# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 23:11:29 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (5S)-2-amino-5-(2,6-diethylpyridin-4-yl)-3-methyl-5-[3-(pyrimidin-5-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(cc(CC)n1)[C@@]2(N=C(N)N(C)C2=O)c3cccc(c3)c4cncnc4
#
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
 BX2  BX2  (5S)-2-amino-5-(2,6-diethylpyridin-4-yl)-3-methyl-5-[3-(pyrimidin-5-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one  ligand  54  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BX2
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
 BX2  C1    C  CH3   0  -0.663  -4.7622   2.7309  -2.0570
 BX2  N1    N  N     0  -0.440  -2.5413   2.7422   0.0286
 BX2  O1    O  O     0  -0.435   0.1238  -1.4612   2.3244
 BX2  C2    C  CH2   0  -0.490  -3.2675   2.4981  -2.2630
 BX2  N2    N  NR5   0  -0.519  -1.5978  -2.8626   1.7419
 BX2  C3    C  CR6   0   0.254  -2.6133   1.9368  -1.0325
 BX2  N3    N  N     0  -0.462  -2.1022  -2.1635  -0.3441
 BX2  C4    C  CR16  0  -0.385  -2.1413   0.6342  -1.0004
 BX2  N4    N  NH2   0  -0.846  -3.3411  -3.9247   0.5666
 BX2  C5    C  CR6   0   0.284  -1.5708   0.1392   0.1685
 BX2  N5    N  N     0  -0.387   4.7913   1.7217   0.6224
 BX2  C6    C  CR16  0  -0.428  -1.5050   0.9843   1.2628
 BX2  N6    N  N     0  -0.387   5.2691   1.8429  -1.6865
 BX2  C7    C  CR6   0   0.248  -2.0039   2.2831   1.1501
 BX2  C8    C  CH2   0  -0.493  -1.9062   3.2405   2.3035
 BX2  C9    C  CH3   0  -0.661  -0.7090   4.1781   2.1574
 BX2  C10   C  CR5   0  -0.255  -1.0574  -1.2954   0.1490
 BX2  C11   C  CR5   0   0.586  -0.7281  -1.8340   1.5519
 BX2  C12   C  CR5   0   0.682  -2.3701  -2.9981   0.5925
 BX2  C14   C  CR6   0   0.188   0.2114  -1.3724  -0.6906
 BX2  C15   C  CR16  0  -0.318   0.3611  -2.3376  -1.6772
 BX2  C16   C  CR16  0  -0.224   1.5364  -2.4002  -2.4159
 BX2  C17   C  CR16  0  -0.317   2.5671  -1.5082  -2.1760
 BX2  C18   C  CR6   0   0.110   2.4290  -0.5314  -1.1882
 BX2  C19   C  CR16  0  -0.345   1.2464  -0.4731  -0.4566
 BX2  C20   C  CR6   0  -0.046   3.5111   0.4265  -0.9180
 BX2  C21   C  CR16  0  -0.047   3.8238   0.8525   0.3701
 BX2  C22   C  CR16  0   0.050   5.4698   2.1752  -0.4205
 BX2  C23   C  CR16  0  -0.046   4.2947   0.9781  -1.9278
 BX2  H1    H  HCH3  0   0.234  -5.2216   3.1302  -2.9613
 BX2  H1A   H  HCH3  0   0.226  -5.2738   1.8010  -1.8051
 BX2  H1B   H  HCH3  0   0.226  -4.9392   3.4405  -1.2489
 BX2  H2    H  HCH2  0   0.238  -3.1101   1.8190  -3.1030
 BX2  H2A   H  HCH2  0   0.243  -2.7844   3.4429  -2.5242
 BX2  H4    H  HCR6  0   0.258  -2.2200   0.0080  -1.8795
 BX2  HN4   H  HNH2  0   0.408  -3.7819  -4.0898  -0.3235
 BX2  HN4A  H  HNH2  0   0.417  -3.2868  -4.7297   1.1685
 BX2  H6    H  HCR6  0   0.259  -1.0738   0.6711   2.2030
 BX2  H8    H  HCH2  0   0.243  -2.8251   3.8278   2.3574
