FMO DATABASE

FMODB ID: VYJK1

Calculation Name: 3KF6-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KF6

Chain ID: B

ChEMBL ID:

UniProt ID: Q0E7J7

Base Structure: X-ray

Registration Date: 2025-10-05

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-799267.281293
FMO2-HF: Nuclear repulsion	757639.861581
FMO2-HF: Total energy	-41627.419712
FMO2-MP2: Total energy	-41747.114222

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:498:PRO)

Summations of interaction energy for fragment #1(A: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.
60.54	63.132	-0.007	-1.147	-1.437	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.903 / q_NPA : 0.926

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	500	GLY	0	0.053	0.046	3.050	8.039	10.397	-0.005	-1.116	-1.237	-0.002
4	A	501	SER	0	0.004	-0.019	4.954	-0.376	-0.309	-0.001	-0.009	-0.056	0.000
81	A	578	LEU	0	-0.045	-0.026	4.311	-3.376	-3.209	-0.001	-0.022	-0.144	0.000
5	A	502	ASP	-1	-0.755	-0.836	7.767	-30.606	-30.606	0.000	0.000	0.000	0.000
6	A	503	SER	0	0.033	0.015	10.091	-2.059	-2.059	0.000	0.000	0.000	0.000
7	A	504	ALA	0	-0.012	-0.006	11.741	-0.131	-0.131	0.000	0.000	0.000	0.000
8	A	505	LYS	1	0.908	0.949	13.560	16.922	16.922	0.000	0.000	0.000	0.000
9	A	506	LEU	0	-0.026	-0.007	16.751	-0.525	-0.525	0.000	0.000	0.000	0.000
10	A	507	ILE	0	-0.004	-0.002	18.219	0.766	0.766	0.000	0.000	0.000	0.000
11	A	508	PHE	0	-0.002	0.001	20.337	-0.282	-0.282	0.000	0.000	0.000	0.000
12	A	509	ILE	0	0.017	0.005	20.105	-0.292	-0.292	0.000	0.000	0.000	0.000
13	A	510	ASN	0	-0.042	-0.033	22.008	-0.164	-0.164	0.000	0.000	0.000	0.000
14	A	511	GLN	0	0.122	0.065	22.550	-0.218	-0.218	0.000	0.000	0.000	0.000
15	A	512	ILE	0	-0.023	-0.004	18.141	-0.382	-0.382	0.000	0.000	0.000	0.000
16	A	513	ASN	0	0.038	0.002	20.787	-0.947	-0.947	0.000	0.000	0.000	0.000
17	A	514	ASP	-1	-0.862	-0.902	23.457	-11.755	-11.755	0.000	0.000	0.000	0.000
18	A	515	CYS	0	-0.157	-0.064	18.745	-0.307	-0.307	0.000	0.000	0.000	0.000
19	A	516	LYS	1	0.977	0.981	18.596	14.113	14.113	0.000	0.000	0.000	0.000
20	A	517	ASP	-1	-0.764	-0.877	16.548	-16.697	-16.697	0.000	0.000	0.000	0.000
21	A	518	GLY	0	-0.009	-0.005	12.344	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	519	GLN	0	0.021	0.007	11.863	-1.696	-1.696	0.000	0.000	0.000	0.000
23	A	520	LYS	1	0.805	0.905	7.255	36.949	36.949	0.000	0.000	0.000	0.000
24	A	521	LEU	0	-0.008	-0.002	12.182	1.670	1.670	0.000	0.000	0.000	0.000
25	A	522	ARG	1	0.898	0.936	12.729	16.608	16.608	0.000	0.000	0.000	0.000
26	A	523	PHE	0	0.041	0.019	14.732	1.110	1.110	0.000	0.000	0.000	0.000
27	A	524	LEU	0	-0.031	-0.008	16.831	-0.613	-0.613	0.000	0.000	0.000	0.000
28	A	525	GLY	0	0.034	0.001	19.591	0.390	0.390	0.000	0.000	0.000	0.000
29	A	526	CYS	0	-0.045	0.008	21.158	-0.174	-0.174	0.000	0.000	0.000	0.000
