data_5S9D # _model_server_result.job_id DPmdC8FQORdZ_BVk1JQBWA _model_server_result.datetime_utc '2024-11-13 01:52:35' _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 5s9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1501}' # _entry.id 5S9D # _exptl.entry_id 5S9D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide _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 100.13 _cell.angle_gamma 90 _cell.entry_id 5S9D _cell.length_a 81.269 _cell.length_b 27.125 _cell.length_c 55.64 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5S9D _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 'C16 H18 N4 O2 S' _chem_comp.formula_weight 330.405 _chem_comp.id Y44 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide _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 O1 C1 Y44 doub 376 n n C1 N1 Y44 sing 377 n n N1 C2 Y44 sing 378 n n C2 C3 Y44 sing 379 n n C3 C4 Y44 doub 380 n y C4 C5 Y44 sing 381 n y C5 C6 Y44 doub 382 n y C6 N2 Y44 sing 383 n y N2 C7 Y44 doub 384 n y C1 N3 Y44 sing 385 n n N3 C8 Y44 sing 386 n n C8 C9 Y44 sing 387 n n C9 N4 Y44 sing 388 n n N4 C10 Y44 sing 389 n n C10 O2 Y44 doub 390 n n C10 C11 Y44 sing 391 n n C11 C12 Y44 doub 392 n y C12 C13 Y44 sing 393 n y C13 C14 Y44 doub 394 n y C14 S1 Y44 sing 395 n y N4 C15 Y44 sing 396 n n C15 C16 Y44 sing 397 n n C3 C7 Y44 sing 398 n y N3 C16 Y44 sing 399 n n C11 S1 Y44 sing 400 n y N1 H1 Y44 sing 401 n n C4 H4 Y44 sing 402 n n C5 H5 Y44 sing 403 n n C6 H6 Y44 sing 404 n n C7 H7 Y44 sing 405 n n C8 H9 Y44 sing 406 n n C8 H8 Y44 sing 407 n n C13 H13 Y44 sing 408 n n C15 H16 Y44 sing 409 n n C15 H15 Y44 sing 410 n n C12 H12 Y44 sing 411 n n C14 H14 Y44 sing 412 n n C16 H18 Y44 sing 413 n n C16 H17 Y44 sing 414 n n C2 H2 Y44 sing 415 n n C2 H3 Y44 sing 416 n n C9 H11 Y44 sing 417 n n C9 H10 Y44 sing 418 n n # _atom_sites.entry_id 5S9D _atom_sites.fract_transf_matrix[1][1] 0.012305 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002198 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.036866 _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] 0.018257 _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 Y44 A 1 1501 1501 Y44 LIG . C 3 HOH A 1 1601 128 HOH HOH . C 3 HOH A 2 1602 151 HOH HOH . C 3 HOH A 3 1603 55 HOH HOH . C 3 HOH A 4 1604 98 HOH HOH . C 3 HOH A 5 1605 172 HOH HOH . C 3 HOH A 6 1606 89 HOH HOH . C 3 HOH A 7 1607 42 HOH HOH . C 3 HOH A 8 1608 85 HOH HOH . C 3 HOH A 9 1609 197 HOH HOH . C 3 HOH A 10 1610 154 HOH HOH . C 3 HOH A 11 1611 7 HOH HOH . C 3 HOH A 12 1612 183 HOH HOH . C 3 