data_8RO
# 
_chem_comp.id                                    8RO 
_chem_comp.name                                  "[(2~{R},3~{S},5~{R})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O6 P S" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-01 
_chem_comp.pdbx_modified_date                    2017-09-15 
_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                        322.275 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8RO 
_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        5XUV 
_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 
8RO P     P1  P 0 1 N N N 3.030  9.324  -14.360 4.670  -1.049 0.064  P     8RO 1  
8RO OP1   O1  O 0 1 N N N 2.259  10.435 -14.973 3.943  -2.448 0.390  OP1   8RO 2  
8RO OP2   O2  O 0 1 N N N 3.996  9.543  -13.263 5.368  -1.357 -1.353 OP2   8RO 3  
8RO "O5'" O3  O 0 1 N N N 1.967  8.264  -13.841 3.428  -0.120 -0.369 "O5'" 8RO 4  
8RO "C5'" C1  C 0 1 N N N 1.024  7.722  -14.745 2.682  0.666  0.563  "C5'" 8RO 5  
8RO "C4'" C2  C 0 1 N N R 0.259  6.650  -14.017 1.578  1.423  -0.178 "C4'" 8RO 6  
8RO "O4'" O4  O 0 1 N N N 1.158  5.579  -13.669 0.599  0.505  -0.709 "O4'" 8RO 7  
8RO "C3'" C3  C 0 1 N N S -0.340 7.140  -12.701 0.759  2.296  0.807  "C3'" 8RO 8  
8RO "O3'" O5  O 0 1 N N N -1.760 7.115  -12.853 1.375  3.572  0.991  "O3'" 8RO 9  
8RO "C2'" C4  C 0 1 N N N 0.237  6.196  -11.608 -0.593 2.437  0.067  "C2'" 8RO 10 
8RO "C1'" C5  C 0 1 N N R 0.848  5.034  -12.408 -0.608 1.256  -0.922 "C1'" 8RO 11 
8RO N1    N1  N 0 1 N N N 2.144  4.389  -11.883 -1.774 0.407  -0.666 N1    8RO 12 
8RO C2    C6  C 0 1 N N N 2.154  3.043  -11.607 -1.816 -0.219 0.528  C2    8RO 13 
8RO O2    O6  O 0 1 N N N 1.146  2.389  -11.753 -1.152 0.176  1.468  O2    8RO 14 
8RO N3    N2  N 0 1 N N N 3.366  2.508  -11.141 -2.615 -1.291 0.646  N3    8RO 15 
8RO C4    C7  C 0 1 N N N 4.582  3.188  -10.911 -3.833 -1.010 -0.090 C4    8RO 16 
8RO S4    S1  S 0 1 N N N 5.671  2.617  -10.483 -3.934 -1.555 1.561  S4    8RO 17 
8RO C5    C8  C 0 1 N N N 4.475  4.623  -11.236 -4.023 -0.385 -1.245 C5    8RO 18 
8RO C7    C9  C 0 1 N N N 5.647  5.545  -11.078 -5.332 -0.379 -1.992 C7    8RO 19 
8RO C6    C10 C 0 1 N N N 3.294  5.134  -11.690 -2.770 0.330  -1.725 C6    8RO 20 
8RO H1    H1  H 0 1 N N N 1.696  10.091 -15.657 3.458  -2.454 1.227  H1    8RO 21 
8RO H2    H2  H 0 1 N N N 4.383  8.713  -13.011 6.154  -1.917 -1.291 H2    8RO 22 
8RO H3    H3  H 0 1 N N N 0.335  8.509  -15.085 2.234  0.013  1.312  H3    8RO 23 
8RO H4    H4  H 0 1 N N N 1.543  7.289  -15.613 3.346  1.378  1.052  H4    8RO 24 
8RO H5    H5  H 0 1 N N N -0.549 6.275  -14.663 2.003  2.035  -0.975 H5    8RO 25 
8RO H6    H6  H 0 1 N N N 0.009  8.165  -12.505 0.630  1.787  1.762  H6    8RO 26 
8RO H7    H7  H 0 1 N N N -2.170 7.415  -12.050 0.900  4.154  1.599  H7    8RO 27 
8RO H8    H8  H 0 1 N N N 1.007  6.710  -11.014 -1.423 2.357  0.770  H8    8RO 28 
