What does "the natural bond angle" mean in the context of Universal Force Field (UFF) potential energy calculation and how are bond angles calculated?
The original article on UFF is from 1992, so it is somewhat dated. The selection of &quot;natural bond&quot; values is explained on page 10028:

a. Standard Bond Angles. The natural angles for the group 15, 17, and 18 main group elements are obtained from standard reference structures of the parent hydrides. Thus 0-3 has Bo = 104.5' from HzO, while S3 has Bo = 92.2' from HzS. Exceptions include 0-32, OR, and N-2. The bond angles for 0-32,O-R, and N-2 are fit to (C13Si)z0, methyl vinyl ether, and dimethyl- diazene angles of 146O, 118.3', and 112.3', respectively. Where structural data are unavailable, the natural angles are extrapolated from the element above it in the periodic table. The remaining elements are all assumed to have regular octahedral, tetrahedral, trigonal, or linear structures. The natural angles are collected in Table I.

So yes, the angles are selected from experimental geometries where available, or where not by extrapolation from geometries for compounds in the same group.
References

A. K. Rappe et al.. UFF, a Full Periodic Table Force Field  for  Molecular Mechanics and  Molecular Dynamics Simulations. J. Am. Chem. Soc. 1992, 114, 10024-10039.