To encode the custom struct (generated by abigen!) you can either use the call_data! macro:
let call_data = calldata!(
MyStruct {
field: 101,
}
)?;
or use ABIEncoder directly:
let instance = MyStruct { field: 101 };
let encoded: Vec<u8> = ABIEncoder::default().encode(&[instance.into_token()])?.resolve(0);
This will give you a Vec<u8> which you can pass as the contract input.