data_A1H3G
# 
_chem_comp.id                                    A1H3G 
_chem_comp.name                                  
;2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (protonated at N1)
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N5 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2024-02-05 
_chem_comp.pdbx_modified_date                    2024-03-08 
_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                        332.230 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     A1H3G 
_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        8RW2 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1H3G N1     N1  N 1 1 Y N N N N N 32.259 30.746 32.957 -5.824 -0.285 -0.597 N1     A1H3G 1  
A1H3G N3     N2  N 0 1 Y N N N N N 31.368 31.660 35.030 -3.910 0.891  -1.142 N3     A1H3G 2  
A1H3G C6     C1  C 0 1 Y N N N N N 33.357 30.173 33.577 -5.156 -1.118 0.195  C6     A1H3G 3  
A1H3G C5     C2  C 0 1 Y N N N N N 33.495 30.415 34.973 -3.769 -0.941 0.334  C5     A1H3G 4  
A1H3G C4     C3  C 0 1 Y N N N N N 32.488 31.120 35.600 -3.159 0.109  -0.373 C4     A1H3G 5  
A1H3G C8     C4  C 0 1 Y N N N N N 34.037 30.524 37.031 -1.651 -0.993 0.799  C8     A1H3G 6  
A1H3G P      P1  P 0 1 N N N N N N 32.445 28.294 42.045 4.752  -0.903 -0.187 P      A1H3G 7  
A1H3G OP3    O1  O 0 1 N Y N N N N 31.263 28.357 42.941 5.285  -1.611 -1.531 OP3    A1H3G 8  
A1H3G OP1    O2  O 0 1 N N N N N N 32.699 27.041 41.292 5.776  0.042  0.312  OP1    A1H3G 9  
A1H3G "O5'"  O3  O 0 1 N N N N N N 32.334 29.503 40.990 3.392  -0.103 -0.504 "O5'"  A1H3G 10 
A1H3G "O3'"  O4  O 0 1 N N N N N N 29.709 32.758 39.594 1.271  3.558  0.836  "O3'"  A1H3G 11 
A1H3G C2     C5  C 0 1 Y N N N N N 31.336 31.446 33.716 -5.207 0.688  -1.242 C2     A1H3G 12 
A1H3G N7     N3  N 0 1 Y N N N N N 34.479 30.051 35.896 -2.793 -1.574 1.029  N7     A1H3G 13 
A1H3G N9     N4  N 0 1 Y N N N N N 32.828 31.164 36.936 -1.825 0.051  -0.060 N9     A1H3G 14 
A1H3G N6     N5  N 0 1 N N N N N N 34.170 29.425 32.820 -5.812 -2.134 0.867  N6     A1H3G 15 
A1H3G "C1'"  C6  C 0 1 N N R N N N 32.042 31.774 38.033 -0.778 0.947  -0.558 "C1'"  A1H3G 16 
A1H3G "O4'"  O5  O 0 1 N N N N N N 32.787 31.768 39.235 0.503  0.301  -0.467 "O4'"  A1H3G 17 
A1H3G "C4'"  C7  C 0 1 N N R N N N 31.865 31.822 40.316 1.473  1.327  -0.167 "C4'"  A1H3G 18 
A1H3G "C3'"  C8  C 0 1 N N S N N N 30.461 31.553 39.747 0.738  2.233  0.853  "C3'"  A1H3G 19 
A1H3G "C2'"  C9  C 0 1 N N N N N N 30.784 30.982 38.370 -0.714 2.215  0.316  "C2'"  A1H3G 20 
A1H3G "C5'"  C10 C 0 1 N N N N N N 32.263 30.852 41.435 2.727  0.716  0.460  "C5'"  A1H3G 21 
A1H3G OP2    O6  O 0 1 N Y N N N N 33.745 28.647 42.936 4.466  -2.025 0.932  OP2    A1H3G 22 
A1H3G H1     H1  H 0 1 N N N N N N 32.134 30.655 31.969 -6.781 -0.396 -0.706 H1     A1H3G 23 
A1H3G H8     H2  H 0 1 N N N N N N 34.576 30.420 37.961 -0.706 -1.294 1.226  H8     A1H3G 24 
A1H3G HOP3   H3  H 0 0 N Y N N N N 30.797 27.530 42.909 6.103  -2.112 -1.414 HOP3   A1H3G 25 
A1H3G "HO3'" H4  H 0 0 N Y N N N N 29.506 33.116 40.450 0.844  4.162  1.459  "HO3'" A1H3G 26 
A1H3G H2     H5  H 0 1 N N N N N N 30.496 31.865 33.182 -5.788 1.343  -1.875 H2     A1H3G 27 
A1H3G H62    H6  H 0 1 N N N N N N 34.962 28.974 33.232 -6.769 -2.245 0.763  H62    A1H3G 28 
A1H3G H61    H7  H 0 1 N N N N N N 33.985 29.317 31.843 -5.313 -2.736 1.442  H61    A1H3G 29 
A1H3G "H1'"  H8  H 0 1 N N N N N N 31.758 32.801 37.758 -0.985 1.220  -1.592 "H1'"  A1H3G 30 
