FMO DATABASE

FMODB ID: JV2Z9

Calculation Name: 2DF6-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2DF6

Chain ID: A

ChEMBL ID:

UniProt ID: O55043

Base Structure: X-ray

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	59
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-335449.684116
FMO2-HF: Nuclear repulsion	312297.991089
FMO2-HF: Total energy	-23151.693027
FMO2-MP2: Total energy	-23221.157932

3D Structure

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:5:GLY)

Summations of interaction energy for fragment #1(A:5:GLY)

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.
-72.261	-70.461	0.007	-0.913	-0.894	-0.006

Interaction energy analysis for fragmet #1(A:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / 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	7	LEU	0	0.029	0.037	3.501	6.508	7.519	0.005	-0.403	-0.613	-0.002
4	A	8	GLY	0	-0.013	-0.004	3.410	-15.130	-14.464	0.003	-0.478	-0.191	-0.004
5	A	9	SER	0	-0.093	-0.047	4.482	3.748	3.871	-0.001	-0.032	-0.090	0.000
6	A	10	VAL	0	0.020	0.005	6.088	5.082	5.082	0.000	0.000	0.000	0.000
7	A	11	VAL	0	-0.011	0.002	8.785	-1.135	-1.135	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.965	0.975	11.216	21.050	21.050	0.000	0.000	0.000	0.000
9	A	13	ALA	0	0.043	0.040	14.928	-0.471	-0.471	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.878	0.943	16.851	17.200	17.200	0.000	0.000	0.000	0.000
11	A	15	PHE	0	-0.037	-0.047	18.595	1.022	1.022	0.000	0.000	0.000	0.000
12	A	16	ASN	0	0.039	0.023	20.908	-0.684	-0.684	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.004	0.005	20.024	0.133	0.133	0.000	0.000	0.000	0.000
14	A	18	GLN	0	-0.016	-0.010	22.589	0.136	0.136	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.028	0.016	23.838	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.087	-0.069	24.312	0.641	0.641	0.000	0.000	0.000	0.000
17	A	21	ASN	0	-0.004	-0.007	23.984	0.949	0.949	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.924	-0.980	25.378	-10.934	-10.934	0.000	0.000	0.000	0.000
19	A	23	ASP	-1	-0.914	-0.947	21.794	-14.396	-14.396	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.776	-0.856	20.470	-14.874	-14.874	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.060	-0.022	16.748	0.612	0.612	0.000	0.000	0.000	0.000
22	A	26	SER	0	-0.010	-0.019	19.989	-0.306	-0.306	0.000	0.000	0.000	0.000
23	A	27	PHE	0	-0.034	-0.019	16.635	-0.205	-0.205	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.002	-0.007	21.773	0.681	0.681	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.900	0.947	21.103	12.971	12.971	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.051	-0.033	19.927	0.636	0.636	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.810	-0.893	19.365	-15.235	-15.235	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.033	-0.017	14.368	-0.941	-0.941	0.000	0.000	0.000	0.000
29	A	33	ILE	0	-0.008	-0.001	12.979	1.131	1.131	0.000	0.000	0.000	0.000
30	A	34	HIS	0	-0.001	0.004	11.012	-3.480	-3.480	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.001	0.005	7.640	2.364	2.364	0.000	0.000	0.000	0.000
32	A	36	THR	0	0.018	-0.008	8.335	-3.818	-3.818	0.000	0.000	0.000	0.000
33	A	37	ARG	1	0.831	0.906	10.047	20.031	20.031	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.045	-0.029	5.789	-1.038	-1.038	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.789	-0.863	8.833	-22.020	-22.020	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.940	-0.981	11.092	-19.783	-19.783	0.000	0.000	0.000	0.000
37	A	41	GLY	0	0.045	0.020	12.726	0.505	0.505	0.000	0.000	0.000	0.000
38	A	42	GLY	0	-0.075	-0.036	14.058	0.934	0.934	0.000	0.000	0.000	0.000
39	A	43	TRP	0	0.011	0.016	14.269	0.215	0.215	0.000	0.000	0.000	0.000
40	A	44	TRP	0	-0.021	-0.019	7.742	-3.015	-3.015	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.861	-0.932	11.994	-17.574	-17.574	0.000	0.000	0.000	0.000
42	A	46	GLY	0	-0.025	-0.017	12.031	-3.006	-3.006	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.015	-0.005	13.715	1.512	1.512	0.000	0.000	0.000	0.000
44	A	48	HIS	0	0.013	-0.005	15.400	-0.348	-0.348	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.036	-0.012	18.119	0.639	0.639	0.000	0.000	0.000	0.000
46	A	50	GLY	0	-0.002	0.003	20.169	-0.362	-0.362	0.000	0.000	0.000	0.000
47	A	51	ARG	1	0.841	0.918	21.081	14.760	14.760	0.000	0.000	0.000	0.000
48	A	52	THR	0	0.042	-0.001	18.284	-0.801	-0.801	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.026	0.020	17.533	0.938	0.938	0.000	0.000	0.000	0.000
50	A	54	TRP	0	0.014	-0.006	13.957	-2.063	-2.063	0.000	0.000	0.000	0.000
51	A	55	PHE	0	-0.008	-0.009	11.684	0.791	0.791	0.000	0.000	0.000	0.000
52	A	56	PRO	0	0.057	0.041	15.296	-1.216	-1.216	0.000	0.000	0.000	0.000
53	A	57	SER	0	0.017	0.006	11.140	0.484	0.484	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.027	0.004	12.939	-0.892	-0.892	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.030	-0.013	15.139	0.919	0.919	0.000	0.000	0.000	0.000
56	A	60	VAL	0	0.004	0.022	11.520	0.929	0.929	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.774	0.863	11.577	21.476	21.476	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.845	-0.924	6.932	-34.518	-34.518	0.000	0.000	0.000	0.000
59	A	63	ILE	-1	-0.984	-0.975	9.971	-22.953	-22.953	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLY)