# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:14:09 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  15  9  .  2022-03-10  2022-03-10
;
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   0.409   1.7833  -0.2462   0.0620
 7YO  O2   O  O      0  -0.601   1.8970  -1.4654  -0.1570
 7YO  C4   C  CR15   0  -0.163   0.4088   0.2700   0.5152
 7YO  N1   N  NR15   0  -0.623  -0.6538  -0.7077   0.4032
 7YO  C3   C  CH2    0  -0.464  -0.1374   1.4295  -0.3295
 7YO  C2   C  CH2    0  -0.589  -1.6517   1.2642  -0.2295
 7YO  C1   C  CR5    0   0.510  -1.8376  -0.2230   0.0058
 7YO  O1   O  O      0  -0.510  -2.8744  -0.8587  -0.1277
 7YO  H23  H  HCR5   0   0.242   0.5060   0.5961   1.5604
 7YO  H24  H  HNR5   0   0.383  -0.5119  -1.6762   0.6421
 7YO  H25  H  HCH2   0   0.245   0.2172   2.3964   0.0195
 7YO  H26  H  HCH2   0   0.239   0.1787   1.3148  -1.3689
 7YO  H27  H  HCH2   0   0.266  -2.0615   1.7996   0.6328
 7YO  H28  H  HCH2   0   0.266  -2.1991   1.5981  -1.1106
 7YO  OXT  O  OC    -1  -0.611   2.6673   0.6276  -0.0178

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  1.223  0.020  1.223
 7YO  C1  C2   single  1.517  0.020  1.517
 7YO  C1  N1   single  1.340  0.020  1.340
 7YO  C2  C3   single  1.527  0.020  1.527
 7YO  N1  C4   single  1.448  0.020  1.448
 7YO  C3  C4   single  1.535  0.020  1.535
 7YO  C4  C5   single  1.537  0.020  1.537
 7YO  C5  O2   deloc   1.244  0.020  1.244
 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  deloc   1.246  0.020  1.246

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   114.71  3.000
 7YO  OXT  C5  O2   127.70  3.000
 7YO  C4   C5  O2   117.58  3.000
 7YO  H23  C4  C3   109.31  3.000
 7YO  H23  C4  N1   109.79  3.000
 7YO  C3   C4  N1   101.91  3.000
 7YO  H23  C4  C5   107.52  3.000
 7YO  C3   C4  C5   114.19  3.000
 7YO  N1   C4  C5   114.00  3.000
 7YO  H24  N1  C1   122.86  3.000
 7YO  H24  N1  C4   121.82  3.000
 7YO  C1   N1  C4   115.28  3.000
 7YO  H26  C3  H25  107.72  3.000
 7YO  H26  C3  C2   109.75  3.000
 7YO  H25  C3  C2   113.50  3.000
 7YO  H26  C3  C4   109.96  3.000
 7YO  H25  C3  C4   112.27  3.000
 7YO  C2   C3  C4   103.60  3.000
 7YO  H28  C2  H27  107.40  3.000
 7YO  H28  C2  C1   111.36  3.000
 7YO  H27  C2  C1   108.15  3.000
 7YO  H28  C2  C3   114.33  3.000
 7YO  H27  C2  C3   111.72  3.000
 7YO  C1   C2  C3   103.76  3.000
 7YO  O1   C1  C2   126.60  3.000
 7YO  C2   C1  N1   107.00  3.000
 7YO  O1   C1  N1   126.39  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  Var_01    C1   C2  C3  C4  -27.40  30.0  1
 7YO  Var_02    C3   C2  C1  N1   17.14  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

