Is Zakat due on a loan amount granted by one company to another without interest and with a deferred payment for five years, and specifically, is Zakat to be paid on the amount by both companies together or by only one company?

Zakat is due on the aforementioned amount once. Zakat on the borrowed amount is obligatory upon the lender (the second company), not the borrower, even if you are both the lender and the borrower simultaneously, because both companies are capitalized solely by you.