# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:05:16 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (5S)-2-amino-5-(4-methoxy-3-methylphenyl)-3-methyl-5-[3-(pyridin-3-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1C)[C@@]2(N=C(N)N(C)C2=O)c3cccc(c3)c4cccnc4
#
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
 X45  X45  (5S)-2-amino-5-(4-methoxy-3-methylphenyl)-3-methyl-5-[3-(pyridin-3-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one  ligand  51  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X45
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
 X45  C1    C  CH3   0  -0.713   1.7151   4.1279  -0.2330
 X45  N1    N  NR5   0  -0.517   1.2822  -2.4611  -1.3894
 X45  O1    O  O2    0  -0.464   4.3281   3.6920   0.5115
 X45  C2    C  CR6   0   0.018   2.2336   2.7586   0.0921
 X45  N2    N  N     0  -0.455   1.4728  -2.0262   0.8175
 X45  O2    O  O     0  -0.440   0.4999  -0.4685  -2.2166
 X45  C3    C  CR16  0  -0.317   1.4108   1.6471   0.0317
 X45  N3    N  NH2   0  -0.846   2.1558  -4.1235   0.0338
 X45  C4    C  CR6   0   0.150   1.8689   0.3633   0.3315
 X45  N4    N  N     0  -0.398  -5.2201   0.3790  -2.0655
 X45  C5    C  CR16  0  -0.318   3.1923   0.2076   0.7019
 X45  C6    C  CR16  0  -0.370   4.0460   1.3047   0.7729
 X45  C7    C  CR6   0   0.339   3.5751   2.5755   0.4684
 X45  C8    C  CH3   0  -0.435   5.6925   3.5769   0.8588
 X45  C9    C  CR5   0  -0.245   0.9365  -0.8312   0.1973
 X45  C10   C  CR5   0   0.570   0.8466  -1.1752  -1.2980
 X45  C11   C  CR5   0   0.668   1.6345  -2.8918  -0.1133
 X45  C13   C  CR6   0   0.206  -0.4210  -0.5287   0.8194
 X45  C14   C  CR16  0  -0.281  -0.4553  -0.2977   2.1944
 X45  C15   C  CR16  0  -0.232  -1.6570  -0.0490   2.8331
 X45  C16   C  CR16  0  -0.324  -2.8439  -0.0250   2.1125
 X45  C17   C  CR6   0   0.113  -2.8307  -0.2537   0.7408
 X45  C18   C  CR16  0  -0.396  -1.6097  -0.5061   0.1063
 X45  C19   C  CR6   0  -0.007  -4.0820  -0.2315  -0.0379
 X45  C20   C  CR16  0  -0.195  -5.2693  -0.7628   0.4615
 X45  C21   C  CR16  0  -0.315  -6.4148  -0.7146  -0.3145
 X45  C22   C  CR16  0  -0.072  -6.3403  -0.1375  -1.5733
 X45  C23   C  CR16  0  -0.101  -4.1296   0.3316  -1.3142
 X45  H1    H  HCH3  0   0.243   1.8158   4.8110   0.6118
 X45  H1A   H  HCH3  0   0.243   2.2547   4.5753  -1.0695
 X45  H1B   H  HCH3  0   0.242   0.6608   4.0848  -0.5021
 X45  H3    H  HCR6  0   0.243   0.3738   1.7962  -0.2473
 X45  HN3   H  HNH2  0   0.406   2.2549  -4.4523   0.9804
 X45  HN3A  H  HNH2  0   0.413   1.9258  -4.8409  -0.6343
 X45  H5    H  HCR6  0   0.253   3.5756  -0.7731   0.9489
 X45  H6    H  HCR6  0   0.275   5.0734   1.1423   1.0701
 X45  H8    H  HCH3  0   0.227   5.8262   3.1896   1.8724
 X45  H8A   H  HCH3  0   0.227   6.2378   2.9344   0.1627
 X45  H8B   H  HCH3  0   0.258   6.1098   4.5798   0.8103
 X45  H12   H  HCH3  0   0.266   2.4698  -3.4981  -2.7706
 X45  H12A  H  HCH3  0   0.264   0.8093  -4.1086  -2.5972
 X45  H12B  H  HCH3  0   0.276   1.1109  -2.5901  -3.4426
 X45  H14   H  HCR6  0   0.256   0.4631  -0.3147   2.7674
 X45  H15   H  HCR6  0   0.260  -1.6722   0.1327   3.8998
 X45  H16   H  HCR6  0   0.257  -3.7754   0.1921   2.6202
 X45  H18   H  HCR6  0   0.250  -1.6152  -0.6994  -0.9577
 X45  H20   H  HCR6  0   0.271  -5.2949  -1.2260   1.4403
 X45  H21   H  HCR6  0   0.274  -7.3488  -1.1243   0.0442
 X45  H22   H  HCR6  0   0.267  -7.2184  -0.0883  -2.2072
