Box 1 is your federal taxable income. It's your gross income, minus certain pre-tax deductions like health insurance premiums and 401k contributions.
Box 3 and 5 is income subject to employment tax (social security and medicare tax). This is your earned income (income earned from performing a service), and most items (like a 401k) that are deductible from your taxable income are not deducted from your earned income, so box 3 and 5 will often be larger than box 1. However, a few items are deductible from both your box 3 wages and your box 1 wages, so it is possible that neither box 1 or box 3 and 5 will represent your gross salary.
Furthermore, for 2022, only the first $147,000 of your income is subject to social security tax, while all your earned income is subject to medicare tax. So the value in box 3 should never be more than $147,000, even your salary and boxes 1 and 5 might be larger.
Box 16 is your state taxable income. It will often be the same as box 1. However, some states do not allow a state tax deduction for items that have federal tax deductions. For example, in California, a health savings account (HSA) is not deductible on your state income tax return, so if you have an HSA, your box 16 state wages will be larger than your box 1 federal taxable wages by the amount of your HSA. Whether box 1 and 16 are the same or different depends on what kinds of benefits you have and your state tax laws.
Box 12 code D is only your elective deferral (your salary reduction).
