fix: correct chain indexing so _atom_site.label_asym_id starts at 'A'

[NessimRaou]

Fixed a bug when saving pdb as mmCIF where label indexing was offset:

• Issue: chain_index was incremented at the start of the loop, causing the first chain being assigned index 1 (label_asym_id 'B')
• Fix: increment chain_index at the end of the loop so label_asym_id correctly starts at 'A' while keeping label_entity_id starting at 1

[douweschulte]

The changes look good, thanks for opening the PR. The failures are because of a renamed dependency and I will fix that outside of this PR.