data_M3X
# 
_chem_comp.id                                    M3X 
_chem_comp.name                                  "(2~{S})-2-azanyl-6-[[4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-1-ium-2-yl]amino]hexanoic acid" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C15 H27 N5 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         
;lysidine 5'-monophosphate
;
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2022-12-22 
_chem_comp.pdbx_modified_date                    2024-03-01 
_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                        452.377 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     M3X 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
M3X N1    N1  N 1 1 Y N N N N N ? ? ? -0.682 1.714  0.217  N1    M3X 1  
M3X C2    C1  C 0 1 Y N N N N N ? ? ? 0.605  1.998  0.078  C2    M3X 2  
M3X C4    C2  C 0 1 Y N N N N N ? ? ? 0.177  4.262  0.002  C4    M3X 3  
M3X C5    C3  C 0 1 Y N N N N N ? ? ? -1.186 3.993  0.143  C5    M3X 4  
M3X C6    C4  C 0 1 Y N N N N N ? ? ? -1.591 2.677  0.250  C6    M3X 5  
M3X N     N2  N 0 1 N N N N N N ? ? ? 7.752  -0.144 -1.766 N     M3X 6  
M3X C     C5  C 0 1 N N N N N N ? ? ? 8.305  -2.029 -0.335 C     M3X 7  
M3X O     O1  O 0 1 N N N N N N ? ? ? 8.575  -2.546 0.874  O     M3X 8  
M3X CB    C6  C 0 1 N N N N N N ? ? ? 6.024  -1.057 -0.289 CB    M3X 9  
M3X CG    C7  C 0 1 N N N N N N ? ? ? 5.233  0.253  -0.280 CG    M3X 10 
M3X CD    C8  C 0 1 N N N N N N ? ? ? 3.742  -0.053 -0.120 CD    M3X 11 
M3X CE    C9  C 0 1 N N N N N N ? ? ? 2.951  1.256  -0.111 CE    M3X 12 
M3X CZ    C10 C 0 1 N N S N N N ? ? ? 7.515  -0.751 -0.449 CZ    M3X 13 
M3X OXT   O2  O 0 1 N N N N N N ? ? ? 8.695  -2.589 -1.332 OXT   M3X 14 
M3X "C1'" C11 C 0 1 N N R N N N ? ? ? -1.105 0.317  0.329  "C1'" M3X 15 
M3X "C2'" C12 C 0 1 N N R N N N ? ? ? -1.077 -0.137 1.806  "C2'" M3X 16 
M3X "C3'" C13 C 0 1 N N S N N N ? ? ? -2.306 -1.064 1.937  "C3'" M3X 17 
M3X "C4'" C14 C 0 1 N N R N N N ? ? ? -2.931 -1.061 0.525  "C4'" M3X 18 
M3X "C5'" C15 C 0 1 N N N N N N ? ? ? -4.458 -1.089 0.618  "C5'" M3X 19 
M3X N2    N3  N 0 1 N N N N N N ? ? ? 1.524  0.964  0.042  N2    M3X 20 
M3X N3    N4  N 0 1 Y N N N N N ? ? ? 1.034  3.246  -0.028 N3    M3X 21 
M3X N4    N5  N 0 1 N N N N N N ? ? ? 0.628  5.567  -0.108 N4    M3X 22 
M3X "O2'" O3  O 0 1 N N N N N N ? ? ? 0.125  -0.856 2.086  "O2'" M3X 23 
M3X "O3'" O4  O 0 1 N N N N N N ? ? ? -1.901 -2.384 2.303  "O3'" M3X 24 
M3X "O4'" O5  O 0 1 N N N N N N ? ? ? -2.485 0.175  -0.074 "O4'" M3X 25 
M3X "O5'" O6  O 0 1 N N N N N N ? ? ? -5.013 -1.204 -0.694 "O5'" M3X 26 
M3X OP2   O7  O 0 1 N N N N N N ? ? ? -6.863 -1.259 -2.562 OP1   M3X 27 
M3X OP3   O8  O 0 1 N Y N N N N ? ? ? -7.207 -2.607 -0.331 OP2   M3X 28 
M3X P     P1  P 0 1 N N N N N N ? ? ? -6.598 -1.262 -0.974 P     M3X 29 
