# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:23:40 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(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
 1RG  1RG  '(4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid'  ligand  60  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1RG
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
 1RG  C     C  C     0   0.534   -6.9591   -5.7668  -0.2704
 1RG  N     N  NH1   0  -0.595   -6.5133   -6.5647   2.0105
 1RG  O     O  O     0  -0.442   -7.9513   -5.1711   0.0912
 1RG  CA    C  CH1   0  -0.201   -6.2039   -6.7587   0.6121
 1RG  CB    C  CH2   0  -0.486   -6.6330   -8.2163   0.3043
 1RG  CD    C  CH2   0  -0.253   -6.6680   -7.8579   2.6463
 1RG  CG    C  CH1   0  -0.417   -7.3541   -8.6834   1.5697
 1RG  CAB   C  CH1   0  -0.446  -10.1550  -11.3052   5.7220
 1RG  CAD   C  CR15  0  -0.074  -10.0002  -10.0428   4.8846
 1RG  CAE   C  CH1   0   0.055   -8.8164  -11.8481   6.2468
 1RG  CAF   C  CH3   0  -0.709   -7.9791  -10.8501   7.0349
 1RG  OAG   O  OH1   0  -0.666   -9.1611  -12.9674   7.0380
 1RG  CAH   C  CR15  0  -0.299   -9.1904  -10.1558   3.5770
 1RG  CAI   C  CR5   0  -0.110   -9.8116   -9.0071   2.8068
 1RG  NAJ   N  NR15  0  -0.660  -11.3030   -9.4920   4.5002
 1RG  SAK   S  S2    0   0.113   -9.1244   -8.2749   1.3974
 1RG  CAL   C  CR5   0   0.153  -11.0345   -8.7572   3.3220
 1RG  CAM   C  C     0   0.486  -11.9967   -7.8207   2.7544
 1RG  OAT   O  O     0  -0.445  -11.8171   -7.2365   1.7077
 1RG  OAU   O  OH1   0  -0.596  -13.0893   -7.6849   3.4964
 1RG  NAX   N  NH1   0  -0.749   -6.4110   -5.6587  -1.5121
 1RG  CAY   C  CR6   0   0.414   -6.8409   -4.9163  -2.6122
 1RG  CAZ   C  CR16  0  -0.374   -6.0476   -4.9763  -3.7569
 1RG  CBA   C  CR6   0  -0.068   -6.3886   -4.2709  -4.9030
 1RG  CBB   C  CR16  0  -0.282   -7.5407   -3.4878  -4.9224
 1RG  CBC   C  CR16  0  -0.231   -8.3295   -3.4327  -3.7857
 1RG  CBD   C  CR16  0  -0.308   -7.9970   -4.1324  -2.6344
 1RG  CBE   C  C     0   0.539   -5.4888   -4.3900  -6.0793
 1RG  OBF   O  OH1   0  -0.593   -5.8837   -3.6549  -7.1082
 1RG  OBG   O  O     0  -0.437   -4.4995   -5.0823  -6.1019
 1RG  HN    H  HNH1  0   0.362   -5.8343   -5.9814   2.4771
 1RG  HA    H  HCH1  0   0.269   -5.1318   -6.6556   0.4007
 1RG  HB    H  HCH2  0   0.276   -7.2343   -8.3169  -0.6005
 1RG  HBA   H  HCH2  0   0.286   -5.7478   -8.8359   0.1635
 1RG  HD    H  HCH2  0   0.226   -5.7170   -8.3461   2.9039
 1RG  HDA   H  HCH2  0   0.242   -7.2521   -7.7728   3.5654
 1RG  HG    H  HCH1  0   0.305   -7.2342   -9.7558   1.7149
 1RG  HAB   H  HCH1  0   0.276  -10.6266  -12.0876   5.1181
 1RG  HAD   H  HCR5  0   0.262   -9.5132   -9.2710   5.4919
 1RG  HAE   H  HCH1  0   0.230   -8.2258  -12.1663   5.3777