 BX2  H8A   H  HCH2  0   0.240  -1.8243   2.6848   3.2396
 BX2  H9    H  HCH3  0   0.228  -0.7770   4.7596   1.2376
 BX2  H9A   H  HCH3  0   0.235  -0.6601   4.8756   2.9937
 BX2  H9B   H  HCH3  0   0.226   0.2281   3.6202   2.1328
 BX2  H13   H  HCH3  0   0.268  -2.6915  -3.6465   3.3443
 BX2  H13A  H  HCH3  0   0.266  -1.4162  -4.7137   2.7156
 BX2  H13B  H  HCH3  0   0.278  -0.9936  -3.2897   3.6703
 BX2  H15   H  HCR6  0   0.260  -0.4404  -3.0359  -1.8735
 BX2  H16   H  HCR6  0   0.262   1.6473  -3.1559  -3.1823
 BX2  H17   H  HCR6  0   0.260   3.4848  -1.5817  -2.7461
 BX2  H19   H  HCR6  0   0.254   1.1207   0.3025   0.2884
 BX2  H21   H  HCR6  0   0.275   3.2818   0.4649   1.2271
 BX2  H22   H  HCR6  0   0.268   6.2651   2.8841  -0.2190
 BX2  H23   H  HCR6  0   0.277   4.1172   0.7218  -2.9673
 BX2  C13   C  CH3   0  -0.557  -1.6854  -3.6795   2.9290

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
 BX2  C2   C1    single    1.527  0.020  1.527
 BX2  C1   H1    single    0.970  0.020  1.090
 BX2  C1   H1A   single    0.970  0.020  1.090
 BX2  C1   H1B   single    0.970  0.020  1.090
 BX2  C3   N1    aromatic  1.334  0.020  1.334
 BX2  N1   C7    aromatic  1.326  0.020  1.326
 BX2  C11  O1    double    1.209  0.020  1.209
 BX2  C2   C3    single    1.502  0.020  1.502
 BX2  C2   H2    single    0.970  0.020  1.090
 BX2  C2   H2A   single    0.970  0.020  1.090
 BX2  C12  N2    single    1.391  0.020  1.391
 BX2  N2   C13   single    1.444  0.020  1.444
 BX2  N2   C11   single    1.360  0.020  1.360
 BX2  C4   C3    aromatic  1.386  0.020  1.386
 BX2  N3   C12   double    1.283  0.020  1.283
 BX2  N3   C10   single    1.445  0.020  1.445
 BX2  C4   C5    aromatic  1.392  0.020  1.392
 BX2  C4   H4    single    0.930  0.020  1.080
 BX2  N4   C12   single    1.342  0.020  1.342
 BX2  N4   HN4   single    0.890  0.020  1.040
 BX2  N4   HN4A  single    0.890  0.020  1.040
 BX2  C10  C5    single    1.524  0.020  1.524
 BX2  C5   C6    aromatic  1.384  0.020  1.384
 BX2  N5   C21   aromatic  1.325  0.020  1.325
 BX2  N5   C22   aromatic  1.324  0.020  1.324
 BX2  C6   C7    aromatic  1.396  0.020  1.396
 BX2  C6   H6    single    0.930  0.020  1.080
 BX2  C22  N6    aromatic  1.324  0.020  1.324
 BX2  N6   C23   aromatic  1.325  0.020  1.325
 BX2  C7   C8    single    1.502  0.020  1.502
 BX2  C8   C9    single    1.528  0.020  1.528
 BX2  C8   H8    single    0.970  0.020  1.090
 BX2  C8   H8A   single    0.970  0.020  1.090
 BX2  C9   H9    single    0.970  0.020  1.090
 BX2  C9   H9A   single    0.970  0.020  1.090
 BX2  C9   H9B   single    0.970  0.020  1.090
 BX2  C14  C10   single    1.523  0.020  1.523
 BX2  C10  C11   single    1.538  0.020  1.538
 BX2  C13  H13   single    0.970  0.020  1.090
 BX2  C13  H13A  single    0.970  0.020  1.090
 BX2  C13  H13B  single    0.970  0.020  1.090
