# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 20:11:01 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-amino-6-[(1S,2R)-2-(3'-methoxybiphenyl-3-yl)cyclopropyl]-3-methylpyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(c2)[C@@H]3C[C@@H]3C4=CC(=O)N(C)C(=N4)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
 0B1  0B1  2-amino-6-[(1S,2R)-2-(3'-methoxybiphenyl-3-yl)cyclopropyl]-3-methylpyrimidin-4(3H)-one  ligand  47  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0B1
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
 0B1  O1   O  O     0  -0.511   1.9964   1.9060  -2.9840
 0B1  C1   C  CR6   0   0.574   2.2196   1.2541  -1.9692
 0B1  N2   N  NR6   0  -0.557   2.1816   1.8815  -0.7088
 0B1  C5   C  CH3   0  -0.580   1.8668   3.2991  -0.6329
 0B1  C4   C  CR6   0   0.721   2.4390   1.1816   0.4314
 0B1  N3   N  NH2   0  -0.843   2.3976   1.8320   1.5986
 0B1  N1   N  N     0  -0.520   2.7251  -0.0981   0.4503
 0B1  C3   C  CR6   0   0.353   2.7375  -0.7521  -0.7207
 0B1  C2   C  CR16  0  -0.529   2.5164  -0.1353  -1.9224
 0B1  C6   C  CH1   0  -0.343   2.9594  -2.2112  -0.6749
 0B1  C21  C  CH2   0  -0.470   3.4495  -2.8819   0.5748
 0B1  C7   C  CH1   0  -0.272   2.0305  -3.0677   0.1681
 0B1  C8   C  CR6   0   0.137   0.9013  -2.4586   0.9246
 0B1  C13  C  CR16  0  -0.317   0.8544  -2.5021   2.3129
 0B1  C12  C  CR16  0  -0.226  -0.2210  -1.9497   2.9946
 0B1  C11  C  CR16  0  -0.329  -1.2528  -1.3404   2.2986
 0B1  C10  C  CR6   0   0.115  -1.2252  -1.2820   0.9043
 0B1  C9   C  CR16  0  -0.352  -0.1460  -1.8556   0.2357
 0B1  C14  C  CR6   0   0.107  -2.3100  -0.6198   0.1502
 0B1  C20  C  CR16  0  -0.337  -2.7528  -1.1364  -1.0717
 0B1  C19  C  CR16  0  -0.227  -3.7704  -0.5009  -1.7603
 0B1  C18  C  CR16  0  -0.396  -4.3703   0.6516  -1.2641
 0B1  C16  C  CR6   0   0.405  -3.9327   1.1710  -0.0486
 0B1  C15  C  CR16  0  -0.413  -2.9051   0.5333   0.6477
 0B1  O2   O  O2    0  -0.473  -4.4326   2.2816   0.5271
 0B1  C17  C  CH3   0  -0.436  -5.4701   2.9778  -0.1331
 0B1  H1   H  HCH3  0   0.288   1.6845   3.6707  -1.6336
 0B1  H2   H  HCH3  0   0.262   0.9709   3.4656  -0.0349
 0B1  H3   H  HCH3  0   0.263   2.6983   3.8591  -0.2046
 0B1  H5   H  HNH2  0   0.428   2.2260   2.8160   1.6947
 0B1  H6   H  HNH2  0   0.413   2.5767   1.3042   2.4349
 0B1  H8   H  HCR6  0   0.254   2.5420  -0.6871  -2.8517
 0B1  H10  H  HCH1  0   0.268   3.2532  -2.6463  -1.6226
 0B1  H11  H  HCH2  0   0.262   4.1314  -3.7141   0.4609
 0B1  H12  H  HCH2  0   0.258   3.6497  -2.2402   1.4231
 0B1  H13  H  HCH1  0   0.284   1.7888  -4.0211  -0.2922
 0B1  H14  H  HCR6  0   0.244   1.6632  -2.9668   2.8633
 0B1  H15  H  HCR6  0   0.251  -0.2571  -1.9971   4.0756
 0B1  H16  H  HCR6  0   0.248  -2.0933  -0.9272   2.8422
 0B1  H17  H  HCR6  0   0.241  -0.0958  -1.7991  -0.8458
 0B1  H18  H  HCR6  0   0.248  -2.3162  -2.0429  -1.4705
 0B1  H19  H  HCR6  0   0.259  -4.1156  -0.9073  -2.7022
 0B1  H20  H  HCR6  0   0.278  -5.1619   1.1197  -1.8329
 0B1  H21  H  HCR6  0   0.256  -2.5642   0.9678   1.5802
