FMO DATABASE

FMODB ID: R5LY8

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1868574.670257
FMO2-HF: Nuclear repulsion	1797196.902707
FMO2-HF: Total energy	-71377.76755
FMO2-MP2: Total energy	-71581.808565

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.
-49.997	-51.469	19.905	-7.563	-10.869	-0.063

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 : 0.907 / q_NPA : 0.917

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	-0.018	0.005	3.816	0.711	2.647	-0.013	-0.808	-1.114	-0.001
4	A	30	VAL	0	0.006	-0.007	6.074	1.748	1.748	0.000	0.000	0.000	0.000
5	A	31	LEU	0	-0.047	-0.030	9.228	0.643	0.643	0.000	0.000	0.000	0.000
6	A	32	LEU	0	-0.022	-0.014	12.570	1.647	1.647	0.000	0.000	0.000	0.000
7	A	33	ASP	-1	-0.858	-0.939	13.515	-19.743	-19.743	0.000	0.000	0.000	0.000
8	A	34	PHE	0	-0.053	-0.019	15.545	0.534	0.534	0.000	0.000	0.000	0.000
9	A	35	ALA	0	0.023	0.011	18.169	0.519	0.519	0.000	0.000	0.000	0.000
10	A	36	ALA	0	-0.018	0.000	15.790	0.462	0.462	0.000	0.000	0.000	0.000
11	A	37	ALA	0	-0.025	-0.015	17.900	0.247	0.247	0.000	0.000	0.000	0.000
12	A	38	GLY	0	0.034	0.023	20.387	0.468	0.468	0.000	0.000	0.000	0.000
13	A	39	GLY	0	-0.017	-0.019	23.401	0.430	0.430	0.000	0.000	0.000	0.000
14	A	40	GLU	-1	-0.950	-0.967	23.824	-11.403	-11.403	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.059	-0.029	20.042	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	42	GLY	0	-0.023	0.000	24.444	0.007	0.007	0.000	0.000	0.000	0.000
17	A	43	TRP	0	0.017	0.003	20.688	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	44	LEU	0	-0.014	0.016	27.256	0.375	0.375	0.000	0.000	0.000	0.000
19	A	45	THR	0	0.010	-0.006	29.855	-0.197	-0.197	0.000	0.000	0.000	0.000
20	A	46	HIS	0	-0.031	0.008	32.441	0.212	0.212	0.000	0.000	0.000	0.000
21	A	47	PRO	0	0.021	-0.002	34.971	-0.152	-0.152	0.000	0.000	0.000	0.000
22	A	48	TYR	0	0.000	-0.025	37.476	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	49	GLY	0	0.013	0.018	37.191	0.196	0.196	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.837	0.923	37.973	8.149	8.149	0.000	0.000	0.000	0.000
25	A	51	GLY	0	-0.015	-0.019	35.494	0.063	0.063	0.000	0.000	0.000	0.000
26	A	52	TRP	0	-0.029	-0.032	28.498	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	53	ASP	-1	-0.853	-0.919	32.886	-8.490	-8.490	0.000	0.000	0.000	0.000
28	A	54	LEU	0	-0.070	-0.041	27.344	-0.293	-0.293	0.000	0.000	0.000	0.000
29	A	55	MET	0	-0.027	-0.004	30.469	0.335	0.335	0.000	0.000	0.000	0.000
30	A	56	GLN	0	0.002	-0.013	29.873	-0.470	-0.470	0.000	0.000	0.000	0.000
31	A	57	ASN	0	-0.010	-0.025	29.948	0.472	0.472	0.000	0.000	0.000	0.000
32	A	58	ILE	0	0.002	0.033	29.593	-0.263	-0.263	0.000	0.000	0.000	0.000
