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How to generate a drug molecule file?

1. Search "Naphthylamine" in PubChem Compound. Find "Isomeric SMILES" [recommended] or "Canonical SMILES" of this molecule.

Note: now the server supports SMILES and PDB file formats, so you will no longer need to go to step 2-3. Instead, you can directly submit the SMILES string to the server, or submit the PDB file generated by Corina in Step 2 [recommended].

2. [Optional] Copy the SMILES into Corina to get the 3D structure of the molecule. Download the PDB file and submit it to our server.

3. [Optional] Add charges of your molecule using Vega ZZ.

Add charges: Left toolbar --> Charges Potential (recommended Force field: "CHARMM", Charges: "Gasteiger");

Save as: mol2 and submit it to our server. Please note you only need to submit one format (SMILES/PDB/MOL2) for each molecule file. This is just a demo and you don't have to go through all the steps.