data_5RKA # _model_server_result.job_id 2mAWHEGb9DthNT0OZhlY4A _model_server_result.datetime_utc '2024-11-14 07:38:36' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5rka # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1501}' # _entry.id 5RKA # _exptl.entry_id 5RKA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 210.253 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(methylsulfonyl)methyl]-1H-benzimidazole _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.73 _cell.angle_gamma 90 _cell.entry_id 5RKA _cell.length_a 82.36 _cell.length_b 27 _cell.length_c 55.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RKA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H10 N2 O2 S' _chem_comp.formula_weight 210.253 _chem_comp.id T6J _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(methylsulfonyl)methyl]-1H-benzimidazole _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C S T6J sing 290 n n O S T6J doub 291 n n S O1 T6J doub 292 n n C1 S T6J sing 293 n n C2 C1 T6J sing 294 n n C2 N T6J doub 295 n y N C3 T6J sing 296 n y C3 C4 T6J sing 297 n y C4 C5 T6J doub 298 n y C5 C6 T6J sing 299 n y C6 C7 T6J doub 300 n y C7 C8 T6J sing 301 n y C3 C8 T6J doub 302 n y C8 N1 T6J sing 303 n y N1 C2 T6J sing 304 n y N1 H9 T6J sing 305 n n C4 H5 T6J sing 306 n n C5 H6 T6J sing 307 n n C6 H7 T6J sing 308 n n C7 H8 T6J sing 309 n n C H1 T6J sing 310 n n C H T6J sing 311 n n C H2 T6J sing 312 n n C1 H4 T6J sing 313 n n C1 H3 T6J sing 314 n n # _atom_sites.entry_id 5RKA _atom_sites.fract_transf_matrix[1][1] 0.012142 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002082 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.037037 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018261 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 T6J A 1 1501 1501 T6J LIG . C 3 HOH A 1 1601 89 HOH HOH . C 3 HOH A 2 1602 197 HOH HOH . C 3 HOH A 3 1603 195 HOH HOH . C 3 HOH A 4 1604 183 HOH HOH . C 3 HOH A 5 1605 42 HOH HOH . C 3 HOH A 6 1606 85 HOH HOH . C 3 HOH A 7 1607 55 HOH HOH . C 3 HOH A 8 1608 187 HOH HOH . C 3 HOH A 9 1609 26 HOH HOH . C 3 HOH A 10 1610 140 HOH HOH . C 3 HOH A 11 1611 7 HOH HOH . C 3 HOH A 12 1612 121 HOH HOH . C 3 HOH A 13 1613 74 HOH HOH . C 3 HOH A 14 1614 17 HOH HOH . C 3 HOH A 15 1615 33 HOH HOH . C 3 HOH A 16 1616 151 HOH HOH . C 3 HOH A 17 1617 9 HOH HOH . C 3 HOH A 18 1618 98 HOH HOH . C 3 HOH A 19 1619 62 HOH HOH . C 3 HOH A 20 1620 25 HOH HOH . C 3 HOH A 21 1621 160 HOH HOH . C 3 HOH A 22 1622 31 HOH HOH . C 3 HOH A 23 1623 123 HOH HOH . C 3 HOH A 24 1624 10 HOH HOH . C 3 HOH A 25 1625 184 HOH HOH . C 3 HOH A 26 1626 12 HOH HOH . C 3 HOH A 27 1627 139 HOH HOH . C 3 HOH A 28 1628 83 HOH HOH . C 3 HOH A 29 1629 60 HOH HOH . C 3 HOH A 30 1630 176 HOH HOH . C 3 HOH A 31 1631 124 HOH HOH . C 3 HOH A 32 1632 14 HOH HOH . C 3 HOH A 33 1633 154 HOH HOH . C 3 HOH A 34 1634 20 HOH HOH . C 3 HOH A 35 1635 50 HOH HOH . C 3 HOH A 36 1636 3 HOH HOH . C 3 HOH A 37 1637 64 HOH HOH . C 3 HOH A 38 1638 182 HOH HOH . C 3 HOH A 39 1639 45 HOH HOH . C 3 HOH A 40 1640 13 HOH HOH . C 3 HOH A 41 1641 1 HOH HOH . C 3 HOH A 42 1642 104 HOH HOH . C 3 HOH A 43 1643 35 HOH HOH . C 3 HOH A 44 1644 52 HOH HOH . C 3 HOH A 45 1645 94 HOH HOH . C 3 HOH A 46 1646 16 HOH HOH . C 3 HOH A 47 1647 58 HOH HOH . C 3 HOH A 48 1648 144 HOH HOH . C 3 HOH A 49 1649 21 HOH HOH . C 3 HOH A 50 1650 54 HOH HOH . C 3 HOH A 51 1651 39 HOH HOH . C 3 HOH A 52 1652 141 HOH HOH . C 3 HOH A 53 1653 65 HOH HOH . C 3 HOH A 54 1654 153 HOH HOH . C 3 HOH A 55 1655 59 HOH HOH . C 3 HOH A 56 1656 14 HOH HOH . C 3 HOH A 57 1657 36 HOH HOH . C 3 HOH A 58 1658 15 HOH HOH . C 3 HOH A 59 1659 105 HOH HOH . C 3 HOH A 60 1660 28 HOH HOH . C 3 HOH A 61 1661 5 HOH HOH . C 3 HOH A 62 1662 24 HOH HOH . C 3 HOH A 63 1663 138 HOH HOH . C 3 HOH A 64 1664 113 HOH HOH . C 3 HOH A 65 1665 69 HOH HOH . C 3 HOH A 66 1666 172 HOH HOH . C 3 HOH A 67 1667 19 HOH HOH . C 3 HOH A 68 1668 88 HOH HOH . C 3 HOH A 69 1669 29 HOH HOH . C 3 HOH A 70 1670 4 HOH HOH . C 3 HOH A 71 1671 40 HOH HOH . C 3 HOH A 72 1672 48 HOH HOH . C 3 HOH A 73 1673 116 HOH HOH . C 3 HOH A 74 1674 130 HOH HOH . C 3 HOH A 75 1675 152 HOH HOH . C 3 HOH A 76 1676 137 HOH HOH . C 3 HOH A 77 1677 56 HOH HOH . C 3 HOH A 78 1678 106 HOH HOH . C 3 HOH A 79 1679 44 HOH HOH . C 3 HOH A 80 1680 19 HOH HOH . C 3 HOH A 81 1681 76 HOH HOH . C 3 HOH A 82 1682 131 HOH HOH . C 3 HOH A 83 1683 70 HOH HOH . C 3 HOH A 84 1684 77 HOH HOH . C 3 HOH A 85 1685 90 HOH HOH . C 3 HOH A 86 1686 191 HOH HOH . C 3 HOH A 87 1687 38 HOH HOH . C 3 HOH A 88 1688 125 HOH HOH . C 3 HOH A 89 1689 167 HOH HOH . C 3 HOH A 90 1690 82 HOH HOH . C 3 HOH A 91 1691 6 HOH HOH . C 3 HOH A 92 1692 86 HOH HOH . C 3 HOH A 93 1693 63 HOH HOH . C 3 HOH A 94 1694 11 HOH HOH . C 3 HOH A 95 1695 119 HOH HOH . C 3 HOH A 96 1696 81 HOH HOH . C 3 HOH A 97 1697 23 HOH HOH . C 3 HOH A 98 1698 71 HOH HOH . C 3 HOH A 99 1699 128 HOH HOH . C 3 HOH A 100 1700 67 HOH HOH . C 3 HOH A 101 1701 15 HOH HOH . C 3 HOH A 102 1702 109 HOH HOH . C 3 HOH A 103 1703 8 HOH HOH . C 3 HOH A 104 1704 6 HOH HOH . C 3 HOH A 105 1705 49 HOH HOH . C 3 HOH A 106 1706 162 HOH HOH . C 3 HOH A 107 1707 145 HOH HOH . C 3 HOH A 108 1708 75 HOH HOH . C 3 HOH A 109 1709 91 HOH HOH . C 3 HOH A 110 1710 134 HOH HOH . C 3 HOH A 111 1711 37 HOH HOH . C 3 HOH A 112 1712 163 HOH HOH . C 3 HOH A 113 1713 127 HOH HOH . C 3 HOH A 114 1714 2 HOH HOH . C 3 HOH A 115 1715 80 HOH HOH . C 3 HOH A 116 1716 72 HOH HOH . C 3 HOH A 117 1717 27 HOH HOH . C 3 HOH A 118 1718 174 HOH HOH . C 3 HOH A 119 1719 118 HOH HOH . C 3 HOH A 120 1720 43 HOH HOH . C 3 HOH A 121 1721 23 HOH HOH . C 3 HOH A 122 1722 158 HOH HOH . C 3 HOH A 123 1723 5 HOH HOH . C 3 HOH A 124 1724 22 HOH HOH . C 3 HOH A 125 1725 4 HOH HOH . C 3 HOH A 126 1726 57 HOH HOH . C 3 HOH A 127 1727 122 HOH HOH . C 3 HOH A 128 1728 175 HOH HOH . C 3 HOH A 129 1729 13 HOH HOH . C 3 HOH A 130 1730 166 HOH HOH . C 3 HOH A 131 1731 53 HOH HOH . C 3 HOH A 132 1732 95 HOH HOH . C 3 HOH A 133 1733 136 HOH HOH . C 3 HOH A 134 1734 93 HOH HOH . C 3 HOH A 135 1735 96 HOH HOH . C 3 HOH A 136 1736 34 HOH HOH . C 3 HOH A 137 1737 120 HOH HOH . C 3 HOH A 138 1738 18 HOH HOH . C 3 HOH A 139 1739 18 HOH HOH . C 3 HOH A 140 1740 165 HOH HOH . C 3 HOH