# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:57:35 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (5S)-2-amino-3-methyl-5-phenyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](C1=O)(c2ccccc2)[C]34CC5[CH2][CH](C[CH]([CH2]5)C3)C4)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
 593  593  (5S)-2-amino-3-methyl-5-phenyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]-3,5-dihydro-4H-imidazol-4-one  ligand  49  24  .  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_593
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
 593  C1    C  CH3   0  -0.557  -2.3364  -3.3319   1.1251
 593  N1    N  NR5   0  -0.520  -1.7596  -2.1931   0.4526
 593  O1    O  O     0  -0.448  -1.0912  -0.9772   2.2659
 593  C2    C  CR5   0   0.576  -1.1785  -1.1220   1.0655
 593  N2    N  N     0  -0.462  -1.0717  -0.9378  -1.2819
 593  C3    C  CR5   0  -0.148  -0.6885  -0.2186  -0.0804
 593  N3    N  NH2   0  -0.845  -2.1062  -2.9881  -1.7420
 593  C4    C  CR5   0   0.663  -1.6559  -2.0149  -0.9210
 593  C5    C  CR6   0   0.138  -1.4139   1.1249  -0.0417
 593  C6    C  CR16  0  -0.299  -1.6694   1.8092   1.1464
 593  C7    C  CR16  0  -0.246  -2.3232   3.0349   1.1374
 593  C8    C  CR16  0  -0.267  -2.7313   3.6072  -0.0587
 593  C9    C  CR16  0  -0.245  -2.4785   2.9376  -1.2479
 593  C10   C  CR16  0  -0.294  -1.8324   1.7094  -1.2371
 593  C11   C  CT    0  -0.048   0.8782  -0.0572  -0.0420
 593  C12   C  CH2   0  -0.404   1.3472   0.6644  -1.3163
 593  C13   C  CH1   0  -0.245   2.8724   0.7897  -1.3387
 593  C14   C  CH2   0  -0.416   3.3391   1.5922  -0.1246
 593  C15   C  CH1   0  -0.242   2.8976   0.8729   1.1496
 593  C16   C  CH2   0  -0.419   1.3698   0.7540   1.1669
 593  C17   C  CH2   0  -0.416   3.5292  -0.5189   1.1944
 593  C18   C  CH1   0  -0.245   3.0691  -1.3188  -0.0242
 593  C19   C  CH2   0  -0.416   3.5025  -0.6030  -1.3033
 593  C20   C  CH2   0  -0.426   1.5432  -1.4448  -0.0000
 593  H1    H  HCH3  0   0.261  -3.4113  -3.3898   0.9542
 593  H1A   H  HCH3  0   0.264  -1.8684  -4.2565   0.7900
 593  H1B   H  HCH3  0   0.274  -2.1652  -3.2279   2.1927
 593  HN3   H  HNH2  0   0.401  -2.1645  -2.7381  -2.7160
 593  HN3A  H  HNH2  0   0.408  -2.8599  -3.5773  -1.4273
 593  H6    H  HCR6  0   0.260  -1.3673   1.3922   2.0961
 593  H7    H  HCR6  0   0.252  -2.5137   3.5410   2.0754
 593  H8    H  HCR6  0   0.252  -3.2426   4.5614  -0.0637
 593  H9    H  HCR6  0   0.251  -2.7877   3.3684  -2.1917
 593  H10   H  HCR6  0   0.253  -1.6519   1.1926  -2.1689
 593  H12   H  HCH2  0   0.228   1.0045   0.1199  -2.1993
 593  H12A  H  HCH2  0   0.228   0.9013   1.6623  -1.3694
 593  H13   H  HCH1  0   0.220   3.1713   1.3027  -2.2581
 593  H14   H  HCH2  0   0.219   4.4284   1.7057  -0.1392
 593  H14A  H  HCH2  0   0.219   2.9170   2.6017  -0.1543
 593  H15   H  HCH1  0   0.221   3.2145   1.4468   2.0258
 593  H16   H  HCH2  0   0.230   0.9371   1.7576   1.1481
 593  H16A  H  HCH2  0   0.234   1.0489   0.2884   2.1013
