# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 21:45:16 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(3S)-1-amino-1,2-dioxopentan-3-yl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](NC(=O)c1ccc(OCc2ccccn2)c(c1Cl)C(F)(F)F)C(=O)C(N)=O
#
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
 O96  O96  N-[(3S)-1-amino-1,2-dioxopentan-3-yl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide  ligand  47  30  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O96
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
 O96  N1    N   NH2   0  -0.787   6.9799   2.2718   1.3019
 O96  C4    C   C     0   0.461   6.5539   1.1655   0.7007
 O96  C5    C   C     0   0.292   5.0891   1.2305   0.2363
 O96  C6    C   CH1   0  -0.170   4.5994   0.0638  -0.6023
 O96  N8    N   NH1   0  -0.624   3.1620   0.0132  -0.5825
 O96  C10   C   C     0   0.516   2.4860  -0.3117   0.5308
 O96  C11   C   CR6   0   0.007   1.0058  -0.1118   0.4328
 O96  C12   C   CR16  0  -0.262   0.5141   1.1520   0.1411
 O96  C14   C   CR16  0  -0.369  -0.8405   1.4037   0.1032
 O96  C16   C   CR6   0   0.403  -1.7552   0.3812   0.3514
 O96  C17   C   CR6   0  -0.250  -1.2865  -0.9122   0.6611
 O96  C18   C   CR6   0  -0.089   0.0941  -1.1271   0.6878
 O96  CL19  CL  CL    0  -0.083   0.7275  -2.7083   0.9822
 O96  C20   C   CT    0   1.074  -2.2042  -2.0744   0.9563
 O96  F21   F   F     0  -0.311  -1.9156  -2.6259   2.1429
 O96  F22   F   F     0  -0.285  -3.4950  -1.7628   1.0037
 O96  F23   F   F     0  -0.312  -2.0798  -3.0366   0.0312
 O96  O24   O   O2    0  -0.459  -3.0727   0.5806   0.3046
 O96  C25   C   CH2   0  -0.235  -3.5759   1.8438  -0.0882
 O96  C28   C   CR6   0   0.205  -5.0744   1.7639  -0.1844
 O96  N29   N   N     0  -0.427  -5.6950   2.9317  -0.0574
 O96  C30   C   CR16  0  -0.075  -7.0161   2.9630  -0.1742
 O96  C32   C   CR16  0  -0.324  -7.7860   1.8352  -0.4137
 O96  C34   C   CR16  0  -0.148  -7.1343   0.6190  -0.5462
 O96  C36   C   CR16  0  -0.326  -5.7529   0.5769  -0.4342
 O96  O38   O   O     0  -0.462   3.0262  -0.7032   1.5505
 O96  C39   C   CH2   0  -0.466   5.1040   0.2140  -2.0435
 O96  C42   C   CH3   0  -0.662   4.7705  -0.9958  -2.9049
 O96  O46   O   O     0  -0.346   4.3946   2.1690   0.5243
 O96  O47   O   O     0  -0.454   7.2105   0.1553   0.5125
 O96  HN1   H   HNH2  0   0.416   7.9169   2.3269   1.6681
 O96  HN1A  H   HNH2  0   0.418   6.3744   3.0646   1.4369
 O96  H6    H   HCH1  0   0.291   5.0057  -0.8627  -0.1893
 O96  HN8   H   HNH1  0   0.417   2.6568   0.3673  -1.3802
 O96  H12   H   HCR6  0   0.288   1.2040   1.9655  -0.0449
 O96  H14   H   HCR6  0   0.311  -1.1739   2.4061  -0.1188
 O96  H25   H   HCH2  0   0.262  -3.3035   2.6192   0.6334
 O96  H25A  H   HCH2  0   0.266  -3.1657   2.1340  -1.0627
 O96  H30   H   HCR6  0   0.266  -7.4861   3.9342  -0.0651
 O96  H32   H   HCR6  0   0.272  -8.8614   1.9125  -0.4917
 O96  H34   H   HCR6  0   0.276  -7.6924  -0.2881  -0.7374
