subjunctive mood - Why might the author have used "to be" instead of "is" in this sentence?

...thinking it to be in the green box when it is really in the yellow box.

The to be does seem to suggest that the green box does not actually contain it. Is to be, as used in the quotation, a subjunctive construction? If it is, then is that construction the most appropriate subjunctive construction; why or why not?

Thank you.