FMO DATABASE

FMODB ID: 9QJL2

Calculation Name: 1VKF-A-Xray549

Preferred Name:

Target Type:

Ligand Name: citric acid | phosphate ion

Ligand 3-letter code: CIT | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1F0

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1729583.70365
FMO2-HF: Nuclear repulsion	1664604.373794
FMO2-HF: Total energy	-64979.329856
FMO2-MP2: Total energy	-65171.510593

3D Structure Molmil

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:1:MET)

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

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.
-29.324	-25.595	3.196	-1.813	-5.112	-0.006

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / 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	A	3	LYS	1	0.924	0.961	3.824	38.029	39.583	-0.005	-0.580	-0.969	0.000
4	A	4	GLY	0	0.028	0.035	5.251	-0.032	0.038	-0.001	-0.007	-0.062	0.000
22	A	22	VAL	0	-0.090	-0.046	2.707	-2.793	-2.013	0.437	-0.223	-0.995	-0.002
46	A	46	THR	0	-0.022	-0.012	2.392	-3.394	-2.855	2.176	-0.711	-2.004	-0.004
47	A	47	VAL	0	-0.018	-0.023	5.145	0.410	0.428	-0.001	-0.003	-0.014	0.000
48	A	48	PHE	0	-0.018	-0.004	3.339	-1.005	-0.288	0.591	-0.285	-1.023	0.000
73	A	73	ASP	-1	-0.823	-0.882	4.431	-28.628	-28.577	-0.001	-0.004	-0.045	0.000
5	A	5	ILE	0	0.027	0.009	8.650	0.573	0.573	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.014	-0.013	5.531	-3.098	-3.098	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.045	0.025	8.732	2.590	2.590	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.032	-0.012	11.145	-0.185	-0.185	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.005	-0.021	13.068	1.059	1.059	0.000	0.000	0.000	0.000
10	A	10	TRP	0	0.010	-0.013	15.675	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.876	-0.955	18.940	-12.363	-12.363	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.054	-0.023	16.787	-0.976	-0.976	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.929	-0.930	20.679	-10.960	-10.960	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.003	-0.007	23.673	0.041	0.041	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.065	-0.016	17.483	-0.420	-0.420	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.036	0.023	19.517	-0.373	-0.373	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.874	-0.940	16.343	-17.882	-17.882	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.070	-0.049	12.041	0.088	0.088	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.769	-0.869	13.206	-19.059	-19.059	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.010	-0.002	9.213	-1.605	-1.605	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.863	-0.921	5.688	-34.432	-34.432	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.031	0.014	5.693	2.755	2.755	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.028	-0.021	5.555	-1.163	-1.163	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.028	0.006	10.060	1.315	1.315	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.016	-0.014	12.784	0.190	0.190	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.964	0.984	15.439	12.833	12.833	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.029	-0.020	17.861	-0.302	-0.302	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.813	-0.895	19.884	-11.150	-11.150	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.009	-0.011	21.558	-0.377	-0.377	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.034	-0.010	22.775	0.034	0.034	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.043	-0.049	22.489	0.012	0.012	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.012	0.024	15.338	-0.436	-0.436	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.878	0.927	17.124	13.380	13.380	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.010	-0.002	17.756	-0.425	-0.425	0.000	0.000	0.000	0.000
36	A	36	HIS	0	0.046	0.033	17.187	-0.767	-0.767	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.041	0.009	11.720	-0.756	-0.756	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.848	0.906	13.512	13.592	13.592	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.018	0.008	15.269	-0.498	-0.498	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.011	-0.010	11.719	-0.410	-0.410	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.805	0.870	7.003	25.703	25.703	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.834	-0.891	11.620	-15.886	-15.886	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.806	0.905	13.288	16.911	16.911	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.027	0.016	10.746	-0.810	-0.810	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.811	0.928	7.993	23.511	23.511	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.018	0.005	8.391	0.754	0.754	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.834	-0.922	12.136	-16.788	-16.788	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.016	-0.010	14.472	0.709	0.709	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.800	-0.883	16.429	