/usr/share/avogadro/fragments/amino_acids/ is in avogadro-data 1.2.0-3.
This file is owned by root:root, with mode 0o755.
..
/usr/share/avogadro/fragments/amino_acids/D-alanine.cml
/usr/share/avogadro/fragments/amino_acids/D-allo-threonine.cml
/usr/share/avogadro/fragments/amino_acids/D-arginine.cml
/usr/share/avogadro/fragments/amino_acids/D-asparagine.cml
/usr/share/avogadro/fragments/amino_acids/D-aspartic_acid.cml
/usr/share/avogadro/fragments/amino_acids/D-cysteine.cml
/usr/share/avogadro/fragments/amino_acids/D-glutamic_acid.cml
/usr/share/avogadro/fragments/amino_acids/D-glutamine.cml
/usr/share/avogadro/fragments/amino_acids/D-histidine.cml
/usr/share/avogadro/fragments/amino_acids/D-isoleucine.cml
/usr/share/avogadro/fragments/amino_acids/D-leucine.cml
/usr/share/avogadro/fragments/amino_acids/D-lysine.cml
/usr/share/avogadro/fragments/amino_acids/D-methionine.cml
/usr/share/avogadro/fragments/amino_acids/D-phenylalanine.cml
/usr/share/avogadro/fragments/amino_acids/D-proline.cml
/usr/share/avogadro/fragments/amino_acids/D-serine.cml
/usr/share/avogadro/fragments/amino_acids/D-threonine.cml
/usr/share/avogadro/fragments/amino_acids/D-tryptophan.cml
/usr/share/avogadro/fragments/amino_acids/D-tyrosine.cml
/usr/share/avogadro/fragments/amino_acids/D-valine.cml
/usr/share/avogadro/fragments/amino_acids/L-4-nitrophenylalanine.cml
/usr/share/avogadro/fragments/amino_acids/L-alanine.cml
/usr/share/avogadro/fragments/amino_acids/L-allo-isoleucine.cml
/usr/share/avogadro/fragments/amino_acids/L-arginine.cml
/usr/share/avogadro/fragments/amino_acids/L-asparagine.cml
/usr/share/avogadro/fragments/amino_acids/L-aspartic_acid.cml
/usr/share/avogadro/fragments/amino_acids/L-cysteine.cml
/usr/share/avogadro/fragments/amino_acids/L-glutamic_acid.cml
/usr/share/avogadro/fragments/amino_acids/L-glutamine.cml
/usr/share/avogadro/fragments/amino_acids/L-histidine.cml
/usr/share/avogadro/fragments/amino_acids/L-isoleucine.cml
/usr/share/avogadro/fragments/amino_acids/L-leucine.cml
/usr/share/avogadro/fragments/amino_acids/L-lysine.cml
/usr/share/avogadro/fragments/amino_acids/L-methionine.cml
/usr/share/avogadro/fragments/amino_acids/L-phenylalanine.cml
/usr/share/avogadro/fragments/amino_acids/L-proline.cml
/usr/share/avogadro/fragments/amino_acids/L-serine.cml
/usr/share/avogadro/fragments/amino_acids/L-threonine.cml
/usr/share/avogadro/fragments/amino_acids/L-tryptophan.cml
/usr/share/avogadro/fragments/amino_acids/L-tyrosine.cml
/usr/share/avogadro/fragments/amino_acids/L-valine.cml
/usr/share/avogadro/fragments/amino_acids/glycine.cml