FMO DATABASE

FMODB ID: K3V23

Calculation Name: 3CZU-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 3CZU

Chain ID: A

ChEMBL ID:

UniProt ID: P20827

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1871697.696223
FMO2-HF: Nuclear repulsion	1800318.992423
FMO2-HF: Total energy	-71378.7038
FMO2-MP2: Total energy	-71582.834282

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:27:LYS)

Summations of interaction energy for fragment #1(A:27:LYS)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-56.957	-60.592	20.031	-7.781	-8.616	-0.072

Interaction energy analysis for fragmet #1(A:27:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.907

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	29	VAL	0	-0.015	-0.004	3.815	0.487	2.259	-0.013	-0.729	-1.030	-0.001
4	A	30	VAL	0	-0.002	-0.007	5.990	1.865	1.865	0.000	0.000	0.000	0.000
5	A	31	LEU	0	-0.043	-0.025	9.635	0.368	0.368	0.000	0.000	0.000	0.000
6	A	32	LEU	0	-0.013	-0.010	12.543	1.604	1.604	0.000	0.000	0.000	0.000
7	A	33	ASP	-1	-0.839	-0.933	14.025	-19.269	-19.269	0.000	0.000	0.000	0.000
8	A	34	PHE	0	-0.042	-0.023	16.078	0.507	0.507	0.000	0.000	0.000	0.000
9	A	35	ALA	0	-0.001	0.007	18.084	0.608	0.608	0.000	0.000	0.000	0.000
10	A	36	ALA	0	-0.029	-0.024	15.611	0.439	0.439	0.000	0.000	0.000	0.000
11	A	37	ALA	0	-0.025	-0.007	17.721	0.281	0.281	0.000	0.000	0.000	0.000
12	A	38	GLY	0	0.028	0.014	20.325	0.518	0.518	0.000	0.000	0.000	0.000
13	A	39	GLY	0	0.020	0.014	23.333	0.474	0.474	0.000	0.000	0.000	0.000
14	A	40	GLU	-1	-0.962	-0.982	24.385	-11.345	-11.345	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.070	-0.033	20.341	0.076	0.076	0.000	0.000	0.000	0.000
16	A	42	GLY	0	0.023	0.019	24.679	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	43	TRP	0	-0.012	-0.006	20.755	0.089	0.089	0.000	0.000	0.000	0.000
18	A	44	LEU	0	0.016	0.027	27.358	0.367	0.367	0.000	0.000	0.000	0.000
19	A	45	THR	0	0.006	-0.004	29.824	-0.236	-0.236	0.000	0.000	0.000	0.000
20	A	46	HIS	0	-0.025	0.004	32.563	0.210	0.210	0.000	0.000	0.000	0.000
21	A	47	PRO	0	0.018	0.001	35.263	-0.134	-0.134	0.000	0.000	0.000	0.000
22	A	48	TYR	0	0.027	-0.011	37.827	-0.109	-0.109	0.000	0.000	0.000	0.000
23	A	49	GLY	0	0.012	0.012	37.886	0.197	0.197	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.835	0.910	38.654	8.083	8.083	0.000	0.000	0.000	0.000
25	A	51	GLY	0	-0.025	-0.009	35.477	0.054	0.054	0.000	0.000	0.000	0.000
26	A	52	TRP	0	-0.047	-0.038	28.452	0.012	0.012	0.000	0.000	0.000	0.000
27	A	53	ASP	-1	-0.860	-0.936	32.947	-8.690	-8.690	0.000	0.000	0.000	0.000
28	A	54	LEU	0	-0.048	-0.021	27.784	-0.274	-0.274	0.000	0.000	0.000	0.000
29	A	55	MET	0	0.010	0.021	31.218	0.247	0.247	0.000	0.000	0.000	0.000
