<?xml version="1.0"?>
<!--
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin; 
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific 
Northwest National Laboratory, operated by Battelle Memorial Institute, 
Pacific Northwest Division for the U.S. Department Energy.; 
Paul Czodrowski & Gerhard Klebe, University of Marburg.

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, 
are permitted provided that the following conditions are met:

	* Redistributions of source code must retain the above copyright notice, 
	  this list of conditions and the following disclaimer.
	* Redistributions in binary form must reproduce the above copyright notice, 
	  this list of conditions and the following disclaimer in the documentation 
	  and/or other materials provided with the distribution.
    * Neither the names of University College Dublin, Battelle Memorial Institute,
      Pacific Northwest National Laboratory, US Department of Energy, or University
      of Marburg nor the names of its contributors may be used to endorse or promote
      products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 
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-->
<topology>
<!-- Amino Acid states -->
	<residue>
		<reference>
			<name>ASP</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>0.043</x>
				<y>-1.017</y>
				<z>1.123</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.229</x>
				<y>-1.966</y>
				<z>1.053</z>
				<bond>CB</bond>
				<bond>OD1</bond>
				<bond>OD2</bond>
			</atom>
			<atom>
				<name>OD1</name>
				<x>2.058</x>
				<y>-1.864</y>
				<z>0.127</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>OD2</name>
				<x>1.319</x>
				<y>-2.810</y>
				<z>1.959</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.511</y>
				<z>-0.860</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>0.086</x>
				<y>-0.524</y>
				<z>1.992</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.796</x>
				<y>-1.559</y>
				<z>1.089</z>
				<bond>CB</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG OD1</dihedral>
		</reference>
<!-- ASH implements the top-level transformation in the decision tree to transform the default ASP -> ASH -->
		<titrationstate>
<!-- No changes to the ASP structure -->
			<name>ASP</name>
			<tautomer>
				<name>ASP</name>
				<conformer>
					<name>ASP</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>ASH</name>
<!-- Protonated aspartate -->
			<tautomer>
				<name>ASH1</name>
<!-- Hydrogen HD1 on OD1 -->
				<conformer>
					<name>ASH1c</name>
<!-- HD1 on OD1 cis-->
					<add>
						<atom>
							<name>HD1</name>
							<altname>1HD</altname>
							<x>2.850</x>
							<y>-2.463</y>
							<z>0.072</z>
							<bond>OD1</bond>
						</atom>
						<dihedral>CB CG OD1 HD1</dihedral>
					</add>
				</conformer>
				<conformer>
					<name>ASH1t</name>
<!-- HD1 on OD1 trans-->
					<add>
						<atom>
							<name>HD1</name>
							<altname>1HD</altname>
							<x>1.955</x>
							<y>-1.180</y>
							<z>-0.588</z>
							<bond>OD1</bond>
						</atom>
						<dihedral>CB CG OD1 HD1</dihedral>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>ASH2</name>
<!-- Hydrogen HD2 on OD2 -->
				<conformer>
					<name>ASH2c</name>
<!-- HD2 on OD2 cis-->
					<add>
						<atom>
							<name>HD2</name>
							<altname>2HD</altname>
							<x>2.105</x>
							<y>-3.427</y>
							<z>1.930</z>
							<bond>OD2</bond>
						</atom>
						<dihedral>CB CG OD2 HD2</dihedral>
					</add>
				</conformer>
				<conformer>
					<name>ASH2t</name>
<!-- HD2 on OD2 trans-->
					<add>
						<atom>
							<name>HD2</name>
							<altname>2HD</altname>
							<x>0.599</x>
							<y>-2.812</y>
							<z>2.652</z>
							<bond>OD2</bond>
						</atom>
						<dihedral>CB CG OD2 HD2</dihedral>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- GLH implements the top-level transformation in the decision tree to transform the default GLU -> GLH -->
	<residue>
		<reference>
			<name>GLU</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>-0.059</x>
				<y>-0.875</y>
				<z>1.258</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.082</x>
				<y>-1.850</y>
				<z>1.501</z>
				<bond>CB</bond>
				<bond>CD</bond>
				<bond>HG2</bond>
				<bond>HG3</bond>
			</atom>
			<atom>
				<name>CD</name>
				<x>0.990</x>
				<y>-2.687</y>
				<z>2.740</z>
				<bond>CG</bond>
				<bond>OE1</bond>
				<bond>OE2</bond>
			</atom>
			<atom>
				<name>OE1</name>
				<x>0.067</x>
				<y>-2.624</y>
				<z>3.539</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>OE2</name>
				<x>1.970</x>
				<y>-3.449</y>
				<z>2.871</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.582</y>
				<z>-0.813</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.099</x>
				<y>-0.260</y>
				<z>2.046</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.903</x>
				<y>-1.409</y>
				<z>1.210</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG2</name>
				<altname>2HG</altname>
				<x>1.124</x>
				<y>-2.469</y>
				<z>0.717</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HG3</name>
				<altname>1HG</altname>
				<altname>HG1</altname>
				<altname>3HG</altname>
				<x>1.929</x>
				<y>-1.321</y>
				<z>1.553</z>
				<bond>CG</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG CD</dihedral>
			<dihedral>CB CG CD OE1</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the GLU structure -->
			<name>GLU</name>
			<tautomer>
				<name>GLU</name>
				<conformer>
					<name>GLU</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>GLH</name>
<!-- Protonated glutamate -->
			<tautomer>
				<name>GLH1</name>
<!-- Hydrogen HE1 on OE1 -->
				<conformer>
					<name>GLH1c</name>
<!-- HE1 on OE1 cis-->
					<add>
						<atom>
							<name>HE1</name>
							<altname>1HE</altname>
							<x>0.036</x>
							<y>-3.194</y>
							<z>4.361</z>
							<bond>OE1</bond>
						</atom>
						<dihedral>CG CD OE1 HE1</dihedral>
					</add>
				</conformer>
				<conformer>
					<name>GLH1t</name>
<!-- HE1 on OE1 trans-->
					<add>
						<atom>
							<name>HE1</name>
							<altname>1HE</altname>
							<x>-0.704</x>
							<y>-1.999</y>
