# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:49:53 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-{[(6-oxo-1,6-dihydropyridin-3-yl)methyl]amino}-N-[4-propyl-3-(trifluoromethyl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1ccc(NC(=O)c2ccccc2NCC3=CNC(=O)C=C3)cc1C(F)(F)F
#
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
 GIN  GIN  2-{[(6-oxo-1,6-dihydropyridin-3-yl)methyl]amino}-N-[4-propyl-3-(trifluoromethyl)phenyl]benzamide  ligand  53  31  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GIN
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
 GIN  C12   C  C     0   0.552   4.9224  -3.3367  -3.5810
 GIN  C16   C  CR6   0   0.395   4.6375  -3.7832  -1.1753
 GIN  C19   C  CR6   0   0.150   5.4265  -4.1562   1.5120
 GIN  C20   C  CR16  0  -0.302   6.2198  -4.5665   0.4430
 GIN  C21   C  CR16  0  -0.271   5.8510  -4.3973  -0.8787
 GIN  C24   C  CH2   0  -0.526   5.9695  -4.3673   2.9017
 GIN  C30   C  CH2   0  -0.417   6.9827  -3.2919   3.3032
 GIN  C31   C  CH3   0  -0.667   7.5651  -3.5495   4.6852
 GIN  C32   C  CH2   0  -0.344   6.2536  -0.7582  -6.7931
 GIN  C33   C  CR6   0  -0.067   7.3365   0.1192  -6.2445
 GIN  C34   C  CR16  0  -0.124   7.0690   1.0727  -5.2251
 GIN  C35   C  CR16  0  -0.458   8.0455   1.8701  -4.7210
 GIN  C01   C  CR6   0  -0.149   4.1661  -3.2287  -4.8534
 GIN  C02   C  CR16  0  -0.292   3.0142  -3.9939  -5.0447
 GIN  C03   C  CR16  0  -0.282   2.2821  -3.9363  -6.2159
 GIN  C04   C  CR16  0  -0.237   2.7161  -3.0877  -7.2268
 GIN  C05   C  CR16  0  -0.357   3.8602  -2.3275  -7.0759
 GIN  C06   C  CR6   0   0.379   4.6229  -2.3787  -5.8957
 GIN  N11   N  NH1   0  -0.698   5.7338  -1.6040  -5.7443
 GIN  N13   N  NH1   0  -0.759   4.1670  -3.6047  -2.4811
 GIN  O14   O  O     0  -0.478   6.1362  -3.1908  -3.5171
 GIN  C17   C  CR16  0  -0.381   3.8232  -3.3675  -0.1281
 GIN  C18   C  CR6   0  -0.267   4.2057  -3.5496   1.1956
 GIN  C23   C  CT    0   1.058   3.2649  -3.0991   2.2749
 GIN  F27   F  F     0  -0.301   2.1906  -2.4678   1.7895
 GIN  F28   F  F     0  -0.315   2.8025  -4.1303   2.9997
 GIN  F29   F  F     0  -0.314   3.8433  -2.2507   3.1372
 GIN  C36   C  CR6   0   0.534   9.4038   1.7867  -5.1952
 GIN  N37   N  NR16  0  -0.659   9.5850   0.8371  -6.1812
 GIN  C38   C  CR16  0   0.021   8.6171   0.0374  -6.6853
 GIN  O41   O  OC    0  -0.512  10.3454   2.4692  -4.8002
 GIN  H20   H  HCR6  0   0.261   7.1629  -5.0540   0.6591
 GIN  H21   H  HCR6  0   0.278   6.4999  -4.7613  -1.6601
 GIN  H241  H  HCH2  0   0.243   5.1851  -4.4319   3.6552
 GIN  H242  H  HCH2  0   0.249   6.4730  -5.3379   2.9208
 GIN  H301  H  HCH2  0   0.226   7.7869  -3.2636   2.5630
 GIN  H302  H  HCH2  0   0.227   6.5088  -2.3084   3.2776
 GIN  H311  H  HCH3  0   0.221   6.7880  -3.5354   5.4511
