I have a 5-sugar units chain in my molecule and I want to substitute sulfate at all the positions but when I try to add sulfate as a derivative on the end terminal sugar, it always gives free OH at position 1 of sugar using "carbohydrate builder” option. If I download that file and add sulfate by replacing OH, the charge of sulfate will still be +0.194 as it was of OH but the charge of sulfate should be same as of other sulfates. If there is any possible way to design a fully sulfated carbohydrate, please suggest.
Also, I would like to add phosphate at the 6th position of mannose by replacing sulfate but couldn't add phosphate as derivative. There is an option to add phosphate as a derivative but it's not functioning. Please suggest what can be the possible way to do that or how the charges of phosphate can be derived.