FMO DATABASE

FMODB ID: 1N38Z

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:

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-465273.884717
FMO2-HF: Nuclear repulsion	430440.681694
FMO2-HF: Total energy	-34833.203022
FMO2-MP2: Total energy	-34930.588408

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.
-0.102	1.403	0.011	-0.87	-0.646	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 : 0.039 / q_NPA : 0.022

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	0.021	0.016	3.329	-0.694	0.811	0.011	-0.870	-0.646	0.003
4	A	10	MET	0	-0.008	0.011	6.480	0.887	0.887	0.000	0.000	0.000	0.000
5	A	11	ARG	1	0.994	1.007	8.828	0.524	0.524	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.031	0.016	8.422	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	13	ILE	0	-0.027	-0.008	11.415	0.073	0.073	0.000	0.000	0.000	0.000
8	A	14	SER	0	0.053	0.030	14.394	0.018	0.018	0.000	0.000	0.000	0.000
9	A	15	TYR	0	0.060	0.008	16.249	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.002	-0.014	18.379	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.909	-0.938	18.662	-0.248	-0.248	0.000	0.000	0.000	0.000
12	A	18	ALA	0	0.056	0.026	18.286	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.916	0.948	20.393	0.111	0.111	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.063	-0.028	23.322	0.012	0.012	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.034	-0.018	23.158	0.016	0.016	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.035	0.047	22.525	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	23	SER	0	0.045	0.007	24.062	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.032	0.013	24.783	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.019	-0.027	19.002	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	26	MET	0	-0.037	-0.024	21.073	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	27	MET	0	0.000	-0.001	23.016	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.839	0.931	20.788	0.349	0.349	0.000	0.000	0.000	0.000
23	A	29	ALA	0	0.005	0.012	19.340	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	30	VAL	0	-0.052	-0.046	20.363	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.917	-0.947	23.532	-0.281	-0.281	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.871	-0.952	19.838	-0.411	-0.411	0.000	0.000	0.000	0.000
27	A	33	HIS	1	0.763	0.893	20.340	0.346	0.346	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.022	0.022	15.718	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	35	PRO	0	-0.039	-0.015	12.342	0.060	0.060	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.016	-0.015	13.012	-0.074	-0.074	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.004	-0.010	7.598	0.052	0.052	0.000	0.000	0.000	0.000
32	A	38	ILE	0	-0.009	-0.001	11.678	0.070	0.070	0.000	0.000	0.000	0.000
33	A	39	THR	0	0.021	0.007	10.088	0.012	0.012	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.860	0.920	13.314	0.019	0.019	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.023	-0.013	14.857	0.032	0.032	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.043	-0.037	16.653	0.003	0.003	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.012	0.016	13.053	0.042	0.042	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.830	-0.910	12.548	0.050	0.050	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.008	-0.001	10.608	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.038	-0.007	12.445	0.013	0.013	0.000	0.000	0.000	0.000
41	A	47	VAL	0	0.027	0.015	10.870	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.036	-0.003	13.524	0.089	0.089	0.000	0.000	0.000	0.000
43	A	49	MET	0	0.031	0.000	14.751	-0.073	-0.073	0.000	0.000	0.000	0.000
44	A	50	SER	0	0.055	0.043	18.205	0.046	0.046	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.038	0.008	21.308	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.897	-0.950	23.573	-0.302	-0.302	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.842	-0.913	18.805	-0.488	-0.488	0.000	0.000	0.000	0.000
48	A	54	TYR	0	-0.047	-0.025	18.355	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.003	-0.019	20.278	0.001	0.001	0.000	0.000	0.000	0.000
50	A	56	SER	0	0.004	0.026	21.371	0.022	0.022	0.000	0.000	0.000	0.000
51	A	57	LEU	0	0.010	0.006	14.733	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	58	GLU	-1	-0.821	-0.895	19.196	-0.287	-0.287	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.863	-0.937	20.886	-0.198	-0.198	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.053	-0.036	19.548	0.021	0.021	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.026	-0.020	18.304	0.015	0.015	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.049	-0.019	20.083	0.040	0.040	0.000	0.000	0.000	0.000
57	A	63	LEU	0	-0.009	0.003	23.626	0.025	0.025	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.035	-0.019	19.672	0.019	0.019	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.837	0.909	19.461	0.271	0.271	0.000	0.000	0.000	0.000
60	A	66	SER	0	0.000	0.008	22.483	0.025	0.025	0.000	0.000	0.000	0.000
61	A	67	PRO	0	0.062	0.018	23.837	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.015	-0.009	25.460	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	69	ASN	0	-0.044	-0.035	26.992	0.014	0.014	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.057	0.033	23.242	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.926	0.970	25.308	0.082	0.082	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.972	0.983	27.238	0.101	0.101	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.030	0.026	25.553	0.003	0.003	0.000	0.000	0.000	0.000
68	A	74	MET	0	0.013	0.000	23.353	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.886	-0.942	26.626	-0.116	-0.116	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.024	-0.020	29.944	0.007	0.007	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.028	-0.020	26.244	0.002	0.002	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.831	-0.900	26.791	-0.191	-0.191	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.044	-0.023	29.500	0.008	0.008	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.003	-0.012	32.040	0.004	0.004	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.863	0.940	24.758	0.228	0.228	0.000	0.000	0.000	0.000
76	A	82	SER	0	-0.103	-0.060	31.555	0.003	0.003	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.011	0.012	33.758	0.008	0.008	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.892	0.948	35.080	0.106	0.106	0.000	0.000	0.000	0.000
79	A	85	GLY	0	-0.001	0.012	38.022	0.003	0.003	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.048	-0.033	38.630	0.005	0.005	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.924	-0.950	41.839	-0.089	-0.089	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.881	0.921	43.929	0.075	0.075	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.836	-0.898	44.804	-0.082	-0.082	0.000	0.000	0.000	0.000
84	A	90	ILE	0	-0.057	-0.037	44.314	0.000	0.000	0.000	0.000	0.000	0.000
85	A	91	ILE	0	-0.075	-0.039	46.835	0.003	0.003	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.945	-0.961	49.172	-0.067	-0.067	0.000	0.000	0.000	0.000

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