# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 08:22:13 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: (3~{S},4~{R},5~{S})-5-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-4-methyl-pyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@@H]1N[C@H]([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O)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
 8FB  8FB  '(3~{S},4~{R},5~{S})-5-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-4-methyl-pyrrolidine-2-carboxylic acid'  ligand  56  27  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8FB
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
 8FB  O    O  O     0  -0.493  12.0721  53.9958  25.8891
 8FB  C    C  C     0   0.579  11.9458  53.6660  24.7183
 8FB  NAY  N  NT    0  -0.446  10.8216  53.9225  24.0132
 8FB  CAC  C  CH3   0  -0.532  10.5811  53.5155  22.6463
 8FB  CAD  C  CH3   0  -0.522   9.6655  54.4980  24.6662
 8FB  CA   C  CH1   0  -0.296  13.0698  52.9173  24.0025
 8FB  CB   C  CH2   0  -0.426  12.7279  51.4243  23.8518
 8FB  N    N  NH1   0  -0.568  14.2811  52.9377  24.8022
 8FB  CD   C  CH2   0  -0.272  14.2039  51.8181  25.7381
 8FB  CG   C  CH1   0  -0.437  13.1161  50.8440  25.2126
 8FB  SAO  S  S2    0   0.026  11.7150  50.7589  26.3831
 8FB  CAT  C  CH1   0  -0.419  11.2034  49.0200  26.3002
 8FB  CAV  C  CH1   0  -0.202  10.9480  48.5014  24.8739
 8FB  CAB  C  CH3   0  -0.676   9.5809  48.8856  24.3432
 8FB  CAS  C  CH1   0  -0.139  12.1556  47.9639  26.9333
 8FB  CAP  C  C     0   0.532  13.3675  48.5402  27.6303
 8FB  OAE  O  O     0  -0.429  14.4839  48.5711  27.1802
 8FB  OAH  O  OH1   0  -0.590  13.0486  48.9844  28.8385
 8FB  NAN  N  NH1   0  -0.605  12.5145  47.1269  25.8136
 8FB  CAZ  C  CH1   0  -0.091  11.3526  47.0180  24.9483
 8FB  CBA  C  CH1   0  -0.413  10.2052  46.0516  25.3995
 8FB  CAQ  C  C     0   0.559  10.5528  45.2429  26.6234
 8FB  OAF  O  OH1   0  -0.579   9.8008  45.5288  27.6747
 8FB  OAI  O  O     0  -0.451  11.4067  44.3820  26.6479
 8FB  CAU  C  CH1   0   0.029   9.8227  45.0364  24.2866
 8FB  OAJ  O  OH1   0  -0.670  10.9358  44.3124  23.8179
 8FB  CAA  C  CH3   0  -0.684   9.1756  45.7081  23.0919
 8FB  H1   H  HCH3  0   0.262  11.4971  53.2793  22.1162
 8FB  H2   H  HCH3  0   0.236   9.9236  52.6427  22.6012
 8FB  H3   H  HCH3  0   0.254  10.0941  54.3290  22.1074
 8FB  H4   H  HCH3  0   0.257   9.9181  54.8333  25.6657
 8FB  H5   H  HCH3  0   0.238   9.3004  55.3508  24.0921
 8FB  H6   H  HCH3  0   0.234   8.8571  53.7655  24.7360
 8FB  H7   H  HCH1  0   0.284  13.2798  53.3841  23.0386
 8FB  H8   H  HCH2  0   0.258  11.6954  51.2125  23.5777
 8FB  H9   H  HCH2  0   0.261  13.3661  50.9985  23.0734
 8FB  H10  H  HNH1  0   0.357  15.0601  52.7892  24.1748
 8FB  H12  H  HCH2  0   0.244  15.1684  51.3146  25.8045
 8FB  H13  H  HCH2  0   0.231  13.9580  52.1683  26.7408
