# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:01:34 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(c2)[C@]3(C)CC(=O)N(C)C(=N3)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
 H24  H24  (6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one  ligand  45  24  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H24
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
 H24  C1    C  CH3   0  -0.405  71.7864  47.1746   0.7753
 H24  O2    O  O2    0  -0.470  71.4004  47.7866   1.9896
 H24  C3    C  CR6   0   0.414  71.8839  47.2878   3.1434
 H24  C4    C  CR16  0  -0.379  72.7231  46.1799   3.2297
 H24  C5    C  CR16  0  -0.204  73.1669  45.7642   4.4803
 H24  C6    C  CR16  0  -0.318  72.7916  46.4282   5.6342
 H24  C7    C  CR6   0   0.110  71.9472  47.5399   5.5538
 H24  C8    C  CR16  0  -0.398  71.5020  47.9590   4.3057
 H24  C9    C  CR6   0   0.127  71.5343  48.2630   6.7751
 H24  C10   C  CR16  0  -0.309  72.4307  48.4564   7.8244
 H24  C11   C  CR16  0  -0.202  72.0336  49.1504   8.9569
 H24  C12   C  CR16  0  -0.299  70.7437  49.6491   9.0595
 H24  C13   C  CR6   0   0.172  69.8231  49.4548   8.0306
 H24  C14   C  CT    0  -0.040  68.4109  50.0394   8.1313
 H24  C15   C  CH3   0  -0.594  68.4967  51.5492   7.9069
 H24  C18   C  CH2   0  -0.569  67.7978  49.7514   9.5023
 H24  C19   C  C     0   0.575  67.5891  48.2770   9.6846
 H24  O20   O  O     0  -0.459  67.6938  47.7068  10.7517
 H24  N21   N  NT    0  -0.535  67.2386  47.6087   8.5381
 H24  C22   C  CH3   0  -0.543  66.9963  46.1743   8.5930
 H24  C23   C  C     0   0.636  67.0389  48.3317   7.3533
 H24  N24   N  NH2   0  -0.817  66.3172  47.6777   6.4019
 H24  N25   N  N     0  -0.426  67.5326  49.4852   7.1214
 H24  C26   C  CR16  0  -0.380  70.2384  48.7675   6.8962
 H24  H1C1  H  HCH3  0   0.247  71.3111  47.7416  -0.0213
 H24  H1C2  H  HCH3  0   0.217  72.8694  47.2036   0.6300
 H24  H1C3  H  HCH3  0   0.216  71.4506  46.1361   0.7147
 H24  H4    H  HCR6  0   0.258  73.0367  45.6342   2.3503
 H24  H8    H  HCR6  0   0.239  70.8655  48.8315   4.2161
 H24  H5    H  HCR6  0   0.239  73.8134  44.8987   4.5459
 H24  H6    H  HCR6  0   0.232  73.1333  46.0715   6.5972
 H24  H10   H  HCR6  0   0.234  73.4456  48.0866   7.7497
 H24  H26   H  HCR6  0   0.239  69.5356  48.6073   6.0894
 H24  H11   H  HCR6  0   0.240  72.7379  49.3108   9.7631
 H24  H12   H  HCR6  0   0.225  70.4639  50.1961   9.9512
 H24  H151  H  HCH3  0   0.218  69.1474  52.0239   8.6419
 H24  H152  H  HCH3  0   0.235  68.8938  51.7612   6.9138
 H24  H153  H  HCH3  0   0.223  67.5067  52.0013   7.9839
 H24  H181  H  HCH2  0   0.268  68.3823  50.1344  10.3376
 H24  H182  H  HCH2  0   0.282  66.8192  50.2427   9.5555
 H24  H221  H  HCH3  0   0.258  67.2824  45.7171   7.6502
 H24  H222  H  HCH3  0   0.271  67.6004  45.7396   9.3826
 H24  H223  H  HCH3  0   0.228  65.9490  45.9474   8.7968
