I submitted my tax return on 3/31/21, with 4/1//21 as date to take out tax due from my bank account. CA Tax dept. took that out on 4/1, but not by Fed Tax Dept till now.

Most likely the IRS is still processing your filing.  Give it time.

Agreed ... just mark the money gone and eventually it will be.   The understaffed overtasked IRS is busy putting out a third stimulus check, refunds and recomputing millions of early filings for the late tax law changes  so returns with balance dues on them are on the very back burner.