# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 19:20:20 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2noc(n2)c3ccccc3F
#
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
 JBF  JBF  "3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid"  ligand  29  21  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JBF
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
 JBF  C02  C  CR6    0   0.554   -7.8385  -33.7121  20.7570
 JBF  C03  C  CR16   0  -0.401   -7.5659  -34.2000  22.0191
 JBF  C04  C  CR16   0  -0.225   -8.0369  -35.4542  22.3724
 JBF  C05  C  CR16   0  -0.252   -8.7742  -36.2069  21.4664
 JBF  C06  C  CR16   0  -0.251   -9.0382  -35.7045  20.2060
 JBF  C07  C  CR6    0  -0.278   -8.5741  -34.4407  19.8237
 JBF  C08  C  CR5    0   0.610   -8.8562  -33.9130  18.4984
 JBF  C10  C  CR5    0   0.335   -9.0463  -32.8614  16.7149
 JBF  C11  C  CR6    0   0.014   -8.8905  -31.8000  15.7219
 JBF  C12  C  CR16   0  -0.336   -9.5098  -31.8852  14.4757
 JBF  C13  C  CR6    0  -0.077   -9.3685  -30.8718  13.5363
 JBF  C14  C  C      0   0.403  -10.0628  -30.9650  12.1775
 JBF  C17  C  CR16   0  -0.288   -8.5849  -29.7659  13.8607
 JBF  C18  C  CR16   0  -0.227   -7.9588  -29.6754  15.0951
 JBF  C19  C  CR16   0  -0.299   -8.1110  -30.6867  16.0305
 JBF  F01  F  F      0  -0.286   -7.3800  -32.5020  20.4402
 JBF  N09  N  N      0  -0.471   -8.4765  -32.8047  17.9531
 JBF  N20  N  N      0  -0.149   -9.7366  -33.9456  16.5130
 JBF  O15  O  OC    -1  -0.582  -10.7166  -32.0017  11.9607
 JBF  O16  O  O      0  -0.584   -9.9106  -29.9922  11.4155
 JBF  O21  O  O      0  -0.337   -9.6141  -34.6390  17.6830
 JBF  H1   H  HCR6   0   0.290   -6.9918  -33.5997  22.7125
 JBF  H2   H  HCR6   0   0.281   -7.8272  -35.8422  23.3600
 JBF  H3   H  HCR6   0   0.274   -9.1426  -37.1852  21.7416
 JBF  H4   H  HCR6   0   0.281   -9.6116  -36.3016  19.5102
 JBF  H5   H  HCR6   0   0.244  -10.1162  -32.7464  14.2274
 JBF  H6   H  HCR6   0   0.248   -8.4646  -28.9713  13.1369
 JBF  H7   H  HCR6   0   0.254   -7.3505  -28.8125  15.3338
 JBF  H8   H  HCR6   0   0.257   -7.6267  -30.6130  16.9948

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
 JBF  O16  C14  deloc     1.245  0.020  1.245
 JBF  O15  C14  deloc     1.245  0.020  1.245
 JBF  C14  C13  single    1.529  0.020  1.529
 JBF  C13  C17  aromatic  1.394  0.020  1.394
 JBF  C13  C12  aromatic  1.389  0.020  1.389
 JBF  C17  C18  aromatic  1.387  0.020  1.387
 JBF  C12  C11  aromatic  1.394  0.020  1.394
 JBF  C18  C19  aromatic  1.386  0.020  1.386
 JBF  C11  C19  aromatic  1.394  0.020  1.394
 JBF  C11  C10  single    1.462  0.020  1.462
 JBF  N20  C10  aromatic  1.301  0.020  1.301
 JBF  N20  O21  aromatic  1.366  0.020  1.366
 JBF  C10  N09  aromatic  1.364  0.020  1.364
 JBF  O21  C08  aromatic  1.329  0.020  1.329
 JBF  N09  C08  aromatic  1.292  0.020  1.292
 JBF  C08  C07  single    1.454  0.020  1.454
 JBF  C07  C06  aromatic  1.400  0.020  1.400
 JBF  C07  C02  aromatic  1.394  0.020  1.394
 JBF  C06  C05  aromatic  1.382  0.020  1.382
 JBF  F01  C02  single    1.332  0.020  1.332
 JBF  C02  C03  aromatic  1.380  0.020  1.380
 JBF  C05  C04  aromatic  1.390  0.020  1.390
 JBF  C03  C04  aromatic  1.386  0.020  1.386
 JBF  C03  H1   single    0.930  0.020  1.080
 JBF  C04  H2   single    0.930  0.020  1.080
 JBF  C05  H3   single    0.930  0.020  1.080
 JBF  C06  H4   single    0.930  0.020  1.080
 JBF  C12  H5   single    0.930  0.020  1.080
 JBF  C17  H6   single    0.930  0.020  1.080
 JBF  C18  H7   single    0.930  0.020  1.080
 JBF  C19  H8   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
 JBF  F01  C02  C07  119.82  3.000
 JBF  F01  C02  C03  118.07  3.000
 JBF  C07  C02  C03  122.11  3.000
 JBF  H1   C03  C04  121.28  3.000
 JBF  H1   C03  C02  119.65  3.000
 JBF  C04  C03  C02  119.08  3.000
 JBF  H2   C04  C05  120.26  3.000
 JBF  H2   C04  C03  119.45  3.000
 JBF  C05  C04  C03  120.29  3.000
 JBF  H3   C05  C06  119.73  3.000
 JBF  H3   C05  C04  120.33  3.000
 JBF  C06  C05  C04  119.93  3.000
 JBF  H4   C06  C07  119.91  3.000
 JBF  H4   C06  C05  119.17  3.000
 JBF  C07  C06  C05  120.92  3.000
 JBF  C08  C07  C06  120.82  3.000
 JBF  C06  C07  C02  117.66  3.000
 JBF  C08  C07  C02  121.53  3.000
 JBF  O21  C08  N09  112.16  3.000
 JBF  N09  C08  C07  129.70  3.000
 JBF  O21  C08  C07  118.14  3.000
 JBF  N20  C10  N09  113.39  3.000
 JBF  N09  C10  C11  122.81  3.000
 JBF  N20  C10  C11  123.79  3.000
 JBF  C19  C11  C12  119.68  3.000
 JBF  C19  C11  C10  119.29  3.000
 JBF  C12  C11  C10  121.03  3.000
 JBF  H5   C12  C13  118.84  3.000
 JBF  H5   C12  C11  120.17  3.000
 JBF  C13  C12  C11  120.98  3.000
 JBF  C17  C13  C14  120.70  3.000
 JBF  C17  C13  C12  118.60  3.000
 JBF  C14  C13  C12  120.70  3.000
 JBF  O16  C14  O15  127.47  3.000
 JBF  O15  C14  C13  116.37  3.000
 JBF  O16  C14  C13  116.16  3.000
 JBF  H6   C17  C18  119.83  3.000
 JBF  H6   C17  C13  119.33  3.000
 JBF  C18  C17  C13  120.84  3.000
 JBF  H7   C18  C19  119.64  3.000
 JBF  H7   C18  C17  120.13  3.000
 JBF  C19  C18  C17  120.23  3.000
 JBF  H8   C19  C18  120.19  3.000
 JBF  H8   C19  C11  120.15  3.000
 JBF  C18  C19  C11  119.66  3.000
 JBF  C10  N09  C08  102.98  3.000
 JBF  O21  N20  C10  104.05  3.000
 JBF  N20  O21  C08  107.42  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
 JBF  CONST_01  O21  C08  C07  C02  180.00   0.0  0
 JBF  CONST_02  N09  C08  C07  C02    0.00   0.0  0
 JBF  CONST_03  C05  C06  C07  C02    0.00   0.0  0
 JBF  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 JBF  CONST_05  C08  C07  C02  C03  180.00   0.0  0
 JBF  CONST_06  C06  C07  C02  C03    0.00   0.0  0
 JBF  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 JBF  CONST_08  C07  C06  C05  C04    0.00   0.0  0
 JBF  CONST_09  C07  C02  C03  C04    0.00   0.0  0
 JBF  CONST_10  C08  C07  C06  C05  180.00   0.0  0
 JBF  CONST_11  O21  C08  C07  C06    0.00   0.0  0
 JBF  CONST_12  N09  C08  C07  C06  180.00   0.0  0
 JBF  CONST_13  N20  O21  C08  C07  180.00   0.0  0
 JBF  CONST_14  C10  N09  C08  C07  180.00   0.0  0
 JBF  CONST_15  C10  N20  O21  C08    0.00   0.0  0
 JBF  CONST_16  C11  C10  N09  C08  180.00   0.0  0
 JBF  CONST_17  N20  C10  N09  C08    0.00   0.0  0
 JBF  CONST_18  C13  C12  C11  C10  180.00   0.0  0
