FMO DATABASE

FMODB ID: YVMJ2

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	OptAll
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	-286503.025528
FMO2-HF: Nuclear repulsion	262571.035899
FMO2-HF: Total energy	-23931.989629
FMO2-MP2: Total energy	-23998.113504

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.
-0.241	1.061	-0.006	-0.68	-0.617	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 : 0.048 / q_NPA : 0.025

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	-0.022	-0.032	3.874	-0.254	1.048	-0.006	-0.680	-0.617	0.003
4	B	10	MET	0	-0.034	-0.009	6.673	0.638	0.638	0.000	0.000	0.000	0.000
5	B	11	ARG	1	0.887	0.920	8.284	1.405	1.405	0.000	0.000	0.000	0.000
6	B	12	THR	0	-0.027	-0.007	11.197	0.139	0.139	0.000	0.000	0.000	0.000
7	B	13	ILE	0	0.033	0.034	11.868	-0.052	-0.052	0.000	0.000	0.000	0.000
8	B	14	SER	0	-0.005	0.002	14.441	0.043	0.043	0.000	0.000	0.000	0.000
9	B	15	TYR	0	0.054	0.008	17.416	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	16	SER	0	-0.035	-0.028	20.857	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	17	GLU	-1	-0.798	-0.890	13.490	-0.195	-0.195	0.000	0.000	0.000	0.000
12	B	18	ALA	0	0.058	0.028	18.450	-0.009	-0.009	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.805	0.902	19.216	0.070	0.070	0.000	0.000	0.000	0.000
14	B	20	GLN	0	-0.010	-0.005	20.643	0.015	0.015	0.000	0.000	0.000	0.000
15	B	21	ASN	0	-0.002	-0.001	16.285	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	22	LEU	0	0.014	0.035	17.857	-0.055	-0.055	0.000	0.000	0.000	0.000
17	B	23	SER	0	0.035	0.012	19.627	-0.042	-0.042	0.000	0.000	0.000	0.000
18	B	24	ALA	0	0.054	0.021	15.132	-0.022	-0.022	0.000	0.000	0.000	0.000
19	B	25	THR	0	-0.039	-0.033	15.147	-0.083	-0.083	0.000	0.000	0.000	0.000
20	B	26	MET	0	-0.033	-0.021	16.361	-0.035	-0.035	0.000	0.000	0.000	0.000
21	B	27	MET	0	-0.003	0.012	17.213	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	28	LYS	1	0.870	0.937	9.157	1.507	1.507	0.000	0.000	0.000	0.000
23	B	29	ALA	0	-0.016	-0.009	14.492	-0.085	-0.085	0.000	0.000	0.000	0.000
24	B	30	VAL	0	-0.001	0.000	16.642	0.016	0.016	0.000	0.000	0.000	0.000
25	B	31	GLU	-1	-0.938	-0.980	13.961	-0.581	-0.581	0.000	0.000	0.000	0.000
26	B	32	ASP	-1	-0.845	-0.895	11.217	-1.651	-1.651	0.000	0.000	0.000	0.000
27	B	33	HIS	0	-0.062	-0.019	14.216	0.032	0.032	0.000	0.000	0.000	0.000
28	B	34	ALA	0	0.027	0.024	14.405	0.010	0.010	0.000	0.000	0.000	0.000
29	B	35	PRO	0	0.024	0.026	15.784	-0.047	-0.047	0.000	0.000	0.000	0.000
30	B	36	ILE	0	-0.055	-0.032	13.173	-0.114	-0.114	0.000	0.000	0.000	0.000
31	B	37	LEU	0	-0.022	-0.008	15.378	0.081	0.081	0.000	0.000	0.000	0.000
32	B	38	ILE	0	0.010	-0.003	16.320	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	39	THR	0	0.008	-0.011	17.124	0.049	0.049	0.000	0.000	0.000	0.000
34	B	40	ARG	1	0.927	0.949	19.480	0.130	0.130	0.000	0.000	0.000	0.000
35	B	41	GLN	0	-0.026	-0.006	22.638	0.010	0.010	0.000	0.000	0.000	0.000
36	B	42	ASN	0	-0.012	-0.020	23.835	0.003	0.003	0.000	0.000	0.000	0.000
37	B	43	GLY	0	0.013	0.010	26.272	0.006	0.006	0.000	0.000	0.000	0.000
38	B	44	GLU	-1	-0.876	-0.928	25.613	-0.124	-0.124	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.050	-0.020	20.932	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	46	CYS	0	-0.035	-0.023	21.850	0.014	0.014	0.000	0.000	0.000	0.000
41	B	47	VAL	0	0.000	-0.006	19.372	-0.023	-0.023	0.000	0.000	0.000	0.000
42	B	48	LEU	0	-0.030	-0.004	18.727	0.034	0.034	0.000	0.000	0.000	0.000
43	B	49	MET	0	-0.017	-0.004	18.739	-0.049	-0.049	0.000	0.000	0.000	0.000
44	B	50	SER	0	0.009	0.005	20.566	0.039	0.039	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.009	0.005	22.196	0.016	0.016	0.000	0.000	0.000	0.000
46	B	52	GLU	-1	-0.875	-0.952	24.281	-0.305	-0.305	0.000	0.000	0.000	0.000
47	B	53	GLU	-1	-0.789	-0.894	19.795	-0.500	-0.500	0.000	0.000	0.000	0.000
48	B	54	TYR	0	-0.096	-0.072	23.825	0.011	0.011	0.000	0.000	0.000	0.000
49	B	55	ASN	0	0.003	-0.005	26.177	0.022	0.022	0.000	0.000	0.000	0.000
50	B	56	SER	0	0.044	0.038	26.036	0.009	0.009	0.000	0.000	0.000	0.000
51	B	57	LEU	0	-0.007	0.004	24.615	0.011	0.011	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.805	-0.883	27.531	-0.163	-0.163	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.939	-0.978	31.010	-0.205	-0.205	0.000	0.000	0.000	0.000
54	B	60	THR	0	-0.073	-0.049	28.848	0.012	0.012	0.000	0.000	0.000	0.000
55	B	61	ALA	0	-0.047	-0.023	31.130	0.012	0.012	0.000	0.000	0.000	0.000
56	B	62	TYR	0	-0.112	-0.067	32.708	0.017	0.017	0.000	0.000	0.000	0.000
57	B	63	LEU	0	-0.067	-0.022	34.819	0.010	0.010	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.080	-0.030	35.062	0.013	0.013	0.000	0.000	0.000	0.000

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