data_M1Y
# 
_chem_comp.id                                    M1Y 
_chem_comp.name                                  "(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-13 
_chem_comp.pdbx_modified_date                    2017-12-01 
_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                        338.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     M1Y 
_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        6AZ1 
_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 
M1Y C1    C1  C 0 1 N N N 123.500 200.477 169.994 5.447  1.096  -1.681 C1    M1Y 1  
M1Y "C1'" C2  C 0 1 N N S 123.033 205.358 170.039 1.080  -1.043 -0.869 "C1'" M1Y 2  
M1Y C2    C3  C 0 1 N N N 121.805 201.543 171.537 4.274  1.408  0.426  C2    M1Y 3  
M1Y "C2'" C4  C 0 1 N N R 123.854 206.065 171.084 1.014  -2.315 -0.001 "C2'" M1Y 4  
M1Y "C3'" C5  C 0 1 N N R 124.937 206.730 170.250 -0.404 -2.277 0.619  "C3'" M1Y 5  
M1Y C4    C6  C 0 1 N N N 121.544 203.949 171.593 2.206  0.417  0.873  C4    M1Y 6  
M1Y "C4'" C7  C 0 1 N N R 125.057 205.865 168.996 -1.158 -1.334 -0.352 "C4'" M1Y 7  
M1Y C5    C8  C 0 1 N N N 122.581 204.062 170.585 2.221  -0.171 -0.414 C5    M1Y 8  
M1Y "C5'" C9  C 0 1 N N N 126.287 205.007 168.849 -2.351 -0.681 0.349  "C5'" M1Y 9  
M1Y C6    C10 C 0 1 N N N 123.157 202.936 170.133 3.276  0.056  -1.227 C6    M1Y 10 
M1Y N1    N1  N 0 1 N N N 122.796 201.684 170.571 4.304  0.850  -0.798 N1    M1Y 11 
M1Y N3    N2  N 0 1 N N N 121.181 202.657 172.056 3.239  1.194  1.258  N3    M1Y 12 
M1Y O2    O1  O 0 1 N N N 121.482 200.428 171.947 5.198  2.111  0.786  O2    M1Y 13 
M1Y "O2'" O2  O 0 1 N N N 123.029 207.055 171.670 1.176  -3.482 -0.809 "O2'" M1Y 14 
M1Y "O3'" O3  O 0 1 N N N 126.180 206.986 170.914 -0.370 -1.729 1.939  "O3'" M1Y 15 
M1Y O4    O4  O 0 1 N N N 120.980 204.913 172.063 1.268  0.224  1.626  O4    M1Y 16 
M1Y "O4'" O5  O 0 1 N N N 123.890 205.019 168.994 -0.166 -0.346 -0.701 "O4'" M1Y 17 
M1Y "O5'" O6  O 0 1 N N N 125.931 203.666 168.549 -3.095 0.090  -0.596 "O5'" M1Y 18 
M1Y OP1   O7  O 0 1 N N N 128.201 203.393 167.579 -5.398 0.009  0.433  OP1   M1Y 19 
M1Y OP2   O8  O 0 1 N N N 126.722 201.334 168.200 -4.032 2.095  0.823  OP2   M1Y 20 
M1Y P     P1  P 0 1 N N N 126.860 202.731 167.664 -4.420 0.918  -0.204 P     M1Y 21 
M1Y H1    H1  H 0 1 N N N 123.093 199.562 170.450 5.255  1.982  -2.286 H1    M1Y 22 
M1Y H2    H2  H 0 1 N N N 123.342 200.446 168.906 6.343  1.254  -1.079 H2    M1Y 23 
M1Y H3    H3  H 0 1 N N N 124.577 200.545 170.206 5.595  0.235  -2.332 H3    M1Y 24 
M1Y H4    H4  H 0 1 N N N 122.185 205.978 169.714 1.216  -1.316 -1.916 H4    M1Y 25 
M1Y H5    H5  H 0 1 N N N 124.279 205.363 171.816 1.775  -2.284 0.780  H5    M1Y 26 
M1Y H6    H6  H 0 1 N N N 124.530 207.698 169.923 -0.853 -3.271 0.625  H6    M1Y 27 
M1Y H7    H7  H 0 1 N N N 125.008 206.535 168.125 -1.486 -1.878 -1.238 H7    M1Y 28 
M1Y H8    H8  H 0 1 N N N 126.856 205.028 169.790 -2.992 -1.454 0.772  H8    M1Y 29 
M1Y H9    H9  H 0 1 N N N 126.910 205.406 168.035 -1.992 -0.030 1.146  H9    M1Y 30 
M1Y H10   H10 H 0 1 N N N 123.939 203.018 169.392 3.307  -0.388 -2.211 H10   M1Y 31 
M1Y H11   H11 H 0 1 N N N 120.475 202.555 172.757 3.235  1.601  2.139  H11   M1Y 32 
