data_8Y9
#

_chem_comp.id                                   8Y9
_chem_comp.name                                 
;[(2~{R},3~{S},5~{R})-5-[(5~{S})-5-carbamimidamido-2,4-bis(oxidanylidene)imidazolidin-1-yl]-3-oxidanyl-oxolan-2-yl]methy
l dihydrogen phosphate
;

_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H16 N5 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(S)-Gh"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-11-07
_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                       353.226
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    8Y9
_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       5YMG
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
8Y9  P      P1   P  0  1  N  N  N  -78.493  302.362  104.730  -4.769  -0.388   0.653  P      8Y9   1  
8Y9  C2     C1   C  0  1  N  N  N  -75.425  304.640  108.757   4.421   1.180   1.343  C2     8Y9   2  
8Y9  N3     N1   N  0  1  N  N  N  -75.316  305.642  107.870   4.092   0.357   0.292  N3     8Y9   3  
8Y9  C4     C2   C  0  1  N  N  S  -74.064  306.229  107.493   3.133  -0.733   0.488  C4     8Y9   4  
8Y9  C5     C3   C  0  1  N  N  N  -73.981  307.479  108.246   3.634  -2.007  -0.162  C5     8Y9   5  
8Y9  O5     O1   O  0  1  N  N  N  -74.038  307.404  109.529   4.646  -2.617   0.107  O5     8Y9   6  
8Y9  N7     N2   N  0  1  N  N  N  -73.862  308.679  107.647   2.718  -2.322  -1.100  N7     8Y9   7  
8Y9  C8     C4   C  0  1  N  N  N  -73.860  308.276  106.359   1.719  -1.432  -1.133  C8     8Y9   8  
8Y9  O8     O2   O  0  1  N  N  N  -73.742  309.060  105.334   0.776  -1.504  -1.896  O8     8Y9   9  
8Y9  N9     N3   N  0  1  N  N  N  -73.982  306.945  106.241   1.876  -0.451  -0.227  N9     8Y9  10  
8Y9  "C1'"  C5   C  0  1  N  N  R  -74.028  306.166  104.998   0.972   0.679   0.005  "C1'"  8Y9  11  
8Y9  N11    N4   N  0  1  N  N  N  -74.365  304.033  109.325   5.239   2.266   1.136  N11    8Y9  12  
8Y9  N12    N5   N  0  1  N  N  N  -76.606  304.245  109.018   3.957   0.932   2.535  N12    8Y9  13  
8Y9  "C2'"  C6   C  0  1  N  N  N  -73.497  304.749  104.957   0.934   1.584  -1.242  "C2'"  8Y9  14  
8Y9  "C3'"  C7   C  0  1  N  N  S  -74.357  304.230  103.813  -0.557   1.598  -1.656  "C3'"  8Y9  15  
8Y9  "O3'"  O3   O  0  1  N  N  N  -73.885  304.784  102.554  -0.965   2.908  -2.056  "O3'"  8Y9  16  
8Y9  "C4'"  C8   C  0  1  N  N  R  -75.712  304.792  104.145  -1.263   1.177  -0.342  "C4'"  8Y9  17  
8Y9  "O4'"  O4   O  0  1  N  N  N  -75.410  306.092  104.650  -0.364   0.198   0.228  "O4'"  8Y9  18  
8Y9  "C5'"  C9   C  0  1  N  N  N  -76.469  303.995  105.203  -2.626   0.548  -0.640  "C5'"  8Y9  19  
8Y9  "O5'"  O5   O  0  1  N  N  N  -76.915  302.783  104.625  -3.304   0.276   0.588  "O5'"  8Y9  20  
8Y9  OP2    O6   O  0  1  N  N  N  -78.626  300.943  104.232  -5.274  -0.427   2.181  OP2    8Y9  21  
8Y9  OP1    O7   O  0  1  N  N  N  -79.343  303.391  104.054  -5.711   0.416  -0.158  OP1    8Y9  22  
8Y9  O1     O8   O  0  1  N  Y  N  -78.823  302.406  106.305  -4.705  -1.887   0.070  O1     8Y9  23  
8Y9  H1     H1   H  0  1  N  N  N  -76.152  305.997  107.451   4.496   0.497  -0.579  H1     8Y9  24  
8Y9  H2     H2   H  0  1  N  N  N  -73.203  305.567  107.669   2.946  -0.891   1.550  H2     8Y9  25  
8Y9  H3     H3   H  0  1  N  N  N  -73.795  309.596  108.040   2.777  -3.097  -1.680  H3     8Y9  26  
8Y9  H4     H4   H  0  1  N  N  N  -73.502  306.738  104.219   1.308   1.252   0.869  H4     8Y9  27  
8Y9  H5     H5   H  0  1  N  N  N  -74.505  303.269  109.955   5.413   2.887   1.860  H5     8Y9  28  
8Y9  H6     H6   H  0  1  N  N  N  -73.439  304.347  109.117   5.643   2.410   0.266  H6     8Y9  29  
8Y9  H7     H7   H  0  1  N  N  N  -76.611  303.477  109.658   4.189   1.513   3.277  H7     8Y9  30  
