data_O2F
# 
_chem_comp.id                                    O2F 
_chem_comp.name                                  "(2S,3R,4R)-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H27 N3 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Meropenem, bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-08-26 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        385.478 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     O2F 
_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        8AKL 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
O2F C1  C1  C 0 1 N N N N N N 17.134 3.943  19.743 7.483  -0.589 -0.970 C1  O2F 1  
O2F C2  C2  C 0 1 N N N N N N 17.339 3.610  22.196 5.631  -2.320 -0.850 C2  O2F 2  
O2F C3  C3  C 0 1 N N S N N N 20.020 4.747  19.756 4.058  -0.579 0.740  C3  O2F 3  
O2F C4  C4  C 0 1 N N N N N N 18.937 5.931  17.959 2.147  0.522  1.680  C4  O2F 4  
O2F C5  C5  C 0 1 N N N N N N 20.088 6.249  20.085 3.008  -0.405 -0.386 C5  O2F 5  
O2F C7  C6  C 0 1 N N R N N N 18.225 8.653  21.109 -0.946 0.759  0.637  C7  O2F 6  
O2F C9  C7  C 0 1 N N N N N N 18.439 10.750 19.507 -1.857 2.924  -0.586 C9  O2F 7  
O2F C11 C8  C 0 1 N N S N N N 14.963 9.370  21.772 -3.943 -1.303 0.159  C11 O2F 8  
O2F C15 C9  C 0 1 N N R N N N 17.443 8.649  22.453 -1.592 -0.639 0.800  C15 O2F 9  
O2F C16 C10 C 0 1 N N N N N N 16.948 7.265  22.888 -1.311 -1.522 -0.417 C16 O2F 10 
O2F N   N1  N 0 1 N N N N N N 18.011 3.844  20.915 6.157  -0.998 -0.500 N   O2F 11 
O2F C   C11 C 0 1 N N N N N N 19.356 3.950  20.885 5.422  -0.159 0.255  C   O2F 12 
O2F O   O1  O 0 1 N N N N N N 20.055 3.451  21.747 5.857  0.936  0.545  O   O2F 13 
O2F C10 C12 C 0 1 N N S N N N 16.360 9.775  22.320 -3.089 -0.258 0.881  C10 O2F 14 
O2F C12 C13 C 0 1 N N N N N N 14.390 10.442 20.885 -3.662 -1.245 -1.321 C12 O2F 15 
O2F C13 C14 C 0 1 N N R N N N 13.927 9.326  22.892 -5.424 -1.013 0.409  C13 O2F 16 
O2F C14 C15 C 0 1 N N N N N N 12.626 8.694  22.449 -6.277 -2.058 -0.313 C14 O2F 17 
O2F C6  C16 C 0 1 N N S N N N 19.142 6.963  19.090 1.696  -0.261 0.429  C6  O2F 18 
O2F C8  C17 C 0 1 N N N N N N 17.883 10.061 20.680 -2.058 1.606  0.060  C8  O2F 19 
O2F N1  N2  N 0 1 N N N N N N 19.309 4.583  18.480 3.599  0.313  1.825  N1  O2F 20 
O2F N2  N3  N 0 1 N N N N N N 16.939 10.670 21.292 -3.190 1.039  0.202  N2  O2F 21 
O2F O1  O2  O 0 1 N N N N N N 19.661 10.418 19.213 -2.921 3.646  -0.988 O1  O2F 22 
O2F O2  O3  O 0 1 N N N N N N 17.805 11.567 18.926 -0.734 3.353  -0.754 O2  O2F 23 
O2F O3  O4  O 0 1 N N N N N N 14.025 10.228 19.708 -3.232 -2.218 -1.893 O3  O2F 24 
O2F O4  O5  O 0 1 N N N N N N 14.465 8.600  24.007 -5.690 -1.068 1.811  O4  O2F 25 
O2F S   S1  S 0 1 N N N N N N 17.582 7.458  19.860 0.460  0.681  -0.507 S   O2F 26 
O2F H7  H1  H 0 1 N N N N N N 16.087 3.820  20.056 7.923  -1.393 -1.561 H7  O2F 27 