-14.025	-14.025	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.047	-0.013	18.365	0.798	0.798	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.024	-0.002	17.464	0.026	0.026	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.020	-0.002	20.279	0.293	0.293	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.013	-0.002	24.086	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.062	-0.009	18.568	0.178	0.178	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.030	0.021	23.025	0.262	0.262	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.868	-0.933	21.089	-12.179	-12.179	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.016	-0.006	20.520	0.505	0.505	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.775	-0.853	19.197	-13.249	-13.249	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.862	-0.946	18.998	-11.781	-11.781	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.004	0.007	19.823	-0.172	-0.172	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.021	0.010	13.884	-0.539	-0.539	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.007	-0.008	14.934	-0.760	-0.760	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.028	-0.001	16.756	-0.199	-0.199	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.045	0.016	12.677	-0.213	-0.213	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.890	0.941	8.893	20.193	20.193	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.946	0.969	13.204	12.098	12.098	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.039	-0.008	15.694	0.355	0.355	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.004	-0.011	13.025	0.353	0.353	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.012	0.032	10.006	-1.010	-1.010	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.006	-0.011	6.355	-0.459	-0.459	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.048	-0.021	7.771	0.878	0.878	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.027	0.007	9.042	-1.273	-1.273	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.006	-0.017	11.834	1.295	1.295	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.011	-0.003	15.421	-0.512	-0.512	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.929	0.974	18.352	12.612	12.612	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.049	0.018	18.240	-0.459	-0.459	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.848	0.907	18.615	11.632	11.632	0.000	0.000	0.000	0.000
82	A	82	ASN	0	0.031	0.008	16.900	0.469	0.469	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.058	0.028	11.088	0.035	0.035	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.020	0.007	14.789	-0.545	-0.545	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.004	0.012	17.294	-0.080	-0.080	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.003	0.007	12.285	0.011	0.011	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.878	0.940	12.877	19.430	19.430	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.813	0.894	13.894	13.162	13.162	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.114	-0.087	14.839	0.959	0.959	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.005	0.017	12.075	-0.109	-0.109	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.068	-0.030	9.588	-1.384	-1.384	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.012	-0.007	5.064	0.216	0.216	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.021	0.012	7.530	1.004	1.004	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.035	-0.009	7.323	-1.444	-1.444	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.007	0.011	10.069	1.371	1.371	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.800	0.885	13.345	16.851	16.851	0.000	0.000	0.000	0.000
97	A	97	PHE	0	0.004	-0.003	15.222	0.918	0.918	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.028	0.007	17.736	-0.174	-0.174	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.002	0.003	20.346	0.606	0.606	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.011	-0.013	22.049	0.189	0.189	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.807	-0.896	25.450	-10.268	-10.268	0.000	0.000	0.000	0.000
102	A	102	SER	0	0.004	-0.016	26.554	-0.294	-0.294	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.828	0.905	27.668	9.630	9.630	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.037	-0.021	24.820	-0.111	-0.111	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.019	-0.010	22.479	-0.466	-0.466	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.809	-0.902	23.397	-10.652	-10.652	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.958	0.980	25.055	10.676	10.676	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.020	0.015	21.449	-0.122	-0.122	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.018	-0.015	20.237	-0.605	-0.605	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.835	-0.889	20.956	-12.190	-12.190	0.000	0.000	0.000	0.000