 0B1  H22  H  HCH3  0   0.228  -5.1580   3.3462  -1.1139
 0B1  H23  H  HCH3  0   0.228  -6.3637   2.3607  -0.2568
 0B1  H24  H  HCH3  0   0.259  -5.7188   3.8298   0.4950

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
 0B1  C21  C6   single    1.501  0.020  1.501
 0B1  C21  C7   single    1.488  0.020  1.488
 0B1  O1   C1   double    1.227  0.020  1.227
 0B1  C2   C1   single    1.422  0.020  1.422
 0B1  C2   C3   double    1.369  0.020  1.369
 0B1  C13  C12  aromatic  1.388  0.020  1.388
 0B1  C13  C8   aromatic  1.390  0.020  1.390
 0B1  C6   C7   single    1.519  0.020  1.519
 0B1  C6   C3   single    1.477  0.020  1.477
 0B1  C7   C8   single    1.489  0.020  1.489
 0B1  C1   N2   single    1.408  0.020  1.408
 0B1  C3   N1   single    1.341  0.020  1.341
 0B1  C12  C11  aromatic  1.386  0.020  1.386
 0B1  C8   C9   aromatic  1.391  0.020  1.391
 0B1  N2   C5   single    1.454  0.020  1.454
 0B1  N2   C4   single    1.362  0.020  1.362
 0B1  N1   C4   double    1.311  0.020  1.311
 0B1  C11  C10  aromatic  1.396  0.020  1.396
 0B1  C9   C10  aromatic  1.393  0.020  1.393
 0B1  C4   N3   single    1.337  0.020  1.337
 0B1  C10  C14  single    1.478  0.020  1.478
 0B1  C14  C15  aromatic  1.390  0.020  1.390
 0B1  C14  C20  aromatic  1.399  0.020  1.399
 0B1  C15  C16  aromatic  1.396  0.020  1.396
 0B1  C20  C19  aromatic  1.383  0.020  1.383
 0B1  C17  O2   single    1.413  0.020  1.413
 0B1  C16  O2   single    1.347  0.020  1.347
 0B1  C16  C18  aromatic  1.392  0.020  1.392
 0B1  C19  C18  aromatic  1.391  0.020  1.391
 0B1  C5   H1   single    0.970  0.020  1.090
 0B1  C5   H2   single    0.970  0.020  1.090
 0B1  C5   H3   single    0.970  0.020  1.090
 0B1  N3   H5   single    0.860  0.020  1.020
 0B1  N3   H6   single    0.860  0.020  1.020
 0B1  C2   H8   single    0.930  0.020  1.080
 0B1  C6   H10  single    0.970  0.020  1.090
 0B1  C21  H11  single    0.970  0.020  1.090
 0B1  C21  H12  single    0.970  0.020  1.090
 0B1  C7   H13  single    0.970  0.020  1.090
 0B1  C13  H14  single    0.930  0.020  1.080
 0B1  C12  H15  single    0.930  0.020  1.080
 0B1  C11  H16  single    0.930  0.020  1.080
 0B1  C9   H17  single    0.930  0.020  1.080
 0B1  C20  H18  single    0.930  0.020  1.080
 0B1  C19  H19  single    0.930  0.020  1.080
 0B1  C18  H20  single    0.930  0.020  1.080
 0B1  C15  H21  single    0.930  0.020  1.080
 0B1  C17  H22  single    0.970  0.020  1.090
 0B1  C17  H23  single    0.970  0.020  1.090
 0B1  C17  H24  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
 0B1  C2   C1   N2   114.31  3.000
 0B1  N2   C1   O1   119.92  3.000
 0B1  C2   C1   O1   125.77  3.000
 0B1  C4   N2   C5   119.87  3.000
 0B1  C4   N2   C1   121.00  3.000
 0B1  C5   N2   C1   119.13  3.000
 0B1  H3   C5   H2   109.44  3.000
 0B1  H3   C5   H1   108.37  3.000
 0B1  H2   C5   H1   108.43  3.000
 0B1  H3   C5   N2   110.87  3.000
 0B1  H2   C5   N2   110.83  3.000
 0B1  H1   C5   N2   108.83  3.000
 0B1  N1   C4   N3   117.96  3.000