 BX2  C19  C14   aromatic  1.391  0.020  1.391
 BX2  C14  C15   aromatic  1.388  0.020  1.388
 BX2  C16  C15   aromatic  1.390  0.020  1.390
 BX2  C15  H15   single    0.930  0.020  1.080
 BX2  C17  C16   aromatic  1.384  0.020  1.384
 BX2  C16  H16   single    0.930  0.020  1.080
 BX2  C18  C17   aromatic  1.396  0.020  1.396
 BX2  C17  H17   single    0.930  0.020  1.080
 BX2  C20  C18   single    1.470  0.020  1.470
 BX2  C18  C19   aromatic  1.392  0.020  1.392
 BX2  C19  H19   single    0.930  0.020  1.080
 BX2  C21  C20   aromatic  1.392  0.020  1.392
 BX2  C20  C23   aromatic  1.392  0.020  1.392
 BX2  C21  H21   single    0.930  0.020  1.080
 BX2  C22  H22   single    0.930  0.020  1.080
 BX2  C23  H23   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
 BX2  H1B   C1   H1A   107.91  3.000
 BX2  H1B   C1   H1    107.95  3.000
 BX2  H1A   C1   H1    107.83  3.000
 BX2  H1B   C1   C2    110.99  3.000
 BX2  H1A   C1   C2    111.12  3.000
 BX2  H1    C1   C2    110.89  3.000
 BX2  C7    N1   C3    119.06  3.000
 BX2  H2A   C2   H2    106.87  3.000
 BX2  H2A   C2   C3    109.04  3.000
 BX2  H2    C2   C3    109.57  3.000
 BX2  H2A   C2   C1    109.47  3.000
 BX2  H2    C2   C1    109.87  3.000
 BX2  C3    C2   C1    111.89  3.000
 BX2  C13   N2   C12   126.19  3.000
 BX2  C13   N2   C11   125.55  3.000
 BX2  C12   N2   C11   108.25  3.000
 BX2  C4    C3   C2    121.23  3.000
 BX2  C4    C3   N1    122.05  3.000
 BX2  C2    C3   N1    116.70  3.000
 BX2  C12   N3   C10   107.02  3.000
 BX2  H4    C4   C5    120.41  3.000
 BX2  H4    C4   C3    120.02  3.000
 BX2  C5    C4   C3    119.56  3.000
 BX2  HN4A  N4   HN4   114.90  3.000
 BX2  HN4A  N4   C12   120.10  3.000
 BX2  HN4   N4   C12   116.55  3.000
 BX2  C10   C5   C6    124.67  3.000
 BX2  C6    C5   C4    117.80  3.000
 BX2  C10   C5   C4    117.53  3.000
 BX2  C22   N5   C21   116.67  3.000
 BX2  H6    C6   C7    118.85  3.000
 BX2  H6    C6   C5    121.99  3.000
 BX2  C7    C6   C5    119.16  3.000
 BX2  C23   N6   C22   116.70  3.000
 BX2  C8    C7   C6    120.52  3.000
 BX2  C8    C7   N1    117.08  3.000
 BX2  C6    C7   N1    122.37  3.000
 BX2  H8A   C8   H8    107.14  3.000
 BX2  H8A   C8   C9    109.61  3.000
 BX2  H8    C8   C9    109.52  3.000
 BX2  H8A   C8   C7    109.80  3.000
 BX2  H8    C8   C7    109.02  3.000
 BX2  C9    C8   C7    111.64  3.000
 BX2  H9B   C9   H9A   107.82  3.000
 BX2  H9B   C9   H9    107.90  3.000
 BX2  H9A   C9   H9    107.98  3.000
 BX2  H9B   C9   C8    111.19  3.000
 BX2  H9A   C9   C8    110.76  3.000
 BX2  H9    C9   C8    111.05  3.000
 BX2  C14   C10  C11   107.86  3.000
 BX2  C11   C10  C5    112.96  3.000
 BX2  C14   C10  C5    109.58  3.000
 BX2  C11   C10  N3    104.81  3.000
 BX2  C14   C10  N3    112.56  3.000
 BX2  C5    C10  N3    109.05  3.000
 BX2  C10   C11  N2    104.79  3.000
 BX2  C10   C11  O1    128.73  3.000
 BX2  N2    C11  O1    126.47  3.000
 BX2  N4    C12  N3    125.88  3.000
 BX2  N4    C12  N2    118.99  3.000
 BX2  N3    C12  N2    115.08  3.000
 BX2  C19   C14  C15   119.26  3.000
 BX2  C15   C14  C10   121.11  3.000
 BX2  C19   C14  C10   119.63  3.000
 BX2  H15   C15  C16   120.09  3.000
 BX2  H15   C15  C14   119.88  3.000
 BX2  C16   C15  C14   120.03  3.000
 BX2  H16   C16  C17   119.77  3.000
 BX2  H16   C16  C15   119.66  3.000
 BX2  C17   C16  C15   120.57  3.000
 BX2  H17   C17  C18   120.26  3.000
 BX2  H17   C17  C16   119.74  3.000
 BX2  C18   C17  C16   119.99  3.000
 BX2  C20   C18  C19   120.10  3.000
 BX2  C19   C18  C17   119.03  3.000
 BX2  C20   C18  C17   120.87  3.000
 BX2  H19   C19  C18   119.36  3.000
 BX2  H19   C19  C14   119.50  3.000
 BX2  C18   C19  C14   121.11  3.000
 BX2  C23   C20  C21   115.05  3.000
 BX2  C23   C20  C18   122.62  3.000
 BX2  C21   C20  C18   122.32  3.000
 BX2  H21   C21  C20   120.60  3.000
 BX2  H21   C21  N5    116.65  3.000
 BX2  C20   C21  N5    122.75  3.000
 BX2  H22   C22  N6    116.93  3.000
 BX2  H22   C22  N5    116.96  3.000
 BX2  N6    C22  N5    126.11  3.000
 BX2  H23   C23  C20   120.61  3.000
 BX2  H23   C23  N6    116.67  3.000
 BX2  C20   C23  N6    122.71  3.000
 BX2  H13B  C13  H13A  108.47  3.000
 BX2  H13B  C13  H13   108.50  3.000
 BX2  H13A  C13  H13   109.37  3.000
 BX2  H13B  C13  N2    108.63  3.000
 BX2  H13A  C13  N2    111.16  3.000
 BX2  H13   C13  N2    110.64  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
 BX2  CONST_01  C5   C4   C3   N1      0.00   0.0  0
 BX2  CONST_02  C5   C6   C7   N1      0.00   0.0  0
 BX2  CONST_03  C6   C7   N1   C3      0.00   0.0  0
 BX2  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 BX2  CONST_05  C7   N1   C3   C4      0.00   0.0  0
 BX2  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 BX2  CONST_07  C18  C20  C21  N5    180.00   0.0  0
 BX2  CONST_08  C23  C20  C21  N5      0.00   0.0  0
 BX2  CONST_09  C23  N6   C22  N5      0.00   0.0  0
 BX2  CONST_10  C21  N5   C22  N6      0.00   0.0  0
 BX2  CONST_11  C18  C20  C23  N6    180.00   0.0  0
 BX2  CONST_12  C21  C20  C23  N6      0.00   0.0  0
 BX2  CONST_13  C17  C18  C19  C14     0.00   0.0  0
 BX2  CONST_14  C20  C18  C19  C14   180.00   0.0  0
 BX2  CONST_15  C17  C16  C15  C14     0.00   0.0  0
 BX2  CONST_16  C18  C19  C14  C15     0.00   0.0  0
 BX2  CONST_17  C18  C17  C16  C15     0.00   0.0  0
 BX2  CONST_18  C19  C14  C15  C16     0.00   0.0  0
 BX2  CONST_19  C20  C18  C17  C16   180.00   0.0  0
 BX2  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 BX2  CONST_25  C22  N5   C21  C20     0.00   0.0  0
 BX2  CONST_26  C22  N6   C23  C20     0.00   0.0  0
 BX2  CONST_27  C10  C5   C4   C3    180.00   0.0  0
 BX2  CONST_28  C10  C5   C6   C7    180.00   0.0  0
 BX2  CONST_29  C18  C19  C14  C10   180.00   0.0  0
 BX2  CONST_30  C16  C15  C14  C10   180.00   0.0  0
 BX2  CONST_31  C10  N3   C12  N2      0.00   0.0  0
 BX2  CONST_32  C11  N2   C12  N3      0.00   0.0  0
 BX2  CONST_33  C12  N2   C11  C10     0.00   0.0  0
 BX2  CONST_34  C7   N1   C3   C2    180.00   0.0  0
 BX2  CONST_35  C5   C4   C3   C2    180.00   0.0  0
 BX2  CONST_36  C8   C7   N1   C3    180.00   0.0  0
 BX2  CONST_37  C8   C7   C6   C5    180.00   0.0  0
 BX2  CONST_38  C12  N2   C11  O1    180.00   0.0  0
 BX2  CONST_39  C13  N2   C12  N3    180.00   0.0  0
 BX2  CONST_40  C11  N2   C12  N4    180.00   0.0  0
 BX2  CONST_41  C10  N3   C12  N4    180.00   0.0  0
 BX2  CONST_42  C13  N2   C11  C10   180.00   0.0  0
 BX2  CONST_43  H4   C4   C3   N1    180.00   0.0  0
 BX2  CONST_44  H6   C6   C7   N1    180.00   0.0  0
 BX2  CONST_45  H19  C19  C14  C10     0.00   0.0  0
 BX2  CONST_46  H15  C15  C14  C10     0.00   0.0  0
 BX2  CONST_47  H16  C16  C15  C14   180.00   0.0  0
 BX2  CONST_48  H17  C17  C16  C15   180.00   0.0  0
 BX2  CONST_49  H21  C21  C20  C18     0.00   0.0  0
 BX2  CONST_50  H23  C23  C20  C18     0.00   0.0  0
 BX2  CONST_51  H22  C22  N5   C21   180.00   0.0  0
 BX2  CONST_52  C13  N2   C11  O1      0.00   0.0  0
 BX2  CONST_53  C13  N2   C12  N4      0.00   0.0  0
 BX2  CONST_54  HN4  N4   C12  N2    180.00   0.0  0
 BX2  Var_01    N1   C3   C2   C1    -67.74  30.0  2
 BX2  Var_02    C9   C8   C7   N1    -80.00  30.0  2
 BX2  Var_03    H13  C13  N2   C11   123.13  30.0  3
 BX2  Var_04    H1   C1   C2   C3   -179.53  30.0  3
 BX2  Var_05    H9   C9   C8   C7     59.20  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
 BX2  chir_01  C10  C5  C14  C11  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
 BX2  plan-1  N1    0.020
 BX2  plan-1  C2    0.020
 BX2  plan-1  C3    0.020
 BX2  plan-1  C4    0.020
 BX2  plan-1  C5    0.020
 BX2  plan-1  C6    0.020
 BX2  plan-1  C7    0.020
 BX2  plan-1  C8    0.020
 BX2  plan-1  C10   0.020
 BX2  plan-1  H4    0.020
 BX2  plan-1  H6    0.020
 BX2  plan-2  N5    0.020
 BX2  plan-2  N6    0.020
 BX2  plan-2  C18   0.020
 BX2  plan-2  C20   0.020
 BX2  plan-2  C21   0.020
 BX2  plan-2  C22   0.020
 BX2  plan-2  C23   0.020
 BX2  plan-2  H21   0.020
 BX2  plan-2  H22   0.020
 BX2  plan-2  H23   0.020
 BX2  plan-3  C10   0.020
 BX2  plan-3  C14   0.020
 BX2  plan-3  C15   0.020
 BX2  plan-3  C16   0.020
 BX2  plan-3  C17   0.020
 BX2  plan-3  C18   0.020
 BX2  plan-3  C19   0.020
 BX2  plan-3  C20   0.020
 BX2  plan-3  H15   0.020
 BX2  plan-3  H16   0.020
 BX2  plan-3  H17   0.020
 BX2  plan-3  H19   0.020
 BX2  plan-4  O1    0.020
 BX2  plan-4  N2    0.020
 BX2  plan-4  N3    0.020
 BX2  plan-4  N4    0.020
 BX2  plan-4  C10   0.020
 BX2  plan-4  C11   0.020
 BX2  plan-4  C12   0.020
 BX2  plan-4  HN4   0.020
 BX2  plan-4  HN4A  0.020
 BX2  plan-4  C13   0.020

