# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:19:40 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2E,5R)-2-imino-5-(3'-methoxybiphenyl-3-yl)-3-methyl-5-phenylimidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(c2)[C@]3(NC(=N)N(C)C3=O)c4ccccc4
#
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
 0KM  0KM  (2E,5R)-2-imino-5-(3'-methoxybiphenyl-3-yl)-3-methyl-5-phenylimidazolidin-4-one  ligand  49  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0KM
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
 0KM  O1   O  O     0  -0.424  -2.8587   0.8297  -2.1326
 0KM  C1   C  C     0   0.568  -2.6148   1.0405  -0.9693
 0KM  C2   C  CT    0  -0.137  -1.9904   0.0458   0.0205
 0KM  N1   N  NH1   0  -0.659  -1.8167   0.8881   1.1808
 0KM  C3   C  C     0   0.612  -2.4304   2.0989   1.0465
 0KM  N2   N  NT    0  -0.521  -2.8315   2.1934  -0.2896
 0KM  N3   N  N     0  -0.677  -2.5727   2.9505   1.9727
 0KM  C4   C  CH3   0  -0.555  -3.4098   3.3907  -0.8508
 0KM  C5   C  CR6   0   0.180  -2.9347  -1.1075   0.3408
 0KM  C6   C  CR16  0  -0.275  -2.4230  -2.2323   0.9847
 0KM  C7   C  CR16  0  -0.245  -3.2620  -3.2612   1.3851
 0KM  C8   C  CR16  0  -0.261  -4.6273  -3.1824   1.1429
 0KM  C9   C  CR16  0  -0.240  -5.1443  -2.0658   0.5030
 0KM  C10  C  CR16  0  -0.318  -4.3042  -1.0325   0.1075
 0KM  C11  C  CR6   0   0.140  -0.6745  -0.4345  -0.5735
 0KM  C12  C  CR16  0  -0.286  -0.6853  -1.3865  -1.5906
 0KM  C13  C  CR16  0  -0.231   0.5070  -1.8044  -2.1582
 0KM  C14  C  CR16  0  -0.317   1.7157  -1.2819  -1.7206
 0KM  C15  C  CR6   0   0.110   1.7441  -0.3268  -0.7071
 0KM  C16  C  CR16  0  -0.370   0.5352   0.0903  -0.1456
 0KM  C17  C  CR16  0  -0.394   5.4619   1.3016   0.6475
 0KM  C18  C  CR16  0  -0.412   4.1478  -0.5692  -0.1181
 0KM  C19  C  CR6   0   0.105   3.0239   0.2400  -0.2331
 0KM  C20  C  CR16  0  -0.334   3.1245   1.5939   0.1015
 0KM  C21  C  CR16  0  -0.227   4.3342   2.1069   0.5333
 0KM  C22  C  CR6   0   0.406   5.3662  -0.0485   0.3198
 0KM  O2   O  O2    0  -0.473   6.3856  -0.9244   0.4006
 0KM  C23  C  CH3   0  -0.437   7.6408  -0.4600   0.8561
 0KM  H1   H  H     0   0.353  -3.0502   3.7867   1.6596
 0KM  H3   H  HCH3  0   0.266  -4.3455   3.6360  -0.3507
 0KM  H4   H  HCH3  0   0.267  -2.7206   4.2283  -0.7545
 0KM  H5   H  HCH3  0   0.278  -3.6119   3.2236  -1.9041
 0KM  H6   H  HCR6  0   0.262  -1.3597  -2.3124   1.1750
 0KM  H7   H  HCR6  0   0.261  -2.8464  -4.1272   1.8834
 0KM  H8   H  HCR6  0   0.261  -5.2829  -3.9866   1.4504
 0KM  H9   H  HCR6  0   0.262  -6.2060  -1.9937   0.3066
 0KM  H10  H  HCR6  0   0.259  -4.7441  -0.1742  -0.3837
 0KM  H11  H  HCR6  0   0.256  -1.6188  -1.8112  -1.9349
 0KM  H12  H  HCR6  0   0.260   0.4959  -2.5409  -2.9506
 0KM  H13  H  HCR6  0   0.257   2.6375  -1.6085  -2.1854
 0KM  H14  H  HCR6  0   0.257   0.5406   0.8193   0.6541
 0KM  H16  H  HCR6  0   0.259   4.0858  -1.6263  -0.3478
 0KM  H17  H  HCR6  0   0.251   2.2676   2.2475   0.0028
 0KM  H18  H  HCR6  0   0.261   4.4126   3.1575   0.7816
 0KM  H19  H  HCH3  0   0.260   8.3069  -1.3191   0.8554
 0KM  H20  H  HCH3  0   0.229   8.0567   0.3072   0.1979
 0KM  H21  H  HCH3  0   0.229   7.5842  -0.0596   1.8717
 0KM  H22  H  HNH1  0   0.405  -1.7284   0.4851   2.1004
