# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 23:07:14 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: methyl D-prolinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1CCCN1
#
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
 PDW  PDW  'methyl D-prolinate       '  D-peptide  20  9  .  2016-04-26  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDW
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
 PDW  CM   C  CH3   0  -0.421  -26.3233  -39.1071   0.8133
 PDW  O    O  O     0  -0.447  -23.7501  -38.8238   0.2072
 PDW  CG   C  CH2   0  -0.463  -22.1873  -36.2589  -1.3498
 PDW  CB   C  CH2   0  -0.470  -22.3479  -36.3305   0.1652
 PDW  CD   C  CH2   0  -0.269  -23.3670  -35.3853  -1.7518
 PDW  OXT  O  O2    0  -0.453  -25.6677  -37.8410   0.7788
 PDW  C    C  C     0   0.616  -24.3840  -37.8259   0.4432
 PDW  CA   C  CH1   0  -0.219  -23.8627  -36.4013   0.3544
 PDW  N    N  NH1   0  -0.612  -24.4424  -35.8154  -0.8614
 PDW  HM1  H  HCH3  0   0.248  -27.3519  -38.9053   1.0981
 PDW  HM2  H  HCH3  0   0.235  -26.3098  -39.5920  -0.1630
 PDW  HM3  H  HCH3  0   0.235  -25.8710  -39.7729   1.5483
 PDW  HG2  H  HCH2  0   0.241  -21.2322  -35.8362  -1.6597
 PDW  HG3  H  HCH2  0   0.231  -22.2743  -37.2530  -1.7930
 PDW  HB2  H  HCH2  0   0.250  -21.8127  -37.1589   0.6267
 PDW  HB3  H  HCH2  0   0.242  -21.9778  -35.4092   0.6192
 PDW  HD2  H  HCH2  0   0.205  -23.1081  -34.3282  -1.6153
 PDW  HD3  H  HCH2  0   0.224  -23.6485  -35.5188  -2.7989
 PDW  HA   H  HCH1  0   0.269  -24.1793  -35.8632   1.2529
 PDW  H    H  HNH1  0   0.358  -25.0845  -35.0680  -0.6459

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
 PDW  CM   OXT  single  1.426  0.020  1.426
 PDW  O    C    double  1.231  0.020  1.231
 PDW  CG   CB   single  1.525  0.020  1.525
 PDW  CG   CD   single  1.522  0.020  1.522
 PDW  CB   CA   single  1.521  0.033  1.521
 PDW  CD   N    single  1.473  0.014  1.473
 PDW  OXT  C    single  1.327  0.020  1.327
 PDW  C    CA   single  1.525  0.021  1.525
 PDW  CA   N    single  1.458  0.019  1.458
 PDW  CM   HM1  single  0.970  0.020  1.090
 PDW  CM   HM2  single  0.970  0.020  1.090
 PDW  CM   HM3  single  0.970  0.020  1.090
 PDW  CG   HG2  single  0.970  0.020  1.090
 PDW  CG   HG3  single  0.970  0.020  1.090
 PDW  CB   HB2  single  0.970  0.020  1.090
 PDW  CB   HB3  single  0.970  0.020  1.090
 PDW  CD   HD2  single  0.970  0.020  1.090
 PDW  CD   HD3  single  0.970  0.020  1.090
 PDW  CA   HA   single  0.970  0.020  0.970
 PDW  N    H    single  0.860  0.020  0.860

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
 PDW  HM3  CM   HM2  109.09  3.000
 PDW  HM3  CM   HM1  109.24  3.000
 PDW  HM2  CM   HM1  109.22  3.000
 PDW  HM3  CM   OXT  111.58  3.000
 PDW  HM2  CM   OXT  111.56  3.000
 PDW  HM1  CM   OXT  106.07  3.000
 PDW  HG3  CG   HG2  107.91  3.000
 PDW  HG3  CG   CD   110.71  3.000
 PDW  HG2  CG   CD   112.44  3.000
 PDW  HG3  CG   CB   110.62  3.000
 PDW  HG2  CG   CB   113.15  3.000
 PDW  CD   CG   CB   101.99  3.000
 PDW  HB3  CB   HB2  107.41  3.000
 PDW  HB3  CB   CA   108.88  3.000
 PDW  HB2  CB   CA   113.54  3.000
 PDW  HB3  CB   CG   109.74  3.000
 PDW  HB2  CB   CG   113.89  3.000
 PDW  CA   CB   CG   103.27  3.000
 PDW  HD3  CD   HD2  107.33  3.000
 PDW  HD3  CD   N    111.01  3.000
 PDW  HD2  CD   N    112.43  3.000
 PDW  HD3  CD   CG   112.50  3.000
 PDW  HD2  CD   CG   109.71  3.000
 PDW  N    CD   CG   103.20  1.500
 PDW  C    OXT  CM   117.45  3.000
 PDW  CA   C    OXT  120.80  1.700
 PDW  CA   C    O    120.80  1.700
 PDW  OXT  C    O    123.28  3.000
 PDW  HA   CA   N    110.00  3.000
 PDW  HA   CA   C    110.00  3.000
 PDW  N    CA   C    111.00  2.800
 PDW  HA   CA   CB   109.00  3.000
 PDW  N    CA   CB   110.40  1.500
 PDW  C    CA   CB   110.50  1.500
 PDW  H    N    CA   114.00  3.000
 PDW  H    N    CD   112.37  3.000
 PDW  CA   N    CD   109.35  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
 PDW  Var_01  CA   N   CD   CG    24.51  30.0  1
 PDW  Var_02  N    CD  CG   CB   -38.14  30.0  1
 PDW  Var_03  CA   CB  CG   CD    37.37  30.0  1
 PDW  Var_04  CA   C   OXT  CM   175.85  30.0  3
 PDW  Var_05  HM1  CM  OXT  C   -179.62  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
 PDW  chir_01  CA  CB  C  N  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
 PDW  plan-1  O    0.020
 PDW  plan-1  OXT  0.020
 PDW  plan-1  C    0.020
 PDW  plan-1  CA   0.020

