# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 20:42:08 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-[(3~{R})-3-oxidanylpiperidin-1-yl]carbonylbenzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCN(C1)C(=O)c2ccc(C=O)cc2
#
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
 V4H  V4H  4-[(3~{R})-3-oxidanylpiperidin-1-yl]carbonylbenzaldehyde  ligand  32  17  .  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_V4H
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
 V4H  C02  C  CH1   0   0.038  -17.6446  23.3551   2.7540
 V4H  C03  C  CH2   0  -0.478  -16.3394  24.1214   2.5901
 V4H  C04  C  CH2   0  -0.448  -15.1501  23.2001   2.8922
 V4H  C05  C  CH2   0  -0.337  -15.4761  21.7565   2.4927
 V4H  C08  C  CR6   0  -0.068  -16.9195  21.5490  -1.0024
 V4H  C09  C  CR16  0  -0.236  -17.9997  20.6733  -0.9735
 V4H  C10  C  CR16  0  -0.266  -18.8398  20.5771  -2.0714
 V4H  C11  C  CR6   0  -0.015  -18.6151  21.3618  -3.1978
 V4H  C12  C  CR16  0  -0.254  -17.5310  22.2387  -3.2267
 V4H  C13  C  CR16  0  -0.257  -16.6810  22.3191  -2.1410
 V4H  C14  C  C1    0   0.118  -19.5320  21.2427  -4.3446
 V4H  C16  C  CH2   0  -0.306  -17.7292  22.2426   1.6967
 V4H  N06  N  NT    0  -0.456  -16.4003  21.7419   1.3709
 V4H  O01  O  OH1   0  -0.666  -18.7943  24.1484   2.5689
 V4H  O15  O  O     0  -0.475  -14.7358  21.4765  -0.1411
 V4H  H1   H  HCH1  0   0.213  -17.6549  22.9033   3.7561
 V4H  H2   H  HCH2  0   0.231  -16.2766  24.5036   1.5666
 V4H  H3   H  HCH2  0   0.247  -16.3243  24.9905   3.2517
 V4H  H4   H  HCH2  0   0.238  -14.9074  23.2228   3.9562
 V4H  H5   H  HCH2  0   0.241  -14.2662  23.5483   2.3567
 V4H  H6   H  HCH2  0   0.257  -15.9559  21.2265   3.3189
 V4H  H7   H  HCH2  0   0.269  -14.5796  21.1985   2.2380
 V4H  H8   H  HCR6  0   0.275  -18.1844  20.0574  -0.1027
 V4H  H9   H  HCR6  0   0.274  -19.6765  19.8886  -2.0512
 V4H  H10  H  HCR6  0   0.269  -17.3503  22.8517  -4.1002
 V4H  H11  H  HCR6  0   0.269  -15.8324  22.9900  -2.1701
 V4H  H12  H  H     0   0.200  -20.3499  20.5143  -4.2026
 V4H  H15  H  HCH2  0   0.264  -18.1839  22.6699   0.8039
 V4H  H16  H  HCH2  0   0.254  -18.3731  21.4305   2.0466
 V4H  H17  H  HOH1  0   0.450  -18.8551  24.7673   3.3032
 V4H  O1   O  O     0  -0.370  -19.4273  21.8716  -5.3703
 V4H  C07  C  C     0   0.525  -15.9251  21.6013   0.1180

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
 V4H  C14  C11  single    1.473  0.020  1.473
 V4H  C12  C11  aromatic  1.395  0.020  1.395
 V4H  C12  C13  aromatic  1.381  0.020  1.381
 V4H  C11  C10  aromatic  1.391  0.020  1.391
 V4H  C13  C08  aromatic  1.395  0.020  1.395
 V4H  C10  C09  aromatic  1.386  0.020  1.386
 V4H  C08  C09  aromatic  1.391  0.020  1.391
 V4H  C08  C07  single    1.499  0.020  1.499
 V4H  O15  C07  double    1.224  0.020  1.224
 V4H  C07  N06  single    1.347  0.020  1.347
 V4H  N06  C16  single    1.457  0.020  1.457
 V4H  N06  C05  single    1.454  0.020  1.454
 V4H  C16  C02  single    1.537  0.020  1.537
 V4H  C05  C04  single    1.533  0.020  1.533
 V4H  O01  C02  single    1.409  0.020  1.409
 V4H  C02  C03  single    1.522  0.020  1.522
 V4H  C03  C04  single    1.534  0.020  1.534
 V4H  C02  H1   single    0.970  0.020  1.090
 V4H  C03  H2   single    0.970  0.020  1.090
 V4H  C03  H3   single    0.970  0.020  1.090
 V4H  C04  H4   single    0.970  0.020  1.090
 V4H  C04  H5   single    0.970  0.020  1.090
 V4H  C05  H6   single    0.970  0.020  1.090
 V4H  C05  H7   single    0.970  0.020  1.090
 V4H  C09  H8   single    0.930  0.020  1.080
 V4H  C10  H9   single    0.930  0.020  1.080
 V4H  C12  H10  single    0.930  0.020  1.080
 V4H  C13  H11  single    0.930  0.020  1.080
 V4H  C14  H12  single    0.930  0.020  1.080
 V4H  C16  H15  single    0.970  0.020  1.090
 V4H  C16  H16  single    0.970  0.020  1.090
 V4H  O01  H17  single    0.850  0.020  0.980
 V4H  C14  O1   double    1.208  0.020  1.208

