FMO DATABASE

FMODB ID: V5ZZ1

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	OptHSide
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	-122167.738037
FMO2-HF: Nuclear repulsion	108274.085078
FMO2-HF: Total energy	-13893.652959
FMO2-MP2: Total energy	-13934.093298

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.
-4.462	-0.774	2.706	-2.571	-3.825	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 : 0.039 / q_NPA : 0.014

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	0.046	0.009	2.898	-3.062	-0.816	0.805	-1.335	-1.717	0.007
4	A	2499	ALA	0	0.023	0.008	2.250	-3.101	-2.243	1.890	-1.057	-1.691	-0.003
5	A	2500	GLN	0	-0.013	-0.004	3.583	0.983	1.567	0.011	-0.179	-0.417	0.000
6	A	2501	ILE	0	0.000	0.008	6.262	0.312	0.312	0.000	0.000	0.000	0.000
7	A	2502	ILE	0	0.044	0.019	6.095	0.021	0.021	0.000	0.000	0.000	0.000
8	A	2503	ALA	0	0.001	0.003	7.582	0.066	0.066	0.000	0.000	0.000	0.000
9	A	2504	ALA	0	-0.005	-0.003	9.472	0.096	0.096	0.000	0.000	0.000	0.000
10	A	2505	GLN	0	-0.008	-0.017	10.985	0.084	0.084	0.000	0.000	0.000	0.000
11	A	2506	GLU	-1	-0.924	-0.963	11.785	-0.131	-0.131	0.000	0.000	0.000	0.000
12	A	2507	GLU	-1	-0.858	-0.904	13.738	-0.209	-0.209	0.000	0.000	0.000	0.000
13	A	2508	MET	0	-0.018	-0.010	15.585	0.036	0.036	0.000	0.000	0.000	0.000
14	A	2509	LEU	0	0.039	0.019	15.840	0.021	0.021	0.000	0.000	0.000	0.000
15	A	2510	ARG	1	0.823	0.901	15.222	0.242	0.242	0.000	0.000	0.000	0.000
16	A	2511	LYS	1	0.809	0.894	19.830	0.164	0.164	0.000	0.000	0.000	0.000
17	A	2512	GLU	-1	-0.907	-0.947	21.119	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	2513	ARG	1	0.917	0.955	19.370	0.075	0.075	0.000	0.000	0.000	0.000
19	A	2514	GLU	-1	-0.792	-0.893	22.847	-0.123	-0.123	0.000	0.000	0.000	0.000
20	A	2515	LEU	0	-0.009	0.002	25.700	0.007	0.007	0.000	0.000	0.000	0.000
21	A	2516	GLU	-1	-0.818	-0.885	27.199	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	2517	GLU	-1	-0.876	-0.924	28.118	-0.065	-0.065	0.000	0.000	0.000	0.000
23	A	2518	ALA	0	-0.029	-0.012	30.088	0.003	0.003	0.000	0.000	0.000	0.000
24	A	2519	ARG	1	0.891	0.928	29.014	0.040	0.040	0.000	0.000	0.000	0.000
25	A	2520	LYS	1	0.865	0.900	30.751	0.037	0.037	0.000	0.000	0.000	0.000
26	A	2521	LYS	1	0.899	0.940	31.344	0.064	0.064	0.000	0.000	0.000	0.000
27	A	2522	LEU	0	-0.008	0.003	36.273	0.002	0.002	0.000	0.000	0.000	0.000
28	A	2523	ALA	0	-0.010	-0.012	37.801	0.002	0.002	0.000	0.000	0.000	0.000
29	A	2524	GLN	0	0.015	0.014	38.481	0.000	0.000	0.000	0.000	0.000	0.000
30	A	2525	ILE	0	0.033	0.018	40.071	0.001	0.001	0.000	0.000	0.000	0.000
31	A	2526	ARG	1	0.901	0.940	41.002	0.028	0.028	0.000	0.000	0.000	0.000
32	A	2527	GLN	0	-0.034	-0.013	41.034	0.001	0.001	0.000	0.000	0.000	0.000
33	A	2528	GLN	0	-0.040	-0.007	43.336	0.000	0.000	0.000	0.000	0.000	0.000
34	A	2529	GLN	0	-0.041	0.001	46.993	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)