data_EW3
#

_chem_comp.id                                   EW3
_chem_comp.name                                 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H14 F N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-02-10
_chem_comp.pdbx_modified_date                   2021-06-04
_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                       328.188
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    EW3
_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       6LWP
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
EW3  F2     F1   F  0  1  N  N  N  -3.827  -14.211  32.509   1.845  -3.271  -0.201  F2     EW3   1  
EW3  "C2'"  C1   C  0  1  N  N  R  -3.871  -15.555  32.432   1.276  -2.114   0.342  "C2'"  EW3   2  
EW3  "C3'"  C2   C  0  1  N  N  R  -5.092  -16.042  31.676  -0.235  -2.319   0.590  "C3'"  EW3   3  
EW3  "O3'"  O1   O  0  1  N  N  N  -6.266  -15.274  32.006  -0.634  -3.634   0.195  "O3'"  EW3   4  
EW3  "C1'"  C3   C  0  1  N  N  R  -4.080  -16.180  33.811   1.336  -0.952  -0.674  "C1'"  EW3   5  
EW3  "O4'"  O2   O  0  1  N  N  N  -4.803  -17.417  33.576   0.095  -0.236  -0.489  "O4'"  EW3   6  
EW3  "C4'"  C4   C  0  1  N  N  R  -5.249  -17.450  32.224  -0.910  -1.257  -0.306  "C4'"  EW3   7  
EW3  "C5'"  C5   C  0  1  N  N  N  -4.388  -18.488  31.528  -2.140  -0.674   0.392  "C5'"  EW3   8  
EW3  "O5'"  O3   O  0  1  N  N  N  -4.650  -18.507  30.131  -2.815   0.218  -0.497  "O5'"  EW3   9  
EW3  P      P1   P  0  1  N  N  N  -4.011  -19.728  29.351  -4.155   1.013  -0.091  P      EW3  10  
EW3  OP2    O4   O  0  1  N  N  N  -4.403  -21.069  29.928  -4.708   1.819  -1.371  OP2    EW3  11  
EW3  OP1    O5   O  0  1  N  N  N  -4.319  -19.459  27.870  -5.181   0.050   0.366  OP1    EW3  12  
EW3  N1     N1   N  0  1  N  N  N  -2.867  -16.442  34.624   2.476  -0.080  -0.385  N1     EW3  13  
EW3  C2     C6   C  0  1  N  N  N  -2.910  -16.224  35.941   2.504   0.615   0.764  C2     EW3  14  
EW3  O2     O6   O  0  1  N  N  N  -3.440  -15.247  36.432   1.633   0.428   1.591  O2     EW3  15  
EW3  N3     N2   N  0  1  N  N  N  -2.381  -17.189  36.717   3.471   1.511   1.022  N3     EW3  16  
EW3  C4     C7   C  0  1  N  N  N  -1.814  -18.305  36.226   4.310   1.923   0.053  C4     EW3  17  
EW3  O4     O7   O  0  1  N  N  N  -1.344  -19.161  36.954   5.226   2.669   0.322  O4     EW3  18  
EW3  C5     C8   C  0  1  N  N  N  -1.748  -18.499  34.719   4.109   1.455  -1.366  C5     EW3  19  
EW3  C6     C9   C  0  1  N  N  N  -1.731  -17.126  34.019   3.573   0.018  -1.350  C6     EW3  20  
EW3  O1     O8   O  0  1  N  Y  N  -2.432  -19.545  29.643  -3.825   2.051   1.095  O1     EW3  21  
EW3  H1     H1   H  0  1  N  N  N  -2.963  -15.974  31.974   1.783  -1.839   1.267  H1     EW3  22  
EW3  H2     H2   H  0  1  N  N  N  -4.902  -16.062  30.593  -0.478  -2.147   1.638  H2     EW3  23  
EW3  H3     H3   H  0  1  N  N  N  -6.174  -14.392  31.666  -0.239  -4.340   0.725  H3     EW3  24  
EW3  H4     H4   H  0  1  N  N  N  -4.731  -15.503  34.383   1.404  -1.341  -1.690  H4     EW3  25  
EW3  H5     H5   H  0  1  N  N  N  -6.306  -17.751  32.167  -1.188  -1.692  -1.266  H5     EW3  26  
EW3  H6     H6   H  0  1  N  N  N  -4.608  -19.480  31.950  -2.814  -1.483   0.676  H6     EW3  27  
EW3  H7     H7   H  0  1  N  N  N  -3.328  -18.246  31.693  -1.828  -0.131   1.285  H7     EW3  28  
EW3  H8     H8   H  0  1  N  N  N  -4.813  -21.597  29.253  -5.516   2.323  -1.199  H8     EW3  29  
EW3  H9     H9   H  0  1  N  N  N  -2.411  -17.070  37.709   3.567   1.866   1.919  H9     EW3  30  
EW3  H10    H10  H  0  1  N  N  N  -2.627  -19.069  34.385   3.394   2.107  -1.867  H10    EW3  31  
EW3  H11    H11  H  0  1  N  N  N  -0.833  -19.052  34.461   5.061   1.482  -1.897  H11    EW3  32  
EW3  H12    H12  H  0  1  N  N  N  -1.866  -17.233  32.933   4.371  -0.668  -1.063  H12    EW3  33  
EW3  H13    H13  H  0  1  N  N  N  -0.792  -16.590  34.221   3.208  -0.245  -2.343  H13    EW3  34  
EW3  H14    H14  H  0  1  N  N  N  -1.987  -19.304  28.839  -3.159   2.713   0.864  H14    EW3  35  
#   #
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
EW3  OP1    P      DOUB  N  N   1  
EW3  P      OP2    SING  N  N   2  
EW3  P      "O5'"  SING  N  N   3  
EW3  "O5'"  "C5'"  SING  N  N   4  
EW3  "C5'"  "C4'"  SING  N  N   5  
EW3  "C3'"  "O3'"  SING  N  N   6  
EW3  "C3'"  "C4'"  SING  N  N   7  
EW3  "C3'"  "C2'"  SING  N  N   8  
EW3  "C4'"  "O4'"  SING  N  N   9  
EW3  "C2'"  F2     SING  N  N  10  
EW3  "C2'"  "C1'"  SING  N  N  11  
EW3  "O4'"  "C1'"  SING  N  N  12  
EW3  "C1'"  N1     SING  N  N  13  
EW3  C6     N1     SING  N  N  14  
EW3  C6     C5     SING  N  N  15  
EW3  N1     C2     SING  N  N  16  
EW3  C5     C4     SING  N  N  17  
EW3  C2     O2     DOUB  N  N  18  
EW3  C2     N3     SING  N  N  19  
EW3  C4     N3     SING  N  N  20  
EW3  C4     O4     DOUB  N  N  21  
EW3  P      O1     SING  N  N  22  
EW3  "C2'"  H1     SING  N  N  23  
EW3  "C3'"  H2     SING  N  N  24  
EW3  "O3'"  H3     SING  N  N  25  
EW3  "C1'"  H4     SING  N  N  26  
EW3  "C4'"  H5     SING  N  N  27  
EW3  "C5'"  H6     SING  N  N  28  
EW3  "C5'"  H7     SING  N  N  29  
EW3  OP2    H8     SING  N  N  30  
EW3  N3     H9     SING  N  N  31  
EW3  C5     H10    SING  N  N  32  
EW3  C5     H11    SING  N  N  33  
EW3  C6     H12    SING  N  N  34  
EW3  C6     H13    SING  N  N  35  
EW3  O1     H14    SING  N  N  36  
#   #
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
EW3  InChI             InChI                 1.03   "InChI=1S/C9H14FN2O8P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)12-2-1-5(13)11-9(12)15/h4,6-8,14H,1-3H2,(H,11,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1"  
EW3  InChIKey          InChI                 1.03   QEKJBDVYKHPUGN-XVFCMESISA-N  
EW3  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O"  
EW3  SMILES            CACTVS                3.385  "O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O"  
EW3  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F"  
EW3  SMILES            "OpenEye OEToolkits"  2.0.7  "C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)F"  
#
_pdbx_chem_comp_identifier.comp_id          EW3
_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},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EW3  "Create component"  2020-02-10  PDBJ  
EW3  "Initial release"   2021-06-09  RCSB  
##
