# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 15:21:29 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCCN1
#
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
 V1L  V1L  'piperidin-2-one          '  ligand  16  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_V1L
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
 V1L  O05  O  O     0  -0.520  -2.3268  -0.0457  -0.0295
 V1L  C04  C  C     0   0.513  -1.1000  -0.0216  -0.0032
 V1L  C06  C  CH2   0  -0.563  -0.3445   1.2866  -0.0763
 V1L  C07  C  CH2   0  -0.451   1.1143   1.2057   0.3516
 V1L  C08  C  CH2   0  -0.467   1.7684  -0.0035  -0.2956
 V1L  C02  C  CH2   0  -0.258   1.0703  -1.2675   0.1655
 V1L  N03  N  NH1   0  -0.620  -0.3730  -1.1497   0.0457
 V1L  H1   H  HCH2  0   0.265  -0.4049   1.6215  -1.1173
 V1L  H2   H  HCH2  0   0.267  -0.8947   2.0230   0.5112
 V1L  H3   H  HCH2  0   0.248   1.6304   2.1258   0.0746
 V1L  H4   H  HCH2  0   0.230   1.1839   1.1207   1.4401
 V1L  H5   H  HCH2  0   0.233   1.7086   0.0807  -1.3845
 V1L  H6   H  HCH2  0   0.250   2.8256  -0.0700  -0.0358
 V1L  H7   H  HCH2  0   0.251   1.3929  -2.1243  -0.4271
 V1L  H8   H  HCH2  0   0.231   1.3390  -1.4785   1.2054
 V1L  H9   H  HNH1  0   0.391  -0.9021  -2.0073   0.1069

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
 V1L  C02  N03  single  1.453  0.020  1.453
 V1L  C02  C08  single  1.516  0.020  1.516
 V1L  N03  C04  single  1.343  0.020  1.343
 V1L  C04  O05  double  1.227  0.020  1.227
 V1L  C04  C06  single  1.513  0.020  1.513
 V1L  C08  C07  single  1.520  0.020  1.520
 V1L  C07  C06  single  1.522  0.020  1.522
 V1L  C06  H1   single  0.970  0.020  1.090
 V1L  C06  H2   single  0.970  0.020  1.090
 V1L  C07  H3   single  0.970  0.020  1.090
 V1L  C07  H4   single  0.970  0.020  1.090
 V1L  C08  H5   single  0.970  0.020  1.090
 V1L  C08  H6   single  0.970  0.020  1.090
 V1L  C02  H7   single  0.970  0.020  1.090
 V1L  C02  H8   single  0.970  0.020  1.090
 V1L  N03  H9   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
 V1L  N03  C04  C06  117.26  3.000
 V1L  C06  C04  O05  121.01  3.000
 V1L  N03  C04  O05  121.70  3.000
 V1L  H2   C06  H1   106.12  3.000
 V1L  H2   C06  C07  111.58  3.000
 V1L  H1   C06  C07  109.65  3.000
 V1L  H2   C06  C04  107.82  3.000
 V1L  H1   C06  C04  106.43  3.000
 V1L  C07  C06  C04  114.77  3.000
 V1L  H4   C07  H3   106.74  3.000
 V1L  H4   C07  C08  109.55  3.000
 V1L  H3   C07  C08  111.06  3.000
 V1L  H4   C07  C06  110.17  3.000
 V1L  H3   C07  C06  109.70  3.000
 V1L  C08  C07  C06  109.58  3.000
 V1L  H6   C08  H5   107.15  3.000
 V1L  H6   C08  C02  108.85  3.000
 V1L  H5   C08  C02  109.99  3.000
 V1L  H6   C08  C07  111.36  3.000
 V1L  H5   C08  C07  109.83  3.000
 V1L  C02  C08  C07  109.62  3.000
 V1L  H8   C02  H7   106.99  3.000
 V1L  H8   C02  N03  109.75  3.000
 V1L  H7   C02  N03  108.22  3.000
 V1L  H8   C02  C08  109.68  3.000
 V1L  H7   C02  C08  110.70  3.000
 V1L  N03  C02  C08  111.39  3.000
 V1L  H9   N03  C02  116.53  3.000
 V1L  H9   N03  C04  115.60  3.000
 V1L  C02  N03  C04  127.50  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
 V1L  CONST_01  C02  N03  C04  C06    0.00   0.0  0
 V1L  CONST_02  C02  N03  C04  O05  180.00   0.0  0
 V1L  CONST_03  H9   N03  C04  C06  180.00   0.0  0
 V1L  Var_01    C08  C02  N03  C04  -22.12  30.0  1
 V1L  Var_02    C08  C07  C06  C04   46.11  30.0  1
 V1L  Var_03    N03  C02  C08  C07   48.65  30.0  1
 V1L  Var_04    N03  C04  C06  C07  -18.49  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
 V1L  plan-1  O05  0.020
 V1L  plan-1  C04  0.020
 V1L  plan-1  C06  0.020
 V1L  plan-1  C02  0.020
 V1L  plan-1  N03  0.020
 V1L  plan-1  H9   0.020

