# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:49:46 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-[(2S)-2-carboxy-2-hydroxyethyl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CN1CCC[C@H]1C(O)=O)C(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
 PR7  PR7  1-[(2S)-2-carboxy-2-hydroxyethyl]-L-proline  L-peptide  25  14  .  2022-07-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PR7
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
 PR7  C     C  C      0   0.381   2.2273   1.2970   0.4029
 PR7  N     N  NT     0  -0.422   0.6328  -0.5929  -0.1614
 PR7  O     O  O      0  -0.599   1.7929   1.9297  -0.5761
 PR7  CA    C  CH1    0  -0.142   1.8143  -0.1742   0.5690
 PR7  CB    C  CH2    0  -0.461   2.9066  -1.1164   0.0376
 PR7  CD    C  CH2    0  -0.280   0.6761  -2.0426  -0.1314
 PR7  CG    C  CH2    0  -0.459   2.1423  -2.3748  -0.4133
 PR7  CAB   C  CH2    0  -0.261  -0.5848  -0.0281   0.3721
 PR7  CAC   C  CH1    0  -0.117  -1.8315  -0.3938  -0.4258
 PR7  CAD   C  C      0   0.396  -3.0873   0.2275   0.2267
 PR7  OAE   O  O      0  -0.612  -3.7432   0.9896  -0.5212
 PR7  OAF   O  OC    -1  -0.596  -3.3411  -0.0730   1.4035
 PR7  OAG   O  OH1    0  -0.695  -1.7369   0.0363  -1.7598
 PR7  O5    O  OC    -1  -0.625   3.0259   1.7165   1.2681
 PR7  HA    H  HCH1   0   0.171   1.6823  -0.3727   1.6505
 PR7  HB    H  HCH2   0   0.225   3.4240  -0.6627  -0.8104
 PR7  HBA   H  HCH2   0   0.227   3.6592  -1.3205   0.7982
 PR7  HD    H  HCH2   0   0.175   0.3830  -2.4389   0.8582
 PR7  HDA   H  HCH2   0   0.226  -0.0024  -2.4839  -0.8645
 PR7  HG    H  HCH2   0   0.228   2.2996  -2.5613  -1.4763
 PR7  HGA   H  HCH2   0   0.227   2.4570  -3.2730   0.1181
 PR7  HAB   H  HCH2   0   0.172  -0.7434  -0.3435   1.4180
 PR7  HABA  H  HCH2   0   0.220  -0.4806   1.0596   0.3767
 PR7  HAC   H  HCH1   0   0.198  -1.9622  -1.4868  -0.3961
 PR7  HOAG  H  HOH1   0   0.423  -2.5109   0.6257  -1.8343

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
 PR7  C    CA    single  1.525  0.021  1.525
 PR7  C    O5    deloc   1.250  0.020  1.250
 PR7  N    CD    single  1.473  0.014  1.473
 PR7  N    CAB   single  1.444  0.020  1.444
 PR7  O    C     deloc   1.231  0.020  1.231
 PR7  CA   N     single  1.466  0.015  1.466
 PR7  CA   CB    single  1.530  0.020  1.530
 PR7  CA   HA    single  0.970  0.020  0.970
 PR7  CB   HB    single  0.970  0.020  1.090
 PR7  CB   HBA   single  0.970  0.020  1.090
 PR7  CD   HD    single  0.970  0.020  1.090
 PR7  CD   HDA   single  0.970  0.020  1.090
 PR7  CG   CB    single  1.540  0.020  1.540
 PR7  CG   CD    single  1.530  0.020  1.530
 PR7  CG   HG    single  0.970  0.020  1.090
 PR7  CG   HGA   single  0.970  0.020  1.090
 PR7  CAB  CAC   single  1.525  0.020  1.525
 PR7  CAB  HAB   single  0.970  0.020  1.090
 PR7  CAB  HABA  single  0.970  0.020  1.090
 PR7  CAC  OAG   single  1.405  0.020  1.405
 PR7  CAC  CAD   single  1.546  0.020  1.546
 PR7  CAC  HAC   single  0.970  0.020  1.090
 PR7  CAD  OAE   deloc   1.253  0.020  1.253
 PR7  CAD  OAF   deloc   1.241  0.020  1.241
 PR7  OAG  HOAG  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
 PR7  O5    C    CA   114.72  3.000
 PR7  O5    C    O    126.67  3.000
 PR7  CA    C    O    119.00  3.000
 PR7  CAB   N    CD   114.10  3.000
 PR7  CAB   N    CA   112.81  3.000
 PR7  CD    N    CA   104.70  3.000
 PR7  HA    CA   CB   109.00  3.000
 PR7  HA    CA   N    110.00  3.000
 PR7  CB    CA   N    103.00  1.100
 PR7  HA    CA   C    109.00  3.000
 PR7  CB    CA   C    110.10  1.900
 PR7  N     CA   C    112.10  2.500
 PR7  HBA   CB   HB   107.02  3.000
 PR7  HBA   CB   CG   113.22  3.000
 PR7  HB    CB   CG   110.32  3.000
 PR7  CG    CB   CA   104.44  3.000
 PR7  HBA   CB   CA   111.37  3.000
 PR7  HB    CB   CA   110.51  3.000
 PR7  HDA   CD   HD   106.94  3.000
 PR7  HDA   CD   CG   112.59  3.000
 PR7  HD    CD   CG   109.95  3.000
 PR7  CG    CD   N    103.20  1.500
 PR7  HDA   CD   N    111.81  3.000
 PR7  HD    CD   N    111.64  3.000
 PR7  HGA   CG   HG   107.01  3.000
 PR7  HGA   CG   CD   111.46  3.000
 PR7  HG    CG   CD   110.79  3.000
 PR7  HGA   CG   CB   112.79  3.000
 PR7  HG    CG   CB   110.71  3.000
 PR7  CD    CG   CB   104.14  3.000
 PR7  HABA  CAB  HAB  107.10  3.000
 PR7  HABA  CAB  CAC  108.59  3.000
 PR7  HAB   CAB  CAC  108.05  3.000
 PR7  HABA  CAB  N    108.09  3.000
 PR7  HAB   CAB  N    111.06  3.000
 PR7  CAC   CAB  N    113.72  3.000
 PR7  HAC   CAC  OAG  109.72  3.000
 PR7  HAC   CAC  CAD  106.93  3.000
 PR7  OAG   CAC  CAD  109.42  3.000
 PR7  HAC   CAC  CAB  108.73  3.000
 PR7  CAD   CAC  CAB  110.31  3.000
 PR7  OAG   CAC  CAB  111.62  3.000
 PR7  OAF   CAD  OAE  127.32  3.000
 PR7  OAF   CAD  CAC  117.98  3.000
 PR7  OAE   CAD  CAC  114.70  3.000
 PR7  HOAG  OAG  CAC  101.77  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
 PR7  Var_01  CB   CG   CD  N    24.68  30.0  1
 PR7  Var_02  CG   CD   N   CA  -42.99  30.0  1
 PR7  Var_03  CAC  CAB  N   CA  176.86  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
 PR7  chir_01  CA   C    N    CB   negativ
 PR7  chir_02  CAC  OAG  CAB  CAD  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
 PR7  plan-1  C    0.020
 PR7  plan-1  O    0.020
 PR7  plan-1  CA   0.020
 PR7  plan-1  O5   0.020
 PR7  plan-2  CAC  0.020
 PR7  plan-2  CAD  0.020
 PR7  plan-2  OAE  0.020
 PR7  plan-2  OAF  0.020

