# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:37:00 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC(=C/c2cc(F)c(O)c(F)c2)\C(=O)N1CC(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
 2ZY  2ZY  (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one  ligand  31  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2ZY
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
 2ZY  O18  O  O     0  -0.430   1.9834  -2.2160   0.5389
 2ZY  C15  C  CR5   0   0.552   1.6670  -1.0479   0.5250
 2ZY  N14  N  NR5   0  -0.579   2.5257   0.0322   0.6415
 2ZY  C16  C  CH2   0  -0.512   3.9485  -0.0838   0.7846
 2ZY  C19  C  CT    0   0.989   4.6452  -0.1522  -0.5599
 2ZY  C13  C  CR5   0   0.521   1.7666   1.1930   0.6327
 2ZY  C17  C  CH3   0  -0.768   2.3763   2.5272   0.8224
 2ZY  C11  C  CR5   0   0.104   0.3423  -0.3998   0.4092
 2ZY  N12  N  N     0  -0.485   0.5055   0.9763   0.4924
 2ZY  C10  C  C1    0  -0.378  -0.7968  -1.1000   0.2538
 2ZY  C2   C  CR6   0   0.163  -2.1547  -0.6172   0.1229
 2ZY  C1   C  CR16  0  -0.483  -3.1706  -1.5682  -0.0327
 2ZY  C6   C  CR6   0   0.496  -4.4783  -1.1679  -0.1634
 2ZY  F8   F  F     0  -0.306  -5.4462  -2.0798  -0.3105
 2ZY  C5   C  CR6   0   0.079  -4.8522   0.1723  -0.1482
 2ZY  O9   O  OH1   0  -0.603  -6.1414   0.4913  -0.2808
 2ZY  C4   C  CR6   0   0.512  -3.8201   1.0959   0.0087
 2ZY  F7   F  F     0  -0.316  -4.1669   2.3938   0.0244
 2ZY  C3   C  CR16  0  -0.495  -2.5018   0.7394   0.1427
 2ZY  F20  F  F     0  -0.297   4.2253  -1.1857  -1.2947
 2ZY  F21  F  F     0  -0.304   4.4346   0.9499  -1.2921
 2ZY  F22  F  F     0  -0.301   5.9653  -0.2800  -0.3976
 2ZY  H1   H  HCH2  0   0.326   4.3437   0.7612   1.3487
 2ZY  H2   H  HCH2  0   0.322   4.1831  -0.9875   1.3488
 2ZY  H4   H  HCH3  0   0.272   3.1287   2.7418   0.0647
 2ZY  H5   H  HCH3  0   0.284   1.6029   3.2881   0.7751
 2ZY  H6   H  HCH3  0   0.280   2.8678   2.5877   1.7954
 2ZY  H7   H  H     0   0.276  -0.6814  -2.1785   0.2207
 2ZY  H9   H  HCR6  0   0.291  -2.9392  -2.6255  -0.0513
 2ZY  H10  H  HOH1  0   0.487  -6.2684   1.4479  -0.2656
 2ZY  H11  H  HCR6  0   0.302  -1.7481   1.5049   0.2602

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
 2ZY  F20  C19  single    1.336  0.020  1.336
 2ZY  F22  C19  single    1.336  0.020  1.336
 2ZY  C19  F21  single    1.340  0.020  1.340
 2ZY  C19  C16  single    1.516  0.020  1.516
 2ZY  C16  N14  single    1.435  0.020  1.435
 2ZY  O18  C15  double    1.210  0.020  1.210
 2ZY  C15  N14  single    1.385  0.020  1.385
 2ZY  C15  C11  single    1.479  0.020  1.479
 2ZY  N14  C13  single    1.387  0.020  1.387
 2ZY  C10  C11  double    1.346  0.020  1.346
