# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:39:08 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (5S)-2-azanyl-5-[3-(2,5-difluorophenyl)phenyl]-3-methyl-5-pyridin-4-yl-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](C1=O)(c2ccncc2)c3cccc(c3)c4cc(F)ccc4F)N
#
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
 Z81  Z81  (5S)-2-azanyl-5-[3-(2,5-difluorophenyl)phenyl]-3-methyl-5-pyridin-4-yl-imidazol-4-one  ligand  44  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z81
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
 Z81  C1    C  CR16  0  -0.231   0.5694   1.7250   2.2704
 Z81  F1    F  F     0  -0.314   6.3341   1.2387  -0.7922
 Z81  N1    N  N     0  -0.407  -4.3283   3.3623  -0.9868
 Z81  O1    O  O     0  -0.435  -2.8322  -0.9249   2.0959
 Z81  C2    C  CR16  0  -0.304   1.7903   1.2523   1.8106
 Z81  F2    F  F     0  -0.304   2.4857  -2.3737   0.3773
 Z81  N2    N  N     0  -0.465  -1.6639  -0.8079  -1.2497
 Z81  C3    C  CR16  0  -0.289  -0.6105   1.3103   1.6752
 Z81  N3    N  NR5   0  -0.519  -2.6377  -2.2234   0.2146
 Z81  C4    C  CR16  0  -0.404   5.6480  -1.0030  -0.6784
 Z81  N4    N  NH2   0  -0.846  -2.0756  -3.0052  -1.9332
 Z81  C5    C  CR16  0  -0.389   4.6501  -1.9189  -0.3809
 Z81  C6    C  CR16  0  -0.345  -2.4571   1.9336  -1.4113
 Z81  C7    C  CR16  0  -0.387  -3.8984   1.4696   0.4178
 Z81  C8    C  CR16  0  -0.357   0.6439  -0.0563   0.1515
 Z81  C9    C  CR16  0  -0.442   4.1569   0.7935  -0.0518
 Z81  C10   C  CR16  0  -0.063  -3.2521   3.0288  -1.6953
 Z81  C11   C  CR16  0  -0.060  -4.6331   2.5892   0.0441
 Z81  C12   C  CR6   0   0.116   1.8365   0.3568   0.7464
 Z81  C13   C  CR6   0  -0.129   3.1427  -0.1169   0.2437
 Z81  C14   C  CR6   0   0.179  -0.5778   0.4154   0.6078
 Z81  C15   C  CR6   0   0.256  -2.7793   1.1240  -0.3249
 Z81  C16   C  CR6   0   0.538   5.3790   0.3402  -0.5046
 Z81  C17   C  CR6   0   0.514   3.4265  -1.4664   0.0710
 Z81  C18   C  CR5   0   0.586  -2.5204  -1.0777   0.9381
 Z81  C19   C  CR5   0   0.685  -2.1151  -1.9936  -1.0541
 Z81  C20   C  CR5   0  -0.249  -1.8775  -0.0668  -0.0276
 Z81  H1    H  HCR6  0   0.262   0.5391   2.4200   3.0989
 Z81  H2    H  HCR6  0   0.260   2.7075   1.5740   2.2882
 Z81  H3    H  HCR6  0   0.261  -1.5530   1.6961   2.0414
 Z81  H4    H  HCR6  0   0.293   6.6127  -1.3347  -1.0372
 Z81  HN4   H  HNH2  0   0.410  -1.8246  -2.7775  -2.8811
 Z81  HN4A  H  HNH2  0   0.418  -2.6889  -3.7961  -1.8278
 Z81  H5    H  HCR6  0   0.292   4.8285  -2.9801  -0.4919
 Z81  H6    H  HCR6  0   0.270  -1.6006   1.7164  -2.0349
 Z81  H7    H  HCR6  0   0.270  -4.2174   0.9030   1.2803
 Z81  H8    H  HCR6  0   0.255   0.6631  -0.7278  -0.6957
 Z81  H9    H  HCR6  0   0.288   3.9802   1.8559   0.0579
 Z81  H10   H  HCR6  0   0.264  -3.0089   3.6674  -2.5375
 Z81  H11   H  HCR6  0   0.266  -5.5116   2.8666   0.6167
 Z81  H21   H  HCH3  0   0.267  -4.0407  -3.7803   0.1518
 Z81  H21A  H  HCH3  0   0.268  -2.4014  -4.2604   0.6440
 Z81  H21B  H  HCH3  0   0.278  -3.4342  -3.3505   1.7511
 Z81  C21   C  CH3   0  -0.557  -3.1553  -3.4773   0.7091

