FMO DATABASE

FMODB ID: QK9LY

Calculation Name: 2J5Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2J5Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q51911

Base Structure: X-ray

Registration Date: 2025-10-04

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	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-323331.227751
FMO2-HF: Nuclear repulsion	299799.628091
FMO2-HF: Total energy	-23531.59966
FMO2-MP2: Total energy	-23601.333673

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:-7:LEU)

Summations of interaction energy for fragment #1(A:-7:LEU)

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.
-48.712	-43.31	6.528	-4.904	-7.024	-0.042

Interaction energy analysis for fragmet #1(A:-7:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.924

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	-5	PRO	0	0.034	0.022	2.997	-2.043	0.053	0.181	-0.925	-1.352	-0.004
4	A	-4	ARG	1	0.890	0.946	5.231	26.961	27.033	-0.001	-0.002	-0.068	0.000
13	A	5	TRP	0	-0.020	-0.027	2.755	-0.957	0.211	0.229	-0.351	-1.046	-0.002
14	A	6	LEU	0	-0.007	0.009	4.716	-4.957	-4.847	-0.001	-0.005	-0.104	0.000
17	A	9	ASN	0	-0.017	-0.018	2.192	-23.340	-22.010	6.120	-3.445	-4.006	-0.035
18	A	10	ALA	0	0.082	0.046	4.902	-0.745	-0.710	-0.001	-0.005	-0.028	0.000
21	A	13	ASP	-1	-0.930	-0.961	4.013	-62.117	-61.526	0.001	-0.171	-0.420	-0.001
5	A	-3	GLY	0	0.036	0.016	7.390	1.613	1.613	0.000	0.000	0.000	0.000
6	A	-2	SER	0	0.010	-0.013	10.990	-0.144	-0.144	0.000	0.000	0.000	0.000
7	A	-1	HIS	0	0.013	0.010	12.185	0.953	0.953	0.000	0.000	0.000	0.000
8	A	0	MET	0	-0.056	0.003	9.015	-0.911	-0.911	0.000	0.000	0.000	0.000
9	A	1	THR	0	0.047	0.007	11.938	-0.779	-0.779	0.000	0.000	0.000	0.000
10	A	2	ILE	0	0.038	-0.004	8.529	-2.086	-2.086	0.000	0.000	0.000	0.000
11	A	3	ASP	-1	-0.827	-0.910	8.801	-21.775	-21.775	0.000	0.000	0.000	0.000
12	A	4	GLN	0	0.040	0.028	10.330	-1.383	-1.383	0.000	0.000	0.000	0.000
15	A	7	LEU	0	0.001	0.012	6.596	-1.615	-1.615	0.000	0.000	0.000	0.000
16	A	8	LYS	1	0.916	0.957	7.317	29.529	29.529	0.000	0.000	0.000	0.000
19	A	11	LYS	1	0.784	0.894	7.450	23.514	23.514	0.000	0.000	0.000	0.000
20	A	12	GLU	-1	-0.935	-0.974	5.371	-32.025	-32.025	0.000	0.000	0.000	0.000
22	A	14	ALA	0	0.006	0.000	6.999	3.663	3.663	0.000	0.000	0.000	0.000
23	A	15	ILE	0	-0.012	-0.009	10.215	2.528	2.528	0.000	0.000	0.000	0.000
24	A	16	ALA	0	-0.026	-0.011	7.787	2.074	2.074	0.000	0.000	0.000	0.000
25	A	17	GLU	-1	-0.875	-0.924	9.783	-21.369	-21.369	0.000	0.000	0.000	0.000
26	A	18	LEU	0	-0.003	-0.005	12.029	1.861	1.861	0.000	0.000	0.000	0.000
