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Import sample files from Avogadro v1.2.
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ghutchis committed Nov 18, 2016
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2 changes: 1 addition & 1 deletion LICENSE
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BSD 3-Clause License

Copyright (c) 2016, Open Chemistry
Copyright (c) 2016, Geoffrey Hutchison, University of Pittsburgh
All rights reserved.

Redistribution and use in source and binary forms, with or without
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35 changes: 33 additions & 2 deletions README.md
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@@ -1,2 +1,33 @@
# molecules
Common molecule fragments for visualization in Avogadro
# OpenChemistry Molecules

Common molecule fragments for visualization in Avogadro.
Includes a variety of organic functional groups, including:

- alcohols
- aldehydes
- alkanes
- alkenes
- alkynes
- amides
- amines
- amino acids
- aromatics
- carbamides
- carbohydrates
- carboxylic acids
- coordination
- cyclic alkanes
- cyclic alkenes
- cyclic sugars
- ethers
- fatty acids
- fullerenes
- heteroaromatics
- ketones
- ligands
- macrocycles
- nitriles
- nucleobases
- steroids
- sulfoxides
- thiols
47 changes: 47 additions & 0 deletions alcohols/2-aminoethanol.cml
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<?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_2-aminoethanol">
<formula concise=" C 2 H 7 N 1 O 1 "/>
<identifier convention="iupac:inchi" value="1/C2H7NO/c3-1-2-4/h4H,1-3H2"/>
<name convention="IUPAC">2-Aminoethanol</name>
<atomArray>
<atom id="a1" elementType="N" x3="1.755238" y3="-0.030552" z3="-0.153047"/>
<atom id="a2" elementType="C" x3="0.461282" y3="0.622572" z3="0.105890"/>
<atom id="a3" elementType="C" x3="-0.744915" y3="-0.320278" z3="-0.012069"/>
<atom id="a4" elementType="O" x3="-1.896750" y3="0.440719" z3="0.260708"/>
<atom id="a5" elementType="H" x3="1.767839" y3="-0.406472" z3="-1.078473"/>
<atom id="a6" elementType="H" x3="1.898014" y3="-0.774237" z3="0.498474"/>
<atom id="a7" elementType="H" x3="0.362383" y3="1.469945" z3="-0.601842"/>
<atom id="a8" elementType="H" x3="0.505654" y3="1.071838" z3="1.118284"/>
<atom id="a9" elementType="H" x3="-0.664866" y3="-1.163290" z3="0.703828"/>
<atom id="a10" elementType="H" x3="-0.809446" y3="-0.761388" z3="-1.027347"/>
<atom id="a11" elementType="H" x3="-2.634433" y3="-0.148857" z3="0.185595"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a1 a5" order="1"/>
<bond atomRefs2="a1 a6" order="1"/>
<bond atomRefs2="a2 a7" order="1"/>
<bond atomRefs2="a2 a8" order="1"/>
<bond atomRefs2="a3 a9" order="1"/>
<bond atomRefs2="a3 a10" order="1"/>
<bond atomRefs2="a4 a11" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">61.0831</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">61.0527638</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">10</scalar>
</property>
</propertyList>
</molecule>
52 changes: 52 additions & 0 deletions alcohols/but-2-yne-1_4-diol.cml
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<?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_but-2-yne-1_4-diol">
<formula concise=" C 4 H 6 O 2 "/>
<identifier convention="iupac:inchi" value="1/C4H6O2/c5-3-1-2-4-6/h5-6H,3-4H2"/>
<name convention="IUPAC">But-2-yne-1,4-diol</name>
<atomArray>
