FMO DATABASE

FMODB ID: QV4ZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-643904.607458
FMO2-HF: Nuclear repulsion	608455.366849
FMO2-HF: Total energy	-35449.240609
FMO2-MP2: Total energy	-35554.12205

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.
-27.117	-19.989	13.804	-5.504	-15.428	-0.022

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 : 0.029 / q_NPA : 0.031

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	-0.010	-0.008	2.972	-2.276	0.649	0.170	-1.453	-1.642	-0.005
4	E	4	ILE	0	0.018	0.018	5.527	-0.157	-0.157	0.000	0.000	0.000	0.000
5	E	5	TRP	0	-0.010	-0.018	7.978	0.355	0.355	0.000	0.000	0.000	0.000
6	E	6	SER	0	-0.013	-0.020	11.087	-0.083	-0.083	0.000	0.000	0.000	0.000
7	E	7	GLU	-1	-0.875	-0.952	14.360	0.114	0.114	0.000	0.000	0.000	0.000
8	E	8	GLU	-1	-0.816	-0.883	17.487	0.181	0.181	0.000	0.000	0.000	0.000
9	E	9	SER	0	-0.046	-0.036	12.544	0.023	0.023	0.000	0.000	0.000	0.000
10	E	10	TRP	0	-0.013	-0.007	13.311	0.107	0.107	0.000	0.000	0.000	0.000
11	E	11	ASP	-1	-0.831	-0.916	15.745	0.237	0.237	0.000	0.000	0.000	0.000
12	E	12	ASP	-1	-0.832	-0.923	16.921	0.412	0.412	0.000	0.000	0.000	0.000
13	E	13	TYR	0	-0.069	-0.085	14.018	0.018	0.018	0.000	0.000	0.000	0.000
14	E	14	LEU	0	0.015	-0.001	16.825	0.023	0.023	0.000	0.000	0.000	0.000
15	E	15	TYR	0	0.040	0.027	19.551	-0.015	-0.015	0.000	0.000	0.000	0.000
16	E	16	TRP	0	-0.012	-0.039	18.235	-0.030	-0.030	0.000	0.000	0.000	0.000
17	E	17	GLN	0	-0.029	-0.008	17.121	-0.004	-0.004	0.000	0.000	0.000	0.000
18	E	18	GLU	-1	-0.986	-0.977	21.062	0.246	0.246	0.000	0.000	0.000	0.000
19	E	19	THR	0	-0.038	-0.008	24.025	-0.035	-0.035	0.000	0.000	0.000	0.000
20	E	20	ASP	-1	-0.803	-0.914	23.856	0.365	0.365	0.000	0.000	0.000	0.000
21	E	21	LYS	1	0.944	0.963	19.972	-0.452	-0.452	0.000	0.000	0.000	0.000
22	E	22	ARG	1	0.856	0.915	20.982	-0.313	-0.313	0.000	0.000	0.000	0.000
23	E	23	ILE	0	-0.019	-0.012	19.507	0.057	0.057	0.000	0.000	0.000	0.000
24	E	24	VAL	0	0.015	0.036	16.871	0.085	0.085	0.000	0.000	0.000	0.000
25	E	25	LYS	1	0.923	0.958	16.111	-0.533	-0.533	0.000	0.000	0.000	0.000
26	E	26	LYS	1	0.883	0.950	15.935	-0.490	-0.490	0.000	0.000	0.000	0.000
27	E	27	ILE	0	0.074	0.046	13.053	0.123	0.123	0.000	0.000	0.000	0.000
28	E	28	ASN	0	0.032	0.027	11.609	0.238	0.238	0.000	0.000	0.000	0.000
29	E	29	GLU	-1	-0.865	-0.919	10.881	1.458	1.458	0.000	0.000	0.000	0.000
30	E	30	LEU	0	0.008	0.006	11.482	0.167	0.167	0.000	0.000	0.000	0.000
31	E	31	ILE	0	0.036	0.045	6.771	0.338	0.338	0.000	0.000	0.000	0.000
32	E	32	LYS	1	0.824	0.888	6.644	-0.430	-0.430	0.000	0.000	0.000	0.000
33	E	33	ASP	-1	-0.860	-0.932	7.587	1.616	1.616	0.000	0.000	0.000	0.000
34	E	34	THR	0	-0.016	-0.013	5.180	-0.429	-0.331	-0.001	-0.009	-0.087	0.000
35	E	35	ARG	1	0.867	0.924	2.180	-10.403	-8.013	2.078	-1.605	-2.863	0.008
36	E	36	ARG	1	0.906	0.969	4.328	-1.750	-1.450	0.010	0.036	-0.346	0.000
37	E	37	THR	0	0.003	-0.008	6.881	-0.696	-0.696	0.000	0.000	0.000	0.000
38	E	38	PRO	0	0.049	0.017	2.759	-0.807	-0.086	0.358	-0.194	-0.886	-0.001
39	E	39	PHE	0	-0.003	-0.010	5.318	-0.020	0.035	-0.001	-0.002	-0.052	0.000
40	E	40	GLU	-1	-0.910	-0.938	8.551	0.106	0.106	0.000	0.000	0.000	0.000
41	E	41	GLY	0	0.031	0.026	10.459	0.246	0.246	0.000	0.000	0.000	0.000