 X45  H23   H  HCR6  0   0.258  -3.2383   0.7834  -1.7385
 X45  C12   C  CH3   0  -0.553   1.4305  -3.2133  -2.6124

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
 X45  C2   C1    single    1.500  0.020  1.500
 X45  C1   H1    single    0.970  0.020  1.090
 X45  C1   H1A   single    0.970  0.020  1.090
 X45  C1   H1B   single    0.970  0.020  1.090
 X45  C11  N1    single    1.392  0.020  1.392
 X45  N1   C10   single    1.361  0.020  1.361
 X45  N1   C12   single    1.443  0.020  1.443
 X45  C8   O1    single    1.413  0.020  1.413
 X45  C7   O1    single    1.347  0.020  1.347
 X45  C7   C2    aromatic  1.405  0.020  1.405
 X45  C3   C2    aromatic  1.384  0.020  1.384
 X45  N2   C11   double    1.281  0.020  1.281
 X45  N2   C9    single    1.449  0.020  1.449
 X45  C10  O2    double    1.210  0.020  1.210
 X45  C4   C3    aromatic  1.396  0.020  1.396
 X45  C3   H3    single    0.930  0.020  1.080
 X45  N3   C11   single    1.346  0.020  1.346
 X45  N3   HN3   single    0.890  0.020  1.040
 X45  N3   HN3A  single    0.890  0.020  1.040
 X45  C5   C4    aromatic  1.383  0.020  1.383
 X45  C9   C4    single    1.521  0.020  1.521
 X45  N4   C23   aromatic  1.325  0.020  1.325
 X45  N4   C22   aromatic  1.328  0.020  1.328
 X45  C5   C6    aromatic  1.392  0.020  1.392
 X45  C5   H5    single    0.930  0.020  1.080
 X45  C6   C7    aromatic  1.389  0.020  1.389
 X45  C6   H6    single    0.930  0.020  1.080
 X45  C8   H8    single    0.970  0.020  1.090
 X45  C8   H8A   single    0.970  0.020  1.090
 X45  C8   H8B   single    0.970  0.020  1.090
 X45  C13  C9    single    1.523  0.020  1.523
 X45  C9   C10   single    1.537  0.020  1.537
 X45  C12  H12   single    0.970  0.020  1.090
 X45  C12  H12A  single    0.970  0.020  1.090
 X45  C12  H12B  single    0.970  0.020  1.090
 X45  C18  C13   aromatic  1.386  0.020  1.386
 X45  C13  C14   aromatic  1.395  0.020  1.395
 X45  C15  C14   aromatic  1.383  0.020  1.383
 X45  C14  H14   single    0.930  0.020  1.080
 X45  C16  C15   aromatic  1.389  0.020  1.389
 X45  C15  H15   single    0.930  0.020  1.080
 X45  C17  C16   aromatic  1.391  0.020  1.391
 X45  C16  H16   single    0.930  0.020  1.080
 X45  C19  C17   single    1.474  0.020  1.474
 X45  C17  C18   aromatic  1.399  0.020  1.399
 X45  C18  H18   single    0.930  0.020  1.080
 X45  C23  C19   aromatic  1.396  0.020  1.396
 X45  C19  C20   aromatic  1.393  0.020  1.393
 X45  C21  C20   aromatic  1.384  0.020  1.384
 X45  C20  H20   single    0.930  0.020  1.080
 X45  C22  C21   aromatic  1.387  0.020  1.387
 X45  C21  H21   single    0.930  0.020  1.080
 X45  C22  H22   single    0.930  0.020  1.080
 X45  C23  H23   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
 X45  H1B   C1   H1A   107.79  3.000
 X45  H1B   C1   H1    107.79  3.000
 X45  H1A   C1   H1    106.93  3.000
 X45  H1B   C1   C2    110.62  3.000
 X45  H1A   C1   C2    111.69  3.000
 X45  H1    C1   C2    111.83  3.000
 X45  C12   N1   C11   126.11  3.000
 X45  C12   N1   C10   125.61  3.000
 X45  C11   N1   C10   108.17  3.000
 X45  C8    O1   C7    118.69  3.000
 X45  C7    C2   C3    118.33  3.000
 X45  C3    C2   C1    121.21  3.000
 X45  C7    C2   C1    120.47  3.000
 X45  C11   N2   C9    107.03  3.000
 X45  H3    C3   C4    119.72  3.000
 X45  H3    C3   C2    117.99  3.000
 X45  C4    C3   C2    122.29  3.000
 X45  HN3A  N3   HN3   114.43  3.000
 X45  HN3A  N3   C11   119.41  3.000
