data_AP2
# 
_chem_comp.id                                    AP2 
_chem_comp.name                                  "PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 N5 O9 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        425.228 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AP2 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1AV5 
_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 
AP2 PB     PB   P 0 1 N N N 43.174 31.463 48.444 1.220  -0.230 -5.985 PB     AP2 1  
AP2 O1B    O1B  O 0 1 N N N 43.269 30.257 47.550 1.784  1.129  -5.829 O1B    AP2 2  
AP2 O2B    O2B  O 0 1 N N N 43.689 32.654 47.774 2.251  -1.145 -6.817 O2B    AP2 3  
AP2 O3B    O3B  O 0 1 N N N 43.745 31.352 49.835 -0.179 -0.143 -6.776 O3B    AP2 4  
AP2 C3A    C3A  C 0 1 N N N 41.443 31.652 48.624 0.945  -0.966 -4.340 C3A    AP2 5  
AP2 PA     PA   P 0 1 N N R 40.545 32.747 49.426 -0.221 0.070  -3.398 PA     AP2 6  
AP2 O1A    O1A  O 0 1 N N N 40.998 34.147 49.336 0.342  1.430  -3.242 O1A    AP2 7  
AP2 O2A    O2A  O 0 1 N N N 39.133 32.830 48.987 -1.621 0.157  -4.189 O2A    AP2 8  
AP2 "O5'"  O5*  O 0 1 N N N 40.596 32.350 50.978 -0.464 -0.579 -1.946 "O5'"  AP2 9  
AP2 "C5'"  C5*  C 0 1 N N N 41.919 32.205 51.571 -1.382 0.274  -1.260 "C5'"  AP2 10 
AP2 "C4'"  C4*  C 0 1 N N R 41.977 32.450 53.114 -1.658 -0.289 0.135  "C4'"  AP2 11 
AP2 "O4'"  O4*  O 0 1 N N N 41.311 31.442 53.940 -0.439 -0.339 0.907  "O4'"  AP2 12 
AP2 "C3'"  C3*  C 0 1 N N S 43.473 32.249 53.389 -2.588 0.656  0.926  "C3'"  AP2 13 
AP2 "O3'"  O3*  O 0 1 N N N 44.075 33.474 53.814 -3.939 0.197  0.865  "O3'"  AP2 14 
AP2 "C2'"  C2*  C 0 1 N N R 43.550 31.113 54.538 -2.054 0.582  2.376  "C2'"  AP2 15 
AP2 "O2'"  O2*  O 0 1 N N N 44.559 31.082 55.582 -3.061 0.077  3.255  "O2'"  AP2 16 
AP2 "C1'"  C1*  C 0 1 N N R 42.185 31.346 55.140 -0.863 -0.397 2.286  "C1'"  AP2 17 
AP2 N9     N9   N 0 1 Y N N 41.606 30.300 56.053 0.220  0.034  3.172  N9     AP2 18 
AP2 C8     C8   C 0 1 Y N N 41.488 28.948 55.787 1.230  0.892  2.852  C8     AP2 19 
AP2 N7     N7   N 0 1 Y N N 41.291 28.175 56.840 2.016  1.054  3.876  N7     AP2 20 
AP2 C5     C5   C 0 1 Y N N 41.280 29.113 57.901 1.559  0.317  4.917  C5     AP2 21 
AP2 C6     C6   C 0 1 Y N N 41.101 28.955 59.366 1.990  0.096  6.236  C6     AP2 22 
AP2 N6     N6   N 0 1 N N N 40.909 27.733 59.917 3.124  0.721  6.724  N6     AP2 23 
AP2 N1     N1   N 0 1 Y N N 41.152 30.113 60.073 1.281  -0.723 7.005  N1     AP2 24 
AP2 C2     C2   C 0 1 Y N N 41.344 31.339 59.532 0.198  -1.323 6.548  C2     AP2 25 
AP2 N3     N3   N 0 1 Y N N 41.514 31.568 58.211 -0.239 -1.151 5.318  N3     AP2 26 
AP2 C4     C4   C 0 1 Y N N 41.470 30.404 57.447 0.404  -0.350 4.476  C4     AP2 27 
AP2 HOB2   2HOB H 0 0 N N N 43.629 33.415 48.338 2.369  -0.722 -7.678 HOB2   AP2 28 
AP2 HOB3   3HOB H 0 0 N N N 43.685 32.113 50.399 -0.511 -1.048 -6.856 HOB3   AP2 29 
AP2 H3A1   1H3A H 0 0 N N N 41.057 31.688 47.578 1.892  -1.025 -3.805 H3A1   AP2 30 
AP2 H3A2   2H3A H 0 0 N N N 41.095 30.667 49.015 0.530  -1.967 -4.455 H3A2   AP2 31 
AP2 HOA2   2HOA H 0 0 N N N 38.608 33.469 49.455 -1.953 -0.747 -4.269 HOA2   AP2 32 
AP2 "H5'1" 1H5* H 0 0 N N N 42.346 31.205 51.322 -2.316 0.329  -1.820 "H5'1" AP2 33 
AP2 "H5'2" 2H5* H 0 0 N N N 42.650 32.863 51.047 -0.953 1.271  -1.170 "H5'2" AP2 34 
AP2 "H4'"  H4*  H 0 1 N N N 41.494 33.425 53.357 -2.101 -1.282 0.061  "H4'"  AP2 35 
AP2 "H3'"  H3*  H 0 1 N N N 44.030 31.934 52.476 -2.514 1.674  0.542  "H3'"  AP2 36 
AP2 "HO3'" *HO3 H 0 0 N N N 45.001 33.349 53.984 -4.471 0.824  1.374  "HO3'" AP2 37 