27	A	19	LYS	1	0.927	0.973	11.706	25.175	25.175	0.000	0.000	0.000	0.000
28	A	20	LYS	1	0.909	0.963	12.664	23.060	23.060	0.000	0.000	0.000	0.000
29	A	21	ALA	0	-0.001	0.008	14.749	0.921	0.921	0.000	0.000	0.000	0.000
30	A	22	GLY	0	0.017	0.011	17.431	1.010	1.010	0.000	0.000	0.000	0.000
31	A	23	ILE	0	-0.033	-0.006	17.384	0.749	0.749	0.000	0.000	0.000	0.000
32	A	24	THR	0	0.007	-0.017	17.574	-0.929	-0.929	0.000	0.000	0.000	0.000
33	A	25	SER	0	0.001	0.018	19.721	0.373	0.373	0.000	0.000	0.000	0.000
34	A	26	ASP	-1	-0.793	-0.915	18.200	-17.325	-17.325	0.000	0.000	0.000	0.000
35	A	27	PHE	0	-0.072	-0.028	19.629	-0.326	-0.326	0.000	0.000	0.000	0.000
36	A	28	TYR	0	0.039	0.005	19.197	0.070	0.070	0.000	0.000	0.000	0.000
37	A	29	PHE	0	0.025	0.009	15.034	-0.906	-0.906	0.000	0.000	0.000	0.000
38	A	30	ASN	0	-0.005	-0.008	15.684	-1.458	-1.458	0.000	0.000	0.000	0.000
39	A	31	ALA	0	-0.054	-0.019	18.212	0.050	0.050	0.000	0.000	0.000	0.000
40	A	32	ILE	0	0.044	0.025	12.710	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	33	ASN	0	0.040	-0.008	12.417	-1.701	-1.701	0.000	0.000	0.000	0.000
42	A	34	LYS	1	0.890	0.954	14.775	13.787	13.787	0.000	0.000	0.000	0.000
43	A	35	ALA	0	-0.007	0.028	15.302	0.661	0.661	0.000	0.000	0.000	0.000
44	A	36	LYS	1	0.910	0.936	15.928	13.831	13.831	0.000	0.000	0.000	0.000
45	A	37	THR	0	0.011	0.015	14.972	-0.464	-0.464	0.000	0.000	0.000	0.000
46	A	38	VAL	0	0.046	0.012	10.154	-0.697	-0.697	0.000	0.000	0.000	0.000
47	A	39	GLU	-1	-0.872	-0.942	12.802	-18.520	-18.520	0.000	0.000	0.000	0.000
48	A	40	GLU	-1	-0.809	-0.900	16.144	-15.351	-15.351	0.000	0.000	0.000	0.000
49	A	41	VAL	0	-0.033	-0.014	10.972	0.295	0.295	0.000	0.000	0.000	0.000
50	A	42	ASN	0	-0.011	-0.010	12.342	-1.006	-1.006	0.000	0.000	0.000	0.000
51	A	43	ALA	0	0.003	0.008	14.682	0.461	0.461	0.000	0.000	0.000	0.000
52	A	44	LEU	0	-0.008	-0.007	17.015	0.491	0.491	0.000	0.000	0.000	0.000
53	A	45	LYS	1	0.852	0.919	12.139	22.774	22.774	0.000	0.000	0.000	0.000
54	A	46	ASN	0	-0.002	-0.016	16.365	-0.297	-0.297	0.000	0.000	0.000	0.000
55	A	47	GLU	-1	-0.899	-0.954	18.559	-12.280	-12.280	0.000	0.000	0.000	0.000
56	A	48	ILE	0	-0.058	-0.030	18.433	0.442	0.442	0.000	0.000	0.000	0.000
57	A	49	LEU	0	-0.022	-0.015	16.052	0.286	0.286	0.000	0.000	0.000	0.000
58	A	50	LYS	1	0.907	0.961	20.532	12.302	12.302	0.000	0.000	0.000	0.000
59	A	51	ALA	0	-0.052	-0.030	23.604	0.539	0.539	0.000	0.000	0.000	0.000
60	A	52	HIS	0	-0.083	-0.042	21.574	0.653	0.653	0.000	0.000	0.000	0.000
61	A	53	ALA	-1	-0.948	-0.947	23.760	-11.810	-11.810	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:LEU)