{"id":6720,"date":"2021-03-16T18:03:36","date_gmt":"2021-03-16T18:03:36","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=6720"},"modified":"2021-03-23T18:03:07","modified_gmt":"2021-03-23T18:03:07","slug":"order-returning-bond-order-information-to-your-docked-poses","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2021\/03\/order-returning-bond-order-information-to-your-docked-poses\/","title":{"rendered":"ORDER!: Returning bond order information to your docked poses"},"content":{"rendered":"\n
\"John<\/figure><\/div>\n\n\n\n

<\/p>\n\n\n\n

Common docking software, such as AutoDock Vina or AutoDock 4, require the ligand and receptor files to be converted into the PDBQT format. Once a correct pose has been identified, the pose will be produced also as a .pdbqt file.<\/p>\n\n\n\n\n\n\n\n

PDBQT and PDB file formats do not contain bond order information and so the software used to view a .pdb\/.pdbqt file will have to make an educated guess as to how the atoms bond to each other. It does through a database of known bond lengths which are used to predict where bonds might exist based on distances between atoms. Sometimes it will get this wrong sadly <\/p>\n\n\n\n

The internet has many solutions to this problem and many are unnecessarily convoluted – luckily there is another way.<\/p>\n\n\n\n

RDKit<\/a> has a simple function for Python 3 however that can return this bond information using a template of the ligand that contains this bond information, for example a SMILES string. These SMILES strings can be found on RSCB <\/a>if the ligand is known or has been used before.<\/p>\n\n\n\n

from rdkit.Chem import AllChem\nstring = \"c1cnccc1[NH]C(=O)Oc2cc(OC)cc(Cl)c2\" #A SMILES STRING OF THE DOCKED LIGAND\ntemplate = AllChem.MolFromSmiles(string)\ndocked_pose = \"docked.pdb\" #PDB FILE OF THE DOCKED POSE WITHOUT THE BOND ORDER INFORMATION\nmol = AllChem.MolFromPDBFile(docked_pose ,removeHs=True)\nnewMol = AllChem.AssignBondOrdersFromTemplate(template, mol)\noutputfile = \"docked_with_bond_order.sdf\" # FILE NAME FOR NEW FILE THAT CONTAINS THIS BOND INFORMATION AND THE 3D COORDINATES OF THE DOCKED POSE COMBINED TOGETHER\nChem.MolToMolFile(newMol, outputfile)<\/pre>\n\n\n\n
It is important to note that if the output file is in the PDB format, the bond information will be lost again! I would recommend using the SDF format. <\/p>\n\n\n\n
E.g. <\/p>\n\n\n\n
Before this using this command:<\/p>\n\n\n\n
\"\"<\/a><\/figure><\/div>\n\n\n\n
<\/p>\n\n\n\n
After using this command:<\/p>\n\n\n\n
\"\"<\/a><\/figure><\/div>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
Common docking software, such as AutoDock Vina or AutoDock 4, require the ligand and receptor files to be converted into the PDBQT format. Once a correct pose has been identified, the pose will be produced also as a .pdbqt file.<\/p>\n","protected":false},"author":80,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,291,227,201],"tags":[366,367,368,370,376,369,377],"ppma_author":[554],"class_list":["post-6720","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-protein-ligand-docking","category-python-code","category-small-molecules","tag-autodock","tag-autodock-4","tag-autodock-vina","tag-bond-order","tag-pdb-format","tag-pdbqt-format","tag-sdf-format"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":554,"user_id":80,"is_guest":0,"slug":"guy","display_name":"Guy Durant","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/012800a6259061320ac59c0ef0f953daa4c2a0ebc3538e9463c6c215d88ed479?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6720","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/80"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=6720"}],"version-history":[{"count":4,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6720\/revisions"}],"predecessor-version":[{"id":6756,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6720\/revisions\/6756"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=6720"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=6720"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=6720"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=6720"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}