# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:11:01 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](C1=O)(c2cscc2)c3cccc(c3)c4cccnc4)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
 532  532  (5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one  ligand  41  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_532
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
 532  C1    C  CH3   0  -0.556   2.3631   3.7151   0.9519
 532  N1    N  NR5   0  -0.517   1.9370   2.4617   0.3757
 532  O1    O  O     0  -0.437   2.2679   1.0465   2.1530
 532  S1    S  S2    0   0.215   4.4270  -2.3134  -0.5289
 532  C2    C  CR5   0   0.575   1.9249   1.2603   1.0138
 532  N2    N  N     0  -0.462   1.0919   1.0751  -1.1933
 532  C3    C  CR5   0  -0.251   1.3665   0.2716  -0.0209
 532  N3    N  NH2   0  -0.847   1.3105   3.3446  -1.7165
 532  C4    C  CR5   0   0.676   1.4382   2.2773  -0.9108
 532  N4    N  N     0  -0.398  -5.0801   1.6573  -0.5119
 532  C5    C  CR6   0   0.181   0.1130  -0.3690   0.5602
 532  C6    C  CR16  0  -0.291   0.2256  -1.3468   1.5457
 532  C7    C  CR16  0  -0.231  -0.9135  -1.9170   2.0912
 532  C8    C  CR16  0  -0.320  -2.1719  -1.5216   1.6618
 532  C9    C  CR6   0   0.111  -2.3016  -0.5459   0.6761
 532  C10   C  CR16  0  -0.384  -1.1474   0.0223   0.1332
 532  C11   C  CR6   0  -0.007  -3.6342  -0.1226   0.2093
 532  C12   C  CR16  0  -0.196  -4.6804  -1.0287   0.0487
 532  C13   C  CR16  0  -0.315  -5.9119  -0.5745  -0.3912
 532  C14   C  CR16  0  -0.072  -6.0628   0.7769  -0.6628
 532  C15   C  CR16  0  -0.100  -3.9059   1.2141  -0.0865
 532  C16   C  CR5   0   0.254   2.3803  -0.7909  -0.3807
 532  C17   C  CR15  0  -0.189   2.1262  -1.7110  -1.4423
 532  C18   C  CR15  0  -0.466   3.1437  -2.5896  -1.6322
 532  C19   C  CR15  0  -0.558   3.5919  -1.0048   0.2025
 532  H1    H  HCH3  0   0.266   3.2621   4.0855   0.4606
 532  H1A   H  HCH3  0   0.267   1.5747   4.4618   0.8735
 532  H1B   H  HCH3  0   0.277   2.5863   3.5572   2.0032
 532  HN3   H  HNH2  0   0.415   1.8736   4.1641  -1.5604
 532  HN3A  H  HNH2  0   0.408   1.0898   3.1584  -2.6810
 532  H6    H  HCR6  0   0.257   1.2016  -1.6746   1.8786
 532  H7    H  HCR6  0   0.260  -0.8229  -2.6740   2.8590
 532  H8    H  HCR6  0   0.257  -3.0529  -1.9656   2.1080
 532  H10   H  HCR6  0   0.254  -1.2291   0.7587  -0.6553
 532  H12   H  HCR6  0   0.271  -4.5302  -2.0825   0.2480
 532  H13   H  HCR6  0   0.274  -6.7392  -1.2564  -0.5316
 532  H14   H  HCR6  0   0.266  -7.0127   1.1630  -1.0144
 532  H15   H  HCR6  0   0.259  -3.1333   1.9646   0.0464
 532  H17   H  HCR5  0   0.265   1.2213  -1.7084  -2.0334
 532  H18   H  HCR5  0   0.296   3.2086  -3.3817  -2.3618
 532  H19   H  HCR5  0   0.291   4.0468  -0.4778   1.0263

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
 532  C1   N1    single    1.444  0.020  1.444
 532  N1   C2    single    1.360  0.020  1.360
 532  N1   C4    single    1.392  0.020  1.392
 532  O1   C2    double    1.209  0.020  1.209
 532  S1   C18   aromatic  1.715  0.020  1.715
 532  S1   C19   aromatic  1.716  0.020  1.716
 532  C2   C3    single    1.536  0.020  1.536
 532  N2   C3    single    1.448  0.020  1.448
 532  N2   C4    double    1.283  0.020  1.283
 532  C3   C5    single    1.523  0.020  1.523
 532  C3   C16   single    1.512  0.020  1.512
 532  N3   C4    single    1.343  0.020  1.343
 532  N4   C14   aromatic  1.328  0.020  1.328
 532  N4   C15   aromatic  1.325  0.020  1.325
 532  C5   C6    aromatic  1.393  0.020  1.393
 532  C5   C10   aromatic  1.387  0.020  1.387
 532  C6   C7    aromatic  1.386  0.020  1.386
 532  C7   C8    aromatic  1.387  0.020  1.387
 532  C8   C9    aromatic  1.393  0.020  1.393
 532  C9   C10   aromatic  1.396  0.020  1.396
 532  C9   C11   single    1.474  0.020  1.474
 532  C11  C12   aromatic  1.393  0.020  1.393
 532  C11  C15   aromatic  1.396  0.020  1.396
 532  C12  C13   aromatic  1.384  0.020  1.384
 532  C13  C14   aromatic  1.387  0.020  1.387
 532  C16  C17   aromatic  1.428  0.020  1.428
 532  C16  C19   aromatic  1.362  0.020  1.362
 532  C17  C18   aromatic  1.358  0.020  1.358
 532  C1   H1    single    0.970  0.020  1.090
 532  C1   H1A   single    0.970  0.020  1.090
 532  C1   H1B   single    0.970  0.020  1.090
 532  N3   HN3   single    0.890  0.020  1.040
 532  N3   HN3A  single    0.890  0.020  1.040
 532  C6   H6    single    0.930  0.020  1.080
 532  C7   H7    single    0.930  0.020  1.080
 532  C8   H8    single    0.930  0.020  1.080
 532  C10  H10   single    0.930  0.020  1.080
 532  C12  H12   single    0.930  0.020  1.080
 532  C13  H13   single    0.930  0.020  1.080
 532  C14  H14   single    0.930  0.020  1.080
 532  C15  H15   single    0.930  0.020  1.080
 532  C17  H17   single    0.930  0.020  1.080
 532  C18  H18   single    0.930  0.020  1.080
 532  C19  H19   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
 532  H1B   C1   H1A  108.56  3.000
 532  H1B   C1   H1   108.45  3.000
 532  H1A   C1   H1   109.39  3.000
 532  H1B   C1   N1   108.70  3.000
 532  H1A   C1   N1   110.66  3.000
 532  H1    C1   N1   111.02  3.000
 532  C4    N1   C2   108.26  3.000
 532  C4    N1   C1   126.13  3.000
 532  C2    N1   C1   125.60  3.000
 532  C19   S1   C18   91.89  3.000
 532  C3    C2   O1   128.62  3.000
 532  C3    C2   N1   104.81  3.000
 532  O1    C2   N1   126.56  3.000
 532  C4    N2   C3   106.91  3.000
 532  C16   C3   C5   110.31  3.000
 532  C16   C3   N2   108.94  3.000
 532  C5    C3   N2   112.73  3.000
 532  C16   C3   C2   111.64  3.000
 532  C5    C3   C2   108.24  3.000
 532  N2    C3   C2   104.90  3.000
 532  HN3A  N3   HN3  114.95  3.000
