Simple, don't change the molecule :-). You only need atom types here to add
hydrogens and you don't need to add hydrogens they're there already when
read from SMILES.
String smiles = "C[N]C(=O)C(=O)C=O";
IAtomContainer mol = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
System.out.println(SmilesGenerator.generic().create(mol));
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