Hi Asu,
Since you have already filed the return by paying late fees and interest there will be no penal provision applicable.
There is also no need to reply to notice since the proceedings stands dropped if filing is done under 30 days.
No need to pay penalty amount.
If you would have delayed it then penalty of Rs. 25000 + 25000 might have been attracted.
Since you have already filed the returns no need to worry.
Hope this helps
Regards
Altamush