/usr/share/avogadro/fragments/amino_acids/D-arginine.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 63 64 65 66 67 68 69 70 71 72 73 74 | <?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-5-diaminomethylideneaminopentanoic_acid">
<formula concise=" C 6 H 14 N 4 O 2 "/>
<identifier convention="iupac:inchi" value="1/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m1/s1"/>
<name convention="IUPAC">(2R)-2-Amino-5-(diaminomethylideneamino)pentanoic acid</name>
<atomArray>
<atom id="a1" elementType="N" x3="2.394391" y3="-0.163075" z3="-2.331156"/>
<atom id="a2" elementType="C" x3="1.802026" y3="-1.217462" z3="-1.473739"/>
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<atom id="a7" elementType="C" x3="-0.244946" y3="-0.059278" z3="-0.529450"/>
<atom id="a8" elementType="C" x3="-0.920206" y3="0.421190" z3="0.751797"/>
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<atom id="a11" elementType="N" x3="-2.268809" y3="2.682035" z3="2.312271"/>
<atom id="a12" elementType="N" x3="-4.073063" y3="1.113452" z3="1.861212"/>
<atom id="a13" elementType="H" x3="3.069777" y3="0.363821" z3="-1.817560"/>
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<atom id="a26" elementType="H" x3="3.466214" y3="-3.986890" z3="-1.110302"/>
</atomArray>
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<bond atomRefs2="a3 a5" order="2"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a7 a8" order="1"/>
<bond atomRefs2="a8 a9" order="1"/>
<bond atomRefs2="a9 a10" order="1"/>
<bond atomRefs2="a10 a11" order="1"/>
<bond atomRefs2="a10 a12" order="2"/>
<bond atomRefs2="a1 a13" order="1"/>
<bond atomRefs2="a1 a14" order="1"/>
<bond atomRefs2="a2 a15" order="1"/>
<bond atomRefs2="a6 a16" order="1"/>
<bond atomRefs2="a6 a17" order="1"/>
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<bond atomRefs2="a12 a25" order="1"/>
<bond atomRefs2="a4 a26" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">174.2010</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">174.1116757</scalar>
</property>
</propertyList>
</molecule>
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