/usr/share/avogadro/fragments/coordination/5-trigonal-bipyramidal.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 18 19 | <?xml version="1.0"?>
<molecule xmlns="http://www.xml-cml.org/schema" id="id5-pcl5.out">
<name>5-pcl5.out</name>
<atomArray>
<atom id="a1" elementType="P" x3="-0.432000" y3="-0.040900" z3="0.000000"/>
<atom id="a2" elementType="Cl" x3="-0.432000" y3="1.969300" z3="-0.000000"/>
<atom id="a3" elementType="Cl" x3="1.319100" y3="-1.032000" z3="0.000000"/>
<atom id="a4" elementType="Cl" x3="-2.183100" y3="-1.031900" z3="0.000000"/>
<atom id="a5" elementType="Cl" x3="-0.432000" y3="-0.051800" z3="2.119300"/>
<atom id="a6" elementType="Cl" x3="-0.432000" y3="-0.051800" z3="-2.119300"/>
</atomArray>
<bondArray>
<bond atomRefs2=" a6 a1" order=" 1"/>
<bond atomRefs2=" a1 a2" order=" 1"/>
<bond atomRefs2=" a1 a3" order=" 1"/>
<bond atomRefs2=" a1 a4" order=" 1"/>
<bond atomRefs2=" a1 a5" order=" 1"/>
</bondArray>
</molecule>
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