							<z>3.412</z>
							<bond>OE1</bond>
						</atom>
						<dihedral>CG CD OE1 HE1</dihedral>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>GLH2</name>
<!-- Hydrogen HE2 on OE2 -->
				<conformer>
					<name>GLH2c</name>
<!-- HE2 on OE2 cis-->
					<add>
						<atom>
							<name>HE2</name>
							<altname>2HE</altname>
							<x>1.977</x>
							<y>-4.036</y>
							<z>3.680</z>
							<bond>OE2</bond>
						</atom>
						<dihedral>CG CD OE2 HE2</dihedral>
					</add>
				</conformer>
				<conformer>
					<name>GLH2t</name>
<!-- HE2 on OE2 trans-->
					<add>
						<atom>
							<name>HE2</name>
							<altname>2HE</altname>
							<x>2.668</x>
							<y>-3.410</y>
							<z>2.156</z>
							<bond>OE2</bond>
						</atom>
						<dihedral>CG CD OE2 HE2</dihedral>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- AR0 implements the top-level transformation in the decision tree to transform ARG -> AR0 -->		
	<residue>
		<reference>
			<name>ARG</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>-0.019</x>
				<y>-0.932</y>
				<z>1.222</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.158</x>
				<y>-1.892</y>
				<z>1.324</z>
				<bond>CB</bond>
				<bond>CD</bond>
				<bond>HG2</bond>
				<bond>HG3</bond>
			</atom>
			<atom>
				<name>CD</name>
				<x>1.060</x>
				<y>-2.755</y>
				<z>2.534</z>
				<bond>CG</bond>
				<bond>NE</bond>
				<bond>HD2</bond>
				<bond>HD3</bond>
			</atom>
			<atom>
				<name>NE</name>
				<x>2.184</x>
				<y>-3.677</y>
				<z>2.638</z>
				<bond>CD</bond>
				<bond>CZ</bond>
				<bond>HE</bond>
			</atom>
			<atom>
				<name>CZ</name>
				<x>2.321</x>
				<y>-4.549</y>
				<z>3.631</z>
				<bond>NE</bond>
				<bond>NH1</bond>
				<bond>NH2</bond>
			</atom>
			<atom>
				<name>NH1</name>
				<x>1.541</x>
				<y>-4.507</y>
				<z>4.705</z>
				<bond>CZ</bond>
				<bond>HH11</bond>
				<bond>HH12</bond>
			</atom>
			<atom>
				<name>NH2</name>
				<x>3.296</x>
				<y>-5.454</y>
				<z>3.573</z>
				<bond>CZ</bond>
				<bond>HH21</bond>
				<bond>HH22</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.558</y>
				<z>-0.830</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.027</x>
				<y>-0.363</y>
				<z>2.044</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.858</x>
				<y>-1.474</y>
				<z>1.184</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG2</name>
				<altname>2HG</altname>
				<x>1.174</x>
				<y>-2.473</y>
				<z>0.510</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HG3</name>
				<altname>1HG</altname>
				<altname>HG1</altname>
				<altname>3HG</altname>
				<x>2.005</x>
				<y>-1.362</y>
				<z>1.371</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HD2</name>
				<altname>2HD</altname>
				<x>1.044</x>
				<y>-2.172</y>
				<z>3.346</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>HD3</name>
				<altname>1HD</altname>
				<altname>HD1</altname>
				<altname>3HD</altname>
				<x>0.212</x>
				<y>-3.283</y>
				<z>2.485</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>HE</name>
				<x>2.887</x>
				<y>-3.652</y>
				<z>1.927</z>
				<bond>NE</bond>
			</atom>
			<atom>
				<name>HH11</name>
				<altname>1HH1</altname>
				<x>0.817</x>
				<y>-3.820</y>
				<z>4.771</z>
				<bond>NH1</bond>
			</atom>
			<atom>
				<name>HH12</name>
				<altname>2HH1</altname>
				<x>1.676</x>
				<y>-5.163</y>
				<z>5.448</z>
				<bond>NH1</bond>
			</atom>
			<atom>
				<name>HH21</name>
				<altname>1HH2</altname>
				<x>3.903</x>
				<y>-5.485</y>
				<z>2.779</z>
				<bond>NH2</bond>
			</atom>
			<atom>
				<name>HH22</name>
				<altname>2HH2</altname>
				<x>3.420</x>
				<y>-6.103</y>
				<z>4.323</z>
				<bond>NH2</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG CD</dihedral>
			<dihedral>CB CG CD NE</dihedral>
			<dihedral>CG CD NE CZ</dihedral>
			<dihedral>CD NE CZ NH1</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the ARG structure -->
			<name>ARG</name>
			<tautomer>
				<name>ARG</name>
				<conformer>
					<name>ARG</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>AR0</name>
            <incomplete>
			<tautomer> <!-- AR0-NH1-H1 -->
				<name>AR0HH11</name>
                <conformer>
					<name>AR0HH11</name>
					<remove>
						<atom>
							<name>HH11</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
			<tautomer> <!-- AR0-NH2-H1 -->
				<name>AR0HH21</name>
                <conformer>
					<name>AR0HH21</name>
					<remove>
						<atom>
							<name>HH21</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
			<tautomer> <!-- AR0-NE-H -->
				<name>AR0HE</name>
                <conformer>
					<name>AR0HE</name>
					<remove>
						<atom>
							<name>HE</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
			<tautomer> <!-- AR0-NH1-H2 -->
				<name>AR0HH12</name>
                <conformer>
					<name>AR0HH12</name>
					<remove>
						<atom>
							<name>HH12</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
			<tautomer> <!-- AR0-NH2-H2 -->
				<name>AR0HH22</name>
                <conformer>
					<name>AR0HH22</name>
					<remove>
						<atom>
							<name>HH22</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
			</incomplete>
		</titrationstate>
	</residue>
<!-- HIS implements the top-level transformation in the decision tree to transform HIS -->
	<residue>
		<reference>
			<name>HIS</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>-0.062</x>
				<y>-0.963</y>
				<z>1.211</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.102</x>
				<y>-1.908</y>
				<z>1.266</z>
				<bond>CB</bond>
				<bond>ND1</bond>
				<bond>CD2</bond>
			</atom>
			<atom>
				<name>ND1</name>
				<x>2.279</x>
				<y>-1.643</y>
				<z>1.921</z>
				<bond>CG</bond>
				<bond>CE1</bond>
				<bond>HD1</bond>
			</atom>
			<atom>
				<name>CD2</name>
				<x>1.195</x>
				<y>-3.189</y>
				<z>0.838</z>
				<bond>CG</bond>
				<bond>NE2</bond>
				<bond>HD2</bond>
			</atom>
			<atom>
				<name>CE1</name>
				<x>3.044</x>
				<y>-2.718</y>
				<z>1.891</z>
				<bond>ND1</bond>
				<bond>NE2</bond>
				<bond>HE1</bond>
			</atom>
			<atom>
				<name>NE2</name>
				<x>2.411</x>
				<y>-3.674</y>
				<z>1.242</z>
				<bond>CD2</bond>
				<bond>CE1</bond>
				<bond>HE2</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.547</y>
				<z>-0.837</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.073</x>
				<y>-0.420</y>
				<z>2.051</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.905</x>
				<y>-1.498</y>
				<z>1.150</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HD1</name>
				<x>2.518</x>
				<y>-0.773</y>
				<z>2.353</z>
				<bond>ND1</bond>
			</atom>
			<atom>
				<name>HD2</name>
				<x>0.502</x>
				<y>-3.690</y>
				<z>0.320</z>
				<bond>CD2</bond>
			</atom>
			<atom>
				<name>HE1</name>
				<x>3.956</x>
				<y>-2.794</y>
				<z>2.294</z>
				<bond>CE1</bond>
			</atom>
			<atom>
				<name>HE2</name>
				<x>2.758</x>
				<y>-4.596</y>
				<z>1.074</z>
				<bond>NE2</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG ND1</dihedral>
		</reference>
		<titrationstate>
			<name>HIS</name>
			<tautomer>
				<name>HSD</name>
				<conformer> <!-- HSD flip 1 -->
					<name>HSD1</name>
					<remove>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
				</conformer>
				<conformer> <!-- HSD flip 2 -->
					<name>HSD2</name>
					<remove>
						<atom>
							<name>ND1</name>
						</atom>
						<atom>
							<name>CD2</name>
						</atom>
						<atom>
							<name>CE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HD1</name>
						</atom>
						<atom>
							<name>HD2</name>
						</atom>
						<atom>
							<name>HE1</name>
						</atom>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>ND1</name>
							<x>1.120</x>
							<y>-3.143</y>
							<z>0.667</z>
							<bond>CG</bond>
							<bond>CE1</bond>
							<bond>HD1</bond>
						</atom>
						<atom>
							<name>CD2</name>
							<x>2.349</x>
							<y>-1.715</y>
							<z>1.757</z>
							<bond>CG</bond>
							<bond>NE2</bond>
							<bond>HD2</bond>
						</atom>
						<atom>
							<name>CE1</name>
							<x>2.325</x>
							<y>-3.668</y>
							<z>0.791</z>
							<bond>ND1</bond>
							<bond>NE2</bond>
							<bond>HE1</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>3.093</x>
							<y>-2.822</y>
							<z>1.446</z>
							<bond>CD2</bond>
							<bond>CE1</bond>
							<bond>HE2</bond>
						</atom>
						<atom>
							<name>HD1</name>
							<x>0.343</x>
							<y>-3.577</y>
							<z>0.210</z>
							<bond>ND1</bond>
						</atom>
						<atom>
							<name>HD2</name>
							<x>2.668</x>
							<y>-0.910</y>
							<z>2.258</z>
							<bond>CD2</bond>
						</atom>
						<atom>
							<name>HE1</name>
							<x>2.608</x>
							<y>-4.562</y>
							<z>0.444</z>
							<bond>CE1</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>HSE</name>
				<conformer> <!-- HSE flip 1 -->
					<name>HSE1</name>
					<remove>
						<atom>
							<name>HD1</name>
						</atom>
					</remove>
				</conformer>
				<conformer> <!-- HSE flip 2 -->
					<name>HSE2</name>
					<remove>
						<atom>
							<name>ND1</name>
						</atom>
						<atom>
							<name>CD2</name>
						</atom>
						<atom>
							<name>CE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HD1</name>
						</atom>
						<atom>
							<name>HD2</name>
						</atom>
						<atom>
							<name>HE1</name>
						</atom>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>ND1</name>
							<x>1.120</x>
							<y>-3.143</y>
							<z>0.667</z>
							<bond>CG</bond>
							<bond>CE1</bond>
							<bond>HD1</bond>
						</atom>
						<atom>
							<name>CD2</name>
							<x>2.349</x>
							<y>-1.715</y>
							<z>1.757</z>
							<bond>CG</bond>
							<bond>NE2</bond>
							<bond>HD2</bond>
						</atom>
						<atom>
							<name>CE1</name>
							<x>2.325</x>
							<y>-3.668</y>
							<z>0.791</z>
							<bond>ND1</bond>
							<bond>NE2</bond>
							<bond>HE1</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>3.093</x>
							<y>-2.822</y>
							<z>1.446</z>
							<bond>CD2</bond>
							<bond>CE1</bond>
							<bond>HE2</bond>
						</atom>
						<atom>
							<name>HD2</name>
							<x>2.668</x>
							<y>-0.910</y>
							<z>2.258</z>
							<bond>CD2</bond>
						</atom>
						<atom>
							<name>HE1</name>
							<x>2.608</x>
							<y>-4.562</y>
							<z>0.444</z>
							<bond>CE1</bond>
						</atom>
						<atom>
							<name>HE2</name>
							<x>4.056</x>
							<y>-2.962</y>
							<z>1.676</z>
							<bond>NE2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>HSP</name>
			<tautomer>
				<name>HSP</name> 
				<conformer> <!-- HSP flip 1 -->
					<name>HSP1</name>
				</conformer>
				<conformer> <!-- HSP flip 2 -->
					<name>HSP2</name>
					<remove>
						<atom>
							<name>ND1</name>
						</atom>
						<atom>
							<name>CD2</name>
						</atom>
						<atom>
							<name>CE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HD1</name>
						</atom>
						<atom>
							<name>HD2</name>
						</atom>
						<atom>
							<name>HE1</name>
						</atom>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>ND1</name>
							<x>1.120</x>
							<y>-3.143</y>
							<z>0.667</z>
							<bond>CG</bond>
							<bond>CE1</bond>
							<bond>HD1</bond>
						</atom>
						<atom>
							<name>CD2</name>
							<x>2.349</x>
							<y>-1.715</y>
							<z>1.757</z>
							<bond>CG</bond>
							<bond>NE2</bond>
							<bond>HD2</bond>
						</atom>
						<atom>
							<name>CE1</name>
							<x>2.325</x>
							<y>-3.668</y>
							<z>0.791</z>
							<bond>ND1</bond>
							<bond>NE2</bond>
							<bond>HE1</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>3.093</x>
							<y>-2.822</y>
							<z>1.446</z>
							<bond>CD2</bond>
							<bond>CE1</bond>
							<bond>HE2</bond>
						</atom>
						<atom>
							<name>HD1</name>
							<x>0.343</x>
							<y>-3.577</y>
							<z>0.210</z>
							<bond>ND1</bond>
						</atom>
						<atom>
							<name>HD2</name>
							<x>2.668</x>
							<y>-0.910</y>
							<z>2.258</z>
							<bond>CD2</bond>
						</atom>
						<atom>
							<name>HE1</name>
							<x>2.608</x>
							<y>-4.562</y>
							<z>0.444</z>
							<bond>CE1</bond>
						</atom>
						<atom>
							<name>HE2</name>
							<x>4.056</x>
							<y>-2.962</y>
							<z>1.676</z>
							<bond>NE2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>HIS-</name>
			<tautomer>
				<name>HIS-</name>
				<conformer> <!-- HIS- flip 1 -->
					<name>HIS-1</name>
					<remove>
						<atom>
							<name>HD1</name>
						</atom>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
				</conformer>
				<conformer> <!-- HIS- flip 2 -->
					<name>HIS-2</name>
					<remove>
						<atom>
							<name>ND1</name>
						</atom>
						<atom>
							<name>CD2</name>
						</atom>
						<atom>
							<name>CE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HD1</name>
						</atom>
						<atom>
							<name>HD2</name>
						</atom>
						<atom>
							<name>HE1</name>
						</atom>
						<atom>
							<name>HE2</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>ND1</name>
							<x>1.120</x>
							<y>-3.143</y>
							<z>0.667</z>
							<bond>CG</bond>
							<bond>CE1</bond>
							<bond>HD1</bond>
						</atom>
						<atom>
							<name>CD2</name>
							<x>2.349</x>
							<y>-1.715</y>
							<z>1.757</z>
							<bond>CG</bond>
							<bond>NE2</bond>
							<bond>HD2</bond>
						</atom>
						<atom>
							<name>CE1</name>
							<x>2.325</x>
							<y>-3.668</y>
							<z>0.791</z>
							<bond>ND1</bond>
							<bond>NE2</bond>
							<bond>HE1</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>3.093</x>
							<y>-2.822</y>
							<z>1.446</z>
							<bond>CD2</bond>
							<bond>CE1</bond>
							<bond>HE2</bond>
						</atom>
						<atom>
							<name>HD2</name>
							<x>2.668</x>
							<y>-0.910</y>
							<z>2.258</z>
							<bond>CD2</bond>
						</atom>
						<atom>
							<name>HE1</name>
							<x>2.608</x>
							<y>-4.562</y>
							<z>0.444</z>
							<bond>CE1</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- NTER implements the top-level transformation in the decision tree to transform [RES] -> N[RES] -->
	<residue>
		<reference>
			<name>NTER</name>
		</reference>
<!-- including PRO, we don't differentiate N-terminal PRO here, we can do it in the program -->
		<titrationstate>
			<name>NTER</name>
<!-- N-terminus -->
			<tautomer>
				<name>NTER</name>
				<conformer>
					<name>NTER</name>
					<add>
						<atom>
							<name>H</name>
							<altname>HT1</altname>
							<altname>H1</altname>
							<altname>1H</altname>
							<x>0.934</x>
							<y>1.811</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
						<atom>
							<name>H2</name>
							<altname>HT2</altname>
							<altname>2H</altname>
							<x>1.746</x>
							<y>0.653</y>
							<z>-0.817</z>
							<bond>N</bond>
						</atom>
						<atom>
							<name>H3</name>
							<altname>HT3</altname>
							<altname>3H</altname>
							<x>1.746</x>
							<y>0.653</y>
							<z>0.817</z>
							<bond>N</bond>
						</atom>
						<atom>
							<name>N+1</name>
							<x>-1.252</x>
							<y>1.877</y>
							<z>1.023</z>
							<bond>C</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>NTER0</name>
<!-- Neutral N-terminus -->
			<tautomer>
				<name>NTER0</name>
				<conformer>
					<name>NTER0</name>
					<remove>
						<atom>
							<name>H3</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>H</name>
							<altname>HT1</altname>
							<altname>H1</altname>
							<altname>1H</altname>
							<x>0.934</x>
							<y>1.811</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
						<atom>
							<name>H2</name>
							<altname>HT2</altname>
							<altname>2H</altname>
							<x>1.746</x>
							<y>0.653</y>
							<z>-0.817</z>
							<bond>N</bond>
						</atom>
						<atom>
							<name>N+1</name>
							<x>-1.252</x>
							<y>1.877</y>
							<z>1.023</z>
							<bond>C</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- CTER implements the top-level transformation in the decision tree to transform [RES] -> C[RES] -->
	<residue>
		<reference>
			<name>CTER</name>
		</reference>
		<titrationstate>
			<name>CTER</name>
<!-- C-terminus -->
			<tautomer>
				<name>CTER</name>
				<conformer>
					<name>CTER</name>
					<add>
						<atom>
							<name>OXT</name>
							<altname>O''</altname>
							<altname>OT2</altname>
							<x>-1.529</x>
							<y>1.858</y>
							<z>0.695</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>O</name>
							<altname>O'</altname>
							<altname>OT1</altname>
							<x>-2.185</x>
							<y>0.660</y>
							<z>-0.784</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>C-1</name>
							<x>2.339</x>
							<y>0.216</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>CTER0</name>
<!-- Neutral C-terminus -->
			<tautomer>
				<name>CTER01</name>
<!-- Hydrogen HO on O' -->
				<conformer>
					<name>CTER01c</name>
<!-- HO on O' cis-->
					<add>
						<atom>
							<name>HO</name>
							<x>-2.998</x>
							<y>1.241</y>
							<z>-0.768</z>
							<bond>O</bond>
						</atom>
						<atom>
							<name>OXT</name>
							<altname>O''</altname>
							<altname>OT2</altname>
							<x>-1.529</x>
							<y>1.858</y>
							<z>0.695</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>O</name>
							<altname>O'</altname>
							<altname>OT1</altname>
							<x>-2.185</x>
							<y>0.660</y>
							<z>-0.784</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>C-1</name>
							<x>2.339</x>
							<y>0.216</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
					</add>
				</conformer>
				<conformer>
					<name>CTER01t</name>
<!-- HO on O' trans-->
					<add>
						<atom>
							<name>HO</name>
							<x>-2.125</x>
							<y>-0.099</y>
							<z>-1.431</z>
							<bond>O</bond>
						</atom>
						<atom>
							<name>OXT</name>
							<altname>O''</altname>
							<altname>OT2</altname>
							<x>-1.529</x>
							<y>1.858</y>
							<z>0.695</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>O</name>
							<altname>O'</altname>
							<altname>OT1</altname>
							<x>-2.185</x>
							<y>0.660</y>
							<z>-0.784</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>C-1</name>
							<x>2.339</x>
							<y>0.216</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>CTER02</name>
<!-- Hydrogen HO on OXT -->
				<conformer>
					<name>CTER02c</name>