 532  HN3A  N3   C4   116.65  3.000
 532  HN3   N3   C4   120.04  3.000
 532  N3    C4   N2   125.94  3.000
 532  N3    C4   N1   118.89  3.000
 532  N2    C4   N1   115.11  3.000
 532  C15   N4   C14  118.06  3.000
 532  C10   C5   C6   119.29  3.000
 532  C10   C5   C3   120.78  3.000
 532  C6    C5   C3   119.92  3.000
 532  H6    C6   C7   119.71  3.000
 532  H6    C6   C5   120.22  3.000
 532  C7    C6   C5   120.07  3.000
 532  H7    C7   C8   119.67  3.000
 532  H7    C7   C6   119.90  3.000
 532  C8    C7   C6   120.43  3.000
 532  H8    C8   C9   120.20  3.000
 532  H8    C8   C7   119.58  3.000
 532  C9    C8   C7   120.21  3.000
 532  C11   C9   C10  120.49  3.000
 532  C11   C9   C8   120.62  3.000
 532  C10   C9   C8   118.89  3.000
 532  H10   C10  C9   119.86  3.000
 532  H10   C10  C5   119.01  3.000
 532  C9    C10  C5   121.11  3.000
 532  C15   C11  C12  116.89  3.000
 532  C15   C11  C9   121.20  3.000
 532  C12   C11  C9   121.91  3.000
 532  H12   C12  C13  120.08  3.000
 532  H12   C12  C11  120.49  3.000
 532  C13   C12  C11  119.42  3.000
 532  H13   C13  C14  120.39  3.000
 532  H13   C13  C12  120.99  3.000
 532  C14   C13  C12  118.61  3.000
 532  H14   C14  C13  120.40  3.000
 532  H14   C14  N4   116.68  3.000
 532  C13   C14  N4   122.91  3.000
 532  H15   C15  C11  119.85  3.000
 532  H15   C15  N4   116.02  3.000
 532  C11   C15  N4   124.12  3.000
 532  C19   C16  C17  112.06  3.000
 532  C19   C16  C3   127.24  3.000
 532  C17   C16  C3   120.70  3.000
 532  H17   C17  C18  123.54  3.000
 532  H17   C17  C16  123.65  3.000
 532  C18   C17  C16  112.81  3.000
 532  H18   C18  C17  127.94  3.000
 532  H18   C18  S1   120.56  3.000
 532  C17   C18  S1   111.51  3.000
 532  H19   C19  C16  128.74  3.000
 532  H19   C19  S1   119.53  3.000
 532  C16   C19  S1   111.73  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
 532  CONST_01  C16   C17  C18  S1     0.00   0.0  0
 532  CONST_02  C17   C16  C19  S1     0.00   0.0  0
 532  CONST_03  C12   C13  C14  N4     0.00   0.0  0
 532  CONST_04  C9    C11  C15  N4   180.00   0.0  0
 532  CONST_05  C12   C11  C15  N4     0.00   0.0  0
 532  CONST_06  C8    C7   C6   C5     0.00   0.0  0
 532  CONST_07  C8    C9   C10  C5     0.00   0.0  0
 532  CONST_08  C11   C9   C10  C5   180.00   0.0  0
 532  CONST_09  C9    C10  C5   C6     0.00   0.0  0
 532  CONST_10  C9    C8   C7   C6     0.00   0.0  0
 532  CONST_11  C10   C5   C6   C7     0.00   0.0  0
 532  CONST_12  C10   C9   C8   C7     0.00   0.0  0
 532  CONST_13  C11   C9   C8   C7   180.00   0.0  0
 532  CONST_16  C13   C12  C11  C9   180.00   0.0  0
 532  CONST_19  C14   C13  C12  C11    0.00   0.0  0
 532  CONST_20  C14   N4   C15  C11    0.00   0.0  0
 532  CONST_21  C15   C11  C12  C13    0.00   0.0  0
 532  CONST_22  C15   N4   C14  C13    0.00   0.0  0