 1RG  HAF   H  HCH3  0   0.250   -7.0498  -11.3251   7.3536
 1RG  HAFA  H  HCH3  0   0.234   -7.6992   -9.9847   6.4341
 1RG  HAFB  H  HCH3  0   0.236   -8.4926  -10.4923   7.9275
 1RG  HOAG  H  HOH1  0   0.456   -8.3500  -13.3704   7.3645
 1RG  HAH   H  HCR5  0   0.276   -8.1297  -10.0043   3.7812
 1RG  HNAJ  H  HNR5  0   0.367  -12.0038  -10.2114   4.3456
 1RG  HNAX  H  HNH1  0   0.416   -5.5615   -6.1817  -1.6661
 1RG  HAZ   H  HCR6  0   0.278   -5.1501   -5.5833  -3.7532
 1RG  HBB   H  HCR6  0   0.267   -7.8270   -2.9280  -5.8012
 1RG  HBC   H  HCR6  0   0.268   -9.2280   -2.8300  -3.7877
 1RG  HBD   H  HCR6  0   0.289   -8.6352   -4.0629  -1.7697
 1RG  HOAU  H  HOH1  0   0.485  -13.7022   -7.0719   3.0645
 1RG  HOBF  H  HOH1  0   0.488   -5.2734   -3.7732  -7.8513
 1RG  CAS   C  CH3   0  -0.665   -9.3793  -11.4520   2.7898
 1RG  CAA   C  C1    0   0.213  -11.0769  -10.9978   6.8765
 1RG  OAC   O  O     0  -0.371  -12.1297  -11.5504   7.0722
 1RG  HAA   H  H     0   0.191  -10.7287  -10.1968   7.5530
 1RG  HAS   H  HCH3  0   0.251   -8.9193  -11.3750   1.8042
 1RG  HASA  H  HCH3  0   0.247   -8.9180  -12.2987   3.2979
 1RG  HASB  H  HCH3  0   0.237  -10.4359  -11.6788   2.6403

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
 1RG  C    O     double    1.212  0.020  1.212
 1RG  C    CA    single    1.527  0.020  1.527
 1RG  C    NAX   single    1.362  0.020  1.362
 1RG  N    CA    single    1.445  0.020  1.445
 1RG  N    CD    single    1.449  0.020  1.449
 1RG  CA   CB    single    1.550  0.020  1.550
 1RG  CB   CG    single    1.529  0.020  1.529
 1RG  CD   CG    single    1.520  0.020  1.520
 1RG  CG   SAK   single    1.825  0.020  1.825
 1RG  CAA  CAB   single    1.509  0.020  1.509
 1RG  CAA  OAC   double    1.205  0.020  1.205
 1RG  CAB  CAD   single    1.523  0.020  1.523
 1RG  CAB  CAE   single    1.537  0.020  1.537
 1RG  CAD  CAH   single    1.542  0.020  1.542
 1RG  CAD  NAJ   single    1.466  0.020  1.466
 1RG  CAE  CAF   single    1.523  0.020  1.523
 1RG  CAE  OAG   single    1.413  0.020  1.413
 1RG  CAH  CAI   single    1.516  0.020  1.516
 1RG  CAH  CAS   single    1.528  0.020  1.528
 1RG  CAI  SAK   single    1.731  0.020  1.731
 1RG  CAI  CAL   double    1.350  0.020  1.350
 1RG  NAJ  CAL   single    1.414  0.020  1.414
 1RG  CAL  CAM   single    1.458  0.020  1.458
 1RG  CAM  OAT   double    1.212  0.020  1.212
 1RG  CAM  OAU   single    1.328  0.020  1.328
 1RG  NAX  CAY   single    1.395  0.020  1.395
 1RG  CAY  CAZ   aromatic  1.394  0.020  1.394
 1RG  CAY  CBD   aromatic  1.397  0.020  1.397
 1RG  CAZ  CBA   aromatic  1.388  0.020  1.388
 1RG  CBA  CBB   aromatic  1.393  0.020  1.393
 1RG  CBA  CBE   single    1.486  0.020  1.486
 1RG  CBB  CBC   aromatic  1.385  0.020  1.385
