# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:54:03 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: (5S)-1-(4-chlorophenyl)-5-methylimidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N(C(=O)NC1=O)c2ccc(Cl)cc2
#
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
 W3Y  W3Y  (5S)-1-(4-chlorophenyl)-5-methylimidazolidine-2,4-dione  ligand  24  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W3Y
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
 W3Y  N1  N   NR15  0  -0.710   0.5267  12.8857  -1.6357
 W3Y  C4  C   CR6   0   0.377  -0.6193  11.4049  -4.6664
 W3Y  C5  C   CR16  0  -0.305  -0.1752  11.6938  -5.9539
 W3Y  C6  C   CR16  0  -0.208  -0.5625  10.9082  -7.0273
 W3Y  C7  C   CR6   0  -0.049  -1.3881   9.8179  -6.8084
 W3Y  C8  C   CR16  0  -0.210  -1.8414   9.5177  -5.5337
 W3Y  CL  CL  CL    0  -0.127  -1.8667   8.8235  -8.1437
 W3Y  C9  C   CR16  0  -0.290  -1.4667  10.3174  -4.4664
 W3Y  N   N   NR5   0  -0.622  -0.2316  12.2277  -3.5976
 W3Y  C2  C   CR5   0   0.710   0.1565  11.7703  -2.3728
 W3Y  O   O   O     0  -0.461   0.1910  10.6289  -1.9789
 W3Y  C3  C   CR5   0   0.566   0.4175  14.0480  -2.3323
 W3Y  O1  O   O     0  -0.425   0.6558  15.1608  -1.9332
 W3Y  C1  C   CR15  0  -0.235  -0.0745  13.6691  -3.7156
 W3Y  C   C   CH3   0  -0.655  -1.3581  14.3915  -4.0872
 W3Y  H1  H   HNR5  0   0.432   0.8367  12.8207  -0.6757
 W3Y  H2  H   HCR6  0   0.284   0.4831  12.5327  -6.1374
 W3Y  H3  H   HCR6  0   0.286  -0.2104  11.1446  -8.0220
 W3Y  H4  H   HCR6  0   0.285  -2.4965   8.6734  -5.3680
 W3Y  H5  H   HCR6  0   0.281  -1.8513  10.0896  -3.4833
 W3Y  H6  H   HCR5  0   0.313   0.7179  13.9165  -4.4302
 W3Y  H7  H   HCH3  0   0.258  -1.1817  15.4654  -4.1127
 W3Y  H8  H   HCH3  0   0.257  -1.7003  14.0887  -5.0761
 W3Y  H9  H   HCH3  0   0.248  -2.1479  14.1823  -3.3664

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
 W3Y  CL  C7  single    1.732  0.020  1.732
 W3Y  C6  C7  aromatic  1.385  0.020  1.385
 W3Y  C6  C5  aromatic  1.385  0.020  1.385
 W3Y  C7  C8  aromatic  1.386  0.020  1.386
 W3Y  C5  C4  aromatic  1.392  0.020  1.392
 W3Y  C8  C9  aromatic  1.385  0.020  1.385
 W3Y  C4  C9  aromatic  1.393  0.020  1.393
 W3Y  C4  N   single    1.403  0.020  1.403
 W3Y  C   C1  single    1.519  0.020  1.519
 W3Y  C1  N   single    1.455  0.020  1.455
 W3Y  C1  C3  single    1.516  0.020  1.516
 W3Y  N   C2  single    1.364  0.020  1.364
 W3Y  C2  O   double    1.208  0.020  1.208
 W3Y  C2  N1  single    1.387  0.020  1.387
 W3Y  C3  O1  double    1.206  0.020  1.206
 W3Y  C3  N1  single    1.359  0.020  1.359
 W3Y  N1  H1  single    0.860  0.020  1.020
 W3Y  C5  H2  single    0.930  0.020  1.080
 W3Y  C6  H3  single    0.930  0.020  1.080
 W3Y  C8  H4  single    0.930  0.020  1.080
 W3Y  C9  H5  single    0.930  0.020  1.080
 W3Y  C1  H6  single    0.970  0.020  1.090
 W3Y  C   H7  single    0.970  0.020  1.090
 W3Y  C   H8  single    0.970  0.020  1.090
 W3Y  C   H9  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
 W3Y  H1  N1  C3  124.49  3.000
 W3Y  H1  N1  C2  122.33  3.000