 8FB  H14  H  HCH1  0   0.298  13.5142  49.8358  25.1144
 8FB  H15  H  HCH1  0   0.298  10.2693  49.0189  26.8669
 8FB  H16  H  HCH1  0   0.275  11.6870  48.9470  24.2054
 8FB  H17  H  HCH3  0   0.239   9.4690  49.9705  24.3868
 8FB  H18  H  HCH3  0   0.241   9.4544  48.5856  23.3036
 8FB  H19  H  HCH3  0   0.229   8.7617  48.4565  24.9216
 8FB  H20  H  HCH1  0   0.265  11.5857  47.4403  27.7130
 8FB  H21  H  HOH1  0   0.481  13.8259  49.3731  29.2668
 8FB  H22  H  HNH1  0   0.359  12.9222  46.2407  26.0791
 8FB  H24  H  HCH1  0   0.263  11.6965  46.6846  23.9679
 8FB  H25  H  HCH1  0   0.279   9.3027  46.6203  25.6340
 8FB  H26  H  HOH1  0   0.483  10.0499  44.9683  28.4267
 8FB  H27  H  HCH1  0   0.229   9.0780  44.3544  24.7229
 8FB  H28  H  HOH1  0   0.448  11.3659  43.8963  24.5744
 8FB  H29  H  HCH3  0   0.233   8.2899  46.2636  23.3984
 8FB  H30  H  HCH3  0   0.233   9.8578  46.3970  22.5919
 8FB  H31  H  HCH3  0   0.249   8.8648  44.9581  22.3639

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
 8FB  CAA  CAU  single  1.516  0.020  1.516
 8FB  CAC  NAY  single  1.446  0.020  1.446
 8FB  OAJ  CAU  single  1.408  0.020  1.408
 8FB  CB   CA   single  1.539  0.020  1.539
 8FB  CB   CG   single  1.529  0.020  1.529
 8FB  CAB  CAV  single  1.516  0.020  1.516
 8FB  CA   C    single  1.528  0.020  1.528
 8FB  CA   N    single  1.452  0.020  1.452
 8FB  NAY  CAD  single  1.447  0.020  1.447
 8FB  NAY  C    single  1.352  0.020  1.352
 8FB  CAU  CBA  single  1.554  0.020  1.554
 8FB  CAV  CAZ  single  1.539  0.020  1.539
 8FB  CAV  CAT  single  1.539  0.020  1.539
 8FB  CAZ  CBA  single  1.567  0.020  1.567
 8FB  CAZ  NAN  single  1.453  0.020  1.453
 8FB  C    O    double  1.223  0.020  1.223
 8FB  N    CD   single  1.461  0.020  1.461
 8FB  CBA  CAQ  single  1.508  0.020  1.508
 8FB  CG   CD   single  1.552  0.020  1.552
 8FB  CG   SAO  single  1.828  0.020  1.828
 8FB  NAN  CAS  single  1.443  0.020  1.443
 8FB  CAT  SAO  single  1.814  0.020  1.814
 8FB  CAT  CAS  single  1.557  0.020  1.557
 8FB  CAS  CAP  single  1.512  0.020  1.512
 8FB  CAQ  OAI  double  1.213  0.020  1.213
 8FB  CAQ  OAF  single  1.324  0.020  1.324
 8FB  CAP  OAE  double  1.204  0.020  1.204
 8FB  CAP  OAH  single  1.326  0.020  1.326
 8FB  CAC  H1   single  0.970  0.020  1.090
 8FB  CAC  H2   single  0.970  0.020  1.090
 8FB  CAC  H3   single  0.970  0.020  1.090
 8FB  CAD  H4   single  0.970  0.020  1.090
 8FB  CAD  H5   single  0.970  0.020  1.090
 8FB  CAD  H6   single  0.970  0.020  1.090
 8FB  CA   H7   single  0.970  0.020  1.090
 8FB  CB   H8   single  0.970  0.020  1.090
 8FB  CB   H9   single  0.970  0.020  1.090
 8FB  N    H10  single  0.890  0.020  1.040
 8FB  CD   H12  single  0.970  0.020  1.090
 8FB  CD   H13  single  0.970  0.020  1.090
 8FB  CG   H14  single  0.970  0.020  1.090
 8FB  CAT  H15  single  0.970  0.020  1.090