 GIN  H312  H  HCH3  0   0.220   8.0556  -4.5237   4.7304
 GIN  H313  H  HCH3  0   0.232   8.3051  -2.7938   4.9500
 GIN  H321  H  HCH2  0   0.245   6.6390  -1.3339  -7.6443
 GIN  H322  H  HCH2  0   0.253   5.4459  -0.1318  -7.1817
 GIN  H34   H  HCR6  0   0.274   6.0582   1.1651  -4.8449
 GIN  H35   H  HCR6  0   0.274   7.8305   2.5950  -3.9477
 GIN  H02   H  HCR6  0   0.264   2.6922  -4.6747  -4.2661
 GIN  H03   H  HCR6  0   0.255   1.3993  -4.5473  -6.3409
 GIN  H04   H  HCR6  0   0.261   2.1654  -3.0272  -8.1570
 GIN  H05   H  HCR6  0   0.277   4.1758  -1.6980  -7.8961
 GIN  HN11  H  HNH1  0   0.397   6.4025  -1.9309  -5.0642
 GIN  HN13  H  HNH1  0   0.420   3.1688  -3.4972  -2.5740
 GIN  H17   H  HCR6  0   0.281   2.8788  -2.8967  -0.3674
 GIN  HN37  H  HNR6  0   0.423  10.5215   0.7402  -6.5497
 GIN  H38   H  HCR6  0   0.307   8.9330  -0.6553  -7.4531

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
 GIN  C12  O14   double    1.224  0.020  1.224
 GIN  C12  C01   single    1.484  0.020  1.484
 GIN  C12  N13   single    1.361  0.020  1.361
 GIN  C16  C17   aromatic  1.390  0.020  1.390
 GIN  C16  N13   single    1.399  0.020  1.399
 GIN  C16  C21   aromatic  1.392  0.020  1.392
 GIN  C19  C18   aromatic  1.399  0.020  1.399
 GIN  C19  C24   single    1.507  0.020  1.507
 GIN  C19  C20   aromatic  1.393  0.020  1.393
 GIN  C20  C21   aromatic  1.383  0.020  1.383
 GIN  C20  H20   single    0.930  0.020  1.080
 GIN  C21  H21   single    0.930  0.020  1.080
 GIN  C24  C30   single    1.531  0.020  1.531
 GIN  C24  H241  single    0.970  0.020  1.090
 GIN  C24  H242  single    0.970  0.020  1.090
 GIN  C30  C31   single    1.522  0.020  1.522
 GIN  C30  H301  single    0.970  0.020  1.090
 GIN  C30  H302  single    0.970  0.020  1.090
 GIN  C31  H311  single    0.970  0.020  1.090
 GIN  C31  H312  single    0.970  0.020  1.090
 GIN  C31  H313  single    0.970  0.020  1.090
 GIN  C32  C33   single    1.498  0.020  1.498
 GIN  C32  N11   single    1.444  0.020  1.444
 GIN  C32  H321  single    0.970  0.020  1.090
 GIN  C32  H322  single    0.970  0.020  1.090
 GIN  C33  C38   aromatic  1.357  0.020  1.357
 GIN  C33  C34   aromatic  1.421  0.020  1.421
 GIN  C34  C35   aromatic  1.358  0.020  1.358
 GIN  C34  H34   single    0.930  0.020  1.080
 GIN  C35  C36   aromatic  1.441  0.020  1.441
 GIN  C35  H35   single    0.930  0.020  1.080
 GIN  C01  C06   aromatic  1.420  0.020  1.420
 GIN  C01  C02   aromatic  1.396  0.020  1.396
 GIN  C02  C03   aromatic  1.382  0.020  1.382
 GIN  C02  H02   single    0.930  0.020  1.080
 GIN  C03  C04   aromatic  1.389  0.020  1.389
 GIN  C03  H03   single    0.930  0.020  1.080
 GIN  C04  C05   aromatic  1.382  0.020  1.382
 GIN  C04  H04   single    0.930  0.020  1.080
 GIN  C05  C06   aromatic  1.406  0.020  1.406
