FMO DATABASE

FMODB ID: 19QMZ

Calculation Name: 6J4W-J-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6J4W

Chain ID: J

ChEMBL ID:

UniProt ID: P04908

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-388496.9438
FMO2-HF: Nuclear repulsion	360208.057672
FMO2-HF: Total energy	-28288.886128
FMO2-MP2: Total energy	-28367.775166

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.
-60.61	-48.758	10.146	-10.041	-11.955	-0.112

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 : 0.769 / q_NPA : 0.883

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	ILE	0	0.022	0.020	2.732	-15.372	-11.652	0.189	-2.185	-1.723	-0.020
4	A	4	PRO	0	-0.016	-0.011	4.322	4.846	4.944	-0.001	-0.008	-0.089	0.000
52	A	52	HIS	0	-0.072	-0.026	2.205	-11.988	-10.602	1.430	-1.171	-1.645	-0.011
53	A	53	VAL	0	0.045	0.023	3.461	5.544	5.992	0.000	-0.175	-0.274	-0.001
54	A	54	ASP	-1	-0.790	-0.903	1.925	-99.416	-96.976	5.315	-4.440	-3.315	-0.067
55	A	55	LEU	0	-0.031	-0.023	2.316	8.336	9.984	1.128	-1.046	-1.729	-0.005
56	A	56	ILE	0	0.033	0.026	3.577	6.680	7.402	0.010	-0.182	-0.549	0.000
57	A	57	GLU	-1	-0.853	-0.925	4.967	-24.805	-24.646	-0.001	-0.009	-0.149	0.000
59	A	59	PHE	0	0.003	-0.018	2.210	-0.674	0.557	2.076	-0.825	-2.482	-0.008
5	A	5	VAL	0	0.079	0.034	6.594	3.507	3.507	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.912	0.936	10.159	21.323	21.323	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.016	0.018	10.646	-1.295	-1.295	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.055	0.002	6.860	2.551	2.551	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.027	0.017	12.918	0.583	0.583	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.048	-0.027	16.179	1.036	1.036	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.067	0.051	15.970	0.772	0.772	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.941	0.967	16.652	16.391	16.391	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.016	0.007	14.315	-1.265	-1.265	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.041	-0.029	10.238	1.542	1.542	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.025	0.023	9.680	-0.761	-0.761	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.840	-0.897	10.573	-20.316	-20.316	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.804	0.874	12.750	20.120	20.120	0.000	0.000	0.000	0.000
18	A	18	TRP	0	0.010	0.005	7.452	0.488	0.488	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.824	-0.919	11.459	-23.571	-23.571	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.060	-0.030	14.109	1.192	1.192	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.010	-0.010	11.789	1.390	1.390	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.023	0.011	10.481	0.745	0.745	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.964	0.981	14.481	15.984	15.984	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.070	-0.031	17.866	0.890	0.890	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.003	-0.001	14.161	0.533	0.533	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.955	-0.966	17.830	-16.407	-16.407	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.946	-0.974	20.153	-12.762	-12.762	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.009	0.004	21.755	0.613	0.613	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.837	0.933	20.696	13.617	13.617	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.016	0.017	20.418	-0.701	-0.701	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.856	-0.940	15.421	-17.548	-17.548	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.077	-0.045	17.833	-0.358	-0.358	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.812	-0.918	20.337	-13.149	-13.149	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.040	0.025	17.838	0.156	0.156	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.037	-0.028	14.239	-0.575	-0.575	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.873	-0.916	18.281	-13.990	-13.990	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.920	-0.961	21.451	-13.316	-13.316	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.023	-0.008	15.724	0.173	0.173	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.895	0.949	19.223	11.980	11.980	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.038	-0.014	14.520	0.171	0.171	0.000	0.000	0.000	0.000
41	A	41	LYS	1	1.001	0.991	18.661	12.061	12.061	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.930	0.964	19.434	15.126	15.126	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.132	0.052	18.125	-1.123	-1.123	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.023	-0.017	16.069	-0.740	-0.740	0.000	0.000	0.000	0.000
45	A	45	CYS	0	-0.048	-0.042	14.257	-0.865	-0.865	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.871	0.926	13.315	14.068	14.068	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.978	0.982	11.374	22.525	22.525	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.086	-0.006	8.265	-1.224	-1.224	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.018	0.014	8.061	-4.033	-4.033	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.002	0.007	9.679	-1.357	-1.357	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.049	-0.044	9.108	0.516	0.516	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.843	0.915	7.050	33.583	33.583	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.046	0.017	6.761	2.496	2.496	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.897	0.962	9.251	22.969	22.969	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.071	-0.017	9.215	1.162	1.162	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.011	-0.011	11.923	-0.548	-0.548	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.009	0.004	13.050	-0.201	-0.201	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.056	-0.039	12.605	0.631	0.631	0.000	0.000	0.000	0.000
66	A	66	GLU	-2	-1.900	-1.919	15.398	-28.550	-28.550	0.000	0.000	0.000	0.000

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