data_A6A
# 
_chem_comp.id                                    A6A 
_chem_comp.name                                  "2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H16 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         "((2R,3S,4S,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-08-26 
_chem_comp.pdbx_modified_date                    2021-03-13 
_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                        361.248 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A6A 
_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        3OK2 
_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 
A6A P      P      P 0 1 N N N -9.601  -0.703 1.990 4.764  0.980  0.120  P      A6A 1  
A6A N1     N1     N 0 1 Y N N -3.814  5.562  4.836 -5.812 0.992  0.110  N1     A6A 2  
A6A C2     C2     C 0 1 Y N N -4.832  6.434  4.861 -5.625 -0.223 0.593  C2     A6A 3  
A6A N3     N3     N 0 1 Y N N -6.110  6.230  4.597 -4.430 -0.765 0.701  N3     A6A 4  
A6A C4     C4     C 0 1 Y N N -6.323  4.914  4.284 -3.346 -0.095 0.321  C4     A6A 5  
A6A C5     C5     C 0 1 Y N N -5.366  3.902  4.230 -3.492 1.202  -0.199 C5     A6A 6  
A6A C6     C6     C 0 1 Y N N -4.054  4.249  4.534 -4.788 1.736  -0.295 C6     A6A 7  
A6A N6     N6     N 0 1 N N N -3.077  3.345  4.528 -4.994 3.009  -0.799 N6     A6A 8  
A6A N7     N7     N 0 1 Y N N -5.914  2.687  3.881 -2.251 1.652  -0.503 N7     A6A 9  
A6A C8     C8     C 0 1 Y N N -7.185  2.973  3.709 -1.374 0.736  -0.210 C8     A6A 10 
A6A N9     N9     N 0 1 Y N N -7.510  4.281  3.921 -2.000 -0.361 0.302  N9     A6A 11 
A6A "C1'"  "C1'"  C 0 1 N N R -8.872  4.861  3.812 -1.355 -1.598 0.750  "C1'"  A6A 12 
A6A "C2'"  "C2'"  C 0 1 N N S -9.345  5.041  2.334 -0.738 -2.318 -0.453 "C2'"  A6A 13 
A6A "O2'"  "O2'"  O 0 1 N N N -10.485 5.917  2.327 -0.167 -3.557 -0.027 "O2'"  A6A 14 
A6A "C3'"  "C3'"  C 0 1 N N S -9.782  3.758  1.671 0.352  -1.431 -1.062 "C3'"  A6A 15 
A6A "O3'"  "O3'"  O 0 1 N N N -10.354 4.004  0.417 0.984  -2.124 -2.140 "O3'"  A6A 16 
A6A "C4'"  "C4'"  C 0 1 N N R -10.737 2.955  2.565 1.391  -1.103 0.014  "C4'"  A6A 17 
A6A "O4'"  "O4'"  O 0 1 N N N -10.022 2.770  3.760 0.747  -0.462 1.117  "O4'"  A6A 18 
A6A "C5'"  "C5'"  C 0 1 N N N -10.966 1.553  2.061 2.452  -0.168 -0.570 "C5'"  A6A 19 
A6A "O5'"  "O5'"  O 0 1 N N N -9.722  0.892  2.030 3.483  0.045  0.396  "O5'"  A6A 20 
A6A "C6'"  "C6'"  C 0 1 N N N -9.915  4.003  4.480 -0.250 -1.263 1.755  "C6'"  A6A 21 
A6A OP1    OP1    O 0 1 N N N -10.337 -1.278 0.823 5.452  0.524  -1.108 OP1    A6A 22 
A6A OP2    OP2    O 0 1 N N N -8.147  -1.043 2.083 4.285  2.506  -0.069 OP2    A6A 23 
A6A OP3    OP3    O 0 1 N Y N -10.424 -1.184 3.297 5.776  0.887  1.368  OP3    A6A 24 
A6A H2     H2     H 0 1 N N N -4.570  7.445  5.136 -6.485 -0.794 0.911  H2     A6A 25 
A6A HN6    HN6    H 0 1 N N N -2.212  3.786  4.768 -4.238 3.543  -1.091 HN6    A6A 26 
A6A HN6A   HN6A   H 0 0 N N N -3.282  2.629  5.195 -5.893 3.367  -0.860 HN6A   A6A 27 
A6A H8     H8     H 0 1 N N N -7.915  2.231  3.422 -0.308 0.831  -0.351 H8     A6A 28 
A6A "H1'"  "H1'"  H 0 1 N N N -8.782  5.838  4.309 -2.094 -2.244 1.223  "H1'"  A6A 29 
A6A "H2'"  "H2'"  H 0 1 N N N -8.482  5.435  1.778 -1.510 -2.510 -1.198 "H2'"  A6A 30 
A6A "HO2'" "HO2'" H 0 0 N N N -10.787 6.038  1.434 0.242  -4.067 -0.739 "HO2'" A6A 31 
A6A "H3'"  "H3'"  H 0 1 N N N -8.881  3.146  1.518 -0.094 -0.508 -1.431 "H3'"  A6A 32 
A6A "HO3'" "HO3'" H 0 0 N Y N -10.620 3.181  0.023 1.687  -1.620 -2.573 "HO3'" A6A 33 
A6A "H4'"  "H4'"  H 0 1 N N N -11.699 3.484  2.630 1.865  -2.023 0.354  "H4'"  A6A 34 
A6A "H5'"  "H5'"  H 0 1 N N N -11.657 1.021  2.732 2.881  -0.619 -1.465 "H5'"  A6A 35 