 W3Y  C3  N1  C2  113.18  3.000
 W3Y  N   C4  C9  121.09  3.000
 W3Y  N   C4  C5  119.64  3.000
 W3Y  C9  C4  C5  119.26  3.000
 W3Y  H2  C5  C6  118.57  3.000
 W3Y  H2  C5  C4  120.79  3.000
 W3Y  C6  C5  C4  120.64  3.000
 W3Y  H3  C6  C7  120.77  3.000
 W3Y  H3  C6  C5  119.85  3.000
 W3Y  C7  C6  C5  119.38  3.000
 W3Y  CL  C7  C8  119.62  3.000
 W3Y  C8  C7  C6  120.72  3.000
 W3Y  CL  C7  C6  119.66  3.000
 W3Y  H4  C8  C9  119.77  3.000
 W3Y  H4  C8  C7  120.55  3.000
 W3Y  C9  C8  C7  119.68  3.000
 W3Y  H5  C9  C8  118.89  3.000
 W3Y  H5  C9  C4  120.80  3.000
 W3Y  C8  C9  C4  120.30  3.000
 W3Y  C1  N   C2  112.00  3.000
 W3Y  C2  N   C4  124.46  3.000
 W3Y  C1  N   C4  123.29  3.000
 W3Y  O   C2  N   128.17  3.000
 W3Y  O   C2  N1  125.37  3.000
 W3Y  N   C2  N1  106.46  3.000
 W3Y  C1  C3  O1  126.63  3.000
 W3Y  O1  C3  N1  127.12  3.000
 W3Y  C1  C3  N1  106.25  3.000
 W3Y  H6  C1  C   110.14  3.000
 W3Y  H6  C1  C3  107.70  3.000
 W3Y  C   C1  C3  112.24  3.000
 W3Y  H6  C1  N   110.79  3.000
 W3Y  C3  C1  N   102.04  3.000
 W3Y  C   C1  N   113.57  3.000
 W3Y  H9  C   H8  108.62  3.000
 W3Y  H9  C   H7  108.81  3.000
 W3Y  H8  C   H7  107.69  3.000
 W3Y  H9  C   C1  111.06  3.000
 W3Y  H8  C   C1  110.81  3.000
 W3Y  H7  C   C1  109.76  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
 W3Y  CONST_01  C7  C6  C5  C4    0.00   0.0  0
 W3Y  CONST_02  C7  C8  C9  C4    0.00   0.0  0
 W3Y  CONST_03  C8  C7  C6  C5    0.00   0.0  0
 W3Y  CONST_04  C8  C9  C4  C5    0.00   0.0  0
 W3Y  CONST_05  C9  C8  C7  C6    0.00   0.0  0
 W3Y  CONST_06  C9  C4  C5  C6    0.00   0.0  0
 W3Y  CONST_07  N   C4  C5  C6  180.00   0.0  0
 W3Y  CONST_08  N   C4  C9  C8  180.00   0.0  0
 W3Y  CONST_09  C4  N   C2  N1  180.00   0.0  0
 W3Y  CONST_10  C1  N   C2  N1    0.00   0.0  0
 W3Y  CONST_11  C3  N1  C2  N     0.00   0.0  0
 W3Y  CONST_12  C1  C3  N1  C2    0.00   0.0  0
 W3Y  CONST_13  CL  C7  C6  C5  180.00   0.0  0
 W3Y  CONST_14  C9  C8  C7  CL  180.00   0.0  0
 W3Y  CONST_15  O   C2  N   C4    0.00   0.0  0
 W3Y  CONST_16  C1  N   C2  O   180.00   0.0  0
 W3Y  CONST_17  C3  N1  C2  O   180.00   0.0  0
 W3Y  CONST_18  H3  C6  C5  C4  180.00   0.0  0
 W3Y  CONST_19  H4  C8  C9  C4  180.00   0.0  0
 W3Y  CONST_20  H5  C9  C4  C5  180.00   0.0  0
 W3Y  CONST_21  H2  C5  C6  C7  180.00   0.0  0
 W3Y  CONST_22  H1  N1  C2  N   180.00   0.0  0
 W3Y  Var_01    C1  N   C4  C5   36.16  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
 W3Y  chir_01  C1  C  N  C3  positiv

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
 W3Y  plan-1  C4  0.020
 W3Y  plan-1  C5  0.020
 W3Y  plan-1  C6  0.020
 W3Y  plan-1  C7  0.020
 W3Y  plan-1  C8  0.020
 W3Y  plan-1  CL  0.020
 W3Y  plan-1  C9  0.020
 W3Y  plan-1  N   0.020
 W3Y  plan-1  H2  0.020
 W3Y  plan-1  H3  0.020
 W3Y  plan-1  H4  0.020
 W3Y  plan-1  H5  0.020
 W3Y  plan-2  N1  0.020
 W3Y  plan-2  C4  0.020
 W3Y  plan-2  N   0.020
 W3Y  plan-2  C2  0.020
 W3Y  plan-2  O   0.020
 W3Y  plan-2  C3  0.020
 W3Y  plan-2  O1  0.020
 W3Y  plan-2  C1  0.020
 W3Y  plan-2  H1  0.020