 X45  HN3   N3   C11   116.09  3.000
 X45  C9    C4   C5    121.45  3.000
 X45  C9    C4   C3    120.14  3.000
 X45  C5    C4   C3    118.37  3.000
 X45  C23   N4   C22   118.04  3.000
 X45  H5    C5   C6    119.05  3.000
 X45  H5    C5   C4    120.16  3.000
 X45  C6    C5   C4    120.79  3.000
 X45  H6    C6   C7    121.30  3.000
 X45  H6    C6   C5    118.57  3.000
 X45  C7    C6   C5    120.13  3.000
 X45  C6    C7   C2    120.10  3.000
 X45  C6    C7   O1    124.17  3.000
 X45  C2    C7   O1    115.73  3.000
 X45  H8B   C8   H8A   108.80  3.000
 X45  H8B   C8   H8    108.74  3.000
 X45  H8A   C8   H8    108.73  3.000
 X45  H8B   C8   O1    106.53  3.000
 X45  H8A   C8   O1    111.91  3.000
 X45  H8    C8   O1    112.02  3.000
 X45  C13   C9   C10   112.93  3.000
 X45  C10   C9   C4    107.30  3.000
 X45  C13   C9   C4    110.75  3.000
 X45  C10   C9   N2    104.68  3.000
 X45  C13   C9   N2    108.59  3.000
 X45  C4    C9   N2    112.51  3.000
 X45  C9    C10  O2    128.66  3.000
 X45  C9    C10  N1    104.96  3.000
 X45  O2    C10  N1    126.35  3.000
 X45  N3    C11  N2    126.00  3.000
 X45  N3    C11  N1    118.79  3.000
 X45  N2    C11  N1    115.15  3.000
 X45  C18   C13  C14   118.89  3.000
 X45  C14   C13  C9    117.22  3.000
 X45  C18   C13  C9    123.87  3.000
 X45  H14   C14  C15   119.70  3.000
 X45  H14   C14  C13   119.88  3.000
 X45  C15   C14  C13   120.42  3.000
 X45  H15   C15  C16   119.77  3.000
 X45  H15   C15  C14   119.83  3.000
 X45  C16   C15  C14   120.39  3.000
 X45  H16   C16  C17   120.24  3.000
 X45  H16   C16  C15   119.70  3.000
 X45  C17   C16  C15   120.05  3.000
 X45  C19   C17  C18   120.27  3.000
 X45  C18   C17  C16   119.03  3.000
 X45  C19   C17  C16   120.70  3.000
 X45  H18   C18  C17   118.30  3.000
 X45  H18   C18  C13   120.49  3.000
 X45  C17   C18  C13   121.20  3.000
 X45  C23   C19  C20   116.90  3.000
 X45  C20   C19  C17   121.89  3.000
 X45  C23   C19  C17   121.21  3.000
 X45  H20   C20  C21   120.12  3.000
 X45  H20   C20  C19   120.47  3.000
 X45  C21   C20  C19   119.40  3.000
 X45  H21   C21  C22   120.35  3.000
 X45  H21   C21  C20   121.04  3.000
 X45  C22   C21  C20   118.61  3.000
 X45  H22   C22  C21   120.40  3.000
 X45  H22   C22  N4    116.67  3.000
 X45  C21   C22  N4    122.92  3.000
 X45  H23   C23  C19   119.82  3.000
 X45  H23   C23  N4    116.05  3.000
 X45  C19   C23  N4    124.12  3.000
 X45  H12B  C12  H12A  108.32  3.000
 X45  H12B  C12  H12   108.65  3.000
 X45  H12A  C12  H12   109.34  3.000
 X45  H12B  C12  N1    108.56  3.000
 X45  H12A  C12  N1    110.97  3.000
 X45  H12   C12  N1    110.94  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
 X45  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 X45  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 X45  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 X45  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 X45  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 X45  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 X45  CONST_07  C17  C19  C23  N4   180.00   0.0  0
 X45  CONST_08  C20  C19  C23  N4     0.00   0.0  0
 X45  CONST_09  C20  C21  C22  N4     0.00   0.0  0
 X45  CONST_10  C16  C17  C18  C13    0.00   0.0  0
 X45  CONST_11  C19  C17  C18  C13  180.00   0.0  0
 X45  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 X45  CONST_13  C17  C18  C13  C14    0.00   0.0  0
 X45  CONST_14  C17  C16  C15  C14    0.00   0.0  0
