Thank you. I will try to answer your question but if you feet that it is not clear, you can ask me again.
From your question, it looks that you want to do ‘partial’ optimization of the distance between Li and graphite only.
In Gaussian, there is a possibility to do partial optimization by some ways. The first, probably you already know it by fixing specific variable and put F (Frezze) next after you difine the variable. It is burdening for large molecule geometry, such as your case.
Another way is by separating the constants and variable in your input section. You can do it by make a blank line or a line containing a space in the first column and put the string Constants:
For example for water, I want to keep the angel of H-O-H, but i want to optimize the H-O distance:

# HF/6-31G(d) Opt Test

Partial optimization for water

0 1
O
H1 O R
H2 O R H1 A
Variables:
R 1.0
Constants:
A 105.4

I don’t know whether it works in cartesian input coordinat or not, caused usually I work on Z-matrix. And for your case, probably you can have R as the distance between Li-graphite and/or dihedral angel of Li to the graphite (depend on what you want and your geometry).
For others, you can put under the ‘constants’.
Oke, I hope this answer is what you want. Or if not, please let me know it.

Thnak you