# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:32:27 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (2R)-piperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCCCN1
#
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
 CPI  CPI  '(2R)-piperidine-2-carboxylic acid'  D-peptide  19  9  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CPI
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
 CPI  N    N  NH1    0  -0.569  17.2009  16.8410  20.5670
 CPI  CE   C  CH2    0  -0.314  18.0357  17.9770  20.9286
 CPI  CD   C  CH2    0  -0.435  19.5259  17.7601  20.6783
 CPI  CG   C  CH2    0  -0.438  19.7642  17.3151  19.2388
 CPI  CB   C  CH2    0  -0.417  18.8930  16.1081  18.9064
 CPI  CA   C  CH1    0  -0.252  17.4145  16.3948  19.1935
 CPI  C    C  C      0   0.405  16.7758  17.3455  18.1386
 CPI  O    O  O      0  -0.598  15.9451  18.1859  18.5304
 CPI  H    H  HNH1   0   0.325  17.4346  16.0710  21.1845
 CPI  HE2  H  HCH2   0   0.209  17.6960  18.8445  20.3571
 CPI  HE3  H  HCH2   0   0.216  17.8605  18.2129  21.9818
 CPI  HD2  H  HCH2   0   0.214  20.0827  18.6742  20.9035
 CPI  HD3  H  HCH2   0   0.201  19.8987  16.9887  21.3620
 CPI  HG2  H  HCH2   0   0.207  19.5273  18.1375  18.5549
 CPI  HG3  H  HCH2   0   0.218  20.8200  17.0792  19.0808
 CPI  HB2  H  HCH2   0   0.214  19.0283  15.8058  17.8683
 CPI  HB3  H  HCH2   0   0.197  19.2145  15.2603  19.5236
 CPI  HA   H  HCH1   0   0.225  16.8670  15.4483  19.0903
 CPI  OXT  O  OC    -1  -0.611  17.1238  17.1437  16.9557

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
 CPI  N   CE   single  1.455  0.020  1.455
 CPI  N   CA   single  1.458  0.019  1.458
 CPI  N   H    single  0.860  0.020  0.860
 CPI  CE  CD   single  1.527  0.020  1.527
 CPI  CE  HE2  single  0.970  0.020  1.090
 CPI  CE  HE3  single  0.970  0.020  1.090
 CPI  CD  CG   single  1.526  0.020  1.526
 CPI  CD  HD2  single  0.970  0.020  1.090
 CPI  CD  HD3  single  0.970  0.020  1.090
 CPI  CG  CB   single  1.525  0.020  1.525
 CPI  CG  HG2  single  0.970  0.020  1.090
 CPI  CG  HG3  single  0.970  0.020  1.090
 CPI  CB  CA   single  1.521  0.033  1.521
 CPI  CB  HB2  single  0.970  0.020  1.090
 CPI  CB  HB3  single  0.970  0.020  1.090
 CPI  CA  C    single  1.525  0.021  1.525
 CPI  CA  HA   single  0.970  0.020  0.970
 CPI  C   O    deloc   1.231  0.020  1.231
 CPI  C   OXT  deloc   1.249  0.020  1.249

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
 CPI  H    N   CA   114.00  3.000
 CPI  H    N   CE   108.00  3.000
 CPI  CA   N   CE   112.85  3.000
 CPI  HE3  CE  HE2  106.41  3.000
 CPI  HE3  CE  CD   110.18  3.000
 CPI  HE2  CE  CD   109.30  3.000
 CPI  HE3  CE  N    108.41  3.000
 CPI  HE2  CE  N    108.14  3.000
 CPI  CD   CE  N    114.10  3.000
 CPI  HD3  CD  HD2  106.66  3.000
 CPI  HD3  CD  CG   109.28  3.000
 CPI  HD2  CD  CG   111.01  3.000
 CPI  HD3  CD  CE   109.25  3.000
 CPI  HD2  CD  CE   110.15  3.000
 CPI  CG   CD  CE   110.41  3.000
 CPI  HG3  CG  HG2  106.29  3.000
 CPI  HG3  CG  CB   110.45  3.000
 CPI  HG2  CG  CB   109.55  3.000
 CPI  HG3  CG  CD   110.50  3.000
 CPI  HG2  CG  CD   109.65  3.000
 CPI  CB   CG  CD   110.32  3.000
 CPI  HB3  CB  HB2  106.58  3.000
 CPI  HB3  CB  CA   108.77  3.000
 CPI  HB2  CB  CA   110.48  3.000
 CPI  HB3  CB  CG   108.76  3.000
 CPI  HB2  CB  CG   110.87  3.000
 CPI  CA   CB  CG   111.23  3.000
 CPI  HA   CA  C    110.00  3.000
 CPI  HA   CA  CB   109.00  3.000
 CPI  C    CA  CB   110.50  1.500
 CPI  HA   CA  N    110.00  3.000
 CPI  C    CA  N    111.00  2.800
 CPI  CB   CA  N    110.40  1.500
 CPI  OXT  C   O    126.36  3.000
 CPI  OXT  C   CA   120.80  1.700
 CPI  O    C   CA   120.80  1.700

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
 CPI  Var_01  CG  CD  CE  N    53.00  30.0  1
 CPI  Var_02  CB  CG  CD  CE  -52.87  30.0  1
 CPI  Var_03  CA  N   CE  CD  -53.60  30.0  1
 CPI  Var_04  CA  CB  CG  CD   54.50  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
 CPI  chir_01  CA  N  CB  C  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
 CPI  plan-1  CA   0.020
 CPI  plan-1  C    0.020
 CPI  plan-1  O    0.020
 CPI  plan-1  OXT  0.020

