# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:45:21 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: (3S)-3-hydroxypiperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCNC1=O
#
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
 XDL  XDL  (3S)-3-hydroxypiperidin-2-one  ligand  17  8  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDL
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
 XDL  N1    N  NH1   0  -0.622  -1.2738  -0.0807  -0.6641
 XDL  C2    C  C     0   0.487  -0.7690   0.0427   0.5685
 XDL  C3    C  CH1   0  -0.023   0.7171   0.3705   0.6908
 XDL  O3    O  OH1   0  -0.668   1.2191  -0.1107   1.9057
 XDL  C4    C  CH2   0  -0.482   1.5174  -0.1785  -0.4750
 XDL  C5    C  CH2   0  -0.483   0.8892   0.3251  -1.7647
 XDL  C6    C  CH2   0  -0.259  -0.5272  -0.2015  -1.9063
 XDL  O2    O  O     0  -0.509  -1.4542  -0.0464   1.5826
 XDL  H1    H  HNH1  0   0.397  -2.2630  -0.2787  -0.7145
 XDL  H3    H  HCH1  0   0.230   0.7755   1.4718   0.6477
 XDL  HA    H  HOH1  0   0.444   0.5265   0.0016   2.5687
 XDL  H4C1  H  HCH2  0   0.257   2.5568   0.1445  -0.3972
 XDL  H4C2  H  HCH2  0   0.237   1.5113  -1.2728  -0.4509
 XDL  H5C1  H  HCH2  0   0.240   0.8861   1.4188  -1.7697
 XDL  H5C2  H  HCH2  0   0.260   1.4673   0.0075  -2.6326
 XDL  H6C1  H  HCH2  0   0.256  -1.0616   0.3440  -2.6844
 XDL  H6C2  H  HCH2  0   0.239  -0.5020  -1.2527  -2.2086

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
 XDL  N1  C2    single  1.338  0.020  1.338
 XDL  N1  C6    single  1.454  0.020  1.454
 XDL  N1  H1    single  0.860  0.020  1.020
 XDL  C2  C3    single  1.527  0.020  1.527
 XDL  C2  O2    double  1.227  0.020  1.227
 XDL  C3  O3    single  1.400  0.020  1.400
 XDL  C3  C4    single  1.517  0.020  1.517
 XDL  C3  H3    single  0.970  0.020  1.090
 XDL  O3  HA    single  0.850  0.020  0.980
 XDL  C4  C5    single  1.520  0.020  1.520
 XDL  C4  H4C1  single  0.970  0.020  1.090
 XDL  C4  H4C2  single  0.970  0.020  1.090
 XDL  C5  C6    single  1.518  0.020  1.518
 XDL  C5  H5C1  single  0.970  0.020  1.090
 XDL  C5  H5C2  single  0.970  0.020  1.090
 XDL  C6  H6C1  single  0.970  0.020  1.090
 XDL  C6  H6C2  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
 XDL  H1    N1  C6    116.35  3.000
 XDL  H1    N1  C2    115.70  3.000
 XDL  C6    N1  C2    126.94  3.000
 XDL  O2    C2  C3    119.53  3.000
 XDL  O2    C2  N1    122.96  3.000
 XDL  C3    C2  N1    117.45  3.000
 XDL  H3    C3  C4    107.65  3.000
 XDL  H3    C3  O3    110.97  3.000
 XDL  C4    C3  O3    110.70  3.000
 XDL  H3    C3  C2    105.22  3.000
 XDL  C4    C3  C2    111.98  3.000
 XDL  O3    C3  C2    110.17  3.000
 XDL  HA    O3  C3    107.39  3.000
 XDL  H4C2  C4  H4C1  107.44  3.000
 XDL  H4C2  C4  C5    110.34  3.000
 XDL  H4C1  C4  C5    110.85  3.000
 XDL  H4C2  C4  C3    109.99  3.000
 XDL  H4C1  C4  C3    109.91  3.000
 XDL  C5    C4  C3    108.31  3.000
 XDL  H5C2  C5  H5C1  106.82  3.000
 XDL  H5C2  C5  C6    108.63  3.000
 XDL  H5C1  C5  C6    110.11  3.000
 XDL  H5C2  C5  C4    111.08  3.000
 XDL  H5C1  C5  C4    109.65  3.000
 XDL  C6    C5  C4    110.47  3.000
 XDL  H6C2  C6  H6C1  107.15  3.000
 XDL  H6C2  C6  C5    109.74  3.000
 XDL  H6C1  C6  C5    110.51  3.000
 XDL  H6C2  C6  N1    109.12  3.000
 XDL  H6C1  C6  N1    108.45  3.000
 XDL  C5    C6  N1    111.75  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
 XDL  CONST_01  C6  N1  C2  C3    0.00   0.0  0
 XDL  CONST_02  O2  C2  N1  C6  180.00   0.0  0
 XDL  CONST_03  H1  N1  C2  C3  180.00   0.0  0
 XDL  Var_01    C4  C5  C6  N1   45.06  30.0  1
 XDL  Var_02    C5  C6  N1  C2  -21.03  30.0  1
 XDL  Var_03    C6  C5  C4  C3  -62.92  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
 XDL  chir_01  C3  C2  O3  C4  negativ

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
 XDL  plan-1  N1  0.020
 XDL  plan-1  C2  0.020
 XDL  plan-1  C3  0.020
 XDL  plan-1  C6  0.020
 XDL  plan-1  O2  0.020
 XDL  plan-1  H1  0.020