<!-- HO on OXT cis-->
					<add>
						<atom>
							<name>HO</name>
							<x>-2.401</x>
							<y>2.330</y>
							<z>0.567</z>
							<bond>OXT</bond>
						</atom>
						<atom>
							<name>OXT</name>
							<altname>O''</altname>
							<altname>OT2</altname>
							<x>-1.529</x>
							<y>1.858</y>
							<z>0.695</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>O</name>
							<altname>O'</altname>
							<altname>OT1</altname>
							<x>-2.185</x>
							<y>0.660</y>
							<z>-0.784</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>C-1</name>
							<x>2.339</x>
							<y>0.216</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
					</add>
				</conformer>
				<conformer>
					<name>CTER02t</name>
<!-- HO on OXT trans-->
					<add>
						<atom>
							<name>HO</name>
							<x>-0.883</x>
							<y>2.180</y>
							<z>1.387</z>
							<bond>OXT</bond>
						</atom>
						<atom>
							<name>OXT</name>
							<altname>O''</altname>
							<altname>OT2</altname>
							<x>-1.529</x>
							<y>1.858</y>
							<z>0.695</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>O</name>
							<altname>O'</altname>
							<altname>OT1</altname>
							<x>-2.185</x>
							<y>0.660</y>
							<z>-0.784</z>
							<bond>C</bond>
						</atom>
						<atom>
							<name>C-1</name>
							<x>2.339</x>
							<y>0.216</y>
							<z>0.000</z>
							<bond>N</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- ASN implements the top-level transformation in the decision tree to transform ASN -> ASN+ -->	
	<residue>
		<reference>
			<name>ASN</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>0.050</x>
				<y>-1.025</y>
				<z>1.129</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.239</x>
				<y>-1.965</y>
				<z>1.044</z>
				<bond>CB</bond>
				<bond>OD1</bond>
				<bond>ND2</bond>
			</atom>
			<atom>
				<name>OD1</name>
				<x>2.060</x>
				<y>-1.867</y>
				<z>0.126</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>ND2</name>
				<x>1.344</x>
				<y>-2.870</y>
				<z>2.015</z>
				<bond>CG</bond>
				<bond>HD21</bond>
				<bond>HD22</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.510</y>
				<z>-0.860</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>0.096</x>
				<y>-0.535</y>
				<z>2.000</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.788</x>
				<y>-1.571</y>
				<z>1.098</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HD21</name>
				<altname>1HD2</altname>
				<x>0.657</x>
				<y>-2.905</y>
				<z>2.741</z>
				<bond>ND2</bond>
			</atom>
			<atom>
				<name>HD22</name>
				<altname>2HD2</altname>
				<x>2.108</x>
				<y>-3.514</y>
				<z>2.018</z>
				<bond>ND2</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG OD1</dihedral>
		</reference>
		<titrationstate>
			<name>ASN</name>
			<tautomer>
				<name>ASN</name>
				<conformer> <!-- ASN flip 1, no changes necessary to the ASN reference -->
					<name>ASN1</name>
				</conformer>
				<conformer> <!-- ASN flip 2 -->
					<name>ASN2</name>
					<remove>
						<atom>
							<name>OD1</name>
						</atom>
						<atom>
							<name>ND2</name>
						</atom>
						<atom>
							<name>HD21</name>
						</atom>
						<atom>
							<name>HD22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OD1</name>
							<x>1.411</x>
							<y>-2.848</y>
							<z>1.891</z>
							<bond>CG</bond>
						</atom>
						<atom>
							<name>ND2</name>
							<x>2.055</x>
							<y>-1.789</y>
							<z>0.007</z>
							<bond>CG</bond>
							<bond>HD21</bond>
							<bond>HD22</bond>
						</atom>
						<atom>
							<name>HD21</name>
							<altname>1HD2</altname>
							<x>1.870</x>
							<y>-1.064</y>
							<z>-0.656</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD22</name>
							<altname>2HD2</altname>
							<x>2.845</x>
							<y>-2.373</y>
							<z>-0.197</z>
							<bond>ND2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>ASN+</name>
			<incomplete> <!-- ASN+ is a little problematic, we don't have exact models for the transitions from NH2 to NH3+, and O to OH+ right now -->
			<tautomer> <!-- ASN+ H-N -->
				<name>ASN+N</name>
				<conformer>
					<name>ASN+11</name> <!-- ASN+ H-N (flip 1) -->
					<remove>
						<atom>
							<name>HD21</name>
						</atom>
						<atom>
							<name>HD22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>HD21</name>
							<altname>1HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD22</name>
							<altname>2HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD23</name>
							<altname>3HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
					</add>
				</conformer>
				<conformer>
					<name>ASN+12</name> <!-- ASN+ H-N (flip 2)-->
					<remove>
						<atom>
							<name>OD1</name>
						</atom>
						<atom>
							<name>ND2</name>
						</atom>
						<atom>
							<name>HD21</name>
						</atom>
						<atom>
							<name>HD22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OD1</name>
							<x>1.411</x>
							<y>-2.848</y>
							<z>1.891</z>
							<bond>CG</bond>
						</atom>
						<atom>
							<name>ND2</name>
							<x>2.055</x>
							<y>-1.789</y>
							<z>0.007</z>
							<bond>CG</bond>
							<bond>HD21</bond>
							<bond>HD22</bond>
						</atom>
						<atom>
							<name>HD21</name>
							<altname>1HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD22</name>
							<altname>2HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD23</name>
							<altname>3HD2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>ND2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>ASN+2</name> <!-- ASN+ H-O -->
				<conformer>
					<name>ASN+21</name> <!-- ASN+ H-O (flip 1) -->
					<add>
						<atom>
							<name>HD1</name>
							<altname>1HD</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>OD1</bond>
						</atom>
					</add>
				</conformer>
				<conformer>
					<name>ASN+22</name> <!-- ASN+ H-O (flip 2) -->
					<remove>
						<atom>
							<name>OD1</name>
						</atom>
						<atom>
							<name>ND2</name>
						</atom>
						<atom>
							<name>HD21</name>
						</atom>
						<atom>
							<name>HD22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OD1</name>
