the way the water molecule is formed gives water its unique properties.

the water molecule is formed 是个定语从句，修饰the way，且省略关系词that/in which/;
gives water its unique properties 是及物动词（give）+间接宾语（water）直接宾语（its unique properties ）。

the way (主语)the water molecule is formed（ 定语从句 ） gives (谓语) water (直接宾语)its unique properties (间接宾语)