# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:47:19 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3,5-di(pyridin-4-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(cc(c1)c2ccncc2)c3ccncc3
#
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
 5F3  5F3  '3,5-di(pyridin-4-yl)benzoic acid'  ligand  32  21  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5F3
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
 5F3  C11  C  C      0   0.415   0.0470   3.5963  -0.3181
 5F3  C12  C  CR6    0   0.173  -2.4985  -0.7220  -0.0132
 5F3  C7   C  CR6    0   0.158  -1.2137   0.0025  -0.0524
 5F3  C8   C  CR16   0  -0.383  -1.1862   1.3906  -0.1569
 5F3  C9   C  CR6    0  -0.048   0.0210   2.0748  -0.1917
 5F3  C10  C  CR16   0  -0.402   1.2065   1.3561  -0.1139
 5F3  C2   C  CR16   0  -0.060   4.8938  -0.8987   0.1296
 5F3  N1   N  N      0  -0.408  -4.9451  -2.0946   0.0733
 5F3  C6   C  CR16   0  -0.419  -0.0120  -0.6955   0.0194
 5F3  C5   C  CR6    0   0.201   1.2162  -0.0351  -0.0058
 5F3  C4   C  CR6    0   0.219   2.4891  -0.7893   0.0842
 5F3  O    O  O      0  -0.587  -1.0581   4.1620  -0.4063
 5F3  O1   O  OC    -1  -0.587   1.1702   4.1329  -0.3219
 5F3  C3   C  CR16   0  -0.407   3.7308  -0.1520   0.0455
 5F3  N    N  N      0  -0.408   4.9188  -2.2206   0.2512
 5F3  C1   C  CR16   0  -0.061   3.7424  -2.8343   0.2915
 5F3  C    C  CR16   0  -0.409   2.5250  -2.1792   0.2130
 5F3  C16  C  CR16   0  -0.377  -3.6104  -0.1905   0.6375
 5F3  C15  C  CR16   0  -0.060  -4.7949  -0.9086   0.6522
 5F3  C14  C  CR16   0  -0.060  -3.8872  -2.6021  -0.5491
 5F3  C13  C  CR16   0  -0.382  -2.6586  -1.9658  -0.6213
 5F3  H5   H  HCR6   0   0.252  -2.1087   1.9522  -0.2338
 5F3  H6   H  HCR6   0   0.249   2.1279   1.9207  -0.1390
 5F3  H2   H  HCR6   0   0.267   5.8538  -0.3952   0.0962
 5F3  H4   H  HCR6   0   0.255  -0.0529  -1.7717   0.1170
 5F3  H3   H  HCR6   0   0.268   3.8218   0.9202  -0.0494
 5F3  H1   H  HCR6   0   0.267   3.7603  -3.9138   0.3934
 5F3  H    H  HCR6   0   0.266   1.6268  -2.7779   0.2532
 5F3  H11  H  HCR6   0   0.269  -3.5577   0.7617   1.1488
 5F3  H10  H  HCR6   0   0.265  -5.6615  -0.5047   1.1639
 5F3  H9   H  HCR6   0   0.265  -4.0209  -3.5678  -1.0241
 5F3  H8   H  HCR6   0   0.269  -1.8497  -2.4339  -1.1665

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
 5F3  C14  N1   aromatic  1.328  0.020  1.328
 5F3  C14  C13  aromatic  1.385  0.020  1.385
 5F3  N1   C15  aromatic  1.328  0.020  1.328
 5F3  C13  C12  aromatic  1.394  0.020  1.394
 5F3  C15  C16  aromatic  1.385  0.020  1.385
 5F3  C12  C16  aromatic  1.394  0.020  1.394
 5F3  C12  C7   single    1.475  0.020  1.475
 5F3  C1   C    aromatic  1.385  0.020  1.385
 5F3  C1   N    aromatic  1.328  0.020  1.328
 5F3  C    C4   aromatic  1.396  0.020  1.396
 5F3  C6   C7   aromatic  1.392  0.020  1.392
 5F3  C6   C5   aromatic  1.395  0.020  1.395
 5F3  C7   C8   aromatic  1.392  0.020  1.392
 5F3  N    C2   aromatic  1.328  0.020  1.328
 5F3  C4   C5   single    1.482  0.020  1.482
