data_JO9
# 
_chem_comp.id                                    JO9 
_chem_comp.name                                  "(2~{R},4~{S})-2-[(1~{R})-2-(azepan-1-yl)-1-formamido-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H25 N3 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "mecillinam degradation product" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-06 
_chem_comp.pdbx_modified_date                    2023-03-03 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        343.442 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     JO9 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7ZO5 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
JO9 C7  C1  C 0 1 N N N 12.893 27.117 30.277 -1.501 -0.001 0.520  C7  JO9 1  
JO9 C8  C2  C 0 1 N N N 13.587 24.994 29.436 -3.716 -0.189 1.432  C8  JO9 2  
JO9 C9  C3  C 0 1 N N N 14.580 23.870 29.616 -4.247 -1.584 1.022  C9  JO9 3  
JO9 C10 C4  C 0 1 N N N 16.041 24.277 29.510 -5.183 -1.462 -0.106 C10 JO9 4  
JO9 C11 C5  C 0 1 N N N 16.425 25.546 30.247 -4.560 -0.905 -1.383 C11 JO9 5  
JO9 C12 C6  C 0 1 N N N 15.826 25.753 31.627 -4.575 0.603  -1.329 C12 JO9 6  
JO9 O1  O1  O 0 1 N N N 11.769 32.641 33.601 3.464  1.678  0.627  O1  JO9 7  
JO9 C1  C7  C 0 1 N N N 11.211 29.117 34.175 3.048  -1.442 -0.177 C1  JO9 8  
JO9 C2  C8  C 0 1 N N N 11.793 28.487 35.443 3.535  -2.581 -1.074 C2  JO9 9  
JO9 C3  C9  C 0 1 N N S 12.136 30.213 33.603 3.171  -0.089 -0.904 C3  JO9 10 
JO9 C4  C10 C 0 1 N N N 11.896 31.607 34.235 4.003  0.842  -0.060 C4  JO9 11 
JO9 C5  C11 C 0 1 N N R 11.884 28.998 31.551 0.895  0.199  -0.090 C5  JO9 12 
JO9 C6  C12 C 0 1 N N R 13.245 28.378 31.067 -0.543 0.422  -0.564 C6  JO9 13 
JO9 O2  O2  O 0 1 N N N 12.001 27.154 29.449 -1.092 -0.609 1.486  O2  JO9 14 
JO9 O3  O3  O 0 1 N N N 15.126 30.447 31.743 -0.252 2.425  1.216  O3  JO9 15 
JO9 N   N1  N 0 1 N N N 12.035 30.307 32.151 1.872  0.540  -1.161 N   JO9 16 
JO9 C   C13 C 0 1 N N N 9.791  29.619 34.410 3.831  -1.421 1.137  C   JO9 17 
JO9 O   O4  O 0 1 N N N 11.838 31.538 35.535 5.341  0.743  -0.071 O   JO9 18 
JO9 C13 C14 C 0 1 N N N 14.315 25.638 31.741 -3.260 1.124  -0.723 C13 JO9 19 
JO9 C14 C15 C 0 1 N N N 14.839 30.205 30.578 -0.572 2.767  0.097  C14 JO9 20 
JO9 N1  N2  N 0 1 N N N 13.588 25.988 30.515 -2.810 0.303  0.419  N1  JO9 21 
JO9 N2  N3  N 0 1 N N N 13.975 29.272 30.188 -0.743 1.841  -0.867 N2  JO9 22 
JO9 S   S1  S 0 1 N N N 11.186 27.861 32.825 1.247  -1.597 0.146  S   JO9 23 
JO9 H12 H1  H 0 1 N N N 13.821 25.511 28.493 -4.553 0.502  1.537  H12 JO9 24 
JO9 H11 H2  H 0 1 N N N 12.580 24.556 29.374 -3.189 -0.266 2.383  H11 JO9 25 
JO9 H14 H3  H 0 1 N N N 14.420 23.430 30.612 -3.410 -2.217 0.729  H14 JO9 26 
JO9 H13 H4  H 0 1 N N N 14.381 23.112 28.844 -4.763 -2.037 1.868  H13 JO9 27 
JO9 H16 H5  H 0 1 N N N 16.651 23.455 29.912 -5.593 -2.449 -0.324 H16 JO9 28 
JO9 H15 H6  H 0 1 N N N 16.276 24.421 28.445 -6.003 -0.809 0.192  H15 JO9 29 
JO9 H18 H7  H 0 1 N N N 17.519 25.547 30.357 -3.532 -1.256 -1.468 H18 JO9 30 
JO9 H17 H8  H 0 1 N N N 16.119 26.398 29.622 -5.133 -1.244 -2.246 H17 JO9 31 
JO9 H19 H9  H 0 1 N N N 16.269 25.002 32.298 -4.690 0.999  -2.339 H19 JO9 32 
JO9 H20 H10 H 0 1 N N N 16.110 26.760 31.966 -5.412 0.934  -0.716 H20 JO9 33 
JO9 H4  H11 H 0 1 N N N 11.809 29.234 36.250 3.404  -3.532 -0.558 H4  JO9 34 
JO9 H5  H12 H 0 1 N N N 11.170 27.633 35.747 2.958  -2.588 -1.999 H5  JO9 35 
JO9 H6  H13 H 0 1 N N N 12.818 28.141 35.243 4.590  -2.436 -1.306 H6  JO9 36 
JO9 H7  H14 H 0 1 N N N 13.167 29.923 33.853 3.678  -0.246 -1.856 H7  JO9 37 
JO9 H10 H15 H 0 1 N N N 11.167 29.017 30.717 1.098  0.763  0.821  H10 JO9 38 
JO9 H   H16 H 0 1 N N N 13.852 28.109 31.944 -0.725 -0.170 -1.461 H   JO9 39 