 H24  H241  H  HNH2  0   0.366  65.5486  47.0969   6.6988
 H24  H242  H  HNH2  0   0.379  66.1016  48.2398   5.5938

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
 H24  C1   O2    single    1.414  0.020  1.414
 H24  O2   C3    single    1.347  0.020  1.347
 H24  C3   C4    aromatic  1.393  0.020  1.393
 H24  C3   C8    aromatic  1.395  0.020  1.395
 H24  C4   C5    aromatic  1.391  0.020  1.391
 H24  C5   C6    aromatic  1.383  0.020  1.383
 H24  C6   C7    aromatic  1.398  0.020  1.398
 H24  C7   C8    aromatic  1.390  0.020  1.390
 H24  C7   C9    single    1.478  0.020  1.478
 H24  C9   C10   aromatic  1.394  0.020  1.394
 H24  C9   C26   aromatic  1.396  0.020  1.396
 H24  C10  C11   aromatic  1.386  0.020  1.386
 H24  C11  C12   aromatic  1.387  0.020  1.387
 H24  C12  C13   aromatic  1.394  0.020  1.394
 H24  C13  C26   aromatic  1.390  0.020  1.390
 H24  C13  C14   single    1.532  0.020  1.532
 H24  C14  C15   single    1.529  0.020  1.529
 H24  C14  C18   single    1.529  0.020  1.529
 H24  C14  N25   single    1.449  0.020  1.449
 H24  C18  C19   single    1.500  0.020  1.500
 H24  C19  O20   double    1.214  0.020  1.214
 H24  C19  N21   single    1.373  0.020  1.373
 H24  N21  C22   single    1.456  0.020  1.456
 H24  N21  C23   single    1.402  0.020  1.402
 H24  C23  N25   double    1.276  0.020  1.276
 H24  C23  N24   single    1.362  0.020  1.362
 H24  C1   H1C1  single    0.970  0.020  1.090
 H24  C1   H1C2  single    0.970  0.020  1.090
 H24  C1   H1C3  single    0.970  0.020  1.090
 H24  C4   H4    single    0.930  0.020  1.080
 H24  C8   H8    single    0.930  0.020  1.080
 H24  C5   H5    single    0.930  0.020  1.080
 H24  C6   H6    single    0.930  0.020  1.080
 H24  C10  H10   single    0.930  0.020  1.080
 H24  C26  H26   single    0.930  0.020  1.080
 H24  C11  H11   single    0.930  0.020  1.080
 H24  C12  H12   single    0.930  0.020  1.080
 H24  C15  H151  single    0.970  0.020  1.090
 H24  C15  H152  single    0.970  0.020  1.090
 H24  C15  H153  single    0.970  0.020  1.090
 H24  C18  H181  single    0.970  0.020  1.090
 H24  C18  H182  single    0.970  0.020  1.090
 H24  C22  H221  single    0.970  0.020  1.090
 H24  C22  H222  single    0.970  0.020  1.090
 H24  C22  H223  single    0.970  0.020  1.090
 H24  N24  H241  single    0.890  0.020  1.040
 H24  N24  H242  single    0.890  0.020  1.040

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
 H24  H1C3  C1   H1C2  108.79  3.000
 H24  H1C3  C1   H1C1  108.70  3.000
 H24  H1C2  C1   H1C1  108.78  3.000
 H24  H1C3  C1   O2    112.03  3.000
 H24  H1C2  C1   O2    111.92  3.000
 H24  H1C1  C1   O2    106.52  3.000
 H24  C3    O2   C1    118.53  3.000
 H24  C8    C3   C4    119.74  3.000
 H24  C8    C3   O2    115.92  3.000
 H24  C4    C3   O2    124.34  3.000
 H24  H4    C4   C5    119.21  3.000
 H24  H4    C4   C3    121.72  3.000
