data_XOD
#

_chem_comp.id                                   XOD
_chem_comp.name                                 "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H33 N5 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-22
_chem_comp.pdbx_modified_date                   2021-10-01
_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                       491.537
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XOD
_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       7KB6
_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
XOD  N1   N1   N   0  1  N  N  N  11.298  22.874  13.147    5.264  -0.202  -0.806  N1   XOD   1  
XOD  N3   N2   N   0  1  Y  N  N  22.019  29.987  14.952   -8.585   2.615   0.219  N3   XOD   2  
XOD  C4   C1   C   0  1  N  N  S   8.967  23.156  12.866    6.926  -1.520   0.418  C4   XOD   3  
XOD  C5   C2   C   0  1  N  N  S  10.315  23.848  12.680    6.482  -1.011  -0.954  C5   XOD   4  
XOD  C6   C3   C   0  1  N  N  N  10.555  24.154  11.191    7.593  -0.153  -1.564  C6   XOD   5  
XOD  C7   C4   C   0  1  N  N  N  10.396  23.242   8.839    8.990   1.896  -1.256  C7   XOD   6  
XOD  C8   C5   C   0  1  N  N  N  12.614  23.479  13.087    4.066  -1.052  -0.803  C8   XOD   7  
XOD  C10  C6   C   0  1  N  N  N  14.747  22.093  13.101    1.572  -1.061  -0.644  C10  XOD   8  
XOD  C13  C7   C   0  1  N  N  N  17.552  24.413  13.044   -2.166  -0.195  -0.329  C13  XOD   9  
XOD  C15  C8   C   0  1  Y  N  N  20.485  25.935  14.538   -5.747  -1.276  -0.069  C15  XOD  10  
XOD  C17  C9   C   0  1  Y  N  N  20.943  28.128  13.696   -7.132   0.680   0.071  C17  XOD  11  
XOD  C20  C10  C   0  1  Y  N  N  21.628  29.502  13.787   -8.474   1.293   0.211  C20  XOD  12  
XOD  C21  C11  C   0  1  Y  N  N  22.599  31.181  15.041   -9.767   3.193   0.342  C21  XOD  13  
XOD  C22  C12  C   0  1  Y  N  N  22.787  31.927  13.885  -10.899   2.400   0.464  C22  XOD  14  
XOD  C1   C13  C   0  1  N  N  S  10.390  22.894  10.327    7.879   1.038  -0.646  C1   XOD  15  
XOD  C11  C14  C   0  1  N  N  N  16.103  22.446  13.716    0.327  -0.185  -0.488  C11  XOD  16  
XOD  C12  C15  C   0  1  N  N  N  17.047  23.021  12.659   -0.921  -1.070  -0.485  C12  XOD  17  
XOD  C14  C16  C   0  1  Y  N  N  19.653  25.669  13.471   -4.624  -0.465  -0.196  C14  XOD  18  
XOD  C16  C17  C   0  1  Y  N  N  21.136  27.162  14.663   -6.996  -0.708   0.061  C16  XOD  19  
XOD  C18  C18  C   0  1  Y  N  N  20.101  27.861  12.625   -6.004   1.491  -0.061  C18  XOD  20  
XOD  C19  C19  C   0  1  Y  N  N  19.458  26.634  12.513   -4.758   0.919  -0.191  C19  XOD  21  
XOD  C2   C20  C   0  1  N  N  S   9.093  22.130  10.598    8.323   0.528   0.726  C2   XOD  22  
