# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:28:28 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (5R)-3-[(3-chlorophenyl)methyl]-2-imino-5-methyl-5-(2-methylpropyl)imidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@]1(C)NC(=N)N(Cc2cccc(Cl)c2)C1=O
#
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
 BDO  BDO  (5R)-3-[(3-chlorophenyl)methyl]-2-imino-5-methyl-5-(2-methylpropyl)imidazolidin-4-one  ligand  40  20  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BDO
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
 BDO  C1   C   CR5   0   0.613  -1.3059  -1.6562  -1.0783
 BDO  N1   N   NR15  0  -0.663  -2.4845  -1.0149  -1.2801
 BDO  O1   O   O     0  -0.431  -1.8865  -0.3766   2.0719
 BDO  C2   C   CR5   0   0.566  -1.9058  -0.6822   0.9031
 BDO  N2   N   NR5   0  -0.527  -1.0087  -1.5000   0.2833
 BDO  C3   C   CR5   0  -0.028  -2.9034  -0.2205  -0.1463
 BDO  N3   N   N     0  -0.683  -0.6469  -2.2625  -1.9785
 BDO  C4   C   CH2   0  -0.383  -2.7687   1.2982  -0.3557
 BDO  C5   C   CH3   0  -0.631  -4.3280  -0.5686   0.2772
 BDO  C6   C   CH2   0  -0.424   0.1805  -1.9915   0.9428
 BDO  C7   C   CR6   0   0.122   1.1878  -0.8898   1.1547
 BDO  C8   C   CR16  0  -0.298   1.6339  -0.5761   2.4313
 BDO  C9   C   CR16  0  -0.263   2.5345   0.4636   2.6238
 BDO  C10  C   CR16  0  -0.249   2.9877   1.2127   1.5485
 BDO  C11  C   CR6   0  -0.025   2.5338   0.8910   0.2772
 BDO  C12  C   CR16  0  -0.246   1.6511  -0.1540   0.0673
 BDO  C13  C   CH3   0  -0.664  -0.9096   1.6543  -2.0963
 BDO  C14  C   CH3   0  -0.648  -1.3903   3.3729  -0.3569
 BDO  C15  C   CH1   0  -0.261  -1.3781   1.8751  -0.6593
 BDO  H1   H   HNR5  0   0.397  -2.7743  -0.7949  -2.2189
 BDO  H2   H   H     0   0.340   0.1963  -2.6972  -1.6274
 BDO  H3   H   HCH2  0   0.240  -3.4671   1.5885  -1.1489
 BDO  H4   H   HCH2  0   0.240  -3.1456   1.7657   0.5585
 BDO  H5   H   HCH3  0   0.245  -4.4331  -1.6375   0.4626
 BDO  H6   H   HCH3  0   0.239  -4.6077  -0.0291   1.1812
 BDO  H7   H   HCH3  0   0.245  -5.0275  -0.2891  -0.5116
 BDO  H8   H   HCH2  0   0.297  -0.1026  -2.4374   1.8959
 BDO  H9   H   HCH2  0   0.286   0.5993  -2.7977   0.3393
 BDO  H10  H   HCR6  0   0.269   1.2701  -1.1412   3.2802
 BDO  H11  H   HCR6  0   0.285   2.8768   0.7041   3.6214
 BDO  H12  H   HCR6  0   0.311   3.6752   2.0340   1.6963
 BDO  H13  H   HCR6  0   0.264   1.3213  -0.3853  -0.9387
 BDO  H14  H   HCH3  0   0.214  -1.6267   2.0762  -2.8050
 BDO  H15  H   HCH3  0   0.229   0.0473   2.1528  -2.2611
 BDO  H16  H   HCH3  0   0.233  -0.7661   0.6064  -2.3541
 BDO  H17  H   HCH3  0   0.226  -1.6467   3.5686   0.6852
 BDO  H18  H   HCH3  0   0.232  -0.4133   3.8177  -0.5513
 BDO  H19  H   HCH3  0   0.208  -2.1210   3.8912  -0.9826
 BDO  H20  H   HCH1  0   0.238  -0.6421   1.4209   0.0142
 BDO  CL1  CL  CL    0  -0.114   3.0742   1.8229  -1.0803

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
 BDO  C1   N1   single    1.357  0.020  1.357
 BDO  C1   N2   single    1.402  0.020  1.402
 BDO  C1   N3   double    1.270  0.020  1.270
 BDO  N1   C3   single    1.446  0.020  1.446
 BDO  N1   H1   single    0.890  0.020  1.040
 BDO  O1   C2   double    1.208  0.020  1.208
 BDO  C2   N2   single    1.363  0.020  1.363