 GIN  C05  H05   single    0.930  0.020  1.080
 GIN  C06  N11   single    1.363  0.020  1.363
 GIN  N11  HN11  single    0.890  0.020  1.040
 GIN  N13  HN13  single    0.860  0.020  1.020
 GIN  C17  C18   aromatic  1.390  0.020  1.390
 GIN  C17  H17   single    0.930  0.020  1.080
 GIN  C18  C23   single    1.501  0.020  1.501
 GIN  C23  F27   single    1.337  0.020  1.337
 GIN  C23  F29   single    1.341  0.020  1.341
 GIN  C23  F28   single    1.343  0.020  1.343
 GIN  C36  O41   double    1.228  0.020  1.228
 GIN  C36  N37   aromatic  1.381  0.020  1.381
 GIN  N37  C38   aromatic  1.353  0.020  1.353
 GIN  N37  HN37  single    0.860  0.020  1.020
 GIN  C38  H38   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
 GIN  O14   C12  N13   122.11  3.000
 GIN  N13   C12  C01   115.11  3.000
 GIN  O14   C12  C01   122.77  3.000
 GIN  C17   C16  N13   117.90  3.000
 GIN  N13   C16  C21   123.24  3.000
 GIN  C17   C16  C21   118.81  3.000
 GIN  C18   C19  C24   125.70  3.000
 GIN  C24   C19  C20   117.47  3.000
 GIN  C18   C19  C20   116.81  3.000
 GIN  H20   C20  C21   118.55  3.000
 GIN  H20   C20  C19   118.37  3.000
 GIN  C21   C20  C19   123.07  3.000
 GIN  H21   C21  C20   119.38  3.000
 GIN  H21   C21  C16   121.25  3.000
 GIN  C20   C21  C16   119.36  3.000
 GIN  H242  C24  H241  105.48  3.000
 GIN  H242  C24  C30   108.31  3.000
 GIN  H241  C24  C30   109.67  3.000
 GIN  H242  C24  C19   107.84  3.000
 GIN  H241  C24  C19   112.74  3.000
 GIN  C30   C24  C19   112.45  3.000
 GIN  H302  C30  H301  106.26  3.000
 GIN  H302  C30  C31   109.87  3.000
 GIN  H301  C30  C31   109.74  3.000
 GIN  H302  C30  C24   109.83  3.000
 GIN  H301  C30  C24   109.11  3.000
 GIN  C31   C30  C24   111.87  3.000
 GIN  H313  C31  H312  107.67  3.000
 GIN  H313  C31  H311  107.70  3.000
 GIN  H312  C31  H311  107.60  3.000
 GIN  H313  C31  C30   111.29  3.000
 GIN  H312  C31  C30   111.14  3.000
 GIN  H311  C31  C30   111.26  3.000
 GIN  H322  C32  H321  106.52  3.000
 GIN  H322  C32  N11   109.14  3.000
 GIN  H321  C32  N11   112.48  3.000
 GIN  H322  C32  C33   109.18  3.000
 GIN  H321  C32  C33   109.72  3.000
 GIN  N11   C32  C33   109.71  3.000
 GIN  C38   C33  C34   116.82  3.000
 GIN  C34   C33  C32   121.30  3.000
 GIN  C38   C33  C32   121.88  3.000
 GIN  H34   C34  C35   119.37  3.000
 GIN  H34   C34  C33   118.97  3.000
 GIN  C35   C34  C33   121.66  3.000
 GIN  H35   C35  C36   117.48  3.000
 GIN  H35   C35  C34   121.07  3.000
 GIN  C36   C35  C34   121.45  3.000
 GIN  C06   C01  C02   119.53  3.000
 GIN  C02   C01  C12   119.87  3.000
 GIN  C06   C01  C12   120.59  3.000
 GIN  H02   C02  C03   118.54  3.000
 GIN  H02   C02  C01   119.43  3.000
 GIN  C03   C02  C01   122.02  3.000
 GIN  H03   C03  C04   121.08  3.000
 GIN  H03   C03  C02   120.46  3.000
