That's great that you are considering giving so much! When people say what percent of their income they are donating, usually they use the pretax income, which is the adjusted gross income (AGI) in the US. This is less than the total compensation because of things like benefits, some contributions to retirement, etc. I am not sure how stock options work, so hopefully someone else can join in on this. Unfortunately your calculator does not tell you the AGI, but you could probably find one that does. It seems to me that the calculator is giving broadly reasonable results. Basically, your net income doesn't decrease as much as your charity amount because of the tax advantage. It used to be that the maximum you could give with a federal tax advantage was 50% of AGI, but that got changed to 60% a couple years ago. And I've read that this year it is actually 100%. Of course even if the tax advantaged limit is 60% of AGI, you could still give more.
I’m not from the US, but based on IRS rules, only up to 60% of AGI (Adjusted Gross Income) is deductible for donations to Public Charities. Your in-hand numbers seem roughly in the right ballpark, though exact take-home depends on deductions, tax brackets, and how stock is taxed. A CPA or detailed tax software would give the most accurate results.