# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:54:39 2022
#   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  18  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.471  -2.6854  13.9675  -34.3364
 SYA  C5  C  CR6    0   0.415  -2.0386  12.8257  -34.7415
 SYA  C6  C  CR6    0   0.351  -0.9162  12.9019  -35.5459
 SYA  C2  C  CR6    0   0.482  -1.1132  15.2825  -35.5325
 SYA  C3  C  CR6    0  -0.312  -2.2373  15.2323  -34.7194
 SYA  O2  O  OC    -1  -0.569  -2.5389  17.5788  -34.4941
 SYA  O1  O  O      0  -0.575  -4.0302  16.2128  -33.5540
 SYA  F1  F  F      0  -0.311  -2.4778  11.6189  -34.3610
 SYA  F   F  F      0  -0.297  -0.2911  11.7891  -35.9302
 SYA  C1  C  CR6    0   0.052  -0.4407  14.1362  -35.9586
 SYA  O   O  O2     0  -0.481   0.6326  14.2157  -36.7759
 SYA  C   C  CH3    0  -0.413   1.8791  14.3621  -36.0979
 SYA  H1  H  HCR6   0   0.286  -3.5629  13.8896  -33.7090
 SYA  H3  H  HCH3   0   0.246   2.6480  14.4344  -36.8637
 SYA  H4  H  HCH3   0   0.231   1.9035  15.2671  -35.4876
 SYA  H5  H  HCH3   0   0.230   2.0921  13.5002  -35.4618
 SYA  C7  C  C      0   0.429  -3.0059  16.4652  -34.2119
 SYA  F2  F  F      0  -0.293  -0.6064  16.4366  -35.9716

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    1.426  0.020  1.426
 SYA  O   C1  single    1.351  0.020  1.351
 SYA  F2  C2  single    1.335  0.020  1.335
 SYA  C1  C2  aromatic  1.396  0.020  1.396
 SYA  C1  C6  aromatic  1.386  0.020  1.386
 SYA  F   C6  single    1.333  0.020  1.333
 SYA  C2  C3  aromatic  1.388  0.020  1.388
 SYA  C6  C5  aromatic  1.383  0.020  1.383
 SYA  C3  C4  aromatic  1.395  0.020  1.395
 SYA  C3  C7  single    1.539  0.020  1.539
 SYA  C5  C4  aromatic  1.373  0.020  1.373
 SYA  C5  F1  single    1.339  0.020  1.339
 SYA  C7  O1  deloc     1.243  0.020  1.243
 SYA  C7  O2  deloc     1.240  0.020  1.240
 SYA  C4  H1  single    0.930  0.020  1.080
 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  119.02  3.000
 SYA  H1  C4  C5  119.56  3.000
 SYA  C3  C4  C5  121.42  3.000
 SYA  F1  C5  C6  118.75  3.000
 SYA  F1  C5  C4  120.72  3.000
 SYA  C6  C5  C4  120.53  3.000
 SYA  C1  C6  F   119.79  3.000
 SYA  F   C6  C5  120.16  3.000
 SYA  C1  C6  C5  120.06  3.000
 SYA  C1  C2  C3  122.63  3.000
 SYA  C3  C2  F2  122.10  3.000
 SYA  C1  C2  F2  115.27  3.000
 SYA  C2  C3  C7  124.65  3.000
 SYA  C7  C3  C4  118.38  3.000
 SYA  C2  C3  C4  116.97  3.000
 SYA  O   C1  C2  121.27  3.000
 SYA  C2  C1  C6  118.38  3.000
 SYA  O   C1  C6  120.34  3.000
 SYA  C   O   C1  114.37  3.000
 SYA  H5  C   H4  108.92  3.000
 SYA  H5  C   H3  108.95  3.000
 SYA  H4  C   H3  108.82  3.000
 SYA  H5  C   O   111.48  3.000
 SYA  H4  C   O   111.73  3.000
 SYA  H3  C   O   106.85  3.000
 SYA  O1  C7  O2  127.80  3.000
 SYA  O2  C7  C3  117.15  3.000
 SYA  O1  C7  C3  115.05  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  Var_01    O1  C7  C3  C4    -4.17  30.0  2
 SYA  Var_02    H3  C   O   C1  -178.83  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  C7  0.020

