data_NEF
#

_chem_comp.id                                   NEF
_chem_comp.name                                 "Nitrocefin - open form"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H18 N4 O9 S2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-09-26
_chem_comp.pdbx_modified_date                   2021-09-06
_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                       534.519
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    NEF
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6HR9
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
NEF  C2   C1   C   0  1  N  N  N  -3.323   0.475  16.773    0.621   0.899   0.161  C2   NEF   1  
NEF  C3   C2   C   0  1  N  N  R  -5.723   2.833  17.157   -3.220  -0.803   0.131  C3   NEF   2  
NEF  C4   C3   C   0  1  N  N  N  -2.589   1.309  16.059    1.165  -0.475  -0.107  C4   NEF   3  
NEF  C6   C4   C   0  1  N  N  N  -1.727   0.677  15.058    2.568  -0.615  -0.168  C6   NEF   4  
NEF  C7   C5   C   0  1  N  N  N  -7.455   0.163  15.115   -6.215   1.575  -0.054  C7   NEF   5  
NEF  C8   C6   C   0  1  Y  N  N  -6.526  -0.990  15.003   -7.665   1.203  -0.229  C8   NEF   6  
NEF  C11  C7   C   0  1  Y  N  N  -4.793  -2.543  14.039   -9.992   0.620  -0.961  C11  NEF   7  
NEF  C13  C8   C   0  1  N  N  R  -4.452   2.488  17.901   -1.795  -0.467  -0.312  C13  NEF   8  
NEF  C14  C9   C   0  1  Y  N  N   0.224  -0.770  14.761    4.823   0.331  -0.155  C14  NEF   9  
NEF  C15  C10  C   0  1  N  N  N  -2.627   2.782  16.234    0.428  -1.578  -0.291  C15  NEF  10  
NEF  C16  C11  C   0  1  N  N  N  -1.348   3.579  16.067    1.160  -2.817  -0.569  C16  NEF  11  
NEF  C17  C12  C   0  1  Y  N  N   0.130  -0.708  13.381    5.394  -0.924  -0.387  C17  NEF  12  
NEF  S19  S1   S   0  1  N  N  N  -4.044   0.818  18.188   -1.069   0.763   0.819  S19  NEF  13  
NEF  C1   C13  C   0  1  N  N  N  -5.590   4.271  16.736   -3.192  -1.368   1.528  C1   NEF  14  
NEF  O2   O1   O   0  1  N  N  N  -5.533   4.585  15.590   -3.793  -0.812   2.417  O2   NEF  15  
NEF  N4   N1   N   0  1  N  N  N  -6.084   1.931  16.109   -4.038   0.413   0.112  N4   NEF  16  
NEF  C5   C14  C   0  1  N  N  N  -6.956   0.951  16.309   -5.374   0.324  -0.035  C5   NEF  17  
NEF  O6   O2   O   0  1  N  N  N  -7.341   0.662  17.408   -5.901  -0.762  -0.152  O6   NEF  18  
NEF  C9   C15  C   0  1  Y  N  N  -6.180  -2.007  15.862   -8.520   0.952   0.763  C9   NEF  19  
NEF  C10  C16  C   0  1  Y  N  N  -5.231  -2.844  15.303   -9.804   0.631   0.359  C10  NEF  20  
NEF  S12  S2   S   0  1  Y  N  N  -5.655  -1.144  13.542   -8.490   1.041  -1.774  S12  NEF  21  
NEF  N14  N2   N   0  1  N  N  N  -3.312   3.245  17.424   -0.954  -1.670  -0.247  N14  NEF  22  
NEF  O17  O3   O   0  1  N  N  N  -0.559   3.340  15.178    1.426  -3.123  -1.716  O17  NEF  23  
NEF  O18  O4   O   0  1  N  N  N  -1.139   4.501  16.844    1.539  -3.619   0.448  O18  NEF  24  
NEF  C12  C17  C   0  1  N  N  N  -0.756  -0.039  15.562    3.361   0.478  -0.091  C12  NEF  25  
NEF  C18  C18  C   0  1  Y  N  N   1.017  -1.388  12.593    6.766  -1.054  -0.440  C18  NEF  26  
