# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:45:47 2022
#   Inital geometry file: a 34 line input string
#   Ligand name: imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NCCN1
#
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
 XJV  XJV  'imidazolidin-2-one       '  ligand  12  6  .  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_XJV
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
 XJV  O01   O  O     0  -0.512  -16.4015  25.1858   1.1801
 XJV  C02   C  CR5   0   0.624  -15.3495  25.7035   0.8443
 XJV  N03   N  NR15  0  -0.654  -14.7018  26.7193   1.4925
 XJV  C04   C  CH2   0  -0.285  -13.3745  26.9147   0.9452
 XJV  C05   C  CH2   0  -0.285  -13.5541  26.3580  -0.4690
 XJV  N06   N  NR15  0  -0.653  -14.5985  25.3774  -0.2521
 XJV  H031  H  HNR5  0   0.394  -14.8712  26.8500   2.4772
 XJV  H041  H  HCH2  0   0.251  -13.0819  27.9634   0.9418
 XJV  H042  H  HCH2  0   0.238  -12.6188  26.3477   1.4977
 XJV  H051  H  HCH2  0   0.238  -13.8709  27.1426  -1.1635
 XJV  H052  H  HCH2  0   0.251  -12.6406  25.9083  -0.8545
 XJV  H061  H  HNR5  0   0.393  -15.0547  24.9384  -1.0360

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
 XJV  C02  O01   double  1.220  0.020  1.220
 XJV  N03  C02   single  1.368  0.020  1.368
 XJV  C04  N03   single  1.449  0.020  1.449
 XJV  C05  C04   single  1.530  0.020  1.530
 XJV  N06  C05   single  1.449  0.020  1.449
 XJV  C02  N06   single  1.368  0.020  1.368
 XJV  N03  H031  single  0.890  0.020  1.040
 XJV  C04  H041  single  0.970  0.020  1.090
 XJV  C04  H042  single  0.970  0.020  1.090
 XJV  C05  H051  single  0.970  0.020  1.090
 XJV  C05  H052  single  0.970  0.020  1.090
 XJV  N06  H061  single  0.890  0.020  1.040

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
 XJV  N06   C02  N03   107.26  3.000
 XJV  N06   C02  O01   126.36  3.000
 XJV  N03   C02  O01   126.38  3.000
 XJV  H031  N03  C04   120.37  3.000
 XJV  H031  N03  C02   118.67  3.000
 XJV  C04   N03  C02   110.78  3.000
 XJV  H042  C04  H041  108.36  3.000
 XJV  H042  C04  C05   111.04  3.000
 XJV  H041  C04  C05   112.27  3.000
 XJV  H042  C04  N03   111.83  3.000
 XJV  H041  C04  N03   112.16  3.000
 XJV  C05   C04  N03   101.10  3.000
 XJV  H052  C05  H051  108.32  3.000
 XJV  H052  C05  N06   112.23  3.000
 XJV  H051  C05  N06   111.80  3.000
 XJV  H052  C05  C04   112.27  3.000
 XJV  H051  C05  C04   111.07  3.000
 XJV  N06   C05  C04   101.09  3.000
 XJV  H061  N06  C05   120.31  3.000
 XJV  H061  N06  C02   118.60  3.000
 XJV  C05   N06  C02   110.75  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
 XJV  CONST_03  C05   N06  C02  N03    0.00   0.0  0
 XJV  CONST_05  N06   C02  N03  C04    0.00   0.0  0
 XJV  CONST_06  C04   N03  C02  O01  180.00   0.0  0
 XJV  CONST_07  C05   N06  C02  O01  180.00   0.0  0
 XJV  CONST_09  H031  N03  C04  C05  180.00   0.0  0
 XJV  Var_01    H041  C04  N03  C02  144.76  30.0  1
 XJV  Var_02    H051  C05  N06  C02  -93.11  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
 XJV  plan-1  O01   0.020
 XJV  plan-1  C02   0.020
 XJV  plan-1  N03   0.020
 XJV  plan-1  C04   0.020
 XJV  plan-1  C05   0.020
 XJV  plan-1  N06   0.020
 XJV  plan-1  H031  0.020
 XJV  plan-1  H061  0.020

