FMO DATABASE

FMODB ID: YY662

Calculation Name: 3KF6-B-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	105
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-799346.908212
FMO2-HF: Nuclear repulsion	757720.144738
FMO2-HF: Total energy	-41626.763473
FMO2-MP2: Total energy	-41746.571341

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.
66.583	69.776	0.017	-1.435	-1.774	-0.005

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 : 1 / q_Mulliken : 0.909 / q_NPA : 0.925

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	0.019	0.039	2.777	9.393	12.392	0.017	-1.411	-1.604	-0.005
4	B	501	SER	0	0.019	-0.011	4.797	-0.782	-0.732	0.000	-0.009	-0.041	0.000
5	B	502	ASP	-1	-0.767	-0.838	7.577	-30.296	-30.296	0.000	0.000	0.000	0.000
6	B	503	SER	0	0.016	0.004	9.428	-2.301	-2.301	0.000	0.000	0.000	0.000
7	B	504	ALA	0	-0.013	-0.013	11.691	0.369	0.369	0.000	0.000	0.000	0.000
8	B	505	LYS	1	0.888	0.940	13.107	17.216	17.216	0.000	0.000	0.000	0.000
9	B	506	LEU	0	-0.055	-0.024	16.784	-0.421	-0.421	0.000	0.000	0.000	0.000
10	B	507	ILE	0	0.006	-0.003	18.600	0.751	0.751	0.000	0.000	0.000	0.000
11	B	508	PHE	0	-0.006	0.002	20.649	-0.229	-0.229	0.000	0.000	0.000	0.000
12	B	509	ILE	0	0.058	0.016	20.403	-0.258	-0.258	0.000	0.000	0.000	0.000
13	B	510	ASN	0	-0.054	-0.037	22.248	-0.194	-0.194	0.000	0.000	0.000	0.000
14	B	511	GLN	0	0.127	0.076	23.000	-0.241	-0.241	0.000	0.000	0.000	0.000
15	B	512	ILE	0	-0.018	0.002	18.478	-0.384	-0.384	0.000	0.000	0.000	0.000
16	B	513	ASN	0	0.004	-0.019	21.078	-0.888	-0.888	0.000	0.000	0.000	0.000
17	B	514	ASP	-1	-0.858	-0.901	23.565	-11.680	-11.680	0.000	0.000	0.000	0.000
18	B	515	CYS	0	-0.168	-0.074	18.971	-0.268	-0.268	0.000	0.000	0.000	0.000
19	B	516	LYS	1	0.973	0.966	18.518	14.154	14.154	0.000	0.000	0.000	0.000
20	B	517	ASP	-1	-0.772	-0.876	16.778	-16.790	-16.790	0.000	0.000	0.000	0.000
21	B	518	GLY	0	-0.014	-0.013	12.617	-0.042	-0.042	0.000	0.000	0.000	0.000
22	B	519	GLN	0	0.050	0.030	12.052	-1.587	-1.587	0.000	0.000	0.000	0.000
23	B	520	LYS	1	0.830	0.912	6.480	38.933	38.933	0.000	0.000	0.000	0.000
24	B	521	LEU	0	-0.015	-0.008	12.005	1.545	1.545	0.000	0.000	0.000	0.000
25	B	522	ARG	1	0.965	0.969	13.048	17.207	17.207	0.000	0.000	0.000	0.000
26	B	523	PHE	0	0.012	0.006	14.979	1.201	1.201	0.000	0.000	0.000	0.000
27	B	524	LEU	0	-0.001	0.009	17.056	-0.632	-0.632	0.000	0.000	0.000	0.000
28	B	525	GLY	0	0.022	0.002	19.746	0.442	0.442	0.000	0.000	0.000	0.000
29	B	526	CYS	0	-0.055	-0.002	21.180	-0.084	-0.084	0.000	0.000	0.000	0.000
30	B	527	VAL	0	0.035	0.016	20.538	0.032	0.032	0.000	0.000	0.000	0.000
31	B	528	GLN	0	-0.009	0.008	23.056	0.647	0.647	0.000	0.000	0.000	0.000
32	B	529	SER	0	-0.035	-0.053	23.661	0.627	0.627	0.000	0.000	0.000	0.000
