/usr/share/avogadro/fragments/amino_acids/D-methionine.cml is in avogadro-data 1.0.3-5.
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 | <?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-4-methylsulfanylbutanoic_acid">
<formula concise=" C 5 H 11 N 1 O 2 S 1 "/>
<identifier convention="iupac:inchi" value="1/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1"/>
<name convention="IUPAC">(2R)-2-Amino-4-methylsulfanylbutanoic acid</name>
<atomArray>
<atom id="a1" elementType="C" x3="1.969676" y3="0.311569" z3="-1.577441"/>
<atom id="a2" elementType="C" x3="1.076813" y3="-0.604309" z3="-0.743482"/>
<atom id="a3" elementType="C" x3="0.282665" y3="0.257205" z3="0.250005"/>
<atom id="a4" elementType="H" x3="0.965425" y3="0.989739" z3="0.727599"/>
<atom id="a5" elementType="H" x3="-0.480556" y3="0.862436" z3="-0.283201"/>
<atom id="a6" elementType="C" x3="-0.379103" y3="-0.592748" z3="1.319008"/>
<atom id="a7" elementType="H" x3="-1.048726" y3="-1.342987" z3="0.857371"/>
<atom id="a8" elementType="H" x3="0.381941" y3="-1.165801" z3="1.883898"/>
<atom id="a9" elementType="S" x3="-1.277700" y3="0.375096" z3="2.570177"/>
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<atom id="a12" elementType="H" x3="-3.360135" y3="0.001998" z3="1.344570"/>
<atom id="a13" elementType="H" x3="-3.408871" y3="1.414113" z3="2.414603"/>
<atom id="a14" elementType="N" x3="0.168830" y3="-1.426257" z3="-1.576297"/>
<atom id="a15" elementType="O" x3="3.129613" y3="0.681331" z3="-0.992397"/>
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<atom id="a18" elementType="H" x3="0.701561" y3="-1.970736" z3="-2.220262"/>
<atom id="a19" elementType="H" x3="-0.467936" y3="-0.842732" z3="-2.077579"/>
<atom id="a20" elementType="H" x3="3.618487" y3="1.259875" z3="-1.569982"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a14" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a3 a5" order="1"/>
<bond atomRefs2="a3 a6" order="1"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a6 a8" order="1"/>
<bond atomRefs2="a6 a9" order="1"/>
<bond atomRefs2="a9 a10" order="1"/>
<bond atomRefs2="a10 a11" order="1"/>
<bond atomRefs2="a10 a12" order="1"/>
<bond atomRefs2="a10 a13" order="1"/>
<bond atomRefs2="a1 a15" order="1"/>
<bond atomRefs2="a1 a16" order="2"/>
<bond atomRefs2="a2 a17" order="1"/>
<bond atomRefs2="a14 a18" order="1"/>
<bond atomRefs2="a14 a19" order="1"/>
<bond atomRefs2="a15 a20" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">149.2113</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">149.0510496</scalar>
</property>
</propertyList>
</molecule>
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