 2ZY  C10  C2   single    1.447  0.020  1.447
 2ZY  C11  N12  single    1.388  0.020  1.388
 2ZY  C13  C17  single    1.479  0.020  1.479
 2ZY  C13  N12  double    1.287  0.020  1.287
 2ZY  C1   C2   aromatic  1.400  0.020  1.400
 2ZY  C1   C6   aromatic  1.374  0.020  1.374
 2ZY  C2   C3   aromatic  1.400  0.020  1.400
 2ZY  F8   C6   single    1.338  0.020  1.338
 2ZY  C6   C5   aromatic  1.392  0.020  1.392
 2ZY  C3   C4   aromatic  1.372  0.020  1.372
 2ZY  C5   C4   aromatic  1.394  0.020  1.394
 2ZY  C5   O9   single    1.335  0.020  1.335
 2ZY  C4   F7   single    1.343  0.020  1.343
 2ZY  C16  H1   single    0.970  0.020  1.090
 2ZY  C16  H2   single    0.970  0.020  1.090
 2ZY  C17  H4   single    0.970  0.020  1.090
 2ZY  C17  H5   single    0.970  0.020  1.090
 2ZY  C17  H6   single    0.970  0.020  1.090
 2ZY  C10  H7   single    0.930  0.020  1.080
 2ZY  C1   H9   single    0.930  0.020  1.080
 2ZY  O9   H10  single    0.850  0.020  0.980
 2ZY  C3   H11  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
 2ZY  C11  C15  N14  102.72  3.000
 2ZY  C11  C15  O18  131.14  3.000
 2ZY  N14  C15  O18  126.14  3.000
 2ZY  C13  N14  C16  127.67  3.000
 2ZY  C13  N14  C15  108.23  3.000
 2ZY  C16  N14  C15  124.08  3.000
 2ZY  H2   C16  H1   107.25  3.000
 2ZY  H2   C16  C19  108.81  3.000
 2ZY  H1   C16  C19  109.10  3.000
 2ZY  H2   C16  N14  109.38  3.000
 2ZY  H1   C16  N14  110.39  3.000
 2ZY  C19  C16  N14  111.78  3.000
 2ZY  F22  C19  F21  107.48  3.000
 2ZY  F21  C19  F20  106.64  3.000
 2ZY  F22  C19  F20  107.66  3.000
 2ZY  F21  C19  C16  112.05  3.000
 2ZY  F22  C19  C16  110.53  3.000
 2ZY  F20  C19  C16  112.23  3.000
 2ZY  N12  C13  C17  124.73  3.000
 2ZY  N12  C13  N14  113.33  3.000
 2ZY  C17  C13  N14  121.90  3.000
 2ZY  H6   C17  H5   108.70  3.000
 2ZY  H6   C17  H4   107.35  3.000
 2ZY  H5   C17  H4   108.88  3.000
 2ZY  H6   C17  C13  110.48  3.000
 2ZY  H5   C17  C13  109.44  3.000
 2ZY  H4   C17  C13  111.92  3.000
 2ZY  C10  C11  N12  128.47  3.000
 2ZY  N12  C11  C15  108.92  3.000
 2ZY  C10  C11  C15  122.61  3.000
 2ZY  C11  N12  C13  106.78  3.000
 2ZY  H7   C10  C2   115.38  3.000
 2ZY  H7   C10  C11  115.50  3.000
 2ZY  C2   C10  C11  129.12  3.000
 2ZY  C3   C2   C1   118.66  3.000
 2ZY  C3   C2   C10  123.68  3.000
 2ZY  C1   C2   C10  117.67  3.000
 2ZY  H9   C1   C6   119.10  3.000
 2ZY  H9   C1   C2   120.67  3.000
 2ZY  C6   C1   C2   120.22  3.000
 2ZY  C5   C6   F8   117.60  3.000
 2ZY  C5   C6   C1   122.37  3.000
 2ZY  F8   C6   C1   120.03  3.000
 2ZY  C4   C5   O9   124.62  3.000
 2ZY  O9   C5   C6   119.25  3.000
 2ZY  C4   C5   C6   116.13  3.000
