SMILES to SDF Converter
Generate an SDF structure file from SMILES. Check “3D coordinates” to get a force-field optimised conformer instead of a flat 2D layout.
SMILES to SDF with 3D coordinates
This converter turns a SMILES string into an SDF structure file. SDF is what most molecular viewers, docking programs and modelling pipelines accept. When the 3D coordinates option is enabled, OpenBabel generates an initial geometry and optimises it with a force field so the file contains a real 3D conformer rather than a flat drawing.
What you get
- A valid V2000 SDF block with atom and bond tables
- 2D layout by default, 3D conformer when 3D coordinates is checked
- Explicit hydrogens when 3D coordinates are generated
Frequently asked questions
Is the 3D conformer the global minimum?
No. OpenBabel performs a fast force-field optimisation (MMFF94 or UFF) from a generated starting geometry. It produces a low-energy conformer, not a guaranteed global minimum, and only one conformer — not an ensemble.
Can I convert many SMILES at once?
Yes. Put one SMILES per line and the output will contain one SDF record per molecule,
separated by $$$$.