data_YD1
#

_chem_comp.id                                   YD1
_chem_comp.name                                 "6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H14 Cl2 N4 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-02-22
_chem_comp.pdbx_modified_date                   2021-02-26
_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                       369.203
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YD1
_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       7LTJ
_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
YD1  C1    C1   C   0  1  N  N  N  60.321  -1.623  104.921  -3.888   0.503  -0.205  C1    YD1   1  
YD1  C2    C2   C   0  1  N  N  N  59.823  -0.449  105.710  -2.815   1.523  -0.113  C2    YD1   2  
YD1  C5    C3   C   0  1  N  N  N  57.783  -1.739  106.399  -0.651   2.279   0.760  C5    YD1   3  
YD1  C6    C4   C   0  1  N  N  N  56.387  -1.364  105.927   0.702   1.715   0.315  C6    YD1   4  
YD1  C8    C5   C   0  1  N  N  N  56.732   0.919  106.706  -0.047  -0.566   0.659  C8    YD1   5  
YD1  C9    C6   C   0  1  N  N  N  58.142   0.564  107.151  -1.440  -0.093   1.118  C9    YD1   6  
YD1  C12   C7   C   0  1  Y  N  N  52.505   1.100  107.597   3.965  -1.660   1.078  C12   YD1   7  
YD1  C14   C8   C   0  1  Y  N  N  52.284  -0.487  105.813   4.380   0.257  -0.304  C14   YD1   8  
YD1  C10   C9   C   0  1  Y  N  N  54.484  -0.026  106.735   2.248  -0.016   0.761  C10   YD1   9  
YD1  C11   C10  C   0  1  Y  N  N  53.875   0.886  107.621   2.686  -1.204   1.331  C11   YD1  10  
YD1  C13   C11  C   0  1  Y  N  N  51.697   0.420  106.701   4.812  -0.932   0.262  C13   YD1  11  
YD1  C16   C12  C   0  1  Y  N  N  53.655  -0.712  105.826   3.102   0.717  -0.054  C16   YD1  12  
YD1  C19   C13  C   0  1  N  N  N  61.548  -3.703  105.175  -4.929  -1.258  -1.403  C19   YD1  13  
YD1  C22   C14  C   0  1  N  N  N  60.653  -3.012  102.961  -5.857  -0.633   0.650  C22   YD1  14  
YD1  C24   C15  C   0  1  N  N  N  60.119  -1.822  103.599  -4.809   0.386   0.787  C24   YD1  15  
YD1  N18   N1   N   0  1  N  N  N  61.005  -2.543  105.680  -3.964  -0.329  -1.301  N18   YD1  16  
YD1  N21   N2   N   0  1  N  N  N  61.336  -3.872  103.819  -5.861  -1.418  -0.447  N21   YD1  17  
YD1  N4    N3   N   0  1  N  N  N  58.659  -0.558  106.367  -1.681   1.247   0.561  N4    YD1  18  
YD1  N7    N4   N   0  1  N  N  N  55.863  -0.256  106.752   0.954   0.448   1.015  N7    YD1  19  
YD1  O20   O1   O   0  1  N  N  N  62.161  -4.502  105.864  -4.961  -1.972  -2.387  O20   YD1  20  
YD1  O23   O2   O   0  1  N  N  N  60.535  -3.292  101.772  -6.702  -0.772   1.514  O23   YD1  21  
YD1  O3    O3   O   0  1  N  N  N  60.528   0.573  105.713  -2.958   2.606  -0.644  O3    YD1  22  
YD1  CL15  CL1  CL  0  0  N  N  N  51.292  -1.363  104.658   5.449   1.171  -1.321  CL15  YD1  23  
YD1  CL17  CL2  CL  0  0  N  N  N  49.974   0.717  106.701   6.419  -1.508  -0.053  CL17  YD1  24  
YD1  H1    H1   H   0  1  N  N  N  57.728  -2.124  107.428  -0.605   2.552   1.815  H1    YD1  25  
YD1  H2    H2   H   0  1  N  N  N  58.195  -2.516  105.738  -0.895   3.159   0.165  H2    YD1  26  
YD1  H3    H3   H   0  1  N  N  N  56.430  -1.048  104.874   0.687   1.539  -0.760  H3    YD1  27  
YD1  H4    H4   H   0  1  N  N  N  55.723  -2.236  106.021   1.491   2.427   0.557  H4    YD1  28  
