FMO DATABASE

FMODB ID: YZ772

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	OptH
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	-121965.655428
FMO2-HF: Nuclear repulsion	108072.271311
FMO2-HF: Total energy	-13893.384117
FMO2-MP2: Total energy	-13933.831299

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.
-5.72	-1.929	2.236	-2.392	-3.636	0.007

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 : 0.030 / q_NPA : 0.012

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	0.042	0.011	2.924	-2.930	-0.684	0.764	-1.331	-1.679	0.008
4	A	2499	ALA	0	0.029	0.006	2.322	-3.807	-2.720	1.464	-0.957	-1.594	-0.001
5	A	2500	GLN	0	-0.006	0.006	3.665	0.550	1.008	0.008	-0.104	-0.363	0.000
6	A	2501	ILE	0	0.003	0.009	6.386	0.241	0.241	0.000	0.000	0.000	0.000
7	A	2502	ILE	0	0.037	0.017	6.027	-0.023	-0.023	0.000	0.000	0.000	0.000
8	A	2503	ALA	0	0.007	0.004	7.659	0.020	0.020	0.000	0.000	0.000	0.000
9	A	2504	ALA	0	-0.004	-0.003	9.537	0.070	0.070	0.000	0.000	0.000	0.000
10	A	2505	GLN	0	-0.009	-0.017	11.217	0.065	0.065	0.000	0.000	0.000	0.000
11	A	2506	GLU	-1	-0.934	-0.965	11.502	-0.088	-0.088	0.000	0.000	0.000	0.000
12	A	2507	GLU	-1	-0.889	-0.942	13.810	-0.176	-0.176	0.000	0.000	0.000	0.000
13	A	2508	MET	0	-0.026	-0.013	15.673	0.028	0.028	0.000	0.000	0.000	0.000
14	A	2509	LEU	0	0.044	0.015	16.324	0.014	0.014	0.000	0.000	0.000	0.000
15	A	2510	ARG	1	0.865	0.948	15.670	0.184	0.184	0.000	0.000	0.000	0.000
16	A	2511	LYS	1	0.887	0.944	19.904	0.131	0.131	0.000	0.000	0.000	0.000
17	A	2512	GLU	-1	-0.904	-0.948	21.429	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	2513	ARG	1	0.906	0.953	19.914	0.041	0.041	0.000	0.000	0.000	0.000
19	A	2514	GLU	-1	-0.854	-0.931	23.355	-0.096	-0.096	0.000	0.000	0.000	0.000
20	A	2515	LEU	0	-0.017	-0.001	25.777	0.005	0.005	0.000	0.000	0.000	0.000
21	A	2516	GLU	-1	-0.877	-0.934	27.281	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	2517	GLU	-1	-0.966	-0.987	27.870	-0.054	-0.054	0.000	0.000	0.000	0.000
23	A	2518	ALA	0	-0.039	-0.020	30.157	0.002	0.002	0.000	0.000	0.000	0.000
24	A	2519	ARG	1	0.895	0.930	29.316	0.022	0.022	0.000	0.000	0.000	0.000
25	A	2520	LYS	1	0.932	0.955	30.424	0.024	0.024	0.000	0.000	0.000	0.000
26	A	2521	LYS	1	0.988	0.998	31.737	0.049	0.049	0.000	0.000	0.000	0.000
27	A	2522	LEU	0	-0.010	0.002	36.347	0.002	0.002	0.000	0.000	0.000	0.000
28	A	2523	ALA	0	-0.012	-0.012	37.878	0.002	0.002	0.000	0.000	0.000	0.000
29	A	2524	GLN	0	0.016	0.008	37.995	0.000	0.000	0.000	0.000	0.000	0.000
30	A	2525	ILE	0	0.029	0.024	40.111	0.001	0.001	0.000	0.000	0.000	0.000
31	A	2526	ARG	1	0.886	0.931	40.597	0.019	0.019	0.000	0.000	0.000	0.000
32	A	2527	GLN	0	-0.024	-0.009	40.963	0.001	0.001	0.000	0.000	0.000	0.000
33	A	2528	GLN	0	-0.028	-0.001	43.314	0.000	0.000	0.000	0.000	0.000	0.000
34	A	2529	GLN	0	-0.043	-0.001	47.060	-0.001	-0.001	0.000	0.000	0.000	0.000

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