# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:46:25 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: ~{N}'-[(2~{S})-2-[3,5-bis(fluoranyl)phenyl]-2-oxidanyl-ethanoyl]-2-ethyl-3-methyl-4-oxidanyl-benzohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C)c(O)ccc1C(=O)NNC(=O)[C@@H](O)c2cc(F)cc(F)c2
#
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
 J4B  J4B  ~{N}'-[(2~{S})-2-[3,5-bis(fluoranyl)phenyl]-2-oxidanyl-ethanoyl]-2-ethyl-3-methyl-4-oxidanyl-benzohydrazide  ligand  44  26  .  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_J4B
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
 J4B  C3   C  C     0   0.478   1.1135   0.2193   0.3763
 J4B  O5   O  O     0  -0.452  -0.9780   2.5613  -0.1749
 J4B  C7   C  CR6   0  -0.120   2.5678   0.3912   0.1053
 J4B  C8   C  CR6   0   0.105   3.4521  -0.6968   0.0559
 J4B  C9   C  CR6   0  -0.057   4.7932  -0.4701  -0.2788
 J4B  C10  C  CR6   0   0.338   5.2159   0.8360  -0.5688
 J4B  C11  C  CR16  0  -0.345   4.3339   1.9081  -0.5132
 J4B  C12  C  CR16  0  -0.261   3.0184   1.6800  -0.1681
 J4B  C14  C  CH2   0  -0.543   2.9726  -2.0948   0.3610
 J4B  C15  C  CH3   0  -0.796   5.8231  -1.5664  -0.3396
 J4B  C16  C  CH3   0  -0.657   2.6907  -2.9037  -0.9040
 J4B  C19  C  CR16  0  -0.492  -3.6311  -0.6192   1.3082
 J4B  C20  C  CR6   0   0.564  -3.9871  -1.8589   0.8114
 J4B  C21  C  CR16  0  -0.564  -4.1147  -2.1128  -0.5389
 J4B  C22  C  CR6   0   0.562  -3.8662  -1.0565  -1.3960
 J4B  N1   N  NH1   0  -0.481  -0.6835   1.1632   1.5812
 J4B  N2   N  NH1   0  -0.489   0.6517   1.0218   1.3768
 J4B  C4   C  C     0   0.517  -1.4330   1.8788   0.7209
 J4B  O6   O  O     0  -0.437   0.3819  -0.5351  -0.2322
 J4B  O13  O  OH1   0  -0.623   6.4875   1.1192  -0.9075
 J4B  C17  C  CH1   0  -0.139  -2.9472   1.7705   0.9250
 J4B  C18  C  CR6   0   0.149  -3.3831   0.4122   0.4126
 J4B  C23  C  CR16  0  -0.457  -3.5055   0.2001  -0.9561
 J4B  O24  O  OH1   0  -0.652  -3.5821   2.8179   0.2660
 J4B  F26  F  F     0  -0.307  -3.9864  -1.2689  -2.7122
 J4B  H1   H  HCR6  0   0.266   4.6815   2.9068  -0.7437
 J4B  H2   H  HCR6  0   0.264   2.3276   2.5138  -0.1443
 J4B  H3   H  HCH2  0   0.248   3.7154  -2.6146   0.9691
 J4B  H4   H  HCH2  0   0.252   2.0730  -2.0644   0.9744
 J4B  H5   H  HCH3  0   0.259   6.2249  -1.6881  -1.3494
 J4B  H6   H  HCH3  0   0.261   6.6645  -1.3654   0.3290
 J4B  H7   H  HCH3  0   0.275   5.4276  -2.5343  -0.0502
 J4B  H8   H  HCH3  0   0.225   3.5762  -2.9821  -1.5359
 J4B  H9   H  HCH3  0   0.231   2.3730  -3.9157  -0.6509
 J4B  H10  H  HCH3  0   0.233   1.9000  -2.4384  -1.4906
 J4B  H11  H  HCR6  0   0.285  -3.5658  -0.4646   2.3782
 J4B  H12  H  HCR6  0   0.306  -4.4019  -3.0880  -0.9087
 J4B  H13  H  HNH1  0   0.420  -1.1105   0.5526   2.2627
