FMO DATABASE

FMODB ID: JVYR9

Calculation Name: 2KCN-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KCN

Chain ID: A

ChEMBL ID:

UniProt ID: Q01701

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-285106.585898
FMO2-HF: Nuclear repulsion	261768.539323
FMO2-HF: Total energy	-23338.046576
FMO2-MP2: Total energy	-23401.144592

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:ALA)

Summations of interaction energy for fragment #1(A:1:ALA)

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.
-20.877	-19.827	10.203	-5.564	-5.689	-0.056

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / q_NPA : 0.907

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

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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	TYR	0	0.041	0.029	3.730	-0.237	1.967	0.006	-1.044	-1.166	-0.003
46	A	46	ASP	-1	-0.832	-0.921	4.485	-68.168	-68.133	-0.001	-0.030	-0.004	0.000
47	A	47	THR	0	-0.043	-0.022	1.880	-20.073	-21.503	10.199	-4.447	-4.322	-0.053
48	A	48	TYR	0	-0.030	-0.007	4.145	4.916	5.157	-0.001	-0.043	-0.197	0.000
4	A	4	THR	0	-0.005	-0.002	6.323	2.001	2.001	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.005	-0.002	9.884	0.502	0.502	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.906	0.952	12.941	18.334	18.334	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.023	0.017	16.640	-0.350	-0.350	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.009	-0.021	19.106	0.289	0.289	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.877	0.920	22.504	10.679	10.679	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.028	0.022	26.032	0.094	0.094	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.839	0.893	22.039	13.644	13.644	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.049	0.038	20.866	-0.770	-0.770	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.839	-0.914	17.687	-15.008	-15.008	0.000	0.000	0.000	0.000
14	A	14	CYS	0	0.015	0.016	11.781	0.238	0.238	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.929	0.988	13.983	15.093	15.093	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.004	-0.016	7.061	-0.807	-0.807	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.962	0.990	9.077	24.199	24.199	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.028	0.000	6.749	-1.780	-1.780	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.929	-0.962	6.673	-23.367	-23.367	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.044	0.026	7.366	-2.366	-2.366	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.081	-0.046	9.251	1.629	1.629	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.977	0.993	10.658	20.040	20.040	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.893	-0.949	11.625	-19.149	-19.149	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.068	-0.032	10.939	0.242	0.242	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.008	-0.009	13.195	-0.412	-0.412	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.016	0.013	12.166	0.535	0.535	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.951	0.966	15.381	13.446	13.446	0.000	0.000	0.000	0.000
28	A	28	CYS	0	0.014	0.023	16.515	-0.471	-0.471	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.053	0.043	16.656	1.268	1.268	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.857	0.907	19.572	15.570	15.570	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.020	-0.002	22.807	0.378	0.378	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.853	-0.922	25.845	-10.949	-10.949	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.024	0.007	25.599	0.259	0.259	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.875	0.896	23.780	13.500	13.500	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.844	0.942	23.501	10.997	10.997	0.000	0.000	0.000	0.000
36	A	36	CYS	0	-0.036	0.004	22.534	0.070	0.070	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.016	0.000	24.098	0.462	0.462	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.981	0.977	24.768	11.660	11.660	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.852	-0.908	24.085	-11.689	-11.689	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.053	-0.034	20.429	0.282	0.282	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.024	0.022	20.579	-0.065	-0.065	0.000	0.000	0.000	0.000
42	A	42	LYS	1	1.013	1.005	15.745	18.254	18.254	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.078	-0.042	14.286	0.090	0.090	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.001	-0.027	10.203	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.032	0.020	7.424	1.741	1.741	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.031	-0.001	6.186	2.078	2.078	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.037	-0.011	7.669	2.324	2.324	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.029	0.039	9.209	3.113	3.113	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.015	-0.023	10.316	-2.213	-2.213	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.828	-0.888	12.820	-22.198	-22.198	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.068	-0.070	15.112	0.631	0.631	0.000	0.000	0.000	0.000
55	A	55	ASP	-2	-1.718	-1.823	18.353	-29.356	-29.356	0.000	0.000	0.000	0.000

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