Late Tax Payment Query

I filed my taxes using Cleartrip back on August 31. Unfortunately, by the time Cleartrip used its algorithm, it had become past midnight - 1 September.

I am yet to e-verify this return. If I do, should I pay the late payment penalty of Rs. 5000? If yes, how do I make this payment?

Thanks in advance for your reply.

Regards,

Varun