data_EXC
#

_chem_comp.id                                   EXC
_chem_comp.name                                 
;3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5'
:5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one radical
;

_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C21 H26 N4 O9 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        "nitroxide spin-labeled nucleotide C-spin"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2010-10-19
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       509.426
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    EXC
_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  Y
_chem_comp.pdbx_model_coordinates_db_code       3OT0
_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
EXC  P       P     P  0  1  N  N  N  -0.153   -7.754  16.419  ?  ?  ?  P     EXC   1  
EXC  C1      C1    C  0  1  N  N  N  -2.100   -5.974  10.714  ?  ?  ?  C1    EXC   2  
EXC  N2      N2    N  0  1  N  N  N  -1.503   -6.616   9.687  ?  ?  ?  N2    EXC   3  
EXC  C3      C3    C  0  1  N  N  N  -0.713   -7.690   9.932  ?  ?  ?  C3    EXC   4  
EXC  N4      N4    N  0  1  N  N  N  -0.500   -8.116  11.194  ?  ?  ?  N4    EXC   5  
EXC  C5      C5    C  0  1  N  N  N  -1.084   -7.521  12.243  ?  ?  ?  C5    EXC   6  
EXC  C6      C6    C  0  1  N  N  N  -1.895   -6.417  12.019  ?  ?  ?  C6    EXC   7  
EXC  N7      N7    N  0  1  N  N  N  -2.899   -4.908  10.469  ?  ?  ?  N7    EXC   8  
EXC  C8      C8    C  0  1  Y  N  N  -3.510   -4.260  11.505  ?  ?  ?  C8    EXC   9  
EXC  C9      C9    C  0  1  Y  N  N  -3.318   -4.701  12.818  ?  ?  ?  C9    EXC  10  
EXC  "C1'"   C1*   C  0  1  N  N  R   0.326   -9.298  11.432  ?  ?  ?  C1*   EXC  11  
EXC  O10     O10   O  0  1  N  N  N  -2.495   -5.775  13.075  ?  ?  ?  O10   EXC  12  
EXC  C11     C11   C  0  1  Y  N  N  -3.937   -4.051  13.887  ?  ?  ?  C11   EXC  13  
EXC  C12     C12   C  0  1  Y  N  N  -4.740   -2.954  13.614  ?  ?  ?  C12   EXC  14  
EXC  C13     C13   C  0  1  Y  N  N  -4.943   -2.519  12.331  ?  ?  ?  C13   EXC  15  
EXC  C14     C14   C  0  1  Y  N  N  -4.334   -3.153  11.251  ?  ?  ?  C14   EXC  16  
EXC  C15     C15   C  0  1  N  N  N  -5.857   -1.325  12.297  ?  ?  ?  C15   EXC  17  
EXC  N16     N16   N  0  1  N  N  N  -6.285   -1.294  13.700  ?  ?  ?  N16   EXC  18  
EXC  C17     C17   C  0  1  N  N  N  -5.511   -2.136  14.610  ?  ?  ?  C17   EXC  19  
EXC  O18     O18   O  0  1  N  N  N  -0.151   -8.273   8.967  ?  ?  ?  O18   EXC  20  
EXC  C19     C19   C  0  1  N  N  N  -5.066   -0.083  11.897  ?  ?  ?  C19   EXC  21  
EXC  "C2'"   C2*   C  0  1  N  N  N   1.803   -8.988  11.487  ?  ?  ?  C2*   EXC  22  
EXC  C20     C20   C  0  1  N  N  N  -7.027   -1.560  11.349  ?  ?  ?  C20   EXC  23  
EXC  O21     O21   O  0  1  N  N  N  -7.237   -0.634  14.089  ?  ?  ?  O21   EXC  24  
EXC  C22     C22   C  0  1  N  N  N  -4.586   -1.350  15.535  ?  ?  ?  C22   EXC  25  
EXC  C23     C23   C  0  1  N  N  N  -6.429   -3.064  15.398  ?  ?  ?  C23   EXC  26  
EXC  "C3'"   C3*   C  0  1  N  N  S   2.124   -9.144  12.956  ?  ?  ?  C3*   EXC  27  
EXC  "O3'"   O3*   O  0  1  N  N  N   3.417   -9.708  13.111  ?  ?  ?  O3*   EXC  28  
EXC  "C4'"   C4*   C  0  1  N  N  R   1.082  -10.099  13.508  ?  ?  ?  C4*   EXC  29  
EXC  "O4'"   O4*   O  0  1  N  N  N  -0.068   -9.876  12.687  ?  ?  ?  O4*   EXC  30  
EXC  "C5'"   C5*   C  0  1  N  N  N   0.767   -9.783  14.966  ?  ?  ?  C5*   EXC  31  
EXC  "O5'"   O5*   O  0  1  N  N  N   0.350   -8.419  15.041  ?  ?  ?  O5*   EXC  32  
EXC  OP1     OP1   O  0  1  N  N  N   0.822   -8.172  17.499  ?  ?  ?  OP1   EXC  33  
EXC  OP2     OP2   O  0  1  N  N  N  -0.429   -6.301  16.123  ?  ?  ?  OP2   EXC  34  
EXC  OP3     OP3   O  0  1  N  Y  N  -1.553   -8.485  16.708  ?  ?  ?  OP3   EXC  35  
EXC  H5      H5    H  0  1  N  N  N  -0.927   -7.894  13.244  ?  ?  ?  H5    EXC  36  
EXC  "H1'"   H1*   H  0  1  N  N  N   0.170   -9.988  10.590  ?  ?  ?  H1*   EXC  37  
EXC  H11     H11   H  0  1  N  N  N  -3.794   -4.394  14.901  ?  ?  ?  H11   EXC  38  
EXC  H14     H14   H  0  1  N  N  N  -4.492   -2.801  10.242  ?  ?  ?  H14   EXC  39  
EXC  H19     H19   H  0  1  N  N  N  -5.737    0.788  11.873  ?  ?  ?  H19   EXC  40  
EXC  H19A    H19A  H  0  0  N  N  N  -4.264    0.092  12.629  ?  ?  ?  H19A  EXC  41  
EXC  H19B    H19B  H  0  0  N  N  N  -4.626   -0.234  10.900  ?  ?  ?  H19B  EXC  42  
EXC  "H2'"   H2*   H  0  1  N  N  N   2.389   -9.682  10.866  ?  ?  ?  H2*   EXC  43  
EXC  "H2'A"  H2*A  H  0  0  N  N  N   2.020   -7.971  11.128  ?  ?  ?  H2*A  EXC  44  
EXC  H20     H20   H  0  1  N  N  N  -7.678   -0.674  11.343  ?  ?  ?  H20   EXC  45  
EXC  H20A    H20A  H  0  0  N  N  N  -6.645   -1.741  10.333  ?  ?  ?  H20A  EXC  46  
EXC  H20B    H20B  H  0  0  N  N  N  -7.602   -2.435  11.686  ?  ?  ?  H20B  EXC  47  
EXC  H22     H22   H  0  1  N  N  N  -5.188   -0.766  16.247  ?  ?  ?  H22   EXC  48  
EXC  H22A    H22A  H  0  0  N  N  N  -3.940   -2.048  16.088  ?  ?  ?  H22A  EXC  49  
EXC  H22B    H22B  H  0  0  N  N  N  -3.963   -0.669  14.937  ?  ?  ?  H22B  EXC  50  
EXC  H23     H23   H  0  1  N  N  N  -7.001   -2.478  16.132  ?  ?  ?  H23   EXC  51  
EXC  H23A    H23A  H  0  0  N  N  N  -7.124   -3.565  14.708  ?  ?  ?  H23A  EXC  52  
EXC  H23B    H23B  H  0  0  N  N  N  -5.825   -3.819  15.922  ?  ?  ?  H23B  EXC  53  
EXC  "H3'"   H3*   H  0  1  N  N  N   2.111   -8.176  13.479  ?  ?  ?  H3*   EXC  54  
EXC  "HO3'"  HO3*  H  0  0  N  N  N   3.613   -9.803  14.036  ?  ?  ?  HO3*  EXC  55  
EXC  "H4'"   H4*   H  0  1  N  N  N   1.423  -11.145  13.488  ?  ?  ?  H4*   EXC  56  
EXC  "H5'"   H5*   H  0  1  N  N  N  -0.036  -10.442  15.328  ?  ?  ?  H5*   EXC  57  
EXC  "H5'A"  H5*A  H  0  0  N  N  N   1.663   -9.937  15.586  ?  ?  ?  H5*A  EXC  58  
EXC  HOP1    HOP1  H  0  0  N  N  N   1.189   -7.399  17.912  ?  ?  ?  HOP1  EXC  59  
EXC  HOP3    HOP3  H  0  0  N  Y  N  -2.261   -7.856  16.633  ?  ?  ?  HOP3  EXC  60  
EXC  H26     H26   H  0  1  N  N  N  -3.042   -4.595   9.530  ?  ?  ?  H26   EXC  61  
#   #
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
EXC  P      OP3     SING  N  N   1  
EXC  P      OP1     SING  N  N   2  
EXC  C1     C6      SING  N  N   3  
EXC  N2     C1      DOUB  N  N   4  
EXC  N2     C3      SING  N  N   5  
EXC  C3     N4      SING  N  N   6  
EXC  N4     "C1'"   SING  N  N   7  
EXC  N4     C5      SING  N  N   8  
EXC  C5     H5      SING  N  N   9  
EXC  C6     C5      DOUB  N  N  10  
EXC  C6     O10     SING  N  N  11  
EXC  N7     C1      SING  N  N  12  
EXC  N7     C8      SING  N  N  13  
EXC  C8     C9      SING  Y  N  14  
EXC  C9     O10     SING  N  N  15  
EXC  C9     C11     DOUB  Y  N  16  
EXC  "C1'"  "C2'"   SING  N  N  17  
EXC  "C1'"  "O4'"   SING  N  N  18  
EXC  "C1'"  "H1'"   SING  N  N  19  
EXC  C11    H11     SING  N  N  20  
EXC  C12    C11     SING  Y  N  21  
EXC  C12    C17     SING  N  N  22  
EXC  C13    C12     DOUB  Y  N  23  
EXC  C14    C8      DOUB  Y  N  24  
EXC  C14    C13     SING  Y  N  25  
EXC  C14    H14     SING  N  N  26  
EXC  C15    C13     SING  N  N  27  
EXC  C15    N16     SING  N  N  28  
EXC  N16    O21     SING  N  N  29  
EXC  N16    C17     SING  N  N  30  
EXC  C17    C23     SING  N  N  31  
EXC  C17    C22     SING  N  N  32  
EXC  O18    C3      DOUB  N  N  33  
EXC  C19    C15     SING  N  N  34  
EXC  C19    H19     SING  N  N  35  
EXC  C19    H19A    SING  N  N  36  
EXC  C19    H19B    SING  N  N  37  
EXC  "C2'"  "C3'"   SING  N  N  38  
EXC  "C2'"  "H2'"   SING  N  N  39  
EXC  "C2'"  "H2'A"  SING  N  N  40  
EXC  C20    C15     SING  N  N  41  
EXC  C20    H20     SING  N  N  42  
EXC  C20    H20A    SING  N  N  43  
EXC  C20    H20B    SING  N  N  44  
EXC  C22    H22     SING  N  N  45  
EXC  C22    H22A    SING  N  N  46  
EXC  C22    H22B    SING  N  N  47  
EXC  C23    H23     SING  N  N  48  
EXC  C23    H23A    SING  N  N  49  
EXC  C23    H23B    SING  N  N  50  
EXC  "C3'"  "O3'"   SING  N  N  51  
EXC  "C3'"  "C4'"   SING  N  N  52  
EXC  "C3'"  "H3'"   SING  N  N  53  
EXC  "O3'"  "HO3'"  SING  N  N  54  
EXC  "C4'"  "C5'"   SING  N  N  55  
EXC  "C4'"  "H4'"   SING  N  N  56  
EXC  "O4'"  "C4'"   SING  N  N  57  
EXC  "C5'"  "O5'"   SING  N  N  58  
EXC  "C5'"  "H5'"   SING  N  N  59  
EXC  "C5'"  "H5'A"  SING  N  N  60  
EXC  "O5'"  P       SING  N  N  61  
EXC  OP1    HOP1    SING  N  N  62  
EXC  OP2    P       DOUB  N  N  63  
EXC  OP3    HOP3    SING  N  N  64  
EXC  N7     H26     SING  N  N  65  
#   #
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
EXC  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC5OC(N4C(=O)N=C2C(Oc1cc3c(cc1N2)C(N(O)C3(C)C)(C)C)=C4)CC5O"  
EXC  SMILES_CANONICAL  CACTVS                3.370  "CC1(C)N([O])C(C)(C)c2cc3OC4=CN([C@H]5C[C@H](O)[C@@H](CO[P](O)(O)=O)O5)C(=O)N=C4Nc3cc12"  
EXC  SMILES            CACTVS                3.370  "CC1(C)N([O])C(C)(C)c2cc3OC4=CN([CH]5C[CH](O)[CH](CO[P](O)(O)=O)O5)C(=O)N=C4Nc3cc12"  
EXC  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "CC1(c2cc3c(cc2C(N1[O])(C)C)OC4=CN(C(=O)N=C4N3)[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O)C"  
EXC  SMILES            "OpenEye OEToolkits"  1.7.0  "CC1(c2cc3c(cc2C(N1[O])(C)C)OC4=CN(C(=O)N=C4N3)C5CC(C(O5)COP(=O)(O)O)O)C"  
EXC  InChI             InChI                 1.03   "InChI=1S/C21H27N4O9P/c1-20(2)10-5-12-14(6-11(10)21(3,4)25(20)28)33-15-8-24(19(27)23-18(15)22-12)17-7-13(26)16(34-17)9-32-35(29,30)31/h5-6,8,13,16-17,26,28H,7,9H2,1-4H3,(H,22,23,27)(H2,29,30,31)/t13-,16+,17+/m0/s1"  
EXC  InChIKey          InChI                 1.03   LNDMWSVZTMCXNG-IAOVAPTHSA-N  
#
_pdbx_chem_comp_identifier.comp_id          EXC
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          ACDLabs
_pdbx_chem_comp_identifier.program_version  12.01
_pdbx_chem_comp_identifier.identifier       "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5':5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EXC  "Create component"      2010-10-19  RCSB  
EXC  "Modify aromatic_flag"  2011-06-04  RCSB  
EXC  "Modify descriptor"     2011-06-04  RCSB  
EXC  "Modify synonyms"       2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     EXC
_pdbx_chem_comp_synonyms.name        "nitroxide spin-labeled nucleotide C-spin"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
