# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 14:58:33 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=CC(=C(C1=O)c2ccc(C[C@H](NC(=O)c3c(Cl)cccc3Cl)C(O)=O)cc2)C(F)(F)F)C
#
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
 0DU  0DU  N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine  ligand  53  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0DU
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
 0DU  C10   C   CR6    0   0.042   2.0590  -0.6660   0.0884
 0DU  C13   C   CR6    0   0.165  -0.2931  -2.2044   0.1668
 0DU  C15   C   CH1    0  -0.206  -2.6917  -2.3273  -0.5997
 0DU  C20   C   CR6    0  -0.093  -4.6646   1.7293   0.3794
 0DU  C22   C   CR16   0  -0.200  -4.8789   2.9190   1.0564
 0DU  C24   C   CR16   0  -0.200  -2.5115   3.3579   0.9736
 0DU  C02   C   CR6    0   0.421   5.4706   1.8923  -0.1772
 0DU  C03   C   CR16   0  -0.486   5.6098   0.6742   0.4195
 0DU  C04   C   CR6    0  -0.075   4.5025  -0.1934   0.5200
 0DU  C05   C   CT     0   1.070   4.6947  -1.5240   1.2016
 0DU  F06   F   F      0  -0.310   4.1459  -1.5300   2.4229
 0DU  F07   F   F      0  -0.302   4.1545  -2.5328   0.5165
 0DU  F08   F   F      0  -0.302   5.9891  -1.8190   1.3619
 0DU  C09   C   CR6    0  -0.200   3.2836   0.1639   0.0231
 0DU  C11   C   CR16   0  -0.257   1.3253  -0.7778   1.2613
 0DU  C12   C   CR16   0  -0.311   0.1623  -1.5371   1.2959
 0DU  C14   C   CH2    0  -0.547  -1.5626  -3.0068   0.1833
 0DU  N16   N   NH1    0  -0.571  -2.9243  -1.0083  -0.0639
 0DU  O18   O   O      0  -0.479  -3.2183   0.0967  -2.0246
 0DU  C19   C   CR6    0   0.074  -3.3913   1.3256  -0.0068
 0DU  C23   C   CR16   0  -0.276  -3.7925   3.7287   1.3500
 0DU  C25   C   CR6    0  -0.095  -2.3231   2.1630   0.2960
 0DU  CL2   CL  CL     0  -0.071  -0.7260   1.7076  -0.1778
 0DU  C27   C   C      0   0.416  -3.9722  -3.2051  -0.6377
 0DU  O28   O   O      0  -0.575  -5.0383  -2.6816  -0.2840
 0DU  O29   O   OC    -1  -0.615  -3.7904  -4.3705  -1.0440
 0DU  C30   C   CR16   0  -0.296   0.4482  -2.0856  -1.0086
 0DU  C31   C   CR16   0  -0.250   1.6006  -1.3229  -1.0514
 0DU  C32   C   CR6    0   0.578   3.1353   1.4437  -0.6371
 0DU  O33   O   O      0  -0.476   2.0885   1.8253  -1.1457
 0DU  N34   N   NR6    0  -0.556   4.2590   2.2641  -0.6749
 0DU  C35   C   CH3    0  -0.543   4.0525   3.5574  -1.3168
 0DU  H15   H   HCH1   0   0.254  -2.3566  -2.1991  -1.6322
 0DU  H24   H   HCR6   0   0.284  -1.6667   3.9927   1.2026
 0DU  H03   H   HCR6   0   0.283   6.5808   0.3960   0.7964
 0DU  H11   H   HCR6   0   0.241   1.6513  -0.2597   2.1545
 0DU  H12   H   HCR6   0   0.239  -0.3964  -1.6082   2.2221