A1H3G "H4'"  H9  H 0 1 N N N N N N 31.864 32.838 40.739 1.729  1.888  -1.067 "H4'"  A1H3G 31 
A1H3G "H3'"  H10 H 0 1 N N N N N N 29.932 30.809 40.362 0.787  1.808  1.856  "H3'"  A1H3G 32 
A1H3G "H2'"  H11 H 0 1 N N N N N N 29.976 31.176 37.649 -0.909 3.103  -0.285 "H2'"  A1H3G 33 
A1H3G "H2''" H12 H 0 0 N N N N N N 30.984 29.901 38.415 -1.425 2.147  1.140  "H2''" A1H3G 34 
A1H3G "H5''" H13 H 0 0 N N N N N N 33.249 31.147 41.823 2.445  0.109  1.319  "H5''" A1H3G 35 
A1H3G "H5'"  H14 H 0 1 N N N N N N 31.517 30.918 42.241 3.397  1.513  0.783  "H5'"  A1H3G 36 
A1H3G HOP2   H15 H 0 0 N N N N N N 34.412 27.984 42.801 3.803  -2.680 0.673  HOP2   A1H3G 37 
# 
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 
A1H3G N6    C6     SING N N 1  
A1H3G N1    C6     DOUB Y N 2  
A1H3G N1    C2     SING Y N 3  
A1H3G C6    C5     SING Y N 4  
A1H3G C2    N3     DOUB Y N 5  
A1H3G C5    C4     DOUB Y N 6  
A1H3G C5    N7     SING Y N 7  
A1H3G N3    C4     SING Y N 8  
A1H3G C4    N9     SING Y N 9  
A1H3G N7    C8     DOUB Y N 10 
A1H3G N9    C8     SING Y N 11 
A1H3G N9    "C1'"  SING N N 12 
A1H3G "C1'" "C2'"  SING N N 13 
A1H3G "C1'" "O4'"  SING N N 14 
A1H3G "C2'" "C3'"  SING N N 15 
A1H3G "O4'" "C4'"  SING N N 16 
A1H3G "O3'" "C3'"  SING N N 17 
A1H3G "C3'" "C4'"  SING N N 18 
A1H3G "C4'" "C5'"  SING N N 19 
A1H3G "O5'" "C5'"  SING N N 20 
A1H3G "O5'" P      SING N N 21 
A1H3G OP1   P      DOUB N N 22 
A1H3G P     OP3    SING N N 23 
A1H3G P     OP2    SING N N 24 
A1H3G N1    H1     SING N N 25 
A1H3G C8    H8     SING N N 26 
A1H3G OP3   HOP3   SING N N 27 
A1H3G "O3'" "HO3'" SING N N 28 
A1H3G C2    H2     SING N N 29 
A1H3G N6    H62    SING N N 30 
A1H3G N6    H61    SING N N 31 
A1H3G "C1'" "H1'"  SING N N 32 
A1H3G "C4'" "H4'"  SING N N 33 
A1H3G "C3'" "H3'"  SING N N 34 
A1H3G "C2'" "H2'"  SING N N 35 
A1H3G "C2'" "H2''" SING N N 36 
A1H3G "C5'" "H5''" SING N N 37 
A1H3G "C5'" "H5'"  SING N N 38 
A1H3G OP2   HOP2   SING N N 39 
# 
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 
A1H3G InChI            InChI                1.06  "InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/p+1/t5-,6+,7+/m0/s1" 
A1H3G InChIKey         InChI                1.06  KHWCHTKSEGGWEX-RRKCRQDMSA-O                                                                                                                          
A1H3G SMILES_CANONICAL CACTVS               3.385 "Nc1[nH+]cnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3"                                                                                         
A1H3G SMILES           CACTVS               3.385 "Nc1[nH+]cnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3"                                                                                             
A1H3G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1[nH+]c(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N"                                                                                       
A1H3G SMILES           "OpenEye OEToolkits" 2.0.7 "c1[nH+]c(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N"                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           A1H3G 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[(2~{R},3~{S},5~{R})-5-(6-azanylpurin-1-ium-9-yl)-3-oxidanyl-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 
A1H3G "Create component" 2024-02-08 PDBE 
A1H3G "Initial release"  2024-03-13 RCSB 
# 
