# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 16:45:32 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C[C@@](C)(CCc2ccccc2)N=C1N
#
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
 0B3  0B3  (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one  ligand  37  18  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0B3
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
 0B3  O    O  O     0  -0.458   3.9618  -1.7567   1.0132
 0B3  C5   C  C     0   0.554   3.1191  -0.9458   0.6817
 0B3  N3   N  NT    0  -0.542   3.4528   0.2857   0.1747
 0B3  C4   C  CH3   0  -0.574   4.8531   0.6643   0.0659
 0B3  C3   C  C     0   0.631   2.4379   1.1981  -0.1667
 0B3  N2   N  NH2   0  -0.842   2.8322   2.5030  -0.2240
 0B3  N1   N  N     0  -0.457   1.2205   0.8876  -0.3682
 0B3  C6   C  CH2   0  -0.574   1.6453  -1.1825   0.8383
 0B3  C2   C  CT    0   0.034   0.8365  -0.5050  -0.2662
 0B3  C1   C  CH3   0  -0.653   1.0818  -1.2135  -1.6034
 0B3  C7   C  CH2   0  -0.387  -0.6475  -0.5768   0.1144
 0B3  C8   C  CH2   0  -0.519  -1.5969   0.1165  -0.8631
 0B3  C9   C  CR6   0   0.143  -3.0085   0.1150  -0.3466
 0B3  C14  C  CR16  0  -0.317  -3.9107  -0.8715  -0.7356
 0B3  C13  C  CR16  0  -0.240  -5.2047  -0.8969  -0.2303
 0B3  C12  C  CR16  0  -0.276  -5.6173   0.0685   0.6783
 0B3  C11  C  CR16  0  -0.240  -4.7263   1.0583   1.0754
 0B3  C10  C  CR16  0  -0.311  -3.4348   1.0782   0.5671
 0B3  H1   H  HCH3  0   0.261   5.0659   1.0668  -0.9233
 0B3  H2   H  HCH3  0   0.259   5.1280   1.3999   0.8223
 0B3  H3   H  HCH3  0   0.281   5.4690  -0.2157   0.2089
 0B3  H4   H  HNH2  0   0.409   3.7887   2.7333  -0.4306
 0B3  H5   H  HNH2  0   0.391   2.1674   3.1137  -0.6701
 0B3  H6   H  HCH2  0   0.272   1.4649  -2.2573   0.8818
 0B3  H7   H  HCH2  0   0.283   1.3528  -0.7670   1.8105
 0B3  H8   H  HCH3  0   0.225   0.7352  -2.2477  -1.5617
 0B3  H9   H  HCH3  0   0.241   0.5579  -0.7124  -2.4166
 0B3  H10  H  HCH3  0   0.232   2.1421  -1.2276  -1.8638
 0B3  H11  H  HCH2  0   0.226  -0.9372  -1.6279   0.2174
 0B3  H12  H  HCH2  0   0.227  -0.7687  -0.1249   1.1042
 0B3  H13  H  HCH2  0   0.243  -1.2554   1.1409  -1.0238
 0B3  H14  H  HCH2  0   0.239  -1.5700  -0.3842  -1.8331
 0B3  H15  H  HCR6  0   0.243  -3.5987  -1.6285  -1.4464
 0B3  H16  H  HCR6  0   0.251  -5.8923  -1.6697  -0.5503
 0B3  H17  H  HCR6  0   0.252  -6.6257   0.0521   1.0715
 0B3  H18  H  HCR6  0   0.251  -5.0390   1.8186   1.7801
 0B3  H19  H  HCR6  0   0.243  -2.7471   1.8547   0.8833

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
 0B3  O    C5   double    1.216  0.020  1.216
 0B3  C6   C5   single    1.501  0.020  1.501
 0B3  C6   C2   single    1.527  0.020  1.527
 0B3  C5   N3   single    1.373  0.020  1.373
 0B3  C1   C2   single    1.533  0.020  1.533
 0B3  C2   C7   single    1.534  0.020  1.534
 0B3  C2   N1   single    1.448  0.020  1.448
 0B3  C7   C8   single    1.529  0.020  1.529
 0B3  N3   C4   single    1.455  0.020  1.455
 0B3  N3   C3   single    1.407  0.020  1.407
 0B3  C14  C13  aromatic  1.389  0.020  1.389
 0B3  C14  C9   aromatic  1.392  0.020  1.392
 0B3  C13  C12  aromatic  1.388  0.020  1.388
 0B3  N1   C3   double    1.272  0.020  1.272
 0B3  C8   C9   single    1.503  0.020  1.503
 0B3  C3   N2   single    1.364  0.020  1.364
 0B3  C9   C10  aromatic  1.394  0.020  1.394
 0B3  C12  C11  aromatic  1.390  0.020  1.390
 0B3  C10  C11  aromatic  1.388  0.020  1.388
 0B3  C4   H1   single    0.970  0.020  1.090
 0B3  C4   H2   single    0.970  0.020  1.090
 0B3  C4   H3   single    0.970  0.020  1.090
 0B3  N2   H4   single    0.890  0.020  1.040
 0B3  N2   H5   single    0.890  0.020  1.040
 0B3  C6   H6   single    0.970  0.020  1.090
 0B3  C6   H7   single    0.970  0.020  1.090
 0B3  C1   H8   single    0.970  0.020  1.090
 0B3  C1   H9   single    0.970  0.020  1.090
 0B3  C1   H10  single    0.970  0.020  1.090
 0B3  C7   H11  single    0.970  0.020  1.090
 0B3  C7   H12  single    0.970  0.020  1.090
 0B3  C8   H13  single    0.970  0.020  1.090
 0B3  C8   H14  single    0.970  0.020  1.090
 0B3  C14  H15  single    0.930  0.020  1.080
 0B3  C13  H16  single    0.930  0.020  1.080
 0B3  C12  H17  single    0.930  0.020  1.080
 0B3  C11  H18  single    0.930  0.020  1.080
 0B3  C10  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
 0B3  C6   C5   N3   114.75  3.000
 0B3  N3   C5   O    122.04  3.000
 0B3  C6   C5   O    123.17  3.000
 0B3  C3   N3   C4   120.50  3.000
 0B3  C3   N3   C5   119.74  3.000
 0B3  C4   N3   C5   119.67  3.000
 0B3  H3   C4   H2   108.24  3.000
 0B3  H3   C4   H1   108.00  3.000
 0B3  H2   C4   H1   109.36  3.000
 0B3  H3   C4   N3   109.02  3.000
 0B3  H2   C4   N3   111.50  3.000
 0B3  H1   C4   N3   110.63  3.000
 0B3  N1   C3   N2   120.21  3.000
 0B3  N2   C3   N3   114.96  3.000
 0B3  N1   C3   N3   124.78  3.000
 0B3  H5   N2   H4   113.46  3.000
 0B3  H5   N2   C3   114.07  3.000
 0B3  H4   N2   C3   120.18  3.000
 0B3  C2   N1   C3   118.50  3.000
 0B3  H7   C6   H6   107.08  3.000
 0B3  H7   C6   C2   109.37  3.000
 0B3  H6   C6   C2   112.24  3.000
 0B3  H7   C6   C5   107.13  3.000
 0B3  H6   C6   C5   108.78  3.000
 0B3  C2   C6   C5   112.00  3.000
 0B3  C7   C2   C1   110.46  3.000
 0B3  C7   C2   C6   108.19  3.000
 0B3  C1   C2   C6   109.94  3.000
 0B3  C7   C2   N1   108.60  3.000
 0B3  C1   C2   N1   109.92  3.000
 0B3  C6   C2   N1   109.70  3.000
 0B3  H10  C1   H9   107.15  3.000
 0B3  H10  C1   H8   107.77  3.000
 0B3  H9   C1   H8   108.16  3.000
 0B3  H10  C1   C2   111.68  3.000
 0B3  H9   C1   C2   111.19  3.000
 0B3  H8   C1   C2   110.72  3.000
 0B3  H12  C7   H11  106.36  3.000
 0B3  H12  C7   C8   108.79  3.000
 0B3  H11  C7   C8   109.34  3.000
 0B3  H12  C7   C2   108.19  3.000
 0B3  H11  C7   C2   108.92  3.000
 0B3  C8   C7   C2   114.90  3.000
