FMO DATABASE

FMODB ID: R8K68

Calculation Name: 2A6Q-E-Xray372

Preferred Name: Antitoxin YefM

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6Q

Chain ID: E

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	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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-644658.94741
FMO2-HF: Nuclear repulsion	609210.232796
FMO2-HF: Total energy	-35448.714614
FMO2-MP2: Total energy	-35553.639016

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(E:1:MET)

Summations of interaction energy for fragment #1(E:1:MET)

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.
-18.475	-14.275	18.602	-5.779	-17.021	-0.032

Interaction energy analysis for fragmet #1(E:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.043

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	E	3	LEU	0	-0.008	-0.009	2.786	-4.073	-0.661	0.379	-1.830	-1.962	-0.005
4	E	4	ILE	0	0.027	0.025	5.305	-0.023	0.064	-0.001	-0.004	-0.082	0.000
5	E	5	TRP	0	-0.018	-0.021	7.804	0.195	0.195	0.000	0.000	0.000	0.000
6	E	6	SER	0	0.019	0.024	10.896	-0.044	-0.044	0.000	0.000	0.000	0.000
7	E	7	GLU	-1	-0.873	-0.953	14.191	0.098	0.098	0.000	0.000	0.000	0.000
8	E	8	GLU	-1	-0.857	-0.928	17.271	0.097	0.097	0.000	0.000	0.000	0.000
9	E	9	SER	0	-0.038	-0.022	12.247	0.021	0.021	0.000	0.000	0.000	0.000
10	E	10	TRP	0	-0.014	-0.009	12.884	0.071	0.071	0.000	0.000	0.000	0.000
11	E	11	ASP	-1	-0.826	-0.913	15.526	0.163	0.163	0.000	0.000	0.000	0.000
12	E	12	ASP	-1	-0.870	-0.942	16.748	0.228	0.228	0.000	0.000	0.000	0.000
13	E	13	TYR	0	-0.081	-0.087	13.565	0.017	0.017	0.000	0.000	0.000	0.000
14	E	14	LEU	0	0.029	0.000	16.597	0.014	0.014	0.000	0.000	0.000	0.000
15	E	15	TYR	0	0.045	0.032	19.316	-0.016	-0.016	0.000	0.000	0.000	0.000
16	E	16	TRP	0	-0.024	-0.048	17.975	-0.020	-0.020	0.000	0.000	0.000	0.000
17	E	17	GLN	0	0.001	-0.011	17.266	-0.010	-0.010	0.000	0.000	0.000	0.000
18	E	18	GLU	-1	-0.982	-0.975	20.828	0.178	0.178	0.000	0.000	0.000	0.000
19	E	19	THR	0	-0.046	-0.005	23.793	-0.022	-0.022	0.000	0.000	0.000	0.000
20	E	20	ASP	-1	-0.860	-0.956	23.634	0.207	0.207	0.000	0.000	0.000	0.000
21	E	21	LYS	1	0.952	0.969	18.841	-0.315	-0.315	0.000	0.000	0.000	0.000
22	E	22	ARG	1	0.940	0.968	20.942	-0.183	-0.183	0.000	0.000	0.000	0.000
23	E	23	ILE	0	-0.010	-0.004	19.218	0.028	0.028	0.000	0.000	0.000	0.000
24	E	24	VAL	0	-0.016	0.028	16.862	0.046	0.046	0.000	0.000	0.000	0.000
25	E	25	LYS	1	0.901	0.947	16.070	-0.325	-0.325	0.000	0.000	0.000	0.000
26	E	26	LYS	1	0.912	0.969	15.904	-0.270	-0.270	0.000	0.000	0.000	0.000
27	E	27	ILE	0	0.080	0.048	12.649	0.062	0.062	0.000	0.000	0.000	0.000
28	E	28	ASN	0	0.023	0.021	11.568	0.150	0.150	0.000	0.000	0.000	0.000
29	E	29	GLU	-1	-0.915	-0.942	10.853	0.666	0.666	0.000	0.000	0.000	0.000
30	E	30	LEU	0	-0.009	0.002	11.466	0.065	0.065	0.000	0.000	0.000	0.000
31	E	31	ILE	0	0.030	0.041	6.693	0.215	0.215	0.000	0.000	0.000	0.000
32	E	32	LYS	1	0.800	0.874	6.620	-0.133	-0.133	0.000	0.000	0.000	0.000
33	E	33	ASP	-1	-0.857	-0.918	7.590	0.740	0.740	0.000	0.000	0.000	0.000
34	E	34	THR	0	-0.018	-0.005	5.243	-0.354	-0.261	-0.001	-0.008	-0.084	0.000
35	E	35	ARG	1	0.855	0.910	2.300	-3.679	-1.300	1.607	-1.353	-2.632	0.002
36	E	36	ARG	1	0.904	0.970	4.332	-1.009	-0.711	0.004	0.001	-0.302	0.000
37	E	37	THR	0	-0.011	-0.022	7.060	-0.414	-0.414	0.000	0.000	0.000	0.000
38	E	38	PRO	0	0.045	0.015	3.171	-0.579	0.003	0.068	-0.121	-0.529	0.000
39	E	39	PHE	0	0.000	-0.015	5.763	-0.003	-0.003	0.000	0.000	0.000	0.000
40	E	40	GLU	-1	-0.912	-0.937	8.927	-0.124	-0.124	0.000	0.000	0.000	0.000
41	E	41	GLY	0	0.044	0.043	10.958	0.158	0.158	0.000	0.000	0.000	0.000
42	E	42	LYS	1	0.917	0.939	13.532	-0.523	-0.523	0.000	0.000	0.000	0.000
43	E	43	GLY	0	0.026	0.002	13.712	0.066	0.066	0.000	0.000	0.000	0.000
44	E	44	LYS	1	0.917	0.970	16.071	-0.152	-0.152	0.000	0.000	0.000	0.000
45	E	45	PRO	0	-0.004	-0.004	11.729	-0.016	-0.016	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.885	-0.937	13.861	0.006	0.006	0.000	0.000	0.000	0.000
47	E	47	PRO	0	-0.018	0.015	13.514	0.033	0.033	0.000	0.000	0.000	0.000
48	E	48	LEU	0	-0.009	-0.010	14.454	0.005	0.005	0.000	0.000	0.000	0.000
49	E	49	LYS	1	0.969	0.969	16.619	0.048	0.048	0.000	0.000	0.000	0.000
50	E	50	HIS	0	0.040	0.020	19.323	0.005	0.005	0.000	0.000	0.000	0.000
51	E	51	ASN	0	0.041	0.018	19.564	-0.029	-0.029	0.000	0.000	0.000	0.000
52	E	52	LEU	0	0.018	0.022	16.986	-0.003	-0.003	0.000	0.000	0.000	0.000
53	E	53	SER	0	-0.036	-0.032	15.576	0.007	0.007	0.000	0.000	0.000	0.000
54	E	54	GLY	0	-0.008	0.001	12.138	-0.028	-0.028	0.000	0.000	0.000	0.000
55	E	55	PHE	0	-0.030	-0.016	10.584	-0.020	-0.020	0.000	0.000	0.000	0.000
56	E	56	TRP	0	0.001	-0.003	9.876	-0.008	-0.008	0.000	0.000	0.000	0.000
57	E	57	SER	0	-0.008	-0.003	12.061	0.092	0.092	0.000	0.000	0.000	0.000
58	E	58	ARG	1	0.812	0.918	9.044	-0.845	-0.845	0.000	0.000	0.000	0.000
59	E	59	ARG	1	0.906	0.939	14.427	-0.192	-0.192	0.000	0.000	0.000	0.000
60	E	60	ILE	0	-0.028	0.014	15.503	0.030	0.030	0.000	0.000	0.000	0.000
61	E	61	THR	0	-0.013	-0.024	18.100	-0.008	-0.008	0.000	0.000	0.000	0.000
62	E	62	GLU	-1	-0.946	-0.980	21.407	0.172	0.172	0.000	0.000	0.000	0.000
63	E	63	GLU	-1	-0.843	-0.877	23.690	0.123	0.123	0.000	0.000	0.000	0.000
64	E	64	HIS	0	0.064	0.042	19.664	0.007	0.007	0.000	0.000	0.000	0.000
65	E	65	ARG	1	0.894	0.932	16.650	-0.186	-0.186	0.000	0.000	0.000	0.000
66	E	66	LEU	0	0.006	0.011	9.747	-0.012	-0.012	0.000	0.000	0.000	0.000
67	E	67	VAL	0	-0.012	-0.009	12.826	0.024	0.024	0.000	0.000	0.000	0.000
68	E	68	TYR	0	-0.001	-0.016	7.078	0.124	0.124	0.000	0.000	0.000	0.000
69	E	69	ALA	0	0.071	0.049	8.318	-0.153	-0.153	0.000	0.000	0.000	0.000
70	E	70	VAL	0	-0.028	-0.024	2.462	0.533	0.274	2.379	-0.446	-1.674	-0.003
71	E	71	THR	0	0.002	0.016	3.699	-0.485	-0.273	0.000	-0.037	-0.175	0.000
72	E	72	ASP	-1	-0.955	-0.989	3.181	-5.472	-4.764	0.061	-0.313	-0.456	-0.003
73	E	73	ASP	-1	-0.769	-0.883	4.450	-2.521	-2.174	-0.001	-0.064	-0.282	0.000
74	E	74	SER	0	-0.119	-0.079	1.843	-2.439	-2.989	8.815	-4.765	-3.499	-0.013
75	E	75	LEU	0	-0.001	-0.011	2.503	2.357	-0.409	5.218	2.669	-5.121	-0.011
76	E	76	LEU	0	-0.020	-0.002	3.620	-0.729	-1.072	0.074	0.492	-0.223	0.001
77	E	77	ILE	0	0.007	-0.004	7.260	0.175	0.175	0.000	0.000	0.000	0.000
78	E	78	ALA	0	0.027	0.012	9.440	-0.123	-0.123	0.000	0.000	0.000	0.000
79	E	79	ALA	0	0.023	0.005	12.954	-0.049	-0.049	0.000	0.000	0.000	0.000
80	E	80	CYS	0	-0.083	-0.023	13.785	0.092	0.092	0.000	0.000	0.000	0.000
81	E	81	ARG	1	0.934	0.986	15.650	-0.171	-0.171	0.000	0.000	0.000	0.000
82	E	82	TYR	0	-0.034	-0.008	19.438	-0.007	-0.007	0.000	0.000	0.000	0.000
83	E	83	HIS	0	-0.044	-0.039	20.736	-0.016	-0.016	0.000	0.000	0.000	0.000
84	E	84	TYR	0	-0.061	-0.059	24.759	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:1:MET)