FMO DATABASE

FMODB ID: 3JR3L

Calculation Name: 3E7U-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E7U

Chain ID: X

ChEMBL ID:

UniProt ID: Q53I06

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	37
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-168682.423836
FMO2-HF: Nuclear repulsion	151508.788816
FMO2-HF: Total energy	-17173.63502
FMO2-MP2: Total energy	-17217.723076

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(X:1:GLY)

Summations of interaction energy for fragment #1(X:1: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.
-16.304	-11.594	6.472	-5.445	-5.736	-0.045

Interaction energy analysis for fragmet #1(X:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.005

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

Sort

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	X	3	GLY	0	0.073	0.029	3.542	0.477	1.399	0.008	-0.403	-0.528	0.001
4	X	4	CYS	0	-0.075	0.033	2.407	1.316	2.461	0.351	-0.527	-0.969	0.002
5	X	5	ASN	0	0.018	-0.005	2.000	-10.998	-10.114	5.825	-3.672	-3.036	-0.047
6	X	6	GLY	0	0.021	0.001	4.699	0.936	0.995	-0.001	-0.009	-0.048	0.000
7	X	7	PRO	0	-0.016	-0.005	7.196	-0.013	-0.013	0.000	0.000	0.000	0.000
8	X	8	TRP	0	-0.067	-0.043	10.236	0.122	0.122	0.000	0.000	0.000	0.000
9	X	9	ASP	-1	-0.931	-0.963	7.997	-1.371	-1.371	0.000	0.000	0.000	0.000
10	X	10	GLU	-1	-0.880	-0.935	6.803	-1.522	-1.522	0.000	0.000	0.000	0.000
11	X	11	ASP	-1	-0.835	-0.933	7.146	-0.701	-0.701	0.000	0.000	0.000	0.000
12	X	12	ASP	-1	-0.792	-0.925	8.207	-0.797	-0.797	0.000	0.000	0.000	0.000
13	X	13	MET	0	-0.038	-0.013	9.683	0.165	0.165	0.000	0.000	0.000	0.000
14	X	14	GLN	0	-0.059	-0.019	6.666	0.033	0.033	0.000	0.000	0.000	0.000
15	X	15	CYS	0	0.061	0.056	3.858	-2.214	-1.719	0.005	-0.243	-0.257	0.002
16	X	16	HIS	0	0.020	0.007	7.994	0.384	0.384	0.000	0.000	0.000	0.000
17	X	17	ASN	0	-0.023	-0.023	11.674	0.183	0.183	0.000	0.000	0.000	0.000
18	X	18	HIS	0	0.037	0.028	7.679	-0.077	-0.077	0.000	0.000	0.000	0.000
19	X	19	CYS	0	0.005	0.023	9.072	-0.059	-0.059	0.000	0.000	0.000	0.000
20	X	20	LYS	1	0.813	0.894	11.548	0.061	0.061	0.000	0.000	0.000	0.000
21	X	21	SER	0	-0.086	-0.037	12.411	0.012	0.012	0.000	0.000	0.000	0.000
22	X	22	ILE	0	-0.024	0.005	10.426	0.034	0.034	0.000	0.000	0.000	0.000
23	X	23	LYS	1	0.980	0.973	14.936	-0.159	-0.159	0.000	0.000	0.000	0.000
24	X	24	GLY	0	0.000	-0.001	17.917	0.028	0.028	0.000	0.000	0.000	0.000
25	X	25	TYR	0	-0.017	0.008	12.671	-0.004	-0.004	0.000	0.000	0.000	0.000
26	X	26	LYS	1	0.912	0.935	16.807	-0.064	-0.064	0.000	0.000	0.000	0.000
27	X	27	GLY	0	0.002	-0.004	14.818	-0.053	-0.053	0.000	0.000	0.000	0.000
28	X	28	GLY	0	0.028	-0.002	10.920	0.116	0.116	0.000	0.000	0.000	0.000
29	X	29	TYR	0	-0.020	-0.010	9.836	-0.046	-0.046	0.000	0.000	0.000	0.000
30	X	31	ALA	0	0.001	-0.007	6.917	0.061	0.061	0.000	0.000	0.000	0.000
31	X	32	LYS	1	0.880	0.921	7.286	-0.411	-0.411	0.000	0.000	0.000	0.000
32	X	33	GLY	0	0.065	0.024	8.503	-0.065	-0.065	0.000	0.000	0.000	0.000
33	X	34	GLY	0	0.119	0.066	7.196	-0.029	-0.029	0.000	0.000	0.000	0.000
34	X	35	PHE	0	-0.049	-0.005	4.066	-0.875	-0.819	-0.001	-0.012	-0.043	0.000
35	X	36	VAL	0	-0.035	-0.009	3.032	-0.793	0.356	0.285	-0.579	-0.855	-0.003
36	X	38	LYS	1	0.899	0.955	5.439	0.014	0.014	0.000	0.000	0.000	0.000
37	X	40	TYR	0	0.042	0.021	11.654	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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