30	A	56	GLN	0	0.031	0.011	30.046	-0.526	-0.526	0.000	0.000	0.000	0.000
31	A	57	ASN	0	-0.060	-0.039	30.183	0.377	0.377	0.000	0.000	0.000	0.000
32	A	58	ILE	0	0.016	0.017	29.942	-0.213	-0.213	0.000	0.000	0.000	0.000
33	A	59	MET	0	-0.014	-0.007	23.650	0.204	0.204	0.000	0.000	0.000	0.000
34	A	60	ASN	0	-0.020	-0.017	23.536	0.004	0.004	0.000	0.000	0.000	0.000
35	A	61	ASP	-1	-0.913	-0.952	27.158	-9.573	-9.573	0.000	0.000	0.000	0.000
36	A	62	MET	0	-0.021	0.002	24.255	0.054	0.054	0.000	0.000	0.000	0.000
37	A	63	PRO	0	-0.008	-0.006	26.765	0.133	0.133	0.000	0.000	0.000	0.000
38	A	64	ILE	0	-0.026	-0.012	24.456	-0.496	-0.496	0.000	0.000	0.000	0.000
39	A	65	TYR	0	0.035	-0.004	25.492	0.384	0.384	0.000	0.000	0.000	0.000
40	A	66	MET	0	-0.035	-0.017	25.503	-0.359	-0.359	0.000	0.000	0.000	0.000
41	A	67	TYR	0	0.018	0.018	25.956	0.308	0.308	0.000	0.000	0.000	0.000
42	A	68	SER	0	-0.073	-0.035	28.308	-0.117	-0.117	0.000	0.000	0.000	0.000
43	A	69	VAL	0	0.043	0.019	31.060	0.173	0.173	0.000	0.000	0.000	0.000
44	A	70	CYS	0	-0.031	-0.021	34.122	0.064	0.064	0.000	0.000	0.000	0.000
45	A	71	ASN	0	0.024	0.021	36.911	0.193	0.193	0.000	0.000	0.000	0.000
46	A	72	VAL	0	0.026	0.007	38.236	0.135	0.135	0.000	0.000	0.000	0.000
47	A	73	MET	0	-0.003	0.013	40.570	0.122	0.122	0.000	0.000	0.000	0.000
48	A	74	SER	0	-0.073	-0.027	42.598	0.131	0.131	0.000	0.000	0.000	0.000
49	A	75	GLY	0	0.028	0.019	44.485	0.028	0.028	0.000	0.000	0.000	0.000
50	A	76	ASP	-1	-0.909	-0.954	41.759	-7.529	-7.529	0.000	0.000	0.000	0.000
51	A	77	GLN	0	-0.006	0.004	37.856	-0.074	-0.074	0.000	0.000	0.000	0.000
52	A	78	ASP	-1	-0.732	-0.854	36.424	-8.864	-8.864	0.000	0.000	0.000	0.000
53	A	79	ASN	0	-0.039	0.003	34.730	0.172	0.172	0.000	0.000	0.000	0.000
54	A	80	TRP	0	-0.054	-0.049	29.714	-0.388	-0.388	0.000	0.000	0.000	0.000
55	A	81	LEU	0	0.005	0.026	26.154	0.231	0.231	0.000	0.000	0.000	0.000
56	A	82	ARG	1	0.812	0.890	26.437	10.977	10.977	0.000	0.000	0.000	0.000
57	A	83	THR	0	0.017	0.011	21.210	0.126	0.126	0.000	0.000	0.000	0.000
58	A	84	ASN	0	0.031	0.007	22.389	0.727	0.727	0.000	0.000	0.000	0.000
59	A	85	TRP	0	-0.043	-0.010	21.222	-0.712	-0.712	0.000	0.000	0.000	0.000
60	A	86	VAL	0	-0.015	0.003	16.006	-0.218	-0.218	0.000	0.000	0.000	0.000
61	A	87	TYR	0	-0.025	-0.014	15.467	0.223	0.223	0.000	0.000	0.000	0.000
62	A	88	ARG	1	0.873	0.918	14.429	18.137	18.137	0.000	0.000	0.000	0.000
63	A	89	GLY	0	0.001	0.002	13.024	-1.768	-1.768	0.000	0.000	0.000	0.000
64	A	90	GLU	-1	-0.811	-0.867	6.824	-36.404	-36.404	0.000	0.000	0.000	0.000
65	A	91	ALA	0	-0.010	0.010	10.239	-1.352	-1.352	0.000	0.000	0.000	0.000
66	A	92	GLU	-1	-0.905	-0.939	11.010	-21.319	-21.319	0.000	0.000	0.000	0.000
67	A	93	ARG	1	0.849	0.906	11.320	21.760	21.760	0.000	0.000	0.000	0.000
68	A	94	ILE	0	-0.020	0.013	11.050	-2.653	-2.653	0.000	0.000	0.000	0.000
69	A	95	PHE	0	-0.016	-0.028	9.687	0.901	0.901	0.000	0.000	0.000	0.000
70	A	96	ILE	0	-0.002	-0.010	12.745	-0.315	-0.315	0.000	0.000	0.000	0.000
71	A	97	GLU	-1	-0.769	-0.865	12.586	-19.673	-19.673	0.000	0.000	0.000	0.000
72	A	98	LEU	0	-0.022	-0.020	15.349	0.412	0.412	0.000	0.000	0.000	0.000
73	A	99	LYS	1	0.888	0.927	15.130	17.289	17.289	0.000	0.000	0.000	0.000
74	A	100	PHE	0	-0.023	-0.017	20.548	0.284	0.284	0.000	0.000	0.000	0.000
75	A	101	THR	0	0.034	0.022	24.348	0.008	0.008	0.000	0.000	0.000	0.000
76	A	102	VAL	0	0.034	0.006	27.810	0.016	0.016	0.000	0.000	0.000	0.000
77	A	103	ARG	1	0.826	0.912	30.832	7.934	7.934	0.000	0.000	0.000	0.000
78	A	104	ASP	-1	-0.766	-0.876	34.494	-7.816	-7.816	0.000	0.000	0.000	0.000
79	A	105	CYS	0	-0.006	0.004	36.969	-0.093	-0.093	0.000	0.000	0.000	0.000
80	A	106	ASN	0	-0.049	-0.029	39.542	0.363	0.363	0.000	0.000	0.000	0.000
81	A	107	SER	0	-0.089	-0.037	39.193	0.170	0.170	0.000	0.000	0.000	0.000
82	A	108	PHE	0	0.018	-0.006	38.063	0.035	0.035	0.000	0.000	0.000	0.000
83	A	109	PRO	0	-0.019	-0.022	43.606	0.077	0.077	0.000	0.000	0.000	0.000
84	A	110	GLY	0	0.017	0.013	46.666	0.160	0.160	0.000	0.000	0.000	0.000
85	A	111	GLY	0	0.002	-0.010	44.363	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	112	ALA	0	0.026	0.034	45.044	0.054	0.054	0.000	0.000	0.000	0.000
87	A	113	SER	0	0.012	-0.003	43.896	-0.120	-0.120	0.000	0.000	0.000	0.000
88	A	114	SER	0	-0.038	-0.018	42.665	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.772	0.881	35.677	8.063	8.063	0.000	0.000	0.000	0.000
90	A	117	GLU	-1	-0.785	-0.907	33.525	-8.605	-8.605	0.000	0.000	0.000	0.000
91	A	118	THR	0	-0.028	-0.014	30.245	-0.217	-0.217	0.000	0.000	0.000	0.000
92	A	119	PHE	0	-0.016	0.000	24.445	0.246	0.246	0.000	0.000	0.000	0.000
93	A	120	ASN	0	-0.020	-0.003	28.160	-0.328	-0.328	0.000	0.000	0.000	0.000
94	A	121	LEU	0	0.059	0.038	20.416	0.038	0.038	0.000	0.000	0.000	0.000
95	A	122	TYR	0	-0.047	-0.043	25.062	0.226	0.226	0.000	0.000	0.000	0.000
96	A	123	TYR	0	-0.010	-0.008	21.141	-0.389	-0.389	0.000	0.000	0.000	0.000
97	A	124	ALA	0	0.041	0.024	23.730	0.569	0.569	0.000	0.000	0.000	0.000
98	A	125	GLU	-1	-0.762	-0.883	20.738	-15.605	-15.605	0.000	0.000	0.000	0.000
99	A	126	SER	0	-0.049	-0.046	22.944	0.797	0.797	0.000	0.000	0.000	0.000
100	A	127	ASP	-1	-0.779	-0.881	23.144	-13.362	-13.362	0.000	0.000	0.000	0.000
101	A	128	LEU	0	-0.054	-0.028	24.678	-0.068	-0.068	0.000	0.000	0.000	0.000
102	A	129	ASP	-1	-0.754	-0.838	25.173	-11.853	-11.853	0.000	0.000	0.000	0.000