							<x>1.411</x>
							<y>-2.848</y>
							<z>1.891</z>
							<bond>CG</bond>
						</atom>
						<atom>
							<name>ND2</name>
							<x>2.055</x>
							<y>-1.789</y>
							<z>0.007</z>
							<bond>CG</bond>
							<bond>HD21</bond>
							<bond>HD22</bond>
						</atom>
						<atom>
							<name>HD21</name>
							<altname>1HD2</altname>
							<x>1.870</x>
							<y>-1.064</y>
							<z>-0.656</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD22</name>
							<altname>2HD2</altname>
							<x>2.845</x>
							<y>-2.373</y>
							<z>-0.197</z>
							<bond>ND2</bond>
						</atom>
						<atom>
							<name>HD1</name>
							<altname>1HD</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>OD1</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			</incomplete>
		</titrationstate>
	</residue>
<!-- GLN implements the top-level transformation in the decision tree to transform GLN -> GLN+ -->	
	<residue>
		<reference>
			<name>GLN</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>-0.018</x>
				<y>-0.986</y>
				<z>1.179</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.159</x>
				<y>-1.939</y>
				<z>1.188</z>
				<bond>CB</bond>
				<bond>CD</bond>
				<bond>HG2</bond>
				<bond>HG3</bond>
			</atom>
			<atom>
				<name>CD</name>
				<x>1.117</x>
				<y>-2.896</y>
				<z>2.354</z>
				<bond>CG</bond>
				<bond>OE1</bond>
				<bond>NE2</bond>
			</atom>
			<atom>
				<name>OE1</name>
				<x>0.214</x>
				<y>-2.882</y>
				<z>3.191</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>NE2</name>
				<x>2.144</x>
				<y>-3.752</y>
				<z>2.427</z>
				<bond>CD</bond>
				<bond>HE21</bond>
				<bond>HE22</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.533</y>
				<z>-0.846</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.007</x>
				<y>-0.462</y>
				<z>2.030</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.860</x>
				<y>-1.524</y>
				<z>1.129</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG2</name>
				<altname>2HG</altname>
				<x>1.151</x>
				<y>-2.468</y>
				<z>0.339</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HG3</name>
				<altname>1HG</altname>
				<altname>HG1</altname>
				<altname>3HG</altname>
				<x>2.004</x>
				<y>-1.406</y>
				<z>1.240</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HE21</name>
				<altname>1HE2</altname>
				<x>2.198</x>
				<y>-4.425</y>
				<z>3.196</z>
				<bond>NE2</bond>
			</atom>
			<atom>
				<name>HE22</name>
				<altname>2HE2</altname>
				<x>2.860</x>
				<y>-3.722</y>
				<z>1.713</z>
				<bond>NE2</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG CD</dihedral>
			<dihedral>CB CG CD OE1</dihedral>
		</reference>
		<titrationstate>
			<name>GLN</name>
			<tautomer>
				<name>GLN</name>
				<conformer> <!-- GLN flip 1, no changes necessary to the GLN model in reference -->
					<name>GLN1</name>
				</conformer>
				<conformer> <!-- GLN flip 2 -->
					<name>GLN2</name>
					<remove>
						<atom>
							<name>OE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HE21</name>
						</atom>
						<atom>
							<name>HE22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OE1</name>
							<x>1.983</x>
							<y>-3.751</y>
							<z>2.542</z>
							<bond>CD</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>0.058</x>
							<y>-2.764</y>
							<z>3.163</z>
							<bond>CD</bond>
							<bond>HE21</bond>
							<bond>HE22</bond>
						</atom>
						<atom>
							<name>HE21</name>
							<altname>1HE2</altname>
							<x>-0.053</x>
							<y>-3.384</y>
							<z>3.969</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE22</name>
							<altname>2HE2</altname>
							<x>-0.625</x>
							<y>-2.045</y>
							<z>2.964</z>
							<bond>NE2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>GLN+</name>
			<incomplete>  <!-- GLN+ is a little problematic, we don't have exact models for the transitions from NH2 to NH3+, and O to OH+ right now -->
			<tautomer> <!-- GLN+ H-N -->
				<name>GLN+1</name>
				<conformer> <!-- GLN+ H-N (flip 1) -->
					<name>GLN+11</name>
					<remove>
						<atom>
							<name>HE21</name>
						</atom>
						<atom>
							<name>HE22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>HE21</name>
							<altname>1HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE22</name>
							<altname>2HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE23</name>
							<altname>3HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
					</add>
				</conformer>
				<conformer> <!-- GLN+ H-N (flip 2) -->
					<name>GLN+12</name>
					<remove>
						<atom>
							<name>OE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HE21</name>
						</atom>
						<atom>
							<name>HE22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OE1</name>
							<x>1.983</x>
							<y>-3.751</y>
							<z>2.542</z>
							<bond>CD</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>0.058</x>
							<y>-2.764</y>
							<z>3.163</z>
							<bond>CD</bond>
							<bond>HE21</bond>
							<bond>HE22</bond>
						</atom>
						<atom>
							<name>HE21</name>
							<altname>1HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE22</name>
							<altname>2HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE23</name>
							<altname>3HE2</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>NE2</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			<tautomer>
				<name>GLN+2</name> <!-- GLN+ H-O -->
				<conformer>
					<name>GLN+21</name>  <!-- GLN+ H-O (flip 1) -->
					<add>
						<atom>
							<name>HE1</name>
							<altname>1HE</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>OE1</bond>
						</atom>
					</add>
				</conformer>
				<conformer>
					<name>GLN+22</name> <!-- GLN+ (flip 2) H-O -->
					<remove>
						<atom>
							<name>OE1</name>
						</atom>
						<atom>
							<name>NE2</name>
						</atom>
						<atom>
							<name>HE21</name>
						</atom>
						<atom>
							<name>HE22</name>
						</atom>
					</remove>
					<add>
						<atom>
							<name>OE1</name>
							<x>1.983</x>
							<y>-3.751</y>
							<z>2.542</z>
							<bond>CD</bond>
						</atom>
						<atom>
