pen vs holding pen

pen and holding pen both are nouns.

Word	Noun	Adjective	Verb	Adverb
pen	Yes	No	Yes	No
holding pen	Yes	No	No	No

As nouns, holding pen is a hyponym of pen; that is, holding pen is a word with a more specific, narrower meaning than pen:

pen (noun)	holding pen (noun)
female swan	a pen where livestock is temporarily confined
a writing implement with a point from which ink flows
an enclosure for confining livestock
a correctional institution for those convicted of major crimes
a portable enclosure in which babies may be left to play

pen (verb)	holding pen (verb)
produce a literary work