 8FB  CAV  H16  single  0.970  0.020  1.090
 8FB  CAB  H17  single  0.970  0.020  1.090
 8FB  CAB  H18  single  0.970  0.020  1.090
 8FB  CAB  H19  single  0.970  0.020  1.090
 8FB  CAS  H20  single  0.970  0.020  1.090
 8FB  OAH  H21  single  0.850  0.020  0.980
 8FB  NAN  H22  single  0.890  0.020  1.040
 8FB  CAZ  H24  single  0.970  0.020  1.090
 8FB  CBA  H25  single  0.970  0.020  1.090
 8FB  OAF  H26  single  0.850  0.020  0.980
 8FB  CAU  H27  single  0.970  0.020  1.090
 8FB  OAJ  H28  single  0.850  0.020  0.980
 8FB  CAA  H29  single  0.970  0.020  1.090
 8FB  CAA  H30  single  0.970  0.020  1.090
 8FB  CAA  H31  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
 8FB  CA   C    NAY  117.41  3.000
 8FB  NAY  C    O    122.29  3.000
 8FB  CA   C    O    120.30  3.000
 8FB  CAD  NAY  CAC  113.92  3.000
 8FB  CAD  NAY  C    120.31  3.000
 8FB  CAC  NAY  C    125.31  3.000
 8FB  H3   CAC  H2   107.85  3.000
 8FB  H3   CAC  H1   107.34  3.000
 8FB  H2   CAC  H1   108.29  3.000
 8FB  H3   CAC  NAY  109.35  3.000
 8FB  H2   CAC  NAY  111.32  3.000
 8FB  H1   CAC  NAY  112.51  3.000
 8FB  H6   CAD  H5   108.06  3.000
 8FB  H6   CAD  H4   108.70  3.000
 8FB  H5   CAD  H4   108.74  3.000
 8FB  H6   CAD  NAY  110.68  3.000
 8FB  H5   CAD  NAY  109.93  3.000
 8FB  H4   CAD  NAY  110.66  3.000
 8FB  H7   CA   N    108.66  3.000
 8FB  H7   CA   CB   111.79  3.000
 8FB  N    CA   CB   104.65  3.000
 8FB  H7   CA   C    110.22  3.000
 8FB  N    CA   C    110.41  3.000
 8FB  CB   CA   C    110.96  3.000
 8FB  H9   CB   H8   107.37  3.000
 8FB  H9   CB   CG   109.73  3.000
 8FB  H8   CB   CG   113.00  3.000
 8FB  H9   CB   CA   108.54  3.000
 8FB  H8   CB   CA   115.08  3.000
 8FB  CG   CB   CA   102.98  3.000
 8FB  H10  N    CD   109.00  3.000
 8FB  H10  N    CA   107.40  3.000
 8FB  CD   N    CA   107.34  3.000
 8FB  H13  CD   H12  106.97  3.000
 8FB  H13  CD   CG   110.79  3.000
 8FB  H12  CD   CG   110.54  3.000
 8FB  H13  CD   N    110.79  3.000
 8FB  H12  CD   N    110.26  3.000
 8FB  CG   CD   N    107.52  3.000
 8FB  H14  CG   SAO  107.15  3.000
 8FB  H14  CG   CD   110.83  3.000
 8FB  SAO  CG   CD   110.47  3.000
 8FB  H14  CG   CB   111.35  3.000
 8FB  SAO  CG   CB   113.14  3.000
 8FB  CD   CG   CB   103.95  3.000
 8FB  CAT  SAO  CG   103.39  3.000
 8FB  H15  CAT  CAS  108.14  3.000
 8FB  H15  CAT  CAV  109.79  3.000
 8FB  CAS  CAT  CAV  104.46  3.000
 8FB  H15  CAT  SAO  102.61  3.000
 8FB  CAS  CAT  SAO  117.33  3.000
 8FB  CAV  CAT  SAO  114.34  3.000
 8FB  H16  CAV  CAZ  104.19  3.000
 8FB  H16  CAV  CAB  107.02  3.000
 8FB  CAZ  CAV  CAB  119.88  3.000
 8FB  H16  CAV  CAT  108.51  3.000
 8FB  CAZ  CAV  CAT  103.67  3.000
 8FB  CAB  CAV  CAT  112.87  3.000
 8FB  H19  CAB  H18  108.09  3.000
 8FB  H19  CAB  H17  107.03  3.000
 8FB  H18  CAB  H17  107.45  3.000
 8FB  H19  CAB  CAV  113.08  3.000
 8FB  H18  CAB  CAV  111.65  3.000
