FMO DATABASE

FMODB ID: 22VYR

Calculation Name: 4A8X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A8X

Chain ID: B

ChEMBL ID:

UniProt ID: Q15287

Base Structure: X-ray

Registration Date: 2023-06-20

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	27
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-85608.364339
FMO2-HF: Nuclear repulsion	74796.746576
FMO2-HF: Total energy	-10811.617763
FMO2-MP2: Total energy	-10843.141502

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:656:LEU)

Summations of interaction energy for fragment #1(B:656: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.
-16.933	-14.14	10.946	-6.081	-7.66	-0.055

Interaction energy analysis for fragmet #1(B:656:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.002

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	658	ASP	-1	-0.814	-0.890	3.357	-1.368	0.425	-0.001	-0.775	-1.018	0.003
4	B	659	ASP	-1	-0.905	-0.936	1.943	-15.694	-15.770	9.700	-4.946	-4.678	-0.056
5	B	660	LEU	0	-0.047	-0.007	2.461	-0.045	1.031	1.247	-0.360	-1.964	-0.002
6	B	661	PHE	0	-0.034	-0.014	5.084	0.720	0.720	0.000	0.000	0.000	0.000
7	B	662	ARG	1	0.913	0.963	8.314	0.534	0.534	0.000	0.000	0.000	0.000
8	B	663	LYS	1	0.888	0.936	7.587	-0.954	-0.954	0.000	0.000	0.000	0.000
9	B	664	THR	0	-0.057	-0.023	11.195	-0.057	-0.057	0.000	0.000	0.000	0.000
10	B	665	LYS	1	0.987	0.975	14.618	0.175	0.175	0.000	0.000	0.000	0.000
11	B	666	GLY	0	0.002	0.017	16.346	0.020	0.020	0.000	0.000	0.000	0.000
12	B	667	THR	0	0.016	0.014	17.662	0.018	0.018	0.000	0.000	0.000	0.000
13	B	668	PRO	0	0.033	0.001	18.463	-0.020	-0.020	0.000	0.000	0.000	0.000
14	B	669	CYS	0	-0.050	-0.023	13.400	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	670	ILE	0	0.010	0.014	14.357	0.072	0.072	0.000	0.000	0.000	0.000
16	B	671	TYR	0	-0.015	-0.047	6.754	0.235	0.235	0.000	0.000	0.000	0.000
17	B	672	TRP	0	0.026	0.009	12.495	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	673	LEU	0	0.019	-0.003	10.367	-0.107	-0.107	0.000	0.000	0.000	0.000
19	B	674	PRO	0	-0.061	-0.011	13.614	0.066	0.066	0.000	0.000	0.000	0.000
20	B	675	LEU	0	0.047	0.020	15.256	-0.038	-0.038	0.000	0.000	0.000	0.000
21	B	676	THR	0	0.029	0.010	13.340	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	677	PRO	0	0.007	-0.007	15.829	0.041	0.041	0.000	0.000	0.000	0.000
23	B	678	GLU	-1	-0.849	-0.923	16.602	-0.381	-0.381	0.000	0.000	0.000	0.000
24	B	679	ALA	0	0.012	0.006	18.066	0.031	0.031	0.000	0.000	0.000	0.000
25	B	680	ILE	0	-0.095	-0.046	19.759	0.028	0.028	0.000	0.000	0.000	0.000
26	B	681	ALA	0	-0.039	-0.014	22.183	0.022	0.022	0.000	0.000	0.000	0.000
27	B	682	GLU	-1	-1.039	-1.009	21.086	-0.182	-0.182	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:656:LEU)