# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:57:25 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-amino-3-methyl-6-[(1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=NC(=CC1=O)[C@H]2C[C@H]2c3ccc(cc3)c4cccc(C)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
 B02  B02  2-amino-3-methyl-6-[(1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl]pyrimidin-4(3H)-one  ligand  46  25  .  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_B02
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
 B02  O    O  O     0  -0.511   3.5229   1.6221  -2.9468
 B02  C1   C  CR6   0   0.573   3.2156   1.1309  -1.8657
 B02  N2   N  NR6   0  -0.555   2.5308   1.9065  -0.9104
 B02  C5   C  CH3   0  -0.578   2.1939   3.2859  -1.2272
 B02  C4   C  CR6   0   0.708   2.1934   1.3860   0.3014
 B02  N3   N  NH2   0  -0.838   1.5745   2.1810   1.1893
 B02  N1   N  N     0  -0.520   2.4706   0.1601   0.6679
 B02  C3   C  CR6   0   0.365   3.0854  -0.6378  -0.2198
 B02  C2   C  CR16  0  -0.532   3.4779  -0.2061  -1.4576
 B02  C6   C  CH1   0  -0.343   3.2840  -2.0459   0.1727
 B02  C21  C  CH2   0  -0.472   3.1209  -2.4822   1.5993
 B02  C7   C  CH1   0  -0.270   2.0713  -2.8551   0.6146
 B02  C8   C  CR6   0   0.100   0.7144  -2.2450   0.6135
 B02  C13  C  CR16  0  -0.280   0.0696  -1.8671   1.7851
 B02  C12  C  CR16  0  -0.298  -1.1920  -1.2943   1.7532
 B02  C11  C  CR6   0   0.075  -1.8509  -1.0756   0.5436
 B02  C10  C  CR16  0  -0.300  -1.2079  -1.4692  -0.6313
 B02  C9   C  CR16  0  -0.271   0.0500  -2.0469  -0.5945
 B02  C14  C  CR6   0   0.108  -3.1846  -0.4429   0.5068
 B02  C19  C  CR16  0  -0.333  -4.1414  -0.7284   1.4823
 B02  C18  C  CR16  0  -0.226  -5.3898  -0.1279   1.4324
 B02  C17  C  CR16  0  -0.315  -5.7011   0.7650   0.4161
 B02  C16  C  CR6   0   0.117  -4.7632   1.0707  -0.5674
 B02  C20  C  CH3   0  -0.723  -5.0723   2.0647  -1.6496
 B02  C15  C  CR16  0  -0.364  -3.5154   0.4570  -0.5068
 B02  H1   H  HCH3  0   0.287   2.5797   3.5206  -2.2111
 B02  H2   H  HCH3  0   0.264   1.1135   3.4294  -1.2372
 B02  H3   H  HCH3  0   0.264   2.6436   3.9673  -0.5057
 B02  H4   H  HNH2  0   0.424   1.1347   3.0461   0.9291
 B02  H5   H  HNH2  0   0.408   1.1998   1.7226   2.0026
 B02  H6   H  HCR6  0   0.255   3.9788  -0.8640  -2.1539
 B02  H7   H  HCH1  0   0.268   3.9994  -2.5852  -0.4364
 B02  H8   H  HCH2  0   0.264   3.7834  -3.2589   1.9584
 B02  H9   H  HCH2  0   0.259   2.8951  -1.7084   2.3218
 B02  H10  H  HCH1  0   0.283   2.0953  -3.8818   0.2624
 B02  H11  H  HCR6  0   0.240   0.5649  -2.0061   2.7379
 B02  H12  H  HCR6  0   0.246  -1.6557  -0.9898   2.6835
 B02  H13  H  HCR6  0   0.247  -1.7010  -1.3364  -1.5865
 B02  H14  H  HCR6  0   0.243   0.5271  -2.3401  -1.5222
 B02  H15  H  HCR6  0   0.249  -3.9197  -1.4393   2.2687
 B02  H16  H  HCR6  0   0.253  -6.1307  -0.3658   2.1850
 B02  H17  H  HCR6  0   0.247  -6.6815   1.2254   0.3866
 B02  H18  H  HCH3  0   0.249  -4.7306   3.0635  -1.3708