A6A "H5'A" "H5'A" H 0 0 N N N -11.400 1.583  1.051 1.993  0.786  -0.828 "H5'A" A6A 36 
A6A "H6'"  "H6'"  H 0 1 N N N -9.620  3.802  5.520 -0.677 -0.712 2.594  "H6'"  A6A 37 
A6A "H6'A" "H6'A" H 0 0 N N N -10.884 4.523  4.473 0.203  -2.186 2.119  "H6'A" A6A 38 
A6A HOP2   HOP2   H 0 0 N N N -7.904  -1.598 1.352 3.825  2.872  0.699  HOP2   A6A 39 
A6A HOP3   HOP3   H 0 0 N Y N -11.168 -1.709 3.028 6.573  1.426  1.270  HOP3   A6A 40 
# 
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 
A6A OP1   P      DOUB N N 1  
A6A P     "O5'"  SING N N 2  
A6A P     OP2    SING N N 3  
A6A P     OP3    SING N N 4  
A6A C6    N1     DOUB Y N 5  
A6A N1    C2     SING Y N 6  
A6A N3    C2     DOUB Y N 7  
A6A C2    H2     SING N N 8  
A6A C4    N3     SING Y N 9  
A6A N9    C4     SING Y N 10 
A6A C5    C4     DOUB Y N 11 
A6A N7    C5     SING Y N 12 
A6A C5    C6     SING Y N 13 
A6A N6    C6     SING N N 14 
A6A N6    HN6    SING N N 15 
A6A N6    HN6A   SING N N 16 
A6A C8    N7     DOUB Y N 17 
A6A C8    N9     SING Y N 18 
A6A C8    H8     SING N N 19 
A6A "C1'" N9     SING N N 20 
A6A "C2'" "C1'"  SING N N 21 
A6A "C1'" "C6'"  SING N N 22 
A6A "C1'" "H1'"  SING N N 23 
A6A "C3'" "C2'"  SING N N 24 
A6A "O2'" "C2'"  SING N N 25 
A6A "C2'" "H2'"  SING N N 26 
A6A "O2'" "HO2'" SING N N 27 
A6A "O3'" "C3'"  SING N N 28 
A6A "C3'" "C4'"  SING N N 29 
A6A "C3'" "H3'"  SING N N 30 
A6A "O3'" "HO3'" SING N N 31 
A6A "C5'" "C4'"  SING N N 32 
A6A "C4'" "O4'"  SING N N 33 
A6A "C4'" "H4'"  SING N N 34 
A6A "O4'" "C6'"  SING N N 35 
A6A "O5'" "C5'"  SING N N 36 
A6A "C5'" "H5'"  SING N N 37 
A6A "C5'" "H5'A" SING N N 38 
A6A "C6'" "H6'"  SING N N 39 
A6A "C6'" "H6'A" SING N N 40 
A6A OP2   HOP2   SING N N 41 
A6A OP3   HOP3   SING N N 42 
# 
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 
A6A SMILES           ACDLabs              12.01 "O=P(O)(O)OCC3OCC(n1cnc2c(ncnc12)N)C(O)C3O"                                                                                                                       
A6A SMILES_CANONICAL CACTVS               3.370 "Nc1ncnc2n(cnc12)[C@@H]3CO[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                   
A6A SMILES           CACTVS               3.370 "Nc1ncnc2n(cnc12)[CH]3CO[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                         
A6A SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)[C@@H]3CO[C@@H]([C@H]([C@H]3O)O)COP(=O)(O)O)N"                                                                                                 
A6A SMILES           "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)C3COC(C(C3O)O)COP(=O)(O)O)N"                                                                                                                   
A6A InChI            InChI                1.03  "InChI=1S/C11H16N5O7P/c12-10-7-11(14-3-13-10)16(4-15-7)5-1-22-6(9(18)8(5)17)2-23-24(19,20)21/h3-6,8-9,17-18H,1-2H2,(H2,12,13,14)(H2,19,20,21)/t5-,6-,8+,9-/m1/s1" 
A6A InChIKey         InChI                1.03  WJZBVGLXFAAYLT-MTSNSDSCSA-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 
A6A "SYSTEMATIC NAME" ACDLabs              12.01 "2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol"                   
A6A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4S,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A6A 
_pdbx_chem_comp_synonyms.name         "((2R,3S,4S,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A6A "Create component"     2010-08-26 RCSB 
A6A "Modify aromatic_flag" 2011-06-04 RCSB 
A6A "Modify descriptor"    2011-06-04 RCSB 
A6A "Modify synonyms"      2021-03-13 RCSB 
# 