JO9 H25 H17 H 0 1 N N N 12.864 30.736 31.793 1.518  0.280  -2.070 H25 JO9 40 
JO9 H2  H19 H 0 1 N N N 9.795  30.369 35.214 4.889  -1.264 0.927  H2  JO9 41 
JO9 H1  H20 H 0 1 N N N 9.406  30.074 33.486 3.462  -0.611 1.767  H1  JO9 42 
JO9 H3  H21 H 0 1 N N N 9.147  28.775 34.699 3.700  -2.372 1.653  H3  JO9 43 
JO9 H8  H22 H 0 1 N N N 11.685 32.405 35.892 5.832  1.362  0.487  H8  JO9 44 
JO9 H21 H23 H 0 1 N N N 13.978 26.309 32.545 -2.487 1.114  -1.492 H21 JO9 45 
JO9 H22 H24 H 0 1 N N N 14.068 24.599 32.003 -3.408 2.149  -0.384 H22 JO9 46 
JO9 H24 H25 H 0 1 N N N 15.322 30.792 29.811 -0.719 3.813  -0.126 H24 JO9 47 
JO9 H23 H26 H 0 1 N N N 13.815 29.179 29.205 -0.999 2.115  -1.762 H23 JO9 48 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
JO9 C8  C9  SING N N 1  
JO9 C8  N1  SING N N 2  
JO9 O2  C7  DOUB N N 3  
JO9 C10 C9  SING N N 4  
JO9 C10 C11 SING N N 5  
JO9 N2  C14 SING N N 6  
JO9 N2  C6  SING N N 7  
JO9 C11 C12 SING N N 8  
JO9 C7  N1  SING N N 9  
JO9 C7  C6  SING N N 10 
JO9 N1  C13 SING N N 11 
JO9 C14 O3  DOUB N N 12 
JO9 C6  C5  SING N N 13 
JO9 C5  N   SING N N 14 
JO9 C5  S   SING N N 15 
JO9 C12 C13 SING N N 16 
JO9 N   C3  SING N N 17 
JO9 S   C1  SING N N 18 
JO9 O1  C4  DOUB N N 19 
JO9 C3  C1  SING N N 20 
JO9 C3  C4  SING N N 21 
JO9 C1  C   SING N N 22 
JO9 C1  C2  SING N N 23 
JO9 C4  O   SING N N 24 
JO9 C8  H12 SING N N 25 
JO9 C8  H11 SING N N 26 
JO9 C9  H14 SING N N 27 
JO9 C9  H13 SING N N 28 
JO9 C10 H16 SING N N 29 
JO9 C10 H15 SING N N 30 
JO9 C11 H18 SING N N 31 
JO9 C11 H17 SING N N 32 
JO9 C12 H19 SING N N 33 
JO9 C12 H20 SING N N 34 
JO9 C2  H4  SING N N 35 
JO9 C2  H5  SING N N 36 
JO9 C2  H6  SING N N 37 
JO9 C3  H7  SING N N 38 
JO9 C5  H10 SING N N 39 
JO9 C6  H   SING N N 40 
JO9 N   H25 SING N N 41 
JO9 C   H2  SING N N 42 
JO9 C   H1  SING N N 43 
JO9 C   H3  SING N N 44 
JO9 O   H8  SING N N 45 
JO9 C13 H21 SING N N 46 
JO9 C13 H22 SING N N 47 
JO9 C14 H24 SING N N 48 
JO9 N2  H23 SING N N 49 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
JO9 InChI            InChI                1.06  "InChI=1S/C15H25N3O4S/c1-15(2)11(14(21)22)17-12(23-15)10(16-9-19)13(20)18-7-5-3-4-6-8-18/h9-12,17H,3-8H2,1-2H3,(H,16,19)(H,21,22)/t10-,11-,12+/m0/s1" 
JO9 InChIKey         InChI                1.06  PMJUGUXXJDBOJL-SDDRHHMPSA-N                                                                                                                           
JO9 SMILES_CANONICAL CACTVS               3.385 "CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC=O)C(=O)N2CCCCCC2"                                                                                               
JO9 SMILES           CACTVS               3.385 "CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC=O)C(=O)N2CCCCCC2"                                                                                                   
JO9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1([C@@H](N[C@H](S1)[C@@H](C(=O)N2CCCCCC2)NC=O)C(=O)O)C"                                                                                            
JO9 SMILES           "OpenEye OEToolkits" 2.0.7 "CC1(C(NC(S1)C(C(=O)N2CCCCCC2)NC=O)C(=O)O)C"                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           JO9 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{R},4~{S})-2-[(1~{R})-2-(azepan-1-yl)-1-formamido-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      JO9 
_pdbx_chem_comp_synonyms.name         "mecillinam degradation product" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
JO9 "Create component"  2022-05-06 PDBE 
JO9 "Modify descriptor" 2022-08-22 RCSB 
JO9 "Initial release"   2023-03-08 RCSB 
# 
