# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:20:28 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)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
 2RG  2RG  '(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid'  ligand  58  33  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2RG
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
 2RG  C     C  C      0   0.522  -2.8418  -0.7354  -0.6459
 2RG  N     N  NH1    0  -0.582  -1.2068  -1.6626  -2.2322
 2RG  O     O  O      0  -0.460  -2.5681   0.4040  -0.9769
 2RG  CA    C  CH1    0  -0.204  -1.9652  -1.9171  -1.0204
 2RG  CB    C  CH2    0  -0.485  -0.9432  -2.2422   0.1177
 2RG  CD    C  CH2    0  -0.317   0.0437  -2.3799  -2.0488
 2RG  CG    C  CH1    0  -0.362   0.4210  -2.1914  -0.5793
 2RG  CAB   C  CH1    0  -0.416   5.2812   1.7007   0.4628
 2RG  CAD   C  CR15   0  -0.094   4.0958   0.7562   0.2313
 2RG  CAE   C  CH1    0   0.057   5.7277   1.6527   1.9518
 2RG  CAF   C  CH3    0  -0.700   6.9063   2.5723   2.2383
 2RG  OAG   O  OH1    0  -0.654   4.6429   1.9404   2.8051
 2RG  CAH   C  CR15   0  -0.246   3.2925   0.9021  -1.0792
 2RG  CAI   C  CR15   0  -0.468   2.6992  -0.5108  -1.1894
 2RG  NAJ   N  N      0  -0.356   4.4921  -0.6445   0.3003
 2RG  SAK   S  S2     0  -0.009   1.1178  -0.5357  -0.2688
 2RG  CAL   C  CR5    0   0.144   3.7437  -1.3241  -0.4670
 2RG  CAM   C  C      0   0.377   3.9108  -2.8261  -0.6595
 2RG  OAT   O  OC    -1  -0.583   4.6763  -3.4129   0.1205
 2RG  OAU   O  O      0  -0.577   3.2643  -3.3065  -1.6101
 2RG  NAX   N  NH1    0  -0.742  -3.9036  -1.0839   0.1182
 2RG  CAY   C  CR6    0   0.395  -4.8776  -0.2812   0.7280
 2RG  CAZ   C  CR16   0  -0.366  -4.8867   1.1119   0.6902
 2RG  CBA   C  CR6    0  -0.087  -5.8957   1.8289   1.3289
 2RG  CBB   C  CR16   0  -0.314  -6.9006   1.1497   2.0089
 2RG  CBC   C  CR16   0  -0.232  -6.8918  -0.2372   2.0514
 2RG  CBD   C  CR16   0  -0.357  -5.8906  -0.9517   1.4174
 2RG  CBE   C  C      0   0.402  -5.8888   3.3548   1.2781
 2RG  OBF   O  O      0  -0.591  -4.9416   3.8920   0.6727
 2RG  OBG   O  OC    -1  -0.594  -6.8330   3.9330   1.8489
 2RG  HN    H  HNH1   0   0.348  -1.0010  -0.6694  -2.2739
 2RG  HA    H  HCH1   0   0.269  -2.5996  -2.7958  -1.1732
 2RG  HB    H  HCH2   0   0.265  -1.0117  -1.5560   0.9646
 2RG  HBA   H  HCH2   0   0.273  -1.1235  -3.2429   0.5097
 2RG  HD    H  HCH2   0   0.238  -0.1119  -3.4475  -2.2354
 2RG  HDA   H  HCH2   0   0.257   0.8029  -2.0371  -2.7494
 2RG  HG    H  HCH1   0   0.288   1.1023  -2.9558  -0.2156
 2RG  HAB   H  HCH1   0   0.265   4.9790   2.7298   0.2346