<atom id="a1" elementType="C" x3="0.589445" y3="0.190529" z3="-0.096238"/>
<atom id="a2" elementType="C" x3="-0.596968" y3="0.179628" z3="0.019026"/>
<atom id="a3" elementType="C" x3="2.031063" y3="0.207955" z3="-0.249785"/>
<atom id="a4" elementType="C" x3="-2.038871" y3="0.177436" z3="0.170368"/>
<atom id="a5" elementType="O" x3="2.726047" y3="0.134014" z3="0.966967"/>
<atom id="a6" elementType="O" x3="-2.651705" y3="-0.989054" z3="-0.312443"/>
<atom id="a7" elementType="H" x3="2.369398" y3="1.166366" z3="-0.682924"/>
<atom id="a8" elementType="H" x3="2.335704" y3="-0.612113" z3="-0.930555"/>
<atom id="a9" elementType="H" x3="-2.460623" y3="1.079108" z3="-0.317346"/>
<atom id="a10" elementType="H" x3="-2.319579" y3="0.193834" z3="1.238834"/>
<atom id="a11" elementType="H" x3="2.432876" y3="-0.645774" z3="1.421168"/>
<atom id="a12" elementType="H" x3="-2.416787" y3="-1.081927" z3="-1.227072"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="3"/>
<bond atomRefs2="a1 a3" order="1"/>
<bond atomRefs2="a2 a4" order="1"/>
<bond atomRefs2="a3 a5" order="1"/>
<bond atomRefs2="a4 a6" order="1"/>
<bond atomRefs2="a3 a7" order="1"/>
<bond atomRefs2="a3 a8" order="1"/>
<bond atomRefs2="a4 a9" order="1"/>
<bond atomRefs2="a4 a10" order="1"/>
<bond atomRefs2="a5 a11" order="1"/>
<bond atomRefs2="a6 a12" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">86.0892</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">86.0367794</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="2.0" dictRef="cml:mp" units="units:celsius">56</scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">238</scalar>
</property>
</propertyList>
</molecule>
67 changes: 67 additions & 0 deletions alcohols/cyclohexanol.cml
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<?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_cyclohexanol">
<formula concise=" C 6 H 12 O 1 "/>
<identifier convention="iupac:inchi" value="1/C6H12O/c7-6-4-2-1-3-5-6/h6-7H,1-5H2"/>
<name convention="IUPAC">Cyclohexanol</name>
<atomArray>
<atom id="a1" elementType="C" x3="-0.112736" y3="1.349145" z3="-0.158962"/>
<atom id="a2" elementType="C" x3="1.197895" y3="0.668690" z3="0.268738"/>
<atom id="a3" elementType="C" x3="-1.036426" y3="-0.943649" z3="0.404201"/>
<atom id="a4" elementType="C" x3="-1.234852" y3="0.321815" z3="-0.409118"/>
<atom id="a5" elementType="O" x3="-0.437090" y3="2.267402" z3="0.869709"/>
<atom id="a6" elementType="H" x3="0.056404" y3="1.929443" z3="-1.099533"/>
<atom id="a7" elementType="H" x3="1.231904" y3="0.542808" z3="1.370726"/>
<atom id="a8" elementType="H" x3="2.057019" y3="1.320237" z3="0.018135"/>
<atom id="a9" elementType="H" x3="-1.030081" y3="-0.689261" z3="1.483051"/>
<atom id="a10" elementType="H" x3="-1.897344" y3="-1.625220" z3="0.263925"/>
<atom id="a11" elementType="H" x3="-2.228206" y3="0.760985" z3="-0.187343"/>
<atom id="a12" elementType="H" x3="-1.257154" y3="0.067295" z3="-1.487286"/>
<atom id="a13" elementType="H" x3="-1.260336" y3="2.669646" z3="0.627341"/>
<atom id="a14" elementType="C" x3="1.348903" y3="-0.683094" z3="-0.404949"/>
<atom id="a15" elementType="C" x3="0.257051" y3="-1.654718" z3="0.026948"/>
<atom id="a16" elementType="H" x3="2.345238" y3="-1.108877" z3="-0.178580"/>
<atom id="a17" elementType="H" x3="1.326335" y3="-0.550692" z3="-1.505348"/>
<atom id="a18" elementType="H" x3="0.602588" y3="-2.261211" z3="0.886629"/>