 0DU  H14   H   HCH2   0   0.258  -1.3953  -3.9878  -0.2619
 0DU  H14A  H   HCH2   0   0.245  -1.8843  -3.1807   1.2150
 0DU  HN16  H   HNH1   0   0.396  -2.9975  -0.9155   0.9371
 0DU  H23   H   HCR6   0   0.280  -3.9476   4.6595   1.8783
 0DU  H30   H   HCR6   0   0.242   0.1185  -2.5995  -1.9051
 0DU  H31   H   HCR6   0   0.241   2.1601  -1.2489  -1.9758
 0DU  H35   H   HCH3   0   0.264   3.8427   3.4268  -2.3769
 0DU  H35A  H   HCH3   0   0.266   3.2106   4.0691  -0.8570
 0DU  H35B  H   HCH3   0   0.279   4.9316   4.1784  -1.2097
 0DU  C17   C   C      0   0.501  -3.1784   0.0660  -0.8034
 0DU  CL1   CL  CL     0  -0.099  -6.0137   0.7125   0.0112
 0DU  C01   C   CH3    0  -0.759   6.6377   2.8166  -0.2961
 0DU  H22   H   HCR6   0   0.287  -5.8782   3.2102   1.3477
 0DU  H01   H   HCH3   0   0.273   6.4847   3.7390   0.2662
 0DU  H01A  H   HCH3   0   0.278   7.5265   2.3323   0.0996
 0DU  H01B  H   HCH3   0   0.272   6.8370   3.0888  -1.3331

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
 0DU  C31  C10   aromatic  1.393  0.020  1.393
 0DU  C09  C10   single    1.481  0.020  1.481
 0DU  C10  C11   aromatic  1.388  0.020  1.388
 0DU  C30  C13   aromatic  1.395  0.020  1.395
 0DU  C13  C14   single    1.502  0.020  1.502
 0DU  C13  C12   aromatic  1.388  0.020  1.388
 0DU  N16  C15   single    1.442  0.020  1.442
 0DU  C15  C14   single    1.533  0.020  1.533
 0DU  C15  C27   single    1.553  0.020  1.553
 0DU  C15  H15   single    0.970  0.020  1.090
 0DU  C19  C17   single    1.505  0.020  1.505
 0DU  C17  O18   double    1.222  0.020  1.222
 0DU  C17  N16   single    1.329  0.020  1.329
 0DU  C22  C20   aromatic  1.385  0.020  1.385
 0DU  C20  C19   aromatic  1.390  0.020  1.390
 0DU  C20  CL1   single    1.729  0.020  1.729
 0DU  C23  C22   aromatic  1.386  0.020  1.386
 0DU  C22  H22   single    0.930  0.020  1.080
 0DU  C23  C24   aromatic  1.386  0.020  1.386
 0DU  C24  C25   aromatic  1.387  0.020  1.387
 0DU  C24  H24   single    0.930  0.020  1.080
 0DU  C02  C01   single    1.493  0.020  1.493
 0DU  C01  H01   single    0.970  0.020  1.090
 0DU  C01  H01A  single    0.970  0.020  1.090
 0DU  C01  H01B  single    0.970  0.020  1.090
 0DU  C03  C02   double    1.364  0.020  1.364
 0DU  C02  N34   single    1.362  0.020  1.362
 0DU  C04  C03   single    1.410  0.020  1.410
 0DU  C03  H03   single    0.930  0.020  1.080
 0DU  C05  C04   single    1.507  0.020  1.507
 0DU  C04  C09   double    1.364  0.020  1.364
 0DU  F06  C05   single    1.339  0.020  1.339
 0DU  F08  C05   single    1.337  0.020  1.337
 0DU  C05  F07   single    1.334  0.020  1.334
 0DU  C09  C32   single    1.448  0.020  1.448
 0DU  C11  C12   aromatic  1.389  0.020  1.389
