S Corp estimated tax mistake

[Xuan Ni]

Hi there, 

I just started an S corp and was trying to pay the estimated tax for 2020 first quarter. I received a letter from EFTPS so I went ahead and paid the tax with Form 1120 -- federal tax deposit, but later I know my S corp doesn't have any federal tax liability and I should pay individual estimated tax with 1040ES as usual. Now the questions are:

1. Is there a way to get the money back? I contacted EFTPS, they said they are merely handling payments and send it to the Treasury, and they don't have authority over any IRS account. All IRS phone lines including tax advocate services are down now.

2. If above is not possible, is there some way to count in the tax paid via EFTPS to my individual estimated tax when doing my tax return for 2020.

Bottom line is, I don't want to lose the money I paid for nothing. Hopefully, someone could help here, and many thanks in advance.

-Sean