FMO DATABASE

FMODB ID: LN4M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-168453.475909
FMO2-HF: Nuclear repulsion	151279.660746
FMO2-HF: Total energy	-17173.815163
FMO2-MP2: Total energy	-17217.907833

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.
-16.657	-12.111	6.482	-5.373	-5.655	-0.044

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 : 0.018 / q_NPA : 0.004

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	X	3	GLY	0	0.079	0.040	3.540	0.542	1.456	0.008	-0.396	-0.525	0.001
4	X	4	CYS	0	-0.077	0.022	2.450	1.418	2.562	0.303	-0.504	-0.943	0.002
5	X	5	ASN	0	-0.024	-0.042	1.997	-11.408	-10.704	5.881	-3.612	-2.973	-0.046
6	X	6	GLY	0	0.020	0.000	4.693	0.954	1.011	-0.001	-0.009	-0.048	0.000
7	X	7	PRO	0	-0.013	-0.008	7.192	-0.018	-0.018	0.000	0.000	0.000	0.000
8	X	8	TRP	0	-0.080	-0.047	10.258	0.116	0.116	0.000	0.000	0.000	0.000
9	X	9	ASP	-1	-0.875	-0.923	7.839	-1.470	-1.470	0.000	0.000	0.000	0.000
10	X	10	GLU	-1	-0.858	-0.916	6.800	-1.498	-1.498	0.000	0.000	0.000	0.000
11	X	11	ASP	-1	-0.819	-0.915	7.133	-0.685	-0.685	0.000	0.000	0.000	0.000
12	X	12	ASP	-1	-0.783	-0.912	8.209	-0.729	-0.729	0.000	0.000	0.000	0.000
13	X	13	MET	0	-0.053	-0.019	9.686	0.171	0.171	0.000	0.000	0.000	0.000
14	X	14	GLN	0	-0.042	-0.019	6.501	-0.067	-0.067	0.000	0.000	0.000	0.000
15	X	15	CYS	0	0.059	0.060	3.843	-2.284	-1.773	0.005	-0.255	-0.261	0.002
16	X	16	HIS	0	0.010	0.002	7.994	0.394	0.394	0.000	0.000	0.000	0.000
17	X	17	ASN	0	-0.066	-0.053	11.647	0.188	0.188	0.000	0.000	0.000	0.000
18	X	18	HIS	0	0.042	0.028	7.447	-0.095	-0.095	0.000	0.000	0.000	0.000
19	X	19	CYS	0	0.003	0.025	9.080	-0.060	-0.060	0.000	0.000	0.000	0.000
20	X	20	LYS	1	0.824	0.909	11.550	0.059	0.059	0.000	0.000	0.000	0.000
21	X	21	SER	0	-0.082	-0.039	12.377	0.013	0.013	0.000	0.000	0.000	0.000
22	X	22	ILE	0	-0.017	0.011	10.370	0.032	0.032	0.000	0.000	0.000	0.000
23	X	23	LYS	1	0.981	0.973	14.938	-0.158	-0.158	0.000	0.000	0.000	0.000
24	X	24	GLY	0	-0.002	-0.002	17.919	0.028	0.028	0.000	0.000	0.000	0.000
25	X	25	TYR	0	-0.027	0.001	12.250	-0.011	-0.011	0.000	0.000	0.000	0.000
26	X	26	LYS	1	0.902	0.932	16.809	-0.065	-0.065	0.000	0.000	0.000	0.000
27	X	27	GLY	0	0.014	-0.007	14.818	-0.053	-0.053	0.000	0.000	0.000	0.000
28	X	28	GLY	0	0.024	-0.006	10.926	0.118	0.118	0.000	0.000	0.000	0.000
29	X	29	TYR	0	-0.002	0.012	9.853	-0.037	-0.037	0.000	0.000	0.000	0.000
30	X	31	ALA	0	0.009	-0.009	6.923	0.058	0.058	0.000	0.000	0.000	0.000
31	X	32	LYS	1	0.887	0.924	7.290	-0.421	-0.421	0.000	0.000	0.000	0.000
32	X	33	GLY	0	0.059	0.023	8.505	-0.062	-0.062	0.000	0.000	0.000	0.000
33	X	34	GLY	0	0.124	0.064	7.197	-0.035	-0.035	0.000	0.000	0.000	0.000
34	X	35	PHE	0	-0.064	-0.012	4.058	-0.884	-0.828	-0.001	-0.012	-0.043	0.000
35	X	36	VAL	0	-0.037	-0.011	3.033	-0.732	0.428	0.287	-0.585	-0.862	-0.003
36	X	38	LYS	1	0.874	0.935	5.446	0.020	0.020	0.000	0.000	0.000	0.000
37	X	40	TYR	0	0.045	0.026	11.654	0.004	0.004	0.000	0.000	0.000	0.000

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