data_AP7
# 
_chem_comp.id                                    AP7 
_chem_comp.name                                  
;N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2004-08-10 
_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                        348.229 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     AP7 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1U6P 
_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 
AP7 "C1'"  "C1'"  C 0 1 N N R 83.398 19.268 -15.697 -0.717 0.818  -0.421 "C1'"  AP7 1  
AP7 N1     N1     N 1 1 Y N N 81.627 20.963 -11.167 -5.765 -0.407 -0.380 N1     AP7 2  
AP7 C2     C2     C 0 1 Y N N 81.943 21.604 -12.315 -5.190 0.712  -0.782 C2     AP7 3  
AP7 N3     N3     N 0 1 Y N N 82.404 21.094 -13.472 -3.887 0.893  -0.738 N3     AP7 4  
AP7 C4     C4     C 0 1 Y N N 82.532 19.744 -13.355 -3.086 -0.063 -0.277 C4     AP7 5  
AP7 C5     C5     C 0 1 Y N N 82.257 18.967 -12.274 -3.649 -1.272 0.163  C5     AP7 6  
AP7 C6     C6     C 0 1 Y N N 81.778 19.612 -11.115 -5.045 -1.418 0.095  C6     AP7 7  
AP7 N6     N6     N 0 1 N N N 81.459 18.977 -9.958  -5.656 -2.586 0.515  N6     AP7 8  
AP7 N7     N7     N 0 1 Y N N 82.513 17.648 -12.539 -2.628 -2.061 0.575  N7     AP7 9  
AP7 C8     C8     C 0 1 Y N N 82.945 17.653 -13.796 -1.501 -1.428 0.420  C8     AP7 10 
AP7 N9     N9     N 0 1 Y N N 82.975 18.891 -14.332 -1.731 -0.191 -0.103 N9     AP7 11 
AP7 "C2'"  "C2'"  C 0 1 N N R 84.896 19.529 -15.819 -0.550 1.814  0.754  "C2'"  AP7 12 
AP7 "O2'"  "O2'"  O 0 1 N N N 85.266 20.498 -16.774 -1.497 2.879  0.659  "O2'"  AP7 13 
AP7 "C3'"  "C3'"  C 0 1 N N S 85.352 18.246 -16.458 0.891  2.335  0.536  "C3'"  AP7 14 
AP7 "O3'"  "O3'"  O 0 1 N N N 86.613 18.403 -17.106 0.871  3.588  -0.151 "O3'"  AP7 15 
AP7 "C4'"  "C4'"  C 0 1 N N R 84.286 17.911 -17.496 1.556  1.253  -0.336 "C4'"  AP7 16 
AP7 "O4'"  "O4'"  O 0 1 N N N 83.197 18.207 -16.604 0.587  0.209  -0.535 "O4'"  AP7 17 
AP7 "C5'"  "C5'"  C 0 1 N N N 84.228 16.451 -17.884 2.786  0.691  0.379  "C5'"  AP7 18 
AP7 "O5'"  "O5'"  O 0 1 N N N 83.813 15.664 -16.770 3.462  -0.226 -0.484 "O5'"  AP7 19 
AP7 OP1    O1P    O 0 1 N N N 83.394 13.586 -18.082 4.562  -1.745 1.206  OP1    AP7 20 
AP7 OP2    O2P    O 0 1 N N N 82.620 13.766 -15.680 5.210  -2.049 -1.215 OP2    AP7 21 
AP7 P      P      P 0 1 N N N 82.836 14.417 -16.992 4.802  -1.008 -0.056 P      AP7 22 
AP7 OP3    O3P    O 0 1 N Y N ?      ?      ?       5.996  0.051  0.160  OP3    AP7 23 
AP7 "H1'"  "H1'"  H 0 1 N N N 82.803 20.168 -15.913 -0.978 1.347  -1.338 "H1'"  AP7 24 
AP7 H1     H1     H 0 1 N N N 81.290 21.471 -10.374 -6.730 -0.491 -0.430 H1     AP7 25 
AP7 H2     H2     H 0 1 N N N 81.806 22.675 -12.301 -5.812 1.509  -1.162 H2     AP7 26 
AP7 H61    H61    H 0 1 N N N 81.559 17.984 -9.889  -6.621 -2.674 0.463  H61    AP7 27 
AP7 H62    H62    H 0 1 N N N 81.124 19.502 -9.175  -5.120 -3.317 0.860  H62    AP7 28 
AP7 H8     H8     H 0 1 N N N 83.240 16.762 -14.331 -0.528 -1.825 0.669  H8     AP7 29 
AP7 "H2'"  "H2'"  H 0 1 N N N 85.293 19.850 -14.845 -0.638 1.303  1.713  "H2'"  AP7 30 
AP7 "HO2'" "HO'2" H 0 0 N N N 86.211 20.593 -16.780 -1.433 3.529  1.372  "HO2'" AP7 31 
AP7 "H3'"  "H3'"  H 0 1 N N N 85.478 17.456 -15.703 1.411  2.432  1.489  "H3'"  AP7 32 
AP7 "HO3'" H3T    H 0 0 N Y N 86.873 17.578 -17.499 0.413  4.292  0.328  "HO3'" AP7 33 
AP7 "H4'"  "H4'"  H 0 1 N N N 84.376 18.415 -18.470 1.845  1.677  -1.298 "H4'"  AP7 34 
AP7 "H5''" "H5'2" H 0 0 N N N 83.509 16.323 -18.707 3.460  1.508  0.639  "H5''" AP7 35 
AP7 "H5'"  "H5'1" H 0 1 N N N 85.226 16.122 -18.209 2.475  0.174  1.286  "H5'"  AP7 36 
AP7 HOP2   HOP2   H 0 0 N N N 82.886 12.855 -15.730 6.011  -2.556 -1.024 HOP2   AP7 37 
AP7 HOP3   HOP3   H 0 0 N N N -0.580 -0.741 -0.132  6.208  0.570  -0.628 HOP3   AP7 38 
# 
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 
AP7 "C1'" N9     SING N N 1  
AP7 "C1'" "C2'"  SING N N 2  
AP7 "C1'" "O4'"  SING N N 3  
AP7 "C1'" "H1'"  SING N N 4  
AP7 N1    C2     SING Y N 5  
AP7 N1    C6     DOUB Y N 6  
AP7 N1    H1     SING N N 7  
AP7 C2    N3     DOUB Y N 8  
AP7 C2    H2     SING N N 9  
AP7 N3    C4     SING Y N 10 
AP7 C4    C5     DOUB Y N 11 
AP7 C4    N9     SING Y N 12 
AP7 C5    C6     SING Y N 13 
AP7 C5    N7     SING Y N 14 
AP7 C6    N6     SING N N 15 
AP7 N6    H61    SING N N 16 
AP7 N6    H62    SING N N 17 
AP7 N7    C8     DOUB Y N 18 
AP7 C8    N9     SING Y N 19 
AP7 C8    H8     SING N N 20 
AP7 "C2'" "O2'"  SING N N 21 
AP7 "C2'" "C3'"  SING N N 22 
AP7 "C2'" "H2'"  SING N N 23 
AP7 "O2'" "HO2'" SING N N 24 
AP7 "C3'" "O3'"  SING N N 25 
AP7 "C3'" "C4'"  SING N N 26 
AP7 "C3'" "H3'"  SING N N 27 
AP7 "O3'" "HO3'" SING N N 28 
AP7 "C4'" "O4'"  SING N N 29 
AP7 "C4'" "C5'"  SING N N 30 
AP7 "C4'" "H4'"  SING N N 31 
AP7 "C5'" "O5'"  SING N N 32 
AP7 "C5'" "H5''" SING N N 33 
AP7 "C5'" "H5'"  SING N N 34 
AP7 "O5'" P      SING N N 35 
AP7 OP1   P      DOUB N N 36 
AP7 OP2   P      SING N N 37 
AP7 OP2   HOP2   SING N N 38 
AP7 P     OP3    SING N N 39 
AP7 OP3   HOP3   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 
AP7 SMILES           ACDLabs              12.01 "O=P(O)(O)OCC3OC(n2cnc1c(N)[nH+]cnc12)C(O)C3O"                                                                                                                       
AP7 SMILES_CANONICAL CACTVS               3.370 "Nc1[nH+]cnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                   
AP7 SMILES           CACTVS               3.370 "Nc1[nH+]cnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                         
AP7 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1[nH+]c(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N"                                                                                               
AP7 SMILES           "OpenEye OEToolkits" 1.7.0 "c1[nH+]c(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N"                                                                                                                 
AP7 InChI            InChI                1.03  "InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p+1/t4-,6-,7-,10-/m1/s1" 
AP7 InChIKey         InChI                1.03  UDMBCSSLTHHNCD-KQYNXXCUSA-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 
AP7 "SYSTEMATIC NAME" ACDLabs              12.01 
;5'-adenylic acid
;
AP7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4R,5R)-5-(6-azanylpurin-1-ium-9-yl)-3,4-dihydroxy-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 
AP7 "Create component"  2004-08-10 RCSB 
AP7 "Modify descriptor" 2011-06-04 RCSB 
# 
