An _atom_ is an atomic sentence i.e. a sentence that is not "decomposable" in further sentences.
This means that is a sentence where no connectives occur.
In the syntax of predicate logic, an _atomic formula_ is a _predicate_ symbol $P(x_1, \ldots, x_n)$ with $n$ "argument places" (place holders to be filled with "inputs") with $n$ _terms_ (i.e. "names") of the language.
According to the syntax specifications of the language, _variables_ : $x,y,\ldots$ are terms.
A _sentence_ is a formula without _free_ occurrences of variables.
Thus, $\text {Is_son_of}(\text{Tom},x)$ is a correct (well-formed) formula but it is not a _sentence_ , because in it we have an occurrence of the free variable $x$.
$\text {Is_son_of}(\text{Tom},\text{Bill})$ instead, is a _sentence_ , and thus an _atomic_ one.