 X45  CONST_15  C18  C13  C14  C15    0.00   0.0  0
 X45  CONST_16  C19  C17  C16  C15  180.00   0.0  0
 X45  CONST_17  C18  C17  C16  C15    0.00   0.0  0
 X45  CONST_20  C21  C20  C19  C17  180.00   0.0  0
 X45  CONST_23  C22  N4   C23  C19    0.00   0.0  0
 X45  CONST_24  C22  C21  C20  C19    0.00   0.0  0
 X45  CONST_25  C23  C19  C20  C21    0.00   0.0  0
 X45  CONST_26  C23  N4   C22  C21    0.00   0.0  0
 X45  CONST_27  C9   C4   C3   C2   180.00   0.0  0
 X45  CONST_28  C9   C4   C5   C6   180.00   0.0  0
 X45  CONST_29  C17  C18  C13  C9   180.00   0.0  0
 X45  CONST_30  C15  C14  C13  C9   180.00   0.0  0
 X45  CONST_31  C9   N2   C11  N1     0.00   0.0  0
 X45  CONST_32  C10  N1   C11  N2     0.00   0.0  0
 X45  CONST_33  C11  N1   C10  C9     0.00   0.0  0
 X45  CONST_34  C6   C7   C2   C1   180.00   0.0  0
 X45  CONST_35  C4   C3   C2   C1   180.00   0.0  0
 X45  CONST_36  C3   C2   C7   O1   180.00   0.0  0
 X45  CONST_37  C5   C6   C7   O1   180.00   0.0  0
 X45  CONST_38  C12  N1   C11  N2   180.00   0.0  0
 X45  CONST_39  C11  N1   C10  O2   180.00   0.0  0
 X45  CONST_40  C10  N1   C11  N3   180.00   0.0  0
 X45  CONST_41  C9   N2   C11  N3   180.00   0.0  0
 X45  CONST_42  C12  N1   C10  C9   180.00   0.0  0
 X45  CONST_43  H6   C6   C7   C2   180.00   0.0  0
 X45  CONST_44  H5   C5   C4   C3   180.00   0.0  0
 X45  CONST_45  H21  C21  C22  N4   180.00   0.0  0
 X45  CONST_46  H3   C3   C4   C5   180.00   0.0  0
 X45  CONST_47  H18  C18  C13  C9     0.00   0.0  0
 X45  CONST_48  H14  C14  C13  C9     0.00   0.0  0
 X45  CONST_49  H15  C15  C14  C13  180.00   0.0  0
 X45  CONST_50  H16  C16  C15  C14  180.00   0.0  0
 X45  CONST_51  H23  C23  C19  C17    0.00   0.0  0
 X45  CONST_52  H20  C20  C19  C17    0.00   0.0  0
 X45  CONST_53  H22  C22  C21  C20  180.00   0.0  0
 X45  CONST_54  C12  N1   C10  O2     0.00   0.0  0
 X45  CONST_55  C12  N1   C11  N3     0.00   0.0  0
 X45  CONST_56  HN3  N3   C11  N1   180.00   0.0  0
 X45  Var_01    H1   C1   C2   C3   120.14  30.0  2
 X45  Var_02    H12  C12  N1   C10  117.81  30.0  3
 X45  Var_03    H8   C8   O1   C7   -62.49  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
 X45  chir_01  C9  C4  C13  C10  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
 X45  plan-1  N4    0.020
 X45  plan-1  C17   0.020
 X45  plan-1  C19   0.020
 X45  plan-1  C20   0.020
 X45  plan-1  C21   0.020
 X45  plan-1  C22   0.020
 X45  plan-1  C23   0.020
 X45  plan-1  H20   0.020
 X45  plan-1  H21   0.020
 X45  plan-1  H22   0.020
 X45  plan-1  H23   0.020
 X45  plan-2  C1    0.020
 X45  plan-2  O1    0.020
 X45  plan-2  C2    0.020
 X45  plan-2  C3    0.020
 X45  plan-2  C4    0.020
 X45  plan-2  C5    0.020
 X45  plan-2  C6    0.020
 X45  plan-2  C7    0.020
 X45  plan-2  C9    0.020
 X45  plan-2  H3    0.020
 X45  plan-2  H5    0.020
 X45  plan-2  H6    0.020
 X45  plan-3  C9    0.020
 X45  plan-3  C13   0.020
 X45  plan-3  C14   0.020
 X45  plan-3  C15   0.020
 X45  plan-3  C16   0.020
 X45  plan-3  C17   0.020
 X45  plan-3  C18   0.020
 X45  plan-3  C19   0.020
 X45  plan-3  H14   0.020
 X45  plan-3  H15   0.020
 X45  plan-3  H16   0.020
 X45  plan-3  H18   0.020
 X45  plan-4  N1    0.020
 X45  plan-4  N2    0.020
 X45  plan-4  O2    0.020
 X45  plan-4  N3    0.020
 X45  plan-4  C9    0.020
 X45  plan-4  C10   0.020
 X45  plan-4  C11   0.020
 X45  plan-4  HN3   0.020
 X45  plan-4  HN3A  0.020
 X45  plan-4  C12   0.020