 532  CONST_23  C18   S1   C19  C16    0.00   0.0  0
 532  CONST_24  C19   S1   C18  C17    0.00   0.0  0
 532  CONST_25  C19   C16  C17  C18    0.00   0.0  0
 532  CONST_26  C3    C16  C19  S1   180.00   0.0  0
 532  CONST_27  C7    C6   C5   C3   180.00   0.0  0
 532  CONST_28  C9    C10  C5   C3   180.00   0.0  0
 532  CONST_29  C18   C17  C16  C3   180.00   0.0  0
 532  CONST_30  C3    N2   C4   N1     0.00   0.0  0
 532  CONST_31  N2    C4   N1   C2     0.00   0.0  0
 532  CONST_32  C4    N1   C2   C3     0.00   0.0  0
 532  CONST_33  C3    C2   N1   C1   180.00   0.0  0
 532  CONST_34  N2    C4   N1   C1   180.00   0.0  0
 532  CONST_35  C4    N1   C2   O1   180.00   0.0  0
 532  CONST_36  N3    C4   N1   C2   180.00   0.0  0
 532  CONST_37  N3    C4   N2   C3   180.00   0.0  0
 532  CONST_38  H17   C17  C18  S1   180.00   0.0  0
 532  CONST_39  H6    C6   C5   C3     0.00   0.0  0
 532  CONST_40  H10   C10  C5   C3     0.00   0.0  0
 532  CONST_41  H19   C19  C16  C3     0.00   0.0  0
 532  CONST_42  H13   C13  C14  N4   180.00   0.0  0
 532  CONST_43  H7    C7   C6   C5   180.00   0.0  0
 532  CONST_44  H8    C8   C7   C6   180.00   0.0  0
 532  CONST_45  H12   C12  C11  C9     0.00   0.0  0
 532  CONST_46  H15   C15  C11  C9     0.00   0.0  0
 532  CONST_47  H14   C14  C13  C12  180.00   0.0  0
 532  CONST_48  H18   C18  C17  C16  180.00   0.0  0
 532  CONST_49  O1    C2   N1   C1     0.00   0.0  0
 532  CONST_50  N3    C4   N1   C1     0.00   0.0  0
 532  CONST_52  HN3A  N3   C4   N1   180.00   0.0  0
 532  Var_01    H1    C1   N1   C2   114.13  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
 532  chir_01  C3  N2  C5  C16  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
 532  plan-1  S1    0.020
 532  plan-1  C3    0.020
 532  plan-1  C16   0.020
 532  plan-1  C17   0.020
 532  plan-1  C18   0.020
 532  plan-1  C19   0.020
 532  plan-1  H17   0.020
 532  plan-1  H18   0.020
 532  plan-1  H19   0.020
 532  plan-2  N4    0.020
 532  plan-2  C9    0.020
 532  plan-2  C11   0.020
 532  plan-2  C12   0.020
 532  plan-2  C13   0.020
 532  plan-2  C14   0.020
 532  plan-2  C15   0.020
 532  plan-2  H12   0.020
 532  plan-2  H13   0.020
 532  plan-2  H14   0.020
 532  plan-2  H15   0.020
 532  plan-3  C3    0.020
 532  plan-3  C5    0.020
 532  plan-3  C6    0.020
 532  plan-3  C7    0.020
 532  plan-3  C8    0.020
 532  plan-3  C9    0.020
 532  plan-3  C10   0.020
 532  plan-3  C11   0.020
 532  plan-3  H6    0.020
 532  plan-3  H7    0.020
 532  plan-3  H8    0.020
 532  plan-3  H10   0.020
 532  plan-4  C1    0.020
 532  plan-4  N1    0.020
 532  plan-4  O1    0.020
 532  plan-4  C2    0.020
 532  plan-4  N2    0.020
 532  plan-4  C3    0.020
 532  plan-4  N3    0.020
 532  plan-4  C4    0.020
 532  plan-4  HN3   0.020
 532  plan-4  HN3A  0.020