 0KM  H15  H  HCR6  0   0.280   6.3905   1.7391   0.9873

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
 0KM  C13  C14  aromatic  1.388  0.020  1.388
 0KM  C13  C12  aromatic  1.385  0.020  1.385
 0KM  C14  C15  aromatic  1.393  0.020  1.393
 0KM  C12  C11  aromatic  1.393  0.020  1.393
 0KM  C15  C19  single    1.478  0.020  1.478
 0KM  C15  C16  aromatic  1.397  0.020  1.397
 0KM  C20  C19  aromatic  1.398  0.020  1.398
 0KM  C20  C21  aromatic  1.383  0.020  1.383
 0KM  C8   C9   aromatic  1.387  0.020  1.387
 0KM  C8   C7   aromatic  1.389  0.020  1.389
 0KM  C9   C10  aromatic  1.389  0.020  1.389
 0KM  C7   C6   aromatic  1.387  0.020  1.387
 0KM  C19  C18  aromatic  1.390  0.020  1.390
 0KM  C11  C16  aromatic  1.386  0.020  1.386
 0KM  C11  C2   single    1.522  0.020  1.522
 0KM  C21  C17  aromatic  1.390  0.020  1.390
 0KM  C10  C5   aromatic  1.391  0.020  1.391
 0KM  C6   C5   aromatic  1.393  0.020  1.393
 0KM  C5   C2   single    1.525  0.020  1.525
 0KM  C18  C22  aromatic  1.395  0.020  1.395
 0KM  C17  C22  aromatic  1.393  0.020  1.393
 0KM  C2   N1   single    1.444  0.020  1.444
 0KM  C2   C1   single    1.536  0.020  1.536
 0KM  C22  O2   single    1.346  0.020  1.346
 0KM  O1   C1   double    1.207  0.020  1.207
 0KM  N1   C3   single    1.364  0.020  1.364
 0KM  C1   N2   single    1.356  0.020  1.356
 0KM  O2   C23  single    1.414  0.020  1.414
 0KM  C3   N2   single    1.398  0.020  1.398
 0KM  C3   N3   double    1.266  0.020  1.266
 0KM  N2   C4   single    1.443  0.020  1.443
 0KM  N3   H1   single    0.890  0.020  1.040
 0KM  C4   H3   single    0.970  0.020  1.090
 0KM  C4   H4   single    0.970  0.020  1.090
 0KM  C4   H5   single    0.970  0.020  1.090
 0KM  C6   H6   single    0.930  0.020  1.080
 0KM  C7   H7   single    0.930  0.020  1.080
 0KM  C8   H8   single    0.930  0.020  1.080
 0KM  C9   H9   single    0.930  0.020  1.080
 0KM  C10  H10  single    0.930  0.020  1.080
 0KM  C12  H11  single    0.930  0.020  1.080
 0KM  C13  H12  single    0.930  0.020  1.080
 0KM  C14  H13  single    0.930  0.020  1.080
 0KM  C16  H14  single    0.930  0.020  1.080
 0KM  C17  H15  single    0.930  0.020  1.080
 0KM  C18  H16  single    0.930  0.020  1.080
 0KM  C20  H17  single    0.930  0.020  1.080
 0KM  C21  H18  single    0.930  0.020  1.080
 0KM  C23  H19  single    0.970  0.020  1.090
 0KM  C23  H20  single    0.970  0.020  1.090
 0KM  C23  H21  single    0.970  0.020  1.090
 0KM  N1   H22  single    0.890  0.020  1.040

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
 0KM  N2   C1   C2   107.02  3.000
 0KM  N2   C1   O1   126.82  3.000
 0KM  C2   C1   O1   126.16  3.000
 0KM  C11  C2   C5   112.26  3.000
 0KM  C5   C2   N1   110.30  3.000
 0KM  C11  C2   N1   113.19  3.000
 0KM  N1   C2   C1   100.89  3.000
 0KM  C5   C2   C1   111.93  3.000
 0KM  C11  C2   C1   107.72  3.000
 0KM  H22  N1   C3   118.95  3.000
 0KM  H22  N1   C2   120.69  3.000
 0KM  C3   N1   C2   112.61  3.000
 0KM  N3   C3   N2   128.41  3.000
 0KM  N3   C3   N1   125.14  3.000
 0KM  N2   C3   N1   106.45  3.000
 0KM  C4   N2   C3   122.86  3.000
 0KM  C4   N2   C1   125.07  3.000
 0KM  C3   N2   C1   112.07  3.000
 0KM  H1   N3   C3   112.47  3.000
 0KM  H5   C4   H4   108.79  3.000
