# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 20:10:34 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2~{R})-5-oxidanylidenepyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCC(=O)N1
#
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
 7YO  7YO  '(2~{R})-5-oxidanylidenepyrrolidine-2-carboxylic acid'  peptide  16  9  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7YO
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
 7YO  C5   C  C     0   0.538   1.7351  -0.2805  -0.0129
 7YO  O2   O  O     0  -0.429   1.8842  -1.3698  -0.5010
 7YO  C4   C  CH1   0  -0.148   0.4240   0.2672   0.4966
 7YO  N1   N  NH1   0  -0.632  -0.6393  -0.6943   0.3892
 7YO  C3   C  CH2   0  -0.474  -0.0896   1.4392  -0.3671
 7YO  C2   C  CH2   0  -0.590  -1.6047   1.2849  -0.3042
 7YO  C1   C  C     0   0.525  -1.8215  -0.1849  -0.0131
 7YO  O1   O  O     0  -0.485  -2.8695  -0.7989  -0.0978
 7YO  H23  H  HCH1  0   0.297   0.5674   0.5928   1.5339
 7YO  H24  H  HNH1  0   0.401  -0.5672  -1.6225   0.7783
 7YO  H25  H  HCH2  0   0.273   0.2680   2.3965   0.0027
 7YO  H26  H  HCH2  0   0.264   0.2520   1.3265  -1.3974
 7YO  H27  H  HCH2  0   0.282  -2.0359   1.8581   0.5214
 7YO  H28  H  HCH2  0   0.282  -2.1149   1.5911  -1.2162
 7YO  OXT  O  OH1   0  -0.590   2.7034   0.6104   0.1400
 7YO  HXT  H  HOH1  0   0.488   3.5397   0.2659  -0.2084

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
 7YO  O1   C1   double  1.218  0.020  1.218
 7YO  C1   C2   single  1.514  0.020  1.514
 7YO  C1   N1   single  1.349  0.020  1.349
 7YO  C2   C3   single  1.524  0.020  1.524
 7YO  N1   C4   single  1.438  0.020  1.438
 7YO  C3   C4   single  1.544  0.020  1.544
 7YO  C4   C5   single  1.510  0.020  1.510
 7YO  C5   O2   double  1.203  0.020  1.203
 7YO  C4   H23  single  0.970  0.020  1.090
 7YO  N1   H24  single  0.860  0.020  1.020
 7YO  C3   H25  single  0.970  0.020  1.090
 7YO  C3   H26  single  0.970  0.020  1.090
 7YO  C2   H27  single  0.970  0.020  1.090
 7YO  C2   H28  single  0.970  0.020  1.090
 7YO  C5   OXT  single  1.325  0.020  1.325
 7YO  OXT  HXT  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
 7YO  OXT  C5   C4   110.60  3.000
 7YO  OXT  C5   O2   124.43  3.000
 7YO  C4   C5   O2   124.97  3.000
 7YO  H23  C4   C3   110.32  3.000
 7YO  H23  C4   N1   111.46  3.000
 7YO  C3   C4   N1   102.70  3.000
 7YO  H23  C4   C5   108.27  3.000
 7YO  C3   C4   C5   112.06  3.000
 7YO  N1   C4   C5   112.00  3.000
 7YO  H24  N1   C1   121.68  3.000
 7YO  H24  N1   C4   122.25  3.000
 7YO  C1   N1   C4   114.70  3.000
 7YO  H26  C3   H25  108.01  3.000
 7YO  H26  C3   C2   109.85  3.000
 7YO  H25  C3   C2   113.71  3.000
 7YO  H26  C3   C4   110.22  3.000
 7YO  H25  C3   C4   111.65  3.000
 7YO  C2   C3   C4   103.34  3.000
 7YO  H28  C2   H27  107.47  3.000
 7YO  H28  C2   C1   111.53  3.000
 7YO  H27  C2   C1   107.89  3.000
 7YO  H28  C2   C3   113.75  3.000
 7YO  H27  C2   C3   111.72  3.000
 7YO  C1   C2   C3   104.39  3.000
 7YO  O1   C1   C2   126.83  3.000
 7YO  C2   C1   N1   107.37  3.000
 7YO  O1   C1   N1   125.78  3.000
 7YO  HXT  OXT  C5   110.50  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
 7YO  CONST_01  C2   C1   N1  C4    0.00   0.0  0
 7YO  CONST_02  O1   C1   N1  C4  180.00   0.0  0
 7YO  CONST_03  H24  N1   C1  C2  180.00   0.0  0
 7YO  CONST_04  HXT  OXT  C5  C4  180.00   0.0  0
 7YO  Var_01    C1   C2   C3  C4  -24.98  30.0  1
 7YO  Var_02    C3   C2   C1  N1   14.51  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
 7YO  chir_01  C4  N1  C3  C5  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
 7YO  plan-1  C4   0.020
 7YO  plan-1  N1   0.020
 7YO  plan-1  C2   0.020
 7YO  plan-1  C1   0.020
 7YO  plan-1  O1   0.020
 7YO  plan-1  H24  0.020
 7YO  plan-2  C5   0.020
 7YO  plan-2  O2   0.020
 7YO  plan-2  C4   0.020
 7YO  plan-2  OXT  0.020
 7YO  plan-2  HXT  0.020

