# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 02:04:09 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=NC(=CC1=O)[C@H]2C[C@H]2c3ccccc3)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
 B00  B00  2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one  ligand  33  18  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B00
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
 B00  O    O  O     0  -0.510  -3.3955  -0.7120   1.9306
 B00  C1   C  CR6   0   0.573  -2.5281  -0.6326   1.0676
 B00  N2   N  NR6   0  -0.553  -2.5399   0.4414   0.1569
 B00  C5   C  CH3   0  -0.577  -3.6040   1.4300   0.2361
 B00  C4   C  CR6   0   0.701  -1.5779   0.5587  -0.7986
 B00  N3   N  NH2   0  -0.837  -1.6461   1.6011  -1.6463
 B00  N1   N  N     0  -0.518  -0.6135  -0.3086  -0.9705
 B00  C3   C  CR6   0   0.371  -0.5477  -1.3504  -0.1256
 B00  C2   C  CR16  0  -0.534  -1.4560  -1.5492   0.8785
 B00  C6   C  CH1   0  -0.344   0.5849  -2.2789  -0.2987
 B00  C14  C  CH2   0  -0.474   1.4178  -2.2506  -1.5468
 B00  C7   C  CH1   0  -0.274   2.0084  -1.7344  -0.2837
 B00  C8   C  CR6   0   0.120   2.2825  -0.2929  -0.0352
 B00  C13  C  CR16  0  -0.295   2.3328   0.1673   1.2797
 B00  C12  C  CR16  0  -0.245   2.6011   1.4995   1.5590
 B00  C11  C  CR16  0  -0.273   2.8255   2.3964   0.5218
 B00  C10  C  CR16  0  -0.242   2.7836   1.9467  -0.7911
 B00  C9   C  CR16  0  -0.289   2.5150   0.6123  -1.0650
 B00  H1   H  HCH3  0   0.287  -4.3024   1.1354   1.0098
 B00  H2   H  HCH3  0   0.264  -3.2065   2.4132   0.4888
 B00  H3   H  HCH3  0   0.265  -4.1394   1.4895  -0.7107
 B00  H4   H  HNH2  0   0.422  -2.1644   2.4327  -1.4214
 B00  H5   H  HNH2  0   0.407  -0.8350   1.7407  -2.2260
 B00  H6   H  HCR6  0   0.256  -1.3783  -2.3918   1.5513
 B00  H7   H  HCH1  0   0.268   0.4596  -3.2355   0.1943
 B00  H8   H  HCH2  0   0.263   1.7747  -3.1972  -1.9309
 B00  H9   H  HCH2  0   0.261   1.1276  -1.5316  -2.3024
 B00  H10  H  HCH1  0   0.280   2.7034  -2.4000   0.2191
 B00  H11  H  HCR6  0   0.242   2.1582  -0.5273   2.0934
 B00  H12  H  HCR6  0   0.249   2.6356   1.8377   2.5871
 B00  H13  H  HCR6  0   0.250   3.0336   3.4369   0.7362
 B00  H14  H  HCR6  0   0.248   2.9600   2.6370  -1.6065
 B00  H15  H  HCR6  0   0.236   2.4830   0.2739  -2.0931

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
 B00  C14  C6   single    1.501  0.020  1.501
 B00  C14  C7   single    1.487  0.020  1.487
 B00  O    C1   double    1.226  0.020  1.226
 B00  C2   C1   single    1.423  0.020  1.423
 B00  C2   C3   double    1.369  0.020  1.369
 B00  C6   C7   single    1.524  0.020  1.524
 B00  C6   C3   single    1.475  0.020  1.475
 B00  C7   C8   single    1.488  0.020  1.488
 B00  C9   C10  aromatic  1.389  0.020  1.389
 B00  C9   C8   aromatic  1.391  0.020  1.391
