# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:01:37 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(NC(=O)C2=C(Oc3ccccc3)C=C(NC2=O)C(F)(F)F)c1
#
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
 J8V  J8V  '3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid'  ligand  42  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J8V
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
 J8V  C14  C  CR6    0   0.553   1.4000  -0.1409   0.3456
 J8V  C13  C  CR6    0  -0.430   0.5775   0.6820   1.0591
 J8V  C01  C  CR16   0  -0.400  -3.8252   0.2001  -0.5320
 J8V  C02  C  CR6    0  -0.087  -5.1802  -0.0910  -0.5900
 J8V  C03  C  CR16   0  -0.307  -5.7993  -0.6314   0.5345
 J8V  C04  C  CR16   0  -0.236  -5.0612  -0.8713   1.6819
 J8V  C05  C  CR16   0  -0.322  -3.7034  -0.5834   1.7423
 J8V  C06  C  CR6    0   0.397  -3.0774  -0.0393   0.6212
 J8V  C08  C  C      0   0.514  -0.7735   0.2312   1.5253
 J8V  C15  C  CR16   0  -0.477   2.7052   0.2810  -0.0321
 J8V  C16  C  CR6    0   0.195   3.0957   1.5146   0.3572
 J8V  C18  C  CR6    0   0.552   1.0044   1.9872   1.4764
 J8V  C20  C  CT     0   1.056   4.4488   2.0771   0.0129
 J8V  C25  C  CR6    0   0.294   1.7460  -2.3151  -0.5157
 J8V  C26  C  CR16   0  -0.293   2.6319  -2.9788   0.3184
 J8V  C27  C  CR16   0  -0.252   3.4223  -3.9883  -0.2131
 J8V  C28  C  CR16   0  -0.249   3.3183  -4.3276  -1.5562
 J8V  C29  C  CR16   0  -0.253   2.4205  -3.6533  -2.3731
 J8V  C30  C  CR16   0  -0.299   1.6286  -2.6361  -1.8568
 J8V  F21  F  F      0  -0.301   4.3260   3.2200  -0.6659
 J8V  F22  F  F      0  -0.301   5.1449   2.3447   1.1199
 J8V  F23  F  F      0  -0.281   5.1596   1.2356  -0.7257
 J8V  N07  N  NH1    0  -0.717  -1.7155   0.2901   0.5613
 J8V  N17  N  NR16   0  -0.746   2.2881   2.3233   1.0785
 J8V  O10  O  OC    -1  -0.592  -7.1804  -0.1128  -1.8409
 J8V  O11  O  O      0  -0.591  -5.3371   0.6649  -2.8233
 J8V  O12  O  O      0  -0.445  -0.9554  -0.1310   2.6717
 J8V  O19  O  O      0  -0.472   0.3268   2.7717   2.1247
 J8V  O24  O  O2     0  -0.494   0.9138  -1.3408   0.0032
 J8V  H2   H  HCR6   0   0.258  -3.3440   0.6228  -1.4064
 J8V  H3   H  HCR6   0   0.244  -6.8551  -0.8628   0.5058
 J8V  H4   H  HCR6   0   0.252  -5.5421  -1.2929   2.5554
 J8V  H5   H  HCR6   0   0.278  -3.1547  -0.7852   2.6474
 J8V  H6   H  HCR6   0   0.322   3.3541  -0.3495  -0.6196
 J8V  H7   H  HCR6   0   0.286   2.7015  -2.7169   1.3667
 J8V  H8   H  HCR6   0   0.270   4.1183  -4.5118   0.4284
 J8V  H9   H  HCR6   0   0.265   3.9333  -5.1183  -1.9647
 J8V  H10  H  HCR6   0   0.270   2.3349  -3.9153  -3.4192
 J8V  H11  H  HCR6   0   0.280   0.9266  -2.1042  -2.4859