 0DU  C11  H11   single    0.930  0.020  1.080
 0DU  C12  H12   single    0.930  0.020  1.080
 0DU  C14  H14   single    0.970  0.020  1.090
 0DU  C14  H14A  single    0.970  0.020  1.090
 0DU  N16  HN16  single    0.860  0.020  1.020
 0DU  C25  C19   aromatic  1.391  0.020  1.391
 0DU  C23  H23   single    0.930  0.020  1.080
 0DU  C25  CL2   single    1.727  0.020  1.727
 0DU  O28  C27   deloc     1.239  0.020  1.239
 0DU  C27  O29   deloc     1.247  0.020  1.247
 0DU  C31  C30   aromatic  1.383  0.020  1.383
 0DU  C30  H30   single    0.930  0.020  1.080
 0DU  C31  H31   single    0.930  0.020  1.080
 0DU  C32  N34   single    1.392  0.020  1.392
 0DU  C32  O33   double    1.225  0.020  1.225
 0DU  N34  C35   single    1.459  0.020  1.459
 0DU  C35  H35   single    0.970  0.020  1.090
 0DU  C35  H35A  single    0.970  0.020  1.090
 0DU  C35  H35B  single    0.970  0.020  1.090

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
 0DU  C31   C10  C11   118.65  3.000
 0DU  C11   C10  C09   121.30  3.000
 0DU  C31   C10  C09   120.02  3.000
 0DU  C30   C13  C14   120.26  3.000
 0DU  C14   C13  C12   121.68  3.000
 0DU  C30   C13  C12   118.05  3.000
 0DU  H15   C15  C27   107.21  3.000
 0DU  H15   C15  N16   107.04  3.000
 0DU  C27   C15  N16   113.14  3.000
 0DU  H15   C15  C14   107.98  3.000
 0DU  C27   C15  C14   111.67  3.000
 0DU  N16   C15  C14   109.54  3.000
 0DU  CL1   C20  C19   118.99  3.000
 0DU  CL1   C20  C22   119.23  3.000
 0DU  C19   C20  C22   121.78  3.000
 0DU  H22   C22  C23   120.67  3.000
 0DU  H22   C22  C20   120.40  3.000
 0DU  C23   C22  C20   118.94  3.000
 0DU  H24   C24  C25   120.22  3.000
 0DU  H24   C24  C23   120.51  3.000
 0DU  C25   C24  C23   119.28  3.000
 0DU  N34   C02  C03   119.65  3.000
 0DU  N34   C02  C01   119.82  3.000
 0DU  C03   C02  C01   120.53  3.000
 0DU  H03   C03  C04   121.56  3.000
 0DU  H03   C03  C02   118.39  3.000
 0DU  C04   C03  C02   120.04  3.000
 0DU  C09   C04  C05   120.66  3.000
 0DU  C09   C04  C03   120.97  3.000
 0DU  C05   C04  C03   118.37  3.000
 0DU  F08   C05  F07   106.67  3.000
 0DU  F07   C05  F06   107.41  3.000
 0DU  F08   C05  F06   106.65  3.000
 0DU  F07   C05  C04   112.57  3.000
 0DU  F08   C05  C04   111.86  3.000
 0DU  F06   C05  C04   111.35  3.000
 0DU  C32   C09  C04   119.29  3.000
 0DU  C32   C09  C10   115.52  3.000
 0DU  C04   C09  C10   125.18  3.000
 0DU  H11   C11  C12   119.53  3.000
 0DU  H11   C11  C10   119.96  3.000
 0DU  C12   C11  C10   120.50  3.000
 0DU  H12   C12  C11   119.25  3.000
 0DU  H12   C12  C13   119.62  3.000
 0DU  C11   C12  C13   121.13  3.000
 0DU  H14A  C14  H14   106.68  3.000
 0DU  H14A  C14  C15   109.59  3.000
 0DU  H14   C14  C15   107.66  3.000
 0DU  H14A  C14  C13   110.10  3.000
 0DU  H14   C14  C13   110.28  3.000
 0DU  C15   C14  C13   112.34  3.000
 0DU  HN16  N16  C17   117.67  3.000
 0DU  HN16  N16  C15   117.69  3.000
 0DU  C17   N16  C15   124.29  3.000
 0DU  C25   C19  C20   117.91  3.000
 0DU  C25   C19  C17   120.69  3.000
 0DU  C20   C19  C17   121.29  3.000
 0DU  H23   C23  C24   119.71  3.000
 0DU  H23   C23  C22   119.59  3.000
 0DU  C24   C23  C22   120.70  3.000
 0DU  CL2   C25  C19   119.46  3.000
 0DU  CL2   C25  C24   119.14  3.000
 0DU  C19   C25  C24   121.40  3.000
 0DU  O29   C27  O28   127.81  3.000
 0DU  O29   C27  C15   114.57  3.000
 0DU  O28   C27  C15   117.62  3.000
 0DU  H30   C30  C31   119.29  3.000
 0DU  H30   C30  C13   119.65  3.000
 0DU  C31   C30  C13   121.07  3.000
 0DU  H31   C31  C30   119.64  3.000
 0DU  H31   C31  C10   119.74  3.000
 0DU  C30   C31  C10   120.60  3.000
 0DU  N34   C32  O33   119.68  3.000
 0DU  O33   C32  C09   123.53  3.000
 0DU  N34   C32  C09   116.79  3.000
 0DU  C35   N34  C32   114.86  3.000
 0DU  C35   N34  C02   121.93  3.000
 0DU  C32   N34  C02   123.20  3.000
 0DU  H35B  C35  H35A  108.50  3.000
 0DU  H35B  C35  H35   108.78  3.000
 0DU  H35A  C35  H35   108.61  3.000
 0DU  H35B  C35  N34   110.52  3.000
 0DU  H35A  C35  N34   109.93  3.000
 0DU  H35   C35  N34   110.45  3.000
 0DU  C19   C17  O18   120.20  3.000
 0DU  O18   C17  N16   125.64  3.000
 0DU  C19   C17  N16   114.14  3.000
 0DU  H01B  C01  H01A  107.94  3.000
 0DU  H01B  C01  H01   107.74  3.000
 0DU  H01A  C01  H01   107.69  3.000
 0DU  H01B  C01  C02   111.90  3.000
 0DU  H01A  C01  C02   109.53  3.000
 0DU  H01   C01  C02   111.87  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
 0DU  CONST_01  C13   C30  C31  C10     0.00   0.0  0
 0DU  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 0DU  CONST_03  C24   C23  C22  C20     0.00   0.0  0
 0DU  CONST_04  C24   C25  C19  C20     0.00   0.0  0
 0DU  CONST_05  C25   C19  C20  C22     0.00   0.0  0
 0DU  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 0DU  CONST_07  C30   C31  C10  C11     0.00   0.0  0
 0DU  CONST_08  C30   C13  C12  C11     0.00   0.0  0
 0DU  CONST_09  C31   C30  C13  C12     0.00   0.0  0
 0DU  CONST_10  C31   C10  C11  C12     0.00   0.0  0
 0DU  CONST_11  C23   C22  C20  C19     0.00   0.0  0
 0DU  CONST_12  C23   C24  C25  C19     0.00   0.0  0
 0DU  CONST_13  C30   C31  C10  C09   180.00   0.0  0
 0DU  CONST_14  C12   C11  C10  C09   180.00   0.0  0
 0DU  CONST_15  C09   C32  N34  C02     0.00   0.0  0
 0DU  CONST_16  C22   C20  C19  C17   180.00   0.0  0
 0DU  CONST_17  C24   C25  C19  C17   180.00   0.0  0
