/usr/share/avogadro/fragments/amino_acids/L-threonine.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 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 | <?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_2S_3R-2-amino-3-hydroxybutanoic_acid">
<formula concise=" C 4 H 9 N 1 O 3 "/>
<identifier convention="iupac:inchi" value="1/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1"/>
<name convention="IUPAC">(2S,3R)-2-Amino-3-hydroxybutanoic acid</name>
<atomArray>
<atom id="a1" elementType="C" x3="-0.231663" y3="0.059440" z3="-2.068577"/>
<atom id="a2" elementType="C" x3="-0.269588" y3="-0.563559" z3="-0.675187"/>
<atom id="a3" elementType="C" x3="-0.030302" y3="0.521071" z3="0.417568"/>
<atom id="a4" elementType="N" x3="1.350901" y3="1.051588" z3="0.369288"/>
<atom id="a5" elementType="O" x3="0.598063" y3="-1.662735" z3="-0.550031"/>
<atom id="a6" elementType="C" x3="-0.402002" y3="-0.025407" z3="1.791394"/>
<atom id="a7" elementType="O" x3="0.327532" y3="-0.250615" z3="2.740447"/>
<atom id="a8" elementType="O" x3="-1.719021" y3="-0.259289" z3="1.988685"/>
<atom id="a9" elementType="H" x3="-0.405311" y3="-0.698785" z3="-2.843686"/>
<atom id="a10" elementType="H" x3="0.733280" y3="0.537713" z3="-2.286038"/>
<atom id="a11" elementType="H" x3="-1.010783" y3="0.824758" z3="-2.176255"/>
<atom id="a12" elementType="H" x3="-1.261369" y3="-1.041863" z3="-0.494815"/>
<atom id="a13" elementType="H" x3="-0.712312" y3="1.379904" z3="0.191531"/>
<atom id="a14" elementType="H" x3="2.006711" y3="0.341575" z3="0.621849"/>
<atom id="a15" elementType="H" x3="1.435301" y3="1.816893" z3="1.003971"/>
<atom id="a16" elementType="H" x3="1.448140" y3="-1.407463" z3="-0.887969"/>
<atom id="a17" elementType="H" x3="-1.857577" y3="-0.623225" z3="2.857825"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a2 a5" order="1"/>
<bond atomRefs2="a3 a6" order="1"/>
<bond atomRefs2="a6 a7" order="2"/>
<bond atomRefs2="a6 a8" order="1"/>
<bond atomRefs2="a1 a9" order="1"/>
<bond atomRefs2="a1 a10" order="1"/>
<bond atomRefs2="a1 a11" order="1"/>
<bond atomRefs2="a2 a12" order="1"/>
<bond atomRefs2="a3 a13" order="1"/>
<bond atomRefs2="a4 a14" order="1"/>
<bond atomRefs2="a4 a15" order="1"/>
<bond atomRefs2="a5 a16" order="1"/>
<bond atomRefs2="a8 a17" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">119.1192</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">119.0582432</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<!-- decomposition -->
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">272</scalar>
</property>
</propertyList>
</molecule>
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