# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:00:40 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: ~{N}-(2-chloranyl-6-fluoranyl-phenyl)-4-[4-ethyl-3-(hydroxymethyl)-5-oxidanylidene-1,2,4-triazol-1-yl]-5-fluoranyl-2-[(2~{S})-1,1,1-tris(fluoranyl)propan-2-yl]oxy-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=NN(C1=O)c2cc(O[C@@H](C)C(F)(F)F)c(cc2F)C(=O)Nc3c(F)cccc3Cl)CO
#
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
 JJE  JJE  ~{N}-(2-chloranyl-6-fluoranyl-phenyl)-4-[4-ethyl-3-(hydroxymethyl)-5-oxidanylidene-1,2,4-triazol-1-yl]-5-fluoranyl-2-[(2~{S})-1,1,1-tris(fluoranyl)propan-2-yl]oxy-benzamide  ligand  53  35  .  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_JJE
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
 JJE  C7   C   CT    0   1.024   1.1716   3.2978  -1.5379
 JJE  C8   C   CH1   0  -0.205  -0.0176   2.9082  -0.6706
 JJE  C13  C   CR16  0  -0.406  -1.5150   0.7046   0.4253
 JJE  C15  C   CR6   0  -0.183   0.6401  -0.2515   0.9180
 JJE  C20  C   CR16  0  -0.419   6.3022  -1.4293   1.5637
 JJE  C21  C   CR16  0  -0.246   7.0202  -1.1045   0.4222
 JJE  C22  C   CR16  0  -0.243   6.3703  -0.7429  -0.7477
 JJE  C23  C   CR6   0  -0.085   4.9854  -0.6959  -0.7633
 JJE  C19  C   CR6   0   0.544   4.9250  -1.3909   1.5090
 JJE  F25  F   F     0  -0.297   4.2173  -1.7243   2.5901
 JJE  C18  C   CR6   0   0.233   4.2321  -1.0265   0.3611
 JJE  N17  N   NH1   0  -0.720   2.8318  -1.0034   0.3450
 JJE  C1   C   C     0   0.529   2.1187  -0.1090   1.0753
 JJE  O2   O   O     0  -0.436   2.6282   0.7171   1.8014
 JJE  C16  C   CR6   0   0.400  -0.1373   0.8392   0.5235
 JJE  O14  O   O2    0  -0.482   0.5115   1.9932   0.2723
 JJE  C3   C   CH3   0  -0.696  -0.6617   4.0972   0.0144
 JJE  F5   F   F     0  -0.301   1.7002   2.2352  -2.1495
 JJE  F6   F   F     0  -0.307   0.8017   4.1659  -2.4864
 JJE  F4   F   F     0  -0.306   2.1481   3.8726  -0.8298
 JJE  C9   C   CR16  0  -0.416   0.0284  -1.4686   1.1847
 JJE  C11  C   CR6   0   0.531  -1.3376  -1.5974   1.0572
 JJE  F10  F   F     0  -0.296  -1.9038  -2.7856   1.2810
 JJE  C12  C   CR6   0   0.221  -2.1250  -0.5170   0.6851
 JJE  N26  N   NR5   0  -0.498  -3.5091  -0.6487   0.5542
 JJE  N30  N   N     0  -0.280  -4.2613  -1.2818   1.5051
 JJE  C27  C   CR5   0   0.693  -4.2555  -0.2475  -0.5250
 JJE  O31  O   O     0  -0.493  -3.8929   0.3198  -1.5372
 JJE  N28  N   NR5   0  -0.549  -5.5228  -0.6499  -0.1825
 JJE  C32  C   CH2   0  -0.334  -6.6765  -0.5100  -1.0529
 JJE  C35  C   CH3   0  -0.659  -6.7640  -1.6264  -2.0785
 JJE  C29  C   CR5   0   0.465  -5.4570  -1.2685   1.0337
 JJE  C34  C   CH2   0  -0.223  -6.6539  -1.8388   1.7127
 JJE  O33  O   OH1   0  -0.654  -6.2448  -2.4085   2.9194