							<name>NE2</name>
							<x>0.058</x>
							<y>-2.764</y>
							<z>3.163</z>
							<bond>CD</bond>
							<bond>HE21</bond>
							<bond>HE22</bond>
						</atom>
						<atom>
							<name>HE21</name>
							<altname>1HE2</altname>
							<x>-0.053</x>
							<y>-3.384</y>
							<z>3.969</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE22</name>
							<altname>2HE2</altname>
							<x>-0.625</x>
							<y>-2.045</y>
							<z>2.964</z>
							<bond>NE2</bond>
						</atom>
						<atom>
							<name>HE1</name>
							<altname>1HE</altname>
							<x>????</x>
							<y>????</y>
							<z>????</z>
							<bond>OE1</bond>
						</atom>
					</add>
				</conformer>
			</tautomer>
			</incomplete>
		</titrationstate>
	</residue>
<!-- LYS0 implements the top-level transformation in the decision tree to transform LYS -> LYS0 -->
	<residue>
		<reference>
			<name>LYS</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>-0.030</x>
				<y>-0.922</y>
				<z>1.219</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.154</x>
				<y>-1.877</y>
				<z>1.315</z>
				<bond>CB</bond>
				<bond>CD</bond>
				<bond>HG2</bond>
				<bond>HG3</bond>
			</atom>
			<atom>
				<name>CD</name>
				<x>1.060</x>
				<y>-2.763</y>
				<z>2.546</z>
				<bond>CG</bond>
				<bond>CE</bond>
				<bond>HD2</bond>
				<bond>HD3</bond>
			</atom>
			<atom>
				<name>CE</name>
				<x>2.224</x>
				<y>-3.719</y>
				<z>2.663</z>
				<bond>CD</bond>
				<bond>NZ</bond>
				<bond>HE2</bond>
				<bond>HE3</bond>
			</atom>
			<atom>
				<name>NZ</name>
				<x>2.090</x>
				<y>-4.562</y>
				<z>3.878</z>
				<bond>CE</bond>
				<bond>HZ1</bond>
				<bond>HZ2</bond>
				<bond>HZ3</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.560</y>
				<z>-0.829</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.040</x>
				<y>-0.354</y>
				<z>2.041</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.868</x>
				<y>-1.466</y>
				<z>1.179</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG2</name>
				<altname>2HG</altname>
				<x>1.171</x>
				<y>-2.456</y>
				<z>0.499</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HG3</name>
				<altname>1HG</altname>
				<altname>HG1</altname>
				<altname>3HG</altname>
				<x>1.999</x>
				<y>-1.344</y>
				<z>1.362</z>
				<bond>CG</bond>
			</atom>
			<atom>
				<name>HD2</name>
				<altname>2HD</altname>
				<x>1.040</x>
				<y>-2.180</y>
				<z>3.359</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>HD3</name>
				<altname>1HD</altname>
				<altname>HD1</altname>
				<altname>3HD</altname>
				<x>0.213</x>
				<y>-3.293</y>
				<z>2.496</z>
				<bond>CD</bond>
			</atom>
			<atom>
				<name>HE2</name>
				<altname>2HE</altname>
				<x>2.248</x>
				<y>-4.308</y>
				<z>1.855</z>
				<bond>CE</bond>
			</atom>
			<atom>
				<name>HE3</name>
				<altname>1HE</altname>
				<altname>HE1</altname>
				<altname>3HE</altname>
				<x>3.075</x>
				<y>-3.196</y>
				<z>2.718</z>
				<bond>CE</bond>
			</atom>
			<atom>
				<name>HZ1</name>
				<altname>1HZ</altname>
				<x>2.070</x>
				<y>-3.977</y>
				<z>4.689</z>
				<bond>NZ</bond>
			</atom>
			<atom>
				<name>HZ2</name>
				<altname>2HZ</altname>
				<x>1.242</x>
				<y>-5.089</y>
				<z>3.826</z>
				<bond>NZ</bond>
			</atom>
			<atom>
				<name>HZ3</name>
				<altname>3HZ</altname>
				<x>2.868</x>
				<y>-5.187</y>
				<z>3.938</z>
				<bond>NZ</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG CD</dihedral>
			<dihedral>CB CG CD CE</dihedral>
			<dihedral>CG CD CE NZ</dihedral>
			<dihedral>CD CE NZ HZ1</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the LYS structure -->
			<name>LYS</name>
			<tautomer>
				<name>LYS</name>
				<conformer>
					<name>LYS</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>LYS0</name>
			<tautomer>
				<name>LYS0</name>
				<conformer>
					<name>LYS0</name>
					<remove>
						<atom>
							<name>HZ3</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- SER- implements the top-level transformation in the decision tree to transform SER -> SER-  -->
	<residue>
		<reference>
			<name>SER</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>0.014</x>
				<y>-0.971</y>
				<z>1.174</z>
				<bond>CA</bond>
				<bond>OG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>OG</name>
				<x>0.056</x>
				<y>-0.296</y>
				<z>2.418</z>
				<bond>CB</bond>
				<bond>HG</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.536</y>
				<z>-0.844</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>-0.812</x>
				<y>-1.533</y>
				<z>1.139</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>0.820</x>
				<y>-1.558</y>
				<z>1.098</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG</name>
				<x>0.067</x>
				<y>0.691</y>
				<z>2.262</z>
				<bond>OG</bond>
			</atom>
			<dihedral>N CA CB OG</dihedral>
			<dihedral>CA CB OG HG</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the SER structure -->
			<name>SER</name>
			<tautomer>
				<name>SER</name>
				<conformer>
					<name>SER</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>SER-</name>
			<tautomer>
				<name>SER-</name>
				<conformer>
					<name>SER-</name>
					<remove>
						<atom>
							<name>HG</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- THR- implements the top-level transformation in the decision tree to transform THR -> THR-  -->
	<residue>
		<reference>
		<name>THR</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>0.001</x>
				<y>-0.981</y>
				<z>1.242</z>
				<bond>CA</bond>
				<bond>OG1</bond>
				<bond>CG2</bond>
				<bond>HB</bond>
			</atom>
			<atom>
				<name>OG1</name>
				<x>1.226</x>
				<y>-1.775</y>
				<z>1.136</z>
				<bond>CB</bond>
				<bond>HG1</bond>
			</atom>
			<atom>
				<name>CG2</name>
				<x>-1.252</x>
				<y>-1.866</y>
				<z>1.324</z>
				<bond>CB</bond>
				<bond>HG21</bond>
				<bond>HG22</bond>
				<bond>HG23</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.549</y>
				<z>-0.836</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB</name>
				<x>0.054</x>
				<y>-0.432</y>
				<z>2.076</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG1</name>
				<altname>1HG</altname>
