# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:31:19 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-[(3-chlorophenyl)methyl]-2-imino-5,5-dimethyl-imidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(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
 BDJ  BDJ  3-[(3-chlorophenyl)methyl]-2-imino-5,5-dimethyl-imidazolidin-4-one  ligand  31  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BDJ
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
 BDJ  C1   C   CR5   0   0.619  -1.6253  -1.5005   0.7152
 BDJ  N1   N   NR15  0  -0.661  -2.7419  -1.5510  -0.0570
 BDJ  O1   O   O     0  -0.436  -2.1392   1.8600   0.1228
 BDJ  C2   C   CR5   0   0.575  -2.1694   0.6523   0.1611
 BDJ  N2   N   NR5   0  -0.530  -1.3389  -0.1394   0.8948
 BDJ  C3   C   CR5   0  -0.035  -3.1161  -0.2613  -0.5992
 BDJ  N3   N   N     0  -0.687  -1.0084  -2.5143   1.1673
 BDJ  C4   C   CH3   0  -0.637  -2.8237  -0.1585  -2.0969
 BDJ  C5   C   CH3   0  -0.631  -4.5675   0.0898  -0.2916
 BDJ  C6   C   CH2   0  -0.435  -0.2622   0.3924   1.6990
 BDJ  C7   C   CR6   0   0.139   0.9382   0.7797   0.8741
 BDJ  C8   C   CR16  0  -0.296   1.4078   2.0865   0.8927
 BDJ  C9   C   CR16  0  -0.246   2.5189   2.4452   0.1414
 BDJ  C10  C   CR16  0  -0.226   3.1701   1.5071  -0.6442
 BDJ  C11  C   CR6   0  -0.020   2.6891   0.2060  -0.6609
 BDJ  C12  C   CR16  0  -0.250   1.5867  -0.1690   0.0876
 BDJ  CL1  CL  CL    0  -0.127   3.4901  -0.9819  -1.6380
 BDJ  H1   H   HNR5  0   0.399  -2.9674  -2.4066  -0.5388
 BDJ  H2   H   H     0   0.343  -0.2069  -2.2699   1.7338
 BDJ  H3   H   HCH3  0   0.252  -3.4468  -0.8663  -2.6444
 BDJ  H4   H   HCH3  0   0.245  -3.0461   0.8426  -2.4651
 BDJ  H5   H   HCH3  0   0.244  -1.7794  -0.3841  -2.3158
 BDJ  H6   H   HCH3  0   0.244  -4.7679   0.0365   0.7784
 BDJ  H7   H   HCH3  0   0.239  -4.8013   1.0946  -0.6406
 BDJ  H8   H   HCH3  0   0.247  -5.2347  -0.6077  -0.7987
 BDJ  H9   H   HCH2  0   0.299  -0.6356   1.2580   2.2450
 BDJ  H10  H   HCH2  0   0.292   0.0034  -0.3494   2.4532
 BDJ  H11  H   HCR6  0   0.263   0.9037   2.8289   1.4982
 BDJ  H12  H   HCR6  0   0.271   2.8789   3.4651   0.1608
 BDJ  H13  H   HCR6  0   0.282   4.0348   1.7835  -1.2318
 BDJ  H14  H   HCR6  0   0.264   1.2392  -1.1942   0.0566

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
 BDJ  C1   N1   single    1.358  0.020  1.358
 BDJ  C1   N2   single    1.402  0.020  1.402
 BDJ  C1   N3   double    1.270  0.020  1.270
 BDJ  N1   C3   single    1.448  0.020  1.448
 BDJ  N1   H1   single    0.890  0.020  1.040
 BDJ  O1   C2   double    1.209  0.020  1.209
 BDJ  C2   N2   single    1.362  0.020  1.362
 BDJ  C2   C3   single    1.520  0.020  1.520
 BDJ  N2   C6   single    1.445  0.020  1.445
 BDJ  C3   C4   single    1.529  0.020  1.529
 BDJ  C3   C5   single    1.525  0.020  1.525
 BDJ  N3   H2   single    0.890  0.020  1.040
 BDJ  C4   H3   single    0.970  0.020  1.090
 BDJ  C4   H4   single    0.970  0.020  1.090
 BDJ  C4   H5   single    0.970  0.020  1.090
 BDJ  C5   H6   single    0.970  0.020  1.090
 BDJ  C5   H7   single    0.970  0.020  1.090
 BDJ  C5   H8   single    0.970  0.020  1.090
 BDJ  C6   C7   single    1.507  0.020  1.507
 BDJ  C6   H9   single    0.970  0.020  1.090
 BDJ  C6   H10  single    0.970  0.020  1.090
 BDJ  C7   C8   aromatic  1.389  0.020  1.389
 BDJ  C7   C12  aromatic  1.393  0.020  1.393
 BDJ  C8   C9   aromatic  1.388  0.020  1.388
 BDJ  C8   H11  single    0.930  0.020  1.080
 BDJ  C9   C10  aromatic  1.386  0.020  1.386
 BDJ  C9   H12  single    0.930  0.020  1.080
 BDJ  C10  C11  aromatic  1.387  0.020  1.387
 BDJ  C10  H13  single    0.930  0.020  1.080
 BDJ  C11  C12  aromatic  1.384  0.020  1.384
 BDJ  C11  CL1  single    1.734  0.020  1.734
 BDJ  C12  H14  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
 BDJ  N3   C1   N2   129.05  3.000
 BDJ  N3   C1   N1   124.88  3.000
 BDJ  N2   C1   N1   106.07  3.000
 BDJ  H1   N1   C3   121.29  3.000
 BDJ  H1   N1   C1   119.17  3.000
 BDJ  C3   N1   C1   113.09  3.000
 BDJ  C3   C2   N2   107.46  3.000
 BDJ  C3   C2   O1   126.90  3.000
 BDJ  N2   C2   O1   125.64  3.000
 BDJ  C6   N2   C2   122.70  3.000
 BDJ  C6   N2   C1   125.49  3.000
 BDJ  C2   N2   C1   111.75  3.000
 BDJ  C5   C3   C4   111.35  3.000
 BDJ  C5   C3   C2   110.71  3.000
 BDJ  C4   C3   C2   109.29  3.000
 BDJ  C5   C3   N1   112.06  3.000
 BDJ  C4   C3   N1   112.16  3.000
 BDJ  C2   C3   N1   100.78  3.000
 BDJ  H2   N3   C1   113.04  3.000
 BDJ  H5   C4   H4   108.52  3.000
 BDJ  H5   C4   H3   108.19  3.000
 BDJ  H4   C4   H3   108.06  3.000
 BDJ  H5   C4   C3   111.46  3.000
 BDJ  H4   C4   C3   110.71  3.000
 BDJ  H3   C4   C3   109.80  3.000
 BDJ  H8   C5   H7   108.05  3.000
 BDJ  H8   C5   H6   108.23  3.000
 BDJ  H7   C5   H6   108.68  3.000
 BDJ  H8   C5   C3   109.96  3.000
 BDJ  H7   C5   C3   110.62  3.000
 BDJ  H6   C5   C3   111.21  3.000
 BDJ  H10  C6   H9   106.10  3.000
 BDJ  H10  C6   C7   111.06  3.000
 BDJ  H9   C6   C7   110.07  3.000
 BDJ  H10  C6   N2   108.42  3.000
 BDJ  H9   C6   N2   108.41  3.000
 BDJ  C7   C6   N2   112.54  3.000
 BDJ  C12  C7   C8   119.42  3.000
 BDJ  C12  C7   C6   120.33  3.000
 BDJ  C8   C7   C6   120.25  3.000
 BDJ  H11  C8   C9   119.87  3.000
 BDJ  H11  C8   C7   119.70  3.000
 BDJ  C9   C8   C7   120.43  3.000
 BDJ  H12  C9   C10  119.47  3.000
 BDJ  H12  C9   C8   120.02  3.000
