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In halogen bonds, the halogen bond donor coordinate in the ligand is assigned to "protcoo" and the acceptor coordinate in the protein in assigned to "ligcoo"
I ran PLIP analysis of the PDB structure 3DV3 via web server. In the report I got (attached), the ligcoo in the halogen bond is:
[44.442, -22.175, 4.419], which is the coordinate of the O atom in V127 of the PDB.
While the protcoo is [42.777, -19.685, 3.455], which is the iodine in the ligand. I believe this is a bug?
<halogen_bonds>
<halogen_bond id="1">
<resnr>127</resnr>
<restype>VAL</restype>
<reschain>A</reschain>
<resnr_lig>9001</resnr_lig>
<restype_lig>MEK</restype_lig>
<reschain_lig>A</reschain_lig>
<sidechain>False</sidechain>
<dist>3.15</dist>
<don_angle>175.26</don_angle>
<acc_angle>126.90</acc_angle>
<don_idx>2333</don_idx>
<donortype>I</donortype>
<acc_idx>524</acc_idx>
<acceptortype>O2</acceptortype>
<ligcoo>
<x>44.442</x>
<y>-22.175</y>
<z>4.419</z>
</ligcoo>
<protcoo>
<x>42.777</x>
<y>-19.685</y>
<z>3.455</z>
</protcoo>
</halogen_bond>
</halogen_bonds>
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