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
 V4H  H1   C02  O01  110.09  3.000
 V4H  H1   C02  C16  109.21  3.000
 V4H  O01  C02  C16  105.80  3.000
 V4H  H1   C02  C03  108.24  3.000
 V4H  O01  C02  C03  113.71  3.000
 V4H  C16  C02  C03  109.72  3.000
 V4H  H3   C03  H2   106.72  3.000
 V4H  H3   C03  C04  110.36  3.000
 V4H  H2   C03  C04  110.45  3.000
 V4H  H3   C03  C02  110.31  3.000
 V4H  H2   C03  C02  109.00  3.000
 V4H  C04  C03  C02  109.95  3.000
 V4H  H5   C04  H4   106.97  3.000
 V4H  H5   C04  C05  110.19  3.000
 V4H  H4   C04  C05  108.72  3.000
 V4H  H5   C04  C03  109.87  3.000
 V4H  H4   C04  C03  110.59  3.000
 V4H  C05  C04  C03  110.44  3.000
 V4H  H7   C05  H6   106.89  3.000
 V4H  H7   C05  N06  109.79  3.000
 V4H  H6   C05  N06  107.43  3.000
 V4H  H7   C05  C04  111.68  3.000
 V4H  H6   C05  C04  110.68  3.000
 V4H  N06  C05  C04  110.23  3.000
 V4H  C13  C08  C09  119.82  3.000
 V4H  C09  C08  C07  121.45  3.000
 V4H  C13  C08  C07  118.51  3.000
 V4H  H8   C09  C10  119.63  3.000
 V4H  H8   C09  C08  120.49  3.000
 V4H  C10  C09  C08  119.87  3.000
 V4H  H9   C10  C11  119.88  3.000
 V4H  H9   C10  C09  119.83  3.000
 V4H  C11  C10  C09  120.29  3.000
 V4H  C14  C11  C12  121.23  3.000
 V4H  C12  C11  C10  119.80  3.000
 V4H  C14  C11  C10  118.96  3.000
 V4H  H10  C12  C13  119.91  3.000
 V4H  H10  C12  C11  120.17  3.000
 V4H  C13  C12  C11  119.92  3.000
 V4H  H11  C13  C12  119.84  3.000
 V4H  H11  C13  C08  119.89  3.000
 V4H  C12  C13  C08  120.27  3.000
 V4H  O1   C14  H12  121.12  3.000
 V4H  O1   C14  C11  124.41  3.000
 V4H  H12  C14  C11  114.47  3.000
 V4H  H16  C16  H15  107.92  3.000
 V4H  H16  C16  N06  110.70  3.000
 V4H  H15  C16  N06  109.40  3.000
 V4H  H16  C16  C02  110.47  3.000
 V4H  H15  C16  C02  107.63  3.000
 V4H  N06  C16  C02  110.63  3.000
 V4H  C16  N06  C07  124.44  3.000
 V4H  C16  N06  C05  113.82  3.000
 V4H  C07  N06  C05  119.63  3.000
 V4H  H17  O01  C02  108.26  3.000
 V4H  O15  C07  N06  123.40  3.000
 V4H  N06  C07  C08  117.69  3.000
 V4H  O15  C07  C08  118.88  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
 V4H  CONST_01  C11  C12  C13  C08     0.00   0.0  0
 V4H  CONST_02  C11  C10  C09  C08     0.00   0.0  0
 V4H  CONST_03  C12  C11  C10  C09     0.00   0.0  0
 V4H  CONST_04  C12  C13  C08  C09     0.00   0.0  0
 V4H  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 V4H  CONST_06  C13  C08  C09  C10     0.00   0.0  0
 V4H  CONST_07  C12  C13  C08  C07   180.00   0.0  0
 V4H  CONST_08  C10  C09  C08  C07   180.00   0.0  0
 V4H  CONST_09  C14  C11  C10  C09   180.00   0.0  0
 V4H  CONST_10  C14  C11  C12  C13   180.00   0.0  0
 V4H  CONST_11  C08  C07  N06  C05   180.00   0.0  0
 V4H  CONST_13  H10  C12  C13  C08   180.00   0.0  0
 V4H  CONST_14  H9   C10  C09  C08   180.00   0.0  0
 V4H  CONST_15  H11  C13  C08  C09   180.00   0.0  0
 V4H  CONST_16  H8   C09  C10  C11   180.00   0.0  0
 V4H  CONST_17  O15  C07  N06  C05     0.00   0.0  0
 V4H  Var_01    C05  N06  C16  C02    33.32  30.0  1
 V4H  Var_02    C05  C04  C03  C02    31.94  30.0  1
 V4H  Var_03    N06  C05  C04  C03    30.25  30.0  1
 V4H  Var_04    C16  N06  C05  C04   -67.57  30.0  1
 V4H  Var_05    N06  C07  C08  C09   -51.53  30.0  2
 V4H  Var_06    O1   C14  C11  C10  -179.77  30.0  2

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
 V4H  chir_01  C02  C16  O01  C03  positiv

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
 V4H  plan-1  C08  0.020
 V4H  plan-1  C09  0.020
 V4H  plan-1  C10  0.020
 V4H  plan-1  C11  0.020
 V4H  plan-1  C12  0.020
 V4H  plan-1  C13  0.020
 V4H  plan-1  C14  0.020
 V4H  plan-1  H8   0.020
 V4H  plan-1  H9   0.020
 V4H  plan-1  H10  0.020
 V4H  plan-1  H11  0.020
 V4H  plan-1  C07  0.020
 V4H  plan-2  C05  0.020
 V4H  plan-2  C08  0.020
 V4H  plan-2  C16  0.020
 V4H  plan-2  N06  0.020
 V4H  plan-2  O15  0.020
 V4H  plan-2  C07  0.020
 V4H  plan-3  C11  0.020
 V4H  plan-3  C14  0.020
 V4H  plan-3  H12  0.020
 V4H  plan-3  O1   0.020