 J4B  H14  H  HNH1  0   0.423   1.2615   1.6596   1.8655
 J4B  H15  H  HOH1  0   0.485   7.0238   0.3212  -0.9695
 J4B  H16  H  HCH1  0   0.297  -3.1710   1.8334   1.9965
 J4B  H17  H  HCR6  0   0.280  -3.3266   0.9899  -1.6740
 J4B  H18  H  HOH1  0   0.453  -2.9591   3.1866  -0.3768
 J4B  F25  F  F     0  -0.306  -4.2310  -2.8529   1.6734

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
 J4B  C16  C14  single    1.528  0.020  1.528
 J4B  C15  C9   single    1.505  0.020  1.505
 J4B  C14  C8   single    1.509  0.020  1.509
 J4B  C9   C8   aromatic  1.401  0.020  1.401
 J4B  C9   C10  aromatic  1.403  0.020  1.403
 J4B  C8   C7   aromatic  1.403  0.020  1.403
 J4B  O13  C10  single    1.346  0.020  1.346
 J4B  C10  C11  aromatic  1.389  0.020  1.389
 J4B  F26  C22  single    1.339  0.020  1.339
 J4B  O6   C3   double    1.214  0.020  1.214
 J4B  C7   C3   single    1.489  0.020  1.489
 J4B  C7   C12  aromatic  1.392  0.020  1.392
 J4B  C3   N2   single    1.363  0.020  1.363
 J4B  C11  C12  aromatic  1.379  0.020  1.379
 J4B  C22  C23  aromatic  1.379  0.020  1.379
 J4B  C22  C21  aromatic  1.383  0.020  1.383
 J4B  C23  C18  aromatic  1.390  0.020  1.390
 J4B  N2   N1   single    1.358  0.020  1.358
 J4B  N1   C4   single    1.347  0.020  1.347
 J4B  C21  C20  aromatic  1.380  0.020  1.380
 J4B  C18  C17  single    1.516  0.020  1.516
 J4B  C18  C19  aromatic  1.388  0.020  1.388
 J4B  C4   C17  single    1.532  0.020  1.532
 J4B  C4   O5   double    1.215  0.020  1.215
 J4B  C17  O24  single    1.391  0.020  1.391
 J4B  C20  C19  aromatic  1.382  0.020  1.382
 J4B  C20  F25  single    1.338  0.020  1.338
 J4B  C11  H1   single    0.930  0.020  1.080
 J4B  C12  H2   single    0.930  0.020  1.080
 J4B  C14  H3   single    0.970  0.020  1.090
 J4B  C14  H4   single    0.970  0.020  1.090
 J4B  C15  H5   single    0.970  0.020  1.090
 J4B  C15  H6   single    0.970  0.020  1.090
 J4B  C15  H7   single    0.970  0.020  1.090
 J4B  C16  H8   single    0.970  0.020  1.090
 J4B  C16  H9   single    0.970  0.020  1.090
 J4B  C16  H10  single    0.970  0.020  1.090
 J4B  C19  H11  single    0.930  0.020  1.080
 J4B  C21  H12  single    0.930  0.020  1.080
 J4B  N1   H13  single    0.860  0.020  1.020
 J4B  N2   H14  single    0.860  0.020  1.020
 J4B  O13  H15  single    0.850  0.020  0.980
 J4B  C17  H16  single    0.970  0.020  1.090
 J4B  C23  H17  single    0.930  0.020  1.080
 J4B  O24  H18  single    0.850  0.020  0.980

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
 J4B  O6   C3   N2   121.97  3.000
 J4B  N2   C3   C7   113.35  3.000
 J4B  O6   C3   C7   124.67  3.000
 J4B  C12  C7   C8   120.46  3.000
 J4B  C12  C7   C3   117.29  3.000
 J4B  C8   C7   C3   122.17  3.000
 J4B  C14  C8   C9   120.16  3.000
 J4B  C9   C8   C7   119.10  3.000
 J4B  C14  C8   C7   120.73  3.000