 2RG  HAD   H  HCR5   0   0.265   3.4023   0.9308   1.0623
 2RG  HAE   H  HCH1   0   0.237   6.0140   0.6237   2.1856
 2RG  HAF   H  HCH3   0   0.229   6.7003   3.5977   1.9214
 2RG  HAFA  H  HCH3   0   0.246   7.1178   2.5812   3.3077
 2RG  HAFB  H  HCH3   0   0.237   7.8142   2.2452   1.7329
 2RG  HOAG  H  HOH1   0   0.446   4.3876   2.8605   2.6738
 2RG  HAH   H  HCR5   0   0.257   2.5197   1.6669  -0.9704
 2RG  HAI   H  HCR5   0   0.292   2.5207  -0.8298  -2.2159
 2RG  HNAX  H  HNH1   0   0.415  -4.0253  -2.0742   0.2697
 2RG  HAZ   H  HCR6   0   0.267  -4.1167   1.6564   0.1703
 2RG  HBB   H  HCR6   0   0.243  -7.6865   1.7046   2.5022
 2RG  HBC   H  HCR6   0   0.253  -7.6705  -0.7720   2.5799
 2RG  HBD   H  HCR6   0   0.266  -5.8928  -2.0352   1.4569
 2RG  CAA   C  C1     0   0.185   6.4603   1.3515  -0.4031
 2RG  OAC   O  O      0  -0.383   7.1350   2.1524  -1.0039
 2RG  HAA   H  H      0   0.199   6.7092   0.2756  -0.4307
 2RG  CAS   C  CH3    0  -0.684   4.1162   1.2202  -2.3206
 2RG  HAS   H  HCH3   0   0.227   4.9057   0.4854  -2.4917
 2RG  HASA  H  HCH3   0   0.252   3.4746   1.2129  -3.2027
 2RG  HASB  H  HCH3   0   0.243   4.5720   2.2085  -2.2661

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
 2RG  O    C     double    1.218  0.020  1.218
 2RG  CA   C     single    1.518  0.020  1.518
 2RG  C    NAX   single    1.354  0.020  1.354
 2RG  N    CD    single    1.453  0.020  1.453
 2RG  N    CA    single    1.452  0.020  1.452
 2RG  N    HN    single    0.890  0.020  1.040
 2RG  CA   CB    single    1.564  0.020  1.564
 2RG  CA   HA    single    0.970  0.020  1.090
 2RG  CG   CB    single    1.533  0.020  1.533
 2RG  CB   HB    single    0.970  0.020  1.090
 2RG  CB   HBA   single    0.970  0.020  1.090
 2RG  CD   CG    single    1.529  0.020  1.529
 2RG  CD   HD    single    0.970  0.020  1.090
 2RG  CD   HDA   single    0.970  0.020  1.090
 2RG  CG   SAK   single    1.823  0.020  1.823
 2RG  CG   HG    single    0.970  0.020  1.090
 2RG  OAC  CAA   double    1.207  0.020  1.207
 2RG  CAB  CAA   single    1.504  0.020  1.504
 2RG  CAA  HAA   single    0.930  0.020  1.080
 2RG  CAB  CAD   single    1.533  0.020  1.533
 2RG  CAB  CAE   single    1.555  0.020  1.555
 2RG  CAB  HAB   single    0.970  0.020  1.090
 2RG  CAH  CAD   single    1.544  0.020  1.544
 2RG  CAD  NAJ   single    1.457  0.020  1.457
 2RG  CAD  HAD   single    0.970  0.020  1.090
 2RG  CAF  CAE   single    1.522  0.020  1.522
 2RG  CAE  OAG   single    1.410  0.020  1.410
 2RG  CAE  HAE   single    0.970  0.020  1.090
 2RG  CAF  HAF   single    0.970  0.020  1.090
 2RG  CAF  HAFA  single    0.970  0.020  1.090
