# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 22:04:17 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-methyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H]1C(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
 PKR  PKR  '1-methyl-L-proline       '  peptide  19  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_PKR
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
 PKR  N    N  NT     0  -0.415   0.9099   0.6851   0.1933
 PKR  CA   C  CH1    0  -0.149  -0.0329  -0.1902  -0.4748
 PKR  C    C  C      0   0.383  -1.5155   0.0468  -0.1489
 PKR  O    O  O      0  -0.602  -1.8005   0.7096   0.8653
 PKR  CB   C  CH2    0  -0.459   0.4241  -1.5887  -0.0261
 PKR  CG   C  CH2    0  -0.462   1.9296  -1.4266   0.2664
 PKR  CD   C  CH2    0  -0.273   2.2003   0.0545  -0.0016
 PKR  C6   C  CH3    0  -0.522   0.8735   2.0503  -0.2628
 PKR  OXT  O  OC    -1  -0.624  -2.3187  -0.5008  -0.9333
 PKR  HA   H  HCH1   0   0.176   0.0942  -0.1207  -1.5728
 PKR  HB2  H  HCH2   0   0.226  -0.1095  -1.8930   0.8767
 PKR  HB3  H  HCH2   0   0.228   0.2184  -2.3380  -0.7895
 PKR  HG2  H  HCH2   0   0.229   2.1534  -1.6823   1.3024
 PKR  HG3  H  HCH2   0   0.228   2.5503  -2.0653  -0.3617
 PKR  HD2  H  HCH2   0   0.178   2.5660   0.1904  -1.0354
 PKR  HD3  H  HCH2   0   0.224   2.9546   0.4855   0.6619
 PKR  HC   H  HCH3   0   0.231  -0.1010   2.4913  -0.0586
 PKR  HE   H  HCH3   0   0.222   1.6237   2.6434   0.2644
 PKR  HF   H  HCH3   0   0.178   1.0760   2.1482  -1.3430

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
 PKR  N   CA   single  1.466  0.015  1.466
 PKR  CA  CB   single  1.530  0.020  1.530
 PKR  CA  HA   single  0.970  0.020  0.970
 PKR  C   CA   single  1.525  0.021  1.525
 PKR  C   OXT  deloc   1.249  0.020  1.249
 PKR  O   C    deloc   1.231  0.020  1.231
 PKR  CB  HB2  single  0.970  0.020  1.090
 PKR  CB  HB3  single  0.970  0.020  1.090
 PKR  CG  CB   single  1.542  0.020  1.542
 PKR  CG  HG2  single  0.970  0.020  1.090
 PKR  CG  HG3  single  0.970  0.020  1.090
 PKR  CD  N    single  1.473  0.014  1.473
 PKR  CD  CG   single  1.529  0.020  1.529
 PKR  CD  HD2  single  0.970  0.020  1.090
 PKR  CD  HD3  single  0.970  0.020  1.090
 PKR  N   C6   single  1.440  0.020  1.440
 PKR  C6  HC   single  0.970  0.020  1.090
 PKR  C6  HE   single  0.970  0.020  1.090
 PKR  C6  HF   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
 PKR  C6   N   CD   113.10  3.000
 PKR  C6   N   CA   114.22  3.000
 PKR  CD   N   CA   104.73  3.000
 PKR  HA   CA  CB   109.00  3.000
 PKR  HA   CA  C    109.00  3.000
 PKR  CB   CA  C    110.10  1.900
 PKR  C    CA  N    112.10  2.500
 PKR  HA   CA  N    110.00  3.000
 PKR  CB   CA  N    103.00  1.100
 PKR  OXT  C   O    126.72  3.000
 PKR  O    C   CA   119.00  3.000
 PKR  OXT  C   CA   114.82  3.000
 PKR  HB3  CB  HB2  107.19  3.000
 PKR  HB3  CB  CG   112.93  3.000
 PKR  HB2  CB  CG   110.45  3.000
 PKR  CG   CB  CA   104.47  3.000
 PKR  HB3  CB  CA   111.40  3.000
 PKR  HB2  CB  CA   110.45  3.000
 PKR  HG3  CG  HG2  107.05  3.000
 PKR  HG3  CG  CD   111.45  3.000
 PKR  HG2  CG  CD   110.94  3.000
 PKR  CD   CG  CB   103.96  3.000
 PKR  HG3  CG  CB   112.65  3.000
 PKR  HG2  CG  CB   110.86  3.000
 PKR  HD3  CD  HD2  106.92  3.000
 PKR  HD3  CD  CG   113.43  3.000
 PKR  HD2  CD  CG   109.98  3.000
 PKR  HD3  CD  N    111.17  3.000
 PKR  HD2  CD  N    111.53  3.000
 PKR  CG   CD  N    103.20  1.500
 PKR  HF   C6  HE   107.36  3.000
 PKR  HF   C6  HC   108.17  3.000
 PKR  HE   C6  HC   107.72  3.000
 PKR  HF   C6  N    112.93  3.000
 PKR  HE   C6  N    110.16  3.000
 PKR  HC   C6  N    110.31  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
 PKR  Var_01  CB  CG  CD  N    24.70  30.0  1
 PKR  Var_02  CG  CD  N   CA  -43.57  30.0  1
 PKR  Var_03  HC  C6  N   CA   62.61  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
 PKR  chir_01  CA  N  CB  C  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
 PKR  plan-1  CA   0.020
 PKR  plan-1  C    0.020
 PKR  plan-1  O    0.020
 PKR  plan-1  OXT  0.020

