/usr/share/avogadro/fragments/amino_acids/D-valine.cml is in avogadro-data 1.0.3-1ubuntu4.
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 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | <?xml version="1.0" encoding="UTF-8"?>
<molecule xmlns="http://www.xml-cml.org/schema"
xmlns:cml="http://www.xml-cml.org/dict/cml"
xmlns:units="http://www.xml-cml.org/units/units"
xmlns:xsd="http://www.w3c.org/2001/XMLSchema"
xmlns:iupac="http://www.iupac.org"
id="CS_2R-2-amino-3-methylbutanoic_acid">
<formula concise=" C 5 H 11 N 1 O 2 "/>
<identifier convention="iupac:inchi" value="1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1"/>
<name convention="IUPAC">(2R)-2-Amino-3-methylbutanoic acid</name>
<atomArray>
<atom id="a1" elementType="H" x3="1.374955" y3="0.315825" z3="-0.884766"/>
<atom id="a2" elementType="C" x3="0.590923" y3="-0.401559" z3="-0.529621"/>
<atom id="a3" elementType="N" x3="1.297552" y3="-1.628231" z3="-0.088880"/>
<atom id="a4" elementType="H" x3="2.012165" y3="-1.380660" z3="0.562943"/>
<atom id="a5" elementType="H" x3="0.656921" y3="-2.259492" z3="0.345215"/>
<atom id="a6" elementType="C" x3="-0.257600" y3="0.291336" z3="0.562416"/>
<atom id="a7" elementType="H" x3="-1.048981" y3="-0.418194" z3="0.910782"/>
<atom id="a8" elementType="C" x3="-0.933309" y3="1.533300" z3="0.001597"/>
<atom id="a9" elementType="H" x3="-0.198594" y3="2.270130" z3="-0.350773"/>
<atom id="a10" elementType="H" x3="-1.552206" y3="2.024689" z3="0.763953"/>
<atom id="a11" elementType="H" x3="-1.589339" y3="1.291017" z3="-0.845008"/>
<atom id="a12" elementType="C" x3="0.603505" y3="0.681492" z3="1.754743"/>
<atom id="a13" elementType="H" x3="1.457261" y3="1.304262" z3="1.453986"/>
<atom id="a14" elementType="H" x3="1.001513" y3="-0.193967" z3="2.285293"/>
<atom id="a15" elementType="H" x3="0.020294" y3="1.258527" z3="2.485270"/>
<atom id="a16" elementType="C" x3="-0.272304" y3="-0.779308" z3="-1.730454"/>
<atom id="a17" elementType="O" x3="-0.177113" y3="-0.379137" z3="-2.875701"/>
<atom id="a18" elementType="O" x3="-1.266585" y3="-1.669837" z3="-1.502458"/>
<atom id="a19" elementType="H" x3="-1.719060" y3="-1.860192" z3="-2.318536"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a6" order="1"/>
<bond atomRefs2="a2 a16" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a3 a5" order="1"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a6 a8" order="1"/>
<bond atomRefs2="a6 a12" order="1"/>
<bond atomRefs2="a8 a9" order="1"/>
<bond atomRefs2="a8 a10" order="1"/>
<bond atomRefs2="a8 a11" order="1"/>
<bond atomRefs2="a12 a13" order="1"/>
<bond atomRefs2="a12 a14" order="1"/>
<bond atomRefs2="a12 a15" order="1"/>
<bond atomRefs2="a16 a17" order="2"/>
<bond atomRefs2="a16 a18" order="1"/>
<bond atomRefs2="a18 a19" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">117.1463</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">117.0789786</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<!-- decomposition -->
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">295</scalar>
</property>
</propertyList>
</molecule>
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