Intel-based motherboards are very similar to Arduino. But ATmega chips are microcontrollers, they are equiped with some Flash, ROM and RAM memories on-chip. This is a System-On-a-Chip architecture.
Intel 80x86 chips are CPU. To make a board you will need to use some companion chip called chipset. Also you should be add fast ROM and RAM. All of this is very difficult to solder at home. Much cheaper is to go to computer hardware shop and to buy a motherboard there.
I've got one 