 JJE  H1   H   HCH1  0   0.290  -0.7389   2.4141  -1.3317
 JJE  H2   H   HCR6  0   0.306  -2.1383   1.5495   0.1687
 JJE  H3   H   HCR6  0   0.292   6.8010  -1.7194   2.4786
 JJE  H4   H   HCR6  0   0.284   8.1007  -1.1349   0.4437
 JJE  H5   H   HCR6  0   0.289   6.9331  -0.4883  -1.6346
 JJE  H6   H   HNH1  0   0.422   2.3542  -1.5602  -0.3487
 JJE  H7   H   HCH3  0   0.257  -1.0599   4.7996  -0.7161
 JJE  H8   H   HCH3  0   0.262  -1.4971   3.7635   0.6287
 JJE  H9   H   HCH3  0   0.256   0.0420   4.6232   0.6581
 JJE  H10  H   HCR6  0   0.299   0.6141  -2.3295   1.4820
 JJE  H11  H   HCH2  0   0.274  -7.5679  -0.4822  -0.4276
 JJE  H12  H   HCH2  0   0.276  -6.6074   0.4609  -1.5417
 JJE  H13  H   HCH3  0   0.241  -5.8960  -1.6234  -2.7364
 JJE  H14  H   HCH3  0   0.235  -6.8293  -2.6031  -1.5989
 JJE  H15  H   HCH3  0   0.247  -7.6540  -1.4938  -2.6926
 JJE  H16  H   HCH2  0   0.246  -7.3898  -1.0355   1.8534
 JJE  H17  H   HCH2  0   0.239  -7.1197  -2.5703   1.0375
 JJE  H18  H   HOH1  0   0.469  -7.0300  -2.7256   3.3748
 JJE  CL   CL  CL    0  -0.087   4.1614  -0.2184  -2.2009

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
 JJE  C3   C8   single    1.516  0.020  1.516
 JJE  F6   C7   single    1.338  0.020  1.338
 JJE  F4   C7   single    1.336  0.020  1.336
 JJE  C34  O33  single    1.396  0.020  1.396
 JJE  C34  C29  single    1.490  0.020  1.490
 JJE  C7   C8   single    1.523  0.020  1.523
 JJE  C7   F5   single    1.335  0.020  1.335
 JJE  C8   O14  single    1.416  0.020  1.416
 JJE  CL   C23  single    1.724  0.020  1.724
 JJE  O14  C16  single    1.347  0.020  1.347
 JJE  C29  N30  double    1.285  0.020  1.285
 JJE  C29  N28  single    1.366  0.020  1.366
 JJE  N30  N26  single    1.368  0.020  1.368
 JJE  C13  C16  aromatic  1.388  0.020  1.388
 JJE  C13  C12  aromatic  1.390  0.020  1.390
 JJE  C16  C15  aromatic  1.396  0.020  1.396
 JJE  C23  C22  aromatic  1.386  0.020  1.386
 JJE  C23  C18  aromatic  1.393  0.020  1.393
 JJE  N26  C12  single    1.397  0.020  1.397
 JJE  N26  C27  single    1.372  0.020  1.372
 JJE  N28  C32  single    1.452  0.020  1.452
 JJE  N28  C27  single    1.373  0.020  1.373
 JJE  C22  C21  aromatic  1.386  0.020  1.386
 JJE  C12  C11  aromatic  1.388  0.020  1.388
 JJE  N17  C18  single    1.401  0.020  1.401
 JJE  N17  C1   single    1.357  0.020  1.357
 JJE  C32  C35  single    1.519  0.020  1.519
 JJE  C18  C19  aromatic  1.389  0.020  1.389
 JJE  C15  C1   single    1.494  0.020  1.494
 JJE  C15  C9   aromatic  1.388  0.020  1.388
 JJE  C27  O31  double    1.216  0.020  1.216
 JJE  C1   O2   double    1.212  0.020  1.212
 JJE  C21  C20  aromatic  1.387  0.020  1.387
 JJE  C11  C9   aromatic  1.378  0.020  1.378
 JJE  C11  F10  single    1.335  0.020  1.335
 JJE  C19  C20  aromatic  1.379  0.020  1.379