 B00  C1   N2   single    1.408  0.020  1.408
 B00  C3   N1   single    1.343  0.020  1.343
 B00  C10  C11  aromatic  1.388  0.020  1.388
 B00  C8   C13  aromatic  1.394  0.020  1.394
 B00  N2   C5   single    1.455  0.020  1.455
 B00  N2   C4   single    1.361  0.020  1.361
 B00  N1   C4   double    1.308  0.020  1.308
 B00  C11  C12  aromatic  1.390  0.020  1.390
 B00  C13  C12  aromatic  1.387  0.020  1.387
 B00  C4   N3   single    1.345  0.020  1.345
 B00  C5   H1   single    0.970  0.020  1.090
 B00  C5   H2   single    0.970  0.020  1.090
 B00  C5   H3   single    0.970  0.020  1.090
 B00  N3   H4   single    0.890  0.020  1.040
 B00  N3   H5   single    0.890  0.020  1.040
 B00  C2   H6   single    0.930  0.020  1.080
 B00  C6   H7   single    0.970  0.020  1.090
 B00  C14  H8   single    0.970  0.020  1.090
 B00  C14  H9   single    0.970  0.020  1.090
 B00  C7   H10  single    0.970  0.020  1.090
 B00  C13  H11  single    0.930  0.020  1.080
 B00  C12  H12  single    0.930  0.020  1.080
 B00  C11  H13  single    0.930  0.020  1.080
 B00  C10  H14  single    0.930  0.020  1.080
 B00  C9   H15  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
 B00  C2   C1   N2   114.31  3.000
 B00  N2   C1   O    119.91  3.000
 B00  C2   C1   O    125.79  3.000
 B00  C4   N2   C5   119.78  3.000
 B00  C4   N2   C1   120.92  3.000
 B00  C5   N2   C1   119.29  3.000
 B00  H3   C5   H2   109.35  3.000
 B00  H3   C5   H1   108.60  3.000
 B00  H2   C5   H1   108.35  3.000
 B00  H3   C5   N2   110.45  3.000
 B00  H2   C5   N2   111.02  3.000
 B00  H1   C5   N2   109.01  3.000
 B00  N1   C4   N3   117.92  3.000
 B00  N3   C4   N2   118.25  3.000
 B00  N1   C4   N2   123.78  3.000
 B00  H5   N3   H4   115.43  3.000
 B00  H5   N3   C4   115.43  3.000
 B00  H4   N3   C4   121.75  3.000
 B00  C3   N1   C4   117.89  3.000
 B00  C6   C3   C2   120.29  3.000
 B00  C6   C3   N1   116.89  3.000
 B00  C2   C3   N1   122.80  3.000
 B00  H6   C2   C3   121.48  3.000
 B00  H6   C2   C1   118.26  3.000
 B00  C3   C2   C1   120.26  3.000
 B00  H7   C6   C7   114.76  3.000
 B00  H7   C6   C14  117.34  3.000
 B00  C7   C6   C14   58.88  3.000
 B00  H7   C6   C3   114.44  3.000
 B00  C7   C6   C3   119.42  3.000
 B00  C14  C6   C3   120.80  3.000
 B00  H9   C14  H8   114.93  3.000
 B00  H9   C14  C7   117.96  3.000
 B00  H8   C14  C7   118.31  3.000
 B00  H9   C14  C6   116.37  3.000
 B00  H8   C14  C6   117.50  3.000
 B00  C7   C14  C6    61.35  3.000
 B00  H10  C7   C8   113.49  3.000
 B00  H10  C7   C14  115.77  3.000
 B00  C8   C7   C14  123.46  3.000
 B00  H10  C7   C6   112.54  3.000
 B00  C8   C7   C6   121.31  3.000
 B00  C14  C7   C6    59.77  3.000
 B00  C9   C8   C13  118.53  3.000
 B00  C13  C8   C7   118.94  3.000
 B00  C9   C8   C7   122.52  3.000
 B00  H11  C13  C12  119.69  3.000
