# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:28:13 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-[(2R)-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
 PR4  PR4  1-[(2R)-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_PR4
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
 PR4  C     C  C      0   0.383   2.1385  -1.3907  -0.4771
 PR4  N     N  NT     0  -0.438   0.5560   0.5302   0.0019
 PR4  O     O  O      0  -0.601   1.7642  -1.9339   0.5780
 PR4  CA    C  CH1    0  -0.143   1.7080   0.0605  -0.7470
 PR4  CB    C  CH2    0  -0.457   2.8073   1.0422  -0.3258
 PR4  CD    C  CH2    0  -0.263   0.5741   1.9764  -0.1495
 PR4  CG    C  CH2    0  -0.469   2.0566   2.3576  -0.0574
 PR4  CAC   C  CH1    0  -0.095  -1.8307   0.0772   0.5852
 PR4  CAD   C  C      0   0.391  -3.0156  -0.8479   0.2077
 PR4  OAE   O  OC    -1  -0.591  -2.8051  -2.0663   0.1199
 PR4  OAF   O  O      0  -0.612  -4.1034  -0.2502   0.0293
 PR4  OAG   O  OH1    0  -0.696  -2.3022   1.4015   0.6456
 PR4  O5    O  OC    -1  -0.624   2.8898  -1.8850  -1.3451
 PR4  HA    H  HCH1   0   0.172   1.5393   0.1749  -1.8351
 PR4  HB    H  HCH2   0   0.223   3.2911   0.6881   0.5875
 PR4  HBA   H  HCH2   0   0.227   3.5810   1.1360  -1.0869
 PR4  HD    H  HCH2   0   0.172   0.1680   2.2774  -1.1310
 PR4  HDA   H  HCH2   0   0.225  -0.0351   2.4675   0.6078
 PR4  HG    H  HCH2   0   0.228   2.3053   2.7581   0.9262
 PR4  HGA   H  HCH2   0   0.226   2.3058   3.1300  -0.7856
 PR4  HAB   H  HCH2   0   0.167  -1.0035   0.2305  -1.3995
 PR4  HABA  H  HCH2   0   0.230  -0.4966  -1.1781  -0.4609
 PR4  HAC   H  HCH1   0   0.189  -1.4644  -0.2374   1.5749
 PR4  HOAG  H  HOH1   0   0.425  -3.2445   1.2846   0.4124
 PR4  CAB   C  CH2    0  -0.267  -0.6792  -0.1065  -0.3957

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
 PR4  C    O     deloc   1.231  0.020  1.231
 PR4  C    O5    deloc   1.250  0.020  1.250
 PR4  N    CA    single  1.466  0.015  1.466
 PR4  N    CD    single  1.473  0.014  1.473
 PR4  CA   C     single  1.525  0.021  1.525
 PR4  CA   CB    single  1.530  0.020  1.530
 PR4  CA   HA    single  0.970  0.020  0.970
 PR4  CB   CG    single  1.538  0.020  1.538
 PR4  CB   HB    single  0.970  0.020  1.090
 PR4  CB   HBA   single  0.970  0.020  1.090
 PR4  CD   CG    single  1.533  0.020  1.533
 PR4  CD   HD    single  0.970  0.020  1.090
 PR4  CD   HDA   single  0.970  0.020  1.090
 PR4  CG   HG    single  0.970  0.020  1.090
 PR4  CG   HGA   single  0.970  0.020  1.090
 PR4  CAB  N     single  1.445  0.020  1.445
 PR4  CAB  HAB   single  0.970  0.020  1.090
 PR4  CAB  HABA  single  0.970  0.020  1.090
 PR4  CAC  CAB   single  1.524  0.020  1.524
 PR4  CAC  CAD   single  1.550  0.020  1.550
 PR4  CAC  OAG   single  1.407  0.020  1.407
 PR4  CAC  HAC   single  0.970  0.020  1.090
 PR4  CAD  OAE   deloc   1.240  0.020  1.240
 PR4  OAF  CAD   deloc   1.254  0.020  1.254
 PR4  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
 PR4  O5    C    CA   114.82  3.000
 PR4  CA    C    O    119.00  3.000
 PR4  O5    C    O    126.65  3.000
 PR4  CAB   N    CD   114.84  3.000
 PR4  CAB   N    CA   113.18  3.000
 PR4  CD    N    CA   104.96  3.000
 PR4  HA    CA   CB   109.00  3.000
 PR4  HA    CA   N    110.00  3.000
 PR4  CB    CA   N    103.00  1.100
 PR4  HA    CA   C    109.00  3.000
 PR4  CB    CA   C    110.10  1.900
 PR4  N     CA   C    112.10  2.500
 PR4  HBA   CB   HB   107.31  3.000
 PR4  HBA   CB   CG   113.26  3.000
 PR4  HB    CB   CG   110.33  3.000
 PR4  HBA   CB   CA   111.87  3.000
 PR4  HB    CB   CA   109.86  3.000
 PR4  CG    CB   CA   104.22  3.000
 PR4  HDA   CD   HD   106.83  3.000
 PR4  HDA   CD   CG   112.77  3.000
 PR4  HD    CD   CG   109.95  3.000
 PR4  HDA   CD   N    111.66  3.000
 PR4  HD    CD   N    111.04  3.000
 PR4  CG    CD   N    103.20  1.500
 PR4  HGA   CG   HG   106.86  3.000
 PR4  HGA   CG   CD   110.91  3.000
 PR4  HG    CG   CD   111.46  3.000
 PR4  HGA   CG   CB   112.19  3.000
 PR4  HG    CG   CB   111.11  3.000
 PR4  CD    CG   CB   104.40  3.000
 PR4  HAC   CAC  OAG  109.98  3.000
 PR4  HAC   CAC  CAD  107.62  3.000
 PR4  OAG   CAC  CAD  108.42  3.000
 PR4  HAC   CAC  CAB  107.02  3.000
 PR4  OAG   CAC  CAB  113.22  3.000
 PR4  CAD   CAC  CAB  110.43  3.000
 PR4  OAF   CAD  OAE  127.28  3.000
 PR4  OAF   CAD  CAC  114.42  3.000
 PR4  OAE   CAD  CAC  118.30  3.000
 PR4  HOAG  OAG  CAC  101.55  3.000
 PR4  HABA  CAB  HAB  107.12  3.000
 PR4  HABA  CAB  CAC  106.49  3.000
 PR4  HAB   CAB  CAC  109.00  3.000
 PR4  CAC   CAB  N    114.56  3.000
 PR4  HABA  CAB  N    107.86  3.000
 PR4  HAB   CAB  N    111.44  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
 PR4  Var_01  CB   CG   CD  N    18.40  30.0  1
 PR4  Var_02  CG   CD   N   CA  -39.54  30.0  1
 PR4  Var_03  CAC  CAB  N   CA  164.81  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
 PR4  chir_01  CA   N    C    CB   positiv
 PR4  chir_02  CAC  OAG  CAD  CAB  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
 PR4  plan-1  C    0.020
 PR4  plan-1  O    0.020
 PR4  plan-1  CA   0.020
 PR4  plan-1  O5   0.020
 PR4  plan-2  CAC  0.020
 PR4  plan-2  CAD  0.020
 PR4  plan-2  OAE  0.020
 PR4  plan-2  OAF  0.020

