FMO DATABASE

FMODB ID: 17VVZ

Calculation Name: 2QDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P26039

Base Structure: X-ray

Registration Date: 2023-06-26

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

DOI:

Apendix: None

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	34
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-122717.9171
FMO2-HF: Nuclear repulsion	108824.183936
FMO2-HF: Total energy	-13893.733164
FMO2-MP2: Total energy	-13934.180378

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:2496:GLY)

Summations of interaction energy for fragment #1(A:2496: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.
-3.013	0.723	1.652	-2.18	-3.208	0.004

Interaction energy analysis for fragmet #1(A:2496:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.020

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	2498	ILE	0	0.049	0.014	3.082	-2.094	-0.122	0.392	-1.043	-1.321	0.006
4	A	2499	ALA	0	0.026	0.013	2.332	-2.677	-1.666	1.252	-0.839	-1.424	-0.002
5	A	2500	GLN	0	-0.014	-0.011	3.703	0.982	1.735	0.008	-0.298	-0.463	0.000
6	A	2501	ILE	0	-0.008	0.004	6.429	0.364	0.364	0.000	0.000	0.000	0.000
7	A	2502	ILE	0	0.037	0.016	6.286	0.042	0.042	0.000	0.000	0.000	0.000
8	A	2503	ALA	0	0.003	0.004	7.781	0.063	0.063	0.000	0.000	0.000	0.000
9	A	2504	ALA	0	-0.006	-0.003	9.671	0.095	0.095	0.000	0.000	0.000	0.000
10	A	2505	GLN	0	0.000	-0.012	11.133	0.080	0.080	0.000	0.000	0.000	0.000
11	A	2506	GLU	-1	-0.880	-0.928	12.057	-0.153	-0.153	0.000	0.000	0.000	0.000
12	A	2507	GLU	-1	-0.821	-0.898	13.890	-0.217	-0.217	0.000	0.000	0.000	0.000
13	A	2508	MET	0	-0.025	-0.007	15.705	0.038	0.038	0.000	0.000	0.000	0.000
14	A	2509	LEU	0	0.034	0.014	15.507	0.020	0.020	0.000	0.000	0.000	0.000
15	A	2510	ARG	1	0.783	0.887	14.816	0.253	0.253	0.000	0.000	0.000	0.000
16	A	2511	LYS	1	0.830	0.899	19.876	0.178	0.178	0.000	0.000	0.000	0.000
17	A	2512	GLU	-1	-0.914	-0.959	21.197	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	2513	ARG	1	0.871	0.927	20.528	0.074	0.074	0.000	0.000	0.000	0.000
19	A	2514	GLU	-1	-0.792	-0.890	22.438	-0.131	-0.131	0.000	0.000	0.000	0.000
20	A	2515	LEU	0	-0.011	-0.004	25.795	0.008	0.008	0.000	0.000	0.000	0.000
21	A	2516	GLU	-1	-0.812	-0.879	27.235	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	2517	GLU	-1	-0.892	-0.941	28.090	-0.066	-0.066	0.000	0.000	0.000	0.000
23	A	2518	ALA	0	-0.027	-0.006	30.121	0.004	0.004	0.000	0.000	0.000	0.000
24	A	2519	ARG	1	0.888	0.930	28.883	0.044	0.044	0.000	0.000	0.000	0.000
25	A	2520	LYS	1	0.886	0.918	30.676	0.039	0.039	0.000	0.000	0.000	0.000
26	A	2521	LYS	1	0.916	0.955	31.628	0.065	0.065	0.000	0.000	0.000	0.000
27	A	2522	LEU	0	0.004	0.005	36.168	0.003	0.003	0.000	0.000	0.000	0.000
28	A	2523	ALA	0	-0.014	-0.013	37.590	0.003	0.003	0.000	0.000	0.000	0.000
29	A	2524	GLN	0	0.007	0.010	38.461	0.000	0.000	0.000	0.000	0.000	0.000
30	A	2525	ILE	0	0.027	0.008	39.707	0.002	0.002	0.000	0.000	0.000	0.000
31	A	2526	ARG	1	0.921	0.964	41.145	0.029	0.029	0.000	0.000	0.000	0.000
32	A	2527	GLN	0	-0.028	-0.006	41.234	0.001	0.001	0.000	0.000	0.000	0.000
33	A	2528	GLN	0	-0.034	-0.006	43.043	0.000	0.000	0.000	0.000	0.000	0.000
34	A	2529	GLN	0	-0.090	-0.044	46.793	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2496:GLY)