<?xml version="1.0" encoding="ISO-8859-1"?>

<!--
    Document   : dformula.xml
    Created on : April 12, 2010, 2:37 PM
    Author     : Scooter
    Description:
        Purpose of the document follows.
-->
<compounds>
    <elements>
        <element symbol='C' mono_isotopic_mass = '12.00000000000'/>
        <element symbol='H' mono_isotopic_mass = '1.0078246'/>
        <element symbol='D' mono_isotopic_mass = '2.0141021'/>
        <element symbol='N' mono_isotopic_mass = '14.0030732'/>
        <element symbol='O' mono_isotopic_mass = '15.9949141'/>
        <element symbol='P' mono_isotopic_mass = '30.973762'/>
        <element symbol='S' mono_isotopic_mass = '31.972070'/>
    </elements>
    <amino_acids>
        <amino_acid symbol='A' short='Ala' name='Alanine'>
            <molecular_formula>
                <element symbol='C' count='3'/>
                <element symbol='H' count='5'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='R' short='Arg' name='Arginine'>
            <molecular_formula>
                <element symbol='C' count='6'/>
                <element symbol='H' count='12'/>
                <element symbol='N' count='4'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='N' short='Asn' name='Asparagine'>
            <molecular_formula>
                <element symbol='C' count='4'/>
                <element symbol='H' count='6'/>
                <element symbol='N' count='2'/>
                <element symbol='O' count='2'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='D' short='Asp' name='Aspartic Acid'>
            <molecular_formula>
                <element symbol='C' count='4'/>
                <element symbol='H' count='5'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='3'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='C' short='Cys' name='Cysteine'>
            <molecular_formula>
                <element symbol='C' count='3'/>
                <element symbol='H' count='5'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
                <element symbol='S' count='1'/>
            </molecular_formula>
            <modifications>
                <modification symbol='U' short='capC' name='Carboxamidylmethyl Cysteine' >
                    <molecular_formula>
                        <element symbol='C' count='5'/>
                        <element symbol='H' count='8'/>
                        <element symbol='N' count='2'/>
                        <element symbol='O' count='2'/>
                        <element symbol='S' count='1'/>
                    </molecular_formula>
                </modification>
                <modification symbol='Z' short='pmC' name='Palmytoylated Cysteine' >
                    <molecular_formula>
                        <element symbol='C' count='19'/>
                        <element symbol='H' count='35'/>
                        <element symbol='N' count='1'/>
                        <element symbol='O' count='2'/>
                        <element symbol='S' count='1'/>
                    </molecular_formula>
                </modification>
                <modification symbol='$' short='dsbC' name='Disulfide-bonded Cysteine' >
                    <molecular_formula>
                        <element symbol='C' count='3'/>
                        <element symbol='H' count='4'/>
                        <element symbol='N' count='1'/>
                        <element symbol='O' count='1'/>
                        <element symbol='S' count='1'/>
                    </molecular_formula>
                </modification>
            </modifications>
        </amino_acid>
        <amino_acid symbol='E' short='Glu' name='Glutamic Acid' >
            <molecular_formula>
                <element symbol='C' count='5'/>
                <element symbol='H' count='7'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='3'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='Q' short='Gln' name='Glutamine' >
            <molecular_formula>
                <element symbol='C' count='5'/>
                <element symbol='H' count='8'/>
                <element symbol='N' count='2'/>
                <element symbol='O' count='2'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='G' short='Gly' name='Glycine' >
            <molecular_formula>
                <element symbol='C' count='2'/>
                <element symbol='H' count='3'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='H' short='His' name='Histidine'>
            <molecular_formula>
                <element symbol='C' count='6'/>
                <element symbol='H' count='7'/>
                <element symbol='N' count='3'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='I' short='Ile' name='Isoleucine'>
            <molecular_formula>
                <element symbol='C' count='6'/>
                <element symbol='H' count='11'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='L' short='Leu' name='Leucine' >
            <molecular_formula>
                <element symbol='C' count='6'/>
                <element symbol='H' count='11'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='K' short='Lys' name='Lysine' >
            <molecular_formula>
                <element symbol='C' count='6'/>
                <element symbol='H' count='12'/>
                <element symbol='N' count='2'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='M' short='Met' name='Methionine' >
            <molecular_formula>
                <element symbol='C' count='5'/>
                <element symbol='H' count='9'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
                <element symbol='S' count='1'/>
            </molecular_formula>
            <modifications>
                <modification symbol='O' short='oM' name='Oxidized Methionine' >
                    <molecular_formula>
                        <element symbol='C' count='5'/>
                        <element symbol='H' count='9'/>
                        <element symbol='N' count='1'/>
                        <element symbol='O' count='2'/>
                        <element symbol='S' count='1'/>
                    </molecular_formula>
                </modification>
            </modifications>
        </amino_acid>
        <amino_acid symbol='F' short='Phe' name='Phenylalanine' >
            <molecular_formula>
                <element symbol='C' count='9'/>
                <element symbol='H' count='9'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='P' short='Pro' name='Proline' >
            <molecular_formula>
                <element symbol='C' count='5'/>
                <element symbol='H' count='7'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='S' short='Ser' name='Serine' >
            <molecular_formula>
                <element symbol='C' count='3'/>
                <element symbol='H' count='5'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='2'/>
            </molecular_formula>
            <modifications>
                <modification symbol='X' short='pS' name='Phosphorylate Serine' >
                    <molecular_formula>
                        <element symbol='C' count='3'/>
                        <element symbol='H' count='6'/>
                        <element symbol='N' count='1'/>
                        <element symbol='O' count='5'/>
                        <element symbol='P' count='1'/>
                    </molecular_formula>
                </modification>
            </modifications>
        </amino_acid>
        <amino_acid symbol='T' short='Thr' name='Threonine'>
            <molecular_formula>
                <element symbol='C' count='4'/>
                <element symbol='H' count='7'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='2'/>
            </molecular_formula>
            <modifications>
                <modification symbol='B' short='pT' name='Phosphorylated Threonine' >
                    <molecular_formula>
                        <element symbol='C' count='4'/>
                        <element symbol='H' count='8'/>
                        <element symbol='N' count='1'/>
                        <element symbol='O' count='5'/>
                        <element symbol='P' count='1'/>
                    </molecular_formula>
                </modification>
            </modifications>
        </amino_acid>
        <amino_acid symbol='W' short='Trp' name='Tryptophan'>
            <molecular_formula>
                <element symbol='C' count='11'/>
                <element symbol='H' count='10'/>
                <element symbol='N' count='2'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='Y' short='Tyr' name='Tyrosine' >
            <molecular_formula>
                <element symbol='C' count='9'/>
                <element symbol='H' count='9'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='2'/>
            </molecular_formula>
        </amino_acid>
        <amino_acid symbol='V' short='Val' name='Valine' >
            <molecular_formula>
                <element symbol='C' count='5'/>
                <element symbol='H' count='9'/>
                <element symbol='N' count='1'/>
                <element symbol='O' count='1'/>
            </molecular_formula>
        </amino_acid>
    </amino_acids>
</compounds>
