data_X6H
# 
_chem_comp.id                                    X6H 
_chem_comp.name                                  "(4aM,9M)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,5-dihydropyrimido[1,2-a]purine-6,10-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H14 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-10-31 
_chem_comp.pdbx_modified_date                    2023-07-28 
_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                        399.253 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X6H 
_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        8EVF 
_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 
X6H "C1'"  C1  C 0 1 N N R 60.059 6.323  -1.473 -0.348 0.762  0.058  "C1'"  X6H 1  
X6H C2     C2  C 0 1 N N N 57.110 3.778  -2.779 4.104  0.392  0.419  C2     X6H 2  
X6H "C2'"  C3  C 0 1 N N N 61.209 6.997  -0.750 -0.435 1.788  -1.089 "C2'"  X6H 3  
X6H "C3'"  C4  C 0 1 N N S 60.708 8.432  -0.762 -1.932 1.788  -1.484 "C3'"  X6H 4  
X6H C4     C5  C 0 1 Y N N 59.334 4.457  -2.736 1.953  -0.270 -0.122 C4     X6H 5  
X6H "C4'"  C6  C 0 1 N N R 59.956 8.597  -2.056 -2.604 1.210  -0.212 "C4'"  X6H 6  
X6H C5     C7  C 0 1 Y N N 59.740 3.463  -3.586 2.433  -1.496 -0.601 C5     X6H 7  
X6H "C5'"  C8  C 0 1 N N N 60.894 9.065  -3.154 -3.949 0.568  -0.558 "C5'"  X6H 8  
X6H C6     C9  C 0 1 N N N 58.691 2.537  -4.080 3.824  -1.739 -0.556 C6     X6H 9  
X6H C6A    C10 C 0 1 N N N 54.828 3.267  -2.703 6.264  1.148  1.002  C6A    X6H 10 
X6H C7A    C11 C 0 1 N N N 55.096 2.232  -3.596 6.805  -0.075 0.532  C7A    X6H 11 
X6H C8     C12 C 0 1 Y N N 61.456 4.708  -2.978 0.281  -1.505 -0.857 C8     X6H 12 
X6H C8A    C13 C 0 1 N N N 56.390 1.939  -4.050 5.985  -1.011 0.020  C8A    X6H 13 
X6H N1     N1  N 0 1 N N N 57.413 2.741  -3.649 4.630  -0.784 -0.039 N1     X6H 14 
X6H N2     N2  N 0 1 N N N 55.863 4.037  -2.324 4.935  1.358  0.938  N2     X6H 15 
X6H N3     N3  N 0 1 N N N 58.061 4.599  -2.346 2.809  0.629  0.371  N3     X6H 16 
X6H N7     N4  N 0 1 Y N N 61.077 3.627  -3.731 1.363  -2.205 -1.036 N7     X6H 17 
X6H N9     N5  N 0 1 Y N N 60.361 5.187  -2.371 0.595  -0.302 -0.295 N9     X6H 18 
X6H "O3'"  O1  O 0 1 N N N 59.700 8.639  0.228  -2.390 3.117  -1.743 "O3'"  X6H 19 
X6H "O4'"  O2  O 0 1 N N N 59.446 7.297  -2.339 -1.663 0.212  0.241  "O4'"  X6H 20 
X6H "O5'"  O3  O 0 1 N N N 62.103 8.317  -3.088 -4.599 0.148  0.643  "O5'"  X6H 21 
X6H O6     O4  O 0 1 N N N 58.973 1.612  -4.869 4.286  -2.789 -0.966 O6     X6H 22 
X6H O6A    O5  O 0 1 N N N 53.663 3.508  -2.276 6.997  2.005  1.462  O6A    X6H 23 
X6H OP3    O6  O 0 1 N Y N 63.861 10.151 -3.253 -7.157 0.459  0.118  OP3    X6H 24 
X6H OP1    O7  O 0 1 N N N 64.529 7.821  -3.792 -6.005 -1.761 -0.223 OP1    X6H 25 
X6H P      P1  P 0 1 N N N 63.415 8.837  -3.843 -6.040 -0.570 0.655  P      X6H 26 
X6H OP2    O8  O 0 1 N N N 62.904 9.084  -5.336 -6.403 -1.020 2.157  OP2    X6H 27 
X6H "H1'"  H1  H 0 1 N N N 59.326 5.994  -0.722 -0.022 1.257  0.974  "H1'"  X6H 28 
X6H "H2'"  H2  H 0 1 N N N 61.331 6.614  0.274  -0.132 2.775  -0.741 "H2'"  X6H 29 
X6H "H2''" H3  H 0 0 N N N 62.157 6.889  -1.297 0.183  1.473  -1.929 "H2''" X6H 30 
X6H "H3'"  H4  H 0 1 N N N 61.539 9.148  -0.682 -2.107 1.143  -2.345 "H3'"  X6H 31 
X6H "H4'"  H5  H 0 1 N N N 59.141 9.324  -1.927 -2.733 1.987  0.541  "H4'"  X6H 32 
X6H "H5'"  H6  H 0 1 N N N 61.115 10.134 -3.018 -4.576 1.295  -1.075 "H5'"  X6H 33 
X6H "H5''" H7  H 0 0 N N N 60.419 8.911  -4.134 -3.785 -0.294 -1.204 "H5''" X6H 34 
X6H H1     H8  H 0 1 N N N 54.273 1.630  -3.953 7.870  -0.252 0.579  H1     X6H 35 
X6H H8     H9  H 0 1 N N N 62.457 5.103  -2.890 -0.717 -1.827 -1.116 H8     X6H 36 