AP2 "H2'"  H2*  H 0 1 N N N 43.847 30.147 54.067 -1.715 1.564  2.709  "H2'"  AP2 38 
AP2 "HO2'" *HO2 H 0 0 N N N 44.604 30.414 56.256 -3.800 0.701  3.221  "HO2'" AP2 39 
AP2 "H1'"  H1*  H 0 1 N N N 42.262 32.230 55.814 -1.183 -1.407 2.543  "H1'"  AP2 40 
AP2 H8     H8   H 0 1 N N N 41.548 28.505 54.778 1.358  1.367  1.891  H8     AP2 41 
AP2 HN61   1HN6 H 0 0 N N N 40.786 27.624 60.923 3.409  0.563  7.638  HN61   AP2 42 
AP2 HN62   2HN6 H 0 0 N N N 41.677 27.129 59.624 3.636  1.314  6.152  HN62   AP2 43 
AP2 H2     H2   H 0 1 N N N 41.363 32.207 60.211 -0.349 -1.981 7.207  H2     AP2 44 
# 
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 
AP2 PB    O1B    DOUB N N 1  
AP2 PB    O2B    SING N N 2  
AP2 PB    O3B    SING N N 3  
AP2 PB    C3A    SING N N 4  
AP2 O2B   HOB2   SING N N 5  
AP2 O3B   HOB3   SING N N 6  
AP2 C3A   PA     SING N N 7  
AP2 C3A   H3A1   SING N N 8  
AP2 C3A   H3A2   SING N N 9  
AP2 PA    O1A    DOUB N N 10 
AP2 PA    O2A    SING N N 11 
AP2 PA    "O5'"  SING N N 12 
AP2 O2A   HOA2   SING N N 13 
AP2 "O5'" "C5'"  SING N N 14 
AP2 "C5'" "C4'"  SING N N 15 
AP2 "C5'" "H5'1" SING N N 16 
AP2 "C5'" "H5'2" SING N N 17 
AP2 "C4'" "O4'"  SING N N 18 
AP2 "C4'" "C3'"  SING N N 19 
AP2 "C4'" "H4'"  SING N N 20 
AP2 "O4'" "C1'"  SING N N 21 
AP2 "C3'" "O3'"  SING N N 22 
AP2 "C3'" "C2'"  SING N N 23 
AP2 "C3'" "H3'"  SING N N 24 
AP2 "O3'" "HO3'" SING N N 25 
AP2 "C2'" "O2'"  SING N N 26 
AP2 "C2'" "C1'"  SING N N 27 
AP2 "C2'" "H2'"  SING N N 28 
AP2 "O2'" "HO2'" SING N N 29 
AP2 "C1'" N9     SING N N 30 
AP2 "C1'" "H1'"  SING N N 31 
AP2 N9    C8     SING Y N 32 
AP2 N9    C4     SING Y N 33 
AP2 C8    N7     DOUB Y N 34 
AP2 C8    H8     SING N N 35 
AP2 N7    C5     SING Y N 36 
AP2 C5    C6     SING Y N 37 
AP2 C5    C4     DOUB Y N 38 
AP2 C6    N6     SING N N 39 
AP2 C6    N1     DOUB Y N 40 
AP2 N6    HN61   SING N N 41 
AP2 N6    HN62   SING N N 42 
AP2 N1    C2     SING Y N 43 
AP2 C2    N3     DOUB Y N 44 
AP2 C2    H2     SING N N 45 
AP2 N3    C4     SING Y N 46 
# 
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 
AP2 SMILES           ACDLabs              10.04 "O=P(O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"                                                                                                                                        
AP2 SMILES_CANONICAL CACTVS               3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                                
AP2 SMILES           CACTVS               3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                                        
AP2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(CP(=O)(O)O)O)O)O)N"                                                                                                            
AP2 SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N"                                                                                                                                  
AP2 InChI            InChI                1.03  "InChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1" 
AP2 InChIKey         InChI                1.03  OLCWZBFDIYXLAA-IOSLPCCCSA-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 
AP2 "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]adenosine"                                                           
AP2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methylphosphonic 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 
AP2 "Create component"  1999-07-08 RCSB 
AP2 "Modify descriptor" 2011-06-04 RCSB 
# 
