/usr/share/avogadro/fragments/amino_acids/L-histidine.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 | <?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-2-amino-3-3H-imidazol-4-yl_propanoic_acid">
<formula concise=" C 6 H 9 N 3 O 2 "/>
<identifier convention="iupac:inchi" value="1/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1"/>
<name convention="IUPAC">(2S)-2-Amino-3-(3H-imidazol-4-yl)propanoic acid</name>
<atomArray>
<atom id="a1" elementType="N" x3="0.488838" y3="-1.796078" z3="-0.797589"/>
<atom id="a2" elementType="C" x3="0.873893" y3="-0.373749" z3="-0.939736"/>
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<atom id="a5" elementType="O" x3="2.917137" y3="0.184212" z3="-2.201774"/>
<atom id="a6" elementType="C" x3="0.538827" y3="0.512294" z3="0.272869"/>
<atom id="a7" elementType="H" x3="0.951379" y3="1.528648" z3="0.107133"/>
<atom id="a8" elementType="H" x3="1.040165" y3="0.128343" z3="1.186414"/>
<atom id="a9" elementType="C" x3="-0.922273" y3="0.624823" z3="0.478206"/>
<atom id="a10" elementType="N" x3="-1.565300" y3="0.432041" z3="1.716351"/>
<atom id="a11" elementType="C" x3="-2.928687" y3="0.656403" z3="1.553940"/>
<atom id="a12" elementType="H" x3="-3.698959" y3="0.587839" z3="2.326095"/>
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<atom id="a18" elementType="H" x3="0.868306" y3="-2.176826" z3="0.043844"/>
<atom id="a19" elementType="H" x3="0.327930" y3="0.016497" z3="-1.837519"/>
<atom id="a20" elementType="H" x3="4.096911" y3="-0.721268" z3="-0.560226"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a6" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a3 a5" order="2"/>
<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="a9 a14" order="2"/>
<bond atomRefs2="a10 a11" order="1"/>
<bond atomRefs2="a10 a16" order="1"/>
<bond atomRefs2="a11 a12" order="1"/>
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<bond atomRefs2="a1 a18" order="1"/>
<bond atomRefs2="a2 a19" order="1"/>
<bond atomRefs2="a4 a20" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">155.1546</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">155.0694765</scalar>
</property>
</propertyList>
</molecule>
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