update whole MongoDb Document in PHP

I wants to update whole MongoDb Document in PHP

like: UserCollection.findOneAndUpdate({ _id: user._id }, user, { returnNewDocument: true })

"user": {
_id: "62612f9da4eb57878f89291b",
"name": "VanrC",
"category": "This category",
"payment": {
    "wallet": 546,
    "cashback": 140
},
"createdAt": {
    "$date": {
        "$numberLong": "1650537244950"
    }
},
"updatedAt": {
    "$date": {
        "$numberLong": "1650537300996"
    }
},
"__v": "0"

}

I tried this in PHP

$updateResult = $collName->updateOne(["_id"=> $mid], ['$set' => $doc])

But it's not updating payment, createdAt and updatedAt