A 141 1741 129 HOH HOH . C 3 HOH A 142 1742 157 HOH HOH . C 3 HOH A 143 1743 117 HOH HOH . C 3 HOH A 144 1744 146 HOH HOH . C 3 HOH A 145 1745 181 HOH HOH . C 3 HOH A 146 1746 198 HOH HOH . C 3 HOH A 147 1747 20 HOH HOH . C 3 HOH A 148 1748 126 HOH HOH . C 3 HOH A 149 1749 10 HOH HOH . C 3 HOH A 150 1750 9 HOH HOH . C 3 HOH A 151 1751 101 HOH HOH . C 3 HOH A 152 1752 199 HOH HOH . C 3 HOH A 153 1753 185 HOH HOH . C 3 HOH A 154 1754 156 HOH HOH . C 3 HOH A 155 1755 8 HOH HOH . C 3 HOH A 156 1756 30 HOH HOH . C 3 HOH A 157 1757 114 HOH HOH . C 3 HOH A 158 1758 115 HOH HOH . C 3 HOH A 159 1759 107 HOH HOH . C 3 HOH A 160 1760 22 HOH HOH . C 3 HOH A 161 1761 186 HOH HOH . C 3 HOH A 162 1762 1 HOH HOH . C 3 HOH A 163 1763 61 HOH HOH . C 3 HOH A 164 1764 194 HOH HOH . C 3 HOH A 165 1765 132 HOH HOH . C 3 HOH A 166 1766 188 HOH HOH . C 3 HOH A 167 1767 170 HOH HOH . C 3 HOH A 168 1768 51 HOH HOH . C 3 HOH A 169 1769 112 HOH HOH . C 3 HOH A 170 1770 41 HOH HOH . C 3 HOH A 171 1771 190 HOH HOH . C 3 HOH A 172 1772 110 HOH HOH . C 3 HOH A 173 1773 25 HOH HOH . C 3 HOH A 174 1774 66 HOH HOH . C 3 HOH A 175 1775 205 HOH HOH . C 3 HOH A 176 1776 12 HOH HOH . C 3 HOH A 177 1777 78 HOH HOH . C 3 HOH A 178 1778 204 HOH HOH . C 3 HOH A 179 1779 26 HOH HOH . C 3 HOH A 180 1780 168 HOH HOH . C 3 HOH A 181 1781 102 HOH HOH . C 3 HOH A 182 1782 148 HOH HOH . C 3 HOH A 183 1783 68 HOH HOH . C 3 HOH A 184 1784 16 HOH HOH . C 3 HOH A 185 1785 200 HOH HOH . C 3 HOH A 186 1786 21 HOH HOH . C 3 HOH A 187 1787 201 HOH HOH . C 3 HOH A 188 1788 17 HOH HOH . C 3 HOH A 189 1789 196 HOH HOH . C 3 HOH A 190 1790 73 HOH HOH . C 3 HOH A 191 1791 2 HOH HOH . C 3 HOH A 192 1792 3 HOH HOH . C 3 HOH A 193 1793 7 HOH HOH . C 3 HOH A 194 1794 111 HOH HOH . C 3 HOH A 195 1795 189 HOH HOH . C 3 HOH A 196 1796 24 HOH HOH . C 3 HOH A 197 1797 192 HOH HOH . C 3 HOH A 198 1798 97 HOH HOH . C 3 HOH A 199 1799 79 HOH HOH . C 3 HOH A 200 1800 11 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 T6J . . . B 2 -20.393 13.232 27.665 0.41 14.97 ? N1 T6J 1501 A 1 HETATM 2 C C4 T6J . . . B 2 -22.149 11.45 25.115 0.41 12.02 ? C4 T6J 1501 A 1 HETATM 3 C C5 T6J . . . B 2 -23.477 11.608 25.517 0.41 13.39 ? C5 T6J 1501 A 1 HETATM 4 C C6 T6J . . . B 2 -23.823 12.278 26.692 0.41 13.71 ? C6 T6J 1501 A 1 HETATM 5 C C7 T6J . . . B 2 -22.897 12.827 27.522 0.41 13.31 ? C7 T6J 1501 A 1 HETATM 6 C C8 T6J . . . B 2 -21.551 12.707 27.125 0.41 13.52 ? C8 T6J 1501 A 1 HETATM 7 N N T6J . . . B 2 -19.747 12.09 25.787 0.41 14.46 ? N T6J 1501 A 1 HETATM 8 C C T6J . . . B 2 -16.487 15.62 26.471 0.41 20.12 ? C T6J 1501 A 1 HETATM 9 O O T6J . . . B 2 -18.969 15.805 26.266 0.41 20.77 ? O T6J 1501 A 1 HETATM 10 C C1 T6J . . . B 2 -18.015 13.5 26.955 0.41 17.9 ? C1 T6J 1501 A 1 HETATM 11 C C2 T6J . . . B 2 -19.35 12.864 26.827 0.41 15.74 ? C2 T6J 1501 A 1 HETATM 12 C C3 T6J . . . B 2 -21.163 12.015 25.953 0.41 13.35 ? C3 T6J 1501 A 1 HETATM 13 O O1 T6J . . . B 2 -17.736 14.526 24.596 0.41 21.38 ? O1 T6J 1501 A 1 HETATM 14 S S T6J . . . B 2 -17.883 14.933 25.953 0.41 20.15 ? S T6J 1501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #