/usr/share/pdb2pqr/dat/AMBER.names is in pdb2pqr 2.1.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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<patches>
<residue>
<name>WAT</name>
<atom>
<name>O</name>
<useatomname>OW</useatomname>
</atom>
<atom>
<name>H1</name>
<useatomname>HW</useatomname>
</atom>
<atom>
<name>H2</name>
<useatomname>HW</useatomname>
</atom>
</residue>
<residue>
<name>CYM</name>
<atom>
<name>H</name>
<useatomname>HN</useatomname>
</atom>
</residue>
<residue>
<name>LYN</name>
<atom>
<name>HZ1</name>
<useatomname>HZ3</useatomname>
</atom>
</residue>
<residue>
<name>N...$</name>
<atom>
<name>H</name>
<useatomname>H1</useatomname>
</atom>
</residue>
<residue>
<name>NCYS</name>
<atom>
<name>HG</name>
<useatomname>HSG</useatomname>
</atom>
</residue>
<residue>
<name>CCYS</name>
<atom>
<name>HG</name>
<useatomname>HSG</useatomname>
</atom>
</residue>
<residue>
<name>NPRO</name>
<atom>
<name>H</name>
<useatomname>H3</useatomname>
</atom>
</residue>
<!-- Nucleic Acid Subtitutions -->
<residue>
<name>[RD][ACGTU][35]?$</name>
<atom>
<name>H5'</name>
<useatomname>H5'1</useatomname>
</atom>
<atom>
<name>H5''</name>
<useatomname>H5'2</useatomname>
</atom>
<atom>
<name>H2'</name>
<useatomname>H2'1</useatomname>
</atom>
</residue>
<residue>
<name>D[ACGT][35]?$</name>
<atom>
<name>H2''</name>
<useatomname>H2'2</useatomname>
</atom>
<atom>
<name>OP1</name>
<useatomname>O1P</useatomname>
</atom>
<atom>
<name>OP2</name>
<useatomname>O2P</useatomname>
</atom>
</residue>
<residue>
<name>R[ACGU][35]?$</name>
<atom>
<name>H2''</name>
<useatomname>HO'2</useatomname>
</atom>
<atom>
<name>OP1</name>
<useatomname>O1P</useatomname>
</atom>
<atom>
<name>OP2</name>
<useatomname>O2P</useatomname>
</atom>
</residue>
</patches>
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