 BDO  C2   C3   single    1.520  0.020  1.520
 BDO  N2   C6   single    1.446  0.020  1.446
 BDO  C3   C4   single    1.539  0.020  1.539
 BDO  C3   C5   single    1.526  0.020  1.526
 BDO  N3   H2   single    0.890  0.020  1.040
 BDO  C4   C15  single    1.536  0.020  1.536
 BDO  C4   H3   single    0.970  0.020  1.090
 BDO  C4   H4   single    0.970  0.020  1.090
 BDO  C5   H5   single    0.970  0.020  1.090
 BDO  C5   H6   single    0.970  0.020  1.090
 BDO  C5   H7   single    0.970  0.020  1.090
 BDO  C6   C7   single    1.508  0.020  1.508
 BDO  C6   H8   single    0.970  0.020  1.090
 BDO  C6   H9   single    0.970  0.020  1.090
 BDO  C7   C8   aromatic  1.388  0.020  1.388
 BDO  C7   C12  aromatic  1.392  0.020  1.392
 BDO  C8   C9   aromatic  1.389  0.020  1.389
 BDO  C8   H10  single    0.930  0.020  1.080
 BDO  C9   C10  aromatic  1.387  0.020  1.387
 BDO  C9   H11  single    0.930  0.020  1.080
 BDO  C10  C11  aromatic  1.388  0.020  1.388
 BDO  C10  H12  single    0.930  0.020  1.080
 BDO  C11  C12  aromatic  1.384  0.020  1.384
 BDO  C11  CL1  single    1.733  0.020  1.733
 BDO  C12  H13  single    0.930  0.020  1.080
 BDO  C13  C15  single    1.527  0.020  1.527
 BDO  C13  H14  single    0.970  0.020  1.090
 BDO  C13  H15  single    0.970  0.020  1.090
 BDO  C13  H16  single    0.970  0.020  1.090
 BDO  C14  C15  single    1.528  0.020  1.528
 BDO  C14  H17  single    0.970  0.020  1.090
 BDO  C14  H18  single    0.970  0.020  1.090
 BDO  C14  H19  single    0.970  0.020  1.090
 BDO  C15  H20  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
 BDO  N3   C1   N2   129.17  3.000
 BDO  N3   C1   N1   124.82  3.000
 BDO  N2   C1   N1   106.01  3.000
 BDO  H1   N1   C3   121.83  3.000
 BDO  H1   N1   C1   119.47  3.000
 BDO  C3   N1   C1   113.24  3.000
 BDO  C3   C2   N2   107.48  3.000
 BDO  C3   C2   O1   126.98  3.000
 BDO  N2   C2   O1   125.53  3.000
 BDO  C6   N2   C2   122.54  3.000
 BDO  C6   N2   C1   125.40  3.000
 BDO  C2   N2   C1   111.65  3.000
 BDO  C5   C3   C4   110.15  3.000
 BDO  C5   C3   C2   110.60  3.000
 BDO  C4   C3   C2   109.65  3.000
 BDO  C5   C3   N1   111.26  3.000
 BDO  C4   C3   N1   114.20  3.000
 BDO  C2   C3   N1   100.61  3.000
 BDO  H2   N3   C1   113.06  3.000
 BDO  H4   C4   H3   105.79  3.000
 BDO  H4   C4   C15  108.46  3.000
 BDO  H3   C4   C15  109.54  3.000
 BDO  H4   C4   C3   106.13  3.000
 BDO  H3   C4   C3   107.71  3.000
 BDO  C15  C4   C3   118.48  3.000
 BDO  H7   C5   H6   107.98  3.000
 BDO  H7   C5   H5   108.21  3.000
 BDO  H6   C5   H5   108.65  3.000
 BDO  H7   C5   C3   109.84  3.000
 BDO  H6   C5   C3   110.91  3.000
 BDO  H5   C5   C3   111.15  3.000
 BDO  H9   C6   H8   106.34  3.000
 BDO  H9   C6   C7   111.18  3.000
 BDO  H8   C6   C7   110.47  3.000
 BDO  H9   C6   N2   108.34  3.000
 BDO  H8   C6   N2   108.93  3.000
 BDO  C7   C6   N2   111.41  3.000
 BDO  C12  C7   C8   119.47  3.000
 BDO  C12  C7   C6   119.91  3.000
 BDO  C8   C7   C6   120.60  3.000
 BDO  H10  C8   C9   119.99  3.000
 BDO  H10  C8   C7   119.68  3.000
 BDO  C9   C8   C7   120.33  3.000
 BDO  H11  C9   C10  119.45  3.000
 BDO  H11  C9   C8   119.96  3.000
 BDO  C10  C9   C8   120.59  3.000
 BDO  H12  C10  C11  120.62  3.000
