### PDB entries used for topology testing ###

# proteins
1mru
7s1c

# dna
7qvq

# rna
8d2b

# dna/rna hybrid chain
7een

# d-peptide
7rmr

# carbohydrates ("branched" entities) in addition to linear polymers
2wmg

# only carbohydrates (not counting ions and water)
1c4s

# mostly water residues
1l0r
3p4j

# water molecules 48A from polymer (in a crystal)
1q9j

# tiny unit cell
2ol9

# molecule spanning several unit cells
5xg2

# altlocs
6udz

# altlocs - 3 alternatives for the same atom
8eko
7nnx

# altlocs - 4 alternatives for the same atom
5a7e
6eky

# altlocs - 5 alternatives for the same atom
1alx
7u7j

# altlocs - 5 alternatives: B C D K L instead of usual A B ...
1l3k

# altlocs - 6 alternatives for the same atom
5qy1

# altlocs - 7 alternatives for all atoms except solvent
3b2c

# altlocs - 12 alternatives for CYS SG
2v93

# microheterogeneity
4bsw

# microheterogeneity with 3 alternative residues
# (there are only 7 such PDB entries: 2izq 3jqh 4kl8 4ko2 4ko3 4ko4 3ned)
3jqh
3ned

# microheterogeneity in two consecutive residues
3a0m

# microheterogeneity in three consecutive residues
4mte
6x5x

# microheterogeneity in 4-5 consecutive residues
6ukg

# microheterogeneity in each chain residue (DA/DT)
7w1y

# microheterogeneity with shared atom
1ejg

# alternative conformations with both cis and trans bonds
4ibi

# alternative conformation - partial cleavage
6ozo

# a pair of residues linked with two covalent bonds
4y8l  # THR-05W
173d  # PXZ-PXZ (symmetry-related halves of PXZ)
5jbq  # 05N-BB9 (peptide-linking residues with C-N and C-SG bonds)
3q0q  # CYS-CYS (SS bridge between consecutive residues)

# C-N bond with non-polymer at the chain end
5a5b

# ligand (7PZ) that is absent in CCP4 monomer library and has two conformations
7vlg

# link between conformers A and B
2e7z

# link between conformer A and non-altloc Fe (practically, also conformer A)
8bbc

# aliasing for peptide bond
5c7w  # 50L
#7k00  # MS6

# aliasing for nucleotide bond
7b3b  # F86

# aliasing + microheterogeneity
# 2ci1 has KOR/K1R, KOR has conventional names, K1R uses alias C2->C
2ci1

# link that adds hydrogen
2amq # PJE-CYS
2e84 # CYS-HEMB

# atom on n-fold axis with occupancy 1/n
1pfe

# atom on n-fold axis with occupancy 1

# inversion symmetry
4rwc
5eyq
6ugb

# insertion codes in inverse order

# deuterium
6kl0

# H/D mixture
8dhd

# regression testing for hydrogen generation
6s4n
4zyw
5aco
1q0n
1nlm

# regression testing for link assignment
5uqa

# mistake: no altloc and altloc for the same atom name: 4udf, 4xhy
# (6c5b and 6gob were fixed in 2023?)
6c5b
4xhy

# sum of altloc occupancy > 1
1c5z
3m5q

# Water (A 68 DOD) without O, only D1 and D2
1iu6

# numeric altlocs (1,2,3,4)
1aac

# only UNK residues
3kgv

# chain C has only 1.57% of residues from SEQRES (it's crystal)
3zms
# chain B has only 0.16% of SEQRES (it's not crystal)
8b6z

# 1st residue with altloc A, no B; occupancy 0.75 like in 2nd and 3rd residue
6ey1
# atom with two conformations in a residue w/ partial occupancy (A/200 FLR)
7euv