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
 Z81  C2   C1    aromatic  1.388  0.020  1.388
 Z81  C1   C3    aromatic  1.385  0.020  1.385
 Z81  C1   H1    single    0.930  0.020  1.080
 Z81  F1   C16   single    1.342  0.020  1.342
 Z81  C11  N1    aromatic  1.324  0.020  1.324
 Z81  N1   C10   aromatic  1.331  0.020  1.331
 Z81  C18  O1    double    1.209  0.020  1.209
 Z81  C12  C2    aromatic  1.392  0.020  1.392
 Z81  C2   H2    single    0.930  0.020  1.080
 Z81  C17  F2    single    1.342  0.020  1.342
 Z81  N2   C19   double    1.284  0.020  1.284
 Z81  N2   C20   single    1.445  0.020  1.445
 Z81  C14  C3    aromatic  1.393  0.020  1.393
 Z81  C3   H3    single    0.930  0.020  1.080
 Z81  C19  N3    single    1.391  0.020  1.391
 Z81  N3   C21   single    1.444  0.020  1.444
 Z81  N3   C18   single    1.360  0.020  1.360
 Z81  C16  C4    aromatic  1.381  0.020  1.381
 Z81  C4   C5    aromatic  1.387  0.020  1.387
 Z81  C4   H4    single    0.930  0.020  1.080
 Z81  N4   C19   single    1.341  0.020  1.341
 Z81  N4   HN4   single    0.890  0.020  1.040
 Z81  N4   HN4A  single    0.890  0.020  1.040
 Z81  C5   C17   aromatic  1.381  0.020  1.381
 Z81  C5   H5    single    0.930  0.020  1.080
 Z81  C15  C6    aromatic  1.393  0.020  1.393
 Z81  C6   C10   aromatic  1.383  0.020  1.383
 Z81  C6   H6    single    0.930  0.020  1.080
 Z81  C7   C11   aromatic  1.390  0.020  1.390
 Z81  C7   C15   aromatic  1.387  0.020  1.387
 Z81  C7   H7    single    0.930  0.020  1.080
 Z81  C12  C8    aromatic  1.395  0.020  1.395
 Z81  C8   C14   aromatic  1.387  0.020  1.387
 Z81  C8   H8    single    0.930  0.020  1.080
 Z81  C16  C9    aromatic  1.380  0.020  1.380
 Z81  C9   C13   aromatic  1.394  0.020  1.394
 Z81  C9   H9    single    0.930  0.020  1.080
 Z81  C10  H10   single    0.930  0.020  1.080
 Z81  C11  H11   single    0.930  0.020  1.080
 Z81  C13  C12   single    1.478  0.020  1.478
 Z81  C13  C17   aromatic  1.390  0.020  1.390
 Z81  C14  C20   single    1.525  0.020  1.525
 Z81  C20  C15   single    1.523  0.020  1.523
 Z81  C20  C18   single    1.539  0.020  1.539
 Z81  C21  H21   single    0.970  0.020  1.090
 Z81  C21  H21A  single    0.970  0.020  1.090
 Z81  C21  H21B  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
 Z81  H1    C1   C3    119.84  3.000
 Z81  H1    C1   C2    119.81  3.000
 Z81  C3    C1   C2    120.35  3.000
 Z81  C11   N1   C10   117.02  3.000
 Z81  H2    C2   C12   120.02  3.000
 Z81  H2    C2   C1    119.86  3.000
 Z81  C12   C2   C1    120.12  3.000
 Z81  C20   N2   C19   107.03  3.000
 Z81  H3    C3   C14   120.57  3.000
 Z81  H3    C3   C1    119.33  3.000
 Z81  C14   C3   C1    120.10  3.000
 Z81  C21   N3   C19   126.19  3.000
 Z81  C21   N3   C18   125.47  3.000
 Z81  C19   N3   C18   108.27  3.000
 Z81  H4    C4   C16   120.92  3.000
 Z81  H4    C4   C5    120.70  3.000
 Z81  C16   C4   C5    118.38  3.000
 Z81  HN4A  N4   HN4   115.36  3.000
 Z81  HN4A  N4   C19   120.42  3.000
 Z81  HN4   N4   C19   117.01  3.000
 Z81  H5    C5   C17   120.08  3.000
 Z81  H5    C5   C4    120.48  3.000