 0DU  CONST_18  CL2   C25  C19  C20   180.00   0.0  0
 0DU  CONST_19  C14   C13  C12  C11   180.00   0.0  0
 0DU  CONST_20  C31   C30  C13  C14   180.00   0.0  0
 0DU  CONST_21  C23   C22  C20  CL1   180.00   0.0  0
 0DU  CONST_22  C25   C19  C20  CL1   180.00   0.0  0
 0DU  CONST_23  CL2   C25  C24  C23   180.00   0.0  0
 0DU  CONST_24  O33   C32  N34  C02   180.00   0.0  0
 0DU  CONST_25  C35   N34  C32  C09   180.00   0.0  0
 0DU  CONST_26  H30   C30  C31  C10   180.00   0.0  0
 0DU  CONST_27  H12   C12  C11  C10   180.00   0.0  0
 0DU  CONST_28  H31   C31  C30  C13   180.00   0.0  0
 0DU  CONST_29  H11   C11  C12  C13   180.00   0.0  0
 0DU  CONST_30  H23   C23  C22  C20   180.00   0.0  0
 0DU  CONST_31  H24   C24  C23  C22   180.00   0.0  0
 0DU  CONST_32  H22   C22  C23  C24   180.00   0.0  0
 0DU  CONST_33  C35   N34  C32  O33     0.00   0.0  0
 0DU  CONST_34  C19   C17  N16  C15   180.00   0.0  0
 0DU  CONST_35  HN16  N16  C17  C19     0.00   0.0  0
 0DU  CONST_36  O18   C17  N16  C15     0.00   0.0  0
 0DU  Var_01    C31   C10  C09  C04  -104.76  30.0  2
 0DU  Var_02    C30   C13  C14  C15   -70.37  30.0  2
 0DU  Var_03    O18   C17  C19  C20    88.38  30.0  2
 0DU  Var_04    F06   C05  C04  C03   105.33  30.0  3
 0DU  Var_05    H35   C35  N34  C02   112.94  30.0  3
 0DU  Var_06    H01   C01  C02  C03  -116.35  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0DU  chir_01  C15  N16  C14  C27  negativ

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
 0DU  plan-1  C20   0.020
 0DU  plan-1  C22   0.020
 0DU  plan-1  C24   0.020
 0DU  plan-1  C19   0.020
 0DU  plan-1  C23   0.020
 0DU  plan-1  C25   0.020
 0DU  plan-1  CL2   0.020
 0DU  plan-1  H24   0.020
 0DU  plan-1  H23   0.020
 0DU  plan-1  C17   0.020
 0DU  plan-1  CL1   0.020
 0DU  plan-1  H22   0.020
 0DU  plan-2  C10   0.020
 0DU  plan-2  C02   0.020
 0DU  plan-2  C03   0.020
 0DU  plan-2  C04   0.020
 0DU  plan-2  C05   0.020
 0DU  plan-2  C09   0.020
 0DU  plan-2  C32   0.020
 0DU  plan-2  O33   0.020
 0DU  plan-2  N34   0.020
 0DU  plan-2  C35   0.020
 0DU  plan-2  H03   0.020
 0DU  plan-2  C01   0.020
 0DU  plan-3  C10   0.020
 0DU  plan-3  C13   0.020
 0DU  plan-3  C09   0.020
 0DU  plan-3  C11   0.020
 0DU  plan-3  C12   0.020
 0DU  plan-3  C14   0.020
 0DU  plan-3  C30   0.020
 0DU  plan-3  C31   0.020
 0DU  plan-3  H11   0.020
 0DU  plan-3  H12   0.020
 0DU  plan-3  H30   0.020
 0DU  plan-3  H31   0.020
 0DU  plan-4  C15   0.020
 0DU  plan-4  N16   0.020
 0DU  plan-4  O18   0.020
 0DU  plan-4  C19   0.020
 0DU  plan-4  HN16  0.020
 0DU  plan-4  C17   0.020
 0DU  plan-5  C15   0.020
 0DU  plan-5  C27   0.020
 0DU  plan-5  O28   0.020
 0DU  plan-5  O29   0.020