8RO H9    H9  H 0 1 N N N -0.560 5.836  -10.941 -0.637 3.385  -0.470 H9    8RO 29 
8RO H10   H10 H 0 1 N N N 0.087  4.247  -12.512 -0.637 1.629  -1.946 H10   8RO 30 
8RO H11   H11 H 0 1 N N N 5.355  6.564  -11.373 -6.069 -0.958 -1.437 H11   8RO 31 
8RO H12   H12 H 0 1 N N N 5.973  5.546  -10.027 -5.683 0.647  -2.101 H12   8RO 32 
8RO H13   H13 H 0 1 N N N 6.473  5.201  -11.718 -5.189 -0.821 -2.978 H13   8RO 33 
8RO H14   H14 H 0 1 N N N 3.522  5.585  -12.667 -3.031 1.339  -2.045 H14   8RO 34 
8RO H15   H15 H 0 1 N N N 3.019  5.924  -10.976 -2.353 -0.216 -2.570 H15   8RO 35 
# 
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 
8RO P     OP1   SING N N 1  
8RO P     OP2   SING N N 2  
8RO P     "O5'" SING N N 3  
8RO "O5'" "C5'" SING N N 4  
8RO "C5'" "C4'" SING N N 5  
8RO "C4'" "O4'" SING N N 6  
8RO "C4'" "C3'" SING N N 7  
8RO "O4'" "C1'" SING N N 8  
8RO "C3'" "O3'" SING N N 9  
8RO "C3'" "C2'" SING N N 10 
8RO "C2'" "C1'" SING N N 11 
8RO "C1'" N1    SING N N 12 
8RO N1    C2    SING N N 13 
8RO N1    C6    SING N N 14 
8RO C2    O2    DOUB N N 15 
8RO C2    N3    SING N N 16 
8RO N3    C4    SING N N 17 
8RO N3    S4    SING N N 18 
8RO C4    S4    SING N N 19 
8RO C4    C5    DOUB N N 20 
8RO C5    C7    SING N N 21 
8RO C5    C6    SING N N 22 
8RO OP1   H1    SING N N 23 
8RO OP2   H2    SING N N 24 
8RO "C5'" H3    SING N N 25 
8RO "C5'" H4    SING N N 26 
8RO "C4'" H5    SING N N 27 
8RO "C3'" H6    SING N N 28 
8RO "O3'" H7    SING N N 29 
8RO "C2'" H8    SING N N 30 
8RO "C2'" H9    SING N N 31 
8RO "C1'" H10   SING N N 32 
8RO C7    H11   SING N N 33 
8RO C7    H12   SING N N 34 
8RO C7    H13   SING N N 35 
8RO C6    H14   SING N N 36 
8RO C6    H15   SING N N 37 
# 
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 
8RO InChI            InChI                1.03  "InChI=1S/C10H15N2O6PS/c1-5-3-11(10(14)12-9(5)20-12)8-2-6(13)7(18-8)4-17-19(15)16/h6-8,13,15-16H,2-4H2,1H3/t6-,7+,8+,12?/m0/s1" 
8RO InChIKey         InChI                1.03  GSELOCGYYRGWPL-AARIFPKGSA-N                                                                                                     
8RO SMILES_CANONICAL CACTVS               3.385 "CC1=C2SN2C(=O)N(C1)[C@H]3C[C@H](O)[C@@H](COP(O)O)O3"                                                                           
8RO SMILES           CACTVS               3.385 "CC1=C2SN2C(=O)N(C1)[CH]3C[CH](O)[CH](COP(O)O)O3"                                                                               
8RO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=C2N(S2)C(=O)N(C1)[C@H]3C[C@@H]([C@H](O3)COP(O)O)O"                                                                         
8RO SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=C2N(S2)C(=O)N(C1)C3CC(C(O3)COP(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 
8RO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
8RO "Create component"   2017-09-01 RCSB 
8RO "Other modification" 2017-09-05 PDBJ 
8RO "Initial release"    2017-09-20 RCSB 
# 