 5F3  C4   C3   aromatic  1.396  0.020  1.396
 5F3  C5   C10  aromatic  1.395  0.020  1.395
 5F3  C2   C3   aromatic  1.385  0.020  1.385
 5F3  C8   C9   aromatic  1.388  0.020  1.388
 5F3  C10  C9   aromatic  1.388  0.020  1.388
 5F3  C9   C11  single    1.527  0.020  1.527
 5F3  C11  O    deloc     1.245  0.020  1.245
 5F3  C11  O1   deloc     1.245  0.020  1.245
 5F3  C8   H5   single    0.930  0.020  1.080
 5F3  C10  H6   single    0.930  0.020  1.080
 5F3  C2   H2   single    0.930  0.020  1.080
 5F3  C6   H4   single    0.930  0.020  1.080
 5F3  C3   H3   single    0.930  0.020  1.080
 5F3  C1   H1   single    0.930  0.020  1.080
 5F3  C    H    single    0.930  0.020  1.080
 5F3  C16  H11  single    0.930  0.020  1.080
 5F3  C15  H10  single    0.930  0.020  1.080
 5F3  C14  H9   single    0.930  0.020  1.080
 5F3  C13  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
 5F3  O1   C11  O    127.23  3.000
 5F3  O1   C11  C9   116.43  3.000
 5F3  O    C11  C9   116.34  3.000
 5F3  C13  C12  C16  116.90  3.000
 5F3  C16  C12  C7   121.33  3.000
 5F3  C13  C12  C7   121.78  3.000
 5F3  C6   C7   C8   119.14  3.000
 5F3  C8   C7   C12  120.58  3.000
 5F3  C6   C7   C12  120.29  3.000
 5F3  H5   C8   C9   118.92  3.000
 5F3  H5   C8   C7   120.37  3.000
 5F3  C9   C8   C7   120.69  3.000
 5F3  C10  C9   C8   119.08  3.000
 5F3  C10  C9   C11  120.39  3.000
 5F3  C8   C9   C11  120.53  3.000
 5F3  H6   C10  C5   121.10  3.000
 5F3  H6   C10  C9   117.14  3.000
 5F3  C5   C10  C9   121.76  3.000
 5F3  H2   C2   N    116.64  3.000
 5F3  H2   C2   C3   119.42  3.000
 5F3  N    C2   C3   123.94  3.000
 5F3  C14  N1   C15  117.09  3.000
 5F3  H4   C6   C5   120.41  3.000
 5F3  H4   C6   C7   118.11  3.000
 5F3  C5   C6   C7   121.47  3.000
 5F3  C4   C5   C6   120.94  3.000
 5F3  C4   C5   C10  121.20  3.000
 5F3  C6   C5   C10  117.86  3.000
 5F3  C    C4   C3   115.72  3.000
 5F3  C3   C4   C5   121.99  3.000
 5F3  C    C4   C5   122.29  3.000
 5F3  H3   C3   C4   122.03  3.000
 5F3  H3   C3   C2   118.02  3.000
 5F3  C4   C3   C2   119.95  3.000
 5F3  C1   N    C2   116.51  3.000
 5F3  H1   C1   C    119.40  3.000
 5F3  H1   C1   N    116.64  3.000
 5F3  C    C1   N    123.96  3.000
 5F3  H    C    C1   117.82  3.000
 5F3  H    C    C4   122.26  3.000
 5F3  C1   C    C4   119.92  3.000
 5F3  H11  C16  C15  119.53  3.000
 5F3  H11  C16  C12  121.15  3.000
 5F3  C15  C16  C12  119.31  3.000
 5F3  H10  C15  C16  119.69  3.000
 5F3  H10  C15  N1   116.61  3.000
 5F3  C16  C15  N1   123.70  3.000
 5F3  H9   C14  C13  119.70  3.000
 5F3  H9   C14  N1   116.57  3.000
 5F3  C13  C14  N1   123.73  3.000
 5F3  H8   C13  C14  119.38  3.000
 5F3  H8   C13  C12  121.33  3.000
 5F3  C14  C13  C12  119.28  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
 5F3  CONST_01  N1   C14  C13  C12    0.00   0.0  0
 5F3  CONST_02  N1   C15  C16  C12    0.00   0.0  0
 5F3  CONST_03  C5   C6   C7   C12  180.00   0.0  0
 5F3  CONST_04  C9   C8   C7   C12  180.00   0.0  0
 5F3  CONST_05  C14  C13  C12  C7   180.00   0.0  0