				<x>1.735</x>
				<y>-1.497</y>
				<z>0.321</z>
				<bond>OG1</bond>
			</atom>
			<atom>
				<name>HG21</name>
				<altname>1HG2</altname>
				<x>-2.064</x>
				<y>-1.287</y>
				<z>1.399</z>
				<bond>CG2</bond>
			</atom>
			<atom>
				<name>HG22</name>
				<altname>2HG2</altname>
				<x>-1.318</x>
				<y>-2.427</y>
				<z>0.498</z>
				<bond>CG2</bond>
			</atom>
			<atom>
				<name>HG23</name>
				<altname>3HG2</altname>
				<x>-1.190</x>
				<y>-2.459</y>
				<z>2.126</z>
				<bond>CG2</bond>
			</atom>
			<dihedral>N CA CB OG1</dihedral>
			<dihedral>CA CB OG1 HG1</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the THR structure -->
			<name>THR</name>
			<tautomer>
				<name>THR</name>
				<conformer>
					<name>THR</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>THR-</name>
			<tautomer>
				<name>THR-</name>
				<conformer>
					<name>THR-</name>
					<remove>
						<atom>
							<name>HG1</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- TYR- implements the top-level transformation in the decision tree to transform TYR -> TYR-  -->
	<residue>
		<reference>
			<name>TYR</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>
			<atom>
				<name>CB</name>
				<x>0.012</x>
				<y>-0.963</y>
				<z>1.196</z>
				<bond>CA</bond>
				<bond>CG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>CG</name>
				<x>1.193</x>
				<y>-1.914</y>
				<z>1.235</z>
				<bond>CB</bond>
				<bond>CD1</bond>
				<bond>CD2</bond>
			</atom>
			<atom>
				<name>CD1</name>
				<x>2.381</x>
				<y>-1.570</y>
				<z>1.891</z>
				<bond>CG</bond>
				<bond>CE1</bond>
				<bond>HD1</bond>
			</atom>
			<atom>
				<name>CD2</name>
				<x>1.136</x>
				<y>-3.152</y>
				<z>0.597</z>
				<bond>CG</bond>
				<bond>CE2</bond>
				<bond>HD2</bond>
			</atom>
			<atom>
				<name>CE1</name>
				<x>3.480</x>
				<y>-2.427</y>
				<z>1.889</z>
				<bond>CD1</bond>
				<bond>CZ</bond>
				<bond>HE1</bond>
			</atom>
			<atom>
				<name>CE2</name>
				<x>2.228</x>
				<y>-4.012</y>
				<z>0.583</z>
				<bond>CD2</bond>
				<bond>CZ</bond>
				<bond>HE2</bond>
			</atom>
			<atom>
				<name>CZ</name>
				<x>3.404</x>
				<y>-3.644</y>
				<z>1.219</z>
				<bond>CE1</bond>
				<bond>CE2</bond>
				<bond>OH</bond>
			</atom>
			<atom>
				<name>OH</name>
				<x>4.469</x>
				<y>-4.494</y>
				<z>1.141</z>
				<bond>CZ</bond>
				<bond>HH</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.543</y>
				<z>-0.840</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>0.023</x>
				<y>-0.418</y>
				<z>2.034</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.825</x>
				<y>-1.509</y>
				<z>1.164</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HD1</name>
				<altname>1HD</altname>
				<x>2.443</x>
				<y>-0.694</y>
				<z>2.369</z>
				<bond>CD1</bond>
			</atom>
			<atom>
				<name>HD2</name>
				<altname>2HD</altname>
				<x>0.290</x>
				<y>-3.428</y>
				<z>0.140</z>
				<bond>CD2</bond>
			</atom>
			<atom>
				<name>HE1</name>
				<altname>1HE</altname>
				<x>4.319</x>
				<y>-2.169</y>
				<z>2.368</z>
				<bond>CE1</bond>
			</atom>
			<atom>
				<name>HE2</name>
				<altname>2HE</altname>
				<x>2.166</x>
				<y>-4.894</y>
				<z>0.115</z>
				<bond>CE2</bond>
			</atom>
			<atom>
				<name>HH</name>
				<x>4.215</x>
				<y>-5.298</y>
				<z>0.603</z>
				<bond>OH</bond>
			</atom>
			<dihedral>N CA CB CG</dihedral>
			<dihedral>CA CB CG CD1</dihedral>
			<dihedral>CE2 CZ OH HH</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the TYR structure -->
			<name>TYR</name>
			<tautomer>
				<name>TYR</name>
				<conformer>
					<name>TYR</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>TYR-</name>
			<tautomer>
				<name>TYR-</name>
				<conformer>
					<name>TYR-</name>
					<remove>
						<atom>
							<name>HH</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
<!-- CYS- implements the top-level transformation in the decision tree to transform reduced CYS -> CYS-  -->
	<residue>
		<reference>
			<name>CYS</name>
			<atom>
				<name>N</name>
				<x>1.201</x>
				<y>0.847</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>H</bond>
			</atom>
			<atom>
				<name>CA</name>
				<x>0.000</x>
				<y>0.000</y>
				<z>0.000</z>
				<bond>N</bond>
				<bond>C</bond>
				<bond>CB</bond>
				<bond>HA</bond>
			</atom>
			<atom>
				<name>C</name>
				<x>-1.250</x>
				<y>0.881</y>
				<z>0.000</z>
				<bond>CA</bond>
				<bond>O</bond>
			</atom>
			<atom>
				<name>O</name>
				<x>-2.185</x>
				<y>0.660</y>
				<z>-0.784</z>
				<bond>C</bond>
			</atom>	
			<atom>
				<name>CB</name>
				<x>0.018</x>
				<y>-0.958</y>
				<z>1.184</z>
				<bond>CA</bond>
				<bond>SG</bond>
				<bond>HB2</bond>
				<bond>HB3</bond>
			</atom>
			<atom>
				<name>SG</name>
				<x>1.431</x>
				<y>-2.085</y>
				<z>1.212</z>
				<bond>CB</bond>
				<bond>HG</bond>
			</atom>
			<atom>
				<name>H</name>
				<altname>HN</altname>
				<x>1.201</x>
				<y>1.847</y>
				<z>0.000</z>
				<bond>N</bond>
			</atom>
			<atom>
				<name>HA</name>
				<x>0.000</x>
				<y>-0.542</y>
				<z>-0.840</z>
				<bond>CA</bond>
			</atom>
			<atom>
				<name>HB2</name>
				<altname>2HB</altname>
				<x>0.033</x>
				<y>-0.417</y>
				<z>2.024</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HB3</name>
				<altname>1HB</altname>
				<altname>HB1</altname>
				<altname>3HB</altname>
				<x>-0.818</x>
				<y>-1.506</y>
				<z>1.155</z>
				<bond>CB</bond>
			</atom>
			<atom>
				<name>HG</name>
				<altname>1HG</altname>
				<altname>HG1</altname>
				<x>2.014</x>
				<y>-1.908</y>
				<z>0.419</z>
				<bond>SG</bond>
			</atom>
			<dihedral>N CA CB SG</dihedral>
		</reference>
		<titrationstate> <!-- No changes to the CYS structure -->
			<name>CYS</name>
			<tautomer>
				<name>CYS</name>
				<conformer>
					<name>CYS</name>
				</conformer>
			</tautomer>
		</titrationstate>
		<titrationstate>
			<name>CYS-</name>
			<tautomer>
				<name>CYS-</name>
				<conformer>
					<name>CYS-</name>
					<remove>
						<atom>
							<name>HG</name>
						</atom>
					</remove>
				</conformer>
			</tautomer>
		</titrationstate>
	</residue>
</topology>
