/usr/share/pdb2pqr/dat/PEOEPB.names is in pdb2pqr 1.9.0+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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<peoepb>
<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>[NC]?...$</name>
<atom>
<name>H</name>
<useatomname>HN</useatomname>
</atom>
<atom>
<name>HA3</name>
<useatomname>HA1</useatomname>
</atom>
<atom>
<name>HG3</name>
<useatomname>HG1</useatomname>
</atom>
<atom>
<name>HG</name>
<useatomname>HG1</useatomname>
</atom>
</residue>
<residue>
<name>[NC]?(?!ALA$)...$</name> <!-- ALA has HB1, HB2, HB3 -->
<exclud>ALA</exclud>
<atom>
<name>HB3</name>
<useatomname>HB1</useatomname>
</atom>
</residue>
<residue>
<name>[NC]?(?!ILE$)...$</name> <!-- ILE has HD11, HD12, HD13 -->
<atom>
<name>HD3</name>
<useatomname>HD1</useatomname>
</atom>
</residue>
<residue>
<name>[NC]?(?!MET$|TRP$)...$</name> <!-- both have HE1/HE3 -->
<atom>
<name>HE3</name>
<useatomname>HE1</useatomname>
</atom>
</residue>
<residue>
<name>N...$</name>
<atom>
<name>H</name>
<useatomname>H1</useatomname>
</atom>
</residue>
</peoepb>
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