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37 lines
1.1 KiB
YAML
37 lines
1.1 KiB
YAML
entities:
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- protein:
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id: B
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sequence: 1..3C1..2C1..3 ###1to3 residues before first CYS, 1to2 residues, second CYS, followed by 1to3 residues
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- file:
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path: 4g37.pdb
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include:
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- chain:
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id: A
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- chain:
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id: C # XLX
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- ligand:
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id: D
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smiles: "CC(=O)NCCNC(C)=O"
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constraints:
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## constraints from the file.
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# covalent bond between C3 in XLX (from CCD) and SG in chain A of 4g37.pdb
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- bond:
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atom1: [A, 105, SG]
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atom2: [C, 1, C3]
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# additional covalent bond between C11 in XLX (from CCD) and SG in chain B (design)
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- bond:
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atom1: [B, 2, SG]
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atom2: [C, 1, C11]
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## constraints from the smiles.
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- bond:
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# covalent bond between C1 in D (from smiles) and OG in chain A of 4g37.pdb
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atom1: [A, 339, OG]
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atom2: [D, 1, C1]
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# additional covalent bond between C6 in D (from smiles) and SG in chain B (design)
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- bond:
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atom1: [B, 4, SG]
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atom2: [D, 1, C6]
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#boltzgen run example/small_molecule_from_file_and_smiles/4g37.yaml --output workbench --protocol protein-anything --num_designs 2 --devices 1 --steps design |