 H24  C5    C4   C3    119.07  3.000
 H24  H5    C5   C6    119.70  3.000
 H24  H5    C5   C4    118.96  3.000
 H24  C6    C5   C4    121.35  3.000
 H24  H6    C6   C7    120.25  3.000
 H24  H6    C6   C5    119.90  3.000
 H24  C7    C6   C5    119.83  3.000
 H24  C9    C7   C8    120.33  3.000
 H24  C9    C7   C6    120.67  3.000
 H24  C8    C7   C6    119.00  3.000
 H24  H8    C8   C7    120.34  3.000
 H24  H8    C8   C3    118.63  3.000
 H24  C7    C8   C3    121.02  3.000
 H24  C26   C9   C10   118.80  3.000
 H24  C26   C9   C7    120.52  3.000
 H24  C10   C9   C7    120.68  3.000
 H24  H10   C10  C11   119.72  3.000
 H24  H10   C10  C9    120.24  3.000
 H24  C11   C10  C9    120.03  3.000
 H24  H11   C11  C12   119.79  3.000
 H24  H11   C11  C10   119.75  3.000
 H24  C12   C11  C10   120.45  3.000
 H24  H12   C12  C13   120.49  3.000
 H24  H12   C12  C11   118.88  3.000
 H24  C13   C12  C11   120.63  3.000
 H24  C26   C13  C14   121.19  3.000
 H24  C14   C13  C12   120.48  3.000
 H24  C26   C13  C12   118.28  3.000
 H24  N25   C14  C18   108.05  3.000
 H24  N25   C14  C15   108.03  3.000
 H24  C18   C14  C15   109.88  3.000
 H24  N25   C14  C13   111.54  3.000
 H24  C18   C14  C13   110.90  3.000
 H24  C15   C14  C13   108.40  3.000
 H24  H153  C15  H152  108.31  3.000
 H24  H153  C15  H151  108.28  3.000
 H24  H152  C15  H151  108.18  3.000
 H24  H153  C15  C14   110.36  3.000
 H24  H152  C15  C14   110.25  3.000
 H24  H151  C15  C14   111.37  3.000
 H24  H182  C18  H181  106.52  3.000
 H24  H182  C18  C19   108.08  3.000
 H24  H181  C18  C19   109.09  3.000
 H24  H182  C18  C14   108.48  3.000
 H24  H181  C18  C14   113.96  3.000
 H24  C19   C18  C14   110.47  3.000
 H24  N21   C19  O20   121.84  3.000
 H24  N21   C19  C18   114.36  3.000
 H24  O20   C19  C18   123.79  3.000
 H24  C23   N21  C22   121.08  3.000
 H24  C23   N21  C19   119.41  3.000
 H24  C22   N21  C19   119.39  3.000
 H24  H223  C22  H222  108.38  3.000
 H24  H223  C22  H221  109.12  3.000
 H24  H222  C22  H221  108.44  3.000
 H24  H223  C22  N21   111.83  3.000
 H24  H222  C22  N21   109.24  3.000
 H24  H221  C22  N21   109.77  3.000
 H24  N25   C23  N24   120.82  3.000
 H24  N24   C23  N21   114.72  3.000
 H24  N25   C23  N21   124.38  3.000
 H24  H242  N24  H241  113.23  3.000
 H24  H242  N24  C23   113.94  3.000
 H24  H241  N24  C23   118.37  3.000
 H24  C23   N25  C14   116.98  3.000
 H24  H26   C26  C13   119.19  3.000
 H24  H26   C26  C9    119.00  3.000
 H24  C13   C26  C9    121.80  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
 H24  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 H24  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 H24  CONST_03  C9    C7   C8   C3    180.00   0.0  0
 H24  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 H24  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 H24  CONST_06  C8    C3   C4   C5      0.00   0.0  0
