# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:33:21 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  16  8  .  2022-03-18  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  NR15   0  -0.625   0.7905   1.0395   0.4820
 DPR  CA   C  CR15   0  -0.188  -0.0057  -0.1846   0.5426
 DPR  CB   C  CH2    0  -0.453   0.7116  -1.1887  -0.3718
 DPR  CG   C  CH2    0  -0.475   2.1699  -0.7890  -0.1948
 DPR  CD   C  CH2    0  -0.271   2.0909   0.7379  -0.1277
 DPR  C    C  C      0   0.396  -1.4752   0.0094   0.1314
 DPR  O    O  O      0  -0.604  -1.7853   1.0849  -0.4213
 DPR  OXT  O  OC    -1  -0.618  -2.2302  -0.9551   0.3615
 DPR  H    H  HNR5   0   0.333   0.2776   1.7012  -0.0863
 DPR  HA   H  HCR5   0   0.200   0.0062  -0.5861   1.5649
 DPR  HB2  H  HCH2   0   0.229   0.5038  -2.2265  -0.1112
 DPR  HB3  H  HCH2   0   0.214   0.4072  -1.0379  -1.4132
 DPR  HG2  H  HCH2   0   0.221   2.5571  -1.1948   0.7439
 DPR  HG3  H  HCH2   0   0.234   2.8233  -1.1385  -0.9955
 DPR  HD2  H  HCH2   0   0.203   2.1700   1.1599  -1.1354
 DPR  HD3  H  HCH2   0   0.204   2.9171   1.1582   0.4536

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  1.522  0.020  1.522
 DPR  CB  HB2  single  0.970  0.020  1.090
 DPR  CB  HB3  single  0.970  0.020  1.090
 DPR  CG  CD   single  1.530  0.020  1.530
 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    deloc   1.231  0.020  1.231
 DPR  C   OXT  deloc   1.246  0.020  1.246

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   110.50  3.000
 DPR  H    N   CA   114.00  3.000
 DPR  CD   N   CA   109.14  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  107.78  3.000
 DPR  HB3  CB  CG   109.91  3.000
 DPR  HB2  CB  CG   113.87  3.000
 DPR  HB3  CB  CA   110.26  3.000
 DPR  HB2  CB  CA   113.02  3.000
 DPR  CG   CB  CA   101.92  3.000
 DPR  HG3  CG  HG2  107.40  3.000
 DPR  HG3  CG  CD   112.50  3.000
 DPR  HG2  CG  CD   110.54  3.000
 DPR  HG3  CG  CB   113.84  3.000
 DPR  HG2  CG  CB   109.97  3.000
 DPR  CD   CG  CB   102.56  3.000
 DPR  HD3  CD  HD2  106.63  3.000
 DPR  HD3  CD  CG   111.57  3.000
 DPR  HD2  CD  CG   109.90  3.000
 DPR  HD3  CD  N    111.68  3.000
 DPR  HD2  CD  N    111.53  3.000
 DPR  CG   CD  N    103.20  1.500
 DPR  OXT  C   O    126.73  3.000
 DPR  OXT  C   CA   120.80  1.700
 DPR  O    C   CA   120.80  1.700

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  Var_01  CB  CG  CD  N    31.09  30.0  1
 DPR  Var_02  CG  CD  N   CA  -10.78  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