 B02  H19  H  HCH3  0   0.243  -4.5780   1.8043  -2.5854
 B02  H20  H  HCH3  0   0.244  -6.1431   2.1296  -1.8398
 B02  H21  H  HCR6  0   0.243  -2.7745   0.6998  -1.2607

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
 B02  C21  C6   single    1.501  0.020  1.501
 B02  C21  C7   single    1.487  0.020  1.487
 B02  O    C1   double    1.226  0.020  1.226
 B02  C2   C1   single    1.422  0.020  1.422
 B02  C2   C3   double    1.368  0.020  1.368
 B02  C6   C7   single    1.523  0.020  1.523
 B02  C6   C3   single    1.475  0.020  1.475
 B02  C1   N2   single    1.408  0.020  1.408
 B02  C7   C8   single    1.488  0.020  1.488
 B02  C13  C8   aromatic  1.390  0.020  1.390
 B02  C13  C12  aromatic  1.386  0.020  1.386
 B02  C3   N1   single    1.343  0.020  1.343
 B02  C8   C9   aromatic  1.393  0.020  1.393
 B02  C12  C11  aromatic  1.395  0.020  1.395
 B02  N2   C5   single    1.455  0.020  1.455
 B02  N2   C4   single    1.361  0.020  1.361
 B02  N1   C4   double    1.309  0.020  1.309
 B02  C9   C10  aromatic  1.385  0.020  1.385
 B02  C4   N3   single    1.343  0.020  1.343
 B02  C11  C10  aromatic  1.396  0.020  1.396
 B02  C11  C14  single    1.477  0.020  1.477
 B02  C19  C14  aromatic  1.396  0.020  1.396
 B02  C19  C18  aromatic  1.386  0.020  1.386
 B02  C14  C15  aromatic  1.395  0.020  1.395
 B02  C18  C17  aromatic  1.388  0.020  1.388
 B02  C15  C16  aromatic  1.392  0.020  1.392
 B02  C17  C16  aromatic  1.393  0.020  1.393
 B02  C16  C20  single    1.502  0.020  1.502
 B02  C5   H1   single    0.970  0.020  1.090
 B02  C5   H2   single    0.970  0.020  1.090
 B02  C5   H3   single    0.970  0.020  1.090
 B02  N3   H4   single    0.890  0.020  1.040
 B02  N3   H5   single    0.890  0.020  1.040
 B02  C2   H6   single    0.930  0.020  1.080
 B02  C6   H7   single    0.970  0.020  1.090
 B02  C21  H8   single    0.970  0.020  1.090
 B02  C21  H9   single    0.970  0.020  1.090
 B02  C7   H10  single    0.970  0.020  1.090
 B02  C13  H11  single    0.930  0.020  1.080
 B02  C12  H12  single    0.930  0.020  1.080
 B02  C10  H13  single    0.930  0.020  1.080
 B02  C9   H14  single    0.930  0.020  1.080
 B02  C19  H15  single    0.930  0.020  1.080
 B02  C18  H16  single    0.930  0.020  1.080
 B02  C17  H17  single    0.930  0.020  1.080
 B02  C20  H18  single    0.970  0.020  1.090
 B02  C20  H19  single    0.970  0.020  1.090
 B02  C20  H20  single    0.970  0.020  1.090
 B02  C15  H21  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
 B02  C2   C1   N2   114.37  3.000
 B02  N2   C1   O    119.95  3.000
 B02  C2   C1   O    125.68  3.000
 B02  C4   N2   C5   119.93  3.000
 B02  C4   N2   C1   120.92  3.000
 B02  C5   N2   C1   119.15  3.000
 B02  H3   C5   H2   109.44  3.000
 B02  H3   C5   H1   108.61  3.000
 B02  H2   C5   H1   108.44  3.000
 B02  H3   C5   N2   110.68  3.000
 B02  H2   C5   N2   110.88  3.000
 B02  H1   C5   N2   108.72  3.000
 B02  N1   C4   N3   117.83  3.000
 B02  N3   C4   N2   118.45  3.000