<atom id="a19" elementType="H" x3="0.070889" y3="-2.380744" z3="-0.788284"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a4 a1" order="1"/>
<bond atomRefs2="a1 a5" order="1"/>
<bond atomRefs2="a1 a6" order="1"/>
<bond atomRefs2="a2 a7" order="1"/>
<bond atomRefs2="a2 a8" order="1"/>
<bond atomRefs2="a3 a9" order="1"/>
<bond atomRefs2="a3 a10" order="1"/>
<bond atomRefs2="a4 a11" order="1"/>
<bond atomRefs2="a4 a12" order="1"/>
<bond atomRefs2="a5 a13" order="1"/>
<bond atomRefs2="a2 a14" order="1"/>
<bond atomRefs2="a14 a15" order="1"/>
<bond atomRefs2="a15 a3" order="1"/>
<bond atomRefs2="a14 a16" order="1"/>
<bond atomRefs2="a14 a17" order="1"/>
<bond atomRefs2="a15 a18" order="1"/>
<bond atomRefs2="a15 a19" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">100.1589</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">100.0888150</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="2.0" dictRef="cml:mp" units="units:celsius">23</scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">160</scalar>
</property>
</propertyList>
</molecule>
61 changes: 61 additions & 0 deletions alcohols/cyclopentanol.cml
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<?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_cyclopentanol">
<formula concise=" C 5 H 10 O 1 "/>
<identifier convention="iupac:inchi" value="1/C5H10O/c6-5-3-1-2-4-5/h5-6H,1-4H2"/>
<name convention="IUPAC">Cyclopentanol</name>
<atomArray>
<atom id="a1" elementType="C" x3="0.127209" y3="1.099259" z3="-0.221614"/>
<atom id="a2" elementType="C" x3="1.288733" y3="0.121901" z3="0.035688"/>
<atom id="a3" elementType="C" x3="0.709874" y3="-1.281643" z3="-0.094834"/>
<atom id="a4" elementType="C" x3="-0.780765" y3="-1.155193" z3="0.194044"/>
<atom id="a5" elementType="C" x3="-1.172664" y3="0.265399" z3="-0.193772"/>
<atom id="a6" elementType="O" x3="0.172414" y3="2.094239" z3="0.781138"/>
<atom id="a7" elementType="H" x3="0.244989" y3="1.600180" z3="-1.211721"/>
<atom id="a8" elementType="H" x3="1.726522" y3="0.274794" z3="1.042095"/>
<atom id="a9" elementType="H" x3="2.117399" y3="0.288261" z3="-0.675859"/>
<atom id="a10" elementType="H" x3="1.202489" y3="-1.995146" z3="0.589725"/>
<atom id="a11" elementType="H" x3="0.877471" y3="-1.681007" z3="-1.113160"/>
<atom id="a12" elementType="H" x3="-0.985688" y3="-1.336640" z3="1.266078"/>
<atom id="a13" elementType="H" x3="-1.371863" y3="-1.910101" z3="-0.354803"/>
<atom id="a14" elementType="H" x3="-1.923246" y3="0.679052" z3="0.506008"/>
<atom id="a15" elementType="H" x3="-1.654485" y3="0.281615" z3="-1.189045"/>
<atom id="a16" elementType="H" x3="-0.578386" y3="2.655029" z3="0.640032"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a5 a1" order="1"/>
<bond atomRefs2="a1 a6" order="1"/>
<bond atomRefs2="a1 a7" order="1"/>
<bond atomRefs2="a2 a8" order="1"/>
<bond atomRefs2="a2 a9" order="1"/>
<bond atomRefs2="a3 a10" order="1"/>
<bond atomRefs2="a3 a11" order="1"/>
<bond atomRefs2="a4 a12" order="1"/>
<bond atomRefs2="a4 a13" order="1"/>
<bond atomRefs2="a5 a14" order="1"/>
<bond atomRefs2="a5 a15" order="1"/>
<bond atomRefs2="a6 a16" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">86.1323</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">86.0731649</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">-19</scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">140</scalar>
</property>
</propertyList>
</molecule>
48 changes: 48 additions & 0 deletions alcohols/ethane-1_2-diol.cml
