What is the Ketcher file structure for a molecule structure?

To represent a single molecule in a Ketcher file, you need to include a referenced-object in the "nodes" array as shown below:

{
    "root": {
        "nodes": [
            {    
                "$ref": "mol<seq>"
            }
        ]
    },
    "mol<seq>": {  
        "type": "molecule",
        ...
    }
}

The molecule object structure should include an "atoms" array and a "bonds" array as shown below:

    "mol<seq>": {  
        "type": "molecule",
        "atoms": [
            <atom>,
            <atom>,
            ...
            <atom>
        ],
        "bonds": [
            <bond>,
            <bond>,
            ...
            <bond>
        ]
    }

The "atom" object must have 2 required properties: "label" for the atom symbol, and "location" for the atom coordinates. For example, the following structure represents a carbon atom located at (0, 0, 0):

    {
        "label": "C",
        "location": [ 0, 0, 0 ]
    }

The "bond" object must have 2 required properties: "type" indicating the type of the bond, and "atoms" specifying the connecting atoms of the bond. For example, the following structure represents a single bond connecting atom #0 and atom #1:

    {
        "type": 1,
        "atoms": [ 0, 1 ]
    }

Here is a Ketcher file for a carbon dioxide molecule:

{
    "root": {
        "nodes": [
            { "$ref": "mol0" }
        ]
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "O",
                "location": [ 0, 0, 0 ]
            },
            {
                "label": "C",
                "location": [ 1, 0, 0 ]
            },
            {
                "label": "O",
                "location": [ 2, 0, 0 ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [ 0, 1 ]
            },
            {
                "type": 1,
                "atoms": [ 1, 2 ]
            }
        ]
    }
}

⇒ Molecule Structure with Directed Bonds

⇐ Import Ketcher File to Editor

⇑ Ketcher File Format for Chemical Structures

⇑⇑ Ketcher - Chemical Structure Editor