# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:39:27 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: (5R)-2-amino-5-(4-methoxyphenyl)-3-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@]2(N=C(N)N(C)C2=O)C34CC5CC(CC(C5)C3)C4
#
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
 QL1  QL1  (5R)-2-amino-5-(4-methoxyphenyl)-3-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl]-3,5-dihydro-4H-imidazol-4-one  ligand  53  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QL1
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
 QL1  N1   N  NR5   0  -0.520  15.1509  -47.0170  -16.4206
 QL1  C4   C  CH1   0  -0.244  14.4719  -42.1176  -16.0165
 QL1  C5   C  CH2   0  -0.426  14.5033  -43.6465  -16.0961
 QL1  C6   C  CH2   0  -0.416  13.2519  -41.6719  -15.2104
 QL1  C7   C  CH1   0  -0.245  11.9822  -42.1749  -15.8977
 QL1  C8   C  CH2   0  -0.403  12.0133  -43.7035  -15.9747
 QL1  C10  C  CR5   0  -0.145  13.2539  -45.7557  -16.7937
 QL1  C13  C  CR16  0  -0.375  10.8655  -46.9740  -19.5525
 QL1  C15  C  CR16  0  -0.332   9.8283  -47.3171  -17.4174
 QL1  C20  C  CH3   0  -0.555  16.4219  -47.6911  -16.5259
 QL1  O1   O  O     0  -0.450  15.0074  -46.1517  -18.5286
 QL1  C19  C  CR5   0   0.576  14.5543  -46.2962  -17.4134
 QL1  C18  C  CR5   0   0.663  14.3532  -46.9345  -15.2863
 QL1  N2   N  NH2   0  -0.846  14.7840  -47.5072  -14.1420
 QL1  N    N  N     0  -0.461  13.2848  -46.2490  -15.4280
 QL1  C11  C  CR6   0   0.113  12.0514  -46.3510  -17.5233
 QL1  C16  C  CR16  0  -0.279  10.9486  -46.7999  -16.7940
 QL1  C14  C  CR6   0   0.369   9.7748  -47.4112  -18.8083
 QL1  O    O  O2    0  -0.473   8.6495  -47.9331  -19.3354
 QL1  C12  C  CR16  0  -0.283  11.9821  -46.4523  -18.9083
 QL1  C    C  CT    0  -0.046  13.2330  -44.1840  -16.7788
 QL1  C3   C  CH2   0  -0.416  14.3961  -41.5356  -17.4276
 QL1  C9   C  CH2   0  -0.416  11.9015  -41.5880  -17.3072
 QL1  C2   C  CH1   0  -0.242  13.1231  -42.0385  -18.1072
 QL1  C1   C  CH2   0  -0.421  13.1470  -43.5686  -18.1847
 QL1  H1   H  HCH1  0   0.221  15.3859  -41.7716  -15.5240
 QL1  H3   H  HCH2  0   0.225  15.3982  -43.9536  -16.6493
 QL1  H4   H  HCH2  0   0.219  13.3112  -42.0635  -14.1899
 QL1  H5   H  HCH2  0   0.220  13.2314  -40.5800  -15.1275
 QL1  H6   H  HCH1  0   0.219  11.1045  -41.8668  -15.3210
 QL1  H7   H  HCH2  0   0.227  11.0926  -44.0658  -16.4425
 QL1  H8   H  HCH2  0   0.229  12.0437  -44.1240  -14.9674
 QL1  H9   H  HCR6  0   0.274  10.8713  -47.0300  -20.6328
 QL1  H10  H  HCR6  0   0.256   8.9864  -47.6580  -16.8271
 QL1  H11  H  HCH3  0   0.258   7.5956  -48.5134  -20.9503
 QL1  H12  H  HCH3  0   0.227   8.6219  -47.0993  -21.2473
 QL1  H13  H  HCH3  0   0.227   9.3460  -48.7183  -21.1373
 QL1  H14  H  HCH3  0   0.260  16.3151  -48.7609  -16.3478
 QL1  H15  H  HCH3  0   0.273  16.8038  -47.5512  -17.5330
 QL1  H16  H  HCH3  0   0.263  17.1424  -47.2793  -15.8202
 QL1  H17  H  HNH2  0   0.401  14.1068  -47.5565  -13.3983
 QL1  H18  H  HNH2  0   0.407  15.3938  -48.3069  -14.1933
 QL1  H19  H  HCR6  0   0.252  10.9704  -46.7455  -15.7149
 QL1  H20  H  HCR6  0   0.261  12.8085  -46.1253  -19.5221