O2F H8  H2  H 0 1 N N N N N N 17.262 4.929  19.272 7.390  0.305  -1.586 H8  O2F 28 
O2F H6  H3  H 0 1 N N N N N N 17.396 3.155  19.022 8.123  -0.376 -0.114 H6  O2F 29 
O2F H11 H4  H 0 1 N N N N N N 18.089 3.554  22.999 5.924  -3.041 -0.086 H11 O2F 30 
O2F H9  H5  H 0 1 N N N N N N 16.643 4.437  22.401 4.544  -2.275 -0.908 H9  O2F 31 
O2F H10 H6  H 0 1 N N N N N N 16.780 2.664  22.149 6.035  -2.628 -1.814 H10 O2F 32 
O2F H   H7  H 0 1 N N N N N N 21.050 4.378  19.639 4.080  -1.614 1.081  H   O2F 33 
O2F H13 H8  H 0 1 N N N N N N 19.576 6.187  17.101 1.937  1.584  1.548  H13 O2F 34 
O2F H14 H9  H 0 1 N N N N N N 17.883 5.930  17.643 1.628  0.145  2.561  H14 O2F 35 
O2F H16 H10 H 0 1 N N N N N N 21.117 6.618  19.962 3.207  0.495  -0.969 H16 O2F 36 
O2F H15 H11 H 0 1 N N N N N N 19.756 6.427  21.118 2.975  -1.284 -1.029 H15 O2F 37 
O2F H2  H12 H 0 1 N N N N N N 19.304 8.486  21.244 -0.629 1.149  1.605  H2  O2F 38 
O2F H18 H13 H 0 1 N N N N N N 15.018 8.404  21.248 -3.698 -2.296 0.536  H18 O2F 39 
O2F H5  H14 H 0 1 N N N N N N 18.149 8.989  23.225 -1.258 -1.122 1.719  H5  O2F 40 
O2F H25 H15 H 0 1 N N N N N N 16.408 7.351  23.843 -0.245 -1.741 -0.469 H25 O2F 41 
O2F H24 H16 H 0 1 N N N N N N 16.273 6.859  22.120 -1.870 -2.454 -0.327 H24 O2F 42 
O2F H26 H17 H 0 1 N N N N N N 17.808 6.591  23.013 -1.620 -1.000 -1.323 H26 O2F 43 
O2F H3  H18 H 0 1 N N N N N N 16.249 10.299 23.281 -3.402 -0.169 1.921  H3  O2F 44 
O2F H19 H19 H 0 1 N N N N N N 14.289 11.441 21.283 -3.846 -0.334 -1.870 H19 O2F 45 
O2F H4  H20 H 0 1 N N N N N N 13.717 10.360 23.202 -5.668 -0.020 0.031  H4  O2F 46 
O2F H20 H21 H 0 1 N N N N N N 11.916 8.687  23.289 -6.032 -3.051 0.064  H20 O2F 47 
O2F H22 H22 H 0 1 N N N N N N 12.202 9.274  21.616 -7.332 -1.851 -0.135 H22 O2F 48 
O2F H21 H23 H 0 1 N N N N N N 12.814 7.662  22.119 -6.074 -2.016 -1.384 H21 O2F 49 
O2F H1  H24 H 0 1 N N N N N N 19.617 7.874  18.697 1.303  -1.239 0.707  H1  O2F 50 
O2F H12 H26 H 0 1 N N N N N N 18.483 4.038  18.623 4.095  1.192  1.805  H12 O2F 51 
O2F H17 H30 H 0 1 N N N N N N 19.958 10.929 18.469 -2.740 4.500  -1.405 H17 O2F 52 
O2F H23 H31 H 0 1 N N N N N N 13.822 8.571  24.706 -5.495 -1.924 2.216  H23 O2F 53 
# 
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 
O2F C4  N1  SING N N 1  
O2F C4  C6  SING N N 2  
O2F N1  C3  SING N N 3  
O2F O2  C9  DOUB N N 4  
O2F C6  S   SING N N 5  
O2F C6  C5  SING N N 6  
O2F O1  C9  SING N N 7  
O2F C9  C8  SING N N 8  
O2F O3  C12 DOUB N N 9  
O2F C1  N   SING N N 10 
O2F C3  C5  SING N N 11 
O2F C3  C   SING N N 12 
O2F S   C7  SING N N 13 
O2F C8  C7  SING N N 14 
O2F C8  N2  DOUB N N 15 
O2F C   N   SING N N 16 
O2F C   O   DOUB N N 17 
O2F C12 C11 SING N N 18 
O2F N   C2  SING N N 19 
O2F C7  C15 SING N N 20 
O2F N2  C10 SING N N 21 
