# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:13:34 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2~{S},3~{R})-3-oxidanylpyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN[C@@H]1C(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
 G8X  G8X  '(2~{S},3~{R})-3-oxidanylpyrrolidine-2-carboxylic acid'  L-peptide  17  9  .  2022-08-10  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_G8X
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
 G8X  O2   O  OH1    0  -0.710   0.7943  12.9397  62.3507
 G8X  O    O  OC    -1  -0.581  -2.7234  11.2688  63.6879
 G8X  N    N  NH1    0  -0.611  -0.6992  12.9843  64.9502
 G8X  CB   C  CH1    0   0.069  -0.1581  13.8442  62.8523
 G8X  CG   C  CH2    0  -0.490   0.4759  14.7507  63.9226
 G8X  CD   C  CH2    0  -0.282  -0.1254  14.2844  65.2606
 G8X  CA   C  CH1    0  -0.259  -1.2837  13.1424  63.6231
 G8X  C    C  C      0   0.453  -1.7793  11.7902  63.0783
 G8X  O1   O  O      0  -0.610  -1.1925  11.3142  62.0707
 G8X  H1   H  HOH1   0   0.433   0.2389  12.1848  62.0420
 G8X  H    H  HNH1   0   0.339  -1.3976  12.7117  65.6289
 G8X  HB2  H  HCH1   0   0.178  -0.5905  14.4456  62.0396
 G8X  HG2  H  HCH2   0   0.233   1.5612  14.6435  63.9012
 G8X  HG3  H  HCH2   0   0.231   0.2536  15.8024  63.7426
 G8X  HD2  H  HCH2   0   0.219   0.6198  14.2079  66.0551
 G8X  HD3  H  HCH2   0   0.193  -0.8836  15.0076  65.5931
 G8X  HA   H  HCH1   0   0.198  -2.1479  13.8323  63.6405

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
 G8X  O1  C    deloc   1.259  0.020  1.259
 G8X  O2  CB   single  1.406  0.020  1.406
 G8X  CB  CA   single  1.530  0.020  1.530
 G8X  CB  CG   single  1.539  0.020  1.539
 G8X  C   CA   single  1.525  0.021  1.525
 G8X  C   O    deloc   1.231  0.020  1.231
 G8X  CA  N    single  1.466  0.015  1.466
 G8X  CG  CD   single  1.539  0.020  1.539
 G8X  N   CD   single  1.473  0.014  1.473
 G8X  O2  H1   single  0.850  0.020  0.980
 G8X  N   H    single  0.860  0.020  1.020
 G8X  CB  HB2  single  0.970  0.020  1.090
 G8X  CG  HG2  single  0.970  0.020  1.090
 G8X  CG  HG3  single  0.970  0.020  1.090
 G8X  CD  HD2  single  0.970  0.020  1.090
 G8X  CD  HD3  single  0.970  0.020  1.090
 G8X  CA  HA   single  0.970  0.020  0.970

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
 G8X  H1   O2  CB   102.86  3.000
 G8X  H    N   CA   111.29  3.000
 G8X  H    N   CD   111.73  3.000
 G8X  CA   N   CD   104.80  3.000
 G8X  HB2  CB  CA   109.45  3.000
 G8X  HB2  CB  CG   110.72  3.000
 G8X  CA   CB  CG   102.84  3.000
 G8X  HB2  CB  O2   110.76  3.000
 G8X  CG   CB  O2   110.36  3.000
 G8X  CA   CB  O2   112.45  3.000
 G8X  HG3  CG  HG2  107.13  3.000
 G8X  HG3  CG  CD   110.87  3.000
 G8X  HG2  CG  CD   112.08  3.000
 G8X  HG3  CG  CB   111.68  3.000
 G8X  HG2  CG  CB   109.77  3.000
 G8X  CD   CG  CB   105.38  3.000
 G8X  HD3  CD  HD2  107.26  3.000
 G8X  HD3  CD  CG   109.45  3.000
 G8X  HD2  CD  CG   112.78  3.000
 G8X  HD3  CD  N    112.36  3.000
 G8X  HD2  CD  N    111.22  3.000
 G8X  CG   CD  N    103.20  1.500
 G8X  HA   CA  C    109.00  3.000
 G8X  HA   CA  CB   109.00  3.000
 G8X  C    CA  CB   110.10  1.900
 G8X  HA   CA  N    110.00  3.000
 G8X  C    CA  N    112.10  2.500
 G8X  CB   CA  N    103.00  1.100
 G8X  O1   C   CA   117.71  3.000
 G8X  CA   C   O    119.00  3.000
 G8X  O1   C   O    126.13  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
 G8X  Var_01  CB  CG  CD  N    15.82  30.0  1
 G8X  Var_02  CA  N   CD  CG  -39.12  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
 G8X  chir_01  CB  O2  CA  CG  negativ
 G8X  chir_02  CA  N   C   CB  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
 G8X  plan-1  O   0.020
 G8X  plan-1  CA  0.020
 G8X  plan-1  C   0.020
 G8X  plan-1  O1  0.020