 BDO  H12  C10  C9   120.81  3.000
 BDO  C11  C10  C9   118.57  3.000
 BDO  CL1  C11  C12  119.08  3.000
 BDO  CL1  C11  C10  119.41  3.000
 BDO  C12  C11  C10  121.51  3.000
 BDO  H13  C12  C11  119.75  3.000
 BDO  H13  C12  C7   120.73  3.000
 BDO  C11  C12  C7   119.52  3.000
 BDO  H16  C13  H15  106.75  3.000
 BDO  H16  C13  H14  107.73  3.000
 BDO  H15  C13  H14  107.52  3.000
 BDO  H16  C13  C15  113.73  3.000
 BDO  H15  C13  C15  110.18  3.000
 BDO  H14  C13  C15  110.67  3.000
 BDO  H19  C14  H18  107.67  3.000
 BDO  H19  C14  H17  107.74  3.000
 BDO  H18  C14  H17  107.91  3.000
 BDO  H19  C14  C15  110.91  3.000
 BDO  H18  C14  C15  110.93  3.000
 BDO  H17  C14  C15  111.52  3.000
 BDO  H20  C15  C14  106.85  3.000
 BDO  H20  C15  C13  108.19  3.000
 BDO  C14  C15  C13  109.29  3.000
 BDO  H20  C15  C4   109.32  3.000
 BDO  C14  C15  C4   108.78  3.000
 BDO  C13  C15  C4   114.17  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
 BDO  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 BDO  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 BDO  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 BDO  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 BDO  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 BDO  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 BDO  CONST_07  C3   C2   N2   C1     0.00   0.0  0
 BDO  CONST_08  C2   N2   C1   N1     0.00   0.0  0
 BDO  CONST_09  C3   N1   C1   N2     0.00   0.0  0
 BDO  CONST_10  C9   C8   C7   C6   180.00   0.0  0
 BDO  CONST_11  C11  C12  C7   C6   180.00   0.0  0
 BDO  CONST_12  CL1  C11  C12  C7   180.00   0.0  0
 BDO  CONST_13  CL1  C11  C10  C9   180.00   0.0  0
 BDO  CONST_14  O1   C2   N2   C1   180.00   0.0  0
 BDO  CONST_15  C6   N2   C1   N1   180.00   0.0  0
 BDO  CONST_16  N3   C1   N2   C2   180.00   0.0  0
 BDO  CONST_17  N3   C1   N1   C3   180.00   0.0  0
 BDO  CONST_18  C6   N2   C2   C3   180.00   0.0  0
 BDO  CONST_19  H11  C9   C8   C7   180.00   0.0  0
 BDO  CONST_20  H13  C12  C7   C8   180.00   0.0  0
 BDO  CONST_21  H12  C10  C9   C8   180.00   0.0  0
 BDO  CONST_22  H10  C8   C9   C10  180.00   0.0  0
 BDO  CONST_24  C6   N2   C2   O1     0.00   0.0  0
 BDO  CONST_25  C6   N2   C1   N3     0.00   0.0  0
 BDO  CONST_26  H2   N3   C1   N1   180.00   0.0  0
 BDO  Var_01    C7   C6   N2   C1   101.24  30.0  3
 BDO  Var_02    C8   C7   C6   N2   121.70  30.0  2
 BDO  Var_03    C13  C15  C4   C3    76.81  30.0  3
 BDO  Var_04    H14  C13  C15  C4    56.96  30.0  3
 BDO  Var_05    H17  C14  C15  C4    59.10  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
 BDO  chir_01  C3  C2  N1  C5  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
 BDO  plan-1  C6   0.020
 BDO  plan-1  C7   0.020
 BDO  plan-1  C8   0.020
 BDO  plan-1  C9   0.020
 BDO  plan-1  C10  0.020
 BDO  plan-1  C11  0.020
 BDO  plan-1  C12  0.020
 BDO  plan-1  H10  0.020
 BDO  plan-1  H11  0.020
 BDO  plan-1  H12  0.020
 BDO  plan-1  H13  0.020
 BDO  plan-1  CL1  0.020
 BDO  plan-2  C1   0.020
 BDO  plan-2  N1   0.020
 BDO  plan-2  O1   0.020
 BDO  plan-2  C2   0.020
 BDO  plan-2  N2   0.020
 BDO  plan-2  C3   0.020
 BDO  plan-2  N3   0.020
 BDO  plan-2  C6   0.020
 BDO  plan-2  H1   0.020
 BDO  plan-2  H2   0.020