 JJE  C19  F25  single    1.334  0.020  1.334
 JJE  C8   H1   single    0.970  0.020  1.090
 JJE  C13  H2   single    0.930  0.020  1.080
 JJE  C20  H3   single    0.930  0.020  1.080
 JJE  C21  H4   single    0.930  0.020  1.080
 JJE  C22  H5   single    0.930  0.020  1.080
 JJE  N17  H6   single    0.860  0.020  1.020
 JJE  C3   H7   single    0.970  0.020  1.090
 JJE  C3   H8   single    0.970  0.020  1.090
 JJE  C3   H9   single    0.970  0.020  1.090
 JJE  C9   H10  single    0.930  0.020  1.080
 JJE  C32  H11  single    0.970  0.020  1.090
 JJE  C32  H12  single    0.970  0.020  1.090
 JJE  C35  H13  single    0.970  0.020  1.090
 JJE  C35  H14  single    0.970  0.020  1.090
 JJE  C35  H15  single    0.970  0.020  1.090
 JJE  C34  H16  single    0.970  0.020  1.090
 JJE  C34  H17  single    0.970  0.020  1.090
 JJE  O33  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
 JJE  F4   C7   F6   107.38  3.000
 JJE  F4   C7   F5   107.20  3.000
 JJE  F6   C7   F5   107.52  3.000
 JJE  F5   C7   C8   111.50  3.000
 JJE  F4   C7   C8   112.27  3.000
 JJE  F6   C7   C8   110.73  3.000
 JJE  H1   C8   C3   110.27  3.000
 JJE  H1   C8   O14  110.87  3.000
 JJE  C3   C8   O14  111.38  3.000
 JJE  H1   C8   C7   106.60  3.000
 JJE  O14  C8   C7   104.65  3.000
 JJE  C3   C8   C7   112.86  3.000
 JJE  H2   C13  C12  118.58  3.000
 JJE  H2   C13  C16  120.90  3.000
 JJE  C12  C13  C16  120.51  3.000
 JJE  C9   C15  C16  119.60  3.000
 JJE  C9   C15  C1   119.98  3.000
 JJE  C16  C15  C1   120.42  3.000
 JJE  H3   C20  C19  120.11  3.000
 JJE  H3   C20  C21  121.34  3.000
 JJE  C19  C20  C21  118.54  3.000
 JJE  H4   C21  C22  119.52  3.000
 JJE  H4   C21  C20  119.63  3.000
 JJE  C22  C21  C20  120.86  3.000
 JJE  H5   C22  C23  120.21  3.000
 JJE  H5   C22  C21  120.65  3.000
 JJE  C23  C22  C21  119.14  3.000
 JJE  C18  C23  CL   118.70  3.000
 JJE  C18  C23  C22  121.54  3.000
 JJE  CL   C23  C22  119.76  3.000
 JJE  C18  C19  F25  118.06  3.000
 JJE  F25  C19  C20  119.38  3.000
 JJE  C18  C19  C20  122.56  3.000
 JJE  N17  C18  C19  120.82  3.000
 JJE  C19  C18  C23  117.35  3.000
 JJE  N17  C18  C23  121.83  3.000
 JJE  H6   N17  C1   118.99  3.000
 JJE  H6   N17  C18  118.15  3.000
 JJE  C1   N17  C18  122.01  3.000
 JJE  O2   C1   N17  123.41  3.000
 JJE  O2   C1   C15  122.97  3.000
 JJE  N17  C1   C15  113.61  3.000
 JJE  O14  C16  C15  116.97  3.000
 JJE  C15  C16  C13  119.80  3.000
 JJE  O14  C16  C13  123.22  3.000
 JJE  C16  O14  C8   119.83  3.000
 JJE  H9   C3   H8   108.07  3.000
 JJE  H9   C3   H7   108.74  3.000
 JJE  H8   C3   H7   107.19  3.000
 JJE  H9   C3   C8   111.79  3.000
 JJE  H8   C3   C8   109.90  3.000
 JJE  H7   C3   C8   110.99  3.000
 JJE  H10  C9   C11  119.16  3.000
