data_D6D
#

_chem_comp.id                                   D6D
_chem_comp.name                                 "(1S,2S,3S,4R,5R)-2-amino-4-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-6,8-dioxabicyclo[3.2.1]octan-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H20 N2 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-20
_chem_comp.pdbx_modified_date                   2020-04-17
_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                       244.287
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D6D
_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       5QB8
_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
D6D  O3   O1   O  0  1  N  N  N  -4.853   1.749   6.705  -1.913   1.985   0.927  O3   D6D   1  
D6D  C4   C1   C  0  1  N  N  R  -3.140   2.073  10.525   0.249  -0.593  -0.798  C4   D6D   2  
D6D  C5   C2   C  0  1  N  N  S  -2.470   2.983   9.427   1.233  -1.414   0.042  C5   D6D   3  
D6D  C6   C3   C  0  1  N  N  S  -1.009   3.224   9.798   1.562  -0.648   1.329  C6   D6D   4  
D6D  N1   N1   N  0  1  N  N  N  -0.282   3.780   8.614   0.369  -0.583   2.183  N1   D6D   5  
D6D  C7   C4   C  0  1  N  N  S  -0.352   1.919  10.241   2.005   0.775   0.951  C7   D6D   6  
D6D  C8   C5   C  0  1  N  N  N  -0.376   1.716  11.750   2.994   0.661  -0.233  C8   D6D   7  
D6D  C9   C6   C  0  1  N  N  R  -2.209   0.831  10.754   0.806   0.829  -0.966  C9   D6D   8  
D6D  C10  C7   C  0  1  N  N  N  -5.603   1.451   7.871  -1.748   1.814  -0.482  C10  D6D   9  
D6D  C2   C8   C  0  1  N  N  S  -4.731   0.767   8.914  -1.995   0.350  -0.852  C2   D6D  10  
D6D  C1   C9   C  0  1  N  N  N  -5.343  -0.536   9.432  -3.395  -0.095  -0.377  C1   D6D  11  
D6D  N    N2   N  0  1  N  N  N  -4.557   1.595  10.181  -1.053  -0.535  -0.120  N    D6D  12  
D6D  C3   C10  C  0  1  N  N  N  -5.272   0.858  11.294  -1.718  -1.863  -0.130  C3   D6D  13  
D6D  C    C11  C  0  1  N  N  N  -6.156  -0.127  10.624  -3.213  -1.552   0.098  C    D6D  14  
D6D  O    O2   O  0  1  N  N  N  -1.557   0.938  11.996   2.171   0.728  -1.412  O    D6D  15  
D6D  O1   O3   O  0  1  N  N  N  -1.179   0.823   9.790   0.863   1.431   0.346  O1   D6D  16  
D6D  O2   O4   O  0  1  N  N  N  -3.176   4.214   9.514   2.432  -1.631  -0.704  O2   D6D  17  
D6D  H1   H1   H  0  1  N  N  N  -5.414   2.175   6.067  -1.771   2.891   1.232  H1   D6D  18  
D6D  H2   H2   H  0  1  N  N  N  -3.182   2.646  11.463   0.130  -1.056  -1.778  H2   D6D  19  
D6D  H3   H3   H  0  1  N  N  N  -2.555   2.514   8.436   0.783  -2.374   0.294  H3   D6D  20  
D6D  H4   H4   H  0  1  N  N  N  -0.964   3.946  10.626   2.368  -1.154   1.859  H4   D6D  21  
D6D  H5   H5   H  0  1  N  N  N   0.676   3.939   8.855   0.562  -0.083   3.037  H5   D6D  22  
D6D  H6   H6   H  0  1  N  N  N  -0.332   3.129   7.857  -0.408  -0.169   1.689  H6   D6D  23  
D6D  H8   H8   H  0  1  N  N  N   0.675   1.848   9.853   2.421   1.322   1.796  H8   D6D  24  
D6D  H9   H9   H  0  1  N  N  N   0.522   1.174  12.082   3.701   1.490  -0.217  H9   D6D  25  
D6D  H10  H10  H  0  1  N  N  N  -0.434   2.683  12.270   3.524  -0.291  -0.194  H10  D6D  26  
D6D  H11  H11  H  0  1  N  N  N  -2.814  -0.086  10.698   0.203   1.413  -1.661  H11  D6D  27  
D6D  H12  H12  H  0  1  N  N  N  -6.002   2.386   8.292  -2.460   2.448  -1.011  H12  D6D  28  
D6D  H13  H13  H  0  1  N  N  N  -6.436   0.784   7.604  -0.733   2.094  -0.765  H13  D6D  29  
