# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:58:49 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: (3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@@](O)(C1)C(O)=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
 VWM  VWM  '(3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid'  ligand  26  13  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VWM
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
 VWM  N1   N  NT    0  -0.430  -29.2210  14.4916  -21.7272
 VWM  C4   C  CH2   0  -0.434  -28.6987  14.7839  -24.0988
 VWM  C5   C  CH2   0  -0.451  -29.9697  15.6120  -24.2626
 VWM  C6   C  CT    0   0.109  -31.0166  15.2432  -23.2017
 VWM  C7   C  CH2   0  -0.347  -30.3704  15.3623  -21.8060
 VWM  C8   C  C     0   0.537  -32.1659  16.2461  -23.2687
 VWM  C1   C  CH3   0  -0.803  -28.1123  12.3819  -21.1668
 VWM  C2   C  C     0   0.515  -29.3149  13.2934  -21.1016
 VWM  O1   O  O     0  -0.505  -30.3190  12.9630  -20.4830
 VWM  C3   C  CH2   0  -0.326  -28.1751  14.8553  -22.6693
 VWM  O2   O  OH1   0  -0.656  -31.4268  13.9320  -23.4614
 VWM  O3   O  O     0  -0.444  -32.0138  17.4279  -23.0763
 VWM  O4   O  OH1   0  -0.576  -33.3331  15.6920  -23.5439
 VWM  H7   H  HCH2  0   0.248  -27.9319  15.1581  -24.7796
 VWM  H6   H  HCH2  0   0.236  -28.8826  13.7416  -24.3682
 VWM  H9   H  HCH2  0   0.247  -29.7287  16.6723  -24.1619
 VWM  H8   H  HCH2  0   0.262  -30.3901  15.4734  -25.2617
 VWM  H12  H  HCH2  0   0.267  -30.0464  16.3916  -21.6373
 VWM  H11  H  HCH2  0   0.286  -31.0833  15.1134  -21.0206
 VWM  H2   H  HCH3  0   0.269  -28.2909  11.5154  -20.5356
 VWM  H1   H  HCH3  0   0.265  -27.9342  12.0308  -22.1845
 VWM  H3   H  HCH3  0   0.266  -27.2020  12.8767  -20.8282
 VWM  H4   H  HCH2  0   0.250  -27.8521  15.8760  -22.4407
 VWM  H5   H  HCH2  0   0.278  -27.3061  14.2152  -22.5458
 VWM  H10  H  HOH1  0   0.451  -31.9197  13.5873  -22.7087
 VWM  H13  H  HOH1  0   0.484  -34.0234  16.3727  -23.5570

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
 VWM  C1  C2   single  1.510  0.020  1.510
 VWM  C2  O1   double  1.225  0.020  1.225
 VWM  C2  N1   single  1.355  0.020  1.355
 VWM  N1  C3   single  1.454  0.020  1.454
 VWM  C3  C4   single  1.524  0.020  1.524
 VWM  C4  C5   single  1.526  0.020  1.526
 VWM  C5  C6   single  1.535  0.020  1.535
 VWM  C6  O2   single  1.398  0.020  1.398
 VWM  C6  C7   single  1.543  0.020  1.543
 VWM  C6  C8   single  1.527  0.020  1.527
 VWM  C8  O3   double  1.207  0.020  1.207
 VWM  C8  O4   single  1.321  0.020  1.321
 VWM  N1  C7   single  1.444  0.020  1.444
 VWM  C4  H7   single  0.970  0.020  1.090
 VWM  C4  H6   single  0.970  0.020  1.090
 VWM  C5  H9   single  0.970  0.020  1.090
 VWM  C5  H8   single  0.970  0.020  1.090
 VWM  C7  H12  single  0.970  0.020  1.090
 VWM  C7  H11  single  0.970  0.020  1.090
