# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 12:16:39 2020
#   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  54  27  .  2021-08-06  2023-02-02
;
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  -0.494   4.7711  -2.1307  -0.6048
 8FB  C    C  C      0   0.564   5.1000  -0.9605  -0.4768
 8FB  NAY  N  NT     0  -0.448   6.1645  -0.6055   0.2767
 8FB  CAC  C  CH3    0  -0.531   6.7313   0.7274   0.3167
 8FB  CAD  C  CH3    0  -0.513   6.9560  -1.6579   0.8840
 8FB  CA   C  CH1    0  -0.269   4.2875   0.1647  -1.1169
 8FB  CB   C  CH2    0  -0.463   3.4698   0.9272  -0.0269
 8FB  N    N  NH1    0  -0.564   3.3329  -0.3790  -2.0707
 8FB  CD   C  CH2    0  -0.293   2.0757  -0.5075  -1.3511
 8FB  CG   C  CH1    0  -0.386   2.0106   0.7278  -0.4524
 8FB  SAO  S  S2     0  -0.037   0.9422   0.5847   1.0013
 8FB  CAT  C  CR15   0  -0.353  -0.6698   0.2223   0.2572
 8FB  CAV  C  CR15   0  -0.231  -1.7358   0.1072   1.3482
 8FB  CAB  C  CH3    0  -0.676  -1.6625  -1.1977   2.1264
 8FB  CAS  C  CR15   0  -0.216  -1.2561   1.2574  -0.7186
 8FB  CAP  C  C      0   0.422  -0.9899   2.7101  -0.2896
 8FB  OAE  O  O      0  -0.599  -1.6575   3.1594   0.6632
 8FB  OAH  O  OC    -1  -0.618  -0.1195   3.3364  -0.9334
 8FB  NAN  N  NR15   0  -0.598  -2.6791   0.9295  -0.7472
 8FB  CAZ  C  CR15   0  -0.027  -3.0600   0.4505   0.5863
 8FB  CBA  C  CH1    0  -0.424  -4.1308  -0.6421   0.5625
 8FB  CAQ  C  C      0   0.444  -3.7839  -1.9754  -0.1426
 8FB  OAF  O  OC    -1  -0.622  -4.5148  -2.9441   0.1485
 8FB  OAI  O  O      0  -0.593  -2.8366  -2.0009  -0.9574
 8FB  CAU  C  CH1    0   0.076  -5.4938  -0.1807   0.0184
 8FB  OAJ  O  OH1    0  -0.672  -5.4393  -0.1807  -1.3991
 8FB  CAA  C  CH3    0  -0.708  -5.9534   1.1709   0.5440
 8FB  H1   H  HCH3   0   0.250   7.1331   0.9186   1.3107
 8FB  H2   H  HCH3   0   0.243   7.5422   0.8487  -0.4063
 8FB  H3   H  HCH3   0   0.261   5.9862   1.4929   0.1246
 8FB  H4   H  HCH3   0   0.235   7.6146  -2.1485   0.1631
 8FB  H5   H  HCH3   0   0.238   7.5744  -1.2259   1.6679
 8FB  H6   H  HCH3   0   0.247   6.3174  -2.4152   1.3328
 8FB  H7   H  HCH1   0   0.284   4.9610   0.8413  -1.6459
 8FB  H8   H  HCH2   0   0.250   3.6526   0.5159   0.9696
 8FB  H9   H  HCH2   0   0.261   3.7341   1.9836   0.0112
 8FB  H10  H  HNH1   0   0.353   3.2096   0.2990  -2.8122
 8FB  H12  H  HCH2   0   0.243   1.2391  -0.5731  -2.0474
 8FB  H13  H  HCH2   0   0.226   2.0815  -1.4179  -0.7459
 8FB  H14  H  HCH1   0   0.283   1.6688   1.5866  -1.0320
 8FB  H15  H  HCR5   0   0.266  -0.6082  -0.7353  -0.2673
 8FB  H16  H  HCR5   0   0.221  -1.5678   0.9195   2.0616
 8FB  H17  H  HCH3   0   0.224  -1.7027  -2.0688   1.4744
 8FB  H18  H  HCH3   0   0.224  -0.7239  -1.2505   2.6820
 8FB  H19  H  HCH3   0   0.221  -2.4690  -1.2805   2.8570
 8FB  H20  H  HCR5   0   0.212  -0.8445   1.1108  -1.7208
 8FB  H22  H  HNR5   0   0.342  -2.7754   0.1312  -1.3623