D6D  H14  H14  H  0  1  N  N  N  -3.743   0.555   8.480  -1.895   0.208  -1.928  H14  D6D  30  
D6D  H15  H15  H  0  1  N  N  N  -5.983  -0.996   8.665  -3.733   0.532   0.447  H15  D6D  31  
D6D  H16  H16  H  0  1  N  N  N  -4.555  -1.245   9.725  -4.106  -0.053  -1.203  H16  D6D  32  
D6D  H18  H18  H  0  1  N  N  N  -4.546   0.343  11.941  -1.574  -2.354  -1.092  H18  D6D  33  
D6D  H19  H19  H  0  1  N  N  N  -5.868   1.559  11.897  -1.331  -2.488   0.676  H19  D6D  34  
D6D  H20  H20  H  0  1  N  N  N  -7.106   0.335  10.317  -3.461  -1.639   1.155  H20  D6D  35  
D6D  H21  H21  H  0  1  N  N  N  -6.361  -0.987  11.279  -3.834  -2.224  -0.495  H21  D6D  36  
D6D  H22  H22  H  0  1  N  N  N  -4.087   4.074   9.285   3.102  -2.143  -0.231  H22  D6D  37  
#   #
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
D6D  O3   C10  SING  N  N   1  
D6D  C10  C2   SING  N  N   2  
D6D  N1   C6   SING  N  N   3  
D6D  C2   C1   SING  N  N   4  
D6D  C2   N    SING  N  N   5  
D6D  C5   O2   SING  N  N   6  
D6D  C5   C6   SING  N  N   7  
D6D  C5   C4   SING  N  N   8  
D6D  C1   C    SING  N  N   9  
D6D  O1   C7   SING  N  N  10  
D6D  O1   C9   SING  N  N  11  
D6D  C6   C7   SING  N  N  12  
D6D  N    C4   SING  N  N  13  
D6D  N    C3   SING  N  N  14  
D6D  C7   C8   SING  N  N  15  
D6D  C4   C9   SING  N  N  16  
D6D  C    C3   SING  N  N  17  
D6D  C9   O    SING  N  N  18  
D6D  C8   O    SING  N  N  19  
D6D  O3   H1   SING  N  N  20  
D6D  C4   H2   SING  N  N  21  
D6D  C5   H3   SING  N  N  22  
D6D  C6   H4   SING  N  N  23  
D6D  N1   H5   SING  N  N  24  
D6D  N1   H6   SING  N  N  25  
D6D  C7   H8   SING  N  N  26  
D6D  C8   H9   SING  N  N  27  
D6D  C8   H10  SING  N  N  28  
D6D  C9   H11  SING  N  N  29  
D6D  C10  H12  SING  N  N  30  
D6D  C10  H13  SING  N  N  31  
D6D  C2   H14  SING  N  N  32  
D6D  C1   H15  SING  N  N  33  
D6D  C1   H16  SING  N  N  34  
D6D  C3   H18  SING  N  N  35  
D6D  C3   H19  SING  N  N  36  
D6D  C    H20  SING  N  N  37  
D6D  C    H21  SING  N  N  38  
D6D  O2   H22  SING  N  N  39  
#   #
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
D6D  SMILES            ACDLabs               12.01  "OCC3CCCN3C1C2OCC(C(C1O)N)O2"  
D6D  InChI             InChI                 1.03   "InChI=1S/C11H20N2O4/c12-8-7-5-16-11(17-7)9(10(8)15)13-3-1-2-6(13)4-14/h6-11,14-15H,1-5,12H2/t6-,7+,8+,9+,10-,11+/m0/s1"  
D6D  InChIKey          InChI                 1.03   NMTUCAAUKBQRDV-ZESFFYIMSA-N  
D6D  SMILES_CANONICAL  CACTVS                3.385  "N[C@H]1[C@H](O)[C@H]([C@@H]2OC[C@H]1O2)N3CCC[C@H]3CO"  
D6D  SMILES            CACTVS                3.385  "N[CH]1[CH](O)[CH]([CH]2OC[CH]1O2)N3CCC[CH]3CO"  
D6D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1C[C@H](N(C1)[C@@H]2[C@H]([C@@H]([C@H]3CO[C@@H]2O3)N)O)CO"  
D6D  SMILES            "OpenEye OEToolkits"  2.0.6  "C1CC(N(C1)C2C(C(C3COC2O3)N)O)CO"  
#   #
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
D6D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3S,4R,5R)-2-amino-4-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)"  
D6D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(1~{S},2~{S},3~{S},4~{R},5~{R})-2-azanyl-4-[(2~{S})-2-(hydroxymethyl)pyrrolidin-1-yl]-6,8-dioxabicyclo[3.2.1]octan-3-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D6D  "Create component"  2017-10-20  RCSB  
D6D  "Initial release"   2020-04-22  RCSB  
##