 B02  N1   C4   N2   123.69  3.000
 B02  H5   N3   H4   116.01  3.000
 B02  H5   N3   C4   115.88  3.000
 B02  H4   N3   C4   122.70  3.000
 B02  C3   N1   C4   117.93  3.000
 B02  C6   C3   C2   120.21  3.000
 B02  C6   C3   N1   116.94  3.000
 B02  C2   C3   N1   122.81  3.000
 B02  H6   C2   C3   121.58  3.000
 B02  H6   C2   C1   118.20  3.000
 B02  C3   C2   C1   120.22  3.000
 B02  H7   C6   C7   115.11  3.000
 B02  H7   C6   C21  117.48  3.000
 B02  C7   C6   C21   58.89  3.000
 B02  H7   C6   C3   114.49  3.000
 B02  C7   C6   C3   118.49  3.000
 B02  C21  C6   C3   121.05  3.000
 B02  H9   C21  H8   114.79  3.000
 B02  H9   C21  C7   118.30  3.000
 B02  H8   C21  C7   118.17  3.000
 B02  H9   C21  C6   116.70  3.000
 B02  H8   C21  C6   117.23  3.000
 B02  C7   C21  C6    61.32  3.000
 B02  H10  C7   C8   114.06  3.000
 B02  H10  C7   C21  115.88  3.000
 B02  C8   C7   C21  122.79  3.000
 B02  H10  C7   C6   112.99  3.000
 B02  C8   C7   C6   120.53  3.000
 B02  C21  C7   C6    59.80  3.000
 B02  C9   C8   C13  118.11  3.000
 B02  C9   C8   C7   119.61  3.000
 B02  C13  C8   C7   122.28  3.000
 B02  H11  C13  C12  119.32  3.000
 B02  H11  C13  C8   119.65  3.000
 B02  C12  C13  C8   121.02  3.000
 B02  H12  C12  C11  119.91  3.000
 B02  H12  C12  C13  119.09  3.000
 B02  C11  C12  C13  120.99  3.000
 B02  C14  C11  C10  121.06  3.000
 B02  C14  C11  C12  121.03  3.000
 B02  C10  C11  C12  117.91  3.000
 B02  H13  C10  C9   119.22  3.000
 B02  H13  C10  C11  119.86  3.000
 B02  C9   C10  C11  120.91  3.000
 B02  H14  C9   C10  119.34  3.000
 B02  H14  C9   C8   119.61  3.000
 B02  C10  C9   C8   121.05  3.000
 B02  C15  C14  C19  118.50  3.000
 B02  C15  C14  C11  120.57  3.000
 B02  C19  C14  C11  120.93  3.000
 B02  H15  C19  C18  119.66  3.000
 B02  H15  C19  C14  120.09  3.000
 B02  C18  C19  C14  120.23  3.000
 B02  H16  C18  C17  119.79  3.000
 B02  H16  C18  C19  119.75  3.000
 B02  C17  C18  C19  120.46  3.000
 B02  H17  C17  C16  119.78  3.000
 B02  H17  C17  C18  119.74  3.000
 B02  C16  C17  C18  120.47  3.000
 B02  C15  C16  C20  120.52  3.000
 B02  C20  C16  C17  121.03  3.000
 B02  C15  C16  C17  118.43  3.000
 B02  H20  C20  H19  108.07  3.000
 B02  H20  C20  H18  107.31  3.000
 B02  H19  C20  H18  107.21  3.000
 B02  H20  C20  C16  111.57  3.000
 B02  H19  C20  C16  111.55  3.000
 B02  H18  C20  C16  110.92  3.000
 B02  H21  C15  C16  118.91  3.000
 B02  H21  C15  C14  119.17  3.000
 B02  C16  C15  C14  121.91  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
 B02  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 B02  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 B02  CONST_03  C10  C9   C8   C13     0.00   0.0  0
 B02  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 B02  CONST_05  C14  C11  C12  C13   180.00   0.0  0
 B02  CONST_06  C9   C8   C13  C12     0.00   0.0  0
 B02  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 B02  CONST_10  C18  C19  C14  C11   180.00   0.0  0