X6H H10    H10 H 0 1 N N N 56.570 1.097  -4.702 6.392  -1.942 -0.345 H10    X6H 37 
X6H H21    H11 H 0 1 N N N 55.710 4.805  -1.702 4.562  2.194  1.259  H21    X6H 38 
X6H "HO3'" H12 H 0 0 N Y N 60.083 8.554  1.093  -1.934 3.555  -2.475 "HO3'" X6H 39 
X6H HOP3   H13 H 0 0 N Y N 64.763 10.079 -2.963 -7.235 1.265  0.647  HOP3   X6H 40 
X6H HOP2   H14 H 0 0 N N N 63.400 8.539  -5.935 -7.260 -1.461 2.240  HOP2   X6H 41 
# 
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 
X6H O6    C6     DOUB N N 1  
X6H C6    N1     SING N N 2  
X6H C6    C5     SING N N 3  
X6H C8A   N1     SING N N 4  
X6H C8A   C7A    DOUB N N 5  
X6H P     OP1    DOUB N N 6  
X6H P     OP3    SING N N 7  
X6H P     "O5'"  SING N N 8  
X6H N7    C5     SING Y N 9  
X6H N7    C8     DOUB Y N 10 
X6H N1    C2     SING N N 11 
X6H C7A   C6A    SING N N 12 
X6H C5    C4     DOUB Y N 13 
X6H "C5'" "O5'"  SING N N 14 
X6H "C5'" "C4'"  SING N N 15 
X6H C8    N9     SING Y N 16 
X6H C2    N3     DOUB N N 17 
X6H C2    N2     SING N N 18 
X6H C4    N9     SING Y N 19 
X6H C4    N3     SING N N 20 
X6H C6A   N2     SING N N 21 
X6H C6A   O6A    DOUB N N 22 
X6H N9    "C1'"  SING N N 23 
X6H "O4'" "C4'"  SING N N 24 
X6H "O4'" "C1'"  SING N N 25 
X6H "C4'" "C3'"  SING N N 26 
X6H "C1'" "C2'"  SING N N 27 
X6H "C3'" "C2'"  SING N N 28 
X6H "C3'" "O3'"  SING N N 29 
X6H P     OP2    SING N N 30 
X6H "C1'" "H1'"  SING N N 31 
X6H "C2'" "H2'"  SING N N 32 
X6H "C2'" "H2''" SING N N 33 
X6H "C3'" "H3'"  SING N N 34 
X6H "C4'" "H4'"  SING N N 35 
X6H "C5'" "H5'"  SING N N 36 
X6H "C5'" "H5''" SING N N 37 
X6H C7A   H1     SING N N 38 
X6H C8    H8     SING N N 39 
X6H C8A   H10    SING N N 40 
X6H N2    H21    SING N N 41 
X6H "O3'" "HO3'" SING N N 42 
X6H OP3   HOP3   SING N N 43 
X6H OP2   HOP2   SING N N 44 
# 
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 
X6H SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(CC1O)n1cnc2c1N=C1NC(=O)C=CN1C2=O"                                                                                                                        
X6H InChI            InChI                1.06  "InChI=1S/C13H14N5O8P/c19-6-3-9(26-7(6)4-25-27(22,23)24)18-5-14-10-11(18)16-13-15-8(20)1-2-17(13)12(10)21/h1-2,5-7,9,19H,3-4H2,(H,15,16,20)(H2,22,23,24)/t6-,7+,9+/m0/s1" 
X6H InChIKey         InChI                1.06  NJGWJRXLEBYAKE-LKEWCRSYSA-N                                                                                                                                               
X6H SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC(=O)NC4=Nc23"                                                                                                      
X6H SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC(=O)NC4=Nc23"                                                                                                           
X6H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C4NC(=O)C=CN4C2=O"                                                                                                       
X6H SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4NC(=O)C=CN4C2=O"                                                                                                                    
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
X6H "SYSTEMATIC NAME" ACDLabs              12.01 "(4aM,9M)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,5-dihydropyrimido[1,2-a]purine-6,10-dione"                        
X6H "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[6,10-bis(oxidanylidene)-5~{H}-pyrimido[1,2-a]purin-3-yl]-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 
X6H "Create component" 2022-10-31 RCSB 
X6H "Initial release"  2023-08-02 RCSB 
# 