 J4B  C15  C9   C10  117.61  3.000
 J4B  C10  C9   C8   119.25  3.000
 J4B  C15  C9   C8   123.15  3.000
 J4B  O13  C10  C11  116.58  3.000
 J4B  C11  C10  C9   121.25  3.000
 J4B  O13  C10  C9   122.17  3.000
 J4B  H1   C11  C12  120.82  3.000
 J4B  H1   C11  C10  119.97  3.000
 J4B  C12  C11  C10  119.21  3.000
 J4B  H2   C12  C11  119.12  3.000
 J4B  H2   C12  C7   120.13  3.000
 J4B  C11  C12  C7   120.72  3.000
 J4B  H4   C14  H3   105.16  3.000
 J4B  H4   C14  C16  109.19  3.000
 J4B  H3   C14  C16  109.55  3.000
 J4B  H4   C14  C8   110.51  3.000
 J4B  H3   C14  C8   109.72  3.000
 J4B  C16  C14  C8   112.44  3.000
 J4B  H7   C15  H6   106.34  3.000
 J4B  H7   C15  H5   106.32  3.000
 J4B  H6   C15  H5   107.60  3.000
 J4B  H7   C15  C9   112.93  3.000
 J4B  H6   C15  C9   111.58  3.000
 J4B  H5   C15  C9   111.70  3.000
 J4B  H10  C16  H9   108.06  3.000
 J4B  H10  C16  H8   107.95  3.000
 J4B  H9   C16  H8   107.71  3.000
 J4B  H10  C16  C14  110.72  3.000
 J4B  H9   C16  C14  110.67  3.000
 J4B  H8   C16  C14  111.59  3.000
 J4B  H11  C19  C18  121.36  3.000
 J4B  H11  C19  C20  119.91  3.000
 J4B  C18  C19  C20  118.72  3.000
 J4B  F25  C20  C21  118.48  3.000
 J4B  F25  C20  C19  118.80  3.000
 J4B  C21  C20  C19  122.72  3.000
 J4B  H12  C21  C22  121.64  3.000
 J4B  H12  C21  C20  121.66  3.000
 J4B  C22  C21  C20  116.71  3.000
 J4B  F26  C22  C23  118.79  3.000
 J4B  C23  C22  C21  123.04  3.000
 J4B  F26  C22  C21  118.17  3.000
 J4B  H13  N1   C4   121.13  3.000
 J4B  H13  N1   N2   117.02  3.000
 J4B  C4   N1   N2   120.42  3.000
 J4B  H14  N2   N1   117.10  3.000
 J4B  H14  N2   C3   121.54  3.000
 J4B  N1   N2   C3   120.32  3.000
 J4B  C17  C4   N1   115.31  3.000
 J4B  C17  C4   O5   120.55  3.000
 J4B  N1   C4   O5   124.13  3.000
 J4B  H15  O13  C10  111.58  3.000
 J4B  H16  C17  O24  109.06  3.000
 J4B  H16  C17  C18  108.85  3.000
 J4B  O24  C17  C18  112.54  3.000
 J4B  H16  C17  C4   109.15  3.000
 J4B  O24  C17  C4   109.57  3.000
 J4B  C18  C17  C4   107.61  3.000
 J4B  C23  C18  C17  119.66  3.000
 J4B  C17  C18  C19  119.93  3.000
 J4B  C23  C18  C19  120.39  3.000
 J4B  H17  C23  C18  121.81  3.000
 J4B  H17  C23  C22  119.77  3.000
 J4B  C18  C23  C22  118.42  3.000
 J4B  H18  O24  C17  107.92  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
 J4B  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 J4B  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 J4B  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 J4B  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 J4B  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 J4B  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 J4B  CONST_07  C22  C23  C18  C19    0.00   0.0  0
 J4B  CONST_08  C22  C21  C20  C19    0.00   0.0  0
