FMO DATABASE

FMODB ID: 66K1Z

Calculation Name: 3KF6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF6

Chain ID: B

ChEMBL ID:

UniProt ID: Q0E7J7

Base Structure: X-ray

Registration Date: 2023-06-19

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-799327.506679
FMO2-HF: Nuclear repulsion	757700.390986
FMO2-HF: Total energy	-41627.115693
FMO2-MP2: Total energy	-41746.924791

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:498:PRO)

Summations of interaction energy for fragment #1(B:498:PRO)

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.
-0.759	1.832	0.029	-1.142	-1.477	0.002

Interaction energy analysis for fragmet #1(B:498:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.081 / q_NPA : 0.017

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	500	GLY	0	0.016	0.030	2.707	-1.171	1.240	0.031	-1.123	-1.319	0.002
4	B	501	SER	0	0.013	-0.015	4.749	-0.223	-0.177	-0.001	-0.006	-0.039	0.000
5	B	502	ASP	-1	-0.783	-0.846	7.522	-0.246	-0.246	0.000	0.000	0.000	0.000
6	B	503	SER	0	0.006	-0.002	9.449	-0.117	-0.117	0.000	0.000	0.000	0.000
7	B	504	ALA	0	-0.001	-0.006	11.779	-0.004	-0.004	0.000	0.000	0.000	0.000
8	B	505	LYS	1	0.873	0.932	13.174	0.131	0.131	0.000	0.000	0.000	0.000
9	B	506	LEU	0	-0.061	-0.027	16.849	-0.024	-0.024	0.000	0.000	0.000	0.000
10	B	507	ILE	0	0.000	-0.007	18.600	0.020	0.020	0.000	0.000	0.000	0.000
11	B	508	PHE	0	-0.007	0.003	20.650	-0.012	-0.012	0.000	0.000	0.000	0.000
12	B	509	ILE	0	0.065	0.019	20.409	-0.002	-0.002	0.000	0.000	0.000	0.000
13	B	510	ASN	0	-0.054	-0.038	22.253	0.002	0.002	0.000	0.000	0.000	0.000
14	B	511	GLN	0	0.126	0.074	23.001	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	512	ILE	0	-0.014	0.004	18.484	0.001	0.001	0.000	0.000	0.000	0.000
16	B	513	ASN	0	0.006	-0.018	21.080	-0.009	-0.009	0.000	0.000	0.000	0.000
17	B	514	ASP	-1	-0.865	-0.905	23.570	-0.064	-0.064	0.000	0.000	0.000	0.000
18	B	515	CYS	0	-0.169	-0.075	18.971	0.008	0.008	0.000	0.000	0.000	0.000
19	B	516	LYS	1	0.971	0.966	18.512	0.030	0.030	0.000	0.000	0.000	0.000
20	B	517	ASP	-1	-0.773	-0.877	16.771	-0.119	-0.119	0.000	0.000	0.000	0.000
21	B	518	GLY	0	-0.010	-0.011	12.610	0.028	0.028	0.000	0.000	0.000	0.000
22	B	519	GLN	0	0.048	0.029	12.046	-0.024	-0.024	0.000	0.000	0.000	0.000
23	B	520	LYS	1	0.837	0.917	6.514	0.593	0.593	0.000	0.000	0.000	0.000
24	B	521	LEU	0	-0.024	-0.014	12.005	0.059	0.059	0.000	0.000	0.000	0.000
25	B	522	ARG	1	0.966	0.971	13.049	0.150	0.150	0.000	0.000	0.000	0.000
26	B	523	PHE	0	0.010	0.003	14.979	0.037	0.037	0.000	0.000	0.000	0.000
27	B	524	LEU	0	-0.004	0.008	17.059	-0.022	-0.022	0.000	0.000	0.000	0.000
28	B	525	GLY	0	0.024	0.003	19.749	0.011	0.011	0.000	0.000	0.000	0.000
29	B	526	CYS	0	-0.055	-0.002	21.186	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	527	VAL	0	0.034	0.017	20.548	0.001	0.001	0.000	0.000	0.000	0.000
31	B	528	GLN	0	-0.011	0.007	23.067	0.014	0.014	0.000	0.000	0.000	0.000
32	B	529	SER	0	-0.034	-0.054	23.673	0.014	0.014	0.000	0.000	0.000	0.000
33	B	530	TYR	0	0.042	0.020	17.207	-0.016	-0.016	0.000	0.000	0.000	0.000
34	B	531	LYS	1	0.994	0.999	21.650	0.119	0.119	0.000	0.000	0.000	0.000
35	B	532	ASN	0	0.007	0.004	21.117	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	533	GLY	0	0.077	0.049	16.988	0.000	0.000	0.000	0.000	0.000	0.000
37	B	534	ILE	0	-0.032	-0.008	16.247	-0.025	-0.025	0.000	0.000	0.000	0.000
38	B	535	LEU	0	0.007	-0.006	16.192	0.020	0.020	0.000	0.000	0.000	0.000
39	B	536	ARG	1	0.931	0.980	18.914	0.110	0.110	0.000	0.000	0.000	0.000
40	B	537	LEU	0	0.010	0.006	17.515	0.007	0.007	0.000	0.000	0.000	0.000
41	B	538	ILE	0	-0.016	-0.024	21.660	0.006	0.006	0.000	0.000	0.000	0.000
42	B	539	ASP	-1	-0.852	-0.933	24.267	-0.115	-0.115	0.000	0.000	0.000	0.000
43	B	540	GLY	0	0.004	0.029	26.182	0.005	0.005	0.000	0.000	0.000	0.000
44	B	541	SER	0	-0.014	-0.012	29.840	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	542	SER	0	-0.045	-0.020	25.877	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	543	SER	0	-0.047	-0.048	24.214	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	544	VAL	0	0.015	0.016	18.564	0.004	0.004	0.000	0.000	0.000	0.000
48	B	545	THR	0	-0.037	-0.007	18.811	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	546	CYS	0	-0.037	-0.024	14.826	-0.011	-0.011	0.000	0.000	0.000	0.000
50	B	547	ASP	-1	-0.794	-0.880	12.929	-0.307	-0.307	0.000	0.000	0.000	0.000
51	B	548	VAL	0	0.006	-0.024	11.874	-0.061	-0.061	0.000	0.000	0.000	0.000
52	B	549	THR	0	0.010	-0.003	12.532	0.004	0.004	0.000	0.000	0.000	0.000
53	B	550	VAL	0	-0.006	-0.011	7.048	0.021	0.021	0.000	0.000	0.000	0.000
54	B	551	VAL	0	-0.075	-0.026	8.009	-0.078	-0.078	0.000	0.000	0.000	0.000
55	B	552	LEU	0	-0.004	-0.002	9.780	0.048	0.048	0.000	0.000	0.000	0.000
56	B	553	PRO	0	-0.051	-0.020	13.409	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	554	ASP	-1	-0.901	-0.935	14.779	-0.234	-0.234	0.000	0.000	0.000	0.000
58	B	555	VAL	0	-0.021	-0.009	16.877	0.029	0.029	0.000	0.000	0.000	0.000
59	B	556	SER	0	-0.033	-0.030	19.142	-0.013	-0.013	0.000	0.000	0.000	0.000
60	B	557	ILE	0	0.000	0.014	17.138	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	558	GLN	0	-0.041	-0.023	21.565	0.015	0.015	0.000	0.000	0.000	0.000
62	B	559	LYS	1	0.917	0.946	24.430	0.090	0.090	0.000	0.000	0.000	0.000
63	B	560	HIS	0	-0.005	-0.035	25.900	0.010	0.010	0.000	0.000	0.000	0.000
64	B	561	GLU	-1	-0.852	-0.891	21.604	-0.164	-0.164	0.000	0.000	0.000	0.000
65	B	562	TRP	0	0.004	-0.010	22.357	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	563	LEU	0	0.021	0.010	16.849	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	564	ASN	0	-0.031	-0.025	15.599	0.019	0.019	0.000	0.000	0.000	0.000
68	B	565	ILE	0	0.020	0.008	12.448	-0.032	-0.032	0.000	0.000	0.000	0.000
69	B	566	VAL	0	0.000	-0.003	8.940	0.050	0.050	0.000	0.000	0.000	0.000
70	B	567	GLY	0	0.053	0.017	9.181	-0.114	-0.114	0.000	0.000	0.000	0.000
71	B	568	ARG	1	0.797	0.882	6.521	0.531	0.531	0.000	0.000	0.000	0.000
72	B	569	LYS	1	0.786	0.929	11.566	0.113	0.113	0.000	0.000	0.000	0.000
73	B	570	ARG	1	0.835	0.923	13.472	0.255	0.255	0.000	0.000	0.000	0.000
74	B	571	GLN	0	0.049	0.000	15.560	0.022	0.022	0.000	0.000	0.000	0.000
75	B	572	ASP	-1	-0.863	-0.940	19.325	-0.101	-0.101	0.000	0.000	0.000	0.000
76	B	573	GLY	0	-0.020	-0.010	21.740	0.000	0.000	0.000	0.000	0.000	0.000
77	B	574	ILE	0	-0.067	-0.014	15.485	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	575	VAL	0	0.016	-0.007	12.957	0.002	0.002	0.000	0.000	0.000	0.000
79	B	576	ASP	-1	-0.789	-0.882	9.755	-0.342	-0.342	0.000	0.000	0.000	0.000
80	B	577	VAL	0	-0.049	-0.030	9.578	-0.075	-0.075	0.000	0.000	0.000	0.000
81	B	578	LEU	0	-0.034	-0.013	4.590	-0.231	-0.097	-0.001	-0.013	-0.119	0.000
82	B	579	LEU	0	-0.041	-0.029	6.089	-0.048	-0.048	0.000	0.000	0.000	0.000
83	B	580	ILE	0	0.067	0.041	8.547	0.074	0.074	0.000	0.000	0.000	0.000
84	B	581	ARG	1	0.911	0.950	10.590	0.369	0.369	0.000	0.000	0.000	0.000
85	B	582	SER	0	0.072	0.054	14.890	0.013	0.013	0.000	0.000	0.000	0.000
86	B	583	ALA	0	-0.033	-0.020	18.623	0.001	0.001	0.000	0.000	0.000	0.000
87	B	584	VAL	0	0.038	0.008	20.874	0.015	0.015	0.000	0.000	0.000	0.000
88	B	585	GLY	0	0.010	0.005	23.966	0.002	0.002	0.000	0.000	0.000	0.000
89	B	586	ILE	0	-0.035	0.004	22.361	0.008	0.008	0.000	0.000	0.000	0.000
90	B	587	ASN	0	0.048	0.023	25.814	0.004	0.004	0.000	0.000	0.000	0.000
91	B	588	LEU	0	0.067	0.018	25.388	0.001	0.001	0.000	0.000	0.000	0.000
92	B	589	PRO	0	-0.024	-0.014	28.046	0.000	0.000	0.000	0.000	0.000	0.000
93	B	590	ARG	1	0.925	0.947	29.248	0.057	0.057	0.000	0.000	0.000	0.000
94	B	591	TYR	0	0.035	0.020	19.937	0.001	0.001	0.000	0.000	0.000	0.000
95	B	592	ARG	1	1.008	0.993	25.763	0.071	0.071	0.000	0.000	0.000	0.000
96	B	593	GLN	0	0.056	0.042	27.256	0.001	0.001	0.000	0.000	0.000	0.000
97	B	594	MET	0	0.023	0.001	25.963	0.005	0.005	0.000	0.000	0.000	0.000
98	B	595	VAL	0	-0.032	-0.002	22.380	0.002	0.002	0.000	0.000	0.000	0.000
99	B	596	SER	0	0.002	-0.013	24.864	0.003	0.003	0.000	0.000	0.000	0.000
100	B	597	GLU	-1	-0.918	-0.961	27.973	-0.040	-0.040	0.000	0.000	0.000	0.000
101	B	598	ARG	1	0.906	0.951	19.234	0.085	0.085	0.000	0.000	0.000	0.000
102	B	599	GLN	0	-0.089	-0.037	22.943	0.009	0.009	0.000	0.000	0.000	0.000
103	B	600	LYS	1	0.923	0.958	25.892	0.051	0.051	0.000	0.000	0.000	0.000
104	B	601	CYS	0	-0.058	-0.006	28.482	0.005	0.005	0.000	0.000	0.000	0.000
105	B	602	ASP	-1	-0.948	-0.964	26.585	-0.019	-0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:498:PRO)