# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:15:24 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (2S,3aS,6aS)-octahydrocyclopenta[b]pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@@H]2CCC[C@@H]2N1
#
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
 XBG  XBG  '(2S,3aS,6aS)-octahydrocyclopenta[b]pyrrole-2-carboxylic acid'  ligand  23  11  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XBG
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
 XBG  NBB   N  NH1    0  -0.601   0.1345  -1.0256  -0.6425
 XBG  CAZ   C  CH1    0  -0.213   1.0136   0.1358  -0.6591
 XBG  CAT   C  C      0   0.398   2.3606  -0.1081   0.0379
 XBG  OAC   O  O      0  -0.607   2.4052  -1.0230   0.8860
 XBG  CAN   C  CH2    0  -0.434  -2.3169   1.1310   0.6799
 XBG  OAF   O  OC    -1  -0.618   3.2854   0.6695  -0.2687
 XBG  CAQ   C  CH2    0  -0.438   0.2163   1.2569   0.0372
 XBG  CAY   C  CH1    0  -0.262  -1.2267   0.9885  -0.3909
 XBG  CBA   C  CH1    0  -0.061  -1.2267  -0.5207  -0.7933
 XBG  CAL   C  CH2    0  -0.443  -3.2433  -0.0625   0.4431
 XBG  CAO   C  CH2    0  -0.462  -2.2740  -1.1926   0.0997
 XBG  HBB   H  HNH1   0   0.321   0.2403  -1.4533   0.2712
 XBG  HBA   H  HCH1   0   0.214  -1.5319  -0.6169  -1.8411
 XBG  HAZ   H  HCH1   0   0.207   1.1973   0.4320  -1.6993
 XBG  HAO1  H  HCH2   0   0.234  -2.7574  -2.0485  -0.3738
 XBG  HAO2  H  HCH2   0   0.215  -1.7977  -1.5516   1.0187
 XBG  HAY   H  HCH1   0   0.230  -1.4787   1.6015  -1.2605
 XBG  HAL1  H  HCH2   0   0.227  -3.8790  -0.2902   1.3008
 XBG  HAL2  H  HCH2   0   0.217  -3.9064   0.1329  -0.4051
 XBG  HAN1  H  HCH2   0   0.213  -1.8742   1.0528   1.6778
 XBG  HAN2  H  HCH2   0   0.228  -2.8370   2.0897   0.6398
 XBG  HAQ1  H  HCH2   0   0.211   0.3127   1.1471   1.1233
 XBG  HAQ2  H  HCH2   0   0.225   0.5714   2.2548  -0.2234

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
 XBG  NBB  CBA   single  1.460  0.020  1.460
 XBG  NBB  CAZ   single  1.457  0.020  1.457
 XBG  CBA  CAO   single  1.532  0.020  1.532
 XBG  CBA  CAY   single  1.562  0.020  1.562
 XBG  CAO  CAL   single  1.528  0.020  1.528
 XBG  CAL  CAN   single  1.529  0.020  1.529
 XBG  CAN  CAY   single  1.535  0.020  1.535
 XBG  CAY  CAQ   single  1.529  0.020  1.529
 XBG  CAQ  CAZ   single  1.542  0.020  1.542
 XBG  CAZ  CAT   single  1.536  0.020  1.536
 XBG  CAT  OAF   deloc   1.247  0.020  1.247
 XBG  CAT  OAC   deloc   1.248  0.020  1.248
 XBG  NBB  HBB   single  0.890  0.020  1.040
 XBG  CBA  HBA   single  0.970  0.020  1.090
 XBG  CAZ  HAZ   single  0.970  0.020  1.090
 XBG  CAO  HAO1  single  0.970  0.020  1.090
 XBG  CAO  HAO2  single  0.970  0.020  1.090