O2F C11 C10 SING N N 22 
O2F C11 C13 SING N N 23 
O2F C10 C15 SING N N 24 
O2F C14 C13 SING N N 25 
O2F C15 C16 SING N N 26 
O2F C13 O4  SING N N 27 
O2F C1  H7  SING N N 28 
O2F C1  H8  SING N N 29 
O2F C1  H6  SING N N 30 
O2F C2  H11 SING N N 31 
O2F C2  H9  SING N N 32 
O2F C2  H10 SING N N 33 
O2F C3  H   SING N N 34 
O2F C4  H13 SING N N 35 
O2F C4  H14 SING N N 36 
O2F C5  H16 SING N N 37 
O2F C5  H15 SING N N 38 
O2F C7  H2  SING N N 39 
O2F C11 H18 SING N N 40 
O2F C15 H5  SING N N 41 
O2F C16 H25 SING N N 42 
O2F C16 H24 SING N N 43 
O2F C16 H26 SING N N 44 
O2F C10 H3  SING N N 45 
O2F C12 H19 SING N N 46 
O2F C13 H4  SING N N 47 
O2F C14 H20 SING N N 48 
O2F C14 H22 SING N N 49 
O2F C14 H21 SING N N 50 
O2F C6  H1  SING N N 51 
O2F N1  H12 SING N N 52 
O2F O1  H17 SING N N 53 
O2F O4  H23 SING N N 54 
# 
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 
O2F InChI            InChI                1.06    "InChI=1S/C17H27N3O5S/c1-8-13(11(7-21)9(2)22)19-14(17(24)25)15(8)26-10-5-12(18-6-10)16(23)20(3)4/h7-13,15,18,22H,5-6H2,1-4H3,(H,24,25)/t8-,9-,10+,11-,12+,13-,15-/m1/s1" 
O2F InChIKey         InChI                1.06    UUIYVKJXUXGPKB-UUDPXGIYSA-N                                                                                                                                              
O2F SMILES_CANONICAL CACTVS               3.385   "C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@H](S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O"                                                                                   
O2F SMILES           CACTVS               3.385   "C[CH](O)[CH](C=O)[CH]1N=C([CH](S[CH]2CN[CH](C2)C(=O)N(C)C)[CH]1C)C(O)=O"                                                                                                
O2F SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@H]1[C@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=O)O)S[C@H]2C[C@H](NC2)C(=O)N(C)C"                                                                                        
O2F SMILES           "OpenEye OEToolkits" 3.1.0.0 "CC1C(C(=NC1C(C=O)C(C)O)C(=O)O)SC2CC(NC2)C(=O)N(C)C"                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           O2F 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   3.1.0.0 
_pdbx_chem_comp_identifier.identifier        "(2~{S},3~{R},4~{R})-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
O2F "Create component" 2022-08-26 PDBE 
O2F "Initial release"  2023-03-08 RCSB 
O2F "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      O2F 
_pdbx_chem_comp_synonyms.name         "Meropenem, bound form" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            O2F 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C12 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