 593  H17   H  HCH2  0   0.220   4.6210  -0.4388   1.2081
 593  H17A  H  HCH2  0   0.219   3.2396  -1.0345   2.1160
 593  H18   H  HCH1  0   0.222   3.5041  -2.3222   0.0051
 593  H19   H  HCH2  0   0.219   3.1938  -1.1800  -2.1812
 593  H19A  H  HCH2  0   0.220   4.5940  -0.5270  -1.3449
 593  H20   H  HCH2  0   0.226   1.2500  -1.9841   0.9072
 593  H20A  H  HCH2  0   0.232   1.2129  -2.0433  -0.8532

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
 593  N1   C1    single    1.443  0.020  1.443
 593  C1   H1    single    0.970  0.020  1.090
 593  C1   H1A   single    0.970  0.020  1.090
 593  C1   H1B   single    0.970  0.020  1.090
 593  C4   N1    single    1.389  0.020  1.389
 593  N1   C2    single    1.364  0.020  1.364
 593  C2   O1    double    1.212  0.020  1.212
 593  C3   C2    single    1.539  0.020  1.539
 593  N2   C4    double    1.277  0.020  1.277
 593  N2   C3    single    1.452  0.020  1.452
 593  C11  C3    single    1.575  0.020  1.575
 593  C3   C5    single    1.527  0.020  1.527
 593  N3   C4    single    1.351  0.020  1.351
 593  N3   HN3   single    0.890  0.020  1.040
 593  N3   HN3A  single    0.890  0.020  1.040
 593  C6   C5    aromatic  1.395  0.020  1.395
 593  C5   C10   aromatic  1.395  0.020  1.395
 593  C6   C7    aromatic  1.389  0.020  1.389
 593  C6   H6    single    0.930  0.020  1.080
 593  C7   C8    aromatic  1.387  0.020  1.387
 593  C7   H7    single    0.930  0.020  1.080
 593  C8   C9    aromatic  1.388  0.020  1.388
 593  C8   H8    single    0.930  0.020  1.080
 593  C10  C9    aromatic  1.388  0.020  1.388
 593  C9   H9    single    0.930  0.020  1.080
 593  C10  H10   single    0.930  0.020  1.080
 593  C20  C11   single    1.539  0.020  1.539
 593  C16  C11   single    1.537  0.020  1.537
 593  C11  C12   single    1.538  0.020  1.538
 593  C13  C12   single    1.530  0.020  1.530
 593  C12  H12   single    0.970  0.020  1.090
 593  C12  H12A  single    0.970  0.020  1.090
 593  C19  C13   single    1.529  0.020  1.529
 593  C14  C13   single    1.528  0.020  1.528
 593  C13  H13   single    0.970  0.020  1.090
 593  C15  C14   single    1.528  0.020  1.528
 593  C14  H14   single    0.970  0.020  1.090
 593  C14  H14A  single    0.970  0.020  1.090
 593  C17  C15   single    1.529  0.020  1.529
 593  C15  C16   single    1.533  0.020  1.533
 593  C15  H15   single    0.970  0.020  1.090
 593  C16  H16   single    0.970  0.020  1.090
 593  C16  H16A  single    0.970  0.020  1.090
 593  C17  C18   single    1.529  0.020  1.529
 593  C17  H17   single    0.970  0.020  1.090
 593  C17  H17A  single    0.970  0.020  1.090
 593  C18  C20   single    1.531  0.020  1.531
 593  C18  C19   single    1.528  0.020  1.528
 593  C18  H18   single    0.970  0.020  1.090
 593  C19  H19   single    0.970  0.020  1.090
 593  C19  H19A  single    0.970  0.020  1.090
 593  C20  H20   single    0.970  0.020  1.090
 593  C20  H20A  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
 593  H1B   C1   H1A  108.41  3.000
 593  H1B   C1   H1   108.33  3.000
 593  H1A   C1   H1   109.29  3.000
 593  H1B   C1   N1   108.63  3.000
 593  H1A   C1   N1   110.79  3.000
 593  H1    C1   N1   111.29  3.000
 593  C4    N1   C2   108.16  3.000
 593  C2    N1   C1   125.50  3.000
 593  C4    N1   C1   126.30  3.000
 593  C3    C2   O1   130.10  3.000
 593  C3    C2   N1   105.19  3.000
 593  O1    C2   N1   124.71  3.000
 593  C4    N2   C3   107.73  3.000
 593  C11   C3   C5   112.43  3.000
 593  C5    C3   N2   109.35  3.000
 593  C11   C3   N2   109.47  3.000
 593  C5    C3   C2   110.26  3.000
 593  C11   C3   C2   111.01  3.000
 593  N2    C3   C2   103.96  3.000
 593  HN3A  N3   HN3  113.83  3.000
 593  HN3A  N3   C4   118.76  3.000
 593  HN3   N3   C4   115.35  3.000
 593  N3    C4   N2   126.04  3.000
 593  N3    C4   N1   118.93  3.000
 593  N2    C4   N1   114.95  3.000
 593  C10   C5   C6   118.00  3.000
 593  C10   C5   C3   119.30  3.000
 593  C6    C5   C3   122.70  3.000
 593  H6    C6   C7   118.55  3.000
 593  H6    C6   C5   120.54  3.000
 593  C7    C6   C5   120.91  3.000
 593  H7    C7   C8   120.16  3.000
 593  H7    C7   C6   119.32  3.000
 593  C8    C7   C6   120.53  3.000
 593  H8    C8   C9   120.48  3.000
 593  H8    C8   C7   120.43  3.000
 593  C9    C8   C7   119.08  3.000
 593  H9    C9   C10  119.47  3.000
 593  H9    C9   C8   120.19  3.000
 593  C10   C9   C8   120.34  3.000
 593  H10   C10  C9   119.62  3.000
 593  H10   C10  C5   119.24  3.000
 593  C9    C10  C5   121.14  3.000
 593  C20   C11  C16  108.43  3.000
 593  C16   C11  C12  107.86  3.000
 593  C20   C11  C12  108.29  3.000
 593  C12   C11  C3   109.34  3.000
 593  C16   C11  C3   113.04  3.000
 593  C20   C11  C3   109.75  3.000
 593  H12A  C12  H12  106.70  3.000
 593  H12A  C12  C13  109.31  3.000
 593  H12   C12  C13  109.97  3.000
 593  H12A  C12  C11  110.11  3.000
 593  H12   C12  C11  109.89  3.000
 593  C13   C12  C11  110.76  3.000
 593  H13   C13  C19  109.50  3.000
 593  H13   C13  C14  109.74  3.000
 593  C19   C13  C14  109.51  3.000
 593  H13   C13  C12  108.83  3.000
 593  C14   C13  C12  109.62  3.000
 593  C19   C13  C12  109.62  3.000
 593  H14A  C14  H14  106.72  3.000
 593  H14A  C14  C15  110.20  3.000
 593  H14   C14  C15  110.32  3.000
 593  H14A  C14  C13  110.18  3.000
 593  H14   C14  C13  110.34  3.000
 593  C15   C14  C13  109.08  3.000
 593  H15   C15  C17  109.53  3.000
 593  H15   C15  C16  108.68  3.000
 593  C17   C15  C16  109.93  3.000
 593  H15   C15  C14  109.70  3.000
 593  C16   C15  C14  109.51  3.000
 593  C17   C15  C14  109.48  3.000
 593  H16A  C16  H16  106.85  3.000
 593  H16A  C16  C15  109.61  3.000
 593  H16   C16  C15  108.85  3.000
 593  H16A  C16  C11  110.73  3.000
 593  H16   C16  C11  110.15  3.000
 593  C15   C16  C11  110.55  3.000
 593  H17A  C17  H17  106.71  3.000
 593  H17A  C17  C18  110.18  3.000
 593  H17   C17  C18  110.39  3.000
 593  H17A  C17  C15  110.13  3.000
 593  H17   C17  C15  110.22  3.000
 593  C18   C17  C15  109.19  3.000
