# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 18:30:13 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5S)-2-amino-3-methyl-5-(pyridin-4-yl)-5-[3-(pyridin-3-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](c2ccncc2)(c3cccc(c3)c4cccnc4)C1=O)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
 472  472  (5S)-2-amino-3-methyl-5-(pyridin-4-yl)-5-[3-(pyridin-3-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one  ligand  43  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_472
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
 472  C1    C  CH3   0  -0.557   2.7217   2.2424   2.5998
 472  N1    N  NT    0  -0.520   2.3792   1.5583   1.3751
 472  O1    O  O     0  -0.436   0.9623  -0.0520   2.1880
 472  C2    C  C     0   0.589   1.5458   0.4880   1.2773
 472  N2    N  N     0  -0.464   2.4856   1.0450  -0.8191
 472  C3    C  CT    0  -0.254   1.5576   0.1169  -0.2171
 472  N3    N  NH2   0  -0.846   3.8071   2.8003  -0.0275
 472  C4    C  C     0   0.687   2.9011   1.8222   0.1127
 472  N4    N  N     0  -0.407   2.9145  -3.9745  -0.5115
 472  C5    C  CR6   0   0.258   2.0330  -1.3251  -0.3312
 472  N5    N  N     0  -0.398  -4.7786  -0.4242   1.7713
 472  C6    C  CR16  0  -0.378   3.2943  -1.6309  -0.8206
 472  C7    C  CR16  0  -0.059   3.6823  -2.9621  -0.8908
 472  C8    C  CR16  0  -0.064   1.7071  -3.6762  -0.0418
 472  C9    C  CR16  0  -0.351   1.2221  -2.3837   0.0663
 472  C10   C  CR6   0   0.193   0.1900   0.2547  -0.8822
 472  C11   C  CR16  0  -0.286   0.1603   0.3385  -2.2734
 472  C12   C  CR16  0  -0.228  -1.0482   0.4420  -2.9409
 472  C13   C  CR16  0  -0.321  -2.2426   0.4664  -2.2351
 472  C14   C  CR6   0   0.117  -2.2327   0.3822  -0.8463
 472  C15   C  CR16  0  -0.394  -1.0073   0.2757  -0.1819
 472  C16   C  CR6   0  -0.007  -3.4928   0.4057  -0.0822
 472  C17   C  CR16  0  -0.195  -4.5610   1.2205  -0.4509
 472  C18   C  CR16  0  -0.315  -5.7231   1.1995   0.3012
 472  C19   C  CR16  0  -0.071  -5.7837   0.3632   1.4059
 472  C20   C  CR16  0  -0.101  -3.6715  -0.3994   1.0439
 472  H1    H  HCH3  0   0.269   3.7837   2.1394   2.8187
 472  H1A   H  HCH3  0   0.266   2.4659   3.2994   2.5386
 472  H1B   H  HCH3  0   0.278   2.1544   1.8010   3.4139
 472  HN3   H  HNH2  0   0.409   4.0580   3.0586  -0.9674
 472  HN3A  H  HNH2  0   0.416   3.8840   3.5344   0.6562
 472  H6    H  HCR6  0   0.268   3.9669  -0.8522  -1.1504
 472  H7    H  HCR6  0   0.264   4.6641  -3.2154  -1.2756
 472  H8    H  HCR6  0   0.265   1.0859  -4.5107   0.2640
 472  H9    H  HCR6  0   0.268   0.2225  -2.2239   0.4470
 472  H11   H  HCR6  0   0.260   1.0845   0.3298  -2.8355
 472  H12   H  HCR6  0   0.261  -1.0616   0.4999  -4.0213
 472  H13   H  HCR6  0   0.258  -3.1806   0.5339  -2.7722
 472  H15   H  HCR6  0   0.257  -1.0089   0.2287   0.8983
 472  H17   H  HCR6  0   0.271  -4.4786   1.8776  -1.3076
 472  H18   H  HCR6  0   0.274  -6.5656   1.8263   0.0435
 472  H19   H  HCR6  0   0.267  -6.6777   0.3265   2.0180
 472  H20   H  HCR6  0   0.257  -2.8792  -1.0719   1.3583

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
 472  N1   C1    single    1.444  0.020  1.444
 472  C1   H1    single    0.970  0.020  1.090
 472  C1   H1A   single    0.970  0.020  1.090
 472  C1   H1B   single    0.970  0.020  1.090
 472  C4   N1    single    1.391  0.020  1.391
 472  N1   C2    single    1.360  0.020  1.360
 472  C2   O1    double    1.209  0.020  1.209
 472  C3   C2    single    1.540  0.020  1.540
 472  N2   C4    double    1.283  0.020  1.283
 472  N2   C3    single    1.444  0.020  1.444
 472  C10  C3    single    1.527  0.020  1.527
 472  C3   C5    single    1.523  0.020  1.523
 472  N3   C4    single    1.341  0.020  1.341
 472  N3   HN3   single    0.890  0.020  1.040
 472  N3   HN3A  single    0.890  0.020  1.040
 472  C7   N4    aromatic  1.326  0.020  1.326
 472  N4   C8    aromatic  1.329  0.020  1.329
 472  C6   C5    aromatic  1.387  0.020  1.387
 472  C5   C9    aromatic  1.391  0.020  1.391
 472  N5   C20   aromatic  1.325  0.020  1.325
 472  N5   C19   aromatic  1.328  0.020  1.328
 472  C6   C7    aromatic  1.388  0.020  1.388
 472  C6   H6    single    0.930  0.020  1.080
 472  C7   H7    single    0.930  0.020  1.080
 472  C9   C8    aromatic  1.385  0.020  1.385
 472  C8   H8    single    0.930  0.020  1.080
 472  C9   H9    single    0.930  0.020  1.080
 472  C15  C10   aromatic  1.387  0.020  1.387
 472  C10  C11   aromatic  1.394  0.020  1.394
 472  C12  C11   aromatic  1.384  0.020  1.384
 472  C11  H11   single    0.930  0.020  1.080
 472  C13  C12   aromatic  1.388  0.020  1.388
 472  C12  H12   single    0.930  0.020  1.080
 472  C14  C13   aromatic  1.391  0.020  1.391
 472  C13  H13   single    0.930  0.020  1.080
 472  C16  C14   single    1.474  0.020  1.474
 472  C14  C15   aromatic  1.398  0.020  1.398
 472  C15  H15   single    0.930  0.020  1.080
 472  C20  C16   aromatic  1.396  0.020  1.396
 472  C16  C17   aromatic  1.393  0.020  1.393
 472  C18  C17   aromatic  1.384  0.020  1.384
 472  C17  H17   single    0.930  0.020  1.080
 472  C19  C18   aromatic  1.387  0.020  1.387
 472  C18  H18   single    0.930  0.020  1.080
 472  C19  H19   single    0.930  0.020  1.080
 472  C20  H20   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
 472  H1B   C1   H1A  108.29  3.000
 472  H1B   C1   H1   108.68  3.000
 472  H1A   C1   H1   109.39  3.000
 472  H1B   C1   N1   108.62  3.000
 472  H1A   C1   N1   110.88  3.000
 472  H1    C1   N1   110.91  3.000
 472  C4    N1   C2   108.29  3.000
 472  C2    N1   C1   125.40  3.000
 472  C4    N1   C1   126.20  3.000
 472  C3    C2   O1   128.84  3.000
 472  C3    C2   N1   104.76  3.000
 472  O1    C2   N1   126.38  3.000
 472  C4    N2   C3   107.14  3.000
 472  C10   C3   C5   109.42  3.000
 472  C5    C3   N2   112.14  3.000
 472  C10   C3   N2   109.63  3.000
 472  C5    C3   C2   107.66  3.000
 472  C10   C3   C2   113.21  3.000
 472  N2    C3   C2   104.75  3.000
 472  HN3A  N3   HN3  115.36  3.000
 472  HN3A  N3   C4   120.86  3.000
 472  HN3   N3   C4   116.95  3.000
 472  N3    C4   N2   125.81  3.000
 472  N3    C4   N1   119.13  3.000
 472  N2    C4   N1   115.01  3.000
 472  C8    N4   C7   117.10  3.000
 472  C9    C5   C6   117.58  3.000
 472  C9    C5   C3   121.14  3.000
 472  C6    C5   C3   121.27  3.000
 472  C20   N5   C19  118.05  3.000
 472  H6    C6   C7   120.10  3.000
 472  H6    C6   C5   120.99  3.000
 472  C7    C6   C5   118.90  3.000
 472  H7    C7   C6   119.66  3.000
 472  H7    C7   N4   116.57  3.000
 472  C6    C7   N4   123.76  3.000
 472  H8    C8   C9   119.71  3.000
 472  H8    C8   N4   116.57  3.000
 472  C9    C8   N4   123.72  3.000
 472  H9    C9   C8   119.28  3.000
 472  H9    C9   C5   121.79  3.000
 472  C8    C9   C5   118.93  3.000
 472  C15   C10  C11  118.97  3.000
 472  C11   C10  C3   117.34  3.000
 472  C15   C10  C3   123.68  3.000
 472  H11   C11  C12  119.73  3.000
 472  H11   C11  C10  119.99  3.000
 472  C12   C11  C10  120.28  3.000
 472  H12   C12  C13  119.75  3.000
 472  H12   C12  C11  119.75  3.000
 472  C13   C12  C11  120.50  3.000
 472  H13   C13  C14  120.33  3.000
 472  H13   C13  C12  119.63  3.000
 472  C14   C13  C12  120.03  3.000
 472  C16   C14  C15  120.28  3.000
 472  C15   C14  C13  119.03  3.000
 472  C16   C14  C13  120.69  3.000
 472  H15   C15  C14  118.48  3.000
 472  H15   C15  C10  120.32  3.000
 472  C14   C15  C10  121.18  3.000
 472  C20   C16  C17  116.92  3.000
 472  C17   C16  C14  121.85  3.000
 472  C20   C16  C14  121.23  3.000
 472  H17   C17  C18  120.19  3.000
 472  H17   C17  C16  120.40  3.000
 472  C18   C17  C16  119.40  3.000
 472  H18   C18  C19  120.36  3.000
 472  H18   C18  C17  121.05  3.000
 472  C19   C18  C17  118.59  3.000
 472  H19   C19  C18  120.41  3.000
 472  H19   C19  N5   116.66  3.000
 472  C18   C19  N5   122.93  3.000
 472  H20   C20  C16  119.83  3.000
 472  H20   C20  N5   116.05  3.000
 472  C16   C20  N5   124.11  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
 472  CONST_01  C5   C6   C7   N4     0.00   0.0  0
 472  CONST_02  C5   C9   C8   N4     0.00   0.0  0
 472  CONST_03  C14  C16  C20  N5   180.00   0.0  0
 472  CONST_04  C17  C16  C20  N5     0.00   0.0  0
 472  CONST_05  C17  C18  C19  N5     0.00   0.0  0
 472  CONST_06  C8   C9   C5   C6     0.00   0.0  0
 472  CONST_07  C8   N4   C7   C6     0.00   0.0  0
 472  CONST_08  C9   C8   N4   C7     0.00   0.0  0
 472  CONST_09  C9   C5   C6   C7     0.00   0.0  0
 472  CONST_10  C13  C14  C15  C10    0.00   0.0  0
 472  CONST_11  C16  C14  C15  C10  180.00   0.0  0
 472  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 472  CONST_13  C14  C15  C10  C11    0.00   0.0  0
 472  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 472  CONST_15  C15  C10  C11  C12    0.00   0.0  0
 472  CONST_16  C16  C14  C13  C12  180.00   0.0  0
 472  CONST_17  C15  C14  C13  C12    0.00   0.0  0