 QL1  H21  H  HCH2  0   0.218  15.2762  -41.8356  -18.0061
 QL1  H22  H  HCH2  0   0.220  14.4006  -40.4414  -17.3900
 QL1  H23  H  HCH2  0   0.219  11.8559  -40.4949  -17.2629
 QL1  H24  H  HCH2  0   0.218  10.9828  -41.9204  -17.8024
 QL1  H25  H  HCH1  0   0.220  13.0651  -41.6412  -19.1250
 QL1  H26  H  HCH2  0   0.231  12.2394  -43.9102  -18.6889
 QL1  H27  H  HCH2  0   0.232  13.9920  -43.8880  -18.7985
 QL1  H2   H  HCH2  0   0.232  14.5971  -44.0585  -15.0875
 QL1  C17  C  CH3   0  -0.435   8.5640  -48.0660  -20.7396

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
 QL1  C17  O    single    1.413  0.020  1.413
 QL1  C13  C14  aromatic  1.391  0.020  1.391
 QL1  C13  C12  aromatic  1.391  0.020  1.391
 QL1  O    C14  single    1.348  0.020  1.348
 QL1  C14  C15  aromatic  1.395  0.020  1.395
 QL1  C12  C11  aromatic  1.390  0.020  1.390
 QL1  O1   C19  double    1.212  0.020  1.212
 QL1  C1   C2   single    1.532  0.020  1.532
 QL1  C1   C    single    1.537  0.020  1.537
 QL1  C2   C3   single    1.528  0.020  1.528
 QL1  C2   C9   single    1.528  0.020  1.528
 QL1  C3   C4   single    1.528  0.020  1.528
 QL1  C15  C16  aromatic  1.382  0.020  1.382
 QL1  C11  C16  aromatic  1.396  0.020  1.396
 QL1  C11  C10  single    1.527  0.020  1.527
 QL1  C19  C10  single    1.539  0.020  1.539
 QL1  C19  N1   single    1.364  0.020  1.364
 QL1  C9   C7   single    1.529  0.020  1.529
 QL1  C10  C    single    1.572  0.020  1.572
 QL1  C10  N    single    1.452  0.020  1.452
 QL1  C    C5   single    1.539  0.020  1.539
 QL1  C    C8   single    1.538  0.020  1.538
 QL1  C20  N1   single    1.443  0.020  1.443
 QL1  N1   C18  single    1.389  0.020  1.389
 QL1  C5   C4   single    1.531  0.020  1.531
 QL1  C4   C6   single    1.529  0.020  1.529
 QL1  C8   C7   single    1.531  0.020  1.531
 QL1  C7   C6   single    1.529  0.020  1.529
 QL1  N    C18  double    1.277  0.020  1.277
 QL1  C18  N2   single    1.350  0.020  1.350
 QL1  C4   H1   single    0.970  0.020  1.090
 QL1  C5   H2   single    0.970  0.020  1.090
 QL1  C5   H3   single    0.970  0.020  1.090
 QL1  C6   H4   single    0.970  0.020  1.090
 QL1  C6   H5   single    0.970  0.020  1.090
 QL1  C7   H6   single    0.970  0.020  1.090
 QL1  C8   H7   single    0.970  0.020  1.090
 QL1  C8   H8   single    0.970  0.020  1.090
 QL1  C13  H9   single    0.930  0.020  1.080
 QL1  C15  H10  single    0.930  0.020  1.080
 QL1  C17  H11  single    0.970  0.020  1.090
 QL1  C17  H12  single    0.970  0.020  1.090
 QL1  C17  H13  single    0.970  0.020  1.090
 QL1  C20  H14  single    0.970  0.020  1.090
 QL1  C20  H15  single    0.970  0.020  1.090
 QL1  C20  H16  single    0.970  0.020  1.090
 QL1  N2   H17  single    0.890  0.020  1.040
 QL1  N2   H18  single    0.890  0.020  1.040
 QL1  C16  H19  single    0.930  0.020  1.080
 QL1  C12  H20  single    0.930  0.020  1.080
 QL1  C3   H21  single    0.970  0.020  1.090
 QL1  C3   H22  single    0.970  0.020  1.090
 QL1  C9   H23  single    0.970  0.020  1.090
 QL1  C9   H24  single    0.970  0.020  1.090
 QL1  C2   H25  single    0.970  0.020  1.090
 QL1  C1   H26  single    0.970  0.020  1.090
 QL1  C1   H27  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