 8FB  H17  CAB  CAV  109.29  3.000
 8FB  H20  CAS  NAN  113.78  3.000
 8FB  H20  CAS  CAP  105.68  3.000
 8FB  NAN  CAS  CAP  112.29  3.000
 8FB  H20  CAS  CAT  107.14  3.000
 8FB  CAP  CAS  CAT  114.78  3.000
 8FB  NAN  CAS  CAT  103.30  3.000
 8FB  OAH  CAP  OAE  123.71  3.000
 8FB  OAH  CAP  CAS  110.79  3.000
 8FB  OAE  CAP  CAS  125.48  3.000
 8FB  H21  OAH  CAP  110.13  3.000
 8FB  H22  NAN  CAZ  114.41  3.000
 8FB  H22  NAN  CAS  113.88  3.000
 8FB  CAZ  NAN  CAS  107.86  3.000
 8FB  H24  CAZ  CBA  107.52  3.000
 8FB  H24  CAZ  NAN  107.82  3.000
 8FB  CBA  CAZ  NAN  117.42  3.000
 8FB  H24  CAZ  CAV  109.50  3.000
 8FB  NAN  CAZ  CAV   99.60  3.000
 8FB  CBA  CAZ  CAV  114.57  3.000
 8FB  H25  CBA  CAU  106.89  3.000
 8FB  H25  CBA  CAQ  107.19  3.000
 8FB  CAU  CBA  CAQ  106.72  3.000
 8FB  H25  CBA  CAZ  110.23  3.000
 8FB  CAQ  CBA  CAZ  113.32  3.000
 8FB  CAU  CBA  CAZ  112.15  3.000
 8FB  OAI  CAQ  OAF  122.49  3.000
 8FB  OAF  CAQ  CBA  113.45  3.000
 8FB  OAI  CAQ  CBA  124.02  3.000
 8FB  H26  OAF  CAQ  110.17  3.000
 8FB  H27  CAU  CAA  107.36  3.000
 8FB  H27  CAU  OAJ  110.39  3.000
 8FB  CAA  CAU  OAJ  107.64  3.000
 8FB  H27  CAU  CBA  106.71  3.000
 8FB  OAJ  CAU  CBA  112.32  3.000
 8FB  CAA  CAU  CBA  112.33  3.000
 8FB  H28  OAJ  CAU  108.26  3.000
 8FB  H31  CAA  H30  107.86  3.000
 8FB  H31  CAA  H29  107.87  3.000
 8FB  H30  CAA  H29  108.38  3.000
 8FB  H31  CAA  CAU  110.07  3.000
 8FB  H30  CAA  CAU  111.97  3.000
 8FB  H29  CAA  CAU  110.57  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
 8FB  CONST_01  CA   C    NAY  CAC    0.00   0.0  0
 8FB  CONST_02  CA   C    NAY  CAD  180.00   0.0  0
 8FB  CONST_03  H21  OAH  CAP  CAS  180.00   0.0  0
 8FB  CONST_04  CAC  NAY  C    O    180.00   0.0  0
 8FB  CONST_05  CAD  NAY  C    O      0.00   0.0  0
 8FB  CONST_06  H26  OAF  CAQ  CBA  180.00   0.0  0
 8FB  Var_01    CG   CD   N    CA    17.11  30.0  1
 8FB  Var_02    H1   CAC  NAY  C    -19.61  30.0  3
 8FB  Var_03    H4   CAD  NAY  C     10.56  30.0  3

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
 8FB  chir_01  CA   CB   C    N    negativ
 8FB  chir_02  CG   SAO  CD   CB   positiv
 8FB  chir_03  CAT  SAO  CAS  CAV  positiv
 8FB  chir_04  CAV  CAT  CAZ  CAB  negativ
 8FB  chir_05  CAS  NAN  CAT  CAP  positiv
 8FB  chir_06  CAZ  NAN  CAV  CBA  positiv
 8FB  chir_07  CBA  CAU  CAZ  CAQ  positiv
 8FB  chir_08  CAU  OAJ  CBA  CAA  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
 8FB  plan-1  O    0.020
 8FB  plan-1  C    0.020
 8FB  plan-1  NAY  0.020
 8FB  plan-1  CAC  0.020
 8FB  plan-1  CAD  0.020
 8FB  plan-1  CA   0.020
 8FB  plan-2  CAS  0.020
 8FB  plan-2  CAP  0.020
 8FB  plan-2  OAE  0.020
 8FB  plan-2  OAH  0.020
 8FB  plan-2  H21  0.020
 8FB  plan-3  CBA  0.020
 8FB  plan-3  CAQ  0.020
 8FB  plan-3  OAF  0.020
 8FB  plan-3  OAI  0.020
 8FB  plan-3  H26  0.020