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<?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_ethane-1_2-diol">
<formula concise=" C 2 H 6 O 2 "/>
<identifier convention="iupac:inchi" value="1/C2H6O2/c3-1-2-4/h3-4H,1-2H2"/>
<name convention="IUPAC">Ethane-1,2-diol</name>
<atomArray>
<atom id="a1" elementType="H" x3="1.408675" y3="-0.160093" z3="0.827057"/>
<atom id="a2" elementType="C" x3="0.773787" y3="-0.077623" z3="-0.072111"/>
<atom id="a3" elementType="H" x3="1.066642" y3="0.849125" z3="-0.605433"/>
<atom id="a4" elementType="O" x3="1.131128" y3="-1.207165" z3="-0.817493"/>
<atom id="a5" elementType="H" x3="0.617832" y3="-1.196739" z3="-1.616080"/>
<atom id="a6" elementType="C" x3="-0.725352" y3="-0.057057" z3="0.283874"/>
<atom id="a7" elementType="H" x3="-1.016016" y3="-0.932806" z3="0.889698"/>
<atom id="a8" elementType="H" x3="-1.349636" y3="-0.061309" z3="-0.632238"/>
<atom id="a9" elementType="O" x3="-1.065536" y3="1.024163" z3="1.105157"/>
<atom id="a10" elementType="H" x3="-0.841525" y3="1.819505" z3="0.637568"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a4" order="1"/>
<bond atomRefs2="a2 a6" order="1"/>
<bond atomRefs2="a4 a5" 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"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">62.0678</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">62.0367794</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">-13</scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">197</scalar>
</property>
</propertyList>
</molecule>
46 changes: 46 additions & 0 deletions alcohols/ethanol.cml
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@@ -0,0 +1,46 @@
<?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_ethanol">
<formula concise=" C 2 H 6 O 1 "/>
<identifier convention="iupac:inchi" value="1/C2H6O/c1-2-3/h3H,2H2,1H3"/>
<name convention="IUPAC">Ethanol</name>
<atomArray>
<atom id="a1" elementType="H" x3="1.626544" y3="-0.037693" z3="0.845612"/>
<atom id="a2" elementType="C" x3="1.011200" y3="-0.045292" z3="-0.062605"/>
<atom id="a3" elementType="H" x3="1.325261" y3="0.803088" z3="-0.684698"/>
<atom id="a4" elementType="H" x3="1.250124" y3="-0.961175" z3="-0.618887"/>
<atom id="a5" elementType="C" x3="-0.462076" y3="0.030628" z3="0.294699"/>
<atom id="a6" elementType="H" x3="-0.758002" y3="-0.826323" z3="0.931560"/>
<atom id="a7" elementType="H" x3="-0.682225" y3="0.953690" z3="0.866556"/>
<atom id="a8" elementType="O" x3="-1.198129" y3="0.018094" z3="-0.907245"/>
<atom id="a9" elementType="H" x3="-2.112696" y3="0.064982" z3="-0.664993"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a4" order="1"/>
<bond atomRefs2="a2 a5" order="1"/>
<bond atomRefs2="a5 a6" order="1"/>
<bond atomRefs2="a5 a7" order="1"/>
<bond atomRefs2="a5 a8" order="1"/>
<bond atomRefs2="a8 a9" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
<scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">46.0684</scalar>
</property>
<property dictRef="cml:monoisotopicwt" title="Monoisotopic weight">
<scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">46.0418648</scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">-114</scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
<scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">78</scalar>
</property>
</propertyList>
</molecule>
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