O   0.020
 SYA  plan-1  H1  0.020
 SYA  plan-1  C7  0.020
 SYA  plan-1  F2  0.020
 SYA  plan-2  C3  0.020
 SYA  plan-2  O2  0.020
 SYA  plan-2  O1  0.020
 SYA  plan-2  H2  0.020
 SYA  plan-2  C7  0.020

