FMO DATABASE

FMODB ID: R5678

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

Total energy (hartree)

FMO2-HF: Electronic energy	-799693.181294
FMO2-HF: Nuclear repulsion	758065.408772
FMO2-HF: Total energy	-41627.772521
FMO2-MP2: Total energy	-41747.500302

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.
0.279	2.708	-0.005	-1.116	-1.309	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 : 0.077 / q_NPA : 0.020

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	0.044	0.028	3.076	-0.848	1.362	-0.003	-1.090	-1.117	0.002
4	B	501	SER	0	0.006	-0.023	5.107	-0.043	0.005	-0.001	-0.005	-0.042	0.000
5	B	502	ASP	-1	-0.776	-0.841	7.899	-0.621	-0.621	0.000	0.000	0.000	0.000
6	B	503	SER	0	0.030	0.014	10.122	-0.102	-0.102	0.000	0.000	0.000	0.000
7	B	504	ALA	0	-0.019	-0.007	11.630	-0.007	-0.007	0.000	0.000	0.000	0.000
8	B	505	LYS	1	0.838	0.888	13.333	0.226	0.226	0.000	0.000	0.000	0.000
9	B	506	LEU	0	-0.033	-0.013	16.824	-0.017	-0.017	0.000	0.000	0.000	0.000
10	B	507	ILE	0	-0.013	-0.009	18.120	0.021	0.021	0.000	0.000	0.000	0.000
11	B	508	PHE	0	0.002	0.003	20.197	-0.010	-0.010	0.000	0.000	0.000	0.000
12	B	509	ILE	0	0.022	0.006	19.761	-0.007	-0.007	0.000	0.000	0.000	0.000
13	B	510	ASN	0	-0.074	-0.045	21.661	0.001	0.001	0.000	0.000	0.000	0.000
14	B	511	GLN	0	0.117	0.067	22.506	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	512	ILE	0	-0.036	-0.012	17.797	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	513	ASN	0	0.040	0.000	20.338	-0.020	-0.020	0.000	0.000	0.000	0.000
17	B	514	ASP	-1	-0.890	-0.915	22.978	-0.107	-0.107	0.000	0.000	0.000	0.000
18	B	515	CYS	0	-0.097	-0.018	18.672	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	516	LYS	1	0.980	0.985	19.074	0.103	0.103	0.000	0.000	0.000	0.000
20	B	517	ASP	-1	-0.779	-0.892	16.958	-0.187	-0.187	0.000	0.000	0.000	0.000
21	B	518	GLY	0	0.007	0.007	12.677	0.018	0.018	0.000	0.000	0.000	0.000
22	B	519	GLN	0	0.007	0.004	12.043	-0.068	-0.068	0.000	0.000	0.000	0.000
23	B	520	LYS	1	0.819	0.912	7.182	0.962	0.962	0.000	0.000	0.000	0.000
24	B	521	LEU	0	-0.020	-0.004	12.103	0.076	0.076	0.000	0.000	0.000	0.000
25	B	522	ARG	1	0.903	0.934	12.601	0.181	0.181	0.000	0.000	0.000	0.000
26	B	523	PHE	0	0.037	0.020	14.736	0.037	0.037	0.000	0.000	0.000	0.000
27	B	524	LEU	0	-0.032	-0.014	16.806	-0.014	-0.014	0.000	0.000	0.000	0.000
28	B	525	GLY	0	0.031	0.003	19.487	0.010	0.010	0.000	0.000	0.000	0.000
29	B	526	CYS	0	-0.060	0.008	21.128	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	527	VAL	0	0.058	0.020	20.294	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	528	GLN	0	0.050	0.041	22.807	0.013	0.013	0.000	0.000	0.000	0.000
32	B	529	SER	0	-0.053	-0.046	23.423	0.013	0.013	0.000	0.000	0.000	0.000
33	B	530	TYR	0	0.035	0.013	17.023	-0.015	-0.015	0.000	0.000	0.000	0.000
34	B	531	LYS	1	0.990	0.994	20.984	0.112	0.112	0.000	0.000	0.000	0.000
35	B	532	ASN	0	-0.008	-0.011	20.660	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	533	GLY	0	0.091	0.065	16.484	0.001	0.001	0.000	0.000	0.000	0.000
37	B	534	ILE	0	-0.027	-0.004	15.711	-0.030	-0.030	0.000	0.000	0.000	0.000
38	B	535	LEU	0	0.018	0.002	16.429	0.020	0.020	0.000	0.000	0.000	0.000
39	B	536	ARG	1	0.894	0.950	18.455	0.106	0.106	0.000	0.000	0.000	0.000
40	B	537	LEU	0	0.023	0.014	17.317	0.009	0.009	0.000	0.000	0.000	0.000
41	B	538	ILE	0	-0.029	-0.037	21.257	0.005	0.005	0.000	0.000	0.000	0.000
42	B	539	ASP	-1	-0.829	-0.923	23.878	-0.131	-0.131	0.000	0.000	0.000	0.000
43	B	540	GLY	0	0.027	0.033	25.826	0.004	0.004	0.000	0.000	0.000	0.000
44	B	541	SER	0	-0.010	-0.001	29.632	0.000	0.000	0.000	0.000	0.000	0.000
45	B	542	SER	0	-0.036	-0.020	25.900	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	543	SER	0	-0.023	-0.029	23.785	0.003	0.003	0.000	0.000	0.000	0.000
47	B	544	VAL	0	0.003	0.013	18.007	0.003	0.003	0.000	0.000	0.000	0.000
48	B	545	THR	0	-0.025	-0.008	18.640	0.005	0.005	0.000	0.000	0.000	0.000
49	B	546	CYS	0	-0.014	-0.006	14.549	-0.021	-0.021	0.000	0.000	0.000	0.000
50	B	547	ASP	-1	-0.754	-0.859	13.238	-0.245	-0.245	0.000	0.000	0.000	0.000
51	B	548	VAL	0	-0.001	-0.020	11.520	-0.062	-0.062	0.000	0.000	0.000	0.000
52	B	549	THR	0	0.002	-0.018	12.081	0.001	0.001	0.000	0.000	0.000	0.000
53	B	550	VAL	0	-0.024	-0.012	7.061	0.033	0.033	0.000	0.000	0.000	0.000
54	B	551	VAL	0	-0.066	-0.032	7.667	-0.068	-0.068	0.000	0.000	0.000	0.000
55	B	552	LEU	0	0.006	0.003	9.561	0.025	0.025	0.000	0.000	0.000	0.000
56	B	553	PRO	0	-0.065	-0.030	12.837	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	554	ASP	-1	-0.907	-0.939	14.397	-0.174	-0.174	0.000	0.000	0.000	0.000
58	B	555	VAL	0	-0.016	-0.005	16.080	0.024	0.024	0.000	0.000	0.000	0.000
59	B	556	SER	0	-0.028	-0.027	18.990	-0.013	-0.013	0.000	0.000	0.000	0.000
60	B	557	ILE	0	0.000	0.017	16.866	0.002	0.002	0.000	0.000	0.000	0.000
61	B	558	GLN	0	-0.005	0.001	20.954	0.014	0.014	0.000	0.000	0.000	0.000
62	B	559	LYS	1	0.848	0.915	24.065	0.089	0.089	0.000	0.000	0.000	0.000
63	B	560	HIS	0	-0.019	-0.044	25.718	0.011	0.011	0.000	0.000	0.000	0.000
64	B	561	GLU	-1	-0.788	-0.863	20.990	-0.151	-0.151	0.000	0.000	0.000	0.000
65	B	562	TRP	0	0.003	-0.010	22.181	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	563	LEU	0	0.025	0.016	16.505	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	564	ASN	0	-0.004	-0.002	15.338	0.000	0.000	0.000	0.000	0.000	0.000
68	B	565	ILE	0	0.022	0.014	12.216	-0.019	-0.019	0.000	0.000	0.000	0.000
69	B	566	VAL	0	-0.008	-0.013	9.282	0.036	0.036	0.000	0.000	0.000	0.000
70	B	567	GLY	0	0.067	0.030	8.908	-0.081	-0.081	0.000	0.000	0.000	0.000
71	B	568	ARG	1	0.776	0.864	6.832	0.964	0.964	0.000	0.000	0.000	0.000
72	B	569	LYS	1	0.798	0.915	11.516	0.176	0.176	0.000	0.000	0.000	0.000
73	B	570	ARG	1	0.760	0.841	12.312	0.284	0.284	0.000	0.000	0.000	0.000
74	B	571	GLN	0	0.031	0.006	15.624	0.024	0.024	0.000	0.000	0.000	0.000
75	B	572	ASP	-1	-0.847	-0.924	19.289	-0.144	-0.144	0.000	0.000	0.000	0.000
76	B	573	GLY	0	0.000	0.001	21.624	0.006	0.006	0.000	0.000	0.000	0.000
77	B	574	ILE	0	-0.058	-0.024	15.723	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	575	VAL	0	-0.001	-0.007	12.518	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	576	ASP	-1	-0.773	-0.836	9.513	-0.368	-0.368	0.000	0.000	0.000	0.000
80	B	577	VAL	0	-0.042	-0.023	9.348	-0.076	-0.076	0.000	0.000	0.000	0.000
81	B	578	LEU	0	-0.027	-0.018	4.096	-0.267	-0.096	-0.001	-0.021	-0.150	0.000
82	B	579	LEU	0	-0.040	-0.025	5.644	-0.034	-0.034	0.000	0.000	0.000	0.000
83	B	580	ILE	0	0.070	0.040	8.389	0.056	0.056	0.000	0.000	0.000	0.000
84	B	581	ARG	1	0.892	0.940	10.151	0.339	0.339	0.000	0.000	0.000	0.000
85	B	582	SER	0	0.045	0.007	14.869	0.007	0.007	0.000	0.000	0.000	0.000
86	B	583	ALA	0	-0.033	-0.026	18.582	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	584	VAL	0	0.022	0.014	21.028	0.011	0.011	0.000	0.000	0.000	0.000
88	B	585	GLY	0	0.027	0.017	24.217	0.002	0.002	0.000	0.000	0.000	0.000
89	B	586	ILE	0	-0.036	-0.001	21.922	0.005	0.005	0.000	0.000	0.000	0.000
90	B	587	ASN	0	0.059	0.016	25.680	0.002	0.002	0.000	0.000	0.000	0.000
91	B	588	LEU	0	0.038	0.020	24.713	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	589	PRO	0	-0.023	-0.014	27.575	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	590	ARG	1	0.936	0.953	29.348	0.068	0.068	0.000	0.000	0.000	0.000
94	B	591	TYR	0	0.030	0.018	19.903	-0.003	-0.003	0.000	0.000	0.000	0.000
95	B	592	ARG	1	1.013	0.996	25.576	0.083	0.083	0.000	0.000	0.000	0.000
96	B	593	GLN	0	0.050	0.057	27.016	0.001	0.001	0.000	0.000	0.000	0.000
97	B	594	MET	0	0.017	-0.001	25.754	0.002	0.002	0.000	0.000	0.000	0.000
98	B	595	VAL	0	-0.023	-0.015	22.141	-0.002	-0.002	0.000	0.000	0.000	0.000
99	B	596	SER	0	-0.030	-0.025	24.700	0.000	0.000	0.000	0.000	0.000	0.000
100	B	597	GLU	-1	-0.871	-0.951	27.986	-0.070	-0.070	0.000	0.000	0.000	0.000
101	B	598	ARG	1	0.928	0.959	20.062	0.131	0.131	0.000	0.000	0.000	0.000
102	B	599	GLN	0	-0.076	-0.021	22.642	0.004	0.004	0.000	0.000	0.000	0.000
103	B	600	LYS	1	0.862	0.936	26.535	0.080	0.080	0.000	0.000	0.000	0.000
104	B	601	CYS	0	-0.051	-0.005	28.891	0.007	0.007	0.000	0.000	0.000	0.000
105	B	602	ASP	-1	-0.948	-0.965	26.624	-0.062	-0.062	0.000	0.000	0.000	0.000

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