HOH A 13 1613 184 HOH HOH . C 3 HOH A 14 1614 121 HOH HOH . C 3 HOH A 15 1615 142 HOH HOH . C 3 HOH A 16 1616 17 HOH HOH . C 3 HOH A 17 1617 135 HOH HOH . C 3 HOH A 18 1618 174 HOH HOH . C 3 HOH A 19 1619 187 HOH HOH . C 3 HOH A 20 1620 70 HOH HOH . C 3 HOH A 21 1621 123 HOH HOH . C 3 HOH A 22 1622 179 HOH HOH . C 3 HOH A 23 1623 124 HOH HOH . C 3 HOH A 24 1624 74 HOH HOH . C 3 HOH A 25 1625 10 HOH HOH . C 3 HOH A 26 1626 92 HOH HOH . C 3 HOH A 27 1627 41 HOH HOH . C 3 HOH A 28 1628 171 HOH HOH . C 3 HOH A 29 1629 12 HOH HOH . C 3 HOH A 30 1630 25 HOH HOH . C 3 HOH A 31 1631 167 HOH HOH . C 3 HOH A 32 1632 176 HOH HOH . C 3 HOH A 33 1633 33 HOH HOH . C 3 HOH A 34 1634 141 HOH HOH . C 3 HOH A 35 1635 65 HOH HOH . C 3 HOH A 36 1636 94 HOH HOH . C 3 HOH A 37 1637 31 HOH HOH . C 3 HOH A 38 1638 52 HOH HOH . C 3 HOH A 39 1639 140 HOH HOH . C 3 HOH A 40 1640 160 HOH HOH . C 3 HOH A 41 1641 9 HOH HOH . C 3 HOH A 42 1642 139 HOH HOH . C 3 HOH A 43 1643 45 HOH HOH . C 3 HOH A 44 1644 129 HOH HOH . C 3 HOH A 45 1645 3 HOH HOH . C 3 HOH A 46 1646 20 HOH HOH . C 3 HOH A 47 1647 14 HOH HOH . C 3 HOH A 48 1648 80 HOH HOH . C 3 HOH A 49 1649 149 HOH HOH . C 3 HOH A 50 1650 16 HOH HOH . C 3 HOH A 51 1651 144 HOH HOH . C 3 HOH A 52 1652 50 HOH HOH . C 3 HOH A 53 1653 4 HOH HOH . C 3 HOH A 54 1654 100 HOH HOH . C 3 HOH A 55 1655 75 HOH HOH . C 3 HOH A 56 1656 64 HOH HOH . C 3 HOH A 57 1657 84 HOH HOH . C 3 HOH A 58 1658 162 HOH HOH . C 3 HOH A 59 1659 99 HOH HOH . C 3 HOH A 60 1660 6 HOH HOH . C 3 HOH A 61 1661 83 HOH HOH . C 3 HOH A 62 1662 180 HOH HOH . C 3 HOH A 63 1663 119 HOH HOH . C 3 HOH A 64 1664 182 HOH HOH . C 3 HOH A 65 1665 1 HOH HOH . C 3 HOH A 66 1666 59 HOH HOH . C 3 HOH A 67 1667 108 HOH HOH . C 3 HOH A 68 1668 56 HOH HOH . C 3 HOH A 69 1669 82 HOH HOH . C 3 HOH A 70 1670 39 HOH HOH . C 3 HOH A 71 1671 62 HOH HOH . C 3 HOH A 72 1672 77 HOH HOH . C 3 HOH A 73 1673 27 HOH HOH . C 3 HOH A 74 1674 76 HOH HOH . C 3 HOH A 75 1675 143 HOH HOH . C 3 HOH A 76 1676 35 HOH HOH . C 3 HOH A 77 1677 130 HOH HOH . C 3 HOH A 78 1678 5 HOH HOH . C 3 HOH A 79 1679 145 HOH HOH . C 3 HOH A 80 1680 195 HOH HOH . C 3 HOH A 81 1681 163 HOH HOH . C 3 HOH A 82 1682 91 HOH HOH . C 3 HOH A 83 1683 23 HOH HOH . C 3 HOH A 84 1684 71 HOH HOH . C 3 HOH A 85 1685 157 HOH HOH . C 3 HOH A 86 1686 28 HOH HOH . C 3 HOH A 87 1687 11 HOH HOH . C 3 HOH A 88 1688 150 HOH HOH . C 3 HOH A 89 1689 15 HOH HOH . C 3 HOH A 90 1690 138 HOH HOH . C 3 HOH A 91 1691 29 HOH HOH . C 3 HOH A 92 1692 86 HOH HOH . C 3 HOH A 93 1693 54 HOH HOH . C 3 HOH A 94 1694 90 HOH HOH . C 3 HOH A 95 1695 19 HOH HOH . C 3 HOH A 96 1696 122 HOH HOH . C 3 HOH A 97 1697 152 HOH HOH . C 3 HOH A 98 1698 69 HOH HOH . C 3 HOH A 99 1699 161 HOH HOH . C 3 HOH A 100 1700 113 HOH HOH . C 3 HOH A 101 1701 63 HOH HOH . C 3 HOH A 102 1702 137 HOH HOH . C 3 HOH A 103 1703 37 HOH HOH . C 3 HOH A 104 1704 60 HOH HOH . C 3 HOH A 105 1705 48 HOH HOH . C 3 HOH A 106 1706 44 HOH HOH . C 3 HOH A 107 1707 116 HOH HOH . C 3 HOH A 108 1708 105 HOH HOH . C 3 HOH A 109 1709 36 HOH HOH . C 3 HOH A 110 1710 67 HOH HOH . C 3 HOH A 111 1711 40 HOH HOH . C 3 HOH A 112 1712 118 HOH HOH . C 3 HOH A 113 1713 81 HOH HOH . C 3 HOH A 114 1714 191 HOH HOH . C 3 HOH A 115 1715 159 HOH HOH . C 3 HOH A 116 1716 120 HOH HOH . C 3 HOH A 117 1717 38 HOH HOH . C 3 HOH A 118 1718 178 HOH HOH . C 3 HOH A 119 1719 106 HOH HOH . C 3 HOH A 120 1720 2 HOH HOH . C 3 HOH A 121 1721 72 HOH HOH . C 3 HOH A 122 1722 88 HOH HOH . C 3 HOH A 123 1723 156 HOH HOH . C 3 HOH A 124 1724 49 HOH HOH . C 3 HOH A 125 1725 134 HOH HOH . C 3 HOH A 126 1726 158 HOH HOH . C 3 HOH A 127 1727 96 HOH HOH . C 3 HOH A 128 1728 126 HOH HOH . C 3 HOH A 129 1729 125 HOH HOH . C 3 HOH A 130 1730 22 HOH HOH . C 3 HOH A 131 1731 173 HOH HOH . C 3 HOH A 132 1732 57 HOH HOH . C 3 HOH A 133 1733 165 HOH HOH . C 3 HOH A 134 1734 95 HOH HOH . C 3 HOH A 135 1735 53 HOH HOH . C 3 HOH A 136 1736 34 HOH HOH . C 3 HOH A 137 1737 127 HOH HOH . C 3 HOH A 138 1738 101 HOH HOH . C 3 HOH A 139 1739 13 HOH HOH . C 3 HOH A 140 1740 136 HOH HOH . C 3 HOH A 141 1741 131 HOH HOH . C 3 HOH A 142 1742 109 HOH HOH . C 3 HOH A 143 1743 117 HOH HOH . C 3 HOH A 144 1744 177 HOH HOH . C 3 HOH A 145 1745 181 HOH HOH . C 3 HOH A 146 1746 153 HOH HOH . C 3 HOH A 147 1747 175 HOH HOH . C 3 HOH A 148 1748 164 HOH HOH . C 3 HOH A 149 1749 166 HOH HOH . C 3 HOH A 150 1750 202 HOH HOH . C 3 HOH A 151 1751 104 HOH HOH . C 3 HOH A 152 1752 133 HOH HOH . C 3 HOH A 153 1753 146 HOH HOH . C 3 HOH A 154 1754 114 HOH HOH . C 3 HOH A 155 1755 186 HOH HOH . C 3 HOH A 156 1756 8 HOH HOH . C 3 HOH A 157 1757 185 HOH HOH . C 3 HOH A 158 1758 115 HOH HOH . C 3 HOH A 159 1759 198 HOH HOH . C 3 HOH A 160 1760 93 HOH HOH . C 3 HOH A 161 1761 30 HOH HOH . C 3 HOH A 162 1762 199 HOH HOH . C 3 HOH A 163 1763 61 HOH HOH . C 3 HOH A 164 1764 107 HOH HOH . C 3 HOH A 165 1765 193 HOH HOH . C 3 HOH A 166 1766 51 HOH HOH . C 3 HOH A 167 1767 190 HOH HOH . C 3 HOH A 168 1768 112 HOH HOH . C 3 HOH A 169 1769 132 HOH HOH . C 3 HOH A 170 1770 170 HOH HOH . C 3 HOH A 171 1771 168 HOH HOH . C 3 HOH A 172 1772 110 HOH HOH . C 3 HOH A 173 1773 148 HOH HOH . C 3 HOH A 174 1774 102 HOH HOH . C 3 HOH A 175 1775 188 HOH HOH . C 3 HOH A 176 1776 68 HOH HOH . C 3 HOH A 177 1777 78 HOH HOH . C 3 HOH A 178 1778 103 HOH HOH . C 3 HOH A 179 1779 46 HOH HOH . C 3 HOH A 180 1780 73 HOH HOH . C 3 HOH A 181 1781 196 HOH HOH . C 3 HOH A 182 1782 201 HOH HOH . C 3 HOH A 183 1783 192 HOH HOH . C 3 HOH A 184 1784 200 HOH HOH . C 3 HOH A 185 1785 111 HOH HOH . C 3 HOH A 186 1786 87 HOH HOH . C 3 HOH A 187 1787 97 HOH HOH . C 3 HOH A 188 1788 189 HOH HOH . C 3 HOH A 189 1789 203 HOH HOH . C 3 HOH A 190 1790 79 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 Y44 . . . B 2 -15.872 17.25 25.657 0.35 31 ? N1 Y44 1501 A 1 HETATM 2 N N3 Y44 . . . B 2 -17.285 15.571 26.367 0.35 28.81 ? N3 Y44 1501 A 1 HETATM 3 C C4 Y44 . . . B 2 -13.854 20.066 26.911 0.35 36.64 ? C4 Y44 1501 A 1 HETATM 4 C C5 Y44 . . . B 2 -14.012 21.412 27.146 0.35 36.99 ? C5 Y44 1501 A 1 HETATM 5 C C6 Y44 . . . B 2 -15.04 22.07 26.521 0.35 37.29 ? C6 Y44 1501 A 1 HETATM 6 C C7 Y44 . . . B 2 -15.727 20.153 25.479 0.35 36.44 ? C7 Y44 1501 A 1 HETATM 7 C C8 Y44 . . . B 2 -17.422 14.356 27.17 0.35 28.78 ? C8 Y44 1501 A 1 HETATM 8 C C10 Y44 . . . B 2 -20.165 12.658 25.265 0.35 25.38 ? C10 Y44 1501 A 1 HETATM 9 C C13 Y44 . . . B 2 -23.087 12.956 27.518 0.35 23.31 ? C13 Y44 1501 A 1 HETATM 10 C C15 Y44 . . . B 2 -18.361 14.169 24.705 0.35 27.86 ? C15 Y44 1501 A 1 HETATM 11 C C1 Y44 . . . B 2 -16.432 16.57 26.677 0.35 29.99 ? C1 Y44 1501 A 1 HETATM 12 C C11 Y44 . . . B 2 -21.341 12.528 26.066 0.35 23.93 ? C11 Y44 1501 A 1 HETATM 13 C C12 Y44 . . . B 2 -21.709 13.142 27.25 0.35 22.7 ? C12 Y44 1501 A 1 HETATM 14 C C14 Y44 . . . B 2 -23.667 12.067 26.693 0.35 22.79 ? C14 Y44 1501 A 1 HETATM 15 C C16 Y44 . . . B 2 -18.155 15.581 25.198 0.35 28.28 ? C16 Y44 1501 A 1 HETATM 16 C C2 Y44 . . . B 2 -14.59 17.928 25.773 0.35 32.9 ? C2 Y44 1501 A 1 HETATM 17 C C3 Y44 . . . B 2 -14.725 19.403 26.063 0.35 35.14 ? C3 Y44 1501 A 1 HETATM 18 C C9 Y44 . . . B 2 -18.822 13.781 27.077 0.35 27.69 ? C9 Y44 1501 A 1 HETATM 19 N N2 Y44 . . . B 2 -15.903 21.468 25.69 0.35 37.63 ? N2 Y44 1501 A 1 HETATM 20 N N4 Y44 . . . B 2 -19.165 13.453 25.69 0.35 26.96 ? N4 Y44 1501 A 1 HETATM 21 O O1 Y44 . . . B 2 -16.123 16.792 27.847 0.35 28.3 ? O1 Y44 1501 A 1 HETATM 22 O O2 Y44 . . . B 2 -20.142 12.128 24.157 0.35 24.71 ? O2 Y44 1501 A 1 HETATM 23 S S1 Y44 . . . B 2 -22.599 11.498 25.503 0.35 24.96 ? S1 Y44 1501 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #