No, they are three completely different things:

• Rent – paid to the landlord, usually every month.
• Service fee – a one-time agency fee for finding and securing the property, paid to HomeInZagreb when you book or extend.
• Security deposit – money held as a guarantee for damage/unpaid amounts, usually held by the landlord and returned according to the contract.

Rent does not replace the service fee or deposit, and the service fee/deposit do not replace rent.