 J8V  H12  H  HNH1   0   0.423  -1.4039   0.6379  -0.3336
 J8V  H1   H  HNR6   0   0.435   2.6044   3.2423   1.3655
 J8V  C09  C  C      0   0.404  -5.9701   0.1785  -1.8670

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
 J8V  O11  C09  deloc     1.246  0.020  1.246
 J8V  O10  C09  deloc     1.245  0.020  1.245
 J8V  C09  C02  single    1.526  0.020  1.526
 J8V  C03  C02  aromatic  1.393  0.020  1.393
 J8V  C03  C04  aromatic  1.385  0.020  1.385
 J8V  C02  C01  aromatic  1.387  0.020  1.387
 J8V  C04  C05  aromatic  1.389  0.020  1.389
 J8V  C01  C06  aromatic  1.395  0.020  1.395
 J8V  C05  C06  aromatic  1.395  0.020  1.395
 J8V  C06  N07  single    1.402  0.020  1.402
 J8V  N07  C08  single    1.349  0.020  1.349
 J8V  O19  C18  double    1.223  0.020  1.223
 J8V  C08  O12  double    1.216  0.020  1.216
 J8V  C08  C13  single    1.499  0.020  1.499
 J8V  C18  C13  single    1.435  0.020  1.435
 J8V  C18  N17  single    1.385  0.020  1.385
 J8V  C13  C14  double    1.365  0.020  1.365
 J8V  N17  C16  single    1.351  0.020  1.351
 J8V  C14  O24  single    1.339  0.020  1.339
 J8V  C14  C15  single    1.423  0.020  1.423
 J8V  O24  C25  single    1.382  0.020  1.382
 J8V  C16  C15  double    1.351  0.020  1.351
 J8V  C16  C20  single    1.505  0.020  1.505
 J8V  F21  C20  single    1.335  0.020  1.335
 J8V  C20  F23  single    1.326  0.020  1.326
 J8V  C20  F22  single    1.335  0.020  1.335
 J8V  C25  C26  aromatic  1.386  0.020  1.386
 J8V  C25  C30  aromatic  1.384  0.020  1.384
 J8V  C26  C27  aromatic  1.388  0.020  1.388
 J8V  C30  C29  aromatic  1.389  0.020  1.389
 J8V  C27  C28  aromatic  1.389  0.020  1.389
 J8V  C29  C28  aromatic  1.389  0.020  1.389
 J8V  C01  H2   single    0.930  0.020  1.080
 J8V  C03  H3   single    0.930  0.020  1.080
 J8V  C04  H4   single    0.930  0.020  1.080
 J8V  C05  H5   single    0.930  0.020  1.080
 J8V  C15  H6   single    0.930  0.020  1.080
 J8V  C26  H7   single    0.930  0.020  1.080
 J8V  C27  H8   single    0.930  0.020  1.080
 J8V  C28  H9   single    0.930  0.020  1.080
 J8V  C29  H10  single    0.930  0.020  1.080
 J8V  C30  H11  single    0.930  0.020  1.080
 J8V  N07  H12  single    0.860  0.020  1.020
 J8V  N17  H1   single    0.860  0.020  1.020

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
 J8V  O24  C14  C15  122.07  3.000
 J8V  C15  C14  C13  120.85  3.000
 J8V  O24  C14  C13  117.07  3.000
 J8V  C18  C13  C08  116.83  3.000
 J8V  C18  C13  C14  121.40  3.000
 J8V  C08  C13  C14  121.63  3.000
 J8V  H2   C01  C06  119.72  3.000
 J8V  H2   C01  C02  118.80  3.000
 J8V  C06  C01  C02  121.48  3.000
 J8V  C09  C02  C03  120.95  3.000
 J8V  C03  C02  C01  118.81  3.000
 J8V  C09  C02  C01  120.25  3.000
 J8V  H3   C03  C04  120.35  3.000
 J8V  H3   C03  C02  119.71  3.000
 J8V  C04  C03  C02  119.94  3.000
 J8V  H4   C04  C05  118.67  3.000
 J8V  H4   C04  C03  119.93  3.000
 J8V  C05  C04  C03  121.40  3.000
 J8V  H5   C05  C06  121.31  3.000
 J8V  H5   C05  C04  119.70  3.000
 J8V  C06  C05  C04  118.99  3.000
 J8V  N07  C06  C05  124.19  3.000
 J8V  N07  C06  C01  116.42  3.000
 J8V  C05  C06  C01  119.39  3.000
 J8V  O12  C08  N07  125.61  3.000
 J8V  O12  C08  C13  121.19  3.000
 J8V  N07  C08  C13  113.20  3.000
 J8V  H6   C15  C16  121.11  3.000
 J8V  H6   C15  C14  121.54  3.000
 J8V  C16  C15  C14  117.34  3.000
 J8V  N17  C16  C20  115.83  3.000
 J8V  C20  C16  C15  122.34  3.000
 J8V  N17  C16  C15  121.83  3.000
 J8V  O19  C18  N17  120.67  3.000
 J8V  N17  C18  C13  114.38  3.000
 J8V  O19  C18  C13  124.95  3.000
 J8V  F23  C20  F22  108.03  3.000
 J8V  F22  C20  F21  107.34  3.000
 J8V  F23  C20  F21  108.02  3.000
 J8V  F22  C20  C16  110.73  3.000
 J8V  F23  C20  C16  111.84  3.000
 J8V  F21  C20  C16  110.71  3.000
 J8V  O24  C25  C30  118.43  3.000
 J8V  C30  C25  C26  121.76  3.000
 J8V  O24  C25  C26  119.76  3.000
 J8V  H7   C26  C27  120.67  3.000
 J8V  H7   C26  C25  120.52  3.000
 J8V  C27  C26  C25  118.81  3.000
 J8V  H8   C27  C28  120.23  3.000
 J8V  H8   C27  C26  119.42  3.000
 J8V  C28  C27  C26  120.35  3.000
 J8V  H9   C28  C29  120.02  3.000
 J8V  H9   C28  C27  120.07  3.000
 J8V  C29  C28  C27  119.91  3.000
 J8V  H10  C29  C30  119.46  3.000
 J8V  H10  C29  C28  120.17  3.000
 J8V  C30  C29  C28  120.37  3.000
 J8V  H11  C30  C29  120.91  3.000
 J8V  H11  C30  C25  120.28  3.000
 J8V  C29  C30  C25  118.80  3.000
 J8V  H12  N07  C08  115.66  3.000
 J8V  H12  N07  C06  114.75  3.000
 J8V  C08  N07  C06  129.59  3.000
 J8V  H1   N17  C18  115.33  3.000
 J8V  H1   N17  C16  120.48  3.000
 J8V  C18  N17  C16  124.18  3.000
 J8V  C25  O24  C14  120.59  3.000
 J8V  O11  C09  O10  126.97  3.000
 J8V  O10  C09  C02  116.39  3.000
 J8V  O11  C09  C02  116.64  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
 J8V  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 J8V  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 J8V  CONST_03  C05  C04  C03  C02    0.00   0.0  0
 J8V  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 J8V  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 J8V  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 J8V  CONST_07  C28  C27  C26  C25    0.00   0.0  0
 J8V  CONST_08  C28  C29  C30  C25    0.00   0.0  0
 J8V  CONST_09  C29  C30  C25  C26    0.00   0.0  0
 J8V  CONST_10  C29  C28  C27  C26    0.00   0.0  0