 8FB  H24  H  HCR5   0   0.214  -3.4936   1.2905   1.1321
 8FB  H25  H  HCH1   0   0.223  -4.3260  -0.8851   1.6140
 8FB  H27  H  HCH1   0   0.188  -6.2208  -0.9333   0.3531
 8FB  H28  H  HOH1   0   0.441  -6.3143   0.0484  -1.7267
 8FB  H29  H  HCH3   0   0.228  -6.9789   1.3753   0.2270
 8FB  H30  H  HCH3   0   0.220  -5.9426   1.1948   1.6351
 8FB  H31  H  HCH3   0   0.229  -5.3193   1.9786   0.1762

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  1.521  0.020  1.521
 8FB  CAC  NAY  single  1.449  0.020  1.449
 8FB  OAJ  CAU  single  1.419  0.020  1.419
 8FB  CB   CA   single  1.562  0.020  1.562
 8FB  CB   CG   single  1.533  0.020  1.533
 8FB  CAB  CAV  single  1.521  0.020  1.521
 8FB  CA   C    single  1.528  0.020  1.528
 8FB  CA   N    single  1.455  0.020  1.455
 8FB  NAY  CAD  single  1.450  0.020  1.450
 8FB  NAY  C    single  1.352  0.020  1.352
 8FB  CAU  CBA  single  1.538  0.020  1.538
 8FB  CAV  CAZ  single  1.566  0.020  1.566
 8FB  CAV  CAT  single  1.530  0.020  1.530
 8FB  CAZ  CBA  single  1.530  0.020  1.530
 8FB  CAZ  NAN  single  1.467  0.020  1.467
 8FB  C    O    double  1.222  0.020  1.222
 8FB  N    CD   single  1.454  0.020  1.454
 8FB  CBA  CAQ  single  1.548  0.020  1.548
 8FB  CG   CD   single  1.529  0.020  1.529
 8FB  CG   SAO  single  1.810  0.020  1.810
 8FB  NAN  CAS  single  1.461  0.020  1.461
 8FB  CAT  SAO  single  1.812  0.020  1.812
 8FB  CAT  CAS  single  1.539  0.020  1.539
 8FB  CAS  CAP  single  1.538  0.020  1.538
 8FB  CAQ  OAI  deloc   1.250  0.020  1.250
 8FB  CAQ  OAF  deloc   1.248  0.020  1.248
 8FB  CAP  OAE  deloc   1.247  0.020  1.247
 8FB  CAP  OAH  deloc   1.251  0.020  1.251
 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  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  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  117.31  3.000
 8FB  NAY  C    O    121.45  3.000
 8FB  CA   C    O    121.20  3.000
 8FB  CAD  NAY  CAC  116.27  3.000
 8FB  CAD  NAY  C    118.21  3.000
 8FB  CAC  NAY  C    124.40  3.000
 8FB  H3   CAC  H2   108.30  3.000
 8FB  H3   CAC  H1   106.91  3.000
 8FB  H2   CAC  H1   108.09  3.000
 8FB  H3   CAC  NAY  112.05  3.000
 8FB  H2   CAC  NAY  111.96  3.000
 8FB  H1   CAC  NAY  109.32  3.000
 8FB  H6   CAD  H5   108.23  3.000
 8FB  H6   CAD  H4   108.27  3.000
 8FB  H5   CAD  H4   108.12  3.000
 8FB  H6   CAD  NAY  110.96  3.000
 8FB  H5   CAD  NAY  108.90  3.000
 8FB  H4   CAD  NAY  112.24  3.000
 8FB  H7   CA   N    108.59  3.000
 8FB  H7   CA   CB   111.03  3.000
 8FB  N    CA   CB   107.25  3.000
 8FB  H7   CA   C    109.35  3.000
 8FB  N    CA   C    110.38  3.000
 8FB  CB   CA   C    110.21  3.000
 8FB  H9   CB   H8   107.00  3.000
 8FB  H9   CB   CG   111.51  3.000
 8FB  H8   CB   CG   111.29  3.000
 8FB  H9   CB   CA   111.76  3.000
 8FB  H8   CB   CA   111.41  3.000
 8FB  CG   CB   CA   103.96  3.000
 8FB  H10  N    CD   108.45  3.000
 8FB  H10  N    CA   108.05  3.000
