# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:54:04 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (2S)-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
 YCP  YCP  '(2S)-piperidine-2-carboxylic acid'  L-peptide  19  9  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YCP
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
 YCP  C    C  C      0   0.402  -26.6251  -34.9200  4.0807
 YCP  N    N  NH1    0  -0.580  -24.6907  -36.4447  4.5690
 YCP  O    O  O      0  -0.610  -27.6723  -34.7273  3.4277
 YCP  CA   C  CH1    0  -0.246  -25.7892  -36.1583  3.6547
 YCP  CB   C  CH2    0  -0.440  -26.6518  -37.4112  3.3644
 YCP  CD   C  CH2    0  -0.472  -26.4668  -37.6783  5.8452
 YCP  CE   C  CH2    0  -0.283  -25.1282  -36.9277  5.8770
 YCP  CG   C  CH2    0  -0.434  -26.5970  -38.4158  4.5210
 YCP  OXT  O  OC    -1  -0.599  -26.1766  -34.1903  4.9850
 YCP  HN   H  HNH1   0   0.331  -24.1168  -37.1600  4.1411
 YCP  HA   H  HCH1   0   0.228  -25.3251  -35.8531  2.7085
 YCP  HB   H  HCH2   0   0.217  -27.6829  -37.1085  3.1787
 YCP  HBA  H  HCH2   0   0.207  -26.3096  -37.8990  2.4475
 YCP  HD   H  HCH2   0   0.223  -26.5293  -38.3635  6.6939
 YCP  HDA  H  HCH2   0   0.216  -27.3019  -36.9791  5.9530
 YCP  HE   H  HCH2   0   0.208  -24.3516  -37.5968  6.2560
 YCP  HEA  H  HCH2   0   0.203  -25.1887  -36.0948  6.5810
 YCP  HG   H  HCH2   0   0.222  -27.4839  -39.0528  4.5087
 YCP  HGA  H  HCH2   0   0.206  -25.7413  -39.0889  4.4019

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
 YCP  C   O    deloc   1.231  0.020  1.231
 YCP  C   CA   single  1.525  0.021  1.525
 YCP  C   OXT  deloc   1.246  0.020  1.246
 YCP  N   CA   single  1.458  0.019  1.458
 YCP  N   CE   single  1.461  0.020  1.461
 YCP  CA  CB   single  1.521  0.033  1.521
 YCP  CB  CG   single  1.533  0.020  1.533
 YCP  CD  CE   single  1.535  0.020  1.535
 YCP  CD  CG   single  1.521  0.020  1.521
 YCP  N   HN   single  0.890  0.020  1.040
 YCP  CA  HA   single  0.970  0.020  0.970
 YCP  CB  HB   single  0.970  0.020  1.090
 YCP  CB  HBA  single  0.970  0.020  1.090
 YCP  CD  HD   single  0.970  0.020  1.090
 YCP  CD  HDA  single  0.970  0.020  1.090
 YCP  CE  HE   single  0.970  0.020  1.090
 YCP  CE  HEA  single  0.970  0.020  1.090
 YCP  CG  HG   single  0.970  0.020  1.090
 YCP  CG  HGA  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
 YCP  OXT  C   CA  120.80  1.700
 YCP  OXT  C   O   126.23  3.000
 YCP  CA   C   O   120.80  1.700
 YCP  HN   N   CE  108.34  3.000
 YCP  HN   N   CA  107.53  3.000
 YCP  CE   N   CA  113.62  3.000
 YCP  HA   CA  CB  109.00  3.000
 YCP  HA   CA  N   110.00  3.000
 YCP  CB   CA  N   110.40  1.500
 YCP  HA   CA  C   110.00  3.000
 YCP  CB   CA  C   110.50  1.500
 YCP  N    CA  C   111.00  2.800
 YCP  HBA  CB  HB  106.07  3.000
 YCP  HBA  CB  CG  109.21  3.000
 YCP  HB   CB  CG  110.14  3.000
 YCP  HBA  CB  CA  110.11  3.000
 YCP  HB   CB  CA  109.51  3.000
 YCP  CG   CB  CA  111.64  3.000
 YCP  HDA  CD  HD  106.29  3.000
 YCP  HDA  CD  CG  109.28  3.000
 YCP  HD   CD  CG  111.54  3.000
 YCP  HDA  CD  CE  110.55  3.000
 YCP  HD   CD  CE  109.90  3.000
 YCP  CG   CD  CE  109.25  3.000
 YCP  HEA  CE  HE  106.42  3.000
 YCP  HEA  CE  CD  109.75  3.000
 YCP  HE   CE  CD  109.12  3.000
 YCP  HEA  CE  N   109.97  3.000
 YCP  HE   CE  N   107.45  3.000
 YCP  CD   CE  N   113.84  3.000
 YCP  HGA  CG  HG  105.95  3.000
 YCP  HGA  CG  CD  109.02  3.000
 YCP  HG   CG  CD  111.23  3.000
 YCP  HGA  CG  CB  110.40  3.000
 YCP  HG   CG  CB  110.16  3.000
 YCP  CD   CG  CB  110.00  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
 YCP  Var_01  CG  CD  CE  N    32.72  30.0  1
 YCP  Var_02  CD  CE  N   CA   28.56  30.0  1
 YCP  Var_03  CD  CG  CB  CA   33.40  30.0  1
 YCP  Var_04  CE  CD  CG  CB  -64.18  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
 YCP  chir_01  CA  C  N  CB  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
 YCP  plan-1  C    0.020
 YCP  plan-1  O    0.020
 YCP  plan-1  CA   0.020
 YCP  plan-1  OXT  0.020