 5F3  CONST_06  C15  C16  C12  C7   180.00   0.0  0
 5F3  CONST_07  C4   C5   C6   C7   180.00   0.0  0
 5F3  CONST_08  C10  C5   C6   C7     0.00   0.0  0
 5F3  CONST_09  C10  C9   C8   C7     0.00   0.0  0
 5F3  CONST_12  C5   C6   C7   C8     0.00   0.0  0
 5F3  CONST_13  C5   C10  C9   C8     0.00   0.0  0
 5F3  CONST_14  C6   C7   C8   C9     0.00   0.0  0
 5F3  CONST_15  C6   C5   C10  C9     0.00   0.0  0
 5F3  CONST_16  C4   C5   C10  C9   180.00   0.0  0
 5F3  CONST_17  C    C4   C5   C10  180.00   0.0  0
 5F3  CONST_18  C3   C4   C5   C10    0.00   0.0  0
 5F3  CONST_19  C    C1   N    C2     0.00   0.0  0
 5F3  CONST_20  C    C4   C3   C2     0.00   0.0  0
 5F3  CONST_21  C5   C4   C3   C2   180.00   0.0  0
 5F3  CONST_24  C    C4   C5   C6     0.00   0.0  0
 5F3  CONST_25  C3   C4   C5   C6   180.00   0.0  0
 5F3  CONST_26  C1   C    C4   C5   180.00   0.0  0
 5F3  CONST_27  N    C1   C    C4     0.00   0.0  0
 5F3  CONST_28  N    C2   C3   C4     0.00   0.0  0
 5F3  CONST_29  C1   C    C4   C3     0.00   0.0  0
 5F3  CONST_30  C1   N    C2   C3     0.00   0.0  0
 5F3  CONST_31  C14  N1   C15  C16    0.00   0.0  0
 5F3  CONST_32  C14  C13  C12  C16    0.00   0.0  0
 5F3  CONST_33  C13  C14  N1   C15    0.00   0.0  0
 5F3  CONST_34  C13  C12  C16  C15    0.00   0.0  0
 5F3  CONST_35  C7   C8   C9   C11  180.00   0.0  0
 5F3  CONST_36  C5   C10  C9   C11  180.00   0.0  0
 5F3  CONST_37  H9   C14  C13  C12  180.00   0.0  0
 5F3  CONST_38  H10  C15  C16  C12  180.00   0.0  0
 5F3  CONST_39  H4   C6   C7   C12    0.00   0.0  0
 5F3  CONST_40  H5   C8   C7   C12    0.00   0.0  0
 5F3  CONST_41  H8   C13  C12  C7     0.00   0.0  0
 5F3  CONST_42  H11  C16  C12  C7     0.00   0.0  0
 5F3  CONST_43  H6   C10  C9   C8   180.00   0.0  0
 5F3  CONST_44  H1   C1   N    C2   180.00   0.0  0
 5F3  CONST_45  H    C    C4   C5     0.00   0.0  0
 5F3  CONST_46  H3   C3   C4   C5     0.00   0.0  0
 5F3  CONST_47  H2   C2   C3   C4   180.00   0.0  0
 5F3  Var_01    O    C11  C9   C8    -1.06  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
 5F3  plan-1  C11  0.020
 5F3  plan-1  C12  0.020
 5F3  plan-1  C7   0.020
 5F3  plan-1  C8   0.020
 5F3  plan-1  C9   0.020
 5F3  plan-1  C10  0.020
 5F3  plan-1  C6   0.020
 5F3  plan-1  C5   0.020
 5F3  plan-1  C4   0.020
 5F3  plan-1  H5   0.020
 5F3  plan-1  H6   0.020
 5F3  plan-1  H4   0.020
 5F3  plan-2  C2   0.020
 5F3  plan-2  C5   0.020
 5F3  plan-2  C4   0.020
 5F3  plan-2  C3   0.020
 5F3  plan-2  N    0.020
 5F3  plan-2  C1   0.020
 5F3  plan-2  C    0.020
 5F3  plan-2  H2   0.020
 5F3  plan-2  H3   0.020
 5F3  plan-2  H1   0.020
 5F3  plan-2  H    0.020
 5F3  plan-3  C12  0.020
 5F3  plan-3  C7   0.020
 5F3  plan-3  N1   0.020
 5F3  plan-3  C16  0.020
 5F3  plan-3  C15  0.020
 5F3  plan-3  C14  0.020
 5F3  plan-3  C13  0.020
 5F3  plan-3  H11  0.020
 5F3  plan-3  H10  0.020
 5F3  plan-3  H9   0.020
 5F3  plan-3  H8   0.020
 5F3  plan-4  C11  0.020
 5F3  plan-4  C9   0.020
 5F3  plan-4  O    0.020
 5F3  plan-4  O1   0.020

