FMO DATABASE

FMODB ID: 4JK5N

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-286732.178855
FMO2-HF: Nuclear repulsion	262800.694235
FMO2-HF: Total energy	-23931.484619
FMO2-MP2: Total energy	-23997.662314

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.
-0.853	0.632	-0.01	-0.819	-0.656	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

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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	-0.013	-0.006	3.833	-0.475	1.010	-0.010	-0.819	-0.656	0.003
4	B	10	MET	0	0.008	0.010	6.760	0.384	0.384	0.000	0.000	0.000	0.000
5	B	11	ARG	1	0.885	0.929	8.559	1.244	1.244	0.000	0.000	0.000	0.000
6	B	12	THR	0	-0.032	-0.014	11.308	0.152	0.152	0.000	0.000	0.000	0.000
7	B	13	ILE	0	0.046	0.034	12.212	-0.040	-0.040	0.000	0.000	0.000	0.000
8	B	14	SER	0	0.034	0.042	14.771	0.028	0.028	0.000	0.000	0.000	0.000
9	B	15	TYR	0	0.096	0.019	17.873	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	16	SER	0	-0.060	-0.032	20.607	-0.006	-0.006	0.000	0.000	0.000	0.000
11	B	17	GLU	-1	-0.902	-0.949	13.862	-0.214	-0.214	0.000	0.000	0.000	0.000
12	B	18	ALA	0	0.043	0.010	18.550	-0.015	-0.015	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.836	0.915	19.381	0.083	0.083	0.000	0.000	0.000	0.000
14	B	20	GLN	0	-0.029	-0.023	20.908	0.012	0.012	0.000	0.000	0.000	0.000
15	B	21	ASN	0	0.015	0.028	16.835	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	22	LEU	0	0.026	0.041	18.243	-0.057	-0.057	0.000	0.000	0.000	0.000
17	B	23	SER	0	0.050	0.015	20.069	-0.042	-0.042	0.000	0.000	0.000	0.000
18	B	24	ALA	0	0.054	0.019	15.605	-0.023	-0.023	0.000	0.000	0.000	0.000
19	B	25	THR	0	-0.027	-0.036	15.602	-0.083	-0.083	0.000	0.000	0.000	0.000
20	B	26	MET	0	-0.040	-0.028	16.683	-0.039	-0.039	0.000	0.000	0.000	0.000
21	B	27	MET	0	0.001	0.010	17.104	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	28	LYS	1	0.871	0.955	9.522	1.522	1.522	0.000	0.000	0.000	0.000
23	B	29	ALA	0	-0.042	-0.022	14.747	-0.081	-0.081	0.000	0.000	0.000	0.000
24	B	30	VAL	0	-0.005	-0.013	16.806	0.004	0.004	0.000	0.000	0.000	0.000
25	B	31	GLU	-1	-0.970	-0.986	14.142	-0.629	-0.629	0.000	0.000	0.000	0.000
26	B	32	ASP	-1	-0.845	-0.924	11.813	-1.587	-1.587	0.000	0.000	0.000	0.000
27	B	33	HIS	0	-0.046	-0.001	14.638	0.041	0.041	0.000	0.000	0.000	0.000
28	B	34	ALA	0	0.037	0.021	14.328	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	35	PRO	0	0.001	0.006	16.364	-0.024	-0.024	0.000	0.000	0.000	0.000
30	B	36	ILE	0	-0.065	-0.036	13.741	-0.090	-0.090	0.000	0.000	0.000	0.000
31	B	37	LEU	0	-0.028	-0.008	15.498	0.077	0.077	0.000	0.000	0.000	0.000
32	B	38	ILE	0	0.010	-0.011	16.410	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	39	THR	0	0.020	-0.003	17.236	0.033	0.033	0.000	0.000	0.000	0.000
34	B	40	ARG	1	0.954	0.954	19.761	0.120	0.120	0.000	0.000	0.000	0.000
35	B	41	GLN	0	-0.036	0.002	22.725	0.009	0.009	0.000	0.000	0.000	0.000
36	B	42	ASN	0	-0.009	-0.019	23.858	0.004	0.004	0.000	0.000	0.000	0.000
37	B	43	GLY	0	-0.030	-0.011	27.364	0.001	0.001	0.000	0.000	0.000	0.000
38	B	44	GLU	-1	-0.827	-0.900	26.079	-0.106	-0.106	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.078	-0.044	21.061	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	46	CYS	0	-0.011	-0.004	22.080	0.012	0.012	0.000	0.000	0.000	0.000
41	B	47	VAL	0	0.023	0.011	19.647	-0.023	-0.023	0.000	0.000	0.000	0.000
42	B	48	LEU	0	-0.035	-0.003	19.165	0.032	0.032	0.000	0.000	0.000	0.000
43	B	49	MET	0	-0.002	0.002	19.327	-0.049	-0.049	0.000	0.000	0.000	0.000
44	B	50	SER	0	0.033	0.036	21.089	0.043	0.043	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.047	0.022	22.761	0.012	0.012	0.000	0.000	0.000	0.000
46	B	52	GLU	-1	-0.892	-0.961	24.427	-0.308	-0.308	0.000	0.000	0.000	0.000
47	B	53	GLU	-1	-0.871	-0.950	19.918	-0.502	-0.502	0.000	0.000	0.000	0.000
48	B	54	TYR	0	-0.063	-0.038	23.960	0.013	0.013	0.000	0.000	0.000	0.000
49	B	55	ASN	0	0.051	0.005	26.388	0.022	0.022	0.000	0.000	0.000	0.000
50	B	56	SER	0	0.005	0.028	26.039	0.021	0.021	0.000	0.000	0.000	0.000
51	B	57	LEU	0	-0.002	-0.014	24.179	0.012	0.012	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.895	-0.966	27.601	-0.164	-0.164	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.954	-0.977	31.116	-0.199	-0.199	0.000	0.000	0.000	0.000
54	B	60	THR	0	-0.066	-0.029	29.135	0.011	0.011	0.000	0.000	0.000	0.000
55	B	61	ALA	0	-0.073	-0.029	31.044	0.013	0.013	0.000	0.000	0.000	0.000
56	B	62	TYR	0	-0.028	-0.009	32.656	0.019	0.019	0.000	0.000	0.000	0.000
57	B	63	LEU	0	-0.125	-0.051	34.890	0.010	0.010	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.027	-0.004	35.174	0.009	0.009	0.000	0.000	0.000	0.000

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