diff --git a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
index 7e22be4aa87ce4815e82992383b1a2b773fa7ab6..9338b484f5f6adad14e993870f5adc4309af9313 100644
--- a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+++ b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
@@ -451,6 +451,11 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
             already_mapped = set()
             for mdl_ch in mdl_chains:
                 if mdl_ch not in lddt_chain_mapping:
+
+                    if mdl_ch in self._mdl_chains_without_chem_mapping:
+                        # this mdl chain does not map to any trg chain
+                        continue
+
                     # check which chain in trg is closest
                     chem_grp_idx = None
                     for i, m in enumerate(self._chem_mapping):