 XBG  CAY  HAY   single  0.970  0.020  1.090
 XBG  CAL  HAL1  single  0.970  0.020  1.090
 XBG  CAL  HAL2  single  0.970  0.020  1.090
 XBG  CAN  HAN1  single  0.970  0.020  1.090
 XBG  CAN  HAN2  single  0.970  0.020  1.090
 XBG  CAQ  HAQ1  single  0.970  0.020  1.090
 XBG  CAQ  HAQ2  single  0.970  0.020  1.090

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
 XBG  HBB   NBB  CBA   109.65  3.000
 XBG  HBB   NBB  CAZ   106.47  3.000
 XBG  CBA   NBB  CAZ   106.61  3.000
 XBG  HAZ   CAZ  CAQ   108.57  3.000
 XBG  HAZ   CAZ  CAT   109.04  3.000
 XBG  CAQ   CAZ  CAT   111.34  3.000
 XBG  HAZ   CAZ  NBB   109.10  3.000
 XBG  CAT   CAZ  NBB   113.42  3.000
 XBG  CAQ   CAZ  NBB   105.22  3.000
 XBG  OAF   CAT  OAC   126.71  3.000
 XBG  OAC   CAT  CAZ   117.13  3.000
 XBG  OAF   CAT  CAZ   116.10  3.000
 XBG  HAN2  CAN  HAN1  106.80  3.000
 XBG  HAN2  CAN  CAL   113.02  3.000
 XBG  HAN1  CAN  CAL   109.30  3.000
 XBG  HAN2  CAN  CAY   113.23  3.000
 XBG  HAN1  CAN  CAY   110.01  3.000
 XBG  CAL   CAN  CAY   104.47  3.000
 XBG  HAQ2  CAQ  HAQ1  107.45  3.000
 XBG  HAQ2  CAQ  CAY   113.63  3.000
 XBG  HAQ1  CAQ  CAY   110.05  3.000
 XBG  HAQ2  CAQ  CAZ   112.89  3.000
 XBG  HAQ1  CAQ  CAZ   109.22  3.000
 XBG  CAY   CAQ  CAZ   103.53  3.000
 XBG  HAY   CAY  CBA   109.68  3.000
 XBG  HAY   CAY  CAQ   109.99  3.000
 XBG  CBA   CAY  CAQ   103.99  3.000
 XBG  HAY   CAY  CAN   109.82  3.000
 XBG  CAQ   CAY  CAN   117.31  3.000
 XBG  CBA   CAY  CAN   105.63  3.000
 XBG  HBA   CBA  CAO   109.18  3.000
 XBG  HBA   CBA  CAY   109.35  3.000
 XBG  CAO   CBA  CAY   105.88  3.000
 XBG  HBA   CBA  NBB   109.17  3.000
 XBG  CAY   CBA  NBB   107.91  3.000
 XBG  CAO   CBA  NBB   115.19  3.000
 XBG  HAL2  CAL  HAL1  107.06  3.000
 XBG  HAL2  CAL  CAO   110.02  3.000
 XBG  HAL1  CAL  CAO   113.06  3.000
 XBG  HAL2  CAL  CAN   110.35  3.000
 XBG  HAL1  CAL  CAN   113.20  3.000
 XBG  CAO   CAL  CAN   103.17  3.000
 XBG  HAO2  CAO  HAO1  107.43  3.000
 XBG  HAO2  CAO  CAL   109.25  3.000
 XBG  HAO1  CAO  CAL   113.37  3.000
 XBG  HAO2  CAO  CBA   109.61  3.000
 XBG  HAO1  CAO  CBA   113.21  3.000
 XBG  CAL   CAO  CBA   103.91  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
 XBG  Var_01  CBA  CAO  CAL  CAN  -40.28  30.0  1
 XBG  Var_02  CAO  CAL  CAN  CAY   38.98  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
 XBG  chir_01  CAZ  NBB  CAQ  CAT  negativ
 XBG  chir_02  CAY  CBA  CAN  CAQ  negativ
 XBG  chir_03  CBA  NBB  CAO  CAY  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
 XBG  plan-1  CAZ  0.020
 XBG  plan-1  CAT  0.020
 XBG  plan-1  OAC  0.020
 XBG  plan-1  OAF  0.020