M1Y H12   H12 H 0 1 N N N 122.205 206.664 171.937 1.143  -4.311 -0.313 H12   M1Y 33 
M1Y H13   H13 H 0 1 N N N 126.025 207.527 171.680 0.167  -2.238 2.562  H13   M1Y 34 
M1Y H15   H15 H 0 1 N N N 127.578 201.002 168.445 -3.393 2.730  0.471  H15   M1Y 35 
M1Y OP3   OP3 O 0 1 N Y N 126.183 202.742 166.214 -5.067 1.556  -1.533 OP3   M1Y 36 
M1Y H17   H17 H 0 1 N N N 126.766 203.165 165.595 -5.870 2.070  -1.372 H17   M1Y 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 
M1Y OP1   P     DOUB N N 1  
M1Y P     OP2   SING N N 2  
M1Y P     "O5'" SING N N 3  
M1Y "O5'" "C5'" SING N N 4  
M1Y "C5'" "C4'" SING N N 5  
M1Y "O4'" "C4'" SING N N 6  
M1Y "O4'" "C1'" SING N N 7  
M1Y "C4'" "C3'" SING N N 8  
M1Y C1    N1    SING N N 9  
M1Y "C1'" C5    SING N N 10 
M1Y "C1'" "C2'" SING N N 11 
M1Y C6    N1    SING N N 12 
M1Y C6    C5    DOUB N N 13 
M1Y "C3'" "O3'" SING N N 14 
M1Y "C3'" "C2'" SING N N 15 
M1Y N1    C2    SING N N 16 
M1Y C5    C4    SING N N 17 
M1Y "C2'" "O2'" SING N N 18 
M1Y C2    O2    DOUB N N 19 
M1Y C2    N3    SING N N 20 
M1Y C4    N3    SING N N 21 
M1Y C4    O4    DOUB N N 22 
M1Y C1    H1    SING N N 23 
M1Y C1    H2    SING N N 24 
M1Y C1    H3    SING N N 25 
M1Y "C1'" H4    SING N N 26 
M1Y "C2'" H5    SING N N 27 
M1Y "C3'" H6    SING N N 28 
M1Y "C4'" H7    SING N N 29 
M1Y "C5'" H8    SING N N 30 
M1Y "C5'" H9    SING N N 31 
M1Y C6    H10   SING N N 32 
M1Y N3    H11   SING N N 33 
M1Y "O2'" H12   SING N N 34 
M1Y "O3'" H13   SING N N 35 
M1Y OP2   H15   SING N N 36 
M1Y P     OP3   SING N N 37 
M1Y OP3   H17   SING N N 38 
# 
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 
M1Y SMILES           ACDLabs              12.01 "CN2C(=O)NC(=O)C(C1C(O)C(O)C(COP(=O)(O)O)O1)=C2"                                                                                                         
M1Y InChI            InChI                1.03  "InChI=1S/C10H15N2O9P/c1-12-2-4(9(15)11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6+,7-,8+/m1/s1" 
M1Y InChIKey         InChI                1.03  VORAOZTXNOXTGQ-CWKFCGSDSA-N                                                                                                                              
M1Y SMILES_CANONICAL CACTVS               3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@H](O)[C@H]2O)C(=O)NC1=O"                                                                                          
M1Y SMILES           CACTVS               3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O"                                                                                               
M1Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                          
M1Y SMILES           "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                           
# 
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 
M1Y "SYSTEMATIC NAME" ACDLabs              12.01 "(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol"                                      
M1Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{R},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-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 
M1Y "Create component" 2017-09-13 RCSB 
M1Y "Initial release"  2017-12-06 RCSB 
# 
