data_8RJ
# 
_chem_comp.id                                    8RJ 
_chem_comp.name                                  "(R)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C8 H13 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-03-03 
_chem_comp.pdbx_modified_date                    2022-06-13 
_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                        280.172 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8RJ 
_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        5V1K 
_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 
8RJ P     P1  P 0 1 N N N 25.943 30.276 15.279 4.321  0.010  0.174  P   8RJ 1  
8RJ OP2   O1  O 0 1 N N N 27.239 30.339 14.558 4.796  -1.220 -0.748 O1P 8RJ 2  
8RJ O1    O2  O 0 1 N N N 24.671 30.434 14.543 4.652  1.287  -0.498 O2P 8RJ 3  
8RJ "O5'" O3  O 0 1 N N N 26.031 31.249 16.551 2.730  -0.076 0.408  O3G 8RJ 4  
8RJ O4    O4  O 0 1 N N N 26.044 35.009 23.858 -5.630 0.234  0.909  O4  8RJ 5  
8RJ C4    C1  C 0 1 N N N 25.892 34.274 22.858 -4.509 0.219  0.433  C4  8RJ 6  
8RJ N3    N1  N 0 1 N N N 27.023 34.071 22.082 -3.781 1.352  0.368  N3  8RJ 7  
8RJ C2    C2  C 0 1 N N N 27.036 33.294 20.934 -2.542 1.334  -0.157 C2  8RJ 8  
8RJ O2    O5  O 0 1 N N N 28.114 33.203 20.341 -1.898 2.364  -0.209 O2  8RJ 9  
8RJ C5    C3  C 0 1 N N N 24.709 33.662 22.482 -3.955 -0.991 -0.051 C5  8RJ 10 
8RJ C5M   C4  C 0 1 N N N 23.510 33.804 23.192 -4.745 -2.273 0.015  C5M 8RJ 11 
8RJ C6    C5  C 0 1 N N N 24.735 32.877 21.327 -2.710 -0.981 -0.573 C6  8RJ 12 
8RJ N1    N2  N 0 1 N N N 25.894 32.697 20.558 -2.007 0.192  -0.626 N1  8RJ 13 
8RJ C1G   C6  C 0 1 N N N 25.806 31.848 19.368 -0.656 0.203  -1.192 C1G 8RJ 14 
8RJ C2G   C7  C 0 1 N N R 25.045 32.618 18.289 0.364  -0.071 -0.085 C2G 8RJ 15 
8RJ O2G   O6  O 0 1 N N N 25.910 33.738 17.904 0.176  -1.395 0.419  O2G 8RJ 16 
8RJ C3G   C8  C 0 1 N N N 24.827 31.721 17.105 1.779  0.064  -0.650 C3G 8RJ 17 
8RJ OP3   O7  O 0 1 N Y N 25.907 28.950 16.178 5.076  -0.060 1.594  O1  8RJ 18 
8RJ HOP2  H1  H 0 0 N Y N 27.080 30.486 13.633 4.610  -2.091 -0.370 H1  8RJ 19 
8RJ H2    H2  H 0 1 N N N 27.876 34.509 22.366 -4.153 2.184  0.702  H2  8RJ 20 
8RJ H3    H3  H 0 1 N N N 23.675 34.451 24.066 -5.718 -2.077 0.465  H3  8RJ 21 
8RJ H4    H4  H 0 1 N N N 22.749 34.257 22.539 -4.883 -2.667 -0.992 H4  8RJ 22 
8RJ H5    H5  H 0 1 N N N 23.164 32.815 23.528 -4.205 -3.001 0.620  H5  8RJ 23 
8RJ H6    H6  H 0 1 N N N 23.825 32.388 21.013 -2.271 -1.894 -0.947 H6  8RJ 24 
8RJ H7    H7  H 0 1 N N N 25.269 30.919 19.612 -0.576 -0.568 -1.958 H7  8RJ 25 
8RJ H8    H8  H 0 1 N N N 26.817 31.604 19.009 -0.456 1.179  -1.637 H8  8RJ 26 
8RJ H9    H9  H 0 1 N N N 24.084 32.977 18.685 0.225  0.648  0.723  H9  8RJ 27 
8RJ H10   H10 H 0 1 N N N 26.047 34.305 18.654 0.285  -2.088 -0.247 H10 8RJ 28 
8RJ H11   H11 H 0 1 N N N 24.282 32.284 16.333 1.894  1.044  -1.113 H11 8RJ 29 
8RJ H12   H12 H 0 1 N N N 24.224 30.858 17.424 1.948  -0.712 -1.396 H12 8RJ 30 
8RJ HOP3  H13 H 0 0 N Y N 25.070 28.514 16.067 6.040  -0.013 1.530  H13 8RJ 31 
# 
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 
8RJ O1    P     DOUB N N 1  
8RJ OP2   P     SING N N 2  
8RJ P     "O5'" SING N N 3  
8RJ "O5'" C3G   SING N N 4  
8RJ C3G   C2G   SING N N 5  
8RJ O2G   C2G   SING N N 6  
8RJ C2G   C1G   SING N N 7  
8RJ C1G   N1    SING N N 8  
8RJ O2    C2    DOUB N N 9  
8RJ N1    C2    SING N N 10 
8RJ N1    C6    SING N N 11 
8RJ C2    N3    SING N N 12 
8RJ C6    C5    DOUB N N 13 
8RJ N3    C4    SING N N 14 
8RJ C5    C4    SING N N 15 
8RJ C5    C5M   SING N N 16 
8RJ C4    O4    DOUB N N 17 
8RJ P     OP3   SING N N 18 
8RJ OP2   HOP2  SING N N 19 
8RJ N3    H2    SING N N 20 
8RJ C5M   H3    SING N N 21 
8RJ C5M   H4    SING N N 22 
8RJ C5M   H5    SING N N 23 
8RJ C6    H6    SING N N 24 
8RJ C1G   H7    SING N N 25 
8RJ C1G   H8    SING N N 26 
8RJ C2G   H9    SING N N 27 
8RJ O2G   H10   SING N N 28 
8RJ C3G   H11   SING N N 29 
8RJ C3G   H12   SING N N 30 
8RJ OP3   HOP3  SING N N 31 
# 
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 
8RJ SMILES           ACDLabs              12.01 "P(OCC(CN1C(NC(=O)C(C)=C1)=O)O)(O)(O)=O"                                                                                    
8RJ InChI            InChI                1.03  "InChI=1S/C8H13N2O7P/c1-5-2-10(8(13)9-7(5)12)3-6(11)4-17-18(14,15)16/h2,6,11H,3-4H2,1H3,(H,9,12,13)(H2,14,15,16)/t6-/m1/s1" 
8RJ InChIKey         InChI                1.03  WWYWEFRSGDVKHI-ZCFIWIBFSA-N                                                                                                 
8RJ SMILES_CANONICAL CACTVS               3.385 "CC1=CN(C[C@@H](O)CO[P](O)(O)=O)C(=O)NC1=O"                                                                                 
8RJ SMILES           CACTVS               3.385 "CC1=CN(C[CH](O)CO[P](O)(O)=O)C(=O)NC1=O"                                                                                   
8RJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C[C@H](COP(=O)(O)O)O"                                                                                    
8RJ SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)CC(COP(=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 
8RJ "SYSTEMATIC NAME" ACDLabs              12.01 "(2R)-2-hydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)propyl dihydrogen phosphate"     
8RJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-propyl] 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 
8RJ "Create component"      2017-03-03 RCSB 
8RJ "Initial release"       2017-06-21 RCSB 
8RJ "Modify parent residue" 2022-06-13 RCSB 
# 