 QL1  C18  N1   C19  108.16  3.000
 QL1  C18  N1   C20  126.40  3.000
 QL1  C19  N1   C20  125.38  3.000
 QL1  H1   C4   C3   109.67  3.000
 QL1  H1   C4   C6   109.69  3.000
 QL1  C3   C4   C6   109.65  3.000
 QL1  H1   C4   C5   108.79  3.000
 QL1  C6   C4   C5   109.56  3.000
 QL1  C3   C4   C5   109.47  3.000
 QL1  H3   C5   H2   106.85  3.000
 QL1  H3   C5   C    110.61  3.000
 QL1  H2   C5   C    110.39  3.000
 QL1  H3   C5   C4   108.83  3.000
 QL1  H2   C5   C4   109.27  3.000
 QL1  C    C5   C4   110.79  3.000
 QL1  H5   C6   H4   106.68  3.000
 QL1  H5   C6   C7   110.27  3.000
 QL1  H4   C6   C7   110.26  3.000
 QL1  H5   C6   C4   110.22  3.000
 QL1  H4   C6   C4   110.12  3.000
 QL1  C7   C6   C4   109.26  3.000
 QL1  H6   C7   C9   109.60  3.000
 QL1  H6   C7   C8   108.90  3.000
 QL1  C9   C7   C8   109.75  3.000
 QL1  H6   C7   C6   109.66  3.000
 QL1  C8   C7   C6   109.53  3.000
 QL1  C9   C7   C6   109.39  3.000
 QL1  H8   C8   H7   106.87  3.000
 QL1  H8   C8   C    109.87  3.000
 QL1  H7   C8   C    109.90  3.000
 QL1  H8   C8   C7   109.80  3.000
 QL1  H7   C8   C7   109.57  3.000
 QL1  C    C8   C7   110.76  3.000
 QL1  C    C10  C11  112.57  3.000
 QL1  C    C10  N    109.33  3.000
 QL1  C11  C10  N    109.48  3.000
 QL1  N    C10  C19  103.97  3.000
 QL1  C    C10  C19  111.49  3.000
 QL1  C11  C10  C19  109.64  3.000
 QL1  H9   C13  C12  118.54  3.000
 QL1  H9   C13  C14  121.48  3.000
 QL1  C12  C13  C14  119.98  3.000
 QL1  H10  C15  C14  119.48  3.000
 QL1  H10  C15  C16  120.12  3.000
 QL1  C14  C15  C16  120.39  3.000
 QL1  H16  C20  H15  108.63  3.000
 QL1  H16  C20  H14  109.27  3.000
 QL1  H15  C20  H14  108.21  3.000
 QL1  H16  C20  N1   111.02  3.000
 QL1  H15  C20  N1   108.50  3.000
 QL1  H14  C20  N1   111.13  3.000
 QL1  O1   C19  C10  130.13  3.000
 QL1  C10  C19  N1   105.20  3.000
 QL1  O1   C19  N1   124.68  3.000
 QL1  N    C18  N2   126.06  3.000
 QL1  N2   C18  N1   118.92  3.000
 QL1  N    C18  N1   114.94  3.000
 QL1  H18  N2   H17  113.95  3.000
 QL1  H18  N2   C18  119.14  3.000
 QL1  H17  N2   C18  115.60  3.000
 QL1  C18  N    C10  107.72  3.000
 QL1  C12  C11  C16  117.22  3.000
 QL1  C16  C11  C10  119.84  3.000
 QL1  C12  C11  C10  122.92  3.000
 QL1  H19  C16  C11  119.31  3.000
 QL1  H19  C16  C15  119.04  3.000
 QL1  C11  C16  C15  121.65  3.000
 QL1  O    C14  C15  116.62  3.000
 QL1  C15  C14  C13  118.82  3.000
 QL1  O    C14  C13  124.56  3.000
 QL1  C14  O    C17  118.40  3.000
 QL1  H20  C12  C11  120.38  3.000
 QL1  H20  C12  C13  117.69  3.000
 QL1  C11  C12  C13  121.92  3.000
 QL1  C1   C    C10  113.10  3.000
 QL1  C10  C    C8   109.14  3.000
 QL1  C1   C    C8   107.98  3.000
 QL1  C8   C    C5   108.27  3.000
 QL1  C10  C    C5   110.03  3.000
 QL1  C1   C    C5   108.19  3.000
 QL1  H22  C3   H21  106.78  3.000
 QL1  H22  C3   C2   110.34  3.000
 QL1  H21  C3   C2   110.14  3.000
 QL1  H22  C3   C4   110.41  3.000
 QL1  H21  C3   C4   110.09  3.000
 QL1  C2   C3   C4   109.06  3.000
 QL1  H24  C9   H23  106.64  3.000
 QL1  H24  C9   C2   110.15  3.000
 QL1  H23  C9   C2   110.41  3.000
 QL1  H24  C9   C7   110.15  3.000
