/usr/share/avogadro/fragments/amino_acids/D-glutamic_acid.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-aminopentanedioic_acid">
<formula concise=" C 5 H 9 N 1 O 4 "/>
<identifier convention="iupac:inchi" value="1/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1"/>
<name convention="IUPAC">(2R)-2-Aminopentanedioic acid</name>
<atomArray>
<atom id="a1" elementType="C" x3="2.010765" y3="-0.450274" z3="-1.250501"/>
<atom id="a2" elementType="C" x3="0.672921" y3="-0.828064" z3="-0.618800"/>
<atom id="a3" elementType="N" x3="-0.272758" y3="-1.418382" z3="-1.594073"/>
<atom id="a4" elementType="C" x3="0.071037" y3="0.420495" z3="0.041654"/>
<atom id="a5" elementType="H" x3="0.852021" y3="0.931603" z3="0.640964"/>
<atom id="a6" elementType="H" x3="-0.243571" y3="1.156807" z3="-0.726366"/>
<atom id="a7" elementType="C" x3="-1.105351" y3="0.060311" z3="0.934996"/>
<atom id="a8" elementType="H" x3="-1.898834" y3="-0.450399" z3="0.350655"/>
<atom id="a9" elementType="H" x3="-0.793402" y3="-0.663815" z3="1.715759"/>
<atom id="a10" elementType="C" x3="-1.698973" y3="1.269838" z3="1.607368"/>
<atom id="a11" elementType="O" x3="-1.369091" y3="2.440922" z3="1.551725"/>
<atom id="a12" elementType="O" x3="-2.767469" y3="1.003271" z3="2.397877"/>
<atom id="a13" elementType="H" x3="-3.091305" y3="1.809809" z3="2.786912"/>
<atom id="a14" elementType="O" x3="3.052979" y3="-0.366994" z3="-0.394645"/>
<atom id="a15" elementType="O" x3="2.259360" y3="-0.228425" z3="-2.421934"/>
<atom id="a16" elementType="H" x3="0.854257" y3="-1.612218" z3="0.159965"/>
<atom id="a17" elementType="H" x3="0.141969" y3="-2.216153" z3="-2.026033"/>
<atom id="a18" elementType="H" x3="-0.516408" y3="-0.747652" z3="-2.292697"/>
<atom id="a19" elementType="H" x3="3.841854" y3="-0.110680" z3="-0.862824"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a4" order="1"/>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a4 a6" order="1"/>
<bond atomRefs2="a4 a7" order="1"/>
<bond atomRefs2="a7 a8" order="1"/>
<bond atomRefs2="a7 a9" order="1"/>
<bond atomRefs2="a7 a10" order="1"/>
<bond atomRefs2="a10 a11" order="2"/>
<bond atomRefs2="a10 a12" order="1"/>
<bond atomRefs2="a12 a13" order="1"/>
<bond atomRefs2="a1 a14" order="1"/>
<bond atomRefs2="a1 a15" order="2"/>
<bond atomRefs2="a2 a16" order="1"/>
<bond atomRefs2="a3 a17" order="1"/>
<bond atomRefs2="a3 a18" order="1"/>
<bond atomRefs2="a14 a19" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">147.1293</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">147.0531578</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<!-- decomposition -->
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">205</scalar>
</property>
</propertyList>
</molecule>
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