I was wondering why it was a separate list, so I asked during the OFAC Fall Symposium. The answer is pretty simple: because any Iran sanctions listings still on the SDN List have secondary sanctions attached – by having a separate list, those sanctions targets are only the subject of primary sanctions (e.g. for US persons).
It actually is explaine3d on the 13599 List page OFAC has:
Pursuant to the Joint Comprehensive Plan of Action of July 14, 2015 (JCPOA), the United States committed to lift secondary sanctions with respect to activity with certain persons, including the individuals and entities on the E.O. 13599 List, on Implementation Day. Effective as of Implementation Day, non-U.S. persons will not be subject to secondary sanctions solely for engaging in activity that involves persons included on the E.O. 13599 List, provided that the activity does not involve persons on the SDN List or conduct that remains sanctionable as described in Section VII of the Guidance Relating to the Lifting of Certain Sanctions Pursuant to the Joint Comprehensive Plan of Action on Implementation Day (the “Guidance Document”). For more information on the JCPOA, see the Guidance Document and related Frequently Asked Questions.
Not for nothing, but a program code and a different explainer (secondary sanctions on anyone except those whose only program code is EO13599), would have worked just as well, without the need to download a second file.
But, I did learn something…