 VWM  C1  H2   single  0.970  0.020  1.090
 VWM  C1  H1   single  0.970  0.020  1.090
 VWM  C1  H3   single  0.970  0.020  1.090
 VWM  C3  H4   single  0.970  0.020  1.090
 VWM  C3  H5   single  0.970  0.020  1.090
 VWM  O2  H10  single  0.850  0.020  0.980
 VWM  O4  H13  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
 VWM  C3   N1  C2   124.77  3.000
 VWM  C3   N1  C7   112.73  3.000
 VWM  C2   N1  C7   120.21  3.000
 VWM  H6   C4  H7   106.96  3.000
 VWM  H6   C4  C3   109.51  3.000
 VWM  H7   C4  C3   109.12  3.000
 VWM  H6   C4  C5   110.56  3.000
 VWM  H7   C4  C5   109.40  3.000
 VWM  C3   C4  C5   111.19  3.000
 VWM  H8   C5  H9   107.00  3.000
 VWM  H8   C5  C6   109.81  3.000
 VWM  H9   C5  C6   108.66  3.000
 VWM  H8   C5  C4   110.48  3.000
 VWM  H9   C5  C4   109.47  3.000
 VWM  C6   C5  C4   111.31  3.000
 VWM  O2   C6  C8   112.77  3.000
 VWM  C8   C6  C7   107.72  3.000
 VWM  O2   C6  C7   111.30  3.000
 VWM  C8   C6  C5   108.98  3.000
 VWM  C7   C6  C5   108.72  3.000
 VWM  O2   C6  C5   107.28  3.000
 VWM  H11  C7  H12  107.34  3.000
 VWM  H11  C7  C6   111.13  3.000
 VWM  H12  C7  C6   109.68  3.000
 VWM  H11  C7  N1   110.11  3.000
 VWM  H12  C7  N1   108.88  3.000
 VWM  C6   C7  N1   109.65  3.000
 VWM  O4   C8  O3   123.73  3.000
 VWM  O4   C8  C6   113.50  3.000
 VWM  O3   C8  C6   122.77  3.000
 VWM  H3   C1  H1   107.43  3.000
 VWM  H3   C1  H2   108.59  3.000
 VWM  H1   C1  H2   108.18  3.000
 VWM  H3   C1  C2   112.19  3.000
 VWM  H1   C1  C2   111.37  3.000
 VWM  H2   C1  C2   108.98  3.000
 VWM  O1   C2  C1   120.78  3.000
 VWM  O1   C2  N1   121.91  3.000
 VWM  C1   C2  N1   117.30  3.000
 VWM  H5   C3  H4   106.83  3.000
 VWM  H5   C3  C4   110.73  3.000
 VWM  H4   C3  C4   109.94  3.000
 VWM  H5   C3  N1   110.75  3.000
 VWM  H4   C3  N1   108.07  3.000
 VWM  C4   C3  N1   110.42  3.000
 VWM  H10  O2  C6   109.91  3.000
 VWM  H13  O4  C8   109.71  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
 VWM  CONST_01  C1   C2  N1  C7  180.00   0.0  0
 VWM  CONST_02  O1   C2  N1  C7    0.00   0.0  0
 VWM  CONST_03  C3   N1  C2  C1    0.00   0.0  0
 VWM  CONST_04  C3   N1  C2  O1  180.00   0.0  0
 VWM  CONST_05  H13  O4  C8  C6  180.00   0.0  0
 VWM  Var_01    C5   C4  C3  N1   53.48  30.0  1
 VWM  Var_02    C7   N1  C3  C4  -60.07  30.0  1
 VWM  Var_03    C3   C4  C5  C6  -52.07  30.0  1
 VWM  Var_04    C3   N1  C7  C6   62.91  30.0  1
 VWM  Var_05    H2   C1  C2  N1  173.82  30.0  3

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
 VWM  chir_01  C6  C5  C7  C8  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
 VWM  plan-1  N1   0.020
 VWM  plan-1  C7   0.020
 VWM  plan-1  C1   0.020
 VWM  plan-1  C2   0.020
 VWM  plan-1  O1   0.020
 VWM  plan-1  C3   0.020
 VWM  plan-2  C6   0.020
 VWM  plan-2  C8   0.020
 VWM  plan-2  O3   0.020
 VWM  plan-2  O4   0.020
 VWM  plan-2  H13  0.020

