FMO DATABASE

FMODB ID: LQ689

Calculation Name: 1J3D-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J3D

Chain ID: A

ChEMBL ID:

UniProt ID: P17741

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-458022.46378
FMO2-HF: Nuclear repulsion	426657.259642
FMO2-HF: Total energy	-31365.204139
FMO2-MP2: Total energy	-31456.28199

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.
130.119	132.291	-0.013	-0.916	-1.243	-0.002

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 : 0.880 / q_NPA : 0.917

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	LYS	1	0.907	0.950	3.728	51.695	53.776	-0.012	-0.902	-1.167	-0.002
4	A	4	ASP	-1	-0.793	-0.880	4.734	-38.356	-38.265	-0.001	-0.014	-0.076	0.000
5	A	5	PRO	0	-0.048	-0.030	7.625	-0.316	-0.316	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.022	0.005	9.679	2.476	2.476	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.006	0.025	8.803	1.313	1.313	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.056	0.039	10.959	-0.385	-0.385	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.923	0.945	10.192	23.286	23.286	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.897	0.957	8.127	28.653	28.653	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.042	0.040	10.158	1.278	1.278	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.042	-0.007	13.462	-0.542	-0.542	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.004	-0.015	15.234	0.902	0.902	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.080	0.042	17.489	-0.157	-0.157	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.036	0.039	18.171	-0.086	-0.086	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.005	-0.016	13.088	-0.880	-0.880	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.041	-0.017	17.396	-0.392	-0.392	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.085	0.052	20.033	-0.111	-0.111	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.034	-0.013	17.493	0.258	0.258	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.071	-0.040	17.833	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.832	-0.914	19.228	-12.257	-12.257	0.000	0.000	0.000	0.000
22	A	22	HIS	1	0.852	0.931	22.748	12.669	12.669	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.963	0.989	15.227	18.815	18.815	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.042	-0.028	21.146	0.105	0.105	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.975	0.994	23.278	11.291	11.291	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.019	0.008	24.057	0.336	0.336	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.892	0.938	19.737	14.935	14.935	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.002	0.024	25.056	0.026	0.026	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.896	-0.948	28.607	-9.359	-9.359	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.049	-0.027	26.537	0.387	0.387	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.080	0.045	26.064	-0.638	-0.638	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.001	-0.008	23.658	0.110	0.110	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.042	0.000	22.569	-0.465	-0.465	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.021	0.002	18.601	-0.789	-0.789	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.000	-0.037	14.748	0.123	0.123	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.050	0.034	17.558	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.823	-0.920	19.114	-12.026	-12.026	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.019	0.005	19.852	0.198	0.198	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.015	0.004	18.181	0.240	0.240	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.893	0.938	20.301	12.053	12.053	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.967	0.994	23.120	10.796	10.796	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.019	-0.013	21.280	0.190	0.190	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.011	-0.019	23.214	0.068	0.068	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.946	-0.965	23.750	-9.757	-9.757	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.050	0.016	27.282	0.006	0.006	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.025	-0.024	23.460	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.039	-0.023	26.394	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.902	-0.933	28.254	-8.830	-8.830	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.074	-0.018	28.653	0.070	0.070	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.032	0.004	30.736	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.029	-0.006	31.654	-0.289	-0.289	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.931	0.968	31.850	8.630	8.630	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.862	-0.934	28.581	-10.791	-10.791	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.956	0.958	26.904	9.974	9.974	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.005	0.008	27.146	-0.324	-0.324	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.022	-0.007	27.469	-0.345	-0.345	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.085	-0.053	23.455	-0.686	-0.686	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.863	-0.948	22.727	-12.263	-12.263	0.000	0.000	0.000	0.000
59	A	59	GLN	0	0.056	0.039	23.637	-0.346	-0.346	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.919	0.968	20.603	14.161	14.161	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.030	-0.018	19.146	-0.758	-0.758	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.030	0.018	19.341	-0.766	-0.766	0.000	0.000	0.000	0.000
63	A	63	LYS	1	1.039	1.012	20.974	11.140	11.140	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.029	-0.013	17.471	-0.110	-0.110	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.920	0.951	14.721	17.668	17.668	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.871	-0.936	17.221	-13.945	-13.945	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.914	0.976	18.570	14.022	14.022	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.008	-0.013	9.267	-1.647	-1.647	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.906	-0.959	14.933	-17.060	-17.060	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.856	0.932	16.549	14.725	14.725	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.857	-0.932	15.890	-17.054	-17.054	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.055	-0.034	10.399	-0.789	-0.789	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.030	-0.014	14.051	-0.419	-0.419	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.013	0.002	16.948	0.153	0.153	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.007	-0.029	13.046	-0.250	-0.250	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.864	0.955	12.770	20.570	20.570	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.028	-0.030	14.592	-0.447	-0.447	0.000	0.000	0.000	0.000
78	A	78	LYS	0	0.048	0.059	18.011	0.619	0.619	0.000	0.000	0.000	0.000

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