It is a known issue that for some 3D structures in the CSD, the 3D structure does not necessarily reflect the expected structure. For some structures here are hydrogens missing in the 3D structure. Additionally, the fixed CSD SMILES strings can have incorrect number of implicit hydrogens due to the nature of the fixing procedure. Both these cases can be detected by comparing the formula of our SMILES with the corresponding formula from the CSD API. How this is detected and for which complexes this is the case is shown in the notebook mentioned above.