 GIN  C04   C03  C02   118.46  3.000
 GIN  H04   C04  C05   118.96  3.000
 GIN  H04   C04  C03   120.03  3.000
 GIN  C05   C04  C03   121.00  3.000
 GIN  H05   C05  C06   119.98  3.000
 GIN  H05   C05  C04   118.63  3.000
 GIN  C06   C05  C04   121.38  3.000
 GIN  N11   C06  C05   120.98  3.000
 GIN  N11   C06  C01   121.39  3.000
 GIN  C05   C06  C01   117.60  3.000
 GIN  HN11  N11  C06   115.55  3.000
 GIN  HN11  N11  C32   116.18  3.000
 GIN  C06   N11  C32   123.07  3.000
 GIN  HN13  N13  C16   115.62  3.000
 GIN  HN13  N13  C12   117.00  3.000
 GIN  C16   N13  C12   126.35  3.000
 GIN  H17   C17  C18   120.52  3.000
 GIN  H17   C17  C16   118.34  3.000
 GIN  C18   C17  C16   121.14  3.000
 GIN  C23   C18  C17   118.23  3.000
 GIN  C23   C18  C19   120.95  3.000
 GIN  C17   C18  C19   120.81  3.000
 GIN  F29   C23  F28   106.70  3.000
 GIN  F28   C23  F27   106.38  3.000
 GIN  F29   C23  F27   106.34  3.000
 GIN  F28   C23  C18   111.93  3.000
 GIN  F29   C23  C18   112.45  3.000
 GIN  F27   C23  C18   112.59  3.000
 GIN  O41   C36  N37   120.74  3.000
 GIN  N37   C36  C35   113.48  3.000
 GIN  O41   C36  C35   125.78  3.000
 GIN  HN37  N37  C38   118.05  3.000
 GIN  HN37  N37  C36   116.59  3.000
 GIN  C38   N37  C36   125.36  3.000
 GIN  H38   C38  N37   115.74  3.000
 GIN  H38   C38  C33   123.02  3.000
 GIN  N37   C38  C33   121.23  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
 GIN  CONST_01  C19   C18  C17  C16     0.00   0.0  0
 GIN  CONST_02  C19   C20  C21  C16     0.00   0.0  0
 GIN  CONST_03  C17   C18  C19  C20     0.00   0.0  0
 GIN  CONST_04  C17   C16  C21  C20     0.00   0.0  0
 GIN  CONST_05  C18   C17  C16  C21     0.00   0.0  0
 GIN  CONST_06  C18   C19  C20  C21     0.00   0.0  0
 GIN  CONST_07  C36   N37  C38  C33     0.00   0.0  0
 GIN  CONST_08  C36   C35  C34  C33     0.00   0.0  0
 GIN  CONST_09  N37   C38  C33  C34     0.00   0.0  0
 GIN  CONST_10  N37   C36  C35  C34     0.00   0.0  0
 GIN  CONST_11  C38   C33  C34  C35     0.00   0.0  0
 GIN  CONST_12  C38   N37  C36  C35     0.00   0.0  0
 GIN  CONST_13  C04   C05  C06  C01     0.00   0.0  0
 GIN  CONST_14  C04   C03  C02  C01     0.00   0.0  0
 GIN  CONST_15  C05   C06  C01  C02     0.00   0.0  0
 GIN  CONST_16  C05   C04  C03  C02     0.00   0.0  0
 GIN  CONST_17  C06   C01  C02  C03     0.00   0.0  0
 GIN  CONST_18  C06   C05  C04  C03     0.00   0.0  0
 GIN  CONST_19  C05   C06  C01  C12   180.00   0.0  0
 GIN  CONST_20  C03   C02  C01  C12   180.00   0.0  0
 GIN  CONST_21  C23   C18  C17  C16   180.00   0.0  0
 GIN  CONST_22  C23   C18  C19  C20   180.00   0.0  0
 GIN  CONST_23  N13   C16  C21  C20   180.00   0.0  0
 GIN  CONST_24  C24   C19  C20  C21   180.00   0.0  0
 GIN  CONST_25  C17   C18  C19  C24   180.00   0.0  0
 GIN  CONST_26  N37   C38  C33  C32   180.00   0.0  0
 GIN  CONST_27  C35   C34  C33  C32   180.00   0.0  0
 GIN  CONST_28  O41   C36  C35  C34   180.00   0.0  0
 GIN  CONST_29  N11   C06  C01  C02   180.00   0.0  0
 GIN  CONST_30  N11   C06  C05  C04   180.00   0.0  0
 GIN  CONST_31  C18   C17  C16  N13   180.00   0.0  0
 GIN  CONST_32  O41   C36  N37  C38   180.00   0.0  0
 GIN  CONST_33  H20   C20  C21  C16   180.00   0.0  0
 GIN  CONST_34  H17   C17  C18  C19   180.00   0.0  0
 GIN  CONST_35  H21   C21  C20  C19   180.00   0.0  0
 GIN  CONST_36  HN37  N37  C38  C33   180.00   0.0  0
 GIN  CONST_37  H35   C35  C34  C33   180.00   0.0  0
 GIN  CONST_38  H38   C38  C33  C34   180.00   0.0  0
 GIN  CONST_39  H05   C05  C06  C01   180.00   0.0  0
 GIN  CONST_40  H03   C03  C02  C01   180.00   0.0  0
 GIN  CONST_41  H04   C04  C03  C02   180.00   0.0  0
 GIN  CONST_42  H02   C02  C03  C04   180.00   0.0  0
 GIN  CONST_43  H34   C34  C35  C36   180.00   0.0  0
 GIN  CONST_44  C01   C12  N13  C16   180.00   0.0  0
 GIN  CONST_47  C01   C06  N11  C32   180.00   0.0  0
 GIN  CONST_48  C05   C06  N11  C32     0.00   0.0  0
 GIN  CONST_51  O14   C12  N13  C16     0.00   0.0  0
 GIN  Var_01    F27   C23  C18  C19   176.05  30.0  2
 GIN  Var_02    C30   C24  C19  C20    79.83  30.0  2
 GIN  Var_03    C06   N11  C32  C33   170.91  30.0  3
 GIN  Var_04    N11   C32  C33  C34   -62.53  30.0  2
 GIN  Var_05    O14   C12  C01  C02   148.40  30.0  2
 GIN  Var_06    C31   C30  C24  C19  -177.64  30.0  3
 GIN  Var_07    H311  C31  C30  C24   -61.45  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
 GIN  plan-1  C16   0.020
 GIN  plan-1  C19   0.020
 GIN  plan-1  C20   0.020
 GIN  plan-1  C21   0.020
 GIN  plan-1  C24   0.020
 GIN  plan-1  N13   0.020
 GIN  plan-1  C17   0.020
 GIN  plan-1  C18   0.020
 GIN  plan-1  C23   0.020
 GIN  plan-1  H20   0.020
 GIN  plan-1  H21   0.020
 GIN  plan-1  H17   0.020
 GIN  plan-2  C32   0.020
 GIN  plan-2  C33   0.020
 GIN  plan-2  C34   0.020
 GIN  plan-2  C35   0.020
 GIN  plan-2  C36   0.020
 GIN  plan-2  N37   0.020
 GIN  plan-2  C38   0.020
 GIN  plan-2  O41   0.020
 GIN  plan-2  H34   0.020
 GIN  plan-2  H35   0.020
 GIN  plan-2  HN37  0.020
 GIN  plan-2  H38   0.020
 GIN  plan-3  C12   0.020
 GIN  plan-3  C01   0.020
 GIN  plan-3  C02   0.020
 GIN  plan-3  C03   0.020
 GIN  plan-3  C04   0.020
 GIN  plan-3  C05   0.020
 GIN  plan-3  C06   0.020
 GIN  plan-3  N11   0.020
 GIN  plan-3  H02   0.020
 GIN  plan-3  H03   0.020
 GIN  plan-3  H04   0.020
 GIN  plan-3  H05   0.020
 GIN  plan-4  C12   0.020
 GIN  plan-4  C16   0.020
 GIN  plan-4  C01   0.020
 GIN  plan-4  N13   0.020
 GIN  plan-4  O14   0.020
 GIN  plan-4  HN13  0.020
 GIN  plan-5  C32   0.020
 GIN  plan-5  C06   0.020
 GIN  plan-5  N11   0.020
 GIN  plan-5  HN11  0.020

