FMO DATABASE

FMODB ID: ZV1VN

Calculation Name: 3B8P-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: B

ChEMBL ID:

UniProt ID: Q04866

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	174
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1627512.869421
FMO2-HF: Nuclear repulsion	1560162.453733
FMO2-HF: Total energy	-67350.415688
FMO2-MP2: Total energy	-67550.995751

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(B:55:LYS)

Summations of interaction energy for fragment #1(B:55: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.
-144.387	-152.692	51.748	-21.724	-21.72	-0.102

Interaction energy analysis for fragmet #1(B:55:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.924

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	B	57	THR	0	0.008	-0.005	3.221	0.049	2.110	0.001	-0.863	-1.199	-0.003
4	B	58	SER	0	-0.071	-0.020	5.696	5.074	5.074	0.000	0.000	0.000	0.000
5	B	59	THR	0	0.036	-0.011	9.384	-1.747	-1.747	0.000	0.000	0.000	0.000
6	B	60	ALA	0	-0.023	0.003	11.451	1.724	1.724	0.000	0.000	0.000	0.000
7	B	61	ILE	0	-0.011	-0.011	14.815	-0.518	-0.518	0.000	0.000	0.000	0.000
8	B	62	ILE	0	0.027	0.005	17.519	0.735	0.735	0.000	0.000	0.000	0.000
9	B	63	THR	0	-0.010	-0.022	20.214	0.136	0.136	0.000	0.000	0.000	0.000
10	B	64	GLN	0	0.071	0.032	23.505	0.041	0.041	0.000	0.000	0.000	0.000
11	B	65	PRO	0	-0.012	0.034	26.614	0.028	0.028	0.000	0.000	0.000	0.000
12	B	66	ASP	-1	-0.860	-0.951	28.712	-10.128	-10.128	0.000	0.000	0.000	0.000
13	B	67	ALA	0	0.053	-0.002	31.483	0.086	0.086	0.000	0.000	0.000	0.000
14	B	68	ALA	0	-0.020	-0.002	34.539	0.166	0.166	0.000	0.000	0.000	0.000
15	B	69	GLN	0	0.024	-0.001	27.678	0.102	0.102	0.000	0.000	0.000	0.000
16	B	70	VAL	0	-0.011	0.012	32.441	-0.034	-0.034	0.000	0.000	0.000	0.000
17	B	71	ALA	0	0.009	-0.009	34.777	0.178	0.178	0.000	0.000	0.000	0.000
18	B	72	THR	0	0.040	0.031	36.822	0.241	0.241	0.000	0.000	0.000	0.000
19	B	73	TYR	0	0.053	0.013	36.031	0.281	0.281	0.000	0.000	0.000	0.000
20	B	74	THR	0	-0.003	-0.014	37.284	0.086	0.086	0.000	0.000	0.000	0.000
21	B	75	ASN	0	-0.033	-0.023	39.476	0.317	0.317	0.000	0.000	0.000	0.000
22	B	76	ALA	0	0.022	0.024	41.165	0.204	0.204	0.000	0.000	0.000	0.000
23	B	77	LEU	0	0.015	0.012	38.095	0.154	0.154	0.000	0.000	0.000	0.000
24	B	78	ASN	0	0.005	0.002	42.618	0.104	0.104	0.000	0.000	0.000	0.000
25	B	79	VAL	0	-0.053	-0.025	45.441	0.163	0.163	0.000	0.000	0.000	0.000
26	B	80	LEU	0	-0.020	-0.009	43.514	0.150	0.150	0.000	0.000	0.000	0.000
27	B	81	TYR	0	-0.037	-0.019	43.466	0.045	0.045	0.000	0.000	0.000	0.000
28	B	82	GLY	0	0.013	0.001	47.172	0.060	0.060	0.000	0.000	0.000	0.000
29	B	83	GLY	0	-0.034	-0.017	47.325	-0.109	-0.109	0.000	0.000	0.000	0.000
