data_A1IEA
# 
_chem_comp.id                                    A1IEA 
_chem_comp.name                                  
;N3-methyl adenosine-5'-monophosphate
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         "[(2R,3S,4R,5R)-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2024-06-13 
_chem_comp.pdbx_modified_date                    2025-01-17 
_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                        362.256 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IEA 
_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        9FN2 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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 
A1IEA C4     C1  C 0 1 Y N N N N N 26.593 25.026 -4.120 3.010  -0.219 0.218  C4     A1IEA 1  
A1IEA C5     C2  C 0 1 Y N N N N N 26.162 25.344 -5.381 3.645  -1.316 -0.386 C5     A1IEA 2  
A1IEA C6     C3  C 0 1 Y N N N N N 26.781 26.388 -6.066 5.015  -1.510 -0.137 C6     A1IEA 3  
A1IEA N1     N1  N 0 1 Y N N N N N 27.773 27.051 -5.492 5.642  -0.648 0.657  N1     A1IEA 4  
A1IEA C8     C4  C 0 1 Y N N N N N 24.961 23.711 -4.692 1.566  -1.353 -1.003 C8     A1IEA 5  
A1IEA N3     N2  N 1 1 Y N N N N N 27.610 25.744 -3.585 3.721  0.593  0.994  N3     A1IEA 6  
A1IEA C2     C5  C 0 1 Y N N N N N 28.165 26.718 -4.270 5.001  0.369  1.204  C2     A1IEA 7  
A1IEA N6     N3  N 0 1 N N N N N N 26.313 26.723 -7.415 5.694  -2.573 -0.704 N6     A1IEA 8  
A1IEA "C1'"  C6  C 0 1 N N R N N N 25.898 23.326 -2.431 0.642  0.675  0.179  "C1'"  A1IEA 9  
A1IEA C1P    C7  C 0 1 N N N N N N 28.128 25.469 -2.275 3.073  1.745  1.626  C1P    A1IEA 10 
A1IEA "C2'"  C8  C 0 1 N N R N N N 24.863 22.231 -2.207 0.533  1.799  -0.875 "C2'"  A1IEA 11 
A1IEA "C3'"  C9  C 0 1 N N S N N N 25.549 21.406 -1.125 -0.984 2.076  -0.973 "C3'"  A1IEA 12 
A1IEA "C4'"  C10 C 0 1 N N R N N N 27.021 21.489 -1.533 -1.612 1.087  0.034  "C4'"  A1IEA 13 
A1IEA "C5'"  C11 C 0 1 N N N N N N 27.513 20.321 -2.335 -2.938 0.548  -0.506 "C5'"  A1IEA 14 
A1IEA N7     N4  N 0 1 Y N N N N N 25.157 24.521 -5.716 2.709  -1.967 -1.118 N7     A1IEA 15 
A1IEA N9     N5  N 0 1 Y N N N N N 25.814 23.993 -3.729 1.700  -0.268 -0.189 N9     A1IEA 16 
A1IEA "O2'"  O1  O 0 1 N N N N N N 23.614 22.769 -1.831 1.228  2.967  -0.435 "O2'"  A1IEA 17 
A1IEA "O3'"  O2  O 0 1 N N N N N N 25.374 22.038 0.144  -1.272 3.424  -0.597 "O3'"  A1IEA 18 
A1IEA "O4'"  O3  O 0 1 N N N N N N 27.149 22.687 -2.340 -0.646 0.021  0.156  "O4'"  A1IEA 19 
A1IEA "O5'"  O4  O 0 1 N N N N N N 27.217 19.112 -1.663 -3.558 -0.272 0.486  "O5'"  A1IEA 20 
A1IEA OP3    O5  O 0 1 N Y N N N N 26.303 18.078 -3.739 -5.301 -1.944 1.526  OP3    A1IEA 21 
A1IEA OP2    O6  O 0 1 N N N N N N 26.497 16.744 -1.487 -6.131 0.100  0.095  OP2    A1IEA 22 
A1IEA P      P1  P 0 1 N N N N N N 27.058 17.757 -2.465 -4.973 -1.006 0.259  P      A1IEA 23 
A1IEA H8     H1  H 0 1 N N N N N N 24.213 22.933 -4.650 0.648  -1.659 -1.482 H8     A1IEA 24 
A1IEA H2     H2  H 0 1 N N N N N N 28.975 27.271 -3.818 5.549  1.046  1.843  H2     A1IEA 25 
A1IEA H61    H3  H 0 1 N N N N N N 26.851 27.485 -7.775 6.639  -2.697 -0.524 H61    A1IEA 26 
A1IEA H62    H4  H 0 1 N N N N N N 26.421 25.928 -8.012 5.225  -3.195 -1.283 H62    A1IEA 27 
A1IEA "H1'"  H5  H 0 1 N N N N N N 25.796 24.073 -1.630 0.835  1.098  1.165  "H1'"  A1IEA 28 
A1IEA H1P3   H6  H 0 0 N N N N N N 27.569 24.635 -1.827 2.594  1.430  2.553  H1P3   A1IEA 29 
A1IEA H1     H7  H 0 1 N N N N N N 29.192 25.199 -2.351 3.821  2.508  1.844  H1     A1IEA 30 
A1IEA H3     H8  H 0 1 N N N N N N 28.021 26.363 -1.643 2.323  2.155  0.950  H3     A1IEA 31 
A1IEA "H2'"  H9  H 0 1 N N N N N N 24.770 21.626 -3.121 0.924  1.462  -1.835 "H2'"  A1IEA 32 
A1IEA "H3'"  H10 H 0 1 N N N N N N 25.194 20.365 -1.133 -1.344 1.877  -1.982 "H3'"  A1IEA 33 
A1IEA "H4'"  H11 H 0 1 N N N N N N 27.634 21.585 -0.625 -1.765 1.573  0.998  "H4'"  A1IEA 34 
A1IEA "H5''" H12 H 0 0 N N N N N N 28.601 20.405 -2.471 -3.596 1.381  -0.752 "H5''" A1IEA 35 
A1IEA "H5'"  H13 H 0 1 N N N N N N 27.020 20.321 -3.318 -2.752 -0.044 -1.402 "H5'"  A1IEA 36 
A1IEA "HO2'" H14 H 0 0 N N N N N N 22.992 22.064 -1.699 1.192  3.705  -1.060 "HO2'" A1IEA 37 
A1IEA "HO3'" H15 H 0 0 N Y N N N N 25.802 21.522 0.817  -0.852 4.088  -1.160 "HO3'" A1IEA 38 
A1IEA HOP3   H16 H 0 0 N Y N N N N 26.877 17.959 -4.486 -6.141 -2.418 1.457  HOP3   A1IEA 39 
A1IEA HOP2   H17 H 0 0 N N N N N N 27.165 16.102 -1.278 -6.232 0.681  0.862  HOP2   A1IEA 40 
A1IEA OP1    O1P O 0 1 N N N N N N 28.576 17.319 -2.749 -4.907 -1.836 -0.965 OP1    A1IEA 41 
# 
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 
A1IEA N6    C6     SING N N 1  
A1IEA C6    N1     DOUB Y N 2  
A1IEA C6    C5     SING Y N 3  
A1IEA N7    C5     SING Y N 4  
A1IEA N7    C8     DOUB Y N 5  
A1IEA N1    C2     SING Y N 6  
A1IEA C5    C4     DOUB Y N 7  
A1IEA C8    N9     SING Y N 8  
A1IEA C2    N3     DOUB Y N 9  
A1IEA C4    N9     SING Y N 10 
A1IEA C4    N3     SING Y N 11 
A1IEA OP3   P      SING N N 12 
A1IEA N9    "C1'"  SING N N 13 
A1IEA N3    C1P    SING N N 14 
A1IEA P     "O5'"  SING N N 15 
A1IEA P     OP2    SING N N 16 
A1IEA "C1'" "O4'"  SING N N 17 
A1IEA "C1'" "C2'"  SING N N 18 
A1IEA "O4'" "C4'"  SING N N 19 
A1IEA "C5'" "O5'"  SING N N 20 
A1IEA "C5'" "C4'"  SING N N 21 
A1IEA "C2'" "O2'"  SING N N 22 
A1IEA "C2'" "C3'"  SING N N 23 
A1IEA "C4'" "C3'"  SING N N 24 
A1IEA "C3'" "O3'"  SING N N 25 
A1IEA C8    H8     SING N N 26 
A1IEA C2    H2     SING N N 27 
A1IEA N6    H61    SING N N 28 
A1IEA N6    H62    SING N N 29 
A1IEA "C1'" "H1'"  SING N N 30 
A1IEA C1P   H1P3   SING N N 31 
A1IEA C1P   H1     SING N N 32 
A1IEA C1P   H3     SING N N 33 
A1IEA "C2'" "H2'"  SING N N 34 
A1IEA "C3'" "H3'"  SING N N 35 
A1IEA "C4'" "H4'"  SING N N 36 
A1IEA "C5'" "H5''" SING N N 37 
A1IEA "C5'" "H5'"  SING N N 38 
A1IEA "O2'" "HO2'" SING N N 39 
A1IEA "O3'" "HO3'" SING N N 40 
A1IEA OP3   HOP3   SING N N 41 
A1IEA OP2   HOP2   SING N N 42 
A1IEA P     OP1    DOUB N N 43 
# 
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 
A1IEA InChI            InChI                1.06  "InChI=1S/C11H16N5O7P/c1-15-3-14-9(12)6-10(15)16(4-13-6)11-8(18)7(17)5(23-11)2-22-24(19,20)21/h3-5,7-8,11-12,17-18H,2H2,1H3,(H2,19,20,21)/p+1/t5-,7-,8-,11-/m1/s1" 
A1IEA InChIKey         InChI                1.06  XPHLDSANNGAVEC-IOSLPCCCSA-O                                                                                                                                        
A1IEA SMILES_CANONICAL CACTVS               3.385 "C[n+]1cnc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c12"                                                                                               
A1IEA SMILES           CACTVS               3.385 "C[n+]1cnc(N)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c12"                                                                                                     
A1IEA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[n+]1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N"                                                                                               
A1IEA SMILES           "OpenEye OEToolkits" 2.0.7 "C[n+]1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N"                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           A1IEA 
_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},4~{R},5~{R})-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(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 
A1IEA "Create component" 2024-06-13 PDBE 
A1IEA "Modify name"      2024-08-30 PDBE 
A1IEA "Initial release"  2025-01-22 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1IEA 
_pdbx_chem_comp_synonyms.name         "[(2R,3S,4R,5R)-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
