# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 23:13:56 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: (4S)-imidazolidine-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#C[C@@H]1CNCN1
#
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
 XKY  XKY  (4S)-imidazolidine-4-carbonitrile  ligand  14  7  .  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_XKY
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
 XKY  N01   N  NS    0  -0.262  -23.0877  42.3820  15.1448
 XKY  C02   C  CSP   0   0.098  -23.8230  41.9926  14.3499
 XKY  C03   C  CR15  0  -0.174  -24.7554  41.5236  13.3340
 XKY  C04   C  CH2   0  -0.343  -25.8730  42.5876  13.0088
 XKY  N05   N  NR15  0  -0.569  -27.1084  41.9962  13.4744
 XKY  C06   C  CH2   0  -0.214  -26.8598  40.5734  13.3591
 XKY  N07   N  NR15  0  -0.595  -25.4743  40.3230  13.7653
 XKY  H031  H  HCR5  0   0.309  -24.1700  41.3225  12.4332
 XKY  H041  H  HCH2  0   0.270  -25.6945  43.5587  13.4668
 XKY  H042  H  HCH2  0   0.257  -25.9000  42.7269  11.9271
 XKY  H051  H  HNR5  0   0.355  -27.2420  42.2272  14.4524
 XKY  H061  H  HCH2  0   0.261  -27.5497  39.9874  13.9634
 XKY  H062  H  HCH2  0   0.240  -26.9794  40.2766  12.3135
 XKY  H071  H  HNR5  0   0.366  -25.4452  40.2456  14.7751

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
 XKY  C02  N01   triple  1.151  0.020  1.151
 XKY  C03  C02   single  1.457  0.020  1.457
 XKY  C04  C03   single  1.577  0.020  1.577
 XKY  N05  C04   single  1.447  0.020  1.447
 XKY  C06  N05   single  1.449  0.020  1.449
 XKY  N07  C06   single  1.465  0.020  1.465
 XKY  C03  N07   single  1.464  0.020  1.464
 XKY  C03  H031  single  0.970  0.020  1.090
 XKY  C04  H041  single  0.970  0.020  1.090
 XKY  C04  H042  single  0.970  0.020  1.090
 XKY  N05  H051  single  0.890  0.020  1.040
 XKY  C06  H061  single  0.970  0.020  1.090
 XKY  C06  H062  single  0.970  0.020  1.090
 XKY  N07  H071  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
 XKY  C03   C02  N01   180.00  3.000
 XKY  H031  C03  N07   110.79  3.000
 XKY  H031  C03  C04   109.50  3.000
 XKY  N07   C03  C04   105.43  3.000
 XKY  H031  C03  C02   106.93  3.000
 XKY  N07   C03  C02   111.89  3.000
 XKY  C04   C03  C02   112.35  3.000
 XKY  H042  C04  H041  107.90  3.000
 XKY  H042  C04  N05   110.50  3.000
 XKY  H041  C04  N05   111.68  3.000
 XKY  H042  C04  C03   107.95  3.000
 XKY  H041  C04  C03   113.52  3.000
 XKY  N05   C04  C03   105.25  3.000
 XKY  H051  N05  C06   108.85  3.000
 XKY  H051  N05  C04   109.26  3.000
 XKY  C06   N05  C04   103.26  3.000
 XKY  H062  C06  H061  108.39  3.000
 XKY  H062  C06  N07   108.79  3.000
 XKY  H061  C06  N07   110.70  3.000
 XKY  H062  C06  N05   108.90  3.000
 XKY  H061  C06  N05   112.07  3.000
 XKY  N07   C06  N05   107.94  3.000
 XKY  H071  N07  C06   108.45  3.000
 XKY  H071  N07  C03   110.00  3.000
 XKY  C06   N07  C03   104.03  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
 XKY  Var_01  C06  N05  C04  C03  -28.15  30.0  1
 XKY  Var_02  N07  C06  N05  C04   39.07  30.0  1

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
 XKY  chir_01  C03  C02  C04  N07  positiv