 JJE  H10  C9   C15  120.77  3.000
 JJE  C11  C9   C15  120.07  3.000
 JJE  C12  C11  F10  119.82  3.000
 JJE  F10  C11  C9   119.22  3.000
 JJE  C12  C11  C9   120.96  3.000
 JJE  N26  C12  C11  120.93  3.000
 JJE  C11  C12  C13  119.04  3.000
 JJE  N26  C12  C13  120.02  3.000
 JJE  C27  N26  N30  112.52  3.000
 JJE  C27  N26  C12  125.82  3.000
 JJE  N30  N26  C12  121.57  3.000
 JJE  C29  N30  N26  104.58  3.000
 JJE  N28  C27  O31  128.29  3.000
 JJE  O31  C27  N26  128.99  3.000
 JJE  N28  C27  N26  102.72  3.000
 JJE  C29  N28  C32  128.00  3.000
 JJE  C32  N28  C27  123.75  3.000
 JJE  C29  N28  C27  108.08  3.000
 JJE  H12  C32  H11  106.67  3.000
 JJE  H12  C32  C35  110.85  3.000
 JJE  H11  C32  C35  111.06  3.000
 JJE  H12  C32  N28  107.73  3.000
 JJE  H11  C32  N28  107.97  3.000
 JJE  C35  C32  N28  112.32  3.000
 JJE  H15  C35  H14  107.95  3.000
 JJE  H15  C35  H13  108.08  3.000
 JJE  H14  C35  H13  108.42  3.000
 JJE  H15  C35  C32  109.77  3.000
 JJE  H14  C35  C32  111.41  3.000
 JJE  H13  C35  C32  111.11  3.000
 JJE  C34  C29  N28  122.72  3.000
 JJE  N28  C29  N30  112.09  3.000
 JJE  C34  C29  N30  125.19  3.000
 JJE  H17  C34  H16  106.35  3.000
 JJE  H17  C34  O33  112.56  3.000
 JJE  H16  C34  O33  112.59  3.000
 JJE  H17  C34  C29  108.38  3.000
 JJE  H16  C34  C29  108.46  3.000
 JJE  O33  C34  C29  108.35  3.000
 JJE  H18  O33  C34  107.75  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
 JJE  CONST_01  C9   C15  C16  C13     0.00   0.0  0
 JJE  CONST_02  C9   C11  C12  C13     0.00   0.0  0
 JJE  CONST_03  C12  C13  C16  C15     0.00   0.0  0
 JJE  CONST_04  C12  C11  C9   C15     0.00   0.0  0
 JJE  CONST_05  C23  C22  C21  C20     0.00   0.0  0
 JJE  CONST_06  C23  C18  C19  C20     0.00   0.0  0
 JJE  CONST_07  C18  C23  C22  C21     0.00   0.0  0
 JJE  CONST_08  C18  C19  C20  C21     0.00   0.0  0
 JJE  CONST_09  C19  C18  C23  C22     0.00   0.0  0
 JJE  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 JJE  CONST_11  C11  C12  C13  C16     0.00   0.0  0
 JJE  CONST_12  C11  C9   C15  C16     0.00   0.0  0
 JJE  CONST_13  N26  C12  C13  C16   180.00   0.0  0
 JJE  CONST_14  N26  C12  C11  C9    180.00   0.0  0
 JJE  CONST_15  C29  N30  N26  C12   180.00   0.0  0
 JJE  CONST_16  N28  C27  N26  C12   180.00   0.0  0
 JJE  CONST_17  N28  C29  N30  N26     0.00   0.0  0
 JJE  CONST_18  C29  N28  C27  N26     0.00   0.0  0
 JJE  CONST_19  C27  N28  C29  N30     0.00   0.0  0
 JJE  CONST_20  N28  C27  N26  N30     0.00   0.0  0
 JJE  CONST_21  C29  N30  N26  C27     0.00   0.0  0
 JJE  CONST_22  C1   C15  C16  C13   180.00   0.0  0
 JJE  CONST_23  F10  C11  C12  C13   180.00   0.0  0
 JJE  CONST_24  F10  C11  C9   C15   180.00   0.0  0
 JJE  CONST_25  N17  C18  C19  C20   180.00   0.0  0