XOD  C23  C21  C   0  1  Y  N  N  22.353  31.372  12.689  -10.747   1.021   0.452  C23  XOD  23  
XOD  C3   C22  C   0  1  N  N  R   8.972  21.831  12.093    7.213  -0.330   1.336  C3   XOD  24  
XOD  C9   C23  C   0  1  N  N  N  13.595  22.667  13.923    2.821  -0.176  -0.647  C9   XOD  25  
XOD  N2   N3   N   0  1  N  N  N  18.971  24.382  13.356   -3.361  -1.042  -0.326  N2   XOD  26  
XOD  N4   N4   N   0  1  Y  N  N  21.783  30.176  12.666   -9.536   0.507   0.326  N4   XOD  27  
XOD  N5   N5   N   1  1  N  N  N  20.672  24.914  15.531   -5.602  -2.749  -0.081  N5   XOD  28  
XOD  O1   O1   O   0  1  N  N  N  11.442  22.015  10.622    6.695   1.824  -0.502  O1   XOD  29  
XOD  O2   O2   O   0  1  N  N  N   9.487  24.286   8.609    9.338   2.941  -0.346  O2   XOD  30  
XOD  O3   O3   O   0  1  N  N  N   7.723  21.227  12.300    7.628  -0.805   2.618  O3   XOD  31  
XOD  O4   O4   O   0  1  N  N  N   8.796  22.872  14.235    5.889  -2.321   0.988  O4   XOD  32  
XOD  O5   O5   O   0  1  N  N  N   9.150  20.908   9.907    8.591   1.640   1.583  O5   XOD  33  
XOD  O6   O6   O   0  1  N  N  N  20.575  25.222  16.898   -6.438  -3.439  -0.637  O6   XOD  34  
XOD  O7   O7   O  -1  1  N  N  N  20.956  23.610  15.102   -4.646  -3.271   0.465  O7   XOD  35  
XOD  H1   H1   H   0  1  N  N  N  11.091  22.612  14.089    5.307   0.366   0.027  H1   XOD  36  
XOD  H3   H3   H   0  1  N  N  N   8.162  23.802  12.486    7.830  -2.120   0.308  H3   XOD  37  
XOD  H4   H4   H   0  1  N  N  N  10.356  24.775  13.271    6.278  -1.859  -1.608  H4   XOD  38  
XOD  H5   H5   H   0  1  N  N  N  11.576  24.543  11.065    8.496  -0.752  -1.674  H5   XOD  39  
XOD  H6   H6   H   0  1  N  N  N   9.830  24.913  10.860    7.276   0.210  -2.542  H6   XOD  40  
XOD  H7   H7   H   0  1  N  N  N  10.100  22.360   8.253    9.864   1.275  -1.448  H7   XOD  41  
XOD  H8   H8   H   0  1  N  N  N  11.406  23.559   8.539    8.640   2.331  -2.192  H8   XOD  42  
XOD  H9   H9   H   0  1  N  N  N  12.957  23.503  12.042    4.008  -1.602  -1.742  H9   XOD  43  
XOD  H10  H10  H   0  1  N  N  N  12.562  24.505  13.480    4.121  -1.756   0.027  H10  XOD  44  
XOD  H11  H11  H   0  1  N  N  N  14.699  22.504  12.082    1.628  -1.765   0.186  H11  XOD  45  
XOD  H12  H12  H   0  1  N  N  N  14.647  20.998  13.060    1.515  -1.611  -1.584  H12  XOD  46  
XOD  H13  H13  H   0  1  N  N  N  17.383  25.103  12.204   -2.108   0.355   0.610  H13  XOD  47  
XOD  H14  H14  H   0  1  N  N  N  16.997  24.766  13.926   -2.222   0.509  -1.160  H14  XOD  48  
XOD  H15  H15  H   0  1  N  N  N  22.919  31.565  15.999   -9.851   4.270   0.348  H15  XOD  49  
XOD  H16  H16  H   0  1  N  N  N  23.253  32.901  13.915  -11.877   2.847   0.567  H16  XOD  50  
XOD  H17  H17  H   0  1  N  N  N  16.552  21.538  14.144    0.385   0.364   0.451  H17  XOD  51  
