data_A1L9Q
# 
_chem_comp.id                                    A1L9Q 
_chem_comp.name                                  "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-3-methoxy-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2-thione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N3 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-05-20 
_chem_comp.pdbx_modified_date                    2025-11-07 
_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                        353.289 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1L9Q 
_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        9UYT 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
A1L9Q "C1'" C1  C 0 1 N N R N N N 0.732  9.935  3.190 1.269  0.819  0.876  "C1'" A1L9Q 1  
A1L9Q C2    C2  C 0 1 N N N N N N 3.177  9.762  3.772 2.126  -1.072 -0.393 C2    A1L9Q 2  
A1L9Q "C2'" C3  C 0 1 N N R N N N 0.014  9.387  4.420 1.224  1.826  -0.302 "C2'" A1L9Q 3  
A1L9Q "C3'" C4  C 0 1 N N R N N N -0.819 10.594 4.804 -0.217 2.383  -0.196 "C3'" A1L9Q 4  
A1L9Q C4    C5  C 0 1 N N N N N N 4.499  11.680 4.270 4.105  -2.143 0.127  C4    A1L9Q 5  
A1L9Q "C4'" C6  C 0 1 N N R N N N -1.298 11.071 3.448 -0.978 1.314  0.611  "C4'" A1L9Q 6  
A1L9Q C5    C7  C 0 1 N N N N N N 3.342  12.534 4.059 4.296  -1.260 1.211  C5    A1L9Q 7  
A1L9Q "C5'" C8  C 0 1 N N N N N N -1.776 12.492 3.374 -2.162 0.791  -0.204 "C5'" A1L9Q 8  
A1L9Q C6    C9  C 0 1 N N N N N N 2.150  11.940 3.715 3.370  -0.301 1.446  C6    A1L9Q 9  
A1L9Q CM2   C10 C 0 1 N N N N N N -0.244 7.056  4.131 2.696  3.405  -1.343 CM2   A1L9Q 10 
A1L9Q N1    N1  N 0 1 N N N N N N 2.022  10.571 3.556 2.279  -0.214 0.632  N1    A1L9Q 11 
A1L9Q N3    N2  N 0 1 N N N N N N 4.420  10.342 4.130 3.029  -2.020 -0.637 N3    A1L9Q 12 
A1L9Q N4    N3  N 0 1 N N N N N N 5.733  12.232 4.621 5.031  -3.127 -0.135 N4    A1L9Q 13 
A1L9Q "O2'" O1  O 0 1 N N N N N N -0.822 8.323  3.992 2.187  2.865  -0.122 "O2'" A1L9Q 14 
A1L9Q "O3'" O2  O 0 1 N N N N N N -1.862 10.309 5.714 -0.220 3.632  0.499  "O3'" A1L9Q 15 
A1L9Q "O4'" O3  O 0 1 N N N N N N -0.124 10.904 2.610 -0.055 0.244  0.879  "O4'" A1L9Q 16 
A1L9Q "O5'" O4  O 0 1 N N N N N N -0.714 13.392 3.608 -2.928 -0.113 0.595  "O5'" A1L9Q 17 
A1L9Q OP1   O5  O 0 1 N N N N N N -2.402 15.138 3.821 -5.212 0.154  -0.446 OP1   A1L9Q 18 
A1L9Q OP2   O6  O 0 1 N N N N N N 0.093  15.731 4.217 -3.855 -1.858 -1.140 OP2   A1L9Q 19 
A1L9Q P     P1  P 0 1 N N N N N N -0.952 14.951 3.460 -4.251 -0.854 0.055  P     A1L9Q 20 
A1L9Q S2    S1  S 0 1 N N N N N N 3.083  8.166  3.606 0.745  -0.946 -1.396 S2    A1L9Q 21 
A1L9Q H1    H1  H 0 1 N N N N N N 0.915  9.111  2.485 1.468  1.335  1.815  H1    A1L9Q 22 
A1L9Q H2    H2  H 0 1 N N N N N N 0.720  9.102  5.214 1.375  1.318  -1.254 H2    A1L9Q 23 
A1L9Q H3    H3  H 0 1 N N N N N N -0.151 11.359 5.227 -0.655 2.499  -1.188 H3    A1L9Q 24 
A1L9Q H4    H4  H 0 1 N N N N N N -2.100 10.404 3.100 -1.333 1.740  1.549  H4    A1L9Q 25 
A1L9Q H5    H5  H 0 1 N N N N N N 3.416  13.606 4.169 5.168  -1.347 1.842  H5    A1L9Q 26 
A1L9Q H6    H6  H 0 1 N N N N N N -2.194 12.680 2.374 -2.790 1.628  -0.509 H6    A1L9Q 27 
A1L9Q H7    H7  H 0 1 N N N N N N -2.556 12.650 4.133 -1.794 0.272  -1.089 H7    A1L9Q 28 
A1L9Q H8    H8  H 0 1 N N N N N N 1.282  12.565 3.563 3.493  0.388  2.268  H8    A1L9Q 29 
A1L9Q H9    H9  H 0 1 N N N N N N -0.951 6.290  3.780 3.180  2.614  -1.916 H9    A1L9Q 30 