 0B3  H14  C8   H13  106.96  3.000
 0B3  H14  C8   C9   109.14  3.000
 0B3  H13  C8   C9   110.20  3.000
 0B3  H14  C8   C7   110.16  3.000
 0B3  H13  C8   C7   108.99  3.000
 0B3  C9   C8   C7   111.29  3.000
 0B3  C10  C9   C14  118.32  3.000
 0B3  C10  C9   C8   120.77  3.000
 0B3  C14  C9   C8   120.88  3.000
 0B3  H15  C14  C13  119.58  3.000
 0B3  H15  C14  C9   119.43  3.000
 0B3  C13  C14  C9   120.99  3.000
 0B3  H16  C13  C12  120.06  3.000
 0B3  H16  C13  C14  119.80  3.000
 0B3  C12  C13  C14  120.14  3.000
 0B3  H17  C12  C11  120.28  3.000
 0B3  H17  C12  C13  120.26  3.000
 0B3  C11  C12  C13  119.45  3.000
 0B3  H18  C11  C10  119.80  3.000
 0B3  H18  C11  C12  120.06  3.000
 0B3  C10  C11  C12  120.14  3.000
 0B3  H19  C10  C11  119.57  3.000
 0B3  H19  C10  C9   119.46  3.000
 0B3  C11  C10  C9   120.97  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
 0B3  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 0B3  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 0B3  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 0B3  CONST_04  C11  C10  C9   C14     0.00   0.0  0
 0B3  CONST_05  C10  C9   C14  C13     0.00   0.0  0
 0B3  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 0B3  CONST_08  C2   N1   C3   N3      0.00   0.0  0
 0B3  CONST_09  C6   C5   N3   C3      0.00   0.0  0
 0B3  CONST_10  C13  C14  C9   C8    180.00   0.0  0
 0B3  CONST_11  C11  C10  C9   C8    180.00   0.0  0
 0B3  CONST_12  C3   N3   C5   O     180.00   0.0  0
 0B3  CONST_14  C6   C5   N3   C4    180.00   0.0  0
 0B3  CONST_16  C2   N1   C3   N2    180.00   0.0  0
 0B3  CONST_17  H16  C13  C14  C9    180.00   0.0  0
 0B3  CONST_18  H18  C11  C10  C9    180.00   0.0  0
 0B3  CONST_19  H17  C12  C13  C14   180.00   0.0  0
 0B3  CONST_20  H19  C10  C9   C14   180.00   0.0  0
 0B3  CONST_21  H15  C14  C13  C12   180.00   0.0  0
 0B3  CONST_22  C4   N3   C5   O       0.00   0.0  0
 0B3  CONST_25  H5   N2   C3   N3    180.00   0.0  0
 0B3  Var_01    H6   C6   C5   N3    159.25  30.0  1
 0B3  Var_02    C9   C8   C7   C2   -174.41  30.0  3
 0B3  Var_03    C14  C9   C8   C7    -95.26  30.0  2
 0B3  Var_04    H1   C4   N3   C5    131.62  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
 0B3  chir_01  C2  C6  C7  N1  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
 0B3  plan-1  C8   0.020
 0B3  plan-1  C9   0.020
 0B3  plan-1  C14  0.020
 0B3  plan-1  C13  0.020
 0B3  plan-1  C12  0.020
 0B3  plan-1  C11  0.020
 0B3  plan-1  C10  0.020
 0B3  plan-1  H15  0.020
 0B3  plan-1  H16  0.020
 0B3  plan-1  H17  0.020
 0B3  plan-1  H18  0.020
 0B3  plan-1  H19  0.020
 0B3  plan-2  O    0.020
 0B3  plan-2  C5   0.020
 0B3  plan-2  N3   0.020
 0B3  plan-2  C4   0.020
 0B3  plan-2  C3   0.020
 0B3  plan-2  N2   0.020
 0B3  plan-2  N1   0.020
 0B3  plan-2  C6   0.020
 0B3  plan-2  C2   0.020
 0B3  plan-2  H4   0.020
 0B3  plan-2  H5   0.020