 B02  CONST_11  C16  C15  C14  C11   180.00   0.0  0
 B02  CONST_14  C14  C11  C10  C9    180.00   0.0  0
 B02  CONST_15  C17  C18  C19  C14     0.00   0.0  0
 B02  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 B02  CONST_17  C16  C15  C14  C19     0.00   0.0  0
 B02  CONST_18  C16  C17  C18  C19     0.00   0.0  0
 B02  CONST_19  C15  C14  C19  C18     0.00   0.0  0
 B02  CONST_20  C15  C16  C17  C18     0.00   0.0  0
 B02  CONST_21  C12  C13  C8   C7    180.00   0.0  0
 B02  CONST_22  C10  C9   C8   C7    180.00   0.0  0
 B02  CONST_23  N1   C4   N2   C1      0.00   0.0  0
 B02  CONST_24  C3   N1   C4   N2      0.00   0.0  0
 B02  CONST_25  C2   C1   N2   C4      0.00   0.0  0
 B02  CONST_26  C20  C16  C15  C14   180.00   0.0  0
 B02  CONST_27  C20  C16  C17  C18   180.00   0.0  0
 B02  CONST_28  C4   N2   C1   O     180.00   0.0  0
 B02  CONST_29  N3   C4   N2   C1    180.00   0.0  0
 B02  CONST_30  C2   C1   N2   C5    180.00   0.0  0
 B02  CONST_31  N1   C4   N2   C5    180.00   0.0  0
 B02  CONST_32  C3   N1   C4   N3    180.00   0.0  0
 B02  CONST_33  H11  C13  C8   C7      0.00   0.0  0
 B02  CONST_34  H14  C9   C8   C7      0.00   0.0  0
 B02  CONST_35  H12  C12  C13  C8    180.00   0.0  0
 B02  CONST_36  H13  C10  C9   C8    180.00   0.0  0
 B02  CONST_37  H15  C19  C14  C11     0.00   0.0  0
 B02  CONST_38  H21  C15  C14  C11     0.00   0.0  0
 B02  CONST_39  H16  C18  C19  C14   180.00   0.0  0
 B02  CONST_40  H17  C17  C18  C19   180.00   0.0  0
 B02  CONST_41  C5   N2   C1   O       0.00   0.0  0
 B02  CONST_42  N3   C4   N2   C5      0.00   0.0  0
 B02  CONST_44  H5   N3   C4   N2    180.00   0.0  0
 B02  Var_01    C21  C6   C3   N1    -14.59  30.0  2
 B02  Var_02    C7   C21  C6   C3    106.68  30.0  1
 B02  Var_03    C13  C8   C7   C6   -105.79  30.0  2
 B02  Var_04    H1   C5   N2   C1     -1.79  30.0  3
 B02  Var_05    H18  C20  C16  C17    93.37  30.0  2

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
 B02  chir_01  C6  C21  C7  C3  both
 B02  chir_02  C7  C21  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
 B02  plan-1  O    0.020
 B02  plan-1  C1   0.020
 B02  plan-1  N2   0.020
 B02  plan-1  C5   0.020
 B02  plan-1  C4   0.020
 B02  plan-1  N3   0.020
 B02  plan-1  N1   0.020
 B02  plan-1  C3   0.020
 B02  plan-1  C2   0.020
 B02  plan-1  C6   0.020
 B02  plan-1  H4   0.020
 B02  plan-1  H5   0.020
 B02  plan-1  H6   0.020
 B02  plan-2  C7   0.020
 B02  plan-2  C8   0.020
 B02  plan-2  C13  0.020
 B02  plan-2  C12  0.020
 B02  plan-2  C11  0.020
 B02  plan-2  C10  0.020
 B02  plan-2  C9   0.020
 B02  plan-2  C14  0.020
 B02  plan-2  H11  0.020
 B02  plan-2  H12  0.020
 B02  plan-2  H13  0.020
 B02  plan-2  H14  0.020
 B02  plan-3  C11  0.020
 B02  plan-3  C14  0.020
 B02  plan-3  C19  0.020
 B02  plan-3  C18  0.020
 B02  plan-3  C17  0.020
 B02  plan-3  C16  0.020
 B02  plan-3  C20  0.020
 B02  plan-3  C15  0.020
 B02  plan-3  H15  0.020
 B02  plan-3  H16  0.020
 B02  plan-3  H17  0.020
 B02  plan-3  H21  0.020

