data_LD3
#
_chem_comp.id LD3
_chem_comp.name meta-carboran-propylsulfonamid
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H8 B10 N O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-06-30
_chem_comp.pdbx_modified_date 2023-05-05
_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 254.298
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LD3
_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 8AA6
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
LD3 C7 C1 C 0 1 N N N N N N -4.991 6.149 12.796 -4.991 6.149 12.796 C7 LD3 1
LD3 B10 B1 B 0 1 N N N N N N -3.870 6.357 14.112 -3.870 6.357 14.112 B10 LD3 2
LD3 B6 B2 B 0 1 N N N N N N -3.529 7.027 12.496 -3.529 7.027 12.496 B6 LD3 3
LD3 B11 B3 B 0 1 N N N N N N -3.016 4.794 14.238 -3.016 4.794 14.238 B11 LD3 4
LD3 B5 B4 B 0 1 N N N N N N -2.245 6.162 13.391 -2.245 6.162 13.391 B5 LD3 5
LD3 B9 B5 B 0 1 N N N N N N -4.758 4.834 13.871 -4.758 4.834 13.871 B9 LD3 6
LD3 B8 B6 B 0 1 N N N N N N -4.962 4.576 12.104 -4.962 4.576 12.104 B8 LD3 7
LD3 B3 B7 B 0 1 N N N N N N -4.210 5.932 11.263 -4.210 5.932 11.263 B3 LD3 8
LD3 B12 B8 B 0 1 N N N N N N -2.151 4.513 12.694 -2.151 4.513 12.694 B12 LD3 9
LD3 B2 B9 B 0 1 N N N N N N -3.360 4.380 11.381 -3.360 4.380 11.381 B2 LD3 10
LD3 B4 B10 B 0 1 N N N N N N -2.453 5.901 11.617 -2.453 5.901 11.617 B4 LD3 11
LD3 C1 C2 C 0 1 N N N N N N -3.708 3.801 12.985 -3.708 3.801 12.985 C1 LD3 12
LD3 C18 C3 C 0 1 N N N N N N -3.709 2.281 13.114 -3.709 2.281 13.114 C18 LD3 13
LD3 C27 C4 C 0 1 N N N N N N -4.839 1.723 13.998 -4.839 1.723 13.998 C27 LD3 14
LD3 C28 C5 C 0 1 N N N N N N -4.509 1.993 15.410 -4.509 1.993 15.410 C28 LD3 15
LD3 S31 S1 S 0 1 N N N N N N -5.542 1.012 16.481 -5.542 1.012 16.481 S31 LD3 16
LD3 O34 O1 O 0 1 N N N N N N -5.021 1.353 17.803 -5.021 1.353 17.803 O34 LD3 17
LD3 O35 O2 O 0 1 N N N N N N -6.921 1.348 16.237 -6.921 1.348 16.237 O35 LD3 18
LD3 N36 N1 N 0 1 N N N N N N -5.268 -0.478 16.116 -5.268 -0.478 16.116 N36 LD3 19
LD3 H1 H1 H 0 1 N N N N N N -3.813 1.850 12.108 -3.813 1.849 12.108 H1 LD3 20
LD3 H2 H2 H 0 1 N N N N N N -2.747 1.971 13.548 -2.747 1.971 13.548 H2 LD3 21
LD3 H3 H3 H 0 1 N N N N N N -5.789 2.214 13.739 -5.789 2.214 13.739 H3 LD3 22
LD3 H4 H4 H 0 1 N N N N N N -4.932 0.638 13.840 -4.932 0.638 13.840 H4 LD3 23
LD3 H5 H5 H 0 1 N N N N N N -3.454 1.740 15.591 -3.454 1.740 15.591 H5 LD3 24
LD3 H6 H6 H 0 1 N N N N N N -4.673 3.059 15.624 -4.673 3.059 15.624 H6 LD3 25
LD3 H7 H7 H 0 1 N N N N N N -5.828 -1.072 16.694 -5.828 -1.072 16.694 H7 LD3 26
LD3 H8 H8 H 0 1 N N N N N N -5.499 -0.634 15.156 -5.499 -0.634 15.156 H8 LD3 27
#
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
LD3 C7 B10 SING N N 1
LD3 C7 B6 SING N N 2
LD3 C7 B9 SING N N 3
LD3 C7 B8 SING N N 4
LD3 C7 B3 SING N N 5
LD3 B10 B6 SING N N 6
LD3 B10 B11 SING N N 7
LD3 B10 B5 SING N N 8
LD3 B10 B9 SING N N 9
LD3 B6 B5 SING N N 10
LD3 B6 B3 SING N N 11
LD3 B6 B4 SING N N 12
LD3 B11 B5 SING N N 13
LD3 B11 B9 SING N N 14
LD3 B11 B12 SING N N 15
LD3 B11 C1 SING N N 16
LD3 B5 B12 SING N N 17
LD3 B9 C1 SING N N 18
LD3 B8 B3 SING N N 19
LD3 B8 B2 SING N N 20
LD3 B8 C1 SING N N 21
