Normal LJ simulations are unary, and the single molecule species has only one site. Although the single site need not be placed at the origin in the molecule frame, putting it anywhere else introduces angular dependencies that will slow down convergence. Because the single site has only isotropic interactions, its orientation is irrelevant, and I leave it as 0.0 0.0 0.0.
class 1 site 0.0 0.0 0.0 orient 0.0 0.0 0.0
# lj sig eps rep att
1 1 lj 1.0 1.0 1.0 1.0
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