I can't find my pen.

Literal

I [of-の] pen [subject-が] not [reflective-なぁ].

The ending なぁ is a drawn-out な expressing musing or mild lament — 'hmm, not here...' The が marks ペン as the subject whose existence is being asserted (or denied, with ない). 'Not existing' = 'can't find.' Very casual and introspective in tone.