( ( For example ) ( , ( ( ( any atom ) ( with ( ( six protons ) ( in ( its nucleus ) ) ) ) ) ( ( is ( a ( carbon atom ) ) ) . ) ) ) )
(ROOT (S (PP (IN For) (NP (NN example))) (, ,) (NP (NP (DT any) (NN atom)) (PP (IN with) (NP (NP (CD six) (NNS protons)) (PP (IN in) (NP (PRP$ its) (NN nucleus)))))) (VP (VBZ is) (NP (DT a) (NN carbon) (NN atom))) (. .)))
For example, any atom with six protons in its nucleus is a carbon atom.
(ROOT (S (NP (NNP Carbon) (NNS atoms)) (VP (VBP have) (NP (NP (CD six) (NNS neutrons)) (CONJP (RB as) (RB well) (IN as)) (NP (CD six) (NNS protons)))) (. .)))