data_9O4
# 
_chem_comp.id                                    9O4 
_chem_comp.name                                  "(3R,5R)-5-(6-amino-9H-purin-9-yl)oxolan-3-yl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H12 N5 O5 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-05-19 
_chem_comp.pdbx_modified_date                    2017-12-01 
_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                        301.196 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     9O4 
_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        5VU7 
_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 
9O4 C2    C1  C 0 1 Y N N 16.560 15.496 305.785 4.013  -1.876 -1.061 C2    9O4 1  
9O4 C4    C2  C 0 1 Y N N 14.396 14.670 306.401 2.659  -0.145 -0.392 C4    9O4 2  
9O4 C5    C3  C 0 1 Y N N 14.258 16.156 306.686 3.667  0.291  0.485  C5    9O4 3  
9O4 C6    C4  C 0 1 Y N N 15.074 16.974 306.534 4.866  -0.440 0.532  C6    9O4 4  
9O4 "C1'" C5  C 0 1 N N R 12.714 12.857 306.692 0.335  0.693  -0.944 "C1'" 9O4 5  
9O4 "C2'" C6  C 0 1 N N N 11.599 12.577 307.601 -0.654 -0.259 -0.225 "C2'" 9O4 6  
9O4 "C3'" C7  C 0 1 N N R 10.431 12.431 306.782 -2.026 0.297  -0.677 "C3'" 9O4 7  
9O4 "C4'" C8  C 0 1 N N N 10.849 12.220 305.328 -1.722 1.742  -1.116 "C4'" 9O4 8  
9O4 C8    C9  C 0 1 Y N N 12.339 15.140 307.187 1.995  1.656  0.695  C8    9O4 9  
9O4 N1    N1  N 0 1 Y N N 16.101 16.700 306.134 4.990  -1.506 -0.253 N1    9O4 10 
9O4 N3    N2  N 0 1 Y N N 15.719 14.213 305.870 2.874  -1.223 -1.139 N3    9O4 11 
9O4 N6    N3  N 0 1 N N N 14.784 18.370 306.856 5.895  -0.060 1.376  N6    9O4 12 
9O4 N7    N4  N 0 1 Y N N 12.898 16.219 307.166 3.198  1.393  1.117  N7    9O4 13 
9O4 N9    N5  N 0 1 Y N N 13.101 14.246 306.782 1.617  0.735  -0.237 N9    9O4 14 
9O4 O1P   O1  O 0 1 N N N 7.489  14.851 306.866 -5.298 0.075  -0.758 O1P   9O4 15 
9O4 O2P   O2  O 0 1 N N N 7.511  12.518 306.237 -4.056 -1.957 0.078  O2P   9O4 16 
9O4 "O3'" O3  O 0 1 N N N 9.679  13.639 306.885 -2.952 0.289  0.411  "O3'" 9O4 17 
9O4 "O4'" O4  O 0 1 N N N 12.332 12.551 305.295 -0.324 1.976  -0.878 "O4'" 9O4 18 
9O4 P     P1  P 0 1 N N N 8.257  13.795 306.171 -4.335 -0.535 0.379  P     9O4 19 
9O4 O3P   O5  O 0 1 N Y N 8.478  14.103 304.617 -5.060 -0.423 1.813  O3P   9O4 20 
9O4 H1    H1  H 0 1 N N N 17.575 15.420 305.424 4.157  -2.746 -1.686 H1    9O4 21 
9O4 H2    H2  H 0 1 N N N 13.569 12.224 306.971 0.479  0.386  -1.980 H2    9O4 22 
9O4 H3    H3  H 0 1 N N N 11.789 11.649 308.160 -0.520 -1.286 -0.563 H3    9O4 23 
9O4 H4    H4  H 0 1 N N N 11.466 13.410 308.307 -0.543 -0.190 0.857  H4    9O4 24 
9O4 H5    H5  H 0 1 N N N 9.831  11.571 307.115 -2.416 -0.284 -1.513 H5    9O4 25 
9O4 H6    H6  H 0 1 N N N 10.288 12.892 304.663 -1.943 1.862  -2.177 H6    9O4 26 
9O4 H7    H7  H 0 1 N N N 10.679 11.177 305.024 -2.322 2.441  -0.533 H7    9O4 27 
9O4 H8    H8  H 0 1 N N N 11.322 14.980 307.512 1.386  2.481  1.033  H8    9O4 28 
9O4 H9    H9  H 0 1 N N N 15.590 18.931 306.665 5.793  0.720  1.944  H9    9O4 29 
