data_AP7
# 
_chem_comp.id                                    AP7 
_chem_comp.name                                  
;N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2004-08-10 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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        ? 
_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 0.622  1.976  -0.784 "C1'"  AP7 1  
AP7 N1     N1   N 1 1 Y N N 81.627 20.963 -11.167 -2.648 1.071  -4.593 N1     AP7 2  
AP7 C2     C2   C 0 1 Y N N 81.943 21.604 -12.315 -2.861 1.645  -3.340 C2     AP7 3  
AP7 N3     N3   N 0 1 Y N N 82.404 21.094 -13.472 -1.960 1.843  -2.413 N3     AP7 4  
AP7 C4     C4   C 0 1 Y N N 82.532 19.744 -13.355 -0.744 1.403  -2.841 C4     AP7 5  
AP7 C5     C5   C 0 1 Y N N 82.257 18.967 -12.274 -0.400 0.821  -4.050 C5     AP7 6  
AP7 C6     C6   C 0 1 Y N N 81.778 19.612 -11.115 -1.426 0.628  -5.029 C6     AP7 7  
AP7 N6     N6   N 0 1 N N N 81.459 18.977 -9.958  -1.165 0.069  -6.223 N6     AP7 8  
AP7 N7     N7   N 0 1 Y N N 82.513 17.648 -12.539 0.926  0.511  -4.109 N7     AP7 9  
AP7 C8     C8   C 0 1 Y N N 82.945 17.653 -13.796 1.396  0.902  -2.940 C8     AP7 10 
AP7 N9     N9   N 0 1 Y N N 82.975 18.891 -14.332 0.424  1.450  -2.136 N9     AP7 11 
AP7 "C2'"  C2*  C 0 1 N N R 84.896 19.529 -15.819 0.518  0.913  0.310  "C2'"  AP7 12 
AP7 "O2'"  O2*  O 0 1 N N N 85.266 20.498 -16.774 -0.210 1.445  1.415  "O2'"  AP7 13 
AP7 "C3'"  C3*  C 0 1 N N S 85.352 18.246 -16.458 1.969  0.663  0.677  "C3'"  AP7 14 
AP7 "O3'"  O3*  O 0 1 N N N 86.613 18.403 -17.106 2.143  0.197  1.998  "O3'"  AP7 15 
AP7 "C4'"  C4*  C 0 1 N N R 84.286 17.911 -17.496 2.595  2.031  0.465  "C4'"  AP7 16 
AP7 "O4'"  O4*  O 0 1 N N N 83.197 18.207 -16.604 1.933  2.574  -0.689 "O4'"  AP7 17 
AP7 "C5'"  C5*  C 0 1 N N N 84.228 16.451 -17.884 4.092  1.980  0.223  "C5'"  AP7 18 
AP7 "O5'"  O5*  O 0 1 N N N 83.813 15.664 -16.770 4.566  3.301  0.029  "O5'"  AP7 19 
AP7 OP1    O1P  O 0 1 N N N 83.394 13.586 -18.082 6.560  4.952  -0.444 OP1    AP7 20 
AP7 OP2    O2P  O 0 1 N N N 82.620 13.766 -15.680 6.456  2.538  -1.495 OP2    AP7 21 
AP7 P      P    P 0 1 N N N 82.836 14.417 -16.992 6.145  3.523  -0.251 P      AP7 22 
AP7 OP3    O3P  O 0 1 N Y N ?      ?      ?       6.843  2.773  1.000  OP3    AP7 23 
AP7 "H1'"  H1*  H 0 1 N N N 82.849 20.154 -16.016 -0.125 2.769  -0.673 "H1'"  AP7 24 
AP7 H1     H1   H 0 1 N N N 81.288 21.476 -10.366 -3.444 0.978  -5.218 H1     AP7 25 
AP7 H2     H2   H 0 1 N N N 81.778 22.667 -12.221 -3.911 1.936  -3.181 H2     AP7 26 
AP7 H61    1H6  H 0 1 N N N 81.121 19.507 -9.167  -0.355 0.363  -6.743 H61    AP7 27 
AP7 H62    2H6  H 0 1 N N N 81.560 17.974 -9.887  -1.783 -0.637 -6.587 H62    AP7 28 
AP7 H8     H8   H 0 1 N N N 83.249 16.787 -14.366 2.425  0.816  -2.617 H8     AP7 29 
AP7 "H2'"  H2*  H 0 1 N N N 85.387 19.634 -14.854 -0.000 0.001  -0.003 "H2'"  AP7 30 
AP7 "HO2'" 2HO* H 0 0 N N N 86.160 20.791 -16.580 -1.062 1.768  1.071  "HO2'" AP7 31 
AP7 "H3'"  H3*  H 0 1 N N N 85.463 17.435 -15.736 2.403  -0.065 -0.019 "H3'"  AP7 32 
AP7 "HO3'" H3T  H 0 0 N Y N 86.901 17.593 -17.510 3.003  0.531  2.294  "HO3'" AP7 33 
AP7 "H4'"  H4*  H 0 1 N N N 84.502 18.507 -18.384 2.399  2.693  1.317  "H4'"  AP7 34 
AP7 "H5''" 2H5* H 0 0 N N N 85.217 16.148 -18.231 4.308  1.388  -0.668 "H5''" AP7 35 
AP7 "H5'"  1H5* H 0 1 N N N 83.534 16.344 -18.719 4.597  1.541  1.085  "H5'"  AP7 36 
AP7 HOP2   2HOP H 0 0 N N N 82.040 13.025 -15.812 7.351  2.548  -1.896 HOP2   AP7 37 
AP7 HOP3   3HOP H 0 0 N N N -0.580 -0.741 -0.132  7.814  2.842  1.113  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              10.04 "O=P(O)(O)OCC3OC(n2cnc1c(N)[nH+]cnc12)C(O)C3O"                                                                                                                                                       
AP7 InChI            InChI                1.02b "InChI=1/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/fC10H15N5O7P/h12,18-19H,11H2/q+1" 
AP7 InChIKey         InChI                1.02b UDMBCSSLTHHNCD-MSVWBLHYDK                                                                                                                                                                            
AP7 SMILES_CANONICAL CACTVS               3.341 "Nc1[nH+]cnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                                                   
AP7 SMILES           CACTVS               3.341 "Nc1[nH+]cnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                                                         
AP7 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "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" 1.5.0 "c1[nH+]c(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)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 
AP7 "SYSTEMATIC NAME" ACDLabs              10.04 
;5'-adenylic acid
;
AP7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-1-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