8Y9  H8     H8   H  0  1  N  N  N  -73.683  304.208  105.896   1.270   2.591  -0.993  H8     8Y9  31  
8Y9  H9     H9   H  0  1  N  N  N  -72.423  304.714  104.720   1.549   1.164  -2.037  H9     8Y9  32  
8Y9  H10    H10  H  0  1  N  N  N  -74.373  303.130  103.800  -0.746   0.874  -2.448  H10    8Y9  33  
8Y9  H11    H11  H  0  1  N  N  N  -73.029  304.425  102.351  -0.550   3.216  -2.874  H11    8Y9  34  
8Y9  H12    H12  H  0  1  N  N  N  -76.321  304.858  103.231  -1.371   2.031   0.327  H12    8Y9  35  
8Y9  H13    H13  H  0  1  N  N  N  -75.802  303.778  106.050  -3.221   1.238  -1.238  H13    8Y9  36  
8Y9  H14    H14  H  0  1  N  N  N  -77.333  304.577  105.557  -2.485  -0.382  -1.191  H14    8Y9  37  
8Y9  H15    H15  H  0  1  N  N  N  -79.262  300.913  103.527  -6.152  -0.816   2.295  H15    8Y9  38  
8Y9  H16    H16  H  0  1  N  N  N  -79.482  303.070  106.473  -4.105  -2.472   0.553  H16    8Y9  39  
#   #
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
8Y9  "O3'"  "C3'"  SING  N  N   1  
8Y9  "C3'"  "C4'"  SING  N  N   2  
8Y9  "C3'"  "C2'"  SING  N  N   3  
8Y9  OP1    P      DOUB  N  N   4  
8Y9  "C4'"  "O4'"  SING  N  N   5  
8Y9  "C4'"  "C5'"  SING  N  N   6  
8Y9  OP2    P      SING  N  N   7  
8Y9  "O5'"  P      SING  N  N   8  
8Y9  "O5'"  "C5'"  SING  N  N   9  
8Y9  "O4'"  "C1'"  SING  N  N  10  
8Y9  "C2'"  "C1'"  SING  N  N  11  
8Y9  "C1'"  N9     SING  N  N  12  
8Y9  O8     C8     DOUB  N  N  13  
8Y9  N9     C8     SING  N  N  14  
8Y9  N9     C4     SING  N  N  15  
8Y9  C8     N7     SING  N  N  16  
8Y9  C4     N3     SING  N  N  17  
8Y9  C4     C5     SING  N  N  18  
8Y9  N7     C5     SING  N  N  19  
8Y9  N3     C2     SING  N  N  20  
8Y9  C5     O5     DOUB  N  N  21  
8Y9  C2     N12    DOUB  N  N  22  
8Y9  C2     N11    SING  N  N  23  
8Y9  P      O1     SING  N  N  24  
8Y9  N3     H1     SING  N  N  25  
8Y9  C4     H2     SING  N  N  26  
8Y9  N7     H3     SING  N  N  27  
8Y9  "C1'"  H4     SING  N  N  28  
8Y9  N11    H5     SING  N  N  29  
8Y9  N11    H6     SING  N  N  30  
8Y9  N12    H7     SING  N  N  31  
8Y9  "C2'"  H8     SING  N  N  32  
8Y9  "C2'"  H9     SING  N  N  33  
8Y9  "C3'"  H10    SING  N  N  34  
8Y9  "O3'"  H11    SING  N  N  35  
8Y9  "C4'"  H12    SING  N  N  36  
8Y9  "C5'"  H13    SING  N  N  37  
8Y9  "C5'"  H14    SING  N  N  38  
8Y9  OP2    H15    SING  N  N  39  
8Y9  O1     H16    SING  N  N  40  
#   #
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
8Y9  InChI             InChI                 1.03   "InChI=1S/C9H16N5O8P/c10-8(11)12-6-7(16)13-9(17)14(6)5-1-3(15)4(22-5)2-21-23(18,19)20/h3-6,15H,1-2H2,(H4,10,11,12)(H,13,16,17)(H2,18,19,20)/t3-,4+,5+,6-/m0/s1"  
8Y9  InChIKey          InChI                 1.03   IMJMAQUBWVPHQG-KCDKBNATSA-N  
8Y9  SMILES_CANONICAL  CACTVS                3.385  "NC(=N)N[C@H]1N([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
8Y9  SMILES            CACTVS                3.385  "NC(=N)N[CH]1N([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
8Y9  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "[H]/N=C(/N)\N[C@@H]1C(=O)NC(=O)N1[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
8Y9  SMILES            "OpenEye OEToolkits"  2.0.6  "C1C(C(OC1N2C(C(=O)NC2=O)NC(=N)N)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          8Y9
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},5~{R})-5-[(5~{S})-5-carbamimidamido-2,4-bis(oxidanylidene)imidazolidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     8Y9
_pdbx_chem_comp_synonyms.name        "(S)-Gh"
_pdbx_chem_comp_synonyms.provenance  ?
_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
8Y9  "Create component"     2017-11-07  RCSB  
8Y9  "Modify linking type"  2017-11-07  PDBJ  
8Y9  "Modify synonyms"      2020-06-05  PDBE  
8Y9  "Initial release"      2021-06-09  RCSB  
##
