# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:31:22 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 5-oxo-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCC(=O)N1
#
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
 PCC  PCC  '5-oxo-L-proline          '  L-peptide  15  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PCC
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
 PCC  N    N  NH1    0  -0.597  -0.7141   0.4159  -0.9796
 PCC  CA   C  CH1    0  -0.211   0.4875  -0.3677  -0.7962
 PCC  CB   C  CH2    0  -0.464  -0.0692  -1.5935  -0.0487
 PCC  CG   C  CH2    0  -0.583  -1.2195  -1.0079   0.7645
 PCC  CD   C  C      0   0.508  -1.6483   0.2063  -0.0358
 PCC  C    C  C      0   0.410   1.5594   0.3435   0.0609
 PCC  O    O  O      0  -0.595   1.1807   1.2866   0.7774
 PCC  OE1  O  O      0  -0.507  -2.6578   0.8722   0.1401
 PCC  OXT  O  OC    -1  -0.617   2.7057  -0.1398  -0.0188
 PCC  H    H  HNH1   0   0.384  -0.6966   1.2825  -1.4956
 PCC  HA   H  HCH1   0   0.245   0.9118  -0.6515  -1.7612
 PCC  HB2  H  HCH2   0   0.248  -0.4508  -2.3216  -0.7669
 PCC  HB3  H  HCH2   0   0.249   0.6875  -2.0910   0.5554
 PCC  HG2  H  HCH2   0   0.264  -2.0521  -1.6937   0.9192
 PCC  HG3  H  HCH2   0   0.267  -0.8905  -0.6645   1.7485

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
 PCC  N   CA   single  1.466  0.015  1.466
 PCC  N   CD   single  1.473  0.014  1.473
 PCC  N   H    single  0.860  0.020  1.020
 PCC  CA  CB   single  1.530  0.020  1.530
 PCC  CA  C    single  1.525  0.021  1.525
 PCC  CA  HA   single  0.970  0.020  0.970
 PCC  CB  CG   single  1.526  0.020  1.526
 PCC  CB  HB2  single  0.970  0.020  1.090
 PCC  CB  HB3  single  0.970  0.020  1.090
 PCC  CG  CD   single  1.516  0.020  1.516
 PCC  CG  HG2  single  0.970  0.020  1.090
 PCC  CG  HG3  single  0.970  0.020  1.090
 PCC  CD  OE1  double  1.222  0.020  1.222
 PCC  C   O    deloc   1.231  0.020  1.231
 PCC  C   OXT  deloc   1.247  0.020  1.247

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
 PCC  H    N   CD   120.34  3.000
 PCC  H    N   CA   121.06  3.000
 PCC  CD   N   CA   113.82  3.000
 PCC  HA   CA  C    109.00  3.000
 PCC  HA   CA  CB   109.00  3.000
 PCC  C    CA  CB   110.10  1.900
 PCC  HA   CA  N    110.00  3.000
 PCC  C    CA  N    112.10  2.500
 PCC  CB   CA  N    103.00  1.100
 PCC  HB3  CB  HB2  107.65  3.000
 PCC  HB3  CB  CG   113.82  3.000
 PCC  HB2  CB  CG   110.07  3.000
 PCC  HB3  CB  CA   112.45  3.000
 PCC  HB2  CB  CA   109.75  3.000
 PCC  CG   CB  CA   103.05  3.000
 PCC  HG3  CG  HG2  107.45  3.000
 PCC  HG3  CG  CD   107.98  3.000
 PCC  HG2  CG  CD   111.27  3.000
 PCC  HG3  CG  CB   111.94  3.000
 PCC  HG2  CG  CB   114.22  3.000
 PCC  CD   CG  CB   103.84  3.000
 PCC  OE1  CD  CG   126.44  3.000
 PCC  OE1  CD  N    126.16  3.000
 PCC  CG   CD  N    103.20  1.500
 PCC  OXT  C   O    127.66  3.000
 PCC  OXT  C   CA   115.08  3.000
 PCC  O    C   CA   119.00  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
 PCC  CONST_01  CG   CD  N   CA    0.00   0.0  0
 PCC  CONST_02  OE1  CD  N   CA  180.00   0.0  0
 PCC  CONST_03  H    N   CD  CG  180.00   0.0  0
 PCC  Var_01    CB   CG  CD  N   -10.91  30.0  1
 PCC  Var_02    CD   CG  CB  CA   26.63  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
 PCC  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
 PCC  plan-1  N    0.020
 PCC  plan-1  CA   0.020
 PCC  plan-1  CG   0.020
 PCC  plan-1  CD   0.020
 PCC  plan-1  OE1  0.020
 PCC  plan-1  H    0.020
 PCC  plan-2  CA   0.020
 PCC  plan-2  C    0.020
 PCC  plan-2  O    0.020
 PCC  plan-2  OXT  0.020