 8FB  CD   N    CA   106.02  3.000
 8FB  H13  CD   H12  107.91  3.000
 8FB  H13  CD   CG   110.34  3.000
 8FB  H12  CD   CG   113.03  3.000
 8FB  H13  CD   N    110.06  3.000
 8FB  H12  CD   N    110.65  3.000
 8FB  CG   CD   N    104.85  3.000
 8FB  H14  CG   SAO  107.70  3.000
 8FB  H14  CG   CD   109.69  3.000
 8FB  SAO  CG   CD   115.68  3.000
 8FB  H14  CG   CB   110.08  3.000
 8FB  SAO  CG   CB   110.44  3.000
 8FB  CD   CG   CB   103.16  3.000
 8FB  CAT  SAO  CG   102.19  3.000
 8FB  H15  CAT  CAS  107.84  3.000
 8FB  H15  CAT  CAV  108.39  3.000
 8FB  CAS  CAT  CAV  103.73  3.000
 8FB  H15  CAT  SAO  108.78  3.000
 8FB  CAS  CAT  SAO  117.70  3.000
 8FB  CAV  CAT  SAO  110.01  3.000
 8FB  H16  CAV  CAZ  106.52  3.000
 8FB  H16  CAV  CAB  107.21  3.000
 8FB  CAZ  CAV  CAB  118.54  3.000
 8FB  H16  CAV  CAT  107.59  3.000
 8FB  CAZ  CAV  CAT  103.05  3.000
 8FB  CAB  CAV  CAT  113.32  3.000
 8FB  H19  CAB  H18  106.91  3.000
 8FB  H19  CAB  H17  108.23  3.000
 8FB  H18  CAB  H17  107.32  3.000
 8FB  H19  CAB  CAV  111.84  3.000
 8FB  H18  CAB  CAV  110.07  3.000
 8FB  H17  CAB  CAV  112.22  3.000
 8FB  H20  CAS  NAN  108.59  3.000
 8FB  H20  CAS  CAP  108.49  3.000
 8FB  NAN  CAS  CAP  112.72  3.000
 8FB  H20  CAS  CAT  110.34  3.000
 8FB  CAP  CAS  CAT  113.12  3.000
 8FB  NAN  CAS  CAT  103.45  3.000
 8FB  OAH  CAP  OAE  125.83  3.000
 8FB  OAH  CAP  CAS  116.74  3.000
 8FB  OAE  CAP  CAS  117.43  3.000
 8FB  H22  NAN  CAZ  105.67  3.000
 8FB  H22  NAN  CAS  106.36  3.000
 8FB  CAZ  NAN  CAS  107.97  3.000
 8FB  H24  CAZ  CBA  106.22  3.000
 8FB  H24  CAZ  NAN  107.84  3.000
 8FB  CBA  CAZ  NAN  113.62  3.000
 8FB  H24  CAZ  CAV  105.15  3.000
 8FB  NAN  CAZ  CAV  107.11  3.000
 8FB  CBA  CAZ  CAV  116.29  3.000
 8FB  H25  CBA  CAU  104.35  3.000
 8FB  H25  CBA  CAQ  106.61  3.000
 8FB  CAU  CBA  CAQ  107.21  3.000
 8FB  H25  CBA  CAZ  105.54  3.000
 8FB  CAQ  CBA  CAZ  117.74  3.000
 8FB  CAU  CBA  CAZ  114.29  3.000
 8FB  OAI  CAQ  OAF  125.47  3.000
 8FB  OAF  CAQ  CBA  115.54  3.000
 8FB  OAI  CAQ  CBA  118.98  3.000
 8FB  H27  CAU  CAA  107.67  3.000
 8FB  H27  CAU  OAJ  109.26  3.000
 8FB  CAA  CAU  OAJ  110.90  3.000
 8FB  H27  CAU  CBA  105.85  3.000
 8FB  OAJ  CAU  CBA  108.63  3.000
 8FB  CAA  CAU  CBA  114.32  3.000
 8FB  H28  OAJ  CAU  107.78  3.000
 8FB  H31  CAA  H30  108.37  3.000
 8FB  H31  CAA  H29  108.02  3.000
 8FB  H30  CAA  H29  107.17  3.000
 8FB  H31  CAA  CAU  111.46  3.000
 8FB  H30  CAA  CAU  111.22  3.000
 8FB  H29  CAA  CAU  110.45  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  CAC  NAY  C    O    180.00   0.0  0
 8FB  CONST_04  CAD  NAY  C    O      0.00   0.0  0
 8FB  Var_01    CG   CD   N    CA    38.21  30.0  1
 8FB  Var_02    H1   CAC  NAY  C    147.75  30.0  3
 8FB  Var_03    H4   CAD  NAY  C     76.53  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-3  CBA  0.020
 8FB  plan-3  CAQ  0.020
 8FB  plan-3  OAF  0.020
 8FB  plan-3  OAI  0.020