 H24  CONST_07  C8    C7   C6   C5      0.00   0.0  0
 H24  CONST_08  C9    C7   C6   C5    180.00   0.0  0
 H24  CONST_11  C11   C10  C9   C7    180.00   0.0  0
 H24  CONST_12  C13   C26  C9   C7    180.00   0.0  0
 H24  CONST_15  C12   C11  C10  C9      0.00   0.0  0
 H24  CONST_16  C12   C13  C26  C9      0.00   0.0  0
 H24  CONST_17  C13   C26  C9   C10     0.00   0.0  0
 H24  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 H24  CONST_19  C26   C9   C10  C11     0.00   0.0  0
 H24  CONST_20  C26   C13  C12  C11     0.00   0.0  0
 H24  CONST_21  C14   C13  C26  C9    180.00   0.0  0
 H24  CONST_22  C14   C13  C12  C11   180.00   0.0  0
 H24  CONST_23  N21   C23  N25  C14     0.00   0.0  0
 H24  CONST_24  C23   N21  C19  C18     0.00   0.0  0
 H24  CONST_26  C5    C4   C3   O2    180.00   0.0  0
 H24  CONST_27  C7    C8   C3   O2    180.00   0.0  0
 H24  CONST_28  N24   C23  N25  C14   180.00   0.0  0
 H24  CONST_29  C22   N21  C19  C18   180.00   0.0  0
 H24  CONST_31  C23   N21  C19  O20   180.00   0.0  0
 H24  CONST_33  H5    C5   C4   C3    180.00   0.0  0
 H24  CONST_34  H8    C8   C3   C4    180.00   0.0  0
 H24  CONST_35  H6    C6   C5   C4    180.00   0.0  0
 H24  CONST_36  H4    C4   C5   C6    180.00   0.0  0
 H24  CONST_37  H10   C10  C9   C7      0.00   0.0  0
 H24  CONST_38  H26   C26  C9   C7      0.00   0.0  0
 H24  CONST_39  H11   C11  C10  C9    180.00   0.0  0
 H24  CONST_40  H12   C12  C11  C10   180.00   0.0  0
 H24  CONST_41  C22   N21  C19  O20     0.00   0.0  0
 H24  CONST_44  H242  N24  C23  N21   180.00   0.0  0
 H24  Var_01    H181  C18  C19  N21  -161.01  30.0  1
 H24  Var_02    C4    C3   O2   C1     -1.55  30.0  2
 H24  Var_03    H221  C22  N21  C19  -148.19  30.0  3
 H24  Var_04    H1C1  C1   O2   C3   -178.54  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
 H24  chir_01  C14  C13  C18  N25  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
 H24  plan-1  O2    0.020
 H24  plan-1  C3    0.020
 H24  plan-1  C4    0.020
 H24  plan-1  C5    0.020
 H24  plan-1  C6    0.020
 H24  plan-1  C7    0.020
 H24  plan-1  C8    0.020
 H24  plan-1  C9    0.020
 H24  plan-1  H4    0.020
 H24  plan-1  H8    0.020
 H24  plan-1  H5    0.020
 H24  plan-1  H6    0.020
 H24  plan-2  C7    0.020
 H24  plan-2  C9    0.020
 H24  plan-2  C10   0.020
 H24  plan-2  C11   0.020
 H24  plan-2  C12   0.020
 H24  plan-2  C13   0.020
 H24  plan-2  C14   0.020
 H24  plan-2  C26   0.020
 H24  plan-2  H10   0.020
 H24  plan-2  H26   0.020
 H24  plan-2  H11   0.020
 H24  plan-2  H12   0.020
 H24  plan-3  C14   0.020
 H24  plan-3  C18   0.020
 H24  plan-3  C19   0.020
 H24  plan-3  O20   0.020
 H24  plan-3  N21   0.020
 H24  plan-3  C22   0.020
 H24  plan-3  C23   0.020
 H24  plan-3  N24   0.020
 H24  plan-3  N25   0.020
 H24  plan-3  H241  0.020
 H24  plan-3  H242  0.020