M3X H1    H1  H 0 1 N N N N N N ? ? ? -1.907 4.797  0.172  H1    M3X 30 
M3X H2    H2  H 0 1 N N N N N N ? ? ? -2.638 2.435  0.358  H2    M3X 31 
M3X H3    H3  H 0 1 N N N N N N ? ? ? 8.718  0.126  -1.871 H3    M3X 32 
M3X H5    H5  H 0 1 N N N N N N ? ? ? 7.468  -0.767 -2.507 H5    M3X 33 
M3X H6    H6  H 0 1 N N N N N N ? ? ? 9.085  -3.367 0.896  H6    M3X 34 
M3X H7    H7  H 0 1 N N N N N N ? ? ? 5.861  -1.587 0.649  H7    M3X 35 
M3X H8    H8  H 0 1 N N N N N N ? ? ? 5.690  -1.678 -1.120 H8    M3X 36 
M3X H9    H9  H 0 1 N N N N N N ? ? ? 5.568  0.874  0.551  H9    M3X 37 
M3X H10   H10 H 0 1 N N N N N N ? ? ? 5.397  0.783  -1.218 H10   M3X 38 
M3X H11   H11 H 0 1 N N N N N N ? ? ? 3.408  -0.674 -0.951 H11   M3X 39 
M3X H12   H12 H 0 1 N N N N N N ? ? ? 3.579  -0.583 0.818  H12   M3X 40 
M3X H13   H13 H 0 1 N N N N N N ? ? ? 3.286  1.877  0.720  H13   M3X 41 
M3X H14   H14 H 0 1 N N N N N N ? ? ? 3.115  1.786  -1.049 H14   M3X 42 
M3X H15   H15 H 0 1 N N N N N N ? ? ? 7.829  -0.058 0.332  H15   M3X 43 
M3X H16   H16 H 0 1 N N N N N N ? ? ? -0.465 -0.323 -0.278 H16   M3X 44 
M3X H17   H17 H 0 1 N N N N N N ? ? ? -1.171 0.722  2.471  H17   M3X 45 
M3X H18   H18 H 0 1 N N N N N N ? ? ? -3.010 -0.663 2.667  H18   M3X 46 
M3X H19   H19 H 0 1 N N N N N N ? ? ? -2.571 -1.913 -0.051 H19   M3X 47 
M3X H20   H20 H 0 1 N N N N N N ? ? ? -4.770 -1.942 1.220  H20   M3X 48 
M3X H21   H21 H 0 1 N N N N N N ? ? ? -4.811 -0.168 1.082  H21   M3X 49 
M3X H22   H22 H 0 1 N N N N N N ? ? ? 1.223  0.045  0.118  H22   M3X 50 
M3X H23   H23 H 0 1 N N N N N N ? ? ? -0.004 6.302  -0.089 H23   M3X 51 
M3X H24   H24 H 0 1 N N N N N N ? ? ? 1.577  5.745  -0.206 H24   M3X 52 
M3X H25   H25 H 0 1 N N N N N N ? ? ? 0.195  -1.164 3.000  H25   M3X 53 
M3X H26   H26 H 0 1 N N N N N N ? ? ? -1.448 -2.434 3.156  H26   M3X 54 
M3X H27   H27 H 0 1 N N N N N N ? ? ? -7.798 -1.293 -2.805 H27   M3X 55 
M3X H28   H28 H 0 1 N Y N N N N ? ? ? -6.824 -3.421 -0.686 H28   M3X 56 
M3X OP1   O9  O 0 1 N N N N N N ? ? ? -7.251 -0.083 -0.362 O1    M3X 57 
# 
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 
M3X N4    C4    SING N N 1  
M3X C4    C5    DOUB Y N 2  
M3X C4    N3    SING Y N 3  
M3X C5    C6    SING Y N 4  
M3X N3    C2    DOUB Y N 5  
M3X OP2   P     SING N N 6  
M3X C6    N1    DOUB Y N 7  
M3X P     OP3   SING N N 8  
M3X P     "O5'" SING N N 9  
M3X C2    N1    SING Y N 10 
M3X C2    N2    SING N N 11 
M3X CD    CE    SING N N 12 
M3X CD    CG    SING N N 13 
M3X CE    N2    SING N N 14 
M3X N1    "C1'" SING N N 15 
M3X "O5'" "C5'" SING N N 16 
M3X CB    CG    SING N N 17 
M3X CB    CZ    SING N N 18 
M3X OXT   C     DOUB N N 19 
M3X "C1'" "O4'" SING N N 20 
M3X "C1'" "C2'" SING N N 21 
M3X C     CZ    SING N N 22 
M3X C     O     SING N N 23 
M3X CZ    N     SING N N 24 
