data_B8N
# 
_chem_comp.id                                    B8N 
_chem_comp.name                                  "(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N3 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-25 
_chem_comp.pdbx_modified_date                    2018-01-19 
_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                        439.312 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     B8N 
_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        6EK0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
B8N "O5'" O1  O 0 1 N N N 339.284 283.978 290.376 3.798  0.686  0.600  "O5'" B8N 1  
B8N "C5'" C1  C 0 1 N N N 340.047 285.164 290.233 3.284  0.109  -0.602 "C5'" B8N 2  
B8N "C4'" C2  C 0 1 N N R 339.638 286.199 291.244 2.751  -1.295 -0.307 "C4'" B8N 3  
B8N "O4'" O2  O 0 1 N N N 338.423 285.769 291.895 1.597  -1.229 0.558  "O4'" B8N 4  
B8N "C3'" C3  C 0 1 N N S 340.611 286.416 292.386 2.198  -1.951 -1.598 "C3'" B8N 5  
B8N "O3'" O3  O 0 1 N N N 341.665 287.294 292.032 3.240  -2.607 -2.323 "O3'" B8N 6  
B8N "C2'" C4  C 0 1 N N R 339.717 286.961 293.491 1.188  -2.978 -1.032 "C2'" B8N 7  
B8N "O2'" O4  O 0 1 N N N 339.492 288.347 293.304 1.779  -4.278 -0.967 "O2'" B8N 8  
B8N "C1'" C5  C 0 1 N N S 338.402 286.226 293.226 0.870  -2.456 0.382  "C1'" B8N 9  
B8N C5    C6  C 0 1 N N N 338.193 285.074 294.133 -0.609 -2.199 0.513  C5    B8N 10 
B8N C6    C7  C 0 1 N N N 338.428 283.783 293.692 -1.353 -2.912 1.386  C6    B8N 11 
B8N N1    N1  N 0 1 N N N 338.238 282.737 294.495 -2.695 -2.666 1.492  N1    B8N 12 
B8N C2    C8  C 0 1 N N N 337.780 282.899 295.808 -3.280 -1.720 0.735  C2    B8N 13 
B8N N3    N2  N 0 1 N N N 337.508 284.163 296.324 -2.562 -0.994 -0.142 N3    B8N 14 
B8N C4    C9  C 0 1 N N N 337.700 285.283 295.512 -1.237 -1.202 -0.272 C4    B8N 15 
B8N C34   C10 C 0 1 N N N 335.151 286.748 298.555 -3.745 3.779  -0.389 C34   B8N 16 
B8N CN1   C11 C 0 1 N N N 338.501 281.386 294.005 -3.502 -3.441 2.438  CN1   B8N 17 
B8N N34   N3  N 0 1 N N N 336.195 285.123 300.076 -5.307 2.105  -1.205 N34   B8N 18 
B8N O2    O5  O 0 1 N N N 337.613 281.903 296.528 -4.474 -1.518 0.846  O2    B8N 19 
B8N O4    O6  O 0 1 N N N 337.474 286.429 295.942 -0.586 -0.542 -1.062 O4    B8N 20 
B8N OP1   O7  O 0 1 N N N 338.710 281.633 289.724 5.532  2.264  -0.335 OP1   B8N 21 
B8N OP2   O8  O 0 1 N N N 341.004 282.221 290.805 3.306  3.254  0.328  OP2   B8N 22 
B8N P     P1  P 0 1 N N N 339.864 282.581 289.896 4.440  2.161  0.660  P     B8N 23 
B8N C31   C12 C 0 1 N N N 337.051 284.293 297.700 -3.224 0.030  -0.955 CN31  B8N 24 
B8N C32   C13 C 0 1 N N N 335.544 284.458 297.793 -3.192 1.368  -0.213 CN32  B8N 25 
B8N C33   C14 C 0 1 N N R 335.194 285.320 298.995 -3.883 2.437  -1.062 CN33  B8N 26 
B8N O36   O9  O 0 1 N N N 336.282 287.425 298.397 -2.602 4.473  -0.504 O341  B8N 27 
B8N O35   O10 O 0 1 N N N 334.088 287.302 298.329 -4.663 4.229  0.254  O342  B8N 28 
B8N H1    H1  H 0 1 N N N 341.111 284.925 290.375 2.476  0.731  -0.987 H1    B8N 29 
B8N H2    H2  H 0 1 N N N 339.894 285.570 289.222 4.080  0.047  -1.345 H2    B8N 30 
B8N H3    H3  H 0 1 N N N 339.470 287.157 290.731 3.529  -1.914 0.138  H3    B8N 31 
B8N H4    H4  H 0 1 N N N 341.014 285.442 292.702 1.694  -1.214 -2.224 H4    B8N 32 
B8N H5    H5  H 0 1 N N N 342.250 287.402 292.773 2.943  -3.033 -3.139 H5    B8N 33 
B8N H6    H6  H 0 1 N N N 340.117 286.719 294.487 0.285  -3.001 -1.642 H6    B8N 34 
B8N H7    H7  H 0 1 N N N 338.933 288.674 293.999 2.051  -4.629 -1.826 H7    B8N 35 
B8N H8    H8  H 0 1 N N N 337.576 286.940 293.363 1.189  -3.185 1.127  H8    B8N 36 
B8N H9    H9  H 0 1 N N N 338.771 283.621 292.681 -0.891 -3.674 1.996  H9    B8N 37 
B8N H10   H10 H 0 1 N N N 338.289 280.658 294.802 -3.516 -2.934 3.403  H10   B8N 38 
B8N H11   H11 H 0 1 N N N 337.856 281.178 293.139 -4.520 -3.529 2.059  H11   B8N 39 
