How to specify a directed bond at a stereocenter in a molecule structure in Ketcher file format?

You need to use the optional "stereo" property to specify a directed bond at a stereocenter in a molecule structure. For example:

    "stereo": 1 - for a upward bond
    "stereo": 6 - for a downward bond 

Note that the "atom" object at the stereocenter should also be given the "stereoLabel" property to indicate the type of the stereocenter. For example,

    "stereoLabel": "abs" - absolute stereochemistry, i.e. chirality

Here is a Ketcher file for a molecule with a stereocenter:

{
    "root": {
        "nodes": [
            {
                "$ref": "mol0"
            }
        ]
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "O",
                "location": [
                    1.7419872981077809,
                    -3.7750000000000004,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    2.6080127018922195,
                    -3.2750000000000004,
                    0
                ],
                "stereoLabel": "abs"
            },
            {
                "label": "N",
                "location": [
                    3.199038105676658,
                    -3.9750000000000005,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    2.6080127018922195,
                    -2.2750000000000004,
                    0
                ]
            },
            {
                "label": "H",
                "location": [
                    3.499038105676658,
                    -3.25,
                    0
                ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [
                    0,
                    1
                ]
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    2
                ],
                "stereo": 1
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    3
                ]
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    4
                ],
                "stereo": 6
            }
        ]
    }
}

⇒ Bond Type Codes in Ketcher File

⇐ Ketcher File Structure for Molecule

⇑ Ketcher File Format for Chemical Structures

⇑⇑ Ketcher - Chemical Structure Editor