 Z81  C17   C5   C4    119.44  3.000
 Z81  H6    C6   C15   121.08  3.000
 Z81  H6    C6   C10   119.73  3.000
 Z81  C15   C6   C10   119.19  3.000
 Z81  H7    C7   C15   122.36  3.000
 Z81  H7    C7   C11   118.75  3.000
 Z81  C15   C7   C11   118.89  3.000
 Z81  H8    C8   C14   119.00  3.000
 Z81  H8    C8   C12   120.18  3.000
 Z81  C14   C8   C12   120.80  3.000
 Z81  H9    C9   C16   120.01  3.000
 Z81  H9    C9   C13   120.03  3.000
 Z81  C16   C9   C13   119.95  3.000
 Z81  H10   C10  C6    119.80  3.000
 Z81  H10   C10  N1    116.56  3.000
 Z81  C6    C10  N1    123.64  3.000
 Z81  H11   C11  C7    119.48  3.000
 Z81  H11   C11  N1    116.62  3.000
 Z81  C7    C11  N1    123.90  3.000
 Z81  C13   C12  C8    121.04  3.000
 Z81  C13   C12  C2    119.72  3.000
 Z81  C8    C12  C2    119.22  3.000
 Z81  C17   C13  C12   122.28  3.000
 Z81  C17   C13  C9    117.33  3.000
 Z81  C12   C13  C9    120.38  3.000
 Z81  C20   C14  C8    120.41  3.000
 Z81  C20   C14  C3    120.15  3.000
 Z81  C8    C14  C3    119.42  3.000
 Z81  C20   C15  C7    124.61  3.000
 Z81  C20   C15  C6    118.02  3.000
 Z81  C7    C15  C6    117.36  3.000
 Z81  C9    C16  C4    122.23  3.000
 Z81  C9    C16  F1    118.72  3.000
 Z81  C4    C16  F1    119.05  3.000
 Z81  C13   C17  C5    122.67  3.000
 Z81  C13   C17  F2    119.00  3.000
 Z81  C5    C17  F2    118.31  3.000
 Z81  C20   C18  N3    104.81  3.000
 Z81  C20   C18  O1    128.74  3.000
 Z81  N3    C18  O1    126.42  3.000
 Z81  N4    C19  N3    118.97  3.000
 Z81  N4    C19  N2    125.92  3.000
 Z81  N3    C19  N2    115.06  3.000
 Z81  C18   C20  C15   112.88  3.000
 Z81  C18   C20  C14   107.60  3.000
 Z81  C15   C20  C14   109.80  3.000
 Z81  C18   C20  N2    104.81  3.000
 Z81  C15   C20  N2    108.86  3.000
 Z81  C14   C20  N2    112.87  3.000
 Z81  H21B  C21  H21A  108.61  3.000
 Z81  H21B  C21  H21   108.34  3.000
 Z81  H21A  C21  H21   109.40  3.000
 Z81  H21B  C21  N3    108.62  3.000
 Z81  H21A  C21  N3    110.85  3.000
 Z81  H21   C21  N3    110.96  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
 Z81  CONST_01  C8   C12  C2   C1     0.00   0.0  0
 Z81  CONST_02  C13  C12  C2   C1   180.00   0.0  0
 Z81  CONST_03  C8   C14  C3   C1     0.00   0.0  0
 Z81  CONST_04  C15  C7   C11  N1     0.00   0.0  0
 Z81  CONST_05  C15  C6   C10  N1     0.00   0.0  0
 Z81  CONST_06  C14  C3   C1   C2     0.00   0.0  0
 Z81  CONST_07  C14  C8   C12  C2     0.00   0.0  0
 Z81  CONST_10  C12  C2   C1   C3     0.00   0.0  0
 Z81  CONST_11  C12  C8   C14  C3     0.00   0.0  0
 Z81  CONST_12  C13  C9   C16  C4     0.00   0.0  0
 Z81  CONST_13  C13  C17  C5   C4     0.00   0.0  0
 Z81  CONST_14  C9   C16  C4   C5     0.00   0.0  0
 Z81  CONST_15  C9   C13  C17  C5     0.00   0.0  0
 Z81  CONST_16  C12  C13  C17  C5   180.00   0.0  0
 Z81  CONST_17  C11  C7   C15  C6     0.00   0.0  0
 Z81  CONST_18  C11  N1   C10  C6     0.00   0.0  0
 Z81  CONST_19  C10  N1   C11  C7     0.00   0.0  0
 Z81  CONST_20  C10  C6   C15  C7     0.00   0.0  0
 Z81  CONST_23  C16  C9   C13  C12  180.00   0.0  0