 B00  H11  C13  C8   119.39  3.000
 B00  C12  C13  C8   120.92  3.000
 B00  H12  C12  C11  120.13  3.000
 B00  H12  C12  C13  119.82  3.000
 B00  C11  C12  C13  120.05  3.000
 B00  H13  C11  C10  120.29  3.000
 B00  H13  C11  C12  120.24  3.000
 B00  C10  C11  C12  119.47  3.000
 B00  H14  C10  C9   119.71  3.000
 B00  H14  C10  C11  120.05  3.000
 B00  C9   C10  C11  120.24  3.000
 B00  H15  C9   C10  119.56  3.000
 B00  H15  C9   C8   119.65  3.000
 B00  C10  C9   C8   120.78  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
 B00  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 B00  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 B00  CONST_03  C10  C9   C8   C13    0.00   0.0  0
 B00  CONST_04  C10  C11  C12  C13    0.00   0.0  0
 B00  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 B00  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 B00  CONST_07  C10  C9   C8   C7   180.00   0.0  0
 B00  CONST_08  C12  C13  C8   C7   180.00   0.0  0
 B00  CONST_09  N1   C4   N2   C1     0.00   0.0  0
 B00  CONST_10  C3   N1   C4   N2     0.00   0.0  0
 B00  CONST_11  C2   C1   N2   C4     0.00   0.0  0
 B00  CONST_12  C4   N2   C1   O    180.00   0.0  0
 B00  CONST_13  N3   C4   N2   C1   180.00   0.0  0
 B00  CONST_14  C2   C1   N2   C5   180.00   0.0  0
 B00  CONST_15  N1   C4   N2   C5   180.00   0.0  0
 B00  CONST_16  C3   N1   C4   N3   180.00   0.0  0
 B00  CONST_17  H15  C9   C8   C7     0.00   0.0  0
 B00  CONST_18  H11  C13  C8   C7     0.00   0.0  0
 B00  CONST_19  H14  C10  C9   C8   180.00   0.0  0
 B00  CONST_20  H12  C12  C13  C8   180.00   0.0  0
 B00  CONST_21  H13  C11  C12  C13  180.00   0.0  0
 B00  CONST_22  C5   N2   C1   O      0.00   0.0  0
 B00  CONST_23  N3   C4   N2   C5     0.00   0.0  0
 B00  CONST_25  H5   N3   C4   N2   180.00   0.0  0
 B00  Var_01    C14  C6   C3   N1   -14.37  30.0  1
 B00  Var_02    C7   C14  C6   C3   107.94  30.0  1
 B00  Var_03    C9   C8   C7   C6   -98.14  30.0  2
 B00  Var_04    H1   C5   N2   C1    -3.09  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
 B00  chir_01  C6  C14  C7  C3  both
 B00  chir_02  C7  C14  C6  C8  both

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
 B00  plan-1  O    0.020
 B00  plan-1  C1   0.020
 B00  plan-1  N2   0.020
 B00  plan-1  C5   0.020
 B00  plan-1  C4   0.020
 B00  plan-1  N3   0.020
 B00  plan-1  N1   0.020
 B00  plan-1  C3   0.020
 B00  plan-1  C2   0.020
 B00  plan-1  C6   0.020
 B00  plan-1  H4   0.020
 B00  plan-1  H5   0.020
 B00  plan-1  H6   0.020
 B00  plan-2  C7   0.020
 B00  plan-2  C8   0.020
 B00  plan-2  C13  0.020
 B00  plan-2  C12  0.020
 B00  plan-2  C11  0.020
 B00  plan-2  C10  0.020
 B00  plan-2  C9   0.020
 B00  plan-2  H11  0.020
 B00  plan-2  H12  0.020
 B00  plan-2  H13  0.020
 B00  plan-2  H14  0.020
 B00  plan-2  H15  0.020