33	B	530	TYR	0	0.039	0.019	17.192	-0.708	-0.708	0.000	0.000	0.000	0.000
34	B	531	LYS	1	0.997	0.999	21.647	11.814	11.814	0.000	0.000	0.000	0.000
35	B	532	ASN	0	0.009	0.005	21.114	-0.332	-0.332	0.000	0.000	0.000	0.000
36	B	533	GLY	0	0.074	0.048	16.985	-0.217	-0.217	0.000	0.000	0.000	0.000
37	B	534	ILE	0	-0.033	-0.009	16.245	-0.893	-0.893	0.000	0.000	0.000	0.000
38	B	535	LEU	0	0.009	-0.006	16.180	0.867	0.867	0.000	0.000	0.000	0.000
39	B	536	ARG	1	0.931	0.980	18.901	11.351	11.351	0.000	0.000	0.000	0.000
40	B	537	LEU	0	0.009	0.006	17.506	0.365	0.365	0.000	0.000	0.000	0.000
41	B	538	ILE	0	-0.012	-0.023	21.651	0.134	0.134	0.000	0.000	0.000	0.000
42	B	539	ASP	-1	-0.854	-0.934	24.261	-12.145	-12.145	0.000	0.000	0.000	0.000
43	B	540	GLY	0	0.008	0.031	26.176	0.159	0.159	0.000	0.000	0.000	0.000
44	B	541	SER	0	-0.013	-0.011	29.832	-0.081	-0.081	0.000	0.000	0.000	0.000
45	B	542	SER	0	-0.047	-0.020	25.870	-0.174	-0.174	0.000	0.000	0.000	0.000
46	B	543	SER	0	-0.043	-0.046	24.206	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	544	VAL	0	0.012	0.014	18.554	-0.025	-0.025	0.000	0.000	0.000	0.000
48	B	545	THR	0	-0.034	-0.006	18.784	0.230	0.230	0.000	0.000	0.000	0.000
49	B	546	CYS	0	-0.038	-0.024	14.815	-0.745	-0.745	0.000	0.000	0.000	0.000
50	B	547	ASP	-1	-0.796	-0.882	12.926	-20.003	-20.003	0.000	0.000	0.000	0.000
51	B	548	VAL	0	0.010	-0.023	11.860	-1.702	-1.702	0.000	0.000	0.000	0.000
52	B	549	THR	0	0.011	-0.002	12.529	0.284	0.284	0.000	0.000	0.000	0.000
53	B	550	VAL	0	-0.013	-0.014	7.045	0.167	0.167	0.000	0.000	0.000	0.000
54	B	551	VAL	0	-0.085	-0.031	7.995	-2.002	-2.002	0.000	0.000	0.000	0.000
55	B	552	LEU	0	0.003	0.002	9.765	1.372	1.372	0.000	0.000	0.000	0.000
56	B	553	PRO	0	-0.053	-0.021	13.396	-0.304	-0.304	0.000	0.000	0.000	0.000
57	B	554	ASP	-1	-0.902	-0.934	14.767	-17.362	-17.362	0.000	0.000	0.000	0.000
58	B	555	VAL	0	-0.020	-0.008	16.871	1.079	1.079	0.000	0.000	0.000	0.000
59	B	556	SER	0	-0.032	-0.030	19.130	-0.453	-0.453	0.000	0.000	0.000	0.000
60	B	557	ILE	0	-0.002	0.013	17.127	-0.050	-0.050	0.000	0.000	0.000	0.000
61	B	558	GLN	0	-0.038	-0.022	21.554	0.747	0.747	0.000	0.000	0.000	0.000
62	B	559	LYS	1	0.916	0.946	24.420	9.888	9.888	0.000	0.000	0.000	0.000
63	B	560	HIS	0	-0.005	-0.035	25.891	0.521	0.521	0.000	0.000	0.000	0.000
64	B	561	GLU	-1	-0.851	-0.890	21.596	-13.629	-13.629	0.000	0.000	0.000	0.000
65	B	562	TRP	0	0.009	-0.008	22.350	-0.380	-0.380	0.000	0.000	0.000	0.000
66	B	563	LEU	0	0.016	0.008	16.839	-0.359	-0.359	0.000	0.000	0.000	0.000
67	B	564	ASN	0	-0.027	-0.022	15.597	0.547	0.547	0.000	0.000	0.000	0.000
68	B	565	ILE	0	0.019	0.008	12.441	-1.019	-1.019	0.000	0.000	0.000	0.000
69	B	566	VAL	0	0.000	-0.003	8.940	0.631	0.631	0.000	0.000	0.000	0.000
