Remove execution permission from files (mosdef-hub#960)

* Remove execution permission from files

Previously some of the python files/reference molecules in `mbuild`
had an execution permission enabled by default. This PR removes the
executable flag from those files. This might only be relavent in a
unix context.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: umesh-timalsina