 O96  H36   H   HCR6  0   0.269  -5.2244  -0.3589  -0.5414
 O96  H39   H   HCH2  0   0.248   4.6789   1.1224  -2.4798
 O96  H39A  H   HCH2  0   0.264   6.1849   0.3557  -2.0246
 O96  H42   H   HCH3  0   0.231   5.2011  -1.9054  -2.4849
 O96  H42A  H   HCH3  0   0.230   3.6958  -1.1489  -3.0024
 O96  H42B  H   HCH3  0   0.244   5.1749  -0.8659  -3.9083

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
 O96  N1    C4    single    1.329  0.020  1.329
 O96  N1    HN1   single    0.860  0.020  1.020
 O96  N1    HN1A  single    0.860  0.020  1.020
 O96  C4    O47   double    1.220  0.020  1.220
 O96  C5    C4    single    1.538  0.020  1.538
 O96  C5    C6    single    1.518  0.020  1.518
 O96  C6    C39   single    1.534  0.020  1.534
 O96  C6    H6    single    0.970  0.020  1.090
 O96  N8    C6    single    1.438  0.020  1.438
 O96  N8    C10   single    1.342  0.020  1.342
 O96  N8    HN8   single    0.860  0.020  1.020
 O96  C10   O38   double    1.219  0.020  1.219
 O96  C11   C10   single    1.497  0.020  1.497
 O96  C11   C12   aromatic  1.387  0.020  1.387
 O96  C12   H12   single    0.930  0.020  1.080
 O96  C14   C12   aromatic  1.378  0.020  1.378
 O96  C14   H14   single    0.930  0.020  1.080
 O96  C16   C14   aromatic  1.394  0.020  1.394
 O96  C17   C16   aromatic  1.410  0.020  1.410
 O96  C17   C18   aromatic  1.397  0.020  1.397
 O96  C18   C11   aromatic  1.388  0.020  1.388
 O96  CL19  C18   single    1.729  0.020  1.729
 O96  C20   C17   single    1.510  0.020  1.510
 O96  C20   F23   single    1.341  0.020  1.341
 O96  F21   C20   single    1.340  0.020  1.340
 O96  F22   C20   single    1.329  0.020  1.329
 O96  O24   C16   single    1.333  0.020  1.333
 O96  O24   C25   single    1.415  0.020  1.415
 O96  C25   H25   single    0.970  0.020  1.090
 O96  C25   H25A  single    0.970  0.020  1.090
 O96  C28   C25   single    1.504  0.020  1.504
 O96  C28   C36   aromatic  1.390  0.020  1.390
 O96  N29   C28   aromatic  1.329  0.020  1.329
 O96  C30   N29   aromatic  1.327  0.020  1.327
 O96  C30   C32   aromatic  1.386  0.020  1.386
 O96  C30   H30   single    0.930  0.020  1.080
 O96  C32   C34   aromatic  1.386  0.020  1.386
 O96  C32   H32   single    0.930  0.020  1.080
 O96  C34   C36   aromatic  1.387  0.020  1.387
 O96  C34   H34   single    0.930  0.020  1.080
 O96  C36   H36   single    0.930  0.020  1.080
 O96  C39   C42   single    1.522  0.020  1.522
 O96  C39   H39   single    0.970  0.020  1.090
 O96  C39   H39A  single    0.970  0.020  1.090
 O96  C42   H42   single    0.970  0.020  1.090
 O96  C42   H42A  single    0.970  0.020  1.090
 O96  C42   H42B  single    0.970  0.020  1.090
 O96  O46   C5    double    1.203  0.020  1.203

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
 O96  HN1A  N1   HN1   117.88  3.000
 O96  HN1A  N1   C4    121.55  3.000
 O96  HN1   N1   C4    120.53  3.000
 O96  O47   C4   C5    120.08  3.000
 O96  C5    C4   N1    114.00  3.000
 O96  O47   C4   N1    125.92  3.000
 O96  O46   C5   C6    123.08  3.000
