ChemServerSMILES to 3D structure converter
Turn a list of SMILES or a folder of structures into 3D files for docking and modelling: SDF, PDB, PDBQT and MOL2, in one batch, with bond orders that survive the trip.
Conversions
| From | To |
|---|---|
| SMILES (one per line) | SDF, PDB, PDBQT, MOL2 |
| SDF, MOL, MOL2, PDB, PDBQT, SMI files | SDF, PDB, PDBQT, MOL2 |
Pick any number of output formats at once. Uploaded 3D structures keep their own coordinates.
Choose how the 3D structure is made
- RDKit: ETKDG conformer embedding followed by MMFF94 minimization.
- Open Babel: the gen3d builder.
Choose how PDBQT is written
- Meeko: the preparation tool recommended for AutoDock Vina 1.2 and AutoDock-GPU.
- Open Babel: the classic route used in many published protocols.
RDKit does not write PDBQT or MOL2, so MOL2 is always written by Open Babel.
Bond orders kept
Double bonds and aromatic rings are written so that viewers show them correctly: MOL2 files are kekulized and PDB files carry CONECT records for double bonds. Docked poses on ChemServer get their bond orders back from the original molecule as well.
Next steps
- Dock the converted ligands
- Calculate RDKit descriptors for the same list