103	A	130	TYR	0	-0.004	-0.005	26.725	0.489	0.489	0.000	0.000	0.000	0.000
104	A	131	GLY	0	0.038	0.023	28.853	0.445	0.445	0.000	0.000	0.000	0.000
105	A	132	THR	0	0.009	-0.003	30.171	-0.244	-0.244	0.000	0.000	0.000	0.000
106	A	133	ASN	0	-0.058	-0.018	32.793	0.380	0.380	0.000	0.000	0.000	0.000
107	A	134	PHE	0	0.012	-0.007	30.042	-0.389	-0.389	0.000	0.000	0.000	0.000
108	A	135	GLN	0	0.049	0.032	32.355	0.261	0.261	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.901	0.937	32.544	8.414	8.414	0.000	0.000	0.000	0.000
110	A	137	ARG	1	0.829	0.904	32.772	9.316	9.316	0.000	0.000	0.000	0.000
111	A	138	LEU	0	0.026	0.023	30.063	0.046	0.046	0.000	0.000	0.000	0.000
112	A	139	PHE	0	-0.032	-0.012	25.761	-0.385	-0.385	0.000	0.000	0.000	0.000
113	A	140	THR	0	-0.005	0.003	26.157	0.505	0.505	0.000	0.000	0.000	0.000
114	A	141	LYS	1	0.808	0.889	26.149	10.285	10.285	0.000	0.000	0.000	0.000
115	A	142	ILE	0	-0.036	-0.018	20.025	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	143	ASP	-1	-0.755	-0.859	23.372	-12.455	-12.455	0.000	0.000	0.000	0.000
117	A	144	THR	0	-0.062	-0.043	25.128	0.316	0.316	0.000	0.000	0.000	0.000
118	A	145	ILE	0	-0.016	0.008	22.389	-0.406	-0.406	0.000	0.000	0.000	0.000
119	A	146	ALA	0	0.015	-0.012	25.816	0.533	0.533	0.000	0.000	0.000	0.000
120	A	147	PRO	0	-0.029	-0.005	26.004	-0.450	-0.450	0.000	0.000	0.000	0.000
121	A	148	ASP	-1	-0.877	-0.923	24.200	-11.816	-11.816	0.000	0.000	0.000	0.000
122	A	149	GLU	-1	-0.942	-0.989	27.501	-9.911	-9.911	0.000	0.000	0.000	0.000
123	A	150	ILE	0	-0.017	0.007	29.301	-0.111	-0.111	0.000	0.000	0.000	0.000
124	A	151	THR	0	-0.020	-0.020	31.476	0.032	0.032	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.036	0.003	33.482	0.179	0.179	0.000	0.000	0.000	0.000
126	A	153	SER	0	0.010	-0.013	37.178	-0.072	-0.072	0.000	0.000	0.000	0.000
127	A	154	SER	0	0.022	0.008	38.360	0.050	0.050	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.768	-0.871	34.158	-8.796	-8.796	0.000	0.000	0.000	0.000
129	A	156	PHE	0	-0.039	-0.021	35.645	-0.123	-0.123	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-1.000	-0.996	37.628	-7.277	-7.277	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.038	0.019	36.800	0.005	0.005	0.000	0.000	0.000	0.000
132	A	159	ARG	1	0.871	0.938	33.707	8.418	8.418	0.000	0.000	0.000	0.000
133	A	160	HIS	0	0.019	0.023	28.918	-0.234	-0.234	0.000	0.000	0.000	0.000
134	A	161	VAL	0	-0.026	-0.023	26.842	0.035	0.035	0.000	0.000	0.000	0.000
135	A	162	LYS	1	0.794	0.906	27.198	8.835	8.835	0.000	0.000	0.000	0.000
136	A	163	LEU	0	-0.055	-0.029	21.113	-0.074	-0.074	0.000	0.000	0.000	0.000
137	A	164	ASN	0	0.019	0.018	22.981	-0.361	-0.361	0.000	0.000	0.000	0.000
138	A	165	VAL	0	0.000	-0.020	16.912	-0.334	-0.334	0.000	0.000	0.000	0.000