A1L9Q H10   H10 H 0 1 N N N N N N 0.678  7.006  3.533 1.875  3.825  -1.925 H10   A1L9Q 31 
A1L9Q H11   H11 H 0 1 N N N N N N -0.005 6.876  5.190 3.421  4.188  -1.121 H11   A1L9Q 32 
A1L9Q H12   H12 H 0 1 N N N N N N 6.525  11.638 4.761 5.818  -3.214 0.426  H12   A1L9Q 33 
A1L9Q H13   H13 H 0 1 N N N N N N 5.825  13.222 4.733 4.897  -3.733 -0.880 H13   A1L9Q 34 
A1L9Q H14   H14 H 0 1 N N N N N N -1.492 10.017 6.539 -1.098 4.026  0.595  H14   A1L9Q 35 
A1L9Q H16   H16 H 0 1 N N N N N N -0.330 16.277 4.869 -3.226 -2.546 -0.883 H16   A1L9Q 36 
A1L9Q OP3   OP3 O 0 1 N N N N N N -0.823 15.198 1.886 -4.926 -1.689 1.255  OP3   A1L9Q 37 
A1L9Q H18   H18 H 0 1 N N N N N N -1.677 15.406 1.527 -5.730 -2.163 1.001  H18   A1L9Q 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 
A1L9Q "O4'" "C1'" SING N N 1  
A1L9Q "O4'" "C4'" SING N N 2  
A1L9Q "C1'" N1    SING N N 3  
A1L9Q "C1'" "C2'" SING N N 4  
A1L9Q "C5'" "C4'" SING N N 5  
A1L9Q "C5'" "O5'" SING N N 6  
A1L9Q "C4'" "C3'" SING N N 7  
A1L9Q P     "O5'" SING N N 8  
A1L9Q P     OP1   DOUB N N 9  
A1L9Q P     OP2   SING N N 10 
A1L9Q N1    C6    SING N N 11 
A1L9Q N1    C2    SING N N 12 
A1L9Q S2    C2    DOUB N N 13 
A1L9Q C6    C5    DOUB N N 14 
A1L9Q C2    N3    SING N N 15 
A1L9Q "O2'" CM2   SING N N 16 
A1L9Q "O2'" "C2'" SING N N 17 
A1L9Q C5    C4    SING N N 18 
A1L9Q N3    C4    DOUB N N 19 
A1L9Q C4    N4    SING N N 20 
A1L9Q "C2'" "C3'" SING N N 21 
A1L9Q "C3'" "O3'" SING N N 22 
A1L9Q "C1'" H1    SING N N 23 
A1L9Q "C2'" H2    SING N N 24 
A1L9Q "C3'" H3    SING N N 25 
A1L9Q "C4'" H4    SING N N 26 
A1L9Q C5    H5    SING N N 27 
A1L9Q "C5'" H6    SING N N 28 
A1L9Q "C5'" H7    SING N N 29 
A1L9Q C6    H8    SING N N 30 
A1L9Q CM2   H9    SING N N 31 
A1L9Q CM2   H10   SING N N 32 
A1L9Q CM2   H11   SING N N 33 
A1L9Q N4    H12   SING N N 34 
A1L9Q N4    H13   SING N N 35 
A1L9Q "O3'" H14   SING N N 36 
A1L9Q OP2   H16   SING N N 37 
A1L9Q P     OP3   SING N N 38 
A1L9Q OP3   H18   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 
A1L9Q InChI            InChI                1.06  "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(15,16)17)20-9(8)13-3-2-6(11)12-10(13)22/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,22)(H2,15,16,17)/t5-,7-,8-,9-/m1/s1" 
A1L9Q InChIKey         InChI                1.06  GWFOPAUVJXMOAL-ZOQUXTDFSA-N                                                                                                                                 
A1L9Q SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=S)N"                                                                                              
A1L9Q SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=S)N"                                                                                                    
A1L9Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=S)N)COP(=O)(O)O)O"                                                                                                
A1L9Q SMILES           "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=S)N)COP(=O)(O)O)O"                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           A1L9Q 
_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~{R},4~{R},5~{R})-5-(4-azanyl-2-sulfanylidene-pyrimidin-1-yl)-4-methoxy-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 
A1L9Q "Create component" 2025-05-20 PDBJ 
A1L9Q "Initial release"  2025-11-12 RCSB 
# 