30	A	527	VAL	0	0.046	0.017	20.424	-0.085	-0.085	0.000	0.000	0.000	0.000
31	A	528	GLN	0	0.019	0.015	23.009	0.572	0.572	0.000	0.000	0.000	0.000
32	A	529	SER	0	-0.043	-0.048	23.713	0.631	0.631	0.000	0.000	0.000	0.000
33	A	530	TYR	0	0.009	0.007	17.026	-0.574	-0.574	0.000	0.000	0.000	0.000
34	A	531	LYS	1	0.993	0.990	21.076	11.992	11.992	0.000	0.000	0.000	0.000
35	A	532	ASN	0	0.006	-0.002	20.711	-0.265	-0.265	0.000	0.000	0.000	0.000
36	A	533	GLY	0	0.081	0.056	16.437	-0.171	-0.171	0.000	0.000	0.000	0.000
37	A	534	ILE	0	-0.025	-0.001	15.755	-0.922	-0.922	0.000	0.000	0.000	0.000
38	A	535	LEU	0	0.029	0.007	16.354	0.879	0.879	0.000	0.000	0.000	0.000
39	A	536	ARG	1	0.904	0.956	18.778	11.329	11.329	0.000	0.000	0.000	0.000
40	A	537	LEU	0	0.023	0.013	17.510	0.366	0.366	0.000	0.000	0.000	0.000
41	A	538	ILE	0	-0.031	-0.029	21.478	0.175	0.175	0.000	0.000	0.000	0.000
42	A	539	ASP	-1	-0.867	-0.940	23.889	-12.159	-12.159	0.000	0.000	0.000	0.000
43	A	540	GLY	0	0.025	0.029	25.803	0.191	0.191	0.000	0.000	0.000	0.000
44	A	541	SER	0	-0.010	-0.007	29.571	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	542	SER	0	-0.038	-0.013	25.971	-0.169	-0.169	0.000	0.000	0.000	0.000
46	A	543	SER	0	-0.026	-0.031	24.084	0.086	0.086	0.000	0.000	0.000	0.000
47	A	544	VAL	0	0.006	0.008	18.335	0.077	0.077	0.000	0.000	0.000	0.000
48	A	545	THR	0	-0.017	-0.001	18.558	0.275	0.275	0.000	0.000	0.000	0.000
49	A	546	CYS	0	-0.014	-0.007	14.831	-0.757	-0.757	0.000	0.000	0.000	0.000
50	A	547	ASP	-1	-0.782	-0.858	13.222	-19.482	-19.482	0.000	0.000	0.000	0.000
51	A	548	VAL	0	0.008	-0.019	11.636	-1.656	-1.656	0.000	0.000	0.000	0.000
52	A	549	THR	0	0.007	-0.019	11.967	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	550	VAL	0	-0.033	-0.018	6.922	0.216	0.216	0.000	0.000	0.000	0.000
54	A	551	VAL	0	-0.074	-0.034	7.822	-2.284	-2.284	0.000	0.000	0.000	0.000
55	A	552	LEU	0	0.010	0.007	9.602	1.293	1.293	0.000	0.000	0.000	0.000
56	A	553	PRO	0	-0.076	-0.035	13.050	-0.557	-0.557	0.000	0.000	0.000	0.000
57	A	554	ASP	-1	-0.897	-0.936	14.688	-17.399	-17.399	0.000	0.000	0.000	0.000
58	A	555	VAL	0	-0.020	-0.005	16.663	1.054	1.054	0.000	0.000	0.000	0.000
59	A	556	SER	0	-0.027	-0.027	19.065	-0.503	-0.503	0.000	0.000	0.000	0.000
60	A	557	ILE	0	-0.008	0.011	16.964	0.141	0.141	0.000	0.000	0.000	0.000
61	A	558	GLN	0	-0.002	0.000	21.112	0.711	0.711	0.000	0.000	0.000	0.000
62	A	559	LYS	1	0.870	0.934	24.160	9.959	9.959	0.000	0.000	0.000	0.000
63	A	560	HIS	0	0.004	-0.026	25.905	0.548	0.548	0.000	0.000	0.000	0.000
64	A	561	GLU	-1	-0.821	-0.893	21.177	-13.670	-13.670	0.000	0.000	0.000	0.000
65	A	562	TRP	0	0.001	-0.008	22.326	-0.239	-0.239	0.000	0.000	0.000	0.000
66	A	563	LEU	0	0.029	0.016	16.707	-0.260	-0.260	0.000	0.000	0.000	0.000
67	A	564	ASN	0	-0.019	-0.009	15.337	0.320	0.320	0.000	0.000	0.000	0.000
