# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 15:23:41 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  27  14  .  2022-07-22  2022-11-17
;
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   0.543   2.0725  -1.0361   0.2853
 PR4  N     N  NT    0  -0.427   0.4099   0.6809  -0.2293
 PR4  O     O  O     0  -0.434   1.5892  -1.2556   1.3658
 PR4  CA    C  CH1   0  -0.183   1.6100   0.0293  -0.6930
 PR4  CB    C  CH2   0  -0.484   2.6467   1.1628  -0.8538
 PR4  CD    C  CH2   0  -0.256   0.5760   2.1208  -0.2105
 PR4  CG    C  CH2   0  -0.466   2.0710   2.2927  -0.0065
 PR4  CAC   C  CH1   0  -0.064  -1.7732  -0.1671   0.5448
 PR4  CAD   C  C     0   0.499  -3.0569  -0.8211   0.0611
 PR4  OAE   O  OH1   0  -0.591  -2.8427  -2.0460  -0.3993
 PR4  OAF   O  O     0  -0.437  -4.1359  -0.2859   0.0730
 PR4  OAG   O  OH1   0  -0.649  -2.0537   0.9529   1.3311
 PR4  O5    O  OH1   0  -0.598   3.0996  -1.7234  -0.2081
 PR4  HA    H  HCH1  0   0.269   1.4684  -0.4734  -1.6603
 PR4  HB    H  HCH2  0   0.259   3.6572   0.8739  -0.5678
 PR4  HBA   H  HCH2  0   0.251   2.6803   1.4619  -1.9022
 PR4  HD    H  HCH2  0   0.195   0.2572   2.5864  -1.1572
 PR4  HDA   H  HCH2  0   0.233  -0.0086   2.5776   0.5893
 PR4  HG    H  HCH2  0   0.236   2.3286   2.1597   1.0466
 PR4  HGA   H  HCH2  0   0.246   2.4273   3.2743  -0.3167
 PR4  HAB   H  HCH2  0   0.230  -1.3759   0.8528  -1.3202
 PR4  HABA  H  HCH2  0   0.253  -0.7019  -0.7639  -1.2256
 PR4  HAC   H  HCH1  0   0.272  -1.2459  -0.8764   1.1884
 PR4  HOAE  H  HOH1  0   0.485  -3.6693  -2.4320  -0.7272
 PR4  HOAG  H  HOH1  0   0.447  -2.5473   1.5918   0.8048
 PR4  H13   H  HOH1  0   0.480   3.3908  -2.3904   0.4311
 PR4  CAB   C  CH2   0  -0.307  -0.8580   0.1505  -0.6486

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     double  1.231  0.020  1.231
 PR4  C    O5    single  1.331  0.020  1.331
 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  1.525  0.020  1.525
 PR4  CB   HB    single  0.970  0.020  1.090
 PR4  CB   HBA   single  0.970  0.020  1.090
 PR4  CD   CG    single  1.519  0.020  1.519
 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  1.437  0.020  1.437
 PR4  CAB  HAB   single  0.970  0.020  1.090
 PR4  CAB  HABA  single  0.970  0.020  1.090
 PR4  CAC  CAB   single  1.537  0.020  1.537
 PR4  CAC  CAD   single  1.520  0.020  1.520
 PR4  CAC  OAG   single  1.397  0.020  1.397
 PR4  CAC  HAC   single  0.970  0.020  1.090
 PR4  CAD  OAE   single  1.326  0.020  1.326
 PR4  OAE  HOAE  single  0.850  0.020  0.980
 PR4  OAF  CAD   double  1.205  0.020  1.205
 PR4  OAG  HOAG  single  0.850  0.020  0.980
 PR4  O5   H13   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   111.01  3.000
 PR4  CA    C    O    119.00  3.000
 PR4  O5    C    O    123.26  3.000
 PR4  CAB   N    CD   118.14  3.000
 PR4  CAB   N    CA   118.27  3.000
 PR4  CD    N    CA   110.95  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   107.25  3.000
 PR4  HBA   CB   CG   110.02  3.000
 PR4  HB    CB   CG   113.63  3.000
 PR4  HBA   CB   CA   108.78  3.000
 PR4  HB    CB   CA   113.63  3.000
 PR4  CG    CB   CA   103.45  3.000
 PR4  HDA   CD   HD   107.33  3.000
 PR4  HDA   CD   CG   112.44  3.000
 PR4  HD    CD   CG   110.63  3.000
 PR4  HDA   CD   N    111.35  3.000
 PR4  HD    CD   N    112.04  3.000
 PR4  CG    CD   N    103.20  1.500
 PR4  HGA   CG   HG   107.89  3.000
 PR4  HGA   CG   CD   112.68  3.000
 PR4  HG    CG   CD   110.36  3.000
 PR4  HGA   CG   CB   112.70  3.000
 PR4  HG    CG   CB   110.88  3.000
 PR4  CD    CG   CB   102.31  3.000
 PR4  HAC   CAC  OAG  106.60  3.000
 PR4  HAC   CAC  CAD  108.39  3.000
 PR4  OAG   CAC  CAD  110.77  3.000
 PR4  HAC   CAC  CAB  107.69  3.000
 PR4  OAG   CAC  CAB  113.01  3.000
 PR4  CAD   CAC  CAB  110.17  3.000
 PR4  OAF   CAD  OAE  123.96  3.000
 PR4  OAF   CAD  CAC  124.21  3.000
 PR4  OAE   CAD  CAC  111.82  3.000
 PR4  HOAE  OAE  CAD  110.34  3.000
 PR4  HOAG  OAG  CAC  109.09  3.000
 PR4  H13   O5   C    110.07  3.000
 PR4  HABA  CAB  HAB  106.19  3.000
 PR4  HABA  CAB  CAC  108.79  3.000
 PR4  HAB   CAB  CAC  108.99  3.000
 PR4  CAC   CAB  N    112.03  3.000
 PR4  HABA  CAB  N    109.69  3.000
 PR4  HAB   CAB  N    110.95  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  CONST_01  H13   O5   C    CA   180.00   0.0  0
 PR4  CONST_02  HOAE  OAE  CAD  CAC  180.00   0.0  0
 PR4  Var_01    CB    CG   CD   N     38.15  30.0  1
 PR4  Var_02    CG    CD   N    CA   -27.59  30.0  1
 PR4  Var_03    CAC   CAB  N    CA   125.50  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-1  H13   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
 PR4  plan-2  HOAE  0.020

