FMO DATABASE

FMODB ID: VQ6J1

Calculation Name: 2A6Q-A-Xray372

Preferred Name: Antitoxin YefM

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6Q

Chain ID: A

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-464964.523368
FMO2-HF: Nuclear repulsion	430131.823562
FMO2-HF: Total energy	-34832.699806
FMO2-MP2: Total energy	-34930.107601

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(A:7:GLY)

Summations of interaction energy for fragment #1(A: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.
-0.312	1.081	0.003	-0.806	-0.59	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.018

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	A	9	HIS	0	0.031	0.021	3.565	-0.980	0.413	0.003	-0.806	-0.590	0.003
4	A	10	MET	0	-0.001	0.017	6.476	0.901	0.901	0.000	0.000	0.000	0.000
5	A	11	ARG	1	0.981	0.998	8.826	0.561	0.561	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.013	0.008	8.386	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.023	0.016	11.413	0.072	0.072	0.000	0.000	0.000	0.000
8	A	14	SER	0	0.049	0.028	14.393	0.017	0.017	0.000	0.000	0.000	0.000
9	A	15	TYR	0	0.048	0.003	16.248	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.000	-0.018	18.378	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.913	-0.937	19.172	-0.240	-0.240	0.000	0.000	0.000	0.000
12	A	18	ALA	0	0.055	0.020	18.302	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.907	0.952	20.391	0.110	0.110	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.065	-0.035	23.321	0.010	0.010	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.025	-0.010	23.073	0.018	0.018	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.035	0.038	22.534	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	23	SER	0	0.012	-0.005	24.060	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.078	0.030	24.723	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.025	-0.019	18.997	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	26	MET	0	-0.040	-0.028	21.071	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	27	MET	0	0.001	-0.001	23.014	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.901	0.947	20.477	0.377	0.377	0.000	0.000	0.000	0.000
23	A	29	ALA	0	-0.018	0.003	19.406	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	30	VAL	0	-0.057	-0.048	20.363	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.988	-0.991	23.532	-0.275	-0.275	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.827	-0.907	19.764	-0.426	-0.426	0.000	0.000	0.000	0.000
27	A	33	HIS	1	0.783	0.917	20.340	0.352	0.352	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.029	0.026	15.671	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	35	PRO	0	-0.043	-0.017	12.434	0.059	0.059	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.007	-0.010	13.011	-0.077	-0.077	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.002	-0.012	7.597	0.051	0.051	0.000	0.000	0.000	0.000
32	A	38	ILE	0	-0.008	0.001	11.676	0.072	0.072	0.000	0.000	0.000	0.000
33	A	39	THR	0	0.009	-0.006	10.154	0.018	0.018	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.916	0.966	13.313	0.025	0.025	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.029	-0.014	14.858	0.037	0.037	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.030	-0.045	16.715	0.008	0.008	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.012	0.012	13.055	0.043	0.043	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.877	-0.926	12.549	0.055	0.055	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.007	-0.005	10.599	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.040	-0.008	12.447	0.008	0.008	0.000	0.000	0.000	0.000
41	A	47	VAL	0	0.024	0.013	10.889	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.030	-0.001	13.526	0.091	0.091	0.000	0.000	0.000	0.000
43	A	49	MET	0	0.028	0.002	14.983	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	50	SER	0	0.054	0.043	18.205	0.046	0.046	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.037	0.009	21.308	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.910	-0.957	23.575	-0.309	-0.309	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.874	-0.946	18.803	-0.520	-0.520	0.000	0.000	0.000	0.000
48	A	54	TYR	0	-0.038	-0.023	18.514	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.017	-0.011	20.280	0.000	0.000	0.000	0.000	0.000	0.000
50	A	56	SER	0	-0.011	0.020	21.482	0.020	0.020	0.000	0.000	0.000	0.000
51	A	57	LEU	0	0.016	0.006	14.870	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	58	GLU	-1	-0.862	-0.939	19.199	-0.289	-0.289	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.854	-0.929	20.888	-0.203	-0.203	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.065	-0.037	19.497	0.021	0.021	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.030	-0.025	18.328	0.015	0.015	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.036	-0.015	20.079	0.041	0.041	0.000	0.000	0.000	0.000
57	A	63	LEU	0	-0.013	-0.002	23.628	0.026	0.026	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.034	-0.020	19.531	0.019	0.019	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.864	0.943	19.157	0.277	0.277	0.000	0.000	0.000	0.000
60	A	66	SER	0	-0.006	0.006	22.482	0.026	0.026	0.000	0.000	0.000	0.000
61	A	67	PRO	0	0.058	0.017	23.733	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.011	-0.008	25.460	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	69	ASN	0	-0.038	-0.027	27.140	0.014	0.014	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.055	0.032	23.257	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.944	0.978	25.306	0.081	0.081	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.976	0.984	27.236	0.101	0.101	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.016	0.017	25.760	0.004	0.004	0.000	0.000	0.000	0.000
68	A	74	MET	0	0.021	-0.004	23.552	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.873	-0.922	26.624	-0.118	-0.118	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.066	-0.039	29.942	0.005	0.005	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.008	-0.012	26.495	0.001	0.001	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.904	-0.941	26.953	-0.178	-0.178	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.059	-0.039	29.497	0.008	0.008	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.005	-0.011	32.027	0.004	0.004	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.932	0.975	24.699	0.252	0.252	0.000	0.000	0.000	0.000
76	A	82	SER	0	-0.084	-0.038	31.550	0.003	0.003	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.001	0.008	33.753	0.008	0.008	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.898	0.949	35.770	0.103	0.103	0.000	0.000	0.000	0.000
79	A	85	GLY	0	-0.002	0.011	38.052	0.003	0.003	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.040	-0.026	38.626	0.005	0.005	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.934	-0.957	41.834	-0.089	-0.089	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.879	0.919	43.924	0.075	0.075	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.828	-0.895	44.799	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	90	ILE	0	-0.057	-0.034	44.400	0.000	0.000	0.000	0.000	0.000	0.000
85	A	91	ILE	0	-0.072	-0.034	46.830	0.003	0.003	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.955	-0.971	49.167	-0.071	-0.071	0.000	0.000	0.000	0.000

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