139	A	166	GLU	-1	-0.762	-0.841	18.973	-13.746	-13.746	0.000	0.000	0.000	0.000
140	A	167	GLU	-1	-0.828	-0.886	12.013	-24.859	-24.859	0.000	0.000	0.000	0.000
141	A	168	ARG	1	0.712	0.821	16.613	15.025	15.025	0.000	0.000	0.000	0.000
142	A	169	SER	0	0.021	0.002	13.735	-1.157	-1.157	0.000	0.000	0.000	0.000
143	A	170	VAL	0	-0.024	-0.004	15.687	1.103	1.103	0.000	0.000	0.000	0.000
144	A	171	GLY	0	0.063	0.030	15.851	-1.308	-1.308	0.000	0.000	0.000	0.000
145	A	172	PRO	0	-0.056	-0.018	15.930	0.333	0.333	0.000	0.000	0.000	0.000
146	A	173	LEU	0	-0.020	-0.004	15.544	1.024	1.024	0.000	0.000	0.000	0.000
147	A	174	THR	0	-0.031	-0.039	17.174	-0.370	-0.370	0.000	0.000	0.000	0.000
148	A	175	ARG	1	0.821	0.907	19.664	12.538	12.538	0.000	0.000	0.000	0.000
149	A	176	LYS	1	0.939	0.982	19.171	12.344	12.344	0.000	0.000	0.000	0.000
150	A	177	GLY	0	0.049	0.013	18.678	-0.850	-0.850	0.000	0.000	0.000	0.000
151	A	178	PHE	0	-0.037	-0.011	15.687	0.493	0.493	0.000	0.000	0.000	0.000
152	A	179	TYR	0	-0.042	-0.030	21.066	0.059	0.059	0.000	0.000	0.000	0.000
153	A	180	LEU	0	0.019	0.003	18.335	-0.199	-0.199	0.000	0.000	0.000	0.000
154	A	181	ALA	0	-0.019	-0.019	22.648	0.466	0.466	0.000	0.000	0.000	0.000
155	A	182	PHE	0	0.027	0.010	21.493	-0.337	-0.337	0.000	0.000	0.000	0.000
156	A	183	GLN	0	0.007	0.012	27.130	0.103	0.103	0.000	0.000	0.000	0.000
157	A	184	ASP	-1	-0.695	-0.843	30.734	-9.061	-9.061	0.000	0.000	0.000	0.000
158	A	185	ILE	0	-0.033	-0.016	32.740	0.150	0.150	0.000	0.000	0.000	0.000
159	A	186	GLY	0	-0.020	-0.017	35.824	0.277	0.277	0.000	0.000	0.000	0.000
160	A	187	ALA	0	0.012	0.020	33.380	0.167	0.167	0.000	0.000	0.000	0.000
161	A	189	VAL	0	0.001	0.006	28.367	-0.116	-0.116	0.000	0.000	0.000	0.000
162	A	190	ALA	0	0.027	0.012	28.816	0.182	0.182	0.000	0.000	0.000	0.000
163	A	191	LEU	0	-0.017	-0.016	22.048	-0.278	-0.278	0.000	0.000	0.000	0.000
164	A	192	LEU	0	0.023	0.008	23.026	-0.003	-0.003	0.000	0.000	0.000	0.000
165	A	193	SER	0	-0.030	-0.006	17.651	-0.642	-0.642	0.000	0.000	0.000	0.000
166	A	194	VAL	0	0.034	0.022	17.904	0.165	0.165	0.000	0.000	0.000	0.000
167	A	195	ARG	1	0.852	0.928	7.534	27.177	27.177	0.000	0.000	0.000	0.000
168	A	196	VAL	0	-0.007	-0.002	13.919	-0.302	-0.302	0.000	0.000	0.000	0.000
169	A	197	TYR	0	-0.088	-0.074	7.402	-1.583	-1.583	0.000	0.000	0.000	0.000
170	A	198	TYR	0	-0.004	-0.033	6.402	1.807	1.807	0.000	0.000	0.000	0.000
171	A	199	LYS	1	0.856	0.944	4.879	27.310	27.310	0.000	0.000	0.000	0.000
172	A	200	LYS	1	0.890	0.943	2.152	44.229	45.679	1.304	-0.792	-1.962	-0.003
173	A	201	CYS	0	0.028	0.029	1.704	-39.806	-46.663	18.740	-6.260	-5.624	-0.068

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:LYS)