If the payment was made to the IRS, then you should consider it to be an estimated tax payment. There is no provision to tell the IRS or your tax return that you specifically paid the money to go toward Self-Employment (SE) tax.
When you complete your return all taxes owed are lumped together into one number. Then estimated payments made to the IRS are deducted from the total tax bill. So any estimated payments made to the IRS are applied to the whole tax bill, not just a certain tax like SE.
@Amraotikar
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