FMO DATABASE

FMODB ID: 5JQ4Z

Calculation Name: 2A6Q-B-Xray372

Preferred Name: Antitoxin YefM

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6Q

Chain ID: B

ChEMBL ID: CHEMBL3309007

UniProt ID: P69346

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:

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-286839.320606
FMO2-HF: Nuclear repulsion	262907.546604
FMO2-HF: Total energy	-23931.774002
FMO2-MP2: Total energy	-23997.920118

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(B:7:GLY)

Summations of interaction energy for fragment #1(B:7: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.
-1.03	0.471	-0.01	-0.829	-0.662	0.003

Interaction energy analysis for fragmet #1(B:7:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / 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

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	B	9	HIS	0	-0.046	-0.041	3.833	-0.547	0.954	-0.010	-0.829	-0.662	0.003
4	B	10	MET	0	0.010	0.017	6.761	0.384	0.384	0.000	0.000	0.000	0.000
5	B	11	ARG	1	0.871	0.917	8.559	1.216	1.216	0.000	0.000	0.000	0.000
6	B	12	THR	0	-0.034	-0.021	11.305	0.142	0.142	0.000	0.000	0.000	0.000
7	B	13	ILE	0	0.041	0.033	12.211	-0.037	-0.037	0.000	0.000	0.000	0.000
8	B	14	SER	0	0.038	0.044	14.771	0.032	0.032	0.000	0.000	0.000	0.000
9	B	15	TYR	0	0.098	0.020	17.872	-0.008	-0.008	0.000	0.000	0.000	0.000
10	B	16	SER	0	-0.041	-0.031	20.652	-0.006	-0.006	0.000	0.000	0.000	0.000
11	B	17	GLU	-1	-0.880	-0.942	13.752	-0.208	-0.208	0.000	0.000	0.000	0.000
12	B	18	ALA	0	0.043	0.019	18.549	-0.014	-0.014	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.801	0.904	19.380	0.086	0.086	0.000	0.000	0.000	0.000
14	B	20	GLN	0	-0.017	-0.018	20.889	0.011	0.011	0.000	0.000	0.000	0.000
15	B	21	ASN	0	0.002	0.014	16.827	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	22	LEU	0	0.027	0.042	18.242	-0.056	-0.056	0.000	0.000	0.000	0.000
17	B	23	SER	0	0.044	0.012	20.068	-0.041	-0.041	0.000	0.000	0.000	0.000
18	B	24	ALA	0	0.048	0.021	15.644	-0.024	-0.024	0.000	0.000	0.000	0.000
19	B	25	THR	0	-0.022	-0.035	15.537	-0.082	-0.082	0.000	0.000	0.000	0.000
20	B	26	MET	0	-0.041	-0.025	16.683	-0.038	-0.038	0.000	0.000	0.000	0.000
21	B	27	MET	0	0.003	0.007	17.339	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	28	LYS	1	0.872	0.946	9.485	1.448	1.448	0.000	0.000	0.000	0.000
23	B	29	ALA	0	-0.026	-0.010	14.743	-0.078	-0.078	0.000	0.000	0.000	0.000
24	B	30	VAL	0	-0.006	-0.014	16.807	0.004	0.004	0.000	0.000	0.000	0.000
25	B	31	GLU	-1	-0.952	-0.975	14.180	-0.613	-0.613	0.000	0.000	0.000	0.000
26	B	32	ASP	-1	-0.854	-0.905	11.542	-1.609	-1.609	0.000	0.000	0.000	0.000
27	B	33	HIS	0	-0.035	-0.002	14.631	0.036	0.036	0.000	0.000	0.000	0.000
28	B	34	ALA	0	0.018	0.014	14.358	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	35	PRO	0	0.043	0.034	16.364	-0.022	-0.022	0.000	0.000	0.000	0.000
30	B	36	ILE	0	-0.076	-0.040	13.736	-0.095	-0.095	0.000	0.000	0.000	0.000
31	B	37	LEU	0	-0.022	-0.004	15.497	0.077	0.077	0.000	0.000	0.000	0.000
32	B	38	ILE	0	0.008	-0.011	16.410	-0.007	-0.007	0.000	0.000	0.000	0.000
33	B	39	THR	0	0.032	0.002	17.413	0.031	0.031	0.000	0.000	0.000	0.000
34	B	40	ARG	1	0.945	0.953	19.761	0.123	0.123	0.000	0.000	0.000	0.000
35	B	41	GLN	0	-0.049	-0.011	22.888	0.013	0.013	0.000	0.000	0.000	0.000
36	B	42	ASN	0	0.000	-0.007	23.858	0.002	0.002	0.000	0.000	0.000	0.000
37	B	43	GLY	0	-0.019	-0.008	27.370	0.001	0.001	0.000	0.000	0.000	0.000
38	B	44	GLU	-1	-0.834	-0.908	26.077	-0.111	-0.111	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.082	-0.042	21.078	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	46	CYS	0	-0.021	-0.009	22.085	0.012	0.012	0.000	0.000	0.000	0.000
41	B	47	VAL	0	0.017	0.006	19.606	-0.023	-0.023	0.000	0.000	0.000	0.000
42	B	48	LEU	0	-0.033	-0.003	18.999	0.031	0.031	0.000	0.000	0.000	0.000
43	B	49	MET	0	-0.008	-0.001	19.327	-0.046	-0.046	0.000	0.000	0.000	0.000
44	B	50	SER	0	0.026	0.030	21.080	0.041	0.041	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.037	0.019	22.761	0.012	0.012	0.000	0.000	0.000	0.000
46	B	52	GLU	-1	-0.885	-0.957	24.413	-0.309	-0.309	0.000	0.000	0.000	0.000
47	B	53	GLU	-1	-0.852	-0.944	19.969	-0.492	-0.492	0.000	0.000	0.000	0.000
48	B	54	TYR	0	-0.102	-0.077	23.960	0.012	0.012	0.000	0.000	0.000	0.000
49	B	55	ASN	0	0.033	-0.002	26.388	0.022	0.022	0.000	0.000	0.000	0.000
50	B	56	SER	0	0.013	0.033	26.052	0.009	0.009	0.000	0.000	0.000	0.000
51	B	57	LEU	0	-0.005	-0.008	24.507	0.013	0.013	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.846	-0.918	27.601	-0.165	-0.165	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.931	-0.972	31.116	-0.203	-0.203	0.000	0.000	0.000	0.000
54	B	60	THR	0	-0.078	-0.040	28.957	0.011	0.011	0.000	0.000	0.000	0.000
55	B	61	ALA	0	-0.065	-0.024	30.997	0.013	0.013	0.000	0.000	0.000	0.000
56	B	62	TYR	0	-0.031	-0.009	32.656	0.018	0.018	0.000	0.000	0.000	0.000
57	B	63	LEU	0	-0.101	-0.036	34.893	0.010	0.010	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.063	-0.027	35.164	0.010	0.010	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:7:GLY)