entities:
  # Specification of the target which is extracted from a .cif file
  - file:
      path: 9d3d.cif
      # Which chain and residues in the .cif file to use as target
      # Here we include chains A, B, and C (all residues on each chain)
      include:
        - chain:
            id: A
        - chain:
            id: B
        - chain:
            id: C
      # Include residues that are within a radius of a reference region
      # Here we include residues within a radius 30 of G:106..118
      include_proximity:
        - chain:
            id: G
            res_index: 106..118
            radius: 30
      # Which regions of the target the design should or should NOT bind to
      # Here we specify that the design should bind to residues 91, 128, and 131 on chains A, B, and C
      binding_types:
        - chain:
            id: A
            binding: 91,128,131
        - chain:
            id: B
            binding: 91,128,131
        - chain:
            id: C
            binding: 91,128,131

  # Specify a designed protein chain
  # random number between 8 and 18 of designed residues (inclusive)
  - protein:
      id: E
      sequence: 8..18
      # Make the designed protein chain cyclic
      cyclic: True