 JJE  CONST_26  CL   C23  C22  C21   180.00   0.0  0
 JJE  CONST_27  F25  C19  C20  C21   180.00   0.0  0
 JJE  CONST_28  N17  C18  C23  C22   180.00   0.0  0
 JJE  CONST_29  C19  C18  C23  CL    180.00   0.0  0
 JJE  CONST_30  F25  C19  C18  C23   180.00   0.0  0
 JJE  CONST_31  C11  C9   C15  C1    180.00   0.0  0
 JJE  CONST_32  C12  C13  C16  O14   180.00   0.0  0
 JJE  CONST_33  C9   C15  C16  O14   180.00   0.0  0
 JJE  CONST_34  N26  C12  C11  F10     0.00   0.0  0
 JJE  CONST_35  O31  C27  N26  C12     0.00   0.0  0
 JJE  CONST_36  C34  C29  N30  N26   180.00   0.0  0
 JJE  CONST_37  C32  N28  C27  N26   180.00   0.0  0
 JJE  CONST_38  C32  N28  C29  N30   180.00   0.0  0
 JJE  CONST_39  O31  C27  N26  N30   180.00   0.0  0
 JJE  CONST_40  C34  C29  N28  C27   180.00   0.0  0
 JJE  CONST_41  C29  N28  C27  O31   180.00   0.0  0
 JJE  CONST_42  H2   C13  C16  C15   180.00   0.0  0
 JJE  CONST_43  H5   C22  C21  C20   180.00   0.0  0
 JJE  CONST_44  H3   C20  C21  C22   180.00   0.0  0
 JJE  CONST_45  H4   C21  C22  C23   180.00   0.0  0
 JJE  CONST_46  H10  C9   C15  C16   180.00   0.0  0
 JJE  CONST_47  C18  N17  C1   C15   180.00   0.0  0
 JJE  CONST_50  C32  N28  C27  O31     0.00   0.0  0
 JJE  CONST_51  C34  C29  N28  C32     0.00   0.0  0
 JJE  CONST_53  O2   C1   N17  C18     0.00   0.0  0
 JJE  Var_01    N30  N26  C12  C13  -134.40  30.0  2
 JJE  Var_02    C13  C16  O14  C8    -30.11  30.0  2
 JJE  Var_03    C16  C15  C1   N17  -124.94  30.0  3
 JJE  Var_04    O33  C34  C29  N30    -1.33  30.0  1
 JJE  Var_05    C35  C32  N28  C27    81.71  30.0  3
 JJE  Var_06    H13  C35  C32  N28   -61.81  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
 JJE  chir_01  C8  C3  C7  O14  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
 JJE  plan-1  C12  0.020
 JJE  plan-1  N26  0.020
 JJE  plan-1  N30  0.020
 JJE  plan-1  C27  0.020
 JJE  plan-1  O31  0.020
 JJE  plan-1  N28  0.020
 JJE  plan-1  C32  0.020
 JJE  plan-1  C29  0.020
 JJE  plan-1  C34  0.020
 JJE  plan-2  C13  0.020
 JJE  plan-2  C15  0.020
 JJE  plan-2  C1   0.020
 JJE  plan-2  C16  0.020
 JJE  plan-2  O14  0.020
 JJE  plan-2  C9   0.020
 JJE  plan-2  C11  0.020
 JJE  plan-2  F10  0.020
 JJE  plan-2  C12  0.020
 JJE  plan-2  N26  0.020
 JJE  plan-2  H2   0.020
 JJE  plan-2  H10  0.020
 JJE  plan-3  C20  0.020
 JJE  plan-3  C21  0.020
 JJE  plan-3  C22  0.020
 JJE  plan-3  C23  0.020
 JJE  plan-3  C19  0.020
 JJE  plan-3  F25  0.020
 JJE  plan-3  C18  0.020
 JJE  plan-3  N17  0.020
 JJE  plan-3  H3   0.020
 JJE  plan-3  H4   0.020
 JJE  plan-3  H5   0.020
 JJE  plan-3  CL   0.020
 JJE  plan-4  C15  0.020
 JJE  plan-4  C18  0.020
 JJE  plan-4  N17  0.020
 JJE  plan-4  C1   0.020
 JJE  plan-4  O2   0.020
 JJE  plan-4  H6   0.020