 0KM  H5   C4   H3   108.69  3.000
 0KM  H4   C4   H3   109.27  3.000
 0KM  H5   C4   N2   108.92  3.000
 0KM  H4   C4   N2   110.49  3.000
 0KM  H3   C4   N2   110.65  3.000
 0KM  C10  C5   C6   118.85  3.000
 0KM  C6   C5   C2   118.70  3.000
 0KM  C10  C5   C2   122.25  3.000
 0KM  H6   C6   C7   119.23  3.000
 0KM  H6   C6   C5   120.09  3.000
 0KM  C7   C6   C5   120.68  3.000
 0KM  H7   C7   C8   120.22  3.000
 0KM  H7   C7   C6   119.63  3.000
 0KM  C8   C7   C6   120.15  3.000
 0KM  H8   C8   C9   120.24  3.000
 0KM  H8   C8   C7   120.25  3.000
 0KM  C9   C8   C7   119.51  3.000
 0KM  H9   C9   C10  119.47  3.000
 0KM  H9   C9   C8   120.21  3.000
 0KM  C10  C9   C8   120.32  3.000
 0KM  H10  C10  C9   118.25  3.000
 0KM  H10  C10  C5   121.26  3.000
 0KM  C9   C10  C5   120.49  3.000
 0KM  C16  C11  C12  119.39  3.000
 0KM  C16  C11  C2   120.98  3.000
 0KM  C12  C11  C2   119.61  3.000
 0KM  H11  C12  C13  119.60  3.000
 0KM  H11  C12  C11  120.48  3.000
 0KM  C13  C12  C11  119.92  3.000
 0KM  H12  C13  C14  119.75  3.000
 0KM  H12  C13  C12  119.78  3.000
 0KM  C14  C13  C12  120.46  3.000
 0KM  H13  C14  C15  120.12  3.000
 0KM  H13  C14  C13  119.51  3.000
 0KM  C15  C14  C13  120.36  3.000
 0KM  C19  C15  C16  120.40  3.000
 0KM  C16  C15  C14  118.66  3.000
 0KM  C19  C15  C14  120.93  3.000
 0KM  H14  C16  C15  119.60  3.000
 0KM  H14  C16  C11  119.17  3.000
 0KM  C15  C16  C11  121.21  3.000
 0KM  H15  C17  C22  121.68  3.000
 0KM  H15  C17  C21  119.21  3.000
 0KM  C22  C17  C21  119.11  3.000
 0KM  H16  C18  C22  118.72  3.000
 0KM  H16  C18  C19  120.28  3.000
 0KM  C22  C18  C19  120.98  3.000
 0KM  C20  C19  C18  119.07  3.000
 0KM  C18  C19  C15  120.24  3.000
 0KM  C20  C19  C15  120.69  3.000
 0KM  H17  C20  C21  119.80  3.000
 0KM  H17  C20  C19  120.40  3.000
 0KM  C21  C20  C19  119.79  3.000
 0KM  H18  C21  C20  119.67  3.000
 0KM  H18  C21  C17  118.99  3.000
 0KM  C20  C21  C17  121.34  3.000
 0KM  O2   C22  C18  115.92  3.000
 0KM  O2   C22  C17  124.37  3.000
 0KM  C18  C22  C17  119.71  3.000
 0KM  C23  O2   C22  118.55  3.000
 0KM  H21  C23  H20  108.78  3.000
 0KM  H21  C23  H19  108.77  3.000
 0KM  H20  C23  H19  108.74  3.000
 0KM  H21  C23  O2   111.94  3.000
 0KM  H20  C23  O2   111.98  3.000
 0KM  H19  C23  O2   106.51  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
 0KM  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 0KM  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 0KM  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 0KM  CONST_04  C9   C10  C5   C6     0.00   0.0  0
 0KM  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 0KM  CONST_06  C10  C5   C6   C7     0.00   0.0  0
 0KM  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 0KM  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 0KM  CONST_09  C19  C15  C16  C11  180.00   0.0  0
 0KM  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 0KM  CONST_11  C15  C16  C11  C12    0.00   0.0  0
 0KM  CONST_12  C19  C15  C14  C13  180.00   0.0  0
 0KM  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 0KM  CONST_14  C16  C11  C12  C13    0.00   0.0  0
 0KM  CONST_17  C21  C20  C19  C15  180.00   0.0  0
 0KM  CONST_18  C22  C18  C19  C15  180.00   0.0  0