 2RG  CAF  HAFB  single    0.970  0.020  1.090
 2RG  OAG  HOAG  single    0.850  0.020  0.980
 2RG  CAS  CAH   single    1.523  0.020  1.523
 2RG  CAH  CAI   single    1.536  0.020  1.536
 2RG  CAH  HAH   single    0.970  0.020  1.090
 2RG  CAI  CAL   single    1.508  0.020  1.508
 2RG  CAI  SAK   single    1.830  0.020  1.830
 2RG  CAI  HAI   single    0.970  0.020  1.090
 2RG  CAL  NAJ   double    1.269  0.020  1.269
 2RG  CAM  CAL   single    1.523  0.020  1.523
 2RG  OAU  CAM   deloc     1.246  0.020  1.246
 2RG  CAM  OAT   deloc     1.240  0.020  1.240
 2RG  CAS  HAS   single    0.970  0.020  1.090
 2RG  CAS  HASA  single    0.970  0.020  1.090
 2RG  CAS  HASB  single    0.970  0.020  1.090
 2RG  NAX  CAY   single    1.402  0.020  1.402
 2RG  NAX  HNAX  single    0.860  0.020  1.020
 2RG  CAY  CAZ   aromatic  1.394  0.020  1.394
 2RG  CAY  CBD   aromatic  1.397  0.020  1.397
 2RG  CAZ  CBA   aromatic  1.393  0.020  1.393
 2RG  CAZ  HAZ   single    0.930  0.020  1.080
 2RG  CBA  CBE   single    1.527  0.020  1.527
 2RG  CBA  CBB   aromatic  1.391  0.020  1.391
 2RG  CBC  CBB   aromatic  1.388  0.020  1.388
 2RG  CBB  HBB   single    0.930  0.020  1.080
 2RG  CBD  CBC   aromatic  1.384  0.020  1.384
 2RG  CBC  HBC   single    0.930  0.020  1.080
 2RG  CBD  HBD   single    0.930  0.020  1.080
 2RG  OBF  CBE   deloc     1.246  0.020  1.246
 2RG  CBE  OBG   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
 2RG  NAX   C    CA    113.06  3.000
 2RG  NAX   C    O     124.79  3.000
 2RG  CA    C    O     122.10  3.000
 2RG  HN    N    CD    108.28  3.000
 2RG  HN    N    CA    108.16  3.000
 2RG  CD    N    CA    104.92  3.000
 2RG  HA    CA   CB    108.27  3.000
 2RG  HA    CA   N     109.09  3.000
 2RG  CB    CA   N     107.61  3.000
 2RG  HA    CA   C     108.94  3.000
 2RG  CB    CA   C     111.08  3.000
 2RG  N     CA   C     111.78  3.000
 2RG  HBA   CB   HB    106.72  3.000
 2RG  HBA   CB   CG    109.95  3.000
 2RG  HB    CB   CG    112.80  3.000
 2RG  HBA   CB   CA    110.16  3.000
 2RG  HB    CB   CA    113.13  3.000
 2RG  CG    CB   CA    104.11  3.000
 2RG  HDA   CD   HD    107.25  3.000
 2RG  HDA   CD   CG    114.06  3.000
 2RG  HD    CD   CG    108.61  3.000
 2RG  HDA   CD   N     111.31  3.000
 2RG  HD    CD   N     109.72  3.000
 2RG  CG    CD   N     105.83  3.000
 2RG  HG    CG   SAK   110.01  3.000
 2RG  HG    CG   CD    112.94  3.000
 2RG  SAK   CG   CD    111.72  3.000
 2RG  HG    CG   CB    112.49  3.000
 2RG  SAK   CG   CB    107.03  3.000
 2RG  CD    CG   CB    102.32  3.000
 2RG  HAB   CAB  CAE   107.90  3.000
 2RG  HAB   CAB  CAD   109.49  3.000
