# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:56:51 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(4-fluorophenyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccc(F)cc2
#
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
 S1D  S1D  '3-(4-fluorophenyl)benzoic acid'  ligand  24  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S1D
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
 S1D  C    C  C      0   0.399  -3.6172  -0.9695   0.4856
 S1D  O    O  OC    -1  -0.593  -4.8019  -0.5991   0.3822
 S1D  C1   C  CR6    0  -0.079  -2.5486   0.0710   0.1671
 S1D  C10  C  CR6    0   0.513   3.9011  -0.4515   0.0515
 S1D  C11  C  CR16   0  -0.396   3.5369   0.8099   0.4806
 S1D  C12  C  CR16   0  -0.295   2.1971   1.1649   0.4364
 S1D  C2   C  CR16   0  -0.362  -1.2001  -0.2666   0.2071
 S1D  C3   C  CR6    0   0.112  -0.2009   0.6652  -0.0742
 S1D  C4   C  CR16   0  -0.322  -0.5790   1.9695  -0.3965
 S1D  C5   C  CR16   0  -0.230  -1.9202   2.3206  -0.4360
 S1D  C6   C  CR16   0  -0.305  -2.9005   1.3782  -0.1597
 S1D  C7   C  CR6    0   0.078   1.2245   0.2792  -0.0311
 S1D  C8   C  CR16   0  -0.293   1.6376  -0.9853  -0.4555
 S1D  C9   C  CR16   0  -0.397   2.9719  -1.3595  -0.4176
 S1D  O1   O  O      0  -0.592  -3.2146  -2.0997   0.8218
 S1D  H6   H  HCR6   0   0.280   4.2821   1.5016   0.8513
 S1D  H7   H  HCR6   0   0.264   1.9092   2.1450   0.7943
 S1D  H    H  HCR6   0   0.241  -0.9276  -1.2766   0.4859
 S1D  H1   H  HCR6   0   0.251   0.1738   2.7104  -0.6368
 S1D  H2   H  HCR6   0   0.251  -2.2001   3.3341  -0.6944
 S1D  H3   H  HCR6   0   0.245  -3.9451   1.6573  -0.1982
 S1D  H4   H  HCR6   0   0.264   0.9115  -1.6903  -0.8400
 S1D  H5   H  HCR6   0   0.281   3.2827  -2.3391  -0.7565
 S1D  F    F  F      0  -0.316   5.1958  -0.8065   0.0909

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
 S1D  C5   C6   aromatic  1.388  0.020  1.388
 S1D  C5   C4   aromatic  1.387  0.020  1.387
 S1D  C6   C1   aromatic  1.393  0.020  1.393
 S1D  C4   C3   aromatic  1.396  0.020  1.396
 S1D  C1   C2   aromatic  1.391  0.020  1.391
 S1D  C1   C    single    1.525  0.020  1.525
 S1D  C3   C2   aromatic  1.395  0.020  1.395
 S1D  C3   C7   single    1.477  0.020  1.477
 S1D  O1   C    deloc     1.246  0.020  1.246
 S1D  C    O    deloc     1.245  0.020  1.245
 S1D  C7   C12  aromatic  1.396  0.020  1.396
 S1D  C7   C8   aromatic  1.396  0.020  1.396
 S1D  C12  C11  aromatic  1.387  0.020  1.387
 S1D  C8   C9   aromatic  1.386  0.020  1.386
 S1D  C11  C10  aromatic  1.381  0.020  1.381
 S1D  C9   C10  aromatic  1.381  0.020  1.381
 S1D  C10  F    single    1.343  0.020  1.343
 S1D  C11  H6   single    0.930  0.020  1.080
 S1D  C12  H7   single    0.930  0.020  1.080
 S1D  C2   H    single    0.930  0.020  1.080
 S1D  C4   H1   single    0.930  0.020  1.080
 S1D  C5   H2   single    0.930  0.020  1.080
 S1D  C6   H3   single    0.930  0.020  1.080
 S1D  C8   H4   single    0.930  0.020  1.080
 S1D  C9   H5   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
 S1D  O1   C    C1   116.67  3.000
 S1D  O1   C    O    126.83  3.000
 S1D  C1   C    O    116.50  3.000
 S1D  C6   C1   C2   118.66  3.000
 S1D  C2   C1   C    120.52  3.000
 S1D  C6   C1   C    120.82  3.000
 S1D  F    C10  C9   118.99  3.000
 S1D  F    C10  C11  119.11  3.000
 S1D  C9   C10  C11  121.90  3.000
