Table 1.

Benchmark Set of Wild Type and Mutant Rhodopsins^a

proteinb	code	PDB ID	RET-Cc	chain(s)	${\mathit{\lambda }}_{\mathbf{max}}^{\mathbf{a}}$	ΔES0–S1
m-Set
X-ray Crystallographic Structures
Anabaena sensory rhodopsin (M)	ASRAT	1XIO86	all-trans	A	550	52.0 (2.25)86
	ASR13C	1XIO86	13-cis	A	537	53.2 (2.31)86
Bacteriorhodopsin (M)	bRAT	6G7H87	all-trans	A	568	50.3 (2.18)2
	bR13C	1X0S88	13-cis	A	548	52.2 (2.26)2
Bathorhodopsin (V)	bathoRh	2G8789	all-trans	A, B	529	54.0 (2.34)90,91
Blue proteorhodopsin (M)	BPR	4JQ692	all-trans	A, B, C	490	58.3 (2.52)93
Bovine rhodopsin (V)	Rh	1U1984	11-cis	A, B	498	57.4 (2.49)32,91
Chimaera channelrhodopsin (M)	ChRC1C2	3UG994	all-trans	A	458	62.4 (2.71)40
Squid rhodopsin (I)	SqRh	2Z7395	11-cis	A, B	489	58.5 (2.54)96
Comparative Models
Human melanopsin (V)	hMeOp	2Z73e	11-cis	A	473	60.4 (2.62)d
a-Set
X-ray Crystallographic Structures
Anabaena sensory rhodopsin D217E (M)	ASRAT-D217E	4TL397	all-trans	A, B	552	51.8 (2.25)98
Archaerhodopsin-1 (M)	Arch1	1UAZ99	all-trans	A, B	568	50.3 (2.18)100
Archaerhodopsin-2 (M)	Arch2	3WQJ101	all-trans	A	550	52.0 (2.25)101
Channelrhodopsin-2 (M)	ChR2	6EID70	all-trans	A, B	470	60.8 (2.64)70
Channelrhodopsin-2 N24Q/C128T (M)	ChR2-C128T	6EIG70	all-trans	A, B	485	59.0 (2.56)70
Krokinobacter eikastus rhodopsin 2 (M)	KR2	3X3C102	all-trans	A	525	54.5 (2.36)102
Nonlabens marinus rhodopsin-3 (M)	NM-R3	5B2N71	all-trans	A	517	55.3 (2.40)71
	C1R	5G2872	all-trans	A	517	55.3 (2.40)72
Sensory rhodopsin II (M)	SRII	1JGJ103	all-trans	A	497	57.5 (2.49)103
Squid bathorhodopsin (I)	SqbathoRh	3AYM104	all-trans	A, B	530	53.9 (2.34)104
Comparative Models
Ancestral archosaur rhodopsin (V)	AARh	1U19e	11-cis	A	508	56.3 (2.44)19
Human blue cone (V)	BCone	1U19e	11-cis	A	430	66.5 (2.88)105
Human green cone (V)	GCone	1U19e	11-cis	A	535	53.4 (2.32)105
Human red cone (V)	RCone	1U19e	11-cis	A	575	49.7 (2.15)105
Mouse melanopsin (V)	mMeOp	2Z73e	11-cis	A	467	61.2 (2.65)106
Parvularcula oceani Xenorhodopsin (M)	PoXeRAT	4TL397,e	all-trans	B	568	50.3 (2.18)107
	PoXeR13C	4TL3e	13-cis	B	549	52.1 (2.26)107
Rh Mutants Set
Bovine rhodopsin mutation (V)	A292S	1U19e	11-cis	A	491	58.2 (2.52)32
	A269T	1U19e	11-cis	A	514	55.6 (2.41)43
	E113D	1U19e	11-cis	A	510	56.1 (2.43)108
	E122Q	1U19e	11-cis	A	480	59.6 (2.58)109
	F261Y	1U19e	11-cis	A	510	56.0 (2.43)43
	G90S	1U19e	11-cis	A	489	58.5 (2.54)110
	T94S	1U19e	11-cis	A	494	57.9 (2.51)111
	T118A	1U19e	11-cis	A	484	59.1 (2.56)112
	W265F	1U19e	11-cis	A	480	59.6 (2.58)113
	W265Y	1U19e	11-cis	A	485	59.0 (2.56)110
	D83N-E122Q	1U19e	11-cis	A	475	60.2 (2.61)109
	A292S-A295S-A299C	1U19e	11-cis	A	484	59.1 (2.56)110

^aExperimental maximum absorption wavelength, ${\lambda }_{\text{max}}^{\text{a}}$, in nm, and first vertical excitation energy, ΔE_S0–S1, in kcal mol⁻¹. Values of ΔE_S0–S1 in eV are also provided in parentheses.

^bVertebrate (V), invertebrate (I), and microbial (M).

^cRetinal conformation.

^dAverage of available experimental values in refs 106 and 114.

^eX-ray structure template model.

See the details of the comparative model construction in section S6 of the Supporting Information.