 0KM  CONST_21  C19  C20  C21  C17    0.00   0.0  0
 0KM  CONST_22  C19  C18  C22  C17    0.00   0.0  0
 0KM  CONST_23  C21  C20  C19  C18    0.00   0.0  0
 0KM  CONST_24  C21  C17  C22  C18    0.00   0.0  0
 0KM  CONST_25  C22  C18  C19  C20    0.00   0.0  0
 0KM  CONST_26  C22  C17  C21  C20    0.00   0.0  0
 0KM  CONST_27  C13  C12  C11  C2   180.00   0.0  0
 0KM  CONST_28  C15  C16  C11  C2   180.00   0.0  0
 0KM  CONST_29  C9   C10  C5   C2   180.00   0.0  0
 0KM  CONST_30  C7   C6   C5   C2   180.00   0.0  0
 0KM  CONST_31  N1   C3   N2   C1     0.00   0.0  0
 0KM  CONST_32  N2   C3   N1   C2     0.00   0.0  0
 0KM  CONST_33  C3   N2   C1   C2     0.00   0.0  0
 0KM  CONST_34  O2   C22  C18  C19  180.00   0.0  0
 0KM  CONST_35  O2   C22  C17  C21  180.00   0.0  0
 0KM  CONST_36  C3   N2   C1   O1   180.00   0.0  0
 0KM  CONST_37  N3   C3   N2   C1   180.00   0.0  0
 0KM  CONST_38  N3   C3   N1   C2   180.00   0.0  0
 0KM  CONST_39  C4   N2   C1   C2   180.00   0.0  0
 0KM  CONST_40  C4   N2   C3   N1   180.00   0.0  0
 0KM  CONST_41  H11  C12  C11  C2     0.00   0.0  0
 0KM  CONST_42  H14  C16  C11  C2     0.00   0.0  0
 0KM  CONST_43  H10  C10  C5   C2     0.00   0.0  0
 0KM  CONST_44  H6   C6   C5   C2     0.00   0.0  0
 0KM  CONST_45  H9   C9   C10  C5   180.00   0.0  0
 0KM  CONST_46  H7   C7   C6   C5   180.00   0.0  0
 0KM  CONST_47  H8   C8   C7   C6   180.00   0.0  0
 0KM  CONST_48  H12  C13  C12  C11  180.00   0.0  0
 0KM  CONST_49  H13  C14  C13  C12  180.00   0.0  0
 0KM  CONST_50  H17  C20  C19  C15    0.00   0.0  0
 0KM  CONST_51  H16  C18  C19  C15    0.00   0.0  0
 0KM  CONST_52  H15  C17  C22  C18  180.00   0.0  0
 0KM  CONST_53  H18  C21  C20  C19  180.00   0.0  0
 0KM  CONST_55  C4   N2   C1   O1     0.00   0.0  0
 0KM  CONST_56  C4   N2   C3   N3     0.00   0.0  0
 0KM  CONST_57  H1   N3   C3   N1   180.00   0.0  0
 0KM  Var_01    H3   C4   N2   C1   117.74  30.0  3
 0KM  Var_02    H19  C23  O2   C22  179.34  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
 0KM  chir_01  C2  C5  N1  C1  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
 0KM  plan-1  C2   0.020
 0KM  plan-1  C5   0.020
 0KM  plan-1  C6   0.020
 0KM  plan-1  C7   0.020
 0KM  plan-1  C8   0.020
 0KM  plan-1  C9   0.020
 0KM  plan-1  C10  0.020
 0KM  plan-1  H6   0.020
 0KM  plan-1  H7   0.020
 0KM  plan-1  H8   0.020
 0KM  plan-1  H9   0.020
 0KM  plan-1  H10  0.020
 0KM  plan-2  C2   0.020
 0KM  plan-2  C11  0.020
 0KM  plan-2  C12  0.020
 0KM  plan-2  C13  0.020
 0KM  plan-2  C14  0.020
 0KM  plan-2  C15  0.020
 0KM  plan-2  C16  0.020
 0KM  plan-2  C19  0.020
 0KM  plan-2  H11  0.020
 0KM  plan-2  H12  0.020
 0KM  plan-2  H13  0.020
 0KM  plan-2  H14  0.020
 0KM  plan-3  C15  0.020
 0KM  plan-3  C17  0.020
 0KM  plan-3  C18  0.020
 0KM  plan-3  C19  0.020
 0KM  plan-3  C20  0.020
 0KM  plan-3  C21  0.020
 0KM  plan-3  C22  0.020
 0KM  plan-3  O2   0.020
 0KM  plan-3  H16  0.020
 0KM  plan-3  H17  0.020
 0KM  plan-3  H18  0.020
 0KM  plan-3  H15  0.020
 0KM  plan-4  O1   0.020
 0KM  plan-4  C1   0.020
 0KM  plan-4  C2   0.020
 0KM  plan-4  N1   0.020
 0KM  plan-4  C3   0.020
 0KM  plan-4  N2   0.020
 0KM  plan-4  N3   0.020
 0KM  plan-4  C4   0.020
 0KM  plan-4  H1   0.020
 0KM  plan-4  H22  0.020