 593  H18   C18  C20  108.68  3.000
 593  H18   C18  C19  109.83  3.000
 593  C20   C18  C19  109.53  3.000
 593  H18   C18  C17  109.82  3.000
 593  C19   C18  C17  109.68  3.000
 593  C20   C18  C17  109.29  3.000
 593  H19A  C19  H19  106.69  3.000
 593  H19A  C19  C18  110.30  3.000
 593  H19   C19  C18  110.14  3.000
 593  H19A  C19  C13  110.29  3.000
 593  H19   C19  C13  110.19  3.000
 593  C18   C19  C13  109.21  3.000
 593  H20A  C20  H20  107.21  3.000
 593  H20A  C20  C18  109.50  3.000
 593  H20   C20  C18  108.68  3.000
 593  H20A  C20  C11  109.97  3.000
 593  H20   C20  C11  110.54  3.000
 593  C18   C20  C11  110.85  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
 593  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 593  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 593  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 593  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 593  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 593  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 593  CONST_07  C7   C6   C5   C3   180.00   0.0  0
 593  CONST_08  C9   C10  C5   C3   180.00   0.0  0
 593  CONST_09  C3   N2   C4   N1     0.00   0.0  0
 593  CONST_10  N2   C4   N1   C2     0.00   0.0  0
 593  CONST_11  C4   N1   C2   C3     0.00   0.0  0
 593  CONST_12  N2   C4   N1   C1   180.00   0.0  0
 593  CONST_13  C3   C2   N1   C1   180.00   0.0  0
 593  CONST_14  C4   N1   C2   O1   180.00   0.0  0
 593  CONST_15  N3   C4   N1   C2   180.00   0.0  0
 593  CONST_16  N3   C4   N2   C3   180.00   0.0  0
 593  CONST_17  H6   C6   C5   C3     0.00   0.0  0
 593  CONST_18  H10  C10  C5   C3     0.00   0.0  0
 593  CONST_19  H7   C7   C6   C5   180.00   0.0  0
 593  CONST_20  H9   C9   C10  C5   180.00   0.0  0
 593  CONST_21  H8   C8   C7   C6   180.00   0.0  0
 593  CONST_22  N3   C4   N1   C1     0.00   0.0  0
 593  CONST_23  O1   C2   N1   C1     0.00   0.0  0
 593  CONST_24  HN3  N3   C4   N1   180.00   0.0  0
 593  Var_01    C18  C20  C11  C3   177.52  30.0  3
 593  Var_02    C15  C16  C11  C3   179.87  30.0  1
 593  Var_03    C13  C12  C11  C3  -177.77  30.0  1
 593  Var_04    H1   C1   N1   C2   115.08  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
 593  chir_01  C3   N2   C11  C5   negativ
 593  chir_02  C13  C12  C19  C14  positiv
 593  chir_03  C15  C14  C17  C16  positiv
 593  chir_04  C18  C19  C20  C17  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
 593  plan-1  C3    0.020
 593  plan-1  C5    0.020
 593  plan-1  C6    0.020
 593  plan-1  C7    0.020
 593  plan-1  C8    0.020
 593  plan-1  C9    0.020
 593  plan-1  C10   0.020
 593  plan-1  H6    0.020
 593  plan-1  H7    0.020
 593  plan-1  H8    0.020
 593  plan-1  H9    0.020
 593  plan-1  H10   0.020
 593  plan-2  C1    0.020
 593  plan-2  N1    0.020
 593  plan-2  O1    0.020
 593  plan-2  C2    0.020
 593  plan-2  N2    0.020
 593  plan-2  C3    0.020
 593  plan-2  N3    0.020
 593  plan-2  C4    0.020
 593  plan-2  HN3   0.020
 593  plan-2  HN3A  0.020

