Bond order information missing in output cif files.

Author: alchemistcaiCreated Dec 7, 2024Updated May 21, 2026

Labelsenhancementquestion

Hi,there!

I use 2OWW to model covalent glycan.Here is my json:

json

{
    "name": "2oww",
    "modelSeeds": [42],
    "sequences": [
      {
        "protein": {
          "id": "A",
          "sequence": "GSHMELPRAFGLLLHPTSLPGPYGVGVLGQEARDFLRFLKEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDYGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALKGAHGGLPWNRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAEAEALGIRIIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWDVLEREGFSFWIRRLEKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMKVLQFAFDDGMENPFLPHNYPAHGRVVVYTGTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL",
          "unpairedMsa": "",
          "pairedMsa": "",
          "templates": []
        }
      },
      {
        "ligand": {
          "id": "B",
          "ccdCodes": ["GLC","AC1"]
        }
      }
    ],
    "bondedAtomPairs": [
      [["A", 296, "OD1"], ["B", 1, "C1"]],
      [["B", 1, "O4"], ["B", 2, "C1"]]
    ],
    "dialect": "alphafold3",
    "version": 1
  }

Residue AC1 contains a double bond between C5B and C7B atoms.

Bond order information is lost because the output cif files don't contain _chem_comp_bond.* fields.

In pymol and chimera(also plain txt editor),the double bond is missing.

Would this undermine the inference accuracy?If I just add addition bond in pymol without local minimization,is it acceptable?

The covalent bond angle between glycan and protein is strange,so maybe the missing double bond will lead to wrong bond geometry.

2oww_bad_bonds

Source: google-deepmind/alphafold3

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