LD3 B3 B2 SING N N 22
LD3 B3 B4 SING N N 23
LD3 B12 B2 SING N N 24
LD3 B12 B4 SING N N 25
LD3 B12 C1 SING N N 26
LD3 B2 B4 SING N N 27
LD3 B2 C1 SING N N 28
LD3 C1 C18 SING N N 29
LD3 C18 C27 SING N N 30
LD3 C27 C28 SING N N 31
LD3 C28 S31 SING N N 32
LD3 S31 O34 DOUB N N 33
LD3 S31 O35 DOUB N N 34
LD3 S31 N36 SING N N 35
LD3 C18 H1 SING N N 36
LD3 C18 H2 SING N N 37
LD3 C27 H3 SING N N 38
LD3 C27 H4 SING N N 39
LD3 C28 H5 SING N N 40
LD3 C28 H6 SING N N 41
LD3 N36 H7 SING N N 42
LD3 N36 H8 SING N N 43
LD3 B8 B9 SING N N 44
LD3 B5 B4 SING N N 45
#
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
LD3 InChI InChI 1.06 InChI=1S/C5H8B10NO2S/c16-19(17,18)3-1-2-5-6-4-7(5,6)9(4)10(4)8(4,6)11(5,6)13(5)12(5,7,9)15(9,10,13)14(8,10,11)13/h1-3H2,(H2,16,17,18)
LD3 InChIKey InChI 1.06 GZJGPPMPTGFUSA-UHFFFAOYSA-N
LD3 SMILES_CANONICAL CACTVS 3.385 N[S](=O)(=O)CCC[C]1234[B]567[B]89%10[B]5%11%12[B]8%13%14[B]9%15%16[B]16%10[B]2%15%17[B]3%18%19[B]%11%13([B]47%12%18)[C]%14%16%17%19
LD3 SMILES CACTVS 3.385 N[S](=O)(=O)CCC[C]1234[B]567[B]89%10[B]5%11%12[B]8%13%14[B]9%15%16[B]16%10[B]2%15%17[B]3%18%19[B]%11%13([B]47%12%18)[C]%14%16%17%19
LD3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 B1234B567B189B212B33%10B454B656B787C911B232B715C4%1062CCCS(=O)(=O)N
LD3 SMILES "OpenEye OEToolkits" 2.0.7 B1234B567B189B212B33%10B454B656B787C911B232B715C4%1062CCCS(=O)(=O)N
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LD3 'Create component' 2022-06-30 PDBE
LD3 'Modify descriptor' 2022-08-22 RCSB
LD3 'Initial release' 2023-05-10 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
LD3 C7 C -0.122 -3.029 1
LD3 B10 B 0.163 -2.015 2
LD3 B6 B -0.951 -1.665 3
LD3 B11 B 0.710 -1.497 4
LD3 B5 B -0.137 -1.005 5
LD3 B9 B 1.433 -3.203 6
LD3 B8 B 1.852 -1.959 7
LD3 B3 B -1.161 -2.379 8
LD3 B12 B 0.943 0.429 9
LD3 B2 B 1.673 -0.544 10
LD3 B4 B -0.795 -0.257 11
LD3 C1 C 1.142 -1.329 12
LD3 C18 C 0.671 -0.667 13
LD3 C27 C 0.073 1.210 14
LD3 C28 C -1.168 1.940 15
LD3 S31 S -1.099 3.592 16
LD3 O34 O 0.435 3.622 17
LD3 O35 O -2.566 3.628 18
LD3 N36 N -1.096 5.129 19
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
LD3 C7 B10 SINGLE NONE 1
LD3 C7 B6 SINGLE NONE 2
LD3 C7 B9 SINGLE NONE 3
LD3 C7 B8 SINGLE NONE 4
LD3 C7 B3 SINGLE NONE 5
LD3 B10 B6 SINGLE NONE 6
LD3 B10 B11 SINGLE NONE 7
LD3 B10 B5 SINGLE NONE 8
LD3 B10 B9 SINGLE NONE 9
LD3 B6 B5 SINGLE NONE 10
LD3 B6 B3 SINGLE NONE 11
LD3 B6 B4 SINGLE NONE 12
LD3 B11 B5 SINGLE NONE 13
LD3 B11 B9 SINGLE NONE 14
LD3 B11 B12 SINGLE NONE 15
LD3 B11 C1 SINGLE NONE 16
LD3 B5 B12 SINGLE NONE 17
LD3 B9 C1 SINGLE NONE 18
LD3 B8 B3 SINGLE NONE 19
LD3 B8 B2 SINGLE NONE 20
LD3 B8 C1 SINGLE NONE 21
LD3 B3 B2 SINGLE NONE 22
LD3 B3 B4 SINGLE NONE 23
LD3 B12 B2 SINGLE NONE 24
LD3 B12 B4 SINGLE NONE 25
LD3 B12 C1 SINGLE NONE 26
LD3 B2 B4 SINGLE NONE 27
LD3 B2 C1 SINGLE NONE 28
LD3 C1 C18 SINGLE NONE 29
LD3 C18 C27 SINGLE NONE 30
LD3 C27 C28 SINGLE NONE 31
LD3 C28 S31 SINGLE NONE 32
LD3 S31 O34 DOUBLE NONE 33
LD3 S31 O35 DOUBLE NONE 34
LD3 S31 N36 SINGLE NONE 35
LD3 B8 B9 SINGLE NONE 36
LD3 B5 B4 SINGLE NONE 37
#
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