B8N H12   H12 H 0 1 N N N 339.556 281.304 293.705 -3.070 -4.434 2.556  H12   B8N 40 
B8N H13   H13 H 0 1 N N N 335.955 285.694 300.861 -5.427 1.241  -1.711 H13   B8N 41 
B8N H14   H14 H 0 1 N N N 336.202 284.162 300.353 -5.760 2.064  -0.305 H14   B8N 42 
B8N H17   H17 H 0 1 N N N 340.844 281.368 291.192 2.559  3.244  0.941  H17   B8N 43 
B8N H18   H18 H 0 1 N N N 337.343 283.390 298.257 -2.703 0.130  -1.907 H18   B8N 44 
B8N H19   H19 H 0 1 N N N 337.532 285.174 298.151 -4.258 -0.262 -1.135 H19   B8N 45 
B8N H20   H20 H 0 1 N N N 335.172 284.940 296.877 -3.713 1.267  0.739  H20   B8N 46 
B8N H21   H21 H 0 1 N N N 335.074 283.469 297.903 -2.158 1.659  -0.033 H21   B8N 47 
B8N H22   H22 H 0 1 N N N 334.200 285.027 299.364 -3.418 2.476  -2.047 H22   B8N 48 
B8N H23   H23 H 0 1 N N N 336.085 288.309 298.109 -2.561 5.328  -0.054 H23   B8N 49 
B8N OP3   OP3 O 0 1 N Y N 340.447 282.892 288.437 5.030  2.429  2.133  OP3   B8N 50 
B8N H15   H15 H 0 1 N N N 339.944 282.416 287.786 5.434  3.301  2.242  H15   B8N 51 
# 
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 
B8N OP1   P     DOUB N N 1  
B8N P     "O5'" SING N N 2  
B8N P     OP2   SING N N 3  
B8N "C5'" "O5'" SING N N 4  
B8N "C5'" "C4'" SING N N 5  
B8N "C4'" "O4'" SING N N 6  
B8N "C4'" "C3'" SING N N 7  
B8N "O4'" "C1'" SING N N 8  
B8N "O3'" "C3'" SING N N 9  
B8N "C3'" "C2'" SING N N 10 
B8N "C1'" "C2'" SING N N 11 
B8N "C1'" C5    SING N N 12 
B8N "O2'" "C2'" SING N N 13 
B8N C6    C5    DOUB N N 14 
B8N C6    N1    SING N N 15 
B8N CN1   N1    SING N N 16 
B8N C5    C4    SING N N 17 
B8N N1    C2    SING N N 18 
B8N C4    O4    DOUB N N 19 
B8N C4    N3    SING N N 20 
B8N C2    N3    SING N N 21 
B8N C2    O2    DOUB N N 22 
B8N N3    C31   SING N N 23 
B8N C31   C32   SING N N 24 
B8N C32   C33   SING N N 25 
B8N O35   C34   DOUB N N 26 
B8N O36   C34   SING N N 27 
B8N C34   C33   SING N N 28 
B8N C33   N34   SING N N 29 
B8N "C5'" H1    SING N N 30 
B8N "C5'" H2    SING N N 31 
B8N "C4'" H3    SING N N 32 
B8N "C3'" H4    SING N N 33 
B8N "O3'" H5    SING N N 34 
B8N "C2'" H6    SING N N 35 
B8N "O2'" H7    SING N N 36 
B8N "C1'" H8    SING N N 37 
B8N C6    H9    SING N N 38 
B8N CN1   H10   SING N N 39 
B8N CN1   H11   SING N N 40 
B8N CN1   H12   SING N N 41 
B8N N34   H13   SING N N 42 
B8N N34   H14   SING N N 43 
B8N OP2   H17   SING N N 44 
B8N C31   H18   SING N N 45 
B8N C31   H19   SING N N 46 
B8N C32   H20   SING N N 47 
B8N C32   H21   SING N N 48 
B8N C33   H22   SING N N 49 
B8N O36   H23   SING N N 50 
B8N P     OP3   SING N N 51 
B8N OP3   H15   SING N N 52 
# 
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 
B8N InChI            InChI                1.03  "InChI=1S/C14H22N3O11P/c1-16-4-6(12(20)17(14(16)23)3-2-7(15)13(21)22)11-10(19)9(18)8(28-11)5-27-29(24,25)26/h4,7-11,18-19H,2-3,5,15H2,1H3,(H,21,22)(H2,24,25,26)/t7-,8-,9-,10-,11+/m1/s1" 
B8N InChIKey         InChI                1.03  BVRIEBGMUPJSJF-ILAIQSSSSA-N                                                                                                                                                               
B8N 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)N(CC[C@@H](N)C(O)=O)C1=O"                                                                                                       
B8N SMILES           CACTVS               3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N(CC[CH](N)C(O)=O)C1=O"                                                                                                               
B8N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CC[C@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                        
B8N SMILES           "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CCC(C(=O)O)N)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 
B8N "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
B8N "Create component" 2017-09-25 EBI  
B8N "Initial release"  2018-01-24 RCSB 
# 