30	B	84	ASN	0	-0.057	-0.032	46.445	0.044	0.044	0.000	0.000	0.000	0.000
31	B	85	ALA	0	-0.004	0.023	43.249	-0.157	-0.157	0.000	0.000	0.000	0.000
32	B	86	PRO	0	-0.019	0.002	38.451	0.037	0.037	0.000	0.000	0.000	0.000
33	B	87	LYS	1	0.897	0.923	38.956	7.951	7.951	0.000	0.000	0.000	0.000
34	B	88	ILE	0	0.033	0.010	36.559	-0.173	-0.173	0.000	0.000	0.000	0.000
35	B	89	SER	0	0.033	0.005	34.869	-0.144	-0.144	0.000	0.000	0.000	0.000
36	B	90	GLU	-1	-0.857	-0.916	33.595	-8.612	-8.612	0.000	0.000	0.000	0.000
37	B	91	VAL	0	0.023	0.019	33.566	-0.252	-0.252	0.000	0.000	0.000	0.000
38	B	92	GLN	0	-0.060	-0.033	30.708	0.007	0.007	0.000	0.000	0.000	0.000
39	B	93	ALA	0	0.034	0.012	29.268	-0.456	-0.456	0.000	0.000	0.000	0.000
40	B	94	ASN	0	-0.035	-0.026	28.704	-0.430	-0.430	0.000	0.000	0.000	0.000
41	B	95	PHE	0	0.025	0.021	28.633	-0.267	-0.267	0.000	0.000	0.000	0.000
42	B	96	ILE	0	0.034	0.023	22.489	-0.386	-0.386	0.000	0.000	0.000	0.000
43	B	97	SER	0	-0.072	-0.022	23.983	-0.583	-0.583	0.000	0.000	0.000	0.000
44	B	98	ARG	1	0.858	0.905	24.405	9.771	9.771	0.000	0.000	0.000	0.000
45	B	99	PHE	0	0.014	0.030	18.652	-0.474	-0.474	0.000	0.000	0.000	0.000
46	B	100	SER	0	-0.025	-0.032	19.781	-0.558	-0.558	0.000	0.000	0.000	0.000
47	B	101	SER	0	-0.019	0.002	19.731	-0.874	-0.874	0.000	0.000	0.000	0.000
48	B	102	ALA	0	0.087	0.046	21.176	-0.403	-0.403	0.000	0.000	0.000	0.000
49	B	103	PHE	0	0.013	-0.018	13.632	-0.866	-0.866	0.000	0.000	0.000	0.000
50	B	104	SER	0	-0.067	-0.046	16.064	-1.218	-1.218	0.000	0.000	0.000	0.000
51	B	105	ALA	0	0.025	0.023	16.915	-0.506	-0.506	0.000	0.000	0.000	0.000
52	B	106	LEU	0	-0.012	-0.011	15.290	-0.550	-0.550	0.000	0.000	0.000	0.000
53	B	107	SER	0	0.011	-0.016	12.530	-1.232	-1.232	0.000	0.000	0.000	0.000
54	B	108	GLU	-1	-0.970	-0.962	12.815	-21.366	-21.366	0.000	0.000	0.000	0.000
55	B	109	VAL	0	-0.009	-0.009	14.740	-0.256	-0.256	0.000	0.000	0.000	0.000
56	B	110	LEU	0	-0.015	-0.003	11.381	-0.271	-0.271	0.000	0.000	0.000	0.000
57	B	111	ASP	-1	-0.814	-0.863	9.298	-31.915	-31.915	0.000	0.000	0.000	0.000
58	B	112	ASN	0	-0.082	-0.028	11.555	0.102	0.102	0.000	0.000	0.000	0.000
59	B	113	GLN	0	-0.061	-0.045	12.101	2.708	2.708	0.000	0.000	0.000	0.000
60	B	114	LYS	1	0.907	0.948	13.466	14.006	14.006	0.000	0.000	0.000	0.000
61	B	115	GLU	-1	-0.934	-0.958	9.137	-28.065	-28.065	0.000	0.000	0.000	0.000
62	B	116	ARG	1	0.867	0.919	7.880	27.812	27.812	0.000	0.000	0.000	0.000
63	B	117	GLU	-1	-0.793	-0.847	7.443	-29.381	-29.381	0.000	0.000	0.000	0.000
64	B	118	LYS	1	0.854	0.903	3.725	42.893	43.122	0.001	-0.027	-0.203	0.000
65	B	119	LEU	0	0.062	0.040	6.813	-3.258	-3.258	0.000	0.000	0.000	0.000
66	B	120	THR	0	-0.034	-0.015	8.412	-1.086	-1.086	0.000	0.000	0.000	0.000