33	A	59	MET	0	-0.025	-0.011	24.175	0.223	0.223	0.000	0.000	0.000	0.000
34	A	60	ASN	0	-0.015	-0.009	24.399	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	61	ASP	-1	-0.913	-0.955	27.387	-9.612	-9.612	0.000	0.000	0.000	0.000
36	A	62	MET	0	-0.029	-0.013	24.231	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	63	PRO	0	-0.012	0.000	26.391	0.160	0.160	0.000	0.000	0.000	0.000
38	A	64	ILE	0	-0.012	-0.012	24.300	-0.469	-0.469	0.000	0.000	0.000	0.000
39	A	65	TYR	0	0.053	0.014	25.038	0.371	0.371	0.000	0.000	0.000	0.000
40	A	66	MET	0	-0.023	-0.006	25.325	-0.328	-0.328	0.000	0.000	0.000	0.000
41	A	67	TYR	0	0.034	0.034	25.561	0.257	0.257	0.000	0.000	0.000	0.000
42	A	68	SER	0	-0.053	-0.029	28.333	-0.165	-0.165	0.000	0.000	0.000	0.000
43	A	69	VAL	0	0.052	0.032	31.045	0.181	0.181	0.000	0.000	0.000	0.000
44	A	70	CYS	0	-0.058	-0.026	33.906	0.032	0.032	0.000	0.000	0.000	0.000
45	A	71	ASN	0	0.006	0.009	36.660	0.294	0.294	0.000	0.000	0.000	0.000
46	A	72	VAL	0	0.038	0.006	38.239	0.057	0.057	0.000	0.000	0.000	0.000
47	A	73	MET	0	-0.061	-0.019	40.583	0.126	0.126	0.000	0.000	0.000	0.000
48	A	74	SER	0	-0.040	-0.020	42.936	0.099	0.099	0.000	0.000	0.000	0.000
49	A	75	GLY	0	0.004	0.013	44.161	0.051	0.051	0.000	0.000	0.000	0.000
50	A	76	ASP	-1	-0.917	-0.965	41.667	-7.430	-7.430	0.000	0.000	0.000	0.000
51	A	77	GLN	0	0.031	0.042	37.707	-0.131	-0.131	0.000	0.000	0.000	0.000
52	A	78	ASP	-1	-0.813	-0.908	35.438	-8.913	-8.913	0.000	0.000	0.000	0.000
53	A	79	ASN	0	-0.039	-0.003	34.264	0.161	0.161	0.000	0.000	0.000	0.000
54	A	80	TRP	0	-0.047	-0.034	28.693	-0.369	-0.369	0.000	0.000	0.000	0.000
55	A	81	LEU	0	0.004	0.028	26.155	0.194	0.194	0.000	0.000	0.000	0.000
56	A	82	ARG	1	0.856	0.929	25.897	10.848	10.848	0.000	0.000	0.000	0.000
57	A	83	THR	0	0.024	0.008	21.061	0.116	0.116	0.000	0.000	0.000	0.000
58	A	84	ASN	0	-0.003	-0.017	22.473	0.668	0.668	0.000	0.000	0.000	0.000
59	A	85	TRP	0	-0.032	-0.011	21.688	-0.713	-0.713	0.000	0.000	0.000	0.000
60	A	86	VAL	0	0.009	0.014	15.661	-0.230	-0.230	0.000	0.000	0.000	0.000
61	A	87	TYR	0	-0.026	-0.015	15.190	0.457	0.457	0.000	0.000	0.000	0.000
62	A	88	ARG	1	0.893	0.921	14.724	18.121	18.121	0.000	0.000	0.000	0.000
63	A	89	GLY	0	-0.010	-0.014	13.013	-1.742	-1.742	0.000	0.000	0.000	0.000
64	A	90	GLU	-1	-0.863	-0.926	7.016	-35.442	-35.442	0.000	0.000	0.000	0.000
65	A	91	ALA	0	-0.019	0.013	10.483	-1.421	-1.421	0.000	0.000	0.000	0.000
66	A	92	GLU	-1	-0.892	-0.932	11.140	-21.286	-21.286	0.000	0.000	0.000	0.000
67	A	93	ARG	1	0.914	0.958	10.948	22.315	22.315	0.000	0.000	0.000	0.000
68	A	94	ILE	0	-0.044	-0.009	10.309	-2.666	-2.666	0.000	0.000	0.000	0.000