NEF  C19  C19  C   0  1  Y  N  N   1.996  -2.143  13.197    7.577   0.053  -0.264  C19  NEF  27  
NEF  C20  C20  C   0  1  Y  N  N   2.108  -2.212  14.571    7.019   1.299  -0.034  C20  NEF  28  
NEF  C21  C21  C   0  1  Y  N  N   1.232  -1.510  15.382    5.650   1.446   0.022  C21  NEF  29  
NEF  N22  N3   N   1  1  N  N  N   1.383  -1.662  16.778    5.056   2.778   0.274  N22  NEF  30  
NEF  N23  N4   N   1  1  N  N  N   2.889  -2.831  12.404    9.049  -0.095  -0.322  N23  NEF  31  
NEF  O24  O5   O  -1  1  N  N  N   1.384  -0.624  17.695    5.576   3.535   1.075  O24  NEF  32  
NEF  O25  O6   O   0  1  N  N  N   1.540  -2.967  17.255    4.047   3.118  -0.318  O25  NEF  33  
NEF  O26  O7   O  -1  1  N  N  N   2.747  -2.715  11.042    9.766   0.877  -0.168  O26  NEF  34  
NEF  O27  O8   O   0  1  N  N  N   3.880  -3.618  12.988    9.543  -1.190  -0.524  O27  NEF  35  
NEF  H1   H1   H   0  1  N  N  N  -4.136   0.158  16.103    1.255   1.406   0.888  H1   NEF  36  
NEF  H2   H2   H   0  1  N  N  N  -2.666  -0.382  16.983    0.605   1.471  -0.767  H2   NEF  37  
NEF  H3   H3   H   0  1  N  N  N  -6.531   2.804  17.902   -3.648  -1.539  -0.550  H3   NEF  38  
NEF  H5   H5   H   0  1  N  N  N  -1.880   0.792  13.995    3.008  -1.595  -0.277  H5   NEF  39  
NEF  H7   H7   H   0  1  N  N  N  -7.420   0.778  14.204   -5.900   2.211  -0.881  H7   NEF  40  
NEF  H8   H8   H   0  1  N  N  N  -8.485  -0.185  15.284   -6.089   2.112   0.886  H8   NEF  41  
NEF  H9   H9   H   0  1  N  N  N  -4.051  -3.081  13.468  -10.925   0.392  -1.456  H9   NEF  42  
NEF  H10  H10  H   0  1  N  N  N  -4.629   2.862  18.920   -1.806  -0.075  -1.329  H10  NEF  43  
NEF  H12  H12  H   0  1  N  N  N  -0.650  -0.118  12.923    4.763  -1.790  -0.524  H12  NEF  44  
NEF  H14  H14  H   0  1  N  N  N  -5.670   2.041  15.205   -3.616   1.282   0.206  H14  NEF  45  
NEF  H15  H15  H   0  1  N  N  N  -6.597  -2.136  16.850   -8.232   0.997   1.803  H15  NEF  46  
NEF  H16  H16  H   0  1  N  N  N  -4.850  -3.700  15.840  -10.593   0.402   1.060  H16  NEF  47  
NEF  H19  H19  H   0  1  N  N  N  -0.322   4.928  16.617    2.016  -4.412   0.167  H19  NEF  48  
NEF  H20  H20  H   0  1  N  N  N  -0.673  -0.094  16.637    2.921   1.458   0.018  H20  NEF  49  
NEF  H22  H22  H   0  1  N  N  N   0.950  -1.333  11.516    7.209  -2.023  -0.619  H22  NEF  50  
NEF  H23  H23  H   0  1  N  N  N   2.884  -2.817  15.016    7.659   2.159   0.102  H23  NEF  51  
NEF  OXY  OXY  O   0  1  N  Y  N       ?       ?       ?   -2.499  -2.489   1.785  OXY  NEF  52  
NEF  HXY  HXY  H   0  1  N  Y  N       ?       ?       ?   -2.511  -2.812   2.696  HXY  NEF  53  
NEF  H4   H4   H   0  1  N  N  N  -2.639   3.264  18.164   -1.372  -2.542  -0.172  H4   NEF  54  
#   #
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
NEF  O26  N23  SING  N  N   1  
NEF  N23  O27  DOUB  N  N   2  
NEF  N23  C19  SING  N  N   3  
NEF  C18  C19  DOUB  Y  N   4  
NEF  C18  C17  SING  Y  N   5  
NEF  C19  C20  SING  Y  N   6  
NEF  C17  C14  DOUB  Y  N   7  
NEF  S12  C11  SING  Y  N   8  
NEF  S12  C8   SING  Y  N   9  
NEF  C11  C10  DOUB  Y  N  10  
NEF  C20  C21  DOUB  Y  N  11  
NEF  C14  C21  SING  Y  N  12  
NEF  C14  C12  SING  N  N  13  
NEF  C8   C7   SING  N  N  14  
NEF  C8   C9   DOUB  Y  N  15  
NEF  C6   C12  DOUB  N  E  16  
NEF  C6   C4   SING  N  N  17  
NEF  C7   C5   SING  N  N  18  
NEF  O17  C16  DOUB  N  N  19  
NEF  C10  C9   SING  Y  N  20  
NEF  C21  N22  SING  N  N  21  
NEF  O2   C1   DOUB  N  N  22  
NEF  C4   C15  DOUB  N  N  23  
NEF  C4   C2   SING  N  N  24  
NEF  C16  C15  SING  N  N  25  
NEF  C16  O18  SING  N  N  26  
NEF  N4   C5   SING  N  N  27  
NEF  N4   C3   SING  N  N  28  
NEF  C15  N14  SING  N  N  29  
NEF  C5   O6   DOUB  N  N  30  
NEF  C1   C3   SING  N  N  31  
NEF  C2   S19  SING  N  N  32  
NEF  N22  O25  DOUB  N  N  33  
NEF  N22  O24  SING  N  N  34  
NEF  C3   C13  SING  N  N  35  
NEF  N14  C13  SING  N  N  36  
NEF  C13  S19  SING  N  N  37  
NEF  C2   H1   SING  N  N  38  
NEF  C2   H2   SING  N  N  39  
NEF  C3   H3   SING  N  N  40  
NEF  C6   H5   SING  N  N  41  
NEF  C7   H7   SING  N  N  42  
NEF  C7   H8   SING  N  N  43  
NEF  C11  H9   SING  N  N  44  
NEF  C13  H10  SING  N  N  45  
NEF  C17  H12  SING  N  N  46  
NEF  N4   H14  SING  N  N  47  
NEF  C9   H15  SING  N  N  48  
NEF  C10  H16  SING  N  N  49  
NEF  O18  H19  SING  N  N  50  
NEF  C12  H20  SING  N  N  51  
NEF  C18  H22  SING  N  N  52  
NEF  C20  H23  SING  N  N  53  
NEF  C1   OXY  SING  N  N  54  
NEF  OXY  HXY  SING  N  N  55  
NEF  N14  H4   SING  N  N  56  
#   #
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
NEF  InChI             InChI                 1.03   "InChI=1S/C21H18N4O9S2/c26-16(9-14-2-1-7-35-14)22-18(21(29)30)19-23-17(20(27)28)12(10-36-19)4-3-11-5-6-13(24(31)32)8-15(11)25(33)34/h1-8,18-19,23H,9-10H2,(H,22,26)(H,27,28)(H,29,30)/b4-3+/t18-,19+/m0/s1"  
NEF  InChIKey          InChI                 1.03   PYBZXZZHQKFSGC-CZHQAMEJSA-N  
NEF  SMILES_CANONICAL  CACTVS                3.385  "OC(=O)[C@@H](NC(=O)Cc1sccc1)[C@@H]2NC(=C(CS2)\C=C\c3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O"  
NEF  SMILES            CACTVS                3.385  "OC(=O)[CH](NC(=O)Cc1sccc1)[CH]2NC(=C(CS2)C=Cc3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O"  
NEF  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(sc1)CC(=O)N[C@@H]([C@@H]2NC(=C(CS2)/C=C/c3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O"  
NEF  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(sc1)CC(=O)NC(C2NC(=C(CS2)C=Cc3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O"  
#
_pdbx_chem_comp_identifier.comp_id          NEF
_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})-5-[(~{E})-2-(2,4-dinitrophenyl)ethenyl]-2-[(1~{R})-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2~{H}-1,3-thiazine-4-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
NEF  "Create component"          2018-09-26  EBI   
NEF  "Other modification"        2018-09-27  EBI   
NEF  "Initial release"           2019-10-23  RCSB  
NEF  "Modify leaving atom flag"  2021-08-24  PDBE  
NEF  "Modify aromatic_flag"      2021-09-06  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     NEF
_pdbx_chem_comp_synonyms.name        "(2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