 472  CONST_20  C18  C17  C16  C14  180.00   0.0  0
 472  CONST_23  C19  N5   C20  C16    0.00   0.0  0
 472  CONST_24  C19  C18  C17  C16    0.00   0.0  0
 472  CONST_25  C20  C16  C17  C18    0.00   0.0  0
 472  CONST_26  C20  N5   C19  C18    0.00   0.0  0
 472  CONST_27  C14  C15  C10  C3   180.00   0.0  0
 472  CONST_28  C12  C11  C10  C3   180.00   0.0  0
 472  CONST_29  C7   C6   C5   C3   180.00   0.0  0
 472  CONST_30  C8   C9   C5   C3   180.00   0.0  0
 472  CONST_31  C3   N2   C4   N1     0.00   0.0  0
 472  CONST_32  N2   C4   N1   C2     0.00   0.0  0
 472  CONST_33  C4   N1   C2   C3     0.00   0.0  0
 472  CONST_34  N2   C4   N1   C1   180.00   0.0  0
 472  CONST_35  C3   C2   N1   C1   180.00   0.0  0
 472  CONST_36  C4   N1   C2   O1   180.00   0.0  0
 472  CONST_37  N3   C4   N1   C2   180.00   0.0  0
 472  CONST_38  N3   C4   N2   C3   180.00   0.0  0
 472  CONST_39  H15  C15  C10  C3     0.00   0.0  0
 472  CONST_40  H11  C11  C10  C3     0.00   0.0  0
 472  CONST_41  H6   C6   C5   C3     0.00   0.0  0
 472  CONST_42  H9   C9   C5   C3     0.00   0.0  0
 472  CONST_43  H7   C7   C6   C5   180.00   0.0  0
 472  CONST_44  H8   C8   C9   C5   180.00   0.0  0
 472  CONST_45  H18  C18  C19  N5   180.00   0.0  0
 472  CONST_46  H12  C12  C11  C10  180.00   0.0  0
 472  CONST_47  H13  C13  C12  C11  180.00   0.0  0
 472  CONST_48  H20  C20  C16  C14    0.00   0.0  0
 472  CONST_49  H17  C17  C16  C14    0.00   0.0  0
 472  CONST_50  H19  C19  C18  C17  180.00   0.0  0
 472  CONST_51  N3   C4   N1   C1     0.00   0.0  0
 472  CONST_52  O1   C2   N1   C1     0.00   0.0  0
 472  CONST_53  HN3  N3   C4   N1   180.00   0.0  0
 472  Var_01    H1   C1   N1   C2   115.75  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
 472  chir_01  C3  N2  C10  C5  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
 472  plan-1  N5    0.020
 472  plan-1  C14   0.020
 472  plan-1  C16   0.020
 472  plan-1  C17   0.020
 472  plan-1  C18   0.020
 472  plan-1  C19   0.020
 472  plan-1  C20   0.020
 472  plan-1  H17   0.020
 472  plan-1  H18   0.020
 472  plan-1  H19   0.020
 472  plan-1  H20   0.020
 472  plan-2  C3    0.020
 472  plan-2  N4    0.020
 472  plan-2  C5    0.020
 472  plan-2  C6    0.020
 472  plan-2  C7    0.020
 472  plan-2  C8    0.020
 472  plan-2  C9    0.020
 472  plan-2  H6    0.020
 472  plan-2  H7    0.020
 472  plan-2  H8    0.020
 472  plan-2  H9    0.020
 472  plan-3  C3    0.020
 472  plan-3  C10   0.020
 472  plan-3  C11   0.020
 472  plan-3  C12   0.020
 472  plan-3  C13   0.020
 472  plan-3  C14   0.020
 472  plan-3  C15   0.020
 472  plan-3  C16   0.020
 472  plan-3  H11   0.020
 472  plan-3  H12   0.020
 472  plan-3  H13   0.020
 472  plan-3  H15   0.020
 472  plan-4  C1    0.020
 472  plan-4  N1    0.020
 472  plan-4  O1    0.020
 472  plan-4  C2    0.020
 472  plan-4  N2    0.020
 472  plan-4  C3    0.020
 472  plan-4  N3    0.020
 472  plan-4  C4    0.020
 472  plan-4  HN3   0.020
 472  plan-4  HN3A  0.020

