# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:38:04 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: [(3~{S},5~{S})-5-carboxypyrrolidin-3-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H]1CN[C@@H](C1)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
 JKH  JKH  '[(3~{S},5~{S})-5-carboxypyrrolidin-3-yl]azanium'  L-peptide  19  9  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JKH
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
 JKH  C     C  C      0   0.407  -1.8746   0.0887  -0.0012
 JKH  N     N  NH1    0  -0.608   0.1386  -1.3594   0.3752
 JKH  CA    C  CH1    0  -0.213  -0.4667  -0.0522   0.6067
 JKH  CD    C  CH2    0  -0.267   1.5764  -1.1889   0.1850
 JKH  CB    C  CH2    0  -0.460   0.5062   0.9629  -0.0073
 JKH  CG    C  CH1    0  -0.153   1.8368   0.3195   0.3260
 JKH  NG2   N  NT3    1  -0.787   2.9436   0.7788  -0.5527
 JKH  O     O  O      0  -0.596  -2.2345  -0.7845  -0.8144
 JKH  OXT   O  OC    -1  -0.609  -2.5111   1.0970   0.3549
 JKH  HA    H  HCH1   0   0.227  -0.5345   0.1422   1.6838
 JKH  HD2   H  HCH2   0   0.238   2.1604  -1.7413   0.9247
 JKH  HD3   H  HCH2   0   0.237   1.8909  -1.5451  -0.8008
 JKH  HB3   H  HCH2   0   0.247   0.3708   1.0085  -1.0934
 JKH  HB2   H  HCH2   0   0.264   0.4010   1.9692   0.3960
 JKH  HG    H  HCH1   0   0.313   2.1445   0.5712   1.3405
 JKH  HG22  H  HNT3   0   0.475   3.1089   1.7809  -0.4575
 JKH  HG21  H  HNT3   0   0.474   3.8250   0.3166  -0.3287
 JKH  HG23  H  HNT3   0   0.466   2.7531   0.5984  -1.5389
 JKH  H1    H  HNH1   0   0.345  -0.2876  -1.7401  -0.4602

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
 JKH  CG   NG2   single  1.486  0.020  1.486
 JKH  CG   CB    single  1.515  0.020  1.515
 JKH  CG   CD    single  1.537  0.020  1.537
 JKH  CB   CA    single  1.530  0.020  1.530
 JKH  CD   N     single  1.473  0.014  1.473
 JKH  CA   N     single  1.466  0.015  1.466
 JKH  CA   C     single  1.525  0.021  1.525
 JKH  O    C     deloc   1.231  0.020  1.231
 JKH  C    OXT   deloc   1.244  0.020  1.244
 JKH  N    H1    single  0.890  0.020  1.040
 JKH  CA   HA    single  0.970  0.020  0.970
 JKH  CD   HD2   single  0.970  0.020  1.090
 JKH  CD   HD3   single  0.970  0.020  1.090
 JKH  CB   HB3   single  0.970  0.020  1.090
 JKH  CB   HB2   single  0.970  0.020  1.090
 JKH  CG   HG    single  0.970  0.020  1.090
 JKH  NG2  HG22  single  0.890  0.020  1.040
 JKH  NG2  HG21  single  0.890  0.020  1.040
 JKH  NG2  HG23  single  0.890  0.020  1.040

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
 JKH  OXT   C    O     127.35  3.000
 JKH  OXT   C    CA    115.39  3.000
 JKH  O     C    CA    119.00  3.000
 JKH  H1    N    CD    110.55  3.000
 JKH  H1    N    CA    107.05  3.000
 JKH  CD    N    CA    108.94  3.000
 JKH  HA    CA   CB    109.00  3.000
 JKH  HA    CA   N     110.00  3.000
 JKH  CB    CA   N     103.00  1.100
 JKH  HA    CA   C     109.00  3.000
 JKH  N     CA   C     112.10  2.500
 JKH  CB    CA   C     110.10  1.900
 JKH  HD3   CD   HD2   106.96  3.000
 JKH  HD3   CD   CG    110.69  3.000
 JKH  HD2   CD   CG    110.09  3.000
 JKH  HD3   CD   N     111.24  3.000
 JKH  HD2   CD   N     112.28  3.000
 JKH  CG    CD   N     103.20  1.500
 JKH  HB2   CB   HB3   108.46  3.000
 JKH  HB2   CB   CG    113.31  3.000
 JKH  HB3   CB   CG    110.14  3.000
 JKH  HB2   CB   CA    113.70  3.000
 JKH  HB3   CB   CA    110.24  3.000
 JKH  CG    CB   CA    100.83  3.000
 JKH  HG    CG   NG2   105.59  3.000
 JKH  HG    CG   CB    110.77  3.000
 JKH  NG2   CG   CB    113.13  3.000
 JKH  HG    CG   CD    111.10  3.000
 JKH  CB    CG   CD    104.35  3.000
 JKH  NG2   CG   CD    112.04  3.000
 JKH  HG23  NG2  HG21  107.05  3.000
 JKH  HG23  NG2  HG22  107.10  3.000
 JKH  HG21  NG2  HG22  106.53  3.000
 JKH  HG23  NG2  CG    112.20  3.000
 JKH  HG21  NG2  CG    111.94  3.000
 JKH  HG22  NG2  CG    111.67  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
 JKH  Var_01  CG  CD  N  CA  0.50  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
 JKH  chir_01  CA  CB   N   C   positiv
 JKH  chir_02  CG  NG2  CD  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
 JKH  plan-1  C    0.020
 JKH  plan-1  CA   0.020
 JKH  plan-1  O    0.020
 JKH  plan-1  OXT  0.020