69	A	95	PHE	0	-0.033	-0.041	8.566	0.869	0.869	0.000	0.000	0.000	0.000
70	A	96	ILE	0	-0.016	-0.017	11.993	-0.371	-0.371	0.000	0.000	0.000	0.000
71	A	97	GLU	-1	-0.866	-0.943	13.031	-19.319	-19.319	0.000	0.000	0.000	0.000
72	A	98	LEU	0	-0.016	-0.014	15.296	0.389	0.389	0.000	0.000	0.000	0.000
73	A	99	LYS	1	0.974	0.989	15.971	16.266	16.266	0.000	0.000	0.000	0.000
74	A	100	PHE	0	-0.016	-0.016	20.599	0.278	0.278	0.000	0.000	0.000	0.000
75	A	101	THR	0	0.015	0.018	24.397	0.100	0.100	0.000	0.000	0.000	0.000
76	A	102	VAL	0	0.021	-0.002	27.835	0.002	0.002	0.000	0.000	0.000	0.000
77	A	103	ARG	1	0.861	0.937	30.687	7.962	7.962	0.000	0.000	0.000	0.000
78	A	104	ASP	-1	-0.807	-0.900	34.329	-7.882	-7.882	0.000	0.000	0.000	0.000
79	A	105	CYS	0	-0.041	0.006	36.776	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	106	ASN	0	-0.024	-0.010	39.181	0.343	0.343	0.000	0.000	0.000	0.000
81	A	107	SER	0	-0.116	-0.060	39.133	0.160	0.160	0.000	0.000	0.000	0.000
82	A	108	PHE	0	-0.002	-0.033	37.767	0.027	0.027	0.000	0.000	0.000	0.000
83	A	109	PRO	0	-0.016	-0.010	43.392	0.090	0.090	0.000	0.000	0.000	0.000
84	A	110	GLY	0	-0.019	-0.002	46.719	0.118	0.118	0.000	0.000	0.000	0.000
85	A	111	GLY	0	0.074	0.025	43.931	0.010	0.010	0.000	0.000	0.000	0.000
86	A	112	ALA	0	0.034	0.037	44.878	0.104	0.104	0.000	0.000	0.000	0.000
87	A	113	SER	0	-0.010	-0.009	43.758	-0.101	-0.101	0.000	0.000	0.000	0.000
88	A	114	SER	0	-0.046	-0.043	42.419	0.000	0.000	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.891	0.947	35.231	8.067	8.067	0.000	0.000	0.000	0.000
90	A	117	GLU	-1	-0.769	-0.906	33.079	-8.607	-8.607	0.000	0.000	0.000	0.000
91	A	118	THR	0	-0.046	-0.017	29.960	-0.204	-0.204	0.000	0.000	0.000	0.000
92	A	119	PHE	0	0.000	0.006	24.288	0.247	0.247	0.000	0.000	0.000	0.000
93	A	120	ASN	0	-0.049	-0.027	27.406	-0.403	-0.403	0.000	0.000	0.000	0.000
94	A	121	LEU	0	0.061	0.047	19.736	0.026	0.026	0.000	0.000	0.000	0.000
95	A	122	TYR	0	-0.023	-0.024	24.490	0.145	0.145	0.000	0.000	0.000	0.000
96	A	123	TYR	0	0.039	0.008	21.000	-0.410	-0.410	0.000	0.000	0.000	0.000
97	A	124	ALA	0	0.029	0.018	22.990	0.570	0.570	0.000	0.000	0.000	0.000
98	A	125	GLU	-1	-0.801	-0.897	20.658	-15.666	-15.666	0.000	0.000	0.000	0.000
99	A	126	SER	0	-0.023	-0.027	22.811	0.785	0.785	0.000	0.000	0.000	0.000
100	A	127	ASP	-1	-0.866	-0.938	23.044	-13.156	-13.156	0.000	0.000	0.000	0.000
101	A	128	LEU	0	-0.034	-0.037	24.584	-0.206	-0.206	0.000	0.000	0.000	0.000
102	A	129	ASP	-1	-0.817	-0.894	25.324	-11.875	-11.875	0.000	0.000	0.000	0.000
103	A	130	TYR	0	-0.037	-0.028	26.605	0.487	0.487	0.000	0.000	0.000	0.000
104	A	131	GLY	0	0.038	0.022	28.714	0.423	0.423	0.000	0.000	0.000	0.000
105	A	132	THR	0	0.002	-0.020	30.260	-0.223	-0.223	0.000	0.000	0.000	0.000
106	A	133	ASN	0	-0.014	0.013	32.655	0.376	0.376	0.000	0.000	0.000	0.000
107	A	134	PHE	0	0.003	-0.007	29.118	-0.368	-0.368	0.000	0.000	0.000	0.000
108	A	135	GLN	0	0.038	0.019	32.391	0.254	0.254	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.987	0.988	31.723	8.511	8.511	0.000	0.000	0.000	0.000
110	A	137	ARG	1	0.853	0.924	31.424	9.030	9.030	0.000	0.000	0.000	0.000
111	A	138	LEU	0	0.018	0.020	29.701	0.031	0.031	0.000	0.000	0.000	0.000
112	A	139	PHE	0	-0.041	-0.012	25.256	-0.384	-0.384	0.000	0.000	0.000	0.000
113	A	140	THR	0	-0.022	-0.006	25.080	0.464	0.464	0.000	0.000	0.000	0.000
114	A	141	LYS	1	0.853	0.922	25.291	10.155	10.155	0.000	0.000	0.000	0.000
115	A	142	ILE	0	-0.037	-0.022	19.537	-0.096	-0.096	0.000	0.000	0.000	0.000
116	A	143	ASP	-1	-0.776	-0.878	22.771	-12.490	-12.490	0.000	0.000	0.000	0.000
117	A	144	THR	0	-0.069	-0.036	24.657	0.204	0.204	0.000	0.000	0.000	0.000
118	A	145	ILE	0	-0.036	-0.004	22.247	-0.360	-0.360	0.000	0.000	0.000	0.000
119	A	146	ALA	0	0.017	-0.020	25.702	0.476	0.476	0.000	0.000	0.000	0.000
120	A	147	PRO	0	-0.026	-0.001	25.908	-0.411	-0.411	0.000	0.000	0.000	0.000
121	A	148	ASP	-1	-0.868	-0.916	23.996	-11.806	-11.806	0.000	0.000	0.000	0.000
122	A	149	GLU	-1	-0.991	-1.008	26.584	-10.288	-10.288	0.000	0.000	0.000	0.000
123	A	150	ILE	0	-0.034	-0.005	28.966	-0.120	-0.120	0.000	0.000	0.000	0.000
124	A	151	THR	0	-0.026	-0.016	31.021	0.054	0.054	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.031	0.002	33.270	0.198	0.198	0.000	0.000	0.000	0.000
126	A	153	SER	0	0.000	-0.016	36.933	-0.048	-0.048	0.000	0.000	0.000	0.000
127	A	154	SER	0	0.042	0.008	38.293	0.033	0.033	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.797	-0.881	34.192	-8.727	-8.727	0.000	0.000	0.000	0.000
129	A	156	PHE	0	-0.062	-0.032	35.729	-0.142	-0.142	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-1.003	-0.998	37.927	-7.176	-7.176	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.047	0.031	36.830	0.036	0.036	0.000	0.000	0.000	0.000
132	A	159	ARG	1	0.864	0.932	34.277	8.268	8.268	0.000	0.000	0.000	0.000
133	A	160	HIS	0	0.012	0.016	29.627	-0.294	-0.294	0.000	0.000	0.000	0.000
134	A	161	VAL	0	-0.010	-0.011	27.075	0.048	0.048	0.000	0.000	0.000	0.000
135	A	162	LYS	1	0.891	0.942	27.593	8.898	8.898	0.000	0.000	0.000	0.000
136	A	163	LEU	0	-0.043	-0.023	21.597	-0.034	-0.034	0.000	0.000	0.000	0.000
137	A	164	ASN	0	0.043	0.035	22.974	-0.324	-0.324	0.000	0.000	0.000	0.000
138	A	165	VAL	0	0.001	-0.016	16.536	-0.355	-0.355	0.000	0.000	0.000	0.000
139	A	166	GLU	-1	-0.826	-0.900	19.061	-13.459	-13.459	0.000	0.000	0.000	0.000
140	A	167	GLU	-1	-0.879	-0.940	11.882	-23.675	-23.675	0.000	0.000	0.000	0.000
141	A	168	ARG	1	0.749	0.859	16.215	14.981	14.981	0.000	0.000	0.000	0.000
142	A	169	SER	0	0.001	0.005	13.279	-1.188	-1.188	0.000	0.000	0.000	0.000
143	A	170	VAL	0	-0.009	0.006	15.029	1.046	1.046	0.000	0.000	0.000	0.000
144	A	171	GLY	0	0.001	0.007	15.060	-1.528	-1.528	0.000	0.000	0.000	0.000
145	A	172	PRO	0	-0.067	-0.025	15.892	0.627	0.627	0.000	0.000	0.000	0.000
146	A	173	LEU	0	-0.008	-0.025	15.110	0.973	0.973	0.000	0.000	0.000	0.000
147	A	174	THR	0	-0.048	-0.031	17.401	-0.469	-0.469	0.000	0.000	0.000	0.000
148	A	175	ARG	1	0.920	0.976	19.977	12.621	12.621	0.000	0.000	0.000	0.000
149	A	176	LYS	1	0.939	0.994	19.373	12.539	12.539	0.000	0.000	0.000	0.000
150	A	177	GLY	0	0.044	0.002	18.852	-0.762	-0.762	0.000	0.000	0.000	0.000
151	A	178	PHE	0	-0.007	0.004	15.291	0.442	0.442	0.000	0.000	0.000	0.000
152	A	179	TYR	0	-0.041	-0.006	20.544	0.009	0.009	0.000	0.000	0.000	0.000
153	A	180	LEU	0	0.021	0.005	17.798	-0.178	-0.178	0.000	0.000	0.000	0.000
154	A	181	ALA	0	-0.014	-0.012	22.158	0.436	0.436	0.000	0.000	0.000	0.000
155	A	182	PHE	0	0.018	0.012	21.258	-0.276	-0.276	0.000	0.000	0.000	0.000
156	A	183	GLN	0	-0.007	-0.010	26.831	0.120	0.120	0.000	0.000	0.000	0.000
157	A	184	ASP	-1	-0.718	-0.870	30.242	-9.123	-9.123	0.000	0.000	0.000	0.000
158	A	185	ILE	0	-0.056	-0.033	32.456	0.187	0.187	0.000	0.000	0.000	0.000
159	A	186	GLY	0	-0.020	-0.013	35.412	0.267	0.267	0.000	0.000	0.000	0.000
160	A	187	ALA	0	-0.013	0.008	32.914	0.166	0.166	0.000	0.000	0.000	0.000
161	A	189	VAL	0	0.024	0.015	28.052	-0.109	-0.109	0.000	0.000	0.000	0.000
162	A	190	ALA	0	0.020	0.006	28.727	0.164	0.164	0.000	0.000	0.000	0.000
163	A	191	LEU	0	0.001	-0.008	22.349	-0.270	-0.270	0.000	0.000	0.000	0.000
164	A	192	LEU	0	-0.012	-0.019	22.817	0.097	0.097	0.000	0.000	0.000	0.000
165	A	193	SER	0	0.007	0.002	17.168	-0.312	-0.312	0.000	0.000	0.000	0.000
166	A	194	VAL	0	0.000	0.001	17.948	0.190	0.190	0.000	0.000	0.000	0.000
167	A	195	ARG	1	0.909	0.973	8.145	25.309	25.309	0.000	0.000	0.000	0.000
168	A	196	VAL	0	-0.020	-0.006	13.266	-0.126	-0.126	0.000	0.000	0.000	0.000
169	A	197	TYR	0	-0.009	-0.006	6.880	-1.977	-1.977	0.000	0.000	0.000	0.000
170	A	198	TYR	0	0.029	0.017	6.702	1.940	1.940	0.000	0.000	0.000	0.000
171	A	199	LYS	1	0.953	0.976	3.590	29.564	29.882	0.002	-0.079	-0.241	0.000
172	A	200	LYS	1	0.916	0.960	2.054	46.715	48.287	2.827	-1.310	-3.089	-0.005
173	A	201	CYS	0	0.005	0.020	1.939	-37.414	-42.712	17.089	-5.366	-6.425	-0.057

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