 J4B  CONST_09  C23  C22  C21  C20    0.00   0.0  0
 J4B  CONST_10  C23  C18  C19  C20    0.00   0.0  0
 J4B  CONST_11  C18  C23  C22  C21    0.00   0.0  0
 J4B  CONST_12  C18  C19  C20  C21    0.00   0.0  0
 J4B  CONST_13  C9   C8   C7   C3   180.00   0.0  0
 J4B  CONST_14  C11  C12  C7   C3   180.00   0.0  0
 J4B  CONST_15  C15  C9   C8   C7   180.00   0.0  0
 J4B  CONST_16  O13  C10  C9   C8   180.00   0.0  0
 J4B  CONST_17  C14  C8   C9   C10  180.00   0.0  0
 J4B  CONST_18  C15  C9   C10  C11  180.00   0.0  0
 J4B  CONST_19  C14  C8   C7   C12  180.00   0.0  0
 J4B  CONST_20  O13  C10  C11  C12  180.00   0.0  0
 J4B  CONST_21  F26  C22  C21  C20  180.00   0.0  0
 J4B  CONST_22  C17  C18  C19  C20  180.00   0.0  0
 J4B  CONST_23  C17  C18  C23  C22  180.00   0.0  0
 J4B  CONST_24  F25  C20  C21  C22  180.00   0.0  0
 J4B  CONST_25  F26  C22  C23  C18  180.00   0.0  0
 J4B  CONST_26  F25  C20  C19  C18  180.00   0.0  0
 J4B  CONST_27  H1   C11  C12  C7   180.00   0.0  0
 J4B  CONST_28  H2   C12  C7   C8   180.00   0.0  0
 J4B  CONST_29  H17  C23  C18  C19  180.00   0.0  0
 J4B  CONST_30  H12  C21  C20  C19  180.00   0.0  0
 J4B  CONST_31  H11  C19  C20  C21  180.00   0.0  0
 J4B  CONST_32  N1   N2   C3   C7   180.00   0.0  0
 J4B  CONST_33  H14  N2   C3   C7     0.00   0.0  0
 J4B  CONST_34  N2   N1   C4   O5     0.00   0.0  0
 J4B  CONST_35  O6   C3   N2   N1     0.00   0.0  0
 J4B  CONST_36  C17  C4   N1   N2   180.00   0.0  0
 J4B  CONST_37  H13  N1   C4   O5   180.00   0.0  0
 J4B  Var_01    C16  C14  C8   C7    99.30  30.0  3
 J4B  Var_02    O6   C3   C7   C8   -52.63  30.0  2
 J4B  Var_03    H5   C15  C9   C8   116.93  30.0  2
 J4B  Var_04    H8   C16  C14  C8    58.51  30.0  3
 J4B  Var_05    C4   N1   N2   C3   -72.56  30.0  2

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
 J4B  chir_01  C17  C18  C4  O24  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
 J4B  plan-1  C3   0.020
 J4B  plan-1  C7   0.020
 J4B  plan-1  C8   0.020
 J4B  plan-1  C9   0.020
 J4B  plan-1  C10  0.020
 J4B  plan-1  C11  0.020
 J4B  plan-1  C12  0.020
 J4B  plan-1  C14  0.020
 J4B  plan-1  C15  0.020
 J4B  plan-1  O13  0.020
 J4B  plan-1  H1   0.020
 J4B  plan-1  H2   0.020
 J4B  plan-2  C19  0.020
 J4B  plan-2  C20  0.020
 J4B  plan-2  C21  0.020
 J4B  plan-2  C22  0.020
 J4B  plan-2  C17  0.020
 J4B  plan-2  C18  0.020
 J4B  plan-2  C23  0.020
 J4B  plan-2  F26  0.020
 J4B  plan-2  H11  0.020
 J4B  plan-2  H12  0.020
 J4B  plan-2  H17  0.020
 J4B  plan-2  F25  0.020
 J4B  plan-3  C3   0.020
 J4B  plan-3  C7   0.020
 J4B  plan-3  N1   0.020
 J4B  plan-3  N2   0.020
 J4B  plan-3  O6   0.020
 J4B  plan-3  H14  0.020
 J4B  plan-4  O5   0.020
 J4B  plan-4  N1   0.020
 J4B  plan-4  N2   0.020
 J4B  plan-4  C4   0.020
 J4B  plan-4  C17  0.020
 J4B  plan-4  H13  0.020