111	A	111	GLN	0	-0.003	-0.003	20.285	-0.412	-0.412	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.018	-0.023	15.850	-0.527	-0.527	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.984	-0.986	17.588	-15.085	-15.085	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.030	-0.039	19.938	-0.217	-0.217	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.079	-0.040	18.696	0.193	0.193	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.013	0.010	17.211	-0.529	-0.529	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.046	-0.020	12.989	-0.991	-0.991	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.843	-0.913	9.682	-22.660	-22.660	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.053	-0.035	6.171	-2.271	-2.271	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.011	0.004	9.245	1.953	1.953	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.772	-0.885	10.786	-22.663	-22.663	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.020	-0.019	12.108	1.669	1.669	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.028	0.006	15.359	-0.240	-0.240	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.023	0.001	18.138	0.548	0.548	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.030	0.006	16.954	-0.167	-0.167	0.000	0.000	0.000	0.000
126	A	126	ALA	0	0.066	0.022	17.733	-0.434	-0.434	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.067	-0.030	20.488	0.324	0.324	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.034	0.028	15.438	0.024	0.024	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.032	0.008	17.269	-0.307	-0.307	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.875	0.937	18.336	12.467	12.467	0.000	0.000	0.000	0.000
131	A	131	VAL	0	0.004	0.008	17.245	0.400	0.400	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.055	0.028	14.741	0.110	0.110	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.908	0.954	16.314	15.095	15.095	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.886	0.945	19.177	13.352	13.352	0.000	0.000	0.000	0.000
135	A	135	ILE	0	0.009	0.024	14.926	0.440	0.440	0.000	0.000	0.000	0.000
136	A	136	PRO	0	0.036	0.019	15.256	-1.424	-1.424	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.004	-0.006	12.664	0.623	0.623	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.893	0.962	11.624	16.736	16.736	0.000	0.000	0.000	0.000
139	A	139	THR	0	-0.045	-0.020	5.784	-2.224	-2.224	0.000	0.000	0.000	0.000
140	A	140	VAL	0	0.005	0.003	9.164	0.809	0.809	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.004	-0.001	6.099	-2.407	-2.407	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.006	0.009	10.214	2.262	2.262	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.038	0.009	12.770	-0.995	-0.995	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.014	0.000	14.800	0.948	0.948	0.000	0.000	0.000	0.000
145	A	145	LEU	0	-0.003	-0.017	18.255	-0.203	-0.203	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.034	0.002	16.812	0.041	0.041	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.954	-0.980	19.672	-12.644	-12.644	0.000	0.000	0.000	0.000
148	A	148	THR	0	-0.030	-0.020	22.406	0.139	0.139	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.810	-0.899	19.458	-16.056	-16.056	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.876	-0.948	19.834	-13.773	-13.773	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.830	-0.906	20.826	-14.094	-14.094	0.000	0.000	0.000	0.000
152	A	152	ALA	0	0.010	-0.001	16.313	-0.783	-0.783	0.000	0.000	0.000	0.000
153	A	153	ARG	1	0.756	0.836	16.028	15.719	15.719	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.806	-0.868	17.303	-15.489	-15.489	0.000	0.000	0.000	0.000
155	A	155	ILE	0	-0.001	-0.018	15.018	-0.538	-0.538	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.030	-0.016	10.651	-1.113	-1.113	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.795	0.900	12.887	14.189	14.189	0.000	0.000	0.000	0.000
158	A	158	HIS	0	-0.098	-0.064	15.359	-0.061	-0.061	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.032	-0.010	11.834	0.154	0.154	0.000	0.000	0.000	0.000
160	A	160	SER	0	-0.048	-0.013	6.560	0.966	0.966	0.000	0.000	0.000	0.000
161	A	161	ALA	0	0.012	-0.008	7.167	-2.609	-2.609	0.000	0.000	0.000	0.000
162	A	162	ILE	0	0.006	0.015	9.285	2.677	2.677	0.000	0.000	0.000	0.000
163	A	163	SER	0	-0.021	0.015	9.924	-0.951	-0.951	0.000	0.000	0.000	0.000
164	A	164	THR	0	0.043	-0.007	11.289	2.100	2.100	0.000	0.000	0.000	0.000
165	A	165	SER	0	0.039	0.041	13.908	-0.862	-0.862	0.000	0.000	0.000	0.000
166	A	166	SER	0	0.025	0.017	16.447	0.665	0.665	0.000	0.000	0.000	0.000
167	A	167	ARG	1	0.922	0.938	17.349	15.195	15.195	0.000	0.000	0.000	0.000
168	A	168	ILE	0	0.012	0.013	18.841	-0.055	-0.055	0.000	0.000	0.000	0.000
169	A	169	LEU	0	0.038	0.011	16.319	-0.419	-0.419	0.000	0.000	0.000	0.000
170	A	170	TRP	0	-0.092	-0.066	14.045	-1.157	-1.157	0.000	0.000	0.000	0.000
171	A	171	LYS	1	0.817	0.903	14.514	15.204	15.204	0.000	0.000	0.000	0.000
172	A	172	MET	-1	-0.870	-0.882	15.274	-19.168	-19.168	0.000	0.000	0.000	0.000

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