 0B1  N3   C4   N2   118.35  3.000
 0B1  N1   C4   N2   123.68  3.000
 0B1  H6   N3   H5   117.76  3.000
 0B1  H6   N3   C4   117.74  3.000
 0B1  H5   N3   C4   124.47  3.000
 0B1  C3   N1   C4   117.73  3.000
 0B1  C6   C3   C2   119.79  3.000
 0B1  C6   C3   N1   117.14  3.000
 0B1  C2   C3   N1   123.04  3.000
 0B1  H8   C2   C3   121.39  3.000
 0B1  H8   C2   C1   118.40  3.000
 0B1  C3   C2   C1   120.20  3.000
 0B1  H10  C6   C7   115.14  3.000
 0B1  H10  C6   C21  117.42  3.000
 0B1  C7   C6   C21   59.04  3.000
 0B1  H10  C6   C3   114.23  3.000
 0B1  C7   C6   C3   118.85  3.000
 0B1  C21  C6   C3   121.10  3.000
 0B1  H12  C21  H11  114.96  3.000
 0B1  H12  C21  C7   117.70  3.000
 0B1  H11  C21  C7   118.44  3.000
 0B1  H12  C21  C6   116.63  3.000
 0B1  H11  C21  C6   117.51  3.000
 0B1  C7   C21  C6    61.10  3.000
 0B1  H13  C7   C8   113.93  3.000
 0B1  H13  C7   C21  115.96  3.000
 0B1  C8   C7   C21  122.21  3.000
 0B1  H13  C7   C6   113.32  3.000
 0B1  C8   C7   C6   121.00  3.000
 0B1  C21  C7   C6    59.87  3.000
 0B1  C9   C8   C13  118.87  3.000
 0B1  C9   C8   C7   119.77  3.000
 0B1  C13  C8   C7   121.35  3.000
 0B1  H14  C13  C12  119.99  3.000
 0B1  H14  C13  C8   119.72  3.000
 0B1  C12  C13  C8   120.29  3.000
 0B1  H15  C12  C11  119.73  3.000
 0B1  H15  C12  C13  119.93  3.000
 0B1  C11  C12  C13  120.35  3.000
 0B1  H16  C11  C10  120.06  3.000
 0B1  H16  C11  C12  119.57  3.000
 0B1  C10  C11  C12  120.36  3.000
 0B1  C14  C10  C9   120.55  3.000
 0B1  C14  C10  C11  120.93  3.000
 0B1  C9   C10  C11  118.52  3.000
 0B1  H17  C9   C10  119.55  3.000
 0B1  H17  C9   C8   118.80  3.000
 0B1  C10  C9   C8   121.61  3.000
 0B1  C15  C14  C20  118.92  3.000
 0B1  C20  C14  C10  120.85  3.000
 0B1  C15  C14  C10  120.23  3.000
 0B1  H18  C20  C19  119.87  3.000
 0B1  H18  C20  C14  120.23  3.000
 0B1  C19  C20  C14  119.88  3.000
 0B1  H19  C19  C18  118.95  3.000
 0B1  H19  C19  C20  119.69  3.000
 0B1  C18  C19  C20  121.36  3.000
 0B1  H20  C18  C16  121.85  3.000
 0B1  H20  C18  C19  119.14  3.000
 0B1  C16  C18  C19  119.01  3.000
 0B1  O2   C16  C15  115.89  3.000
 0B1  O2   C16  C18  124.33  3.000
 0B1  C15  C16  C18  119.77  3.000
 0B1  H21  C15  C16  118.54  3.000
 0B1  H21  C15  C14  120.40  3.000
 0B1  C16  C15  C14  121.05  3.000
 0B1  C17  O2   C16  118.62  3.000
 0B1  H24  C17  H23  108.71  3.000
 0B1  H24  C17  H22  108.63  3.000
 0B1  H23  C17  H22  108.79  3.000
 0B1  H24  C17  O2   106.51  3.000
 0B1  H23  C17  O2   112.02  3.000
 0B1  H22  C17  O2   112.06  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
 0B1  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 0B1  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 0B1  CONST_03  C14  C10  C9   C8    180.00   0.0  0
 0B1  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 0B1  CONST_05  C10  C9   C8   C13     0.00   0.0  0
 0B1  CONST_06  C9   C8   C13  C12     0.00   0.0  0
 0B1  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 0B1  CONST_08  C14  C10  C11  C12   180.00   0.0  0