 BDJ  C10  C9   C8   120.52  3.000
 BDJ  H13  C10  C11  120.69  3.000
 BDJ  H13  C10  C9   120.71  3.000
 BDJ  C11  C10  C9   118.60  3.000
 BDJ  CL1  C11  C12  119.14  3.000
 BDJ  CL1  C11  C10  119.28  3.000
 BDJ  C12  C11  C10  121.58  3.000
 BDJ  H14  C12  C11  119.77  3.000
 BDJ  H14  C12  C7   120.77  3.000
 BDJ  C11  C12  C7   119.45  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
 BDJ  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 BDJ  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 BDJ  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 BDJ  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 BDJ  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 BDJ  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 BDJ  CONST_07  C2   C3   N1   C1     0.00   0.0  0
 BDJ  CONST_08  C3   C2   N2   C1     0.00   0.0  0
 BDJ  CONST_09  C2   N2   C1   N1     0.00   0.0  0
 BDJ  CONST_10  N2   C2   C3   N1     0.00   0.0  0
 BDJ  CONST_11  C3   N1   C1   N2     0.00   0.0  0
 BDJ  CONST_12  C9   C8   C7   C6   180.00   0.0  0
 BDJ  CONST_13  C11  C12  C7   C6   180.00   0.0  0
 BDJ  CONST_14  CL1  C11  C12  C7   180.00   0.0  0
 BDJ  CONST_15  CL1  C11  C10  C9   180.00   0.0  0
 BDJ  CONST_16  O1   C2   N2   C1   180.00   0.0  0
 BDJ  CONST_17  C6   N2   C1   N1   180.00   0.0  0
 BDJ  CONST_18  N3   C1   N2   C2   180.00   0.0  0
 BDJ  CONST_19  N3   C1   N1   C3   180.00   0.0  0
 BDJ  CONST_20  C6   N2   C2   C3   180.00   0.0  0
 BDJ  CONST_21  H12  C9   C8   C7   180.00   0.0  0
 BDJ  CONST_22  H14  C12  C7   C8   180.00   0.0  0
 BDJ  CONST_23  H13  C10  C9   C8   180.00   0.0  0
 BDJ  CONST_24  H11  C8   C9   C10  180.00   0.0  0
 BDJ  CONST_26  C6   N2   C2   O1     0.00   0.0  0
 BDJ  CONST_27  C6   N2   C1   N3     0.00   0.0  0
 BDJ  CONST_28  H2   N3   C1   N1   180.00   0.0  0
 BDJ  Var_01    C4   C3   N1   C1   107.00  30.0  1
 BDJ  Var_02    C7   C6   N2   C1    99.14  30.0  3
 BDJ  Var_03    C8   C7   C6   N2   121.13  30.0  2
 BDJ  Var_04    H3   C4   C3   N1    64.87  30.0  3
 BDJ  Var_05    H6   C5   C3   N1    54.68  30.0  3

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
 BDJ  plan-1  C6   0.020
 BDJ  plan-1  C7   0.020
 BDJ  plan-1  C8   0.020
 BDJ  plan-1  C9   0.020
 BDJ  plan-1  C10  0.020
 BDJ  plan-1  C11  0.020
 BDJ  plan-1  C12  0.020
 BDJ  plan-1  CL1  0.020
 BDJ  plan-1  H11  0.020
 BDJ  plan-1  H12  0.020
 BDJ  plan-1  H13  0.020
 BDJ  plan-1  H14  0.020
 BDJ  plan-2  C1   0.020
 BDJ  plan-2  N1   0.020
 BDJ  plan-2  O1   0.020
 BDJ  plan-2  C2   0.020
 BDJ  plan-2  N2   0.020
 BDJ  plan-2  C3   0.020
 BDJ  plan-2  N3   0.020
 BDJ  plan-2  C6   0.020
 BDJ  plan-2  H1   0.020
 BDJ  plan-2  H2   0.020

