FMO DATABASE

FMODB ID: YYJK2

Calculation Name: 2I3T-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3T

Chain ID: B

ChEMBL ID:

UniProt ID: P26449

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	35
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-134824.486246
FMO2-HF: Nuclear repulsion	119542.66845
FMO2-HF: Total energy	-15281.817796
FMO2-MP2: Total energy	-15324.475032

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(B:353:MET)

Summations of interaction energy for fragment #1(B:353: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.
-0.934	0.484	-0.009	-0.687	-0.722	0.002

Interaction energy analysis for fragmet #1(B:353:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.006

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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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	B	355	PRO	0	0.019	0.015	3.842	-1.326	0.092	-0.009	-0.687	-0.722	0.002
4	B	356	GLU	-1	-0.909	-0.958	6.508	0.428	0.428	0.000	0.000	0.000	0.000
5	B	357	LYS	1	0.915	0.950	7.798	-0.180	-0.180	0.000	0.000	0.000	0.000
6	B	358	ILE	0	0.047	0.029	11.353	0.064	0.064	0.000	0.000	0.000	0.000
7	B	359	ASP	-1	-0.965	-0.970	13.821	0.106	0.106	0.000	0.000	0.000	0.000
8	B	360	CYS	0	-0.007	-0.012	16.789	-0.007	-0.007	0.000	0.000	0.000	0.000
9	B	361	ASN	0	-0.018	-0.005	18.839	-0.016	-0.016	0.000	0.000	0.000	0.000
10	B	362	PHE	0	0.090	0.023	16.419	-0.001	-0.001	0.000	0.000	0.000	0.000
11	B	363	LYS	1	0.942	0.967	21.400	0.012	0.012	0.000	0.000	0.000	0.000
12	B	364	LEU	0	-0.046	-0.016	24.617	0.001	0.001	0.000	0.000	0.000	0.000
13	B	365	ILE	0	0.007	0.010	21.047	0.002	0.002	0.000	0.000	0.000	0.000
14	B	366	TYR	0	-0.049	-0.034	21.079	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	367	CYS	0	-0.036	-0.012	25.856	0.001	0.001	0.000	0.000	0.000	0.000
16	B	368	GLU	-1	-1.017	-1.007	28.907	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	377	LEU	0	-0.029	-0.021	29.018	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	378	GLU	-1	-0.883	-0.914	24.310	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	379	PHE	0	-0.041	-0.020	27.341	0.001	0.001	0.000	0.000	0.000	0.000
20	B	380	SER	0	-0.001	-0.034	26.878	0.002	0.002	0.000	0.000	0.000	0.000
21	B	381	LEU	0	0.032	0.003	22.965	0.000	0.000	0.000	0.000	0.000	0.000
22	B	382	GLU	-1	-0.861	-0.947	27.346	0.031	0.031	0.000	0.000	0.000	0.000
23	B	383	GLU	-1	-0.790	-0.838	30.804	0.009	0.009	0.000	0.000	0.000	0.000
24	B	384	VAL	0	0.033	0.023	27.659	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	385	LEU	0	-0.058	-0.010	30.773	0.000	0.000	0.000	0.000	0.000	0.000
26	B	386	ALA	0	0.016	-0.003	32.374	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	387	ILE	0	-0.005	-0.004	32.578	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	388	SER	0	-0.072	-0.045	32.296	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	389	ARG	1	0.888	0.941	34.895	-0.026	-0.026	0.000	0.000	0.000	0.000
30	B	390	ASN	0	-0.046	-0.014	38.233	0.000	0.000	0.000	0.000	0.000	0.000
31	B	391	VAL	0	0.015	0.001	39.146	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	392	TYR	0	-0.065	-0.041	34.322	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	393	LYS	1	0.936	0.963	38.799	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	394	ARG	1	0.963	0.977	42.355	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	395	VAL	0	0.046	0.040	45.931	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:353:MET)