 O96  O46   C5   C4    120.71  3.000
 O96  C6    C5   C4    116.21  3.000
 O96  H6    C6   C39   108.40  3.000
 O96  H6    C6   N8    109.67  3.000
 O96  C39   C6   N8    110.18  3.000
 O96  N8    C6   C5    109.99  3.000
 O96  H6    C6   C5    108.84  3.000
 O96  C39   C6   C5    109.72  3.000
 O96  HN8   N8   C10   119.26  3.000
 O96  HN8   N8   C6    118.52  3.000
 O96  C10   N8   C6    121.54  3.000
 O96  O38   C10  C11   122.42  3.000
 O96  C11   C10  N8    114.29  3.000
 O96  O38   C10  N8    123.27  3.000
 O96  C18   C11  C12   118.17  3.000
 O96  C18   C11  C10   122.67  3.000
 O96  C12   C11  C10   119.08  3.000
 O96  H12   C12  C14   118.97  3.000
 O96  C14   C12  C11   121.37  3.000
 O96  H12   C12  C11   119.66  3.000
 O96  H14   C14  C16   121.00  3.000
 O96  C16   C14  C12   120.40  3.000
 O96  H14   C14  C12   118.61  3.000
 O96  O24   C16  C17   118.26  3.000
 O96  O24   C16  C14   122.16  3.000
 O96  C17   C16  C14   119.58  3.000
 O96  C20   C17  C18   118.58  3.000
 O96  C20   C17  C16   123.15  3.000
 O96  C18   C17  C16   118.27  3.000
 O96  CL19  C18  C17   120.39  3.000
 O96  CL19  C18  C11   117.36  3.000
 O96  C17   C18  C11   122.20  3.000
 O96  F23   C20  F22   106.45  3.000
 O96  F22   C20  F21   105.91  3.000
 O96  F23   C20  F21   107.20  3.000
 O96  F22   C20  C17   114.64  3.000
 O96  F21   C20  C17   111.04  3.000
 O96  F23   C20  C17   111.17  3.000
 O96  C25   O24  C16   119.64  3.000
 O96  H25A  C25  H25   107.80  3.000
 O96  H25A  C25  C28   109.27  3.000
 O96  H25   C25  C28   109.15  3.000
 O96  C28   C25  O24   108.94  3.000
 O96  H25A  C25  O24   110.48  3.000
 O96  H25   C25  O24   111.17  3.000
 O96  C36   C28  N29   122.67  3.000
 O96  N29   C28  C25   114.38  3.000
 O96  C36   C28  C25   122.92  3.000
 O96  C30   N29  C28   118.53  3.000
 O96  H30   C30  C32   120.35  3.000
 O96  H30   C30  N29   116.35  3.000
 O96  C32   C30  N29   123.30  3.000
 O96  H32   C32  C34   121.57  3.000
 O96  H32   C32  C30   120.44  3.000
 O96  C34   C32  C30   117.98  3.000
 O96  H34   C34  C36   120.17  3.000
 O96  H34   C34  C32   120.66  3.000
 O96  C36   C34  C32   119.16  3.000
 O96  H36   C36  C34   120.39  3.000
 O96  H36   C36  C28   121.25  3.000
 O96  C34   C36  C28   118.36  3.000
 O96  H39A  C39  H39   106.52  3.000
 O96  H39A  C39  C42   109.28  3.000
 O96  H39   C39  C42   110.44  3.000
 O96  H39A  C39  C6    108.81  3.000
 O96  H39   C39  C6    109.16  3.000
 O96  C42   C39  C6    112.44  3.000
 O96  H42B  C42  H42A  107.48  3.000
 O96  H42B  C42  H42   107.92  3.000
 O96  H42A  C42  H42   107.85  3.000
 O96  H42B  C42  C39   110.19  3.000
 O96  H42A  C42  C39   112.22  3.000
 O96  H42   C42  C39   111.01  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
 O96  CONST_01  C16   C14  C12  C11    0.00   0.0  0
 O96  CONST_02  C16   C17  C18  C11    0.00   0.0  0
 O96  CONST_03  C17   C18  C11  C12    0.00   0.0  0
 O96  CONST_04  C17   C16  C14  C12    0.00   0.0  0
