# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:33:11 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=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
 DPR  DPR  'D-proline                '  D-peptide  17  8  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DPR
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
 DPR  N    N  NH1   0  -0.604   0.9150   0.8451   0.8470
 DPR  CA   C  CH1   0  -0.185  -0.0425  -0.2243   0.6608
 DPR  CB   C  CH2   0  -0.482   0.7413  -1.3358  -0.0938
 DPR  CG   C  CH2   0  -0.447   2.1409  -0.7445  -0.2962
 DPR  CD   C  CH2   0  -0.286   1.8936   0.7543  -0.2256
 DPR  C    C  C     0   0.516  -1.2674   0.1886  -0.1316
 DPR  O    O  O     0  -0.442  -1.4216   1.2588  -0.6655
 DPR  OXT  O  OH1   0  -0.593  -2.1740  -0.7820  -0.1665
 DPR  H    H  HNH1  0   0.352   0.4725   1.7530   0.8970
 DPR  HA   H  HCH1  0   0.278  -0.4005  -0.5936   1.6272
 DPR  HB2  H  HCH2  0   0.257   0.7560  -2.2647   0.4737
 DPR  HB3  H  HCH2  0   0.249   0.2810  -1.5604  -1.0569
 DPR  HG2  H  HCH2  0   0.234   2.8096  -1.0508   0.5100
 DPR  HG3  H  HCH2  0   0.239   2.5899  -1.0545  -1.2393
 DPR  HD2  H  HCH2  0   0.202   1.5222   1.1235  -1.1920
 DPR  HD3  H  HCH2  0   0.231   2.7924   1.3223   0.0206
 DPR  HXT  H  HOH1  0   0.480  -2.9402  -0.5058  -0.6915

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
 DPR  N    CA   single  1.458  0.019  1.458
 DPR  N    CD   single  1.473  0.014  1.473
 DPR  N    H    single  0.860  0.020  0.860
 DPR  CA   CB   single  1.521  0.033  1.521
 DPR  CA   C    single  1.525  0.021  1.525
 DPR  CA   HA   single  0.970  0.020  0.970
 DPR  CB   CG   single  1.533  0.020  1.533
 DPR  CB   HB2  single  0.970  0.020  1.090
 DPR  CB   HB3  single  0.970  0.020  1.090
 DPR  CG   CD   single  1.521  0.020  1.521
 DPR  CG   HG2  single  0.970  0.020  1.090
 DPR  CG   HG3  single  0.970  0.020  1.090
 DPR  CD   HD2  single  0.970  0.020  1.090
 DPR  CD   HD3  single  0.970  0.020  1.090
 DPR  C    O    double  1.231  0.020  1.231
 DPR  C    OXT  single  1.329  0.020  1.329
 DPR  OXT  HXT  single  0.850  0.020  0.980

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
 DPR  H    N    CD   112.75  3.000
 DPR  H    N    CA   114.00  3.000
 DPR  CD   N    CA   107.70  3.000
 DPR  HA   CA   C    110.00  3.000
 DPR  HA   CA   CB   109.00  3.000
 DPR  C    CA   CB   110.50  1.500
 DPR  HA   CA   N    110.00  3.000
 DPR  C    CA   N    111.00  2.800
 DPR  CB   CA   N    110.40  1.500
 DPR  HB3  CB   HB2  106.87  3.000
 DPR  HB3  CB   CG   110.37  3.000
 DPR  HB2  CB   CG   112.69  3.000
 DPR  HB3  CB   CA   111.27  3.000
 DPR  HB2  CB   CA   111.33  3.000
 DPR  CG   CB   CA   104.39  3.000
 DPR  HG3  CG   HG2  107.88  3.000
 DPR  HG3  CG   CD   112.80  3.000
 DPR  HG2  CG   CD   110.00  3.000
 DPR  HG3  CG   CB   112.39  3.000
 DPR  HG2  CG   CB   110.71  3.000
 DPR  CD   CG   CB   103.04  3.000
 DPR  HD3  CD   HD2  107.57  3.000
 DPR  HD3  CD   CG   112.92  3.000
 DPR  HD2  CD   CG   110.20  3.000
 DPR  HD3  CD   N    110.80  3.000
 DPR  HD2  CD   N    113.58  3.000
 DPR  CG   CD   N    103.20  1.500
 DPR  OXT  C    O    123.33  3.000
 DPR  OXT  C    CA   120.80  1.700
 DPR  O    C    CA   120.80  1.700
 DPR  HXT  OXT  C    110.21  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
 DPR  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 DPR  Var_01    CB   CG   CD  N    39.69  30.0  1
 DPR  Var_02    CG   CD   N   CA  -42.37  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
 DPR  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
 DPR  plan-1  CA   0.020
 DPR  plan-1  C    0.020
 DPR  plan-1  O    0.020
 DPR  plan-1  OXT  0.020
 DPR  plan-1  HXT  0.020