 2RG  CAE   CAB  CAD   110.33  3.000
 2RG  HAB   CAB  CAA   108.31  3.000
 2RG  CAE   CAB  CAA   108.60  3.000
 2RG  CAD   CAB  CAA   112.10  3.000
 2RG  HAD   CAD  NAJ   106.81  3.000
 2RG  HAD   CAD  CAH   107.41  3.000
 2RG  NAJ   CAD  CAH   105.81  3.000
 2RG  HAD   CAD  CAB   106.05  3.000
 2RG  NAJ   CAD  CAB   112.00  3.000
 2RG  CAH   CAD  CAB   118.18  3.000
 2RG  HAE   CAE  OAG   105.32  3.000
 2RG  HAE   CAE  CAF   109.00  3.000
 2RG  OAG   CAE  CAF   111.01  3.000
 2RG  HAE   CAE  CAB   108.00  3.000
 2RG  OAG   CAE  CAB   110.63  3.000
 2RG  CAF   CAE  CAB   112.57  3.000
 2RG  HAFB  CAF  HAFA  107.21  3.000
 2RG  HAFB  CAF  HAF   107.72  3.000
 2RG  HAFA  CAF  HAF   108.26  3.000
 2RG  HAFB  CAF  CAE   112.12  3.000
 2RG  HAFA  CAF  CAE   109.86  3.000
 2RG  HAF   CAF  CAE   111.49  3.000
 2RG  HOAG  OAG  CAE   108.43  3.000
 2RG  HAH   CAH  CAS   108.51  3.000
 2RG  HAH   CAH  CAI   112.19  3.000
 2RG  CAS   CAH  CAI   110.02  3.000
 2RG  HAH   CAH  CAD   110.46  3.000
 2RG  CAI   CAH  CAD   100.07  3.000
 2RG  CAS   CAH  CAD   115.47  3.000
 2RG  HAI   CAI  CAL   114.01  3.000
 2RG  HAI   CAI  SAK   109.17  3.000
 2RG  CAL   CAI  SAK   110.50  3.000
 2RG  HAI   CAI  CAH   113.59  3.000
 2RG  SAK   CAI  CAH   108.06  3.000
 2RG  CAL   CAI  CAH   101.20  3.000
 2RG  CAL   NAJ  CAD   109.01  3.000
 2RG  CAI   SAK  CG    104.89  3.000
 2RG  CAM   CAL  NAJ   122.67  3.000
 2RG  CAM   CAL  CAI   123.17  3.000
 2RG  NAJ   CAL  CAI   114.15  3.000
 2RG  OAU   CAM  OAT   128.14  3.000
 2RG  OAT   CAM  CAL   117.04  3.000
 2RG  OAU   CAM  CAL   114.81  3.000
 2RG  HNAX  NAX  CAY   114.38  3.000
 2RG  HNAX  NAX  C     115.59  3.000
 2RG  CAY   NAX  C     130.02  3.000
 2RG  CBD   CAY  CAZ   119.24  3.000
 2RG  CBD   CAY  NAX   116.34  3.000
 2RG  CAZ   CAY  NAX   124.42  3.000
 2RG  HAZ   CAZ  CBA   118.62  3.000
 2RG  HAZ   CAZ  CAY   120.92  3.000
 2RG  CBA   CAZ  CAY   120.46  3.000
 2RG  CBE   CBA  CBB   120.51  3.000
 2RG  CBB   CBA  CAZ   119.75  3.000
 2RG  CBE   CBA  CAZ   119.73  3.000
 2RG  HBB   CBB  CBC   120.24  3.000
 2RG  HBB   CBB  CBA   119.85  3.000
 2RG  CBC   CBB  CBA   119.91  3.000
 2RG  HBC   CBC  CBD   119.28  3.000
 2RG  HBC   CBC  CBB   120.28  3.000
 2RG  CBD   CBC  CBB   120.44  3.000
 2RG  HBD   CBD  CBC   119.86  3.000
 2RG  HBD   CBD  CAY   119.94  3.000
 2RG  CBC   CBD  CAY   120.20  3.000
 2RG  OBG   CBE  OBF   126.79  3.000
 2RG  OBG   CBE  CBA   116.44  3.000
 2RG  OBF   CBE  CBA   116.78  3.000
 2RG  HAA   CAA  OAC   120.52  3.000
 2RG  HAA   CAA  CAB   114.66  3.000
 2RG  OAC   CAA  CAB   124.79  3.000
 2RG  HASB  CAS  HASA  107.01  3.000