 JBF  CONST_19  C18  C19  C11  C10  180.00   0.0  0
 JBF  CONST_20  O21  C08  N09  C10    0.00   0.0  0
 JBF  CONST_21  C17  C13  C12  C11    0.00   0.0  0
 JBF  CONST_22  C17  C18  C19  C11    0.00   0.0  0
 JBF  CONST_23  O21  N20  C10  C11  180.00   0.0  0
 JBF  CONST_24  C18  C17  C13  C12    0.00   0.0  0
 JBF  CONST_25  C18  C19  C11  C12    0.00   0.0  0
 JBF  CONST_26  N20  C10  C11  C12    0.00   0.0  0
 JBF  CONST_27  N09  C10  C11  C12  180.00   0.0  0
 JBF  CONST_28  C19  C18  C17  C13    0.00   0.0  0
 JBF  CONST_29  C19  C11  C12  C13    0.00   0.0  0
 JBF  CONST_30  N20  C10  C11  C19  180.00   0.0  0
 JBF  CONST_31  N09  C10  C11  C19    0.00   0.0  0
 JBF  CONST_32  O21  N20  C10  N09    0.00   0.0  0
 JBF  CONST_33  N20  O21  C08  N09    0.00   0.0  0
 JBF  CONST_34  F01  C02  C03  C04  180.00   0.0  0
 JBF  CONST_35  F01  C02  C07  C06  180.00   0.0  0
 JBF  CONST_36  F01  C02  C07  C08    0.00   0.0  0
 JBF  CONST_37  C14  C13  C12  C11  180.00   0.0  0
 JBF  CONST_38  C18  C17  C13  C14  180.00   0.0  0
 JBF  CONST_39  H4   C06  C07  C02  180.00   0.0  0
 JBF  CONST_40  H2   C04  C03  C02  180.00   0.0  0
 JBF  CONST_41  H3   C05  C04  C03  180.00   0.0  0
 JBF  CONST_42  H4   C06  C05  C04  180.00   0.0  0
 JBF  CONST_43  H1   C03  C04  C05  180.00   0.0  0
 JBF  CONST_44  H2   C04  C05  C06  180.00   0.0  0
 JBF  CONST_45  H3   C05  C06  C07  180.00   0.0  0
 JBF  CONST_46  H1   C03  C02  C07  180.00   0.0  0
 JBF  CONST_47  H4   C06  C07  C08    0.00   0.0  0
 JBF  CONST_48  H5   C12  C11  C10    0.00   0.0  0
 JBF  CONST_49  H8   C19  C11  C10    0.00   0.0  0
 JBF  CONST_50  H7   C18  C19  C11  180.00   0.0  0
 JBF  CONST_51  H6   C17  C13  C12  180.00   0.0  0
 JBF  CONST_52  H8   C19  C11  C12  180.00   0.0  0
 JBF  CONST_53  H7   C18  C17  C13  180.00   0.0  0
 JBF  CONST_54  H5   C12  C13  C17  180.00   0.0  0
 JBF  CONST_55  H8   C19  C18  C17  180.00   0.0  0
 JBF  CONST_56  H6   C17  C18  C19  180.00   0.0  0
 JBF  CONST_57  H5   C12  C11  C19  180.00   0.0  0
 JBF  Var_01    O16  C14  C13  C12  177.97  30.0  2
 JBF  Var_02    O15  C14  C13  C12   -1.90  30.0  2
 JBF  Var_03    O16  C14  C13  C17   -1.77  30.0  2
 JBF  Var_04    O15  C14  C13  C17  178.36  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
 JBF  plan-1  C07  0.020
 JBF  plan-1  C08  0.020
 JBF  plan-1  C10  0.020
 JBF  plan-1  C11  0.020
 JBF  plan-1  N09  0.020
 JBF  plan-1  N20  0.020
 JBF  plan-1  O21  0.020
 JBF  plan-2  C02  0.020
 JBF  plan-2  C03  0.020
 JBF  plan-2  C04  0.020
 JBF  plan-2  C05  0.020
 JBF  plan-2  C06  0.020
 JBF  plan-2  C07  0.020
 JBF  plan-2  C08  0.020
 JBF  plan-2  F01  0.020
 JBF  plan-2  H1   0.020
 JBF  plan-2  H2   0.020
 JBF  plan-2  H3   0.020
 JBF  plan-2  H4   0.020
 JBF  plan-3  C10  0.020
 JBF  plan-3  C11  0.020
 JBF  plan-3  C12  0.020
 JBF  plan-3  C13  0.020
 JBF  plan-3  C14  0.020
 JBF  plan-3  C17  0.020
 JBF  plan-3  C18  0.020
 JBF  plan-3  C19  0.020
 JBF  plan-3  H5   0.020
 JBF  plan-3  H6   0.020
 JBF  plan-3  H7   0.020
 JBF  plan-3  H8   0.020
 JBF  plan-4  C13  0.020
 JBF  plan-4  C14  0.020
 JBF  plan-4  O15  0.020
 JBF  plan-4  O16  0.020

