Bond order information missing in output cif files.

[alchemistcai]

Hi,there!

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

[joshabramson]

AlphaFold 3 doesn't take bond type as a direct input, only whether a bond exists. However it does take in the positions and inter-atom distances of the generated conformer and the conformer generation uses the bond types.

Once the inference is complete, you can add particular bond types and run local minimisation to ensure the bond types are respected.

As for the bonds not being included in the output, this is something we should consider adding to the output. Will leave this open for now.