try {
		FileReader file_reader = new FileReader(file_name);
		MDLReader reader = new MDLReader(file_reader);

		IChemFile content = (IChemFile) reader.read(new ChemFile());
		Molecule mol2d =
			(Molecule) ChemFileManipulator.getAllAtomContainers(content).get(0);

		ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
		IMolecule mol3d = mb3d.generate3DCoordinates(mol2d, false);

		FileWriter pdb_file = new FileWriter( "....(filename) ");
		PDBWriter writer = new PDBWriter(pdb_file);
		writer.write(mol3d);
		writer.close();
	}
	catch (Exception e)
	{
		e.printStackTrace();
	}