YD1  H5    H5   H   0  1  N  N  N  56.765   1.304  105.676   0.198  -1.508   1.150  H5    YD1  29  
YD1  H6    H6   H   0  1  N  N  N  56.327   1.694  107.374  -0.052  -0.710  -0.421  H6    YD1  30  
YD1  H7    H7   H   0  1  N  N  N  58.127   0.286  108.215  -2.200  -0.785   0.756  H7    YD1  31  
YD1  H8    H8   H   0  1  N  N  N  58.797   1.437  107.010  -1.471  -0.050   2.207  H8    YD1  32  
YD1  H9    H9   H   0  1  N  N  N  52.063   1.805  108.285   4.306  -2.584   1.522  H9    YD1  33  
YD1  H10   H10  H   0  1  N  N  N  54.485   1.427  108.330   2.027  -1.771   1.972  H10   YD1  34  
YD1  H11   H11  H   0  1  N  N  N  54.089  -1.418  105.134   2.765   1.644  -0.495  H11   YD1  35  
YD1  H12   H12  H   0  1  N  N  N  59.563  -1.099  103.020  -4.771   1.026   1.656  H12   YD1  36  
YD1  H13   H13  H   0  1  N  N  N  61.115  -2.359  106.657  -3.309  -0.242  -2.011  H13   YD1  37  
YD1  H14   H14  H   0  1  N  N  N  61.714  -4.702  103.409  -6.547  -2.096  -0.552  H14   YD1  38  
#   #
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
YD1  O23   C22   DOUB  N  N   1  
YD1  C22   C24   SING  N  N   2  
YD1  C22   N21   SING  N  N   3  
YD1  C24   C1    DOUB  N  N   4  
YD1  N21   C19   SING  N  N   5  
YD1  CL15  C14   SING  N  N   6  
YD1  C1    N18   SING  N  N   7  
YD1  C1    C2    SING  N  N   8  
YD1  C19   N18   SING  N  N   9  
YD1  C19   O20   DOUB  N  N  10  
YD1  C2    O3    DOUB  N  N  11  
YD1  C2    N4    SING  N  N  12  
YD1  C14   C16   DOUB  Y  N  13  
YD1  C14   C13   SING  Y  N  14  
YD1  C16   C10   SING  Y  N  15  
YD1  C6    C5    SING  N  N  16  
YD1  C6    N7    SING  N  N  17  
YD1  N4    C5    SING  N  N  18  
YD1  N4    C9    SING  N  N  19  
YD1  C13   CL17  SING  N  N  20  
YD1  C13   C12   DOUB  Y  N  21  
YD1  C8    N7    SING  N  N  22  
YD1  C8    C9    SING  N  N  23  
YD1  C10   N7    SING  N  N  24  
YD1  C10   C11   DOUB  Y  N  25  
YD1  C12   C11   SING  Y  N  26  
YD1  C5    H1    SING  N  N  27  
YD1  C5    H2    SING  N  N  28  
YD1  C6    H3    SING  N  N  29  
YD1  C6    H4    SING  N  N  30  
YD1  C8    H5    SING  N  N  31  
YD1  C8    H6    SING  N  N  32  
YD1  C9    H7    SING  N  N  33  
YD1  C9    H8    SING  N  N  34  
YD1  C12   H9    SING  N  N  35  
YD1  C11   H10   SING  N  N  36  
YD1  C16   H11   SING  N  N  37  
YD1  C24   H12   SING  N  N  38  
YD1  N18   H13   SING  N  N  39  
YD1  N21   H14   SING  N  N  40  
#   #
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
YD1  InChI             InChI                 1.03   "InChI=1S/C15H14Cl2N4O3/c16-10-2-1-9(7-11(10)17)20-3-5-21(6-4-20)14(23)12-8-13(22)19-15(24)18-12/h1-2,7-8H,3-6H2,(H2,18,19,22,24)"  
YD1  InChIKey          InChI                 1.03   XREZIAMDGRLMGZ-UHFFFAOYSA-N  
YD1  SMILES_CANONICAL  CACTVS                3.385  "Clc1ccc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3"  
YD1  SMILES            CACTVS                3.385  "Clc1ccc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3"  
YD1  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(c(cc1N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3)Cl)Cl"  
YD1  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(c(cc1N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3)Cl)Cl"  
#
_pdbx_chem_comp_identifier.comp_id          YD1
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YD1  "Create component"  2021-02-22  RCSB  
YD1  "Initial release"   2021-03-03  RCSB  
##