 O96  CONST_05  C18   C11  C12  C14    0.00   0.0  0
 O96  CONST_06  C18   C17  C16  C14    0.00   0.0  0
 O96  CONST_07  C32   C34  C36  C28    0.00   0.0  0
 O96  CONST_08  C32   C30  N29  C28    0.00   0.0  0
 O96  CONST_09  C34   C36  C28  N29    0.00   0.0  0
 O96  CONST_10  C34   C32  C30  N29    0.00   0.0  0
 O96  CONST_11  C36   C28  N29  C30    0.00   0.0  0
 O96  CONST_12  C36   C34  C32  C30    0.00   0.0  0
 O96  CONST_13  C14   C12  C11  C10  180.00   0.0  0
 O96  CONST_14  C17   C18  C11  C10  180.00   0.0  0
 O96  CONST_15  C20   C17  C18  C11  180.00   0.0  0
 O96  CONST_16  CL19  C18  C11  C12  180.00   0.0  0
 O96  CONST_17  O24   C16  C14  C12  180.00   0.0  0
 O96  CONST_18  C20   C17  C16  C14  180.00   0.0  0
 O96  CONST_19  CL19  C18  C17  C16  180.00   0.0  0
 O96  CONST_20  O24   C16  C17  C18  180.00   0.0  0
 O96  CONST_21  C34   C36  C28  C25  180.00   0.0  0
 O96  CONST_22  C30   N29  C28  C25  180.00   0.0  0
 O96  CONST_23  H14   C14  C12  C11  180.00   0.0  0
 O96  CONST_24  H12   C12  C14  C16  180.00   0.0  0
 O96  CONST_25  H34   C34  C36  C28  180.00   0.0  0
 O96  CONST_26  H30   C30  N29  C28  180.00   0.0  0
 O96  CONST_27  H36   C36  C28  N29  180.00   0.0  0
 O96  CONST_28  H32   C32  C30  N29  180.00   0.0  0
 O96  CONST_29  C11   C10  N8   C6   180.00   0.0  0
 O96  CONST_30  HN8   N8   C10  C11    0.00   0.0  0
 O96  CONST_31  O38   C10  N8   C6     0.00   0.0  0
 O96  CONST_32  HN1   N1   C4   C5   180.00   0.0  0
 O96  CONST_33  HN1A  N1   C4   C5     0.00   0.0  0
 O96  Var_01    C12   C11  C10  N8   -58.49  30.0  2
 O96  Var_02    F23   C20  C17  C16  115.83  30.0  3
 O96  Var_03    C28   C25  O24  C16  174.62  30.0  3
 O96  Var_04    C36   C28  C25  O24  -25.75  30.0  1
 O96  Var_05    C6    C5   C4   N1   172.89  30.0  2
 O96  Var_06    H42   C42  C39  C6   -58.53  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
 O96  chir_01  C6  C5  C39  N8  positiv

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
 O96  plan-1  C10   0.020
 O96  plan-1  C11   0.020
 O96  plan-1  C12   0.020
 O96  plan-1  C14   0.020
 O96  plan-1  C16   0.020
 O96  plan-1  C17   0.020
 O96  plan-1  C18   0.020
 O96  plan-1  CL19  0.020
 O96  plan-1  C20   0.020
 O96  plan-1  O24   0.020
 O96  plan-1  H12   0.020
 O96  plan-1  H14   0.020
 O96  plan-2  C25   0.020
 O96  plan-2  C28   0.020
 O96  plan-2  N29   0.020
 O96  plan-2  C30   0.020
 O96  plan-2  C32   0.020
 O96  plan-2  C34   0.020
 O96  plan-2  C36   0.020
 O96  plan-2  H30   0.020
 O96  plan-2  H32   0.020
 O96  plan-2  H34   0.020
 O96  plan-2  H36   0.020
 O96  plan-3  N1    0.020
 O96  plan-3  C4    0.020
 O96  plan-3  C5    0.020
 O96  plan-3  O47   0.020
 O96  plan-3  HN1   0.020
 O96  plan-3  HN1A  0.020
 O96  plan-4  C6    0.020
 O96  plan-4  N8    0.020
 O96  plan-4  C10   0.020
 O96  plan-4  C11   0.020
 O96  plan-4  O38   0.020
 O96  plan-4  HN8   0.020
 O96  plan-5  C4    0.020
 O96  plan-5  C5    0.020
 O96  plan-5  C6    0.020
 O96  plan-5  O46   0.020