 J8V  CONST_11  C30  C25  C26  C27    0.00   0.0  0
 J8V  CONST_12  C30  C29  C28  C27    0.00   0.0  0
 J8V  CONST_13  C16  N17  C18  C13    0.00   0.0  0
 J8V  CONST_14  N07  C06  C01  C02  180.00   0.0  0
 J8V  CONST_15  C09  C02  C03  C04  180.00   0.0  0
 J8V  CONST_16  N07  C06  C05  C04  180.00   0.0  0
 J8V  CONST_17  C09  C02  C01  C06  180.00   0.0  0
 J8V  CONST_18  O24  C25  C26  C27  180.00   0.0  0
 J8V  CONST_19  O24  C25  C30  C29  180.00   0.0  0
 J8V  CONST_20  O19  C18  N17  C16  180.00   0.0  0
 J8V  CONST_21  H3   C03  C02  C01  180.00   0.0  0
 J8V  CONST_22  H5   C05  C06  C01  180.00   0.0  0
 J8V  CONST_23  H4   C04  C03  C02  180.00   0.0  0
 J8V  CONST_24  H2   C01  C02  C03  180.00   0.0  0
 J8V  CONST_25  H8   C27  C26  C25  180.00   0.0  0
 J8V  CONST_26  H10  C29  C30  C25  180.00   0.0  0
 J8V  CONST_27  H11  C30  C25  C26  180.00   0.0  0
 J8V  CONST_28  H9   C28  C27  C26  180.00   0.0  0
 J8V  CONST_29  H7   C26  C27  C28  180.00   0.0  0
 J8V  CONST_30  H1   N17  C18  C13  180.00   0.0  0
 J8V  CONST_31  C06  N07  C08  C13  180.00   0.0  0
 J8V  CONST_32  C08  N07  C06  C01  180.00   0.0  0
 J8V  CONST_33  C08  N07  C06  C05    0.00   0.0  0
 J8V  CONST_34  H12  N07  C06  C01    0.00   0.0  0
 J8V  CONST_35  O12  C08  N07  C06    0.00   0.0  0
 J8V  Var_01    C26  C25  O24  C14   73.72  30.0  2
 J8V  Var_02    N07  C08  C13  C14  -80.21  30.0  2
 J8V  Var_03    O11  C09  C02  C01   -0.14  30.0  2
 J8V  Var_04    F21  C20  C16  C15  122.05  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
 J8V  plan-1  C01  0.020
 J8V  plan-1  C02  0.020
 J8V  plan-1  C03  0.020
 J8V  plan-1  C04  0.020
 J8V  plan-1  C05  0.020
 J8V  plan-1  C06  0.020
 J8V  plan-1  N07  0.020
 J8V  plan-1  H2   0.020
 J8V  plan-1  H3   0.020
 J8V  plan-1  H4   0.020
 J8V  plan-1  H5   0.020
 J8V  plan-1  C09  0.020
 J8V  plan-2  C14  0.020
 J8V  plan-2  C13  0.020
 J8V  plan-2  C08  0.020
 J8V  plan-2  C15  0.020
 J8V  plan-2  C16  0.020
 J8V  plan-2  C18  0.020
 J8V  plan-2  C20  0.020
 J8V  plan-2  N17  0.020
 J8V  plan-2  O19  0.020
 J8V  plan-2  O24  0.020
 J8V  plan-2  H6   0.020
 J8V  plan-2  H1   0.020
 J8V  plan-3  C25  0.020
 J8V  plan-3  C26  0.020
 J8V  plan-3  C27  0.020
 J8V  plan-3  C28  0.020
 J8V  plan-3  C29  0.020
 J8V  plan-3  C30  0.020
 J8V  plan-3  O24  0.020
 J8V  plan-3  H7   0.020
 J8V  plan-3  H8   0.020
 J8V  plan-3  H9   0.020
 J8V  plan-3  H10  0.020
 J8V  plan-3  H11  0.020
 J8V  plan-4  C13  0.020
 J8V  plan-4  C06  0.020
 J8V  plan-4  C08  0.020
 J8V  plan-4  N07  0.020
 J8V  plan-4  O12  0.020
 J8V  plan-4  H12  0.020
 J8V  plan-5  C02  0.020
 J8V  plan-5  O10  0.020
 J8V  plan-5  O11  0.020
 J8V  plan-5  C09  0.020