 2ZY  H10  O9   C5   111.25  3.000
 2ZY  C3   C4   F7   119.86  3.000
 2ZY  F7   C4   C5   116.76  3.000
 2ZY  C3   C4   C5   123.38  3.000
 2ZY  H11  C3   C4   119.78  3.000
 2ZY  H11  C3   C2   120.99  3.000
 2ZY  C4   C3   C2   119.24  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
 2ZY  CONST_01  C5   C6   C1   C2      0.00   0.0  0
 2ZY  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 2ZY  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 2ZY  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 2ZY  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 2ZY  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 2ZY  CONST_07  N12  C13  N14  C15     0.00   0.0  0
 2ZY  CONST_08  C13  N12  C11  C15     0.00   0.0  0
 2ZY  CONST_09  N12  C11  C15  N14     0.00   0.0  0
 2ZY  CONST_10  C11  N12  C13  N14     0.00   0.0  0
 2ZY  CONST_11  C11  C15  N14  C13     0.00   0.0  0
 2ZY  CONST_12  C6   C1   C2   C10   180.00   0.0  0
 2ZY  CONST_13  C4   C3   C2   C10   180.00   0.0  0
 2ZY  CONST_14  F8   C6   C1   C2    180.00   0.0  0
 2ZY  CONST_15  F7   C4   C3   C2    180.00   0.0  0
 2ZY  CONST_16  O9   C5   C6   C1    180.00   0.0  0
 2ZY  CONST_17  F7   C4   C5   C6    180.00   0.0  0
 2ZY  CONST_18  C4   C5   C6   F8    180.00   0.0  0
 2ZY  CONST_19  C3   C4   C5   O9    180.00   0.0  0
 2ZY  CONST_20  C13  N14  C15  O18   180.00   0.0  0
 2ZY  CONST_21  C17  C13  N14  C15   180.00   0.0  0
 2ZY  CONST_22  C11  C15  N14  C16   180.00   0.0  0
 2ZY  CONST_23  N12  C13  N14  C16   180.00   0.0  0
 2ZY  CONST_24  C11  N12  C13  C17   180.00   0.0  0
 2ZY  CONST_25  H11  C3   C2   C1    180.00   0.0  0
 2ZY  CONST_26  H9   C1   C6   C5    180.00   0.0  0
 2ZY  CONST_27  C16  N14  C15  O18     0.00   0.0  0
 2ZY  CONST_28  C17  C13  N14  C16     0.00   0.0  0
 2ZY  Var_01    C2   C10  C11  C15  -179.78  30.0  2
 2ZY  Var_02    C1   C2   C10  C11   179.84  30.0  2
 2ZY  Var_03    C19  C16  N14  C15    87.57  30.0  1
 2ZY  Var_04    H4   C17  C13  N14    58.97  30.0  3
 2ZY  Var_05    F20  C19  C16  N14   -58.87  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
 2ZY  plan-1  O18  0.020
 2ZY  plan-1  C15  0.020
 2ZY  plan-1  N14  0.020
 2ZY  plan-1  C16  0.020
 2ZY  plan-1  C13  0.020
 2ZY  plan-1  C17  0.020
 2ZY  plan-1  C11  0.020
 2ZY  plan-1  N12  0.020
 2ZY  plan-1  C10  0.020
 2ZY  plan-2  C10  0.020
 2ZY  plan-2  C2   0.020
 2ZY  plan-2  C1   0.020
 2ZY  plan-2  C6   0.020
 2ZY  plan-2  F8   0.020
 2ZY  plan-2  C5   0.020
 2ZY  plan-2  O9   0.020
 2ZY  plan-2  C4   0.020
 2ZY  plan-2  F7   0.020
 2ZY  plan-2  C3   0.020
 2ZY  plan-2  H9   0.020
 2ZY  plan-2  H11  0.020