 1RG  CBC  CBD   aromatic  1.388  0.020  1.388
 1RG  CBE  OBF   single    1.325  0.020  1.325
 1RG  CBE  OBG   double    1.208  0.020  1.208
 1RG  N    HN    single    0.890  0.020  1.040
 1RG  CA   HA    single    0.970  0.020  1.090
 1RG  CB   HB    single    0.970  0.020  1.090
 1RG  CB   HBA   single    0.970  0.020  1.090
 1RG  CD   HD    single    0.970  0.020  1.090
 1RG  CD   HDA   single    0.970  0.020  1.090
 1RG  CG   HG    single    0.970  0.020  1.090
 1RG  CAA  HAA   single    0.930  0.020  1.080
 1RG  CAB  HAB   single    0.970  0.020  1.090
 1RG  CAD  HAD   single    0.970  0.020  1.090
 1RG  CAE  HAE   single    0.970  0.020  1.090
 1RG  CAF  HAF   single    0.970  0.020  1.090
 1RG  CAF  HAFA  single    0.970  0.020  1.090
 1RG  CAF  HAFB  single    0.970  0.020  1.090
 1RG  OAG  HOAG  single    0.850  0.020  0.980
 1RG  CAH  HAH   single    0.970  0.020  1.090
 1RG  NAJ  HNAJ  single    0.890  0.020  1.040
 1RG  CAS  HAS   single    0.970  0.020  1.090
 1RG  CAS  HASA  single    0.970  0.020  1.090
 1RG  CAS  HASB  single    0.970  0.020  1.090
 1RG  NAX  HNAX  single    0.860  0.020  1.020
 1RG  CAZ  HAZ   single    0.930  0.020  1.080
 1RG  CBB  HBB   single    0.930  0.020  1.080
 1RG  CBC  HBC   single    0.930  0.020  1.080
 1RG  CBD  HBD   single    0.930  0.020  1.080
 1RG  OAU  HOAU  single    0.850  0.020  0.980
 1RG  OBF  HOBF  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
 1RG  NAX   C    CA    112.30  3.000
 1RG  NAX   C    O     124.22  3.000
 1RG  CA    C    O     123.46  3.000
 1RG  HN    N    CD    112.62  3.000
 1RG  HN    N    CA    112.38  3.000
 1RG  CD    N    CA    109.12  3.000
 1RG  HA    CA   CB    108.69  3.000
 1RG  HA    CA   N     112.51  3.000
 1RG  CB    CA   N     105.01  3.000
 1RG  HA    CA   C     108.10  3.000
 1RG  CB    CA   C     111.04  3.000
 1RG  N     CA   C     111.47  3.000
 1RG  HBA   CB   HB    106.74  3.000
 1RG  HBA   CB   CG    108.44  3.000
 1RG  HB    CB   CG    113.46  3.000
 1RG  HBA   CB   CA    109.60  3.000
 1RG  HB    CB   CA    113.82  3.000
 1RG  CG    CB   CA    104.68  3.000
 1RG  HDA   CD   HD    107.46  3.000
 1RG  HDA   CD   CG    113.38  3.000
 1RG  HD    CD   CG    108.37  3.000
 1RG  HDA   CD   N     110.89  3.000
 1RG  HD    CD   N     113.99  3.000
 1RG  CG    CD   N     102.82  3.000
 1RG  HG    CG   SAK   109.87  3.000
 1RG  HG    CG   CD    112.99  3.000
 1RG  SAK   CG   CD    112.52  3.000
 1RG  HG    CG   CB    111.05  3.000
 1RG  SAK   CG   CB    108.12  3.000
 1RG  CD    CG   CB    101.96  3.000
 1RG  HAB   CAB  CAE   108.12  3.000
 1RG  HAB   CAB  CAD   109.44  3.000
 1RG  CAE   CAB  CAD   113.09  3.000
 1RG  HAB   CAB  CAA   107.72  3.000
 1RG  CAE   CAB  CAA   110.05  3.000