42	E	42	LYS	1	0.823	0.909	12.990	-1.329	-1.329	0.000	0.000	0.000	0.000
43	E	43	GLY	0	0.021	0.003	13.564	0.095	0.095	0.000	0.000	0.000	0.000
44	E	44	LYS	1	0.928	0.974	15.937	-0.347	-0.347	0.000	0.000	0.000	0.000
45	E	45	PRO	0	0.004	0.006	11.346	-0.030	-0.030	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.911	-0.949	13.524	0.153	0.153	0.000	0.000	0.000	0.000
47	E	47	PRO	0	-0.010	0.018	13.334	0.043	0.043	0.000	0.000	0.000	0.000
48	E	48	LEU	0	-0.022	-0.015	14.328	-0.014	-0.014	0.000	0.000	0.000	0.000
49	E	49	LYS	1	0.971	0.970	16.599	-0.075	-0.075	0.000	0.000	0.000	0.000
50	E	50	HIS	0	0.051	0.025	19.353	0.006	0.006	0.000	0.000	0.000	0.000
51	E	51	ASN	0	0.046	0.028	19.716	-0.028	-0.028	0.000	0.000	0.000	0.000
52	E	52	LEU	0	0.014	0.017	17.167	-0.002	-0.002	0.000	0.000	0.000	0.000
53	E	53	SER	0	-0.035	-0.035	15.687	0.025	0.025	0.000	0.000	0.000	0.000
54	E	54	GLY	0	-0.009	0.000	12.283	-0.034	-0.034	0.000	0.000	0.000	0.000
55	E	55	PHE	0	-0.038	-0.018	10.714	0.019	0.019	0.000	0.000	0.000	0.000
56	E	56	TRP	0	-0.005	-0.010	9.845	-0.030	-0.030	0.000	0.000	0.000	0.000
57	E	57	SER	0	-0.001	-0.001	11.973	0.112	0.112	0.000	0.000	0.000	0.000
58	E	58	ARG	1	0.828	0.927	8.575	-1.441	-1.441	0.000	0.000	0.000	0.000
59	E	59	ARG	1	0.912	0.944	14.342	-0.390	-0.390	0.000	0.000	0.000	0.000
60	E	60	ILE	0	-0.022	0.018	15.591	0.054	0.054	0.000	0.000	0.000	0.000
61	E	61	THR	0	0.006	-0.013	18.011	-0.012	-0.012	0.000	0.000	0.000	0.000
62	E	62	GLU	-1	-0.905	-0.961	21.327	0.343	0.343	0.000	0.000	0.000	0.000
63	E	63	GLU	-1	-0.861	-0.885	23.613	0.251	0.251	0.000	0.000	0.000	0.000
64	E	64	HIS	0	0.035	0.023	19.747	0.025	0.025	0.000	0.000	0.000	0.000
65	E	65	ARG	1	0.869	0.919	16.590	-0.369	-0.369	0.000	0.000	0.000	0.000
66	E	66	LEU	0	0.010	0.011	9.709	-0.014	-0.014	0.000	0.000	0.000	0.000
67	E	67	VAL	0	-0.011	-0.010	12.792	0.037	0.037	0.000	0.000	0.000	0.000
68	E	68	TYR	0	-0.009	-0.019	6.875	0.159	0.159	0.000	0.000	0.000	0.000
69	E	69	ALA	0	0.067	0.044	8.408	-0.191	-0.191	0.000	0.000	0.000	0.000
70	E	70	VAL	0	-0.038	-0.029	2.584	0.117	0.420	1.578	-0.341	-1.540	-0.002
71	E	71	THR	0	0.021	0.023	4.177	-0.689	-0.542	-0.001	-0.020	-0.126	0.000
72	E	72	ASP	-1	-0.935	-0.972	3.435	-4.856	-4.355	0.016	-0.200	-0.316	-0.002
73	E	73	ASP	-1	-0.755	-0.850	4.689	-3.346	-3.104	-0.001	-0.047	-0.194	0.000
74	E	74	SER	0	-0.136	-0.098	2.029	-3.273	-2.683	5.784	-3.427	-2.947	-0.011
75	E	75	LEU	0	-0.001	-0.006	2.604	1.476	0.451	3.763	1.519	-4.258	-0.009
76	E	76	LEU	0	-0.015	0.000	3.703	-0.912	-1.031	0.051	0.239	-0.171	0.000
77	E	77	ILE	0	0.007	-0.005	7.372	0.213	0.213	0.000	0.000	0.000	0.000
78	E	78	ALA	0	0.027	0.023	9.600	-0.179	-0.179	0.000	0.000	0.000	0.000
79	E	79	ALA	0	0.012	0.008	13.102	-0.080	-0.080	0.000	0.000	0.000	0.000
80	E	80	CYS	0	-0.102	-0.046	13.882	0.149	0.149	0.000	0.000	0.000	0.000
81	E	81	ARG	1	0.945	0.999	15.834	-0.292	-0.292	0.000	0.000	0.000	0.000
82	E	82	TYR	0	-0.048	-0.015	19.620	-0.009	-0.009	0.000	0.000	0.000	0.000
83	E	83	HIS	0	-0.035	-0.039	20.786	-0.030	-0.030	0.000	0.000	0.000	0.000
84	E	84	TYR	0	-0.044	-0.042	24.925	-0.014	-0.014	0.000	0.000	0.000	0.000

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