/usr/share/avogadro/fragments/amino_acids/L-phenylalanine.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 65 66 67 68 69 70 71 72 73 | <?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-phenylpropanoic_acid">
<formula concise=" C 9 H 11 N 1 O 2 "/>
<identifier convention="iupac:inchi" value="1/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1"/>
<name convention="IUPAC">(2S)-2-Amino-3-phenylpropanoic acid</name>
<atomArray>
<atom id="a1" elementType="N" x3="1.049085" y3="-2.055661" z3="-0.142277"/>
<atom id="a2" elementType="C" x3="1.464179" y3="-0.692396" z3="-0.548019"/>
<atom id="a3" elementType="C" x3="0.972167" y3="0.430761" z3="0.381882"/>
<atom id="a4" elementType="C" x3="-0.517238" y3="0.548209" z3="0.355820"/>
<atom id="a5" elementType="C" x3="-1.156800" y3="1.080097" z3="-0.766052"/>
<atom id="a6" elementType="C" x3="-2.540897" y3="1.201101" z3="-0.788525"/>
<atom id="a7" elementType="C" x3="-3.295285" y3="0.795601" z3="0.308103"/>
<atom id="a8" elementType="C" x3="-2.662105" y3="0.268874" z3="1.428336"/>
<atom id="a9" elementType="C" x3="-1.277097" y3="0.144369" z3="1.454287"/>
<atom id="a10" elementType="C" x3="2.986010" y3="-0.650074" z3="-0.600374"/>
<atom id="a11" elementType="O" x3="3.503453" y3="-0.261814" z3="-1.787924"/>
<atom id="a12" elementType="O" x3="3.790819" y3="-0.899869" z3="0.278073"/>
<atom id="a13" elementType="H" x3="0.051436" y3="-2.094371" z3="-0.121011"/>
<atom id="a14" elementType="H" x3="1.408389" y3="-2.271310" z3="0.764455"/>
<atom id="a15" elementType="H" x3="1.042067" y3="-0.528698" z3="-1.573294"/>
<atom id="a16" elementType="H" x3="1.416800" y3="1.394579" z3="0.062287"/>
<atom id="a17" elementType="H" x3="1.332711" y3="0.262445" z3="1.417990"/>
<atom id="a18" elementType="H" x3="-0.562691" y3="1.403506" z3="-1.628860"/>
<atom id="a19" elementType="H" x3="-3.037611" y3="1.617531" z3="-1.671040"/>
<atom id="a20" elementType="H" x3="-4.385680" y3="0.892670" z3="0.289271"/>
<atom id="a21" elementType="H" x3="-3.253695" y3="-0.048099" z3="2.293537"/>
<atom id="a22" elementType="H" x3="-0.782939" y3="-0.265389" z3="2.342942"/>
<atom id="a23" elementType="H" x3="4.454920" y3="-0.272062" z3="-1.749607"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a10" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a4 a9" order="2"/>
<bond atomRefs2="a5 a6" order="2"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a7 a8" order="2"/>
<bond atomRefs2="a8 a9" 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="a3 a16" order="1"/>
<bond atomRefs2="a3 a17" order="1"/>
<bond atomRefs2="a5 a18" order="1"/>
<bond atomRefs2="a6 a19" order="1"/>
<bond atomRefs2="a7 a20" order="1"/>
<bond atomRefs2="a8 a21" order="1"/>
<bond atomRefs2="a9 a22" order="1"/>
<bond atomRefs2="a11 a23" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">165.1891</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">165.0789786</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<!-- decomposition -->
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">266</scalar>
</property>
</propertyList>
</molecule>
|