 S1D  H6   C11  C12  120.84  3.000
 S1D  H6   C11  C10  120.56  3.000
 S1D  C12  C11  C10  118.60  3.000
 S1D  H7   C12  C7   119.99  3.000
 S1D  H7   C12  C11  118.57  3.000
 S1D  C7   C12  C11  121.42  3.000
 S1D  H    C2   C3   119.66  3.000
 S1D  H    C2   C1   118.55  3.000
 S1D  C3   C2   C1   121.78  3.000
 S1D  C7   C3   C4   120.81  3.000
 S1D  C7   C3   C2   120.71  3.000
 S1D  C4   C3   C2   118.47  3.000
 S1D  H1   C4   C5   119.51  3.000
 S1D  H1   C4   C3   120.14  3.000
 S1D  C5   C4   C3   120.34  3.000
 S1D  H2   C5   C6   120.04  3.000
 S1D  H2   C5   C4   119.59  3.000
 S1D  C6   C5   C4   120.37  3.000
 S1D  H3   C6   C5   119.99  3.000
 S1D  H3   C6   C1   119.63  3.000
 S1D  C5   C6   C1   120.38  3.000
 S1D  C8   C7   C3   120.88  3.000
 S1D  C8   C7   C12  118.05  3.000
 S1D  C3   C7   C12  121.08  3.000
 S1D  H4   C8   C9   118.65  3.000
 S1D  H4   C8   C7   119.95  3.000
 S1D  C9   C8   C7   121.39  3.000
 S1D  H5   C9   C8   120.81  3.000
 S1D  H5   C9   C10  120.55  3.000
 S1D  C8   C9   C10  118.64  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
 S1D  CONST_01  C4  C5   C6   C1     0.00   0.0  0
 S1D  CONST_02  C4  C3   C2   C1     0.00   0.0  0
 S1D  CONST_03  C7  C3   C2   C1   180.00   0.0  0
 S1D  CONST_04  C7  C12  C11  C10    0.00   0.0  0
 S1D  CONST_05  C7  C8   C9   C10    0.00   0.0  0
 S1D  CONST_06  C3  C7   C12  C11  180.00   0.0  0
 S1D  CONST_07  C8  C7   C12  C11    0.00   0.0  0
 S1D  CONST_08  C8  C9   C10  C11    0.00   0.0  0
 S1D  CONST_11  C9  C8   C7   C12    0.00   0.0  0
 S1D  CONST_12  C9  C10  C11  C12    0.00   0.0  0
 S1D  CONST_13  C5  C6   C1   C2     0.00   0.0  0
 S1D  CONST_14  C5  C4   C3   C2     0.00   0.0  0
 S1D  CONST_16  C6  C5   C4   C3     0.00   0.0  0
 S1D  CONST_17  C6  C1   C2   C3     0.00   0.0  0
 S1D  CONST_18  C9  C8   C7   C3   180.00   0.0  0
 S1D  CONST_20  C7  C3   C4   C5   180.00   0.0  0
 S1D  CONST_21  C5  C6   C1   C    180.00   0.0  0
 S1D  CONST_22  C3  C2   C1   C    180.00   0.0  0
 S1D  CONST_23  F   C10  C11  C12  180.00   0.0  0
 S1D  CONST_24  F   C10  C9   C8   180.00   0.0  0
 S1D  CONST_25  H2  C5   C6   C1   180.00   0.0  0
 S1D  CONST_26  H7  C12  C11  C10  180.00   0.0  0
 S1D  CONST_27  H4  C8   C9   C10  180.00   0.0  0
 S1D  CONST_28  H5  C9   C10  C11  180.00   0.0  0
 S1D  CONST_29  H3  C6   C1   C2   180.00   0.0  0
 S1D  CONST_30  H1  C4   C3   C2   180.00   0.0  0
 S1D  CONST_31  H   C2   C3   C4   180.00   0.0  0
 S1D  CONST_32  H6  C11  C12  C7   180.00   0.0  0
 S1D  Var_01    C6  C1   C    O      2.87  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
 S1D  plan-1  C    0.020
 S1D  plan-1  C1   0.020
 S1D  plan-1  C2   0.020
 S1D  plan-1  C3   0.020
 S1D  plan-1  C4   0.020
 S1D  plan-1  C5   0.020
 S1D  plan-1  C6   0.020
 S1D  plan-1  C7   0.020
 S1D  plan-1  H    0.020
 S1D  plan-1  H1   0.020
 S1D  plan-1  H2   0.020
 S1D  plan-1  H3   0.020
 S1D  plan-2  C10  0.020
 S1D  plan-2  C11  0.020
 S1D  plan-2  C12  0.020
 S1D  plan-2  C3   0.020
 S1D  plan-2  C7   0.020
 S1D  plan-2  C8   0.020
 S1D  plan-2  C9   0.020
 S1D  plan-2  H6   0.020
 S1D  plan-2  H7   0.020
 S1D  plan-2  H4   0.020
 S1D  plan-2  H5   0.020
 S1D  plan-2  F    0.020
 S1D  plan-3  C    0.020
 S1D  plan-3  O    0.020
 S1D  plan-3  C1   0.020
 S1D  plan-3  O1   0.020