 0B1  CONST_11  C16  C15  C14  C10   180.00   0.0  0
 0B1  CONST_12  C19  C20  C14  C10   180.00   0.0  0
 0B1  CONST_15  C18  C16  C15  C14     0.00   0.0  0
 0B1  CONST_16  C18  C19  C20  C14     0.00   0.0  0
 0B1  CONST_17  C16  C15  C14  C20     0.00   0.0  0
 0B1  CONST_18  C16  C18  C19  C20     0.00   0.0  0
 0B1  CONST_19  C15  C14  C20  C19     0.00   0.0  0
 0B1  CONST_20  C15  C16  C18  C19     0.00   0.0  0
 0B1  CONST_21  C12  C13  C8   C7    180.00   0.0  0
 0B1  CONST_22  C10  C9   C8   C7    180.00   0.0  0
 0B1  CONST_23  N1   C4   N2   C1      0.00   0.0  0
 0B1  CONST_24  C3   N1   C4   N2      0.00   0.0  0
 0B1  CONST_25  C2   C1   N2   C4      0.00   0.0  0
 0B1  CONST_26  O2   C16  C15  C14   180.00   0.0  0
 0B1  CONST_27  O2   C16  C18  C19   180.00   0.0  0
 0B1  CONST_28  C4   N2   C1   O1    180.00   0.0  0
 0B1  CONST_29  N3   C4   N2   C1    180.00   0.0  0
 0B1  CONST_30  C2   C1   N2   C5    180.00   0.0  0
 0B1  CONST_31  N1   C4   N2   C5    180.00   0.0  0
 0B1  CONST_32  C3   N1   C4   N3    180.00   0.0  0
 0B1  CONST_33  H14  C13  C8   C7      0.00   0.0  0
 0B1  CONST_34  H17  C9   C8   C7      0.00   0.0  0
 0B1  CONST_35  H15  C12  C13  C8    180.00   0.0  0
 0B1  CONST_36  H16  C11  C12  C13   180.00   0.0  0
 0B1  CONST_37  H21  C15  C14  C10     0.00   0.0  0
 0B1  CONST_38  H18  C20  C14  C10     0.00   0.0  0
 0B1  CONST_39  H19  C19  C20  C14   180.00   0.0  0
 0B1  CONST_40  H20  C18  C19  C20   180.00   0.0  0
 0B1  CONST_41  C5   N2   C1   O1      0.00   0.0  0
 0B1  CONST_42  N3   C4   N2   C5      0.00   0.0  0
 0B1  CONST_43  H5   N3   C4   N2      0.00   0.0  0
 0B1  CONST_44  H6   N3   C4   N2    180.00   0.0  0
 0B1  Var_01    C21  C6   C3   N1    -13.24  30.0  3
 0B1  Var_02    C7   C21  C6   C3    107.17  30.0  1
 0B1  Var_03    C13  C8   C7   C6   -116.34  30.0  2
 0B1  Var_04    H1   C5   N2   C1      0.84  30.0  3
 0B1  Var_05    H22  C17  O2   C16   -61.24  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
 0B1  chir_01  C6  C21  C7  C3  both
 0B1  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
 0B1  plan-1  O1   0.020
 0B1  plan-1  C1   0.020
 0B1  plan-1  N2   0.020
 0B1  plan-1  C5   0.020
 0B1  plan-1  C4   0.020
 0B1  plan-1  N3   0.020
 0B1  plan-1  N1   0.020
 0B1  plan-1  C3   0.020
 0B1  plan-1  C2   0.020
 0B1  plan-1  C6   0.020
 0B1  plan-1  H5   0.020
 0B1  plan-1  H6   0.020
 0B1  plan-1  H8   0.020
 0B1  plan-2  C7   0.020
 0B1  plan-2  C8   0.020
 0B1  plan-2  C13  0.020
 0B1  plan-2  C12  0.020
 0B1  plan-2  C11  0.020
 0B1  plan-2  C10  0.020
 0B1  plan-2  C9   0.020
 0B1  plan-2  C14  0.020
 0B1  plan-2  H14  0.020
 0B1  plan-2  H15  0.020
 0B1  plan-2  H16  0.020
 0B1  plan-2  H17  0.020
 0B1  plan-3  C10  0.020
 0B1  plan-3  C14  0.020
 0B1  plan-3  C20  0.020
 0B1  plan-3  C19  0.020
 0B1  plan-3  C18  0.020
 0B1  plan-3  C16  0.020
 0B1  plan-3  C15  0.020
 0B1  plan-3  O2   0.020
 0B1  plan-3  H18  0.020
 0B1  plan-3  H19  0.020
 0B1  plan-3  H20  0.020
 0B1  plan-3  H21  0.020