68	A	565	ILE	0	0.028	0.016	12.350	-0.902	-0.902	0.000	0.000	0.000	0.000
69	A	566	VAL	0	0.001	-0.012	9.223	0.654	0.654	0.000	0.000	0.000	0.000
70	A	567	GLY	0	0.046	0.018	9.159	-1.751	-1.751	0.000	0.000	0.000	0.000
71	A	568	ARG	1	0.771	0.856	6.826	35.203	35.203	0.000	0.000	0.000	0.000
72	A	569	LYS	1	0.769	0.898	11.693	15.434	15.434	0.000	0.000	0.000	0.000
73	A	570	ARG	1	0.768	0.840	13.175	19.238	19.238	0.000	0.000	0.000	0.000
74	A	571	GLN	0	0.042	0.012	15.609	0.111	0.111	0.000	0.000	0.000	0.000
75	A	572	ASP	-1	-0.839	-0.914	19.392	-13.699	-13.699	0.000	0.000	0.000	0.000
76	A	573	GLY	0	-0.010	-0.005	22.078	0.145	0.145	0.000	0.000	0.000	0.000
77	A	574	ILE	0	-0.070	-0.027	15.600	0.019	0.019	0.000	0.000	0.000	0.000
78	A	575	VAL	0	0.005	-0.005	12.810	-0.422	-0.422	0.000	0.000	0.000	0.000
79	A	576	ASP	-1	-0.767	-0.836	9.886	-22.725	-22.725	0.000	0.000	0.000	0.000
80	A	577	VAL	0	-0.042	-0.025	9.524	-1.376	-1.376	0.000	0.000	0.000	0.000
82	A	579	LEU	0	-0.051	-0.033	5.704	-2.474	-2.474	0.000	0.000	0.000	0.000
83	A	580	ILE	0	0.086	0.048	8.350	1.933	1.933	0.000	0.000	0.000	0.000
84	A	581	ARG	1	0.886	0.936	10.266	22.910	22.910	0.000	0.000	0.000	0.000
85	A	582	SER	0	0.065	0.040	14.726	0.535	0.535	0.000	0.000	0.000	0.000
86	A	583	ALA	0	-0.038	-0.029	18.474	-0.361	-0.361	0.000	0.000	0.000	0.000
87	A	584	VAL	0	0.028	0.011	20.817	0.625	0.625	0.000	0.000	0.000	0.000
88	A	585	GLY	0	0.023	0.013	23.966	-0.043	-0.043	0.000	0.000	0.000	0.000
89	A	586	ILE	0	-0.035	0.001	21.754	0.215	0.215	0.000	0.000	0.000	0.000
90	A	587	ASN	0	0.048	0.012	25.473	0.304	0.304	0.000	0.000	0.000	0.000
91	A	588	LEU	0	0.064	0.028	25.060	-0.073	-0.073	0.000	0.000	0.000	0.000
92	A	589	PRO	0	-0.037	-0.020	27.758	-0.124	-0.124	0.000	0.000	0.000	0.000
93	A	590	ARG	1	0.928	0.953	28.817	9.517	9.517	0.000	0.000	0.000	0.000
94	A	591	TYR	0	0.034	0.017	20.039	-0.309	-0.309	0.000	0.000	0.000	0.000
95	A	592	ARG	1	1.003	0.990	25.567	9.708	9.708	0.000	0.000	0.000	0.000
96	A	593	GLN	0	0.064	0.063	27.163	0.016	0.016	0.000	0.000	0.000	0.000
97	A	594	MET	0	0.023	0.003	25.571	0.006	0.006	0.000	0.000	0.000	0.000
98	A	595	VAL	0	-0.035	-0.014	22.127	-0.295	-0.295	0.000	0.000	0.000	0.000
99	A	596	SER	0	-0.035	-0.031	24.593	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	597	GLU	-1	-0.909	-0.966	27.907	-9.852	-9.852	0.000	0.000	0.000	0.000
101	A	598	ARG	1	0.921	0.951	19.711	14.559	14.559	0.000	0.000	0.000	0.000
102	A	599	GLN	0	-0.072	-0.025	22.657	0.073	0.073	0.000	0.000	0.000	0.000
103	A	600	LYS	1	0.882	0.949	26.324	10.243	10.243	0.000	0.000	0.000	0.000
104	A	601	CYS	0	-0.079	-0.025	28.851	0.468	0.468	0.000	0.000	0.000	0.000
105	A	602	ASP	-2	-1.877	-1.922	27.332	-22.370	-22.370	0.000	0.000	0.000	0.000

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