 QL1  H23  C9   C7   110.37  3.000
 QL1  C2   C9   C7   109.11  3.000
 QL1  H25  C2   C1   108.45  3.000
 QL1  H25  C2   C9   109.73  3.000
 QL1  C1   C2   C9   109.47  3.000
 QL1  H25  C2   C3   109.78  3.000
 QL1  C9   C2   C3   109.64  3.000
 QL1  C1   C2   C3   109.76  3.000
 QL1  H27  C1   H26  106.96  3.000
 QL1  H27  C1   C2   109.42  3.000
 QL1  H26  C1   C2   108.81  3.000
 QL1  H27  C1   C    110.72  3.000
 QL1  H26  C1   C    110.08  3.000
 QL1  C2   C1   C    110.76  3.000
 QL1  H13  C17  H12  108.70  3.000
 QL1  H13  C17  H11  108.72  3.000
 QL1  H12  C17  H11  108.73  3.000
 QL1  H13  C17  O    111.98  3.000
 QL1  H12  C17  O    112.03  3.000
 QL1  H11  C17  O    106.57  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
 QL1  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 QL1  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 QL1  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 QL1  CONST_04  C12  C11  C16  C15     0.00   0.0  0
 QL1  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 QL1  CONST_06  C14  C15  C16  C11     0.00   0.0  0
 QL1  CONST_07  C13  C12  C11  C10   180.00   0.0  0
 QL1  CONST_08  C15  C16  C11  C10   180.00   0.0  0
 QL1  CONST_09  C10  N    C18  N1      0.00   0.0  0
 QL1  CONST_10  C18  N1   C19  C10     0.00   0.0  0
 QL1  CONST_11  N    C18  N1   C19     0.00   0.0  0
 QL1  CONST_12  O    C14  C15  C16   180.00   0.0  0
 QL1  CONST_13  C12  C13  C14  O     180.00   0.0  0
 QL1  CONST_14  C20  N1   C19  C10   180.00   0.0  0
 QL1  CONST_15  N2   C18  N    C10   180.00   0.0  0
 QL1  CONST_16  N    C18  N1   C20   180.00   0.0  0
 QL1  CONST_17  C18  N1   C19  O1    180.00   0.0  0
 QL1  CONST_18  N2   C18  N1   C19   180.00   0.0  0
 QL1  CONST_19  H20  C12  C11  C10     0.00   0.0  0
 QL1  CONST_20  H19  C16  C11  C10     0.00   0.0  0
 QL1  CONST_21  H10  C15  C14  C13   180.00   0.0  0
 QL1  CONST_22  H9   C13  C14  C15   180.00   0.0  0
 QL1  CONST_23  O1   C19  N1   C20     0.00   0.0  0
 QL1  CONST_24  N2   C18  N1   C20     0.00   0.0  0
 QL1  CONST_25  H17  N2   C18  N1    180.00   0.0  0
 QL1  Var_01    C1   C    C5   C4     58.50  30.0  1
 QL1  Var_02    C2   C1   C    C5    -58.14  30.0  3
 QL1  Var_03    C7   C8   C    C5     58.39  30.0  1
 QL1  Var_04    H14  C20  N1   C19  -120.50  30.0  3
 QL1  Var_05    H11  C17  O    C14   179.25  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
 QL1  chir_01  C4   C3   C5   C6  positiv
 QL1  chir_02  C7   C6   C8   C9  positiv
 QL1  chir_03  C10  C11  C19  C   negativ
 QL1  chir_04  C2   C1   C3   C9  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
 QL1  plan-1  C10  0.020
 QL1  plan-1  C13  0.020
 QL1  plan-1  C15  0.020
 QL1  plan-1  C11  0.020
 QL1  plan-1  C16  0.020
 QL1  plan-1  C14  0.020
 QL1  plan-1  O    0.020
 QL1  plan-1  C12  0.020
 QL1  plan-1  H9   0.020
 QL1  plan-1  H10  0.020
 QL1  plan-1  H19  0.020
 QL1  plan-1  H20  0.020
 QL1  plan-2  N1   0.020
 QL1  plan-2  C10  0.020
 QL1  plan-2  C20  0.020
 QL1  plan-2  O1   0.020
 QL1  plan-2  C19  0.020
 QL1  plan-2  C18  0.020
 QL1  plan-2  N2   0.020
 QL1  plan-2  N    0.020
 QL1  plan-2  H17  0.020
 QL1  plan-2  H18  0.020

