FMO DATABASE

FMODB ID: YR1J2

Calculation Name: 2KMT-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KMT

Chain ID: A

ChEMBL ID:

UniProt ID: Q84B82

Base Structure: SolutionNMR

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	-832495.729178
FMO2-HF: Nuclear repulsion	790848.212347
FMO2-HF: Total energy	-41647.516831
FMO2-MP2: Total energy	-41768.846795

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.
-137.448	-132.988	-0.004	-1.891	-2.564	-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 : 0.871 / q_NPA : 0.921

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	GLN	0	0.087	0.039	3.354	0.395	3.602	-0.003	-1.357	-1.847	-0.006
4	A	4	PHE	0	-0.013	-0.013	3.782	-9.594	-9.311	-0.001	-0.153	-0.130	-0.001
5	A	5	THR	0	-0.005	0.001	3.944	1.004	1.308	0.002	-0.072	-0.233	0.000
7	A	7	TYR	0	-0.050	-0.039	4.032	2.726	3.262	-0.001	-0.303	-0.231	0.001
31	A	31	ASN	0	-0.067	-0.066	4.311	6.050	6.180	-0.001	-0.006	-0.123	0.000
6	A	6	LEU	0	-0.016	-0.001	6.340	3.357	3.357	0.000	0.000	0.000	0.000
8	A	8	LYS	0	0.102	0.039	9.728	1.925	1.925	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.088	-0.034	13.212	-0.889	-0.889	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.857	0.929	13.664	18.310	18.310	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.864	-0.909	14.664	-15.812	-15.812	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.943	0.962	14.396	19.599	19.599	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.006	-0.010	18.496	0.613	0.613	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.023	-0.035	19.138	1.051	1.051	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.051	0.022	19.481	0.274	0.274	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.866	0.947	20.992	12.259	12.259	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.044	-0.015	23.381	0.525	0.525	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.004	-0.006	19.899	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.032	0.031	17.887	-0.516	-0.516	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.006	-0.010	13.414	-1.298	-1.298	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.035	0.026	12.858	1.634	1.634	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.002	0.024	9.320	-2.177	-2.177	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.905	-0.950	6.789	-39.534	-39.534	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.037	0.009	8.440	-2.471	-2.471	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.028	0.014	10.265	2.755	2.755	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.006	0.003	11.579	0.336	0.336	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.885	-0.923	8.099	-33.816	-33.816	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.063	-0.045	8.697	0.018	0.018	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.054	-0.045	9.624	-0.406	-0.406	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.701	-0.843	6.461	-41.826	-41.826	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.056	-0.005	7.150	1.859	1.859	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.002	-0.019	9.504	2.023	2.023	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.056	-0.034	11.738	0.980	0.980	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.917	1.021	8.798	29.547	29.547	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.034	-0.030	11.904	1.616	1.616	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.024	-0.011	12.021	-1.725	-1.725	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.069	0.042	14.159	1.623	1.623	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.052	-0.036	15.665	-1.044	-1.044	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.013	0.015	13.969	0.556	0.556	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.017	-0.020	17.689	0.135	0.135	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.064	0.025	20.878	-0.085	-0.085	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.036	0.016	23.263	0.429	0.429	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-1.014	-1.016	25.875	-10.102	-10.102	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.025	0.012	25.164	0.294	0.294	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.060	-0.020	24.964	0.189	0.189	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.901	-0.933	28.576	-9.480	-9.480	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.926	0.949	28.450	10.530	10.530	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.889	0.950	30.845	8.739	8.739	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.055	0.039	28.706	0.268	0.268	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.042	-0.019	30.726	0.062	0.062	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.004	-0.002	28.063	-0.468	-0.468	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.002	-0.013	27.895	0.322	0.322	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.041	0.020	24.031	-0.195	-0.195	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.105	-0.020	22.072	0.141	0.141	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.041	0.040	18.987	0.341	0.341	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.014	-0.006	20.484	-0.198	-0.198	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.065	-0.020	15.647	-0.462	-0.462	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.025	-0.035	18.390	0.593	0.593	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.050	-0.031	14.764	-1.045	-1.045	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.857	-0.923	15.897	-16.724	-16.724	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.953	-0.970	16.948	-15.720	-15.720	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.026	-0.010	19.543	0.843	0.843	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.861	-0.925	20.207	-14.290	-14.290	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.061	-0.029	18.891	0.299	0.299	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.035	0.013	20.783	-0.103	-0.103	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.019	0.014	14.641	-0.211	-0.211	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.025	0.018	19.199	0.715	0.715	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.006	-0.056	19.332	0.008	0.008	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.005	-0.001	21.449	0.088	0.088	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.092	-0.031	22.747	0.409	0.409	0.000	0.000	0.000	0.000
72	A	72	MET	0	0.026	0.024	18.338	-0.270	-0.270	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.007	0.001	18.261	0.589	0.589	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.001	0.006	15.881	-1.111	-1.111	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.009	0.000	12.357	0.989	0.989	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.009	-0.024	12.743	-1.572	-1.572	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.060	0.026	9.221	0.269	0.269	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.896	0.946	11.126	16.544	16.544	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.035	-0.021	13.787	0.468	0.468	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.021	0.003	7.242	0.503	0.503	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.009	-0.033	8.916	-2.959	-2.959	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.866	-0.907	10.087	-21.336	-21.336	0.000	0.000	0.000	0.000
83	A	83	PRO	0	-0.045	-0.041	7.159	1.271	1.271	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.065	0.039	9.506	0.741	0.741	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.045	-0.037	10.462	1.229	1.229	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.958	-0.988	7.115	-40.535	-40.535	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.013	0.019	9.259	2.654	2.654	0.000	0.000	0.000	0.000
88	A	88	SER	0	0.062	0.023	7.264	0.117	0.117	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.030	-0.013	9.336	1.090	1.090	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.027	0.019	12.838	0.840	0.840	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.931	0.971	9.986	23.896	23.896	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.030	-0.027	11.598	0.680	0.680	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.757	-0.887	15.205	-16.301	-16.301	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.077	-0.038	10.411	0.341	0.341	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.006	0.002	12.549	0.303	0.303	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.059	0.029	14.982	0.671	0.671	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.024	0.000	16.816	0.909	0.909	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.007	-0.008	14.543	0.793	0.793	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.857	-0.950	18.104	-14.644	-14.644	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.033	0.005	20.141	0.799	0.799	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.073	-0.046	19.193	0.437	0.437	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.089	-0.046	18.293	0.291	0.291	0.000	0.000	0.000	0.000
103	A	103	THR	0	-0.122	-0.054	21.156	0.572	0.572	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.031	-0.004	23.979	0.557	0.557	0.000	0.000	0.000	0.000
105	A	105	ILE	-1	-0.990	-0.993	22.059	-11.516	-11.516	0.000	0.000	0.000	0.000

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