# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:19:01 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1NCC=C[C@H]1O
#
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
 KGE  KGE  (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol  ligand  20  9  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KGE
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
 KGE  O1   O  OH1   0  -0.669  45.2962  -11.5918   -5.8568
 KGE  C1   C  CH2   0  -0.194  45.7487  -12.9133   -5.6774
 KGE  C2   C  CH1   0  -0.127  46.6987  -13.3032   -6.7942
 KGE  N1   N  NH1   0  -0.612  47.8846  -12.4659   -6.7895
 KGE  C3   C  CH2   0  -0.315  48.9432  -13.0060   -7.6186
 KGE  C4   C  C1    0  -0.244  48.4195  -13.3871   -8.9655
 KGE  C5   C  C1    0  -0.246  47.1197  -13.4633   -9.2282
 KGE  C6   C  CH1   0   0.036  46.0694  -13.2044   -8.1885
 KGE  O2   O  OH1   0  -0.681  45.0407  -14.1584   -8.3733
 KGE  H1   H  HOH1  0   0.456  44.6261  -11.4134   -5.1914
 KGE  H2   H  HCH2  0   0.204  44.9180  -13.6304   -5.6583
 KGE  H3   H  HCH2  0   0.211  46.2741  -13.0320   -4.7188
 KGE  H4   H  HCH1  0   0.207  46.9424  -14.3675   -6.6222
 KGE  H5   H  HNH1  0   0.353  48.2247  -12.3506   -5.8433
 KGE  H7   H  HCH2  0   0.213  49.4339  -13.8895   -7.1759
 KGE  H8   H  HCH2  0   0.242  49.7294  -12.2543   -7.7336
 KGE  H9   H  H     0   0.248  49.1501  -13.6039   -9.7364
 KGE  H10  H  H     0   0.245  46.7748  -13.7219  -10.2242
 KGE  H11  H  HCH1  0   0.220  45.6755  -12.1888   -8.3290
 KGE  H12  H  HOH1  0   0.452  44.2531  -13.8511   -7.9156

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
 KGE  C5  C4   double  1.328  0.020  1.328
 KGE  C5  C6   single  1.500  0.020  1.500
 KGE  C4  C3   single  1.495  0.020  1.495
 KGE  O2  C6   single  1.415  0.020  1.415
 KGE  C6  C2   single  1.533  0.020  1.533
 KGE  C3  N1   single  1.449  0.020  1.449
 KGE  C2  N1   single  1.452  0.020  1.452
 KGE  C2  C1   single  1.517  0.020  1.517
 KGE  O1  C1   single  1.408  0.020  1.408
 KGE  O1  H1   single  0.850  0.020  0.980
 KGE  C1  H2   single  0.970  0.020  1.090
 KGE  C1  H3   single  0.970  0.020  1.090
 KGE  C2  H4   single  0.970  0.020  1.090
 KGE  N1  H5   single  0.890  0.020  1.040
 KGE  C3  H7   single  0.970  0.020  1.090
 KGE  C3  H8   single  0.970  0.020  1.090
 KGE  C4  H9   single  0.930  0.020  1.080
 KGE  C5  H10  single  0.930  0.020  1.080
 KGE  C6  H11  single  0.970  0.020  1.090
 KGE  O2  H12  single  0.850  0.020  0.980

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
 KGE  H1   O1  C1  108.06  3.000
 KGE  H3   C1  H2  106.02  3.000
 KGE  H3   C1  C2  108.35  3.000
 KGE  H2   C1  C2  108.59  3.000
 KGE  H3   C1  O1  111.47  3.000
 KGE  H2   C1  O1  111.85  3.000
 KGE  C2   C1  O1  110.40  3.000
 KGE  H4   C2  C6  107.10  3.000
 KGE  H4   C2  N1  112.02  3.000
 KGE  C6   C2  N1  107.53  3.000
 KGE  H4   C2  C1  105.72  3.000
 KGE  N1   C2  C1  111.16  3.000
 KGE  C6   C2  C1  113.32  3.000
 KGE  H5   N1  C3  109.39  3.000
 KGE  H5   N1  C2  110.07  3.000
 KGE  C3   N1  C2  112.33  3.000
 KGE  H8   C3  H7  105.83  3.000
 KGE  H8   C3  C4  109.41  3.000
 KGE  H7   C3  C4  108.26  3.000
 KGE  H8   C3  N1  109.21  3.000
 KGE  H7   C3  N1  113.19  3.000
 KGE  C4   C3  N1  110.78  3.000
 KGE  H9   C4  C5  120.49  3.000
 KGE  H9   C4  C3  117.11  3.000
 KGE  C5   C4  C3  122.40  3.000
 KGE  H10  C5  C6  117.04  3.000
 KGE  H10  C5  C4  120.41  3.000
 KGE  C6   C5  C4  122.55  3.000
 KGE  H11  C6  O2  110.24  3.000
 KGE  H11  C6  C5  108.79  3.000
 KGE  O2   C6  C5  107.58  3.000
 KGE  H11  C6  C2  108.86  3.000
 KGE  O2   C6  C2  111.95  3.000
 KGE  C5   C6  C2  109.38  3.000
 KGE  H12  O2  C6  108.53  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
 KGE  Var_01  C4  C3  N1  C2   48.69  30.0  1
 KGE  Var_02  C5  C4  C3  N1  -12.63  30.0  1
 KGE  Var_03  C6  C5  C4  C3   -1.43  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
 KGE  chir_01  C2  C6  N1  C1  negativ
 KGE  chir_02  C6  O2  C2  C5  negativ

