entities:
  - protein:
      id: B
      sequence: 1..3C1..2C1..3 ###1to3 residues before first CYS, 1to2 residues, second CYS, followed by 1to3 residues
  - file:
      path: 4g37.pdb

      include:
        - chain:
            id: A
        - chain:
            id: C # XLX
  - ligand:
      id: D
      smiles: "CC(=O)NCCNC(C)=O"

constraints:
  ## constraints from the file.
  # covalent bond between C3 in XLX (from CCD) and SG in chain A of 4g37.pdb
  - bond:
      atom1: [A, 105, SG]
      atom2: [C, 1, C3]
  # additional covalent bond between C11 in XLX (from CCD) and SG in chain B (design)
  - bond:
      atom1: [B, 2, SG]
      atom2: [C, 1, C11]
  ## constraints from the smiles.
  - bond:
      # covalent bond between C1 in D (from smiles) and OG in chain A of 4g37.pdb
      atom1: [A, 339, OG]
      atom2: [D, 1, C1]
  # additional covalent bond between C6 in D (from smiles) and SG in chain B (design)
  - bond:
      atom1: [B, 4, SG]
      atom2: [D, 1, C6]