XOD  H18  H18  H   0  1  N  N  N  15.955  23.192  14.511    0.272   0.518  -1.319  H18  XOD  52  
XOD  H19  H19  H   0  1  N  N  N  16.510  23.090  11.702   -0.865  -1.774   0.345  H19  XOD  53  
XOD  H20  H20  H   0  1  N  N  N  17.910  22.348  12.548   -0.979  -1.620  -1.425  H20  XOD  54  
XOD  H21  H21  H   0  1  N  N  N  21.783  27.354  15.506   -7.869  -1.337   0.154  H21  XOD  55  
XOD  H22  H22  H   0  1  N  N  N  19.944  28.616  11.869   -6.109   2.566  -0.061  H22  XOD  56  
XOD  H23  H23  H   0  1  N  N  N  18.806  26.440  11.674   -3.885   1.546  -0.293  H23  XOD  57  
XOD  H24  H24  H   0  1  N  N  N   8.234  22.735  10.273    9.227  -0.071   0.616  H24  XOD  58  
XOD  H25  H25  H   0  1  N  N  N  22.481  31.921  11.768  -11.608   0.376   0.545  H25  XOD  59  
XOD  H26  H26  H   0  1  N  N  N   9.806  21.196  12.427    6.310   0.270   1.446  H26  XOD  60  
XOD  H27  H27  H   0  1  N  N  N  14.013  23.319  14.705    2.878   0.374   0.292  H27  XOD  61  
XOD  H28  H28  H   0  1  N  N  N  13.050  21.834  14.392    2.765   0.528  -1.477  H28  XOD  62  
XOD  H29  H29  H   0  1  N  N  N  19.078  23.905  14.228   -3.274  -2.004  -0.416  H29  XOD  63  
XOD  H30  H30  H   0  1  N  N  N  11.430  21.805  11.548    6.803   2.598   0.068  H30  XOD  64  
XOD  H31  H31  H   0  1  N  N  N   9.486  24.508   7.685   10.038   3.525  -0.668  H31  XOD  65  
XOD  H32  H32  H   0  1  N  N  N   7.616  21.028  13.223    6.971  -1.358   3.064  H32  XOD  66  
XOD  H33  H33  H   0  1  N  N  N   8.791  23.683  14.729    6.102  -2.679   1.861  H33  XOD  67  
XOD  H34  H34  H   0  1  N  N  N   8.351  20.418  10.063    8.878   1.391   2.472  H34  XOD  68  
#   #
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
XOD  O2   C7   SING  N  N   1  
XOD  C7   C1   SING  N  N   2  
XOD  O5   C2   SING  N  N   3  
XOD  C1   C2   SING  N  N   4  
XOD  C1   O1   SING  N  N   5  
XOD  C1   C6   SING  N  N   6  
XOD  C2   C3   SING  N  N   7  
XOD  C6   C5   SING  N  N   8  
XOD  C3   O3   SING  N  N   9  
XOD  C3   C4   SING  N  N  10  
XOD  C19  C18  DOUB  Y  N  11  
XOD  C19  C14  SING  Y  N  12  
XOD  C18  C17  SING  Y  N  13  
XOD  C12  C13  SING  N  N  14  
XOD  C12  C11  SING  N  N  15  
XOD  N4   C23  DOUB  Y  N  16  
XOD  N4   C20  SING  Y  N  17  
XOD  C5   C4   SING  N  N  18  
XOD  C5   N1   SING  N  N  19  
XOD  C23  C22  SING  Y  N  20  
XOD  C4   O4   SING  N  N  21  
XOD  C13  N2   SING  N  N  22  
XOD  C8   N1   SING  N  N  23  
XOD  C8   C9   SING  N  N  24  
XOD  C10  C11  SING  N  N  25  
XOD  C10  C9   SING  N  N  26  
XOD  N2   C14  SING  N  N  27  
XOD  C14  C15  DOUB  Y  N  28  
XOD  C17  C20  SING  N  N  29  
XOD  C17  C16  DOUB  Y  N  30  
XOD  C20  N3   DOUB  Y  N  31  
XOD  C22  C21  DOUB  Y  N  32  
XOD  C15  C16  SING  Y  N  33  
XOD  C15  N5   SING  N  N  34  
XOD  N3   C21  SING  Y  N  35  
XOD  O7   N5   SING  N  N  36  
XOD  N5   O6   DOUB  N  N  37  
XOD  N1   H1   SING  N  N  38  
XOD  C4   H3   SING  N  N  39  
XOD  C5   H4   SING  N  N  40  
XOD  C6   H5   SING  N  N  41  
XOD  C6   H6   SING  N  N  42  
XOD  C7   H7   SING  N  N  43  
XOD  C7   H8   SING  N  N  44  
XOD  C8   H9   SING  N  N  45  
XOD  C8   H10  SING  N  N  46  
XOD  C10  H11  SING  N  N  47  
XOD  C10  H12  SING  N  N  48  
XOD  C13  H13  SING  N  N  49  
XOD  C13  H14  SING  N  N  50  
XOD  C21  H15  SING  N  N  51  
XOD  C22  H16  SING  N  N  52  
XOD  C11  H17  SING  N  N  53  
XOD  C11  H18  SING  N  N  54  
XOD  C12  H19  SING  N  N  55  
XOD  C12  H20  SING  N  N  56  
XOD  C16  H21  SING  N  N  57  
XOD  C18  H22  SING  N  N  58  
XOD  C19  H23  SING  N  N  59  
XOD  C2   H24  SING  N  N  60  
XOD  C23  H25  SING  N  N  61  
XOD  C3   H26  SING  N  N  62  
XOD  C9   H27  SING  N  N  63  
XOD  C9   H28  SING  N  N  64  
XOD  N2   H29  SING  N  N  65  
XOD  O1   H30  SING  N  N  66  
XOD  O2   H31  SING  N  N  67  
XOD  O3   H32  SING  N  N  68  
XOD  O4   H33  SING  N  N  69  
XOD  O5   H34  SING  N  N  70  
#   #
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
XOD  SMILES            ACDLabs               12.01  "N(C1C(O)C(C(C(C1)(CO)O)O)O)CCCCCCNc3c(cc(c2ncccn2)cc3)[N+](=O)[O-]"  
XOD  InChI             InChI                 1.03   "InChI=1S/C23H33N5O7/c29-14-23(33)13-17(19(30)20(31)21(23)32)25-9-4-2-1-3-8-24-16-7-6-15(12-18(16)28(34)35)22-26-10-5-11-27-22/h5-7,10-12,17,19-21,24-25,29-33H,1-4,8-9,13-14H2/t17-,19-,20+,21-,23-/m0/s1"  
XOD  InChIKey          InChI                 1.03   MZOLIRUJMQEVFZ-BYGOBXPBSA-N  
XOD  SMILES_CANONICAL  CACTVS                3.385  "OC[C@@]1(O)C[C@H](NCCCCCCNc2ccc(cc2[N+]([O-])=O)c3ncccn3)[C@H](O)[C@@H](O)[C@@H]1O"  
XOD  SMILES            CACTVS                3.385  "OC[C]1(O)C[CH](NCCCCCCNc2ccc(cc2[N+]([O-])=O)c3ncccn3)[CH](O)[CH](O)[CH]1O"  
XOD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cnc(nc1)c2ccc(c(c2)[N+](=O)[O-])NCCCCCCN[C@H]3C[C@@]([C@H]([C@@H]([C@H]3O)O)O)(CO)O"  
XOD  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cnc(nc1)c2ccc(c(c2)[N+](=O)[O-])NCCCCCCNC3CC(C(C(C3O)O)O)(CO)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
XOD  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol"  
XOD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(1~{S},2~{S},3~{R},4~{S},5~{S})-1-(hydroxymethyl)-5-[6-[(2-nitro-4-pyrimidin-2-yl-phenyl)amino]hexylamino]cyclohexane-1,2,3,4-tetrol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XOD  "Create component"  2020-12-22  RCSB  
XOD  "Initial release"   2021-10-06  RCSB  
##