67	B	121	ILE	0	0.016	0.013	10.514	0.805	0.805	0.000	0.000	0.000	0.000
68	B	122	GLU	-1	-0.831	-0.898	12.023	-23.230	-23.230	0.000	0.000	0.000	0.000
69	B	123	GLN	0	0.017	0.004	14.878	0.146	0.146	0.000	0.000	0.000	0.000
70	B	124	SER	0	0.017	-0.007	16.398	-0.357	-0.357	0.000	0.000	0.000	0.000
71	B	125	VAL	0	-0.002	0.006	17.461	-0.340	-0.340	0.000	0.000	0.000	0.000
72	B	126	LYS	1	0.798	0.875	14.385	21.025	21.025	0.000	0.000	0.000	0.000
73	B	127	GLY	0	0.037	0.022	19.650	0.554	0.554	0.000	0.000	0.000	0.000
74	B	128	GLN	0	-0.103	-0.045	22.271	0.884	0.884	0.000	0.000	0.000	0.000
75	B	129	ALA	0	-0.017	-0.015	22.468	-0.524	-0.524	0.000	0.000	0.000	0.000
76	B	130	LEU	0	0.036	0.031	22.676	-0.390	-0.390	0.000	0.000	0.000	0.000
77	B	131	PRO	0	-0.026	-0.008	20.342	0.504	0.504	0.000	0.000	0.000	0.000
78	B	132	LEU	0	0.052	0.037	18.087	-0.266	-0.266	0.000	0.000	0.000	0.000
79	B	133	SER	0	-0.025	0.002	14.004	0.724	0.724	0.000	0.000	0.000	0.000
80	B	134	VAL	0	0.018	0.014	12.760	-0.883	-0.883	0.000	0.000	0.000	0.000
81	B	135	SER	0	-0.002	-0.005	7.802	-0.301	-0.301	0.000	0.000	0.000	0.000
82	B	136	TYR	0	-0.002	-0.044	8.102	-0.384	-0.384	0.000	0.000	0.000	0.000
83	B	137	VAL	0	-0.041	-0.007	2.258	-6.146	-8.276	6.773	-1.464	-3.180	-0.007
84	B	138	SER	0	0.050	0.034	4.101	6.067	6.284	-0.001	-0.032	-0.184	0.000
85	B	139	THR	0	0.001	-0.012	2.744	-9.994	-7.712	0.745	-1.668	-1.359	-0.015
86	B	140	THR	0	0.023	0.003	3.050	-3.160	-1.613	0.085	-0.956	-0.676	-0.009
87	B	141	ALA	0	0.021	0.015	5.488	-0.392	-0.392	0.000	0.000	0.000	0.000
88	B	142	GLU	-1	-0.767	-0.878	7.378	-19.214	-19.214	0.000	0.000	0.000	0.000
89	B	143	GLY	0	0.007	0.009	8.483	1.112	1.112	0.000	0.000	0.000	0.000
90	B	144	ALA	0	0.027	0.004	6.306	0.460	0.460	0.000	0.000	0.000	0.000
91	B	145	GLN	0	-0.096	-0.055	8.318	1.733	1.733	0.000	0.000	0.000	0.000
92	B	146	ARG	1	0.843	0.896	11.589	19.272	19.272	0.000	0.000	0.000	0.000
93	B	147	ARG	1	0.893	0.934	10.067	21.427	21.427	0.000	0.000	0.000	0.000
94	B	148	LEU	0	-0.044	-0.006	11.211	0.957	0.957	0.000	0.000	0.000	0.000
95	B	149	ALA	0	0.015	-0.003	13.018	1.063	1.063	0.000	0.000	0.000	0.000
96	B	150	GLU	-1	-0.827	-0.871	15.453	-16.580	-16.580	0.000	0.000	0.000	0.000
97	B	151	TYR	0	0.007	-0.037	11.787	1.392	1.392	0.000	0.000	0.000	0.000
98	B	152	ILE	0	-0.050	-0.028	15.508	0.605	0.605	0.000	0.000	0.000	0.000
99	B	153	GLN	0	-0.099	-0.049	18.499	0.455	0.455	0.000	0.000	0.000	0.000
100	B	154	GLN	0	0.000	-0.004	19.200	0.364	0.364	0.000	0.000	0.000	0.000
101	B	155	VAL	0	0.021	0.006	18.719	0.557	0.557	0.000	0.000	0.000	0.000
102	B	156	ASP	-1	-0.781	-0.910	21.601	-11.908	-11.908	0.000	0.000	0.000	0.000