M3X "C5'" "C4'" SING N N 25 
M3X "O4'" "C4'" SING N N 26 
M3X "C3'" "C2'" SING N N 27 
M3X "C3'" "C4'" SING N N 28 
M3X "C3'" "O3'" SING N N 29 
M3X "C2'" "O2'" SING N N 30 
M3X C5    H1    SING N N 31 
M3X C6    H2    SING N N 32 
M3X N     H3    SING N N 33 
M3X N     H5    SING N N 34 
M3X O     H6    SING N N 35 
M3X CB    H7    SING N N 36 
M3X CB    H8    SING N N 37 
M3X CG    H9    SING N N 38 
M3X CG    H10   SING N N 39 
M3X CD    H11   SING N N 40 
M3X CD    H12   SING N N 41 
M3X CE    H13   SING N N 42 
M3X CE    H14   SING N N 43 
M3X CZ    H15   SING N N 44 
M3X "C1'" H16   SING N N 45 
M3X "C2'" H17   SING N N 46 
M3X "C3'" H18   SING N N 47 
M3X "C4'" H19   SING N N 48 
M3X "C5'" H20   SING N N 49 
M3X "C5'" H21   SING N N 50 
M3X N2    H22   SING N N 51 
M3X N4    H23   SING N N 52 
M3X N4    H24   SING N N 53 
M3X "O2'" H25   SING N N 54 
M3X "O3'" H26   SING N N 55 
M3X OP2   H27   SING N N 56 
M3X OP3   H28   SING N N 57 
M3X P     OP1   DOUB N N 58 
# 
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 
M3X InChI            InChI                1.06  "InChI=1S/C15H26N5O9P/c16-8(14(23)24)3-1-2-5-18-15-19-10(17)4-6-20(15)13-12(22)11(21)9(29-13)7-28-30(25,26)27/h4,6,8-9,11-13,21-22H,1-3,5,7,16H2,(H5,17,18,19,23,24,25,26,27)/p+1/t8-,9+,11+,12+,13+/m0/s1" 
M3X InChIKey         InChI                1.06  HXUVGGWPASIJQK-IINAIABHSA-O                                                                                                                                                                                 
M3X SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCCNc1nc(N)cc[n+]1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(O)=O"                                                                                                                            
M3X SMILES           CACTVS               3.385 "N[CH](CCCCNc1nc(N)cc[n+]1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(O)=O"                                                                                                                                    
M3X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                                          
M3X SMILES           "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           M3X 
_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~{S})-2-azanyl-6-[[4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-1-ium-2-yl]amino]hexanoic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      M3X 
_pdbx_chem_comp_synonyms.name         
;lysidine 5'-monophosphate
;
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_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 
M3X "Create component" 2022-12-22 PDBJ 
M3X "Modify atom id"   2022-12-23 PDBJ 
M3X "Modify synonyms"  2023-01-06 PDBJ 
M3X "Initial release"  2024-03-06 RCSB 
# 