 1RG  CAD   CAB  CAA   108.30  3.000
 1RG  HAD   CAD  NAJ   106.00  3.000
 1RG  HAD   CAD  CAH   106.74  3.000
 1RG  NAJ   CAD  CAH   105.78  3.000
 1RG  HAD   CAD  CAB   108.91  3.000
 1RG  NAJ   CAD  CAB   111.43  3.000
 1RG  CAH   CAD  CAB   117.32  3.000
 1RG  HAE   CAE  OAG   110.17  3.000
 1RG  HAE   CAE  CAF   107.69  3.000
 1RG  OAG   CAE  CAF   111.31  3.000
 1RG  HAE   CAE  CAB   107.49  3.000
 1RG  OAG   CAE  CAB   104.98  3.000
 1RG  CAF   CAE  CAB   115.10  3.000
 1RG  HAFB  CAF  HAFA  108.16  3.000
 1RG  HAFB  CAF  HAF   107.75  3.000
 1RG  HAFA  CAF  HAF   106.73  3.000
 1RG  HAFB  CAF  CAE   112.33  3.000
 1RG  HAFA  CAF  CAE   112.11  3.000
 1RG  HAF   CAF  CAE   109.53  3.000
 1RG  HOAG  OAG  CAE   108.41  3.000
 1RG  HAH   CAH  CAS   109.54  3.000
 1RG  HAH   CAH  CAI   112.85  3.000
 1RG  CAS   CAH  CAI   109.28  3.000
 1RG  HAH   CAH  CAD   109.99  3.000
 1RG  CAS   CAH  CAD   115.72  3.000
 1RG  CAI   CAH  CAD    99.21  3.000
 1RG  CAL   CAI  SAK   126.30  3.000
 1RG  CAL   CAI  CAH   108.51  3.000
 1RG  SAK   CAI  CAH   124.86  3.000
 1RG  HNAJ  NAJ  CAL   111.84  3.000
 1RG  HNAJ  NAJ  CAD   112.76  3.000
 1RG  CAL   NAJ  CAD   104.18  3.000
 1RG  CAI   SAK  CG    102.34  3.000
 1RG  CAM   CAL  NAJ   122.19  3.000
 1RG  CAM   CAL  CAI   124.62  3.000
 1RG  NAJ   CAL  CAI   113.18  3.000
 1RG  OAU   CAM  OAT   123.73  3.000
 1RG  OAU   CAM  CAL   113.04  3.000
 1RG  OAT   CAM  CAL   123.23  3.000
 1RG  HOAU  OAU  CAM   109.65  3.000
 1RG  HNAX  NAX  CAY   114.51  3.000
 1RG  HNAX  NAX  C     115.90  3.000
 1RG  CAY   NAX  C     129.59  3.000
 1RG  CBD   CAY  CAZ   118.82  3.000
 1RG  CBD   CAY  NAX   124.48  3.000
 1RG  CAZ   CAY  NAX   116.70  3.000
 1RG  HAZ   CAZ  CBA   119.39  3.000
 1RG  HAZ   CAZ  CAY   119.52  3.000
 1RG  CBA   CAZ  CAY   121.08  3.000
 1RG  CBE   CBA  CBB   122.33  3.000
 1RG  CBE   CBA  CAZ   117.66  3.000
 1RG  CBB   CBA  CAZ   120.01  3.000
 1RG  HBB   CBB  CBC   119.74  3.000
 1RG  HBB   CBB  CBA   121.44  3.000
 1RG  CBC   CBB  CBA   118.82  3.000
 1RG  HBC   CBC  CBD   118.78  3.000
 1RG  HBC   CBC  CBB   119.58  3.000
 1RG  CBD   CBC  CBB   121.64  3.000
 1RG  HBD   CBD  CBC   119.45  3.000
 1RG  HBD   CBD  CAY   120.92  3.000
 1RG  CBC   CBD  CAY   119.63  3.000
 1RG  OBG   CBE  OBF   123.21  3.000
 1RG  OBG   CBE  CBA   123.84  3.000
 1RG  OBF   CBE  CBA   112.95  3.000
 1RG  HOBF  OBF  CBE   109.89  3.000
 1RG  HASB  CAS  HASA  108.19  3.000
 1RG  HASB  CAS  HAS   107.42  3.000
 1RG  HASA  CAS  HAS   107.32  3.000
 1RG  HASB  CAS  CAH   111.51  3.000
 1RG  HASA  CAS  CAH   111.50  3.000
 1RG  HAS   CAS  CAH   110.71  3.000
 1RG  HAA   CAA  OAC   120.56  3.000
 1RG  HAA   CAA  CAB   115.06  3.000
 1RG  OAC   CAA  CAB   124.38  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