103	B	157	GLU	-1	-0.855	-0.921	24.162	-12.031	-12.031	0.000	0.000	0.000	0.000
104	B	158	GLU	-1	-1.000	-0.989	23.073	-12.806	-12.806	0.000	0.000	0.000	0.000
105	B	159	VAL	0	-0.004	0.003	24.419	0.455	0.455	0.000	0.000	0.000	0.000
106	B	160	ALA	0	0.031	0.008	27.171	0.522	0.522	0.000	0.000	0.000	0.000
107	B	161	LYS	1	0.966	0.983	29.453	10.539	10.539	0.000	0.000	0.000	0.000
108	B	162	GLU	-1	-0.906	-0.956	29.650	-10.468	-10.468	0.000	0.000	0.000	0.000
109	B	163	LEU	0	0.022	0.018	30.693	0.353	0.353	0.000	0.000	0.000	0.000
110	B	164	GLU	-1	-0.827	-0.909	33.210	-9.018	-9.018	0.000	0.000	0.000	0.000
111	B	165	VAL	0	-0.090	-0.042	34.888	0.366	0.366	0.000	0.000	0.000	0.000
112	B	166	ASP	-1	-0.758	-0.876	34.816	-9.031	-9.031	0.000	0.000	0.000	0.000
113	B	167	LEU	0	-0.011	0.006	37.740	0.317	0.317	0.000	0.000	0.000	0.000
114	B	168	LYS	1	0.802	0.885	37.254	8.902	8.902	0.000	0.000	0.000	0.000
115	B	169	ASP	-1	-0.915	-0.933	40.560	-7.477	-7.477	0.000	0.000	0.000	0.000
116	B	170	ASN	0	0.007	-0.032	40.592	0.391	0.391	0.000	0.000	0.000	0.000
117	B	171	ILE	0	-0.044	-0.005	42.997	0.191	0.191	0.000	0.000	0.000	0.000
118	B	172	THR	0	-0.019	0.002	45.527	0.268	0.268	0.000	0.000	0.000	0.000
119	B	173	LEU	0	-0.053	-0.040	44.379	0.244	0.244	0.000	0.000	0.000	0.000
120	B	174	GLN	0	-0.007	0.011	47.338	0.067	0.067	0.000	0.000	0.000	0.000
121	B	175	THR	0	0.008	-0.027	48.977	0.079	0.079	0.000	0.000	0.000	0.000
122	B	176	LYS	1	0.895	0.952	48.667	6.741	6.741	0.000	0.000	0.000	0.000
123	B	177	THR	0	0.018	0.015	52.436	0.001	0.001	0.000	0.000	0.000	0.000
124	B	178	LEU	0	-0.083	-0.042	51.704	0.113	0.113	0.000	0.000	0.000	0.000
125	B	179	GLN	0	-0.029	-0.028	55.198	0.069	0.069	0.000	0.000	0.000	0.000
126	B	180	GLU	-1	-0.800	-0.897	55.675	-5.823	-5.823	0.000	0.000	0.000	0.000
127	B	181	SER	0	-0.070	-0.029	58.610	0.083	0.083	0.000	0.000	0.000	0.000
128	B	182	LEU	0	-0.025	-0.035	59.960	0.101	0.101	0.000	0.000	0.000	0.000
129	B	183	GLU	-1	-0.858	-0.934	61.548	-5.077	-5.077	0.000	0.000	0.000	0.000
130	B	184	THR	0	-0.112	-0.039	61.864	0.041	0.041	0.000	0.000	0.000	0.000
131	B	185	GLN	0	-0.137	-0.058	64.503	-0.008	-0.008	0.000	0.000	0.000	0.000
132	B	186	GLU	-1	-0.897	-0.930	66.643	-4.629	-4.629	0.000	0.000	0.000	0.000
133	B	251	SER	0	0.031	0.008	67.035	0.031	0.031	0.000	0.000	0.000	0.000
134	B	252	PRO	0	-0.001	-0.012	66.946	-0.055	-0.055	0.000	0.000	0.000	0.000
135	B	253	ALA	0	0.049	0.026	62.210	-0.038	-0.038	0.000	0.000	0.000	0.000
136	B	254	TYR	0	0.021	-0.005	61.805	-0.065	-0.065	0.000	0.000	0.000	0.000
137	B	255	TYR	0	0.018	0.016	61.878	-0.071	-0.071	0.000	0.000	0.000	0.000
138	B	256	GLN	0	0.018	-0.006	58.415	0.028	0.028	0.000	0.000	0.000	0.000
139	B	257	THR	0	0.034	0.018	56.586	-0.103	-0.103	0.000	0.000	0.000	0.000