 Z81  CONST_24  C14  C8   C12  C13  180.00   0.0  0
 Z81  CONST_25  C17  C5   C4   C16    0.00   0.0  0
 Z81  CONST_26  C17  C13  C9   C16    0.00   0.0  0
 Z81  CONST_27  C20  C14  C3   C1   180.00   0.0  0
 Z81  CONST_28  C20  C15  C6   C10  180.00   0.0  0
 Z81  CONST_29  C20  C15  C7   C11  180.00   0.0  0
 Z81  CONST_30  C20  C14  C8   C12  180.00   0.0  0
 Z81  CONST_31  C18  N3   C19  N2     0.00   0.0  0
 Z81  CONST_32  C20  N2   C19  N3     0.00   0.0  0
 Z81  CONST_33  C20  C18  N3   C19    0.00   0.0  0
 Z81  CONST_34  C5   C4   C16  F1   180.00   0.0  0
 Z81  CONST_35  C13  C9   C16  F1   180.00   0.0  0
 Z81  CONST_36  C4   C5   C17  F2   180.00   0.0  0
 Z81  CONST_37  C9   C13  C17  F2   180.00   0.0  0
 Z81  CONST_38  C12  C13  C17  F2     0.00   0.0  0
 Z81  CONST_39  C19  N3   C18  O1   180.00   0.0  0
 Z81  CONST_40  C21  N3   C19  N2   180.00   0.0  0
 Z81  CONST_41  C20  N2   C19  N4   180.00   0.0  0
 Z81  CONST_42  C18  N3   C19  N4   180.00   0.0  0
 Z81  CONST_43  C21  N3   C18  C20  180.00   0.0  0
 Z81  CONST_44  H7   C7   C11  N1   180.00   0.0  0
 Z81  CONST_45  H6   C6   C10  N1   180.00   0.0  0
 Z81  CONST_46  H3   C3   C1   C2   180.00   0.0  0
 Z81  CONST_47  H8   C8   C12  C2   180.00   0.0  0
 Z81  CONST_48  H2   C2   C1   C3   180.00   0.0  0
 Z81  CONST_49  H9   C9   C16  C4   180.00   0.0  0
 Z81  CONST_50  H4   C4   C16  C9   180.00   0.0  0
 Z81  CONST_51  H11  C11  N1   C10  180.00   0.0  0
 Z81  CONST_52  H10  C10  N1   C11  180.00   0.0  0
 Z81  CONST_53  H1   C1   C2   C12  180.00   0.0  0
 Z81  CONST_54  H5   C5   C17  C13  180.00   0.0  0
 Z81  CONST_55  C21  N3   C18  O1     0.00   0.0  0
 Z81  CONST_56  C21  N3   C19  N4     0.00   0.0  0
 Z81  CONST_57  HN4  N4   C19  N2     0.00   0.0  0
 Z81  Var_01    H21  C21  N3   C18  119.02  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
 Z81  chir_01  C20  C14  C15  C18  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
 Z81  plan-1  C1    0.020
 Z81  plan-1  C2    0.020
 Z81  plan-1  C3    0.020
 Z81  plan-1  C8    0.020
 Z81  plan-1  C12   0.020
 Z81  plan-1  C13   0.020
 Z81  plan-1  C14   0.020
 Z81  plan-1  C20   0.020
 Z81  plan-1  H1    0.020
 Z81  plan-1  H2    0.020
 Z81  plan-1  H3    0.020
 Z81  plan-1  H8    0.020
 Z81  plan-2  N1    0.020
 Z81  plan-2  C6    0.020
 Z81  plan-2  C7    0.020
 Z81  plan-2  C10   0.020
 Z81  plan-2  C11   0.020
 Z81  plan-2  C15   0.020
 Z81  plan-2  C20   0.020
 Z81  plan-2  H6    0.020
 Z81  plan-2  H7    0.020
 Z81  plan-2  H10   0.020
 Z81  plan-2  H11   0.020
 Z81  plan-3  F1    0.020
 Z81  plan-3  F2    0.020
 Z81  plan-3  C4    0.020
 Z81  plan-3  C5    0.020
 Z81  plan-3  C9    0.020
 Z81  plan-3  C12   0.020
 Z81  plan-3  C13   0.020
 Z81  plan-3  C16   0.020
 Z81  plan-3  C17   0.020
 Z81  plan-3  H4    0.020
 Z81  plan-3  H5    0.020
 Z81  plan-3  H9    0.020
 Z81  plan-4  O1    0.020
 Z81  plan-4  N2    0.020
 Z81  plan-4  N3    0.020
 Z81  plan-4  N4    0.020
 Z81  plan-4  C18   0.020
 Z81  plan-4  C19   0.020
 Z81  plan-4  C20   0.020
 Z81  plan-4  HN4   0.020
 Z81  plan-4  HN4A  0.020
 Z81  plan-4  C21   0.020

