Here is the tutorial on programming smart key for Honda Civic 2013 under all keys lost situation by using SuperOBD SKP900 Key programmer
Instruction:
Connect OBD plug with vehicle
Connect Main Test cable with SKP-900
Select IMMOBILIZER
Select vehicle brand:Honda

Select Honda immo system: IMMOBILIZER3

Loading
Select IMMOBILIZER SYSTEM
Choose OBDII adapter and turn ignition ON

Communicating
Select All key lost Add remote

Enter key number and confirm

Turn ignition OFF
Turn ignition ON
Programming
Turn ignition OFF within 15 seconds

Turn ignition ON
Turn ignition OFF
Turn ignition ON
(Do follow every IGN ON and OFF operation SKP900 prompt you)
Indicator light off? If yes, Press Yes to continue.
Turn ignition ON

Adapt key success.