# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:22:48 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CNC(=O)N1
#
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
 HYN  HYN  'imidazolidine-2,4-dione  '  ligand  11  7  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HYN
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
 HYN  O    O  O     0  -0.436  -2.2920  -0.5036   0.0199
 HYN  C    C  CR5   0   0.523  -1.1451  -0.1256   0.0066
 HYN  C1   C  CH2   0  -0.372  -0.6524   1.3069  -0.0279
 HYN  N    N  NR15  0  -0.657   0.7747   1.1391  -0.0348
 HYN  N1   N  NR15  0  -0.693  -0.0256  -0.8993   0.0188
 HYN  C2   C  CR5   0   0.679   1.1535  -0.1517  -0.0034
 HYN  O1   O  O     0  -0.483   2.2737  -0.6135   0.0041
 HYN  H1   H  HCH2  0   0.295  -1.0253   1.8131  -0.9212
 HYN  H1A  H  HCH2  0   0.295  -1.0121   1.8510   0.8485
 HYN  HN   H  HNR5  0   0.421   1.4346   1.8983  -0.0445
 HYN  HN1  H  HNR5  0   0.428  -0.0306  -1.9091   0.0404

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
 HYN  O   C    double  1.208  0.020  1.208
 HYN  C   C1   single  1.515  0.020  1.515
 HYN  C   N1   single  1.361  0.020  1.361
 HYN  C1  N    single  1.437  0.020  1.437
 HYN  N   C2   single  1.346  0.020  1.346
 HYN  N1  C2   single  1.396  0.020  1.396
 HYN  C2  O1   double  1.212  0.020  1.212
 HYN  C1  H1   single  0.970  0.020  1.090
 HYN  C1  H1A  single  0.970  0.020  1.090
 HYN  N   HN   single  0.860  0.020  1.020
 HYN  N1  HN1  single  0.860  0.020  1.020

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
 HYN  N1   C   C1  105.68  3.000
 HYN  N1   C   O   127.10  3.000
 HYN  C1   C   O   127.22  3.000
 HYN  H1A  C1  H1  108.23  3.000
 HYN  H1A  C1  N   112.90  3.000
 HYN  H1   C1  N   112.91  3.000
 HYN  H1A  C1  C   110.21  3.000
 HYN  H1   C1  C   110.23  3.000
 HYN  N    C1  C   102.27  3.000
 HYN  HN   N   C2  122.65  3.000
 HYN  HN   N   C1  124.29  3.000
 HYN  C2   N   C1  113.05  3.000
 HYN  HN1  N1  C2  122.66  3.000
 HYN  HN1  N1  C   124.37  3.000
 HYN  C2   N1  C   112.96  3.000
 HYN  O1   C2  N1  125.21  3.000
 HYN  O1   C2  N   128.75  3.000
 HYN  N1   C2  N   106.03  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
 HYN  CONST_01  C2   N   C1  C     0.00   0.0  0
 HYN  CONST_02  N    C2  N1  C     0.00   0.0  0
 HYN  CONST_03  C2   N1  C   C1    0.00   0.0  0
 HYN  CONST_04  N1   C2  N   C1    0.00   0.0  0
 HYN  CONST_05  N1   C   C1  N     0.00   0.0  0
 HYN  CONST_06  C2   N1  C   O   180.00   0.0  0
 HYN  CONST_07  O1   C2  N1  C   180.00   0.0  0
 HYN  CONST_08  O1   C2  N   C1  180.00   0.0  0
 HYN  CONST_09  HN   N   C1  C   180.00   0.0  0
 HYN  CONST_10  HN1  N1  C   C1  180.00   0.0  0
 HYN  Var_01    H1   C1  C   N1  120.48  30.0  1

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
 HYN  plan-1  O    0.020
 HYN  plan-1  C    0.020
 HYN  plan-1  C1   0.020
 HYN  plan-1  N    0.020
 HYN  plan-1  N1   0.020
 HYN  plan-1  C2   0.020
 HYN  plan-1  O1   0.020
 HYN  plan-1  HN   0.020
 HYN  plan-1  HN1  0.020