 1RG  CONST_01  CBB   CBA  CAZ  CAY     0.00   0.0  0
 1RG  CONST_02  CBB   CBC  CBD  CAY     0.00   0.0  0
 1RG  CONST_03  CBC   CBD  CAY  CAZ     0.00   0.0  0
 1RG  CONST_04  CBC   CBB  CBA  CAZ     0.00   0.0  0
 1RG  CONST_05  CBD   CAY  CAZ  CBA     0.00   0.0  0
 1RG  CONST_06  CBD   CBC  CBB  CBA     0.00   0.0  0
 1RG  CONST_07  CBA   CAZ  CAY  NAX   180.00   0.0  0
 1RG  CONST_08  CBC   CBD  CAY  NAX   180.00   0.0  0
 1RG  CONST_09  CBE   CBA  CAZ  CAY   180.00   0.0  0
 1RG  CONST_10  CBE   CBA  CBB  CBC   180.00   0.0  0
 1RG  CONST_11  HBC   CBC  CBD  CAY   180.00   0.0  0
 1RG  CONST_12  HBD   CBD  CAY  CAZ   180.00   0.0  0
 1RG  CONST_13  HBB   CBB  CBA  CAZ   180.00   0.0  0
 1RG  CONST_14  HAZ   CAZ  CBA  CBB   180.00   0.0  0
 1RG  CONST_15  CAY   NAX  C    CA    180.00   0.0  0
 1RG  CONST_16  CAZ   CAY  NAX  C     180.00   0.0  0
 1RG  CONST_17  CBD   CAY  NAX  C       0.00   0.0  0
 1RG  CONST_18  HNAX  NAX  CAY  CAZ     0.00   0.0  0
 1RG  CONST_19  CAY   NAX  C    O       0.00   0.0  0
 1RG  CONST_20  HOAU  OAU  CAM  CAL   180.00   0.0  0
 1RG  CONST_21  HOBF  OBF  CBE  CBA   180.00   0.0  0
 1RG  Var_01    CG    CD   N    CA    -37.16  30.0  1
 1RG  Var_02    CAI   CAL  NAJ  CAD    12.28  30.0  1
 1RG  Var_03    NAJ   CAL  CAI  CAH     7.61  30.0  1
 1RG  Var_04    CAH   CAI  SAK  CG    -23.13  30.0  1
 1RG  Var_05    OAT   CAM  CAL  CAI     4.88  30.0  2
 1RG  Var_06    OBF   CBE  CBA  CAZ  -178.45  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
 1RG  chir_01  CA   C    N    CB   negativ
 1RG  chir_02  CG   SAK  CD   CB   positiv
 1RG  chir_03  CAB  CAE  CAD  CAA  positiv
 1RG  chir_04  CAD  NAJ  CAB  CAH  negativ
 1RG  chir_05  CAE  OAG  CAB  CAF  negativ
 1RG  chir_06  CAH  CAD  CAI  CAS  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
 1RG  plan-1  C     0.020
 1RG  plan-1  O     0.020
 1RG  plan-1  CA    0.020
 1RG  plan-1  NAX   0.020
 1RG  plan-1  CAY   0.020
 1RG  plan-1  HNAX  0.020
 1RG  plan-2  NAX   0.020
 1RG  plan-2  CAY   0.020
 1RG  plan-2  CAZ   0.020
 1RG  plan-2  CBA   0.020
 1RG  plan-2  CBB   0.020
 1RG  plan-2  CBC   0.020
 1RG  plan-2  CBD   0.020
 1RG  plan-2  CBE   0.020
 1RG  plan-2  HAZ   0.020
 1RG  plan-2  HBB   0.020
 1RG  plan-2  HBC   0.020
 1RG  plan-2  HBD   0.020
 1RG  plan-3  CAD   0.020
 1RG  plan-3  NAJ   0.020
 1RG  plan-3  CAL   0.020
 1RG  plan-3  HNAJ  0.020
 1RG  plan-4  CAL   0.020
 1RG  plan-4  CAM   0.020
 1RG  plan-4  OAT   0.020
 1RG  plan-4  OAU   0.020
 1RG  plan-4  HOAU  0.020
 1RG  plan-5  CBA   0.020
 1RG  plan-5  CBE   0.020
 1RG  plan-5  OBF   0.020
 1RG  plan-5  OBG   0.020
 1RG  plan-5  HOBF  0.020
 1RG  plan-6  CAB   0.020
 1RG  plan-6  CAA   0.020
 1RG  plan-6  OAC   0.020
 1RG  plan-6  HAA   0.020

