/usr/share/avogadro/fragments/coordination/5-square-pyramidal.cml is in avogadro-data 1.0.3-10.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | <molecule>
<atomArray>
<atom id="a1" elementType="S" x3="-0.404487" y3="0.310293" z3="0.271055"/>
<atom id="a2" elementType="F" x3="-1.387820" y3="-0.263361" z3="-1.005676"/>
<atom id="a3" elementType="F" x3="0.173190" y3="-0.401702" z3="1.715100"/>
<atom id="a4" elementType="F" x3="0.106858" y3="1.928912" z3="0.061578"/>
<atom id="a5" elementType="F" x3="-1.885256" y3="0.169764" z3="1.115781"/>
<atom id="a6" elementType="F" x3="0.672698" y3="-0.834895" z3="-0.402895"/>
</atomArray>
<bondArray>
<bond atomRefs2=" a1 a2" order=" 1"/>
<bond atomRefs2=" a1 a3" order=" 1"/>
<bond atomRefs2=" a1 a4" order=" 1"/>
<bond atomRefs2=" a1 a5" order=" 1"/>
<bond atomRefs2=" a1 a6" order=" 1"/>
</bondArray>
</molecule>
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