# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 18:11:29 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (~{Z})-2-sulfanyl-3-[2,3,6-tris(fluoranyl)phenyl]prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)\C(S)=C\c1c(F)ccc(F)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
 BY5  BY5  '(~{Z})-2-sulfanyl-3-[2,3,6-tris(fluoranyl)phenyl]prop-2-enoic acid'  ligand  19  15  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BY5
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
 BY5  C4  C  CR6    0   0.539   1.3924  -1.6359  -0.1307
 BY5  C5  C  CR16   0  -0.409   2.7492  -1.5699  -0.3627
 BY5  C6  C  CR16   0  -0.403   3.4025  -0.3585  -0.1784
 BY5  C7  C  CR6    0   0.397   2.6825   0.7418   0.2323
 BY5  C8  C  CR6    0   0.418   1.3199   0.6479   0.4592
 BY5  C   C  C      0   0.444  -3.2537  -0.1788   0.3030
 BY5  O   O  O      0  -0.573  -3.5057  -0.9554   1.2360
 BY5  C1  C  C      0  -0.265  -1.7863  -0.0250  -0.1044
 BY5  C3  C  CR6    0  -0.366   0.6318  -0.5436   0.2750
 BY5  F   F  F      0  -0.298   0.7561  -2.8002  -0.3104
 BY5  F1  F  F      0  -0.287   0.6626   1.7301   0.8751
 BY5  F2  F  F      0  -0.306   3.2904   1.9168   0.4278
 BY5  O1  O  OC    -1  -0.588  -4.0454   0.5174  -0.3573
 BY5  S   S  S2     0  -0.161  -1.6203   1.0588  -1.4742
 BY5  H1  H  HCR6   0   0.295   3.2940  -2.4460  -0.6863
 BY5  H2  H  HCR6   0   0.303   4.4666  -0.2734  -0.3523
 BY5  H3  H  H      0   0.277  -1.1052  -1.3470   1.3282
 BY5  H5  H  HSH1   0   0.206  -0.3117   0.8819  -1.7083
 BY5  C2  C  C1     0  -0.226  -0.8076  -0.6653   0.5388

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
 BY5  F2  C7  single    1.337  0.020  1.337
 BY5  F1  C8  single    1.333  0.020  1.333
 BY5  S   C1  single    1.755  0.020  1.755
 BY5  C7  C8  aromatic  1.385  0.020  1.385
 BY5  C7  C6  aromatic  1.378  0.020  1.378
 BY5  C8  C3  aromatic  1.388  0.020  1.388
 BY5  O   C   deloc     1.240  0.020  1.240
 BY5  C1  C   single    1.531  0.020  1.531
 BY5  C1  C2  double    1.335  0.020  1.335
 BY5  C6  C5  aromatic  1.389  0.020  1.389
 BY5  C   O1  deloc     1.244  0.020  1.244
 BY5  C3  C2  single    1.468  0.020  1.468
 BY5  C3  C4  aromatic  1.391  0.020  1.391
 BY5  C5  C4  aromatic  1.378  0.020  1.378
 BY5  C4  F   single    1.339  0.020  1.339
 BY5  C5  H1  single    0.930  0.020  1.080
 BY5  C6  H2  single    0.930  0.020  1.080
 BY5  C2  H3  single    0.930  0.020  1.080
 BY5  S   H5  single    1.200  0.020  1.300

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
 BY5  F   C4  C3  117.51  3.000
 BY5  F   C4  C5  119.14  3.000
 BY5  C3  C4  C5  123.34  3.000
 BY5  H1  C5  C6  120.63  3.000
 BY5  H1  C5  C4  120.51  3.000
 BY5  C6  C5  C4  118.86  3.000
 BY5  H2  C6  C7  119.95  3.000
 BY5  H2  C6  C5  120.67  3.000
 BY5  C7  C6  C5  119.37  3.000
 BY5  F2  C7  C8  118.88  3.000
 BY5  C8  C7  C6  120.60  3.000
 BY5  F2  C7  C6  120.52  3.000
 BY5  F1  C8  C3  119.60  3.000
 BY5  C3  C8  C7  121.62  3.000
 BY5  F1  C8  C7  118.78  3.000
 BY5  O1  C   C1  114.37  3.000
 BY5  O1  C   O   128.36  3.000
 BY5  C1  C   O   117.26  3.000
 BY5  S   C1  C2  127.10  3.000
 BY5  C2  C1  C   121.77  3.000
 BY5  S   C1  C   111.13  3.000
 BY5  C2  C3  C8  122.22  3.000
 BY5  C2  C3  C4  121.54  3.000
 BY5  C8  C3  C4  116.20  3.000
 BY5  H5  S   C1   98.46  3.000
 BY5  H3  C2  C3  116.86  3.000
 BY5  H3  C2  C1  116.81  3.000
 BY5  C3  C2  C1  126.33  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
 BY5  CONST_01  C7  C8  C3  C4     0.00   0.0  0
 BY5  CONST_02  C7  C6  C5  C4     0.00   0.0  0
 BY5  CONST_03  C8  C7  C6  C5     0.00   0.0  0
 BY5  CONST_04  C8  C3  C4  C5     0.00   0.0  0
 BY5  CONST_05  C3  C8  C7  C6     0.00   0.0  0
 BY5  CONST_06  C3  C4  C5  C6     0.00   0.0  0
 BY5  CONST_07  F1  C8  C3  C4   180.00   0.0  0
 BY5  CONST_08  F2  C7  C6  C5   180.00   0.0  0
 BY5  CONST_09  C2  C3  C4  C5   180.00   0.0  0
 BY5  CONST_10  F1  C8  C7  C6   180.00   0.0  0
 BY5  CONST_11  F   C4  C5  C6   180.00   0.0  0
 BY5  CONST_12  C2  C3  C8  C7   180.00   0.0  0
 BY5  CONST_13  F   C4  C3  C8   180.00   0.0  0
 BY5  CONST_14  F2  C7  C8  C3   180.00   0.0  0
 BY5  CONST_15  H2  C6  C5  C4   180.00   0.0  0
 BY5  CONST_16  H1  C5  C6  C7   180.00   0.0  0
 BY5  Var_01    C1  C2  C3  C4  -118.43  30.0  2
 BY5  Var_02    C3  C2  C1  C   -176.97   0.0  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
 BY5  plan-1  C4  0.020
 BY5  plan-1  C5  0.020
 BY5  plan-1  C6  0.020
 BY5  plan-1  C7  0.020
 BY5  plan-1  C8  0.020
 BY5  plan-1  C3  0.020
 BY5  plan-1  F   0.020
 BY5  plan-1  F1  0.020
 BY5  plan-1  F2  0.020
 BY5  plan-1  H1  0.020
 BY5  plan-1  H2  0.020
 BY5  plan-1  C2  0.020
 BY5  plan-2  C   0.020
 BY5  plan-2  O   0.020
 BY5  plan-2  C1  0.020
 BY5  plan-2  O1  0.020
 BY5  plan-3  C   0.020
 BY5  plan-3  C1  0.020
 BY5  plan-3  C3  0.020
 BY5  plan-3  S   0.020
 BY5  plan-3  H3  0.020
 BY5  plan-3  C2  0.020