140	B	258	LYS	1	0.888	0.946	56.935	5.151	5.151	0.000	0.000	0.000	0.000
141	B	259	GLN	0	-0.013	-0.001	57.263	-0.050	-0.050	0.000	0.000	0.000	0.000
142	B	260	THR	0	0.070	0.037	52.789	-0.054	-0.054	0.000	0.000	0.000	0.000
143	B	261	LEU	0	0.014	0.016	52.449	-0.143	-0.143	0.000	0.000	0.000	0.000
144	B	262	LEU	0	-0.005	0.001	53.368	-0.073	-0.073	0.000	0.000	0.000	0.000
145	B	263	ASP	-1	-0.839	-0.926	50.533	-6.303	-6.303	0.000	0.000	0.000	0.000
146	B	264	ILE	0	-0.071	-0.036	48.508	-0.130	-0.130	0.000	0.000	0.000	0.000
147	B	265	LYS	1	0.839	0.924	48.987	6.266	6.266	0.000	0.000	0.000	0.000
148	B	266	ASN	0	-0.055	-0.017	49.943	-0.158	-0.158	0.000	0.000	0.000	0.000
149	B	267	LEU	0	0.027	0.037	44.518	-0.085	-0.085	0.000	0.000	0.000	0.000
150	B	268	LYS	1	0.869	0.913	43.841	6.777	6.777	0.000	0.000	0.000	0.000
151	B	269	VAL	0	0.013	0.014	38.219	-0.079	-0.079	0.000	0.000	0.000	0.000
152	B	270	THR	0	-0.009	-0.017	37.586	-0.145	-0.145	0.000	0.000	0.000	0.000
153	B	271	ALA	0	0.029	0.009	34.279	-0.083	-0.083	0.000	0.000	0.000	0.000
154	B	272	ASP	-1	-0.934	-0.959	31.723	-10.124	-10.124	0.000	0.000	0.000	0.000
155	B	273	THR	0	-0.127	-0.057	33.497	0.015	0.015	0.000	0.000	0.000	0.000
156	B	274	VAL	0	-0.029	-0.008	31.900	-0.075	-0.075	0.000	0.000	0.000	0.000
157	B	275	HIS	0	0.005	0.003	27.527	-0.032	-0.032	0.000	0.000	0.000	0.000
158	B	276	VAL	0	-0.008	-0.017	25.051	0.222	0.222	0.000	0.000	0.000	0.000
159	B	277	TYR	0	-0.045	-0.026	21.347	-0.651	-0.651	0.000	0.000	0.000	0.000
160	B	278	ARG	1	0.915	0.973	24.169	11.887	11.887	0.000	0.000	0.000	0.000
161	B	279	TYR	0	0.005	-0.002	18.134	-0.744	-0.744	0.000	0.000	0.000	0.000
162	B	280	VAL	0	-0.046	-0.013	21.020	0.690	0.690	0.000	0.000	0.000	0.000
163	B	281	MET	0	-0.078	-0.042	16.919	0.037	0.037	0.000	0.000	0.000	0.000
164	B	282	LYS	1	1.010	1.008	18.141	13.290	13.290	0.000	0.000	0.000	0.000
165	B	283	PRO	0	0.001	0.003	13.875	-0.226	-0.226	0.000	0.000	0.000	0.000
166	B	284	THR	0	0.038	0.032	12.139	0.148	0.148	0.000	0.000	0.000	0.000
167	B	285	LEU	0	0.049	0.035	10.916	-2.016	-2.016	0.000	0.000	0.000	0.000
168	B	286	PRO	0	-0.080	-0.006	7.469	1.173	1.173	0.000	0.000	0.000	0.000
169	B	287	VAL	0	0.057	0.017	9.684	0.510	0.510	0.000	0.000	0.000	0.000
170	B	288	ARG	1	0.935	0.963	9.441	24.855	24.855	0.000	0.000	0.000	0.000
171	B	289	ARG	1	0.869	0.922	1.787	19.175	11.938	18.716	-5.888	-5.591	0.048
172	B	290	ASP	-1	-0.761	-0.895	1.650	-122.145	-128.060	25.429	-10.735	-8.779	-0.116
173	B	291	SER	0	0.010	0.001	4.161	7.880	8.276	0.000	-0.068	-0.328	0.000
174	B	292	PRO	0	-0.017	0.004	4.422	-7.566	-7.321	-0.001	-0.023	-0.221	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:55:LYS)