9O4 H10   H10 H 0 1 N N N 14.017 18.688 306.299 6.718  -0.573 1.399  H10   9O4 30 
9O4 H11   H11 H 0 1 N N N 6.681  14.484 307.206 -5.523 1.006  -0.625 H11   9O4 31 
9O4 H12   H12 H 0 1 N N N 8.088  13.410 304.098 -5.901 -0.896 1.866  H12   9O4 32 
# 
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 
9O4 "O4'" "C4'" SING N N 1  
9O4 "O4'" "C1'" SING N N 2  
9O4 "C4'" "C3'" SING N N 3  
9O4 C2    N3    DOUB Y N 4  
9O4 C2    N1    SING Y N 5  
9O4 N3    C4    SING Y N 6  
9O4 N1    C6    DOUB Y N 7  
9O4 P     O2P   DOUB N N 8  
9O4 P     O1P   SING N N 9  
9O4 P     "O3'" SING N N 10 
9O4 C4    C5    DOUB Y N 11 
9O4 C4    N9    SING Y N 12 
9O4 C6    C5    SING Y N 13 
9O4 C6    N6    SING N N 14 
9O4 C5    N7    SING Y N 15 
9O4 "C1'" N9    SING N N 16 
9O4 "C1'" "C2'" SING N N 17 
9O4 "C3'" "O3'" SING N N 18 
9O4 "C3'" "C2'" SING N N 19 
9O4 N9    C8    SING Y N 20 
9O4 N7    C8    DOUB Y N 21 
9O4 P     O3P   SING N N 22 
9O4 C2    H1    SING N N 23 
9O4 "C1'" H2    SING N N 24 
9O4 "C2'" H3    SING N N 25 
9O4 "C2'" H4    SING N N 26 
9O4 "C3'" H5    SING N N 27 
9O4 "C4'" H6    SING N N 28 
9O4 "C4'" H7    SING N N 29 
9O4 C8    H8    SING N N 30 
9O4 N6    H9    SING N N 31 
9O4 N6    H10   SING N N 32 
9O4 O1P   H11   SING N N 33 
9O4 O3P   H12   SING N N 34 
# 
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 
9O4 SMILES           ACDLabs              12.01 "c3nc1c(ncn1C2CC(OP(O)(=O)O)CO2)c(N)n3"                                                                                             
9O4 InChI            InChI                1.03  "InChI=1S/C9H12N5O5P/c10-8-7-9(12-3-11-8)14(4-13-7)6-1-5(2-18-6)19-20(15,16)17/h3-6H,1-2H2,(H2,10,11,12)(H2,15,16,17)/t5-,6-/m1/s1" 
9O4 InChIKey         InChI                1.03  SRZMSIWIQAVZRP-PHDIDXHHSA-N                                                                                                         
9O4 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](CO3)O[P](O)(O)=O"                                                                                     
9O4 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](CO3)O[P](O)(O)=O"                                                                                       
9O4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@H](CO3)OP(=O)(O)O)N"                                                                                   
9O4 SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(CO3)OP(=O)(O)O)N"                                                                                           
# 
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 
9O4 "SYSTEMATIC NAME" ACDLabs              12.01 "(3R,5R)-5-(6-amino-9H-purin-9-yl)oxolan-3-yl dihydrogen phosphate"     
9O4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(3~{R},5~{R})-5-(6-aminopurin-9-yl)oxolan-3-yl] 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 
9O4 "Create component" 2017-05-19 RCSB 
9O4 "Initial release"  2017-12-06 RCSB 
# 