 2RG  HASB  CAS  HAS   108.40  3.000
 2RG  HASA  CAS  HAS   107.10  3.000
 2RG  HASB  CAS  CAH   112.01  3.000
 2RG  HASA  CAS  CAH   109.86  3.000
 2RG  HAS   CAS  CAH   112.21  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
 2RG  CONST_01  CBB   CBA  CAZ  CAY    0.00   0.0  0
 2RG  CONST_02  CBB   CBC  CBD  CAY    0.00   0.0  0
 2RG  CONST_03  CBC   CBD  CAY  CAZ    0.00   0.0  0
 2RG  CONST_04  CBC   CBB  CBA  CAZ    0.00   0.0  0
 2RG  CONST_05  CBD   CAY  CAZ  CBA    0.00   0.0  0
 2RG  CONST_06  CBD   CBC  CBB  CBA    0.00   0.0  0
 2RG  CONST_07  CBA   CAZ  CAY  NAX  180.00   0.0  0
 2RG  CONST_08  CBC   CBD  CAY  NAX  180.00   0.0  0
 2RG  CONST_09  CBE   CBA  CAZ  CAY  180.00   0.0  0
 2RG  CONST_10  CBE   CBA  CBB  CBC  180.00   0.0  0
 2RG  CONST_11  HBC   CBC  CBD  CAY  180.00   0.0  0
 2RG  CONST_12  HBD   CBD  CAY  CAZ  180.00   0.0  0
 2RG  CONST_13  HBB   CBB  CBA  CAZ  180.00   0.0  0
 2RG  CONST_14  HAZ   CAZ  CBA  CBB  180.00   0.0  0
 2RG  CONST_15  CAY   NAX  C    CA   180.00   0.0  0
 2RG  CONST_16  CAZ   CAY  NAX  C      0.00   0.0  0
 2RG  CONST_17  CBD   CAY  NAX  C    180.00   0.0  0
 2RG  CONST_18  HNAX  NAX  CAY  CAZ  180.00   0.0  0
 2RG  CONST_19  CAY   NAX  C    O      0.00   0.0  0
 2RG  Var_01    CG    CD   N    CA   -39.05  30.0  1
 2RG  Var_02    CAI   CAL  NAJ  CAD   -0.34  30.0  1
 2RG  Var_03    OAU   CAM  CAL  CAI   10.73  30.0  2
 2RG  Var_04    OBF   CBE  CBA  CAZ   -1.34  30.0  2

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
 2RG  chir_01  CA   C    N    CB   negativ
 2RG  chir_02  CG   SAK  CD   CB   positiv
 2RG  chir_03  CAB  CAE  CAD  CAA  positiv
 2RG  chir_04  CAD  NAJ  CAB  CAH  negativ
 2RG  chir_05  CAE  OAG  CAB  CAF  negativ
 2RG  chir_06  CAH  CAI  CAS  CAD  positiv
 2RG  chir_07  CAI  SAK  CAL  CAH  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
 2RG  plan-1  C     0.020
 2RG  plan-1  O     0.020
 2RG  plan-1  CA    0.020
 2RG  plan-1  NAX   0.020
 2RG  plan-1  CAY   0.020
 2RG  plan-1  HNAX  0.020
 2RG  plan-2  NAX   0.020
 2RG  plan-2  CAY   0.020
 2RG  plan-2  CAZ   0.020
 2RG  plan-2  CBA   0.020
 2RG  plan-2  CBB   0.020
 2RG  plan-2  CBC   0.020
 2RG  plan-2  CBD   0.020
 2RG  plan-2  CBE   0.020
 2RG  plan-2  HAZ   0.020
 2RG  plan-2  HBB   0.020
 2RG  plan-2  HBC   0.020
 2RG  plan-2  HBD   0.020
 2RG  plan-3  CAL   0.020
 2RG  plan-3  CAM   0.020
 2RG  plan-3  OAT   0.020
 2RG  plan-3  OAU   0.020
 2RG  plan-4  CBA   0.020
 2RG  plan-4  CBE   0.020
 2RG  plan-4  OBF   0.020
 2RG  plan-4  OBG   0.020
 2RG  plan-5  CAB   0.020
 2RG  plan-5  CAA   0.020
 2RG  plan-5  OAC   0.020
 2RG  plan-5  HAA   0.020

