# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 18:20:27 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  24  11  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.590   0.1503  -1.0685  -0.5153
 XBG  CAZ   C  CH1   0  -0.214   1.0215   0.0888  -0.5925
 XBG  CAT   C  C     0   0.530   2.3514  -0.1532   0.0676
 XBG  OAC   O  O     0  -0.439   2.6021  -1.0818   0.7948
 XBG  CAN   C  CH2   0  -0.433  -2.2811   1.0961   0.7141
 XBG  OAF   O  OH1   0  -0.592   3.2173   0.8110  -0.2157
 XBG  CAQ   C  CH2   0  -0.442   0.2453   1.2543   0.0613
 XBG  CAY   C  CH1   0  -0.265  -1.1969   0.9644  -0.3609
 XBG  CBA   C  CH1   0  -0.071  -1.1927  -0.5451  -0.7636
 XBG  CAL   C  CH2   0  -0.445  -3.2401  -0.0555   0.4155
 XBG  CAO   C  CH2   0  -0.466  -2.3041  -1.2094   0.0544
 XBG  HBB   H  HNH1  0   0.338   0.1896  -1.4372   0.4293
 XBG  HBA   H  HCH1  0   0.234  -1.4105  -0.6385  -1.8317
 XBG  HAZ   H  HCH1  0   0.277   1.1985   0.3352  -1.6458
 XBG  HAO1  H  HCH2  0   0.240  -2.8035  -2.0166  -0.4825
 XBG  HAO2  H  HCH2  0   0.222  -1.8873  -1.6383   0.9723
 XBG  HAY   H  HCH1  0   0.244  -1.4614   1.5746  -1.2279
 XBG  HAL1  H  HCH2  0   0.232  -3.9044  -0.2904   1.2487
 XBG  HAL2  H  HCH2  0   0.220  -3.8739   0.1942  -0.4405
 XBG  HAN1  H  HCH2  0   0.218  -1.8445   0.9598   1.7082
 XBG  HAN2  H  HCH2  0   0.234  -2.7698   2.0717   0.7119
 XBG  HAQ1  H  HCH2  0   0.234   0.3460   1.2005   1.1497
 XBG  HAQ2  H  HCH2  0   0.249   0.6059   2.2314  -0.2582
 XBG  HAF   H  HOH1  0   0.483   4.0499   0.6598   0.2565

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  1.463  0.020  1.463
 XBG  NBB  CAZ   single  1.451  0.020  1.451
 XBG  CBA  CAO   single  1.532  0.020  1.532
 XBG  CBA  CAY   single  1.562  0.020  1.562
 XBG  CAO  CAL   single  1.529  0.020  1.529
 XBG  CAL  CAN   single  1.528  0.020  1.528
 XBG  CAN  CAY   single  1.532  0.020  1.532
 XBG  CAY  CAQ   single  1.530  0.020  1.530
 XBG  CAQ  CAZ   single  1.545  0.020  1.545
 XBG  CAZ  CAT   single  1.504  0.020  1.504
 XBG  CAT  OAF   single  1.327  0.020  1.327
 XBG  CAT  OAC   double  1.206  0.020  1.206
 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
 XBG  OAF  HAF   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
 XBG  HBB   NBB  CBA   108.88  3.000
 XBG  HBB   NBB  CAZ   108.43  3.000
 XBG  CBA   NBB  CAZ   104.89  3.000
 XBG  HAZ   CAZ  CAQ   108.55  3.000
 XBG  HAZ   CAZ  CAT   108.37  3.000
 XBG  CAQ   CAZ  CAT   112.32  3.000
 XBG  HAZ   CAZ  NBB   109.11  3.000
 XBG  CAT   CAZ  NBB   112.29  3.000
 XBG  CAQ   CAZ  NBB   106.11  3.000
 XBG  OAF   CAT  OAC   123.56  3.000
 XBG  OAC   CAT  CAZ   124.91  3.000
 XBG  OAF   CAT  CAZ   111.49  3.000
 XBG  HAN2  CAN  HAN1  106.97  3.000
 XBG  HAN2  CAN  CAL   113.10  3.000
 XBG  HAN1  CAN  CAL   109.52  3.000
 XBG  HAN2  CAN  CAY   113.10  3.000
 XBG  HAN1  CAN  CAY   110.14  3.000
 XBG  CAL   CAN  CAY   104.01  3.000
 XBG  HAF   OAF  CAT   110.08  3.000
 XBG  HAQ2  CAQ  HAQ1  107.78  3.000
 XBG  HAQ2  CAQ  CAY   113.64  3.000
 XBG  HAQ1  CAQ  CAY   110.59  3.000
 XBG  HAQ2  CAQ  CAZ   112.71  3.000
 XBG  HAQ1  CAQ  CAZ   109.72  3.000
 XBG  CAY   CAQ  CAZ   102.34  3.000
 XBG  HAY   CAY  CBA   109.61  3.000
 XBG  HAY   CAY  CAQ   109.95  3.000
 XBG  CBA   CAY  CAQ   104.58  3.000
 XBG  HAY   CAY  CAN   109.71  3.000
 XBG  CAQ   CAY  CAN   117.19  3.000
 XBG  CBA   CAY  CAN   105.41  3.000
 XBG  HBA   CBA  CAO   109.88  3.000
 XBG  HBA   CBA  CAY   109.49  3.000
 XBG  CAO   CBA  CAY   106.23  3.000
 XBG  HBA   CBA  NBB   108.54  3.000
 XBG  CAY   CBA  NBB   107.72  3.000
 XBG  CAO   CBA  NBB   114.86  3.000
 XBG  HAL2  CAL  HAL1  107.08  3.000
 XBG  HAL2  CAL  CAO   110.01  3.000
 XBG  HAL1  CAL  CAO   112.99  3.000
 XBG  HAL2  CAL  CAN   110.15  3.000
 XBG  HAL1  CAL  CAN   113.27  3.000
 XBG  CAO   CAL  CAN   103.34  3.000
 XBG  HAO2  CAO  HAO1  107.27  3.000
 XBG  HAO2  CAO  CAL   109.30  3.000
 XBG  HAO1  CAO  CAL   113.24  3.000
 XBG  HAO2  CAO  CBA   109.96  3.000
 XBG  HAO1  CAO  CBA   112.98  3.000
 XBG  CAL   CAO  CBA   104.06  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  CONST_01  HAF  OAF  CAT  CAZ  180.00   0.0  0
 XBG  Var_01    CBA  CAO  CAL  CAN  -38.96  30.0  1
 XBG  Var_02    CAO  CAL  CAN  CAY   40.35  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
 XBG  plan-1  HAF  0.020

