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[Bug] In halogen bonds ligand coordinate is assigned to "protcoo" #166

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andrew0901 opened this issue Dec 18, 2024 · 0 comments
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@andrew0901
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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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