1099r box 2a blank

Filed for extension finally got 1099r I have a non qualified annuity put 100,000 I needed 50,000 took withdrawal minus surrender charge other fees net 42000 that was box 1 box 2 taxable is blank 2b checked not determined I know I have to pay 10% early withdrawal when I put numbers in saying I owe taxes on whole distribution that was made after taxes I'm confused company says I have to figure taxable amount 

Box 5 42,000

Box 7. 2 codes D and 1

Need help thanks