70	B	567	GLY	0	0.048	0.013	9.176	-2.098	-2.098	0.000	0.000	0.000	0.000
71	B	568	ARG	1	0.788	0.876	6.528	36.169	36.169	0.000	0.000	0.000	0.000
72	B	569	LYS	1	0.788	0.931	11.566	15.905	15.905	0.000	0.000	0.000	0.000
73	B	570	ARG	1	0.836	0.924	13.469	18.858	18.858	0.000	0.000	0.000	0.000
74	B	571	GLN	0	0.051	-0.001	15.559	0.112	0.112	0.000	0.000	0.000	0.000
75	B	572	ASP	-1	-0.858	-0.937	19.333	-13.526	-13.526	0.000	0.000	0.000	0.000
76	B	573	GLY	0	-0.019	-0.009	21.740	0.133	0.133	0.000	0.000	0.000	0.000
77	B	574	ILE	0	-0.069	-0.014	15.481	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	575	VAL	0	0.023	-0.004	12.949	-0.530	-0.530	0.000	0.000	0.000	0.000
79	B	576	ASP	-1	-0.794	-0.885	9.753	-22.780	-22.780	0.000	0.000	0.000	0.000
80	B	577	VAL	0	-0.041	-0.025	9.578	-1.940	-1.940	0.000	0.000	0.000	0.000
81	B	578	LEU	0	-0.051	-0.024	4.584	-3.161	-3.017	0.000	-0.015	-0.129	0.000
82	B	579	LEU	0	-0.050	-0.036	6.081	-2.169	-2.169	0.000	0.000	0.000	0.000
83	B	580	ILE	0	0.075	0.046	8.541	1.947	1.947	0.000	0.000	0.000	0.000
84	B	581	ARG	1	0.908	0.948	10.587	23.213	23.213	0.000	0.000	0.000	0.000
85	B	582	SER	0	0.073	0.055	14.886	0.583	0.583	0.000	0.000	0.000	0.000
86	B	583	ALA	0	-0.034	-0.020	18.618	-0.221	-0.221	0.000	0.000	0.000	0.000
87	B	584	VAL	0	0.039	0.009	20.871	0.692	0.692	0.000	0.000	0.000	0.000
88	B	585	GLY	0	0.011	0.005	23.961	-0.019	-0.019	0.000	0.000	0.000	0.000
89	B	586	ILE	0	-0.036	0.004	22.361	0.255	0.255	0.000	0.000	0.000	0.000
90	B	587	ASN	0	0.049	0.022	25.812	0.349	0.349	0.000	0.000	0.000	0.000
91	B	588	LEU	0	0.064	0.017	25.384	-0.102	-0.102	0.000	0.000	0.000	0.000
92	B	589	PRO	0	-0.024	-0.014	28.044	-0.145	-0.145	0.000	0.000	0.000	0.000
93	B	590	ARG	1	0.927	0.947	29.249	9.602	9.602	0.000	0.000	0.000	0.000
94	B	591	TYR	0	0.034	0.020	19.937	-0.131	-0.131	0.000	0.000	0.000	0.000
95	B	592	ARG	1	1.003	0.990	25.764	9.760	9.760	0.000	0.000	0.000	0.000
96	B	593	GLN	0	0.059	0.043	27.256	-0.081	-0.081	0.000	0.000	0.000	0.000
97	B	594	MET	0	0.025	0.003	25.966	0.044	0.044	0.000	0.000	0.000	0.000
98	B	595	VAL	0	-0.038	-0.005	22.382	-0.276	-0.276	0.000	0.000	0.000	0.000
99	B	596	SER	0	-0.006	-0.017	24.866	-0.065	-0.065	0.000	0.000	0.000	0.000
100	B	597	GLU	-1	-0.916	-0.962	27.927	-9.951	-9.951	0.000	0.000	0.000	0.000
101	B	598	ARG	1	0.912	0.954	19.166	14.781	14.781	0.000	0.000	0.000	0.000
102	B	599	GLN	0	-0.091	-0.039	22.866	0.271	0.271	0.000	0.000	0.000	0.000
103	B	600	LYS	1	0.904	0.945	25.826	10.279	10.279	0.000	0.000	0.000	0.000
104	B	601	CYS	0	-0.090	-0.024	28.420	0.431	0.431	0.000	0.000	0.000	0.000
105	B	602	ASP	-2	-1.878	-1.922	27.004	-22.607	-22.607	0.000	0.000	0.000	0.000

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