FMO DATABASE

FMODB ID: G54Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-466032.975115
FMO2-HF: Nuclear repulsion	431199.527052
FMO2-HF: Total energy	-34833.448063
FMO2-MP2: Total energy	-34930.831146

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.
0.199	1.673	0.014	-0.815	-0.673	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 : 0.045 / q_NPA : 0.023

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	0.008	0.012	3.225	-0.212	1.262	0.014	-0.815	-0.673	0.003
4	A	10	MET	0	0.004	0.019	6.608	0.773	0.773	0.000	0.000	0.000	0.000
5	A	11	ARG	1	0.942	0.986	8.570	0.386	0.386	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.039	0.023	7.992	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	13	ILE	0	-0.055	-0.018	10.712	0.075	0.075	0.000	0.000	0.000	0.000
8	A	14	SER	0	0.032	0.017	14.189	0.025	0.025	0.000	0.000	0.000	0.000
9	A	15	TYR	0	0.037	-0.002	15.894	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.008	-0.006	18.093	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.805	-0.893	17.293	-0.217	-0.217	0.000	0.000	0.000	0.000
12	A	18	ALA	0	0.051	0.019	17.871	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.913	0.949	19.992	0.090	0.090	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.056	-0.019	22.975	0.013	0.013	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.030	-0.019	22.804	0.013	0.013	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.030	0.039	22.140	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	23	SER	0	0.048	0.009	23.731	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.039	0.016	24.729	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.037	-0.027	18.752	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	26	MET	0	-0.033	-0.024	20.703	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	27	MET	0	-0.018	0.003	22.606	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.799	0.896	20.423	0.319	0.319	0.000	0.000	0.000	0.000
23	A	29	ALA	0	0.029	0.014	18.747	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	30	VAL	0	-0.054	-0.037	19.998	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.905	-0.941	23.283	-0.259	-0.259	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.864	-0.938	19.438	-0.387	-0.387	0.000	0.000	0.000	0.000
27	A	33	HIS	1	0.774	0.888	20.094	0.342	0.342	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.023	0.027	15.758	-0.059	-0.059	0.000	0.000	0.000	0.000
29	A	35	PRO	0	-0.030	-0.016	12.250	0.051	0.051	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.015	-0.017	12.709	-0.060	-0.060	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.002	-0.010	7.431	0.030	0.030	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.009	0.006	11.388	0.093	0.093	0.000	0.000	0.000	0.000
33	A	39	THR	0	0.014	-0.001	9.939	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.814	0.887	13.178	0.017	0.017	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.010	-0.012	14.843	0.038	0.038	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.074	-0.046	16.300	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.032	0.026	13.255	0.032	0.032	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.789	-0.863	12.422	0.049	0.049	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.016	0.001	10.339	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.056	-0.032	12.433	0.012	0.012	0.000	0.000	0.000	0.000
41	A	47	VAL	0	0.006	0.005	10.573	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.020	0.003	13.149	0.088	0.088	0.000	0.000	0.000	0.000
43	A	49	MET	0	0.033	0.005	14.842	-0.081	-0.081	0.000	0.000	0.000	0.000
44	A	50	SER	0	0.073	0.045	18.010	0.042	0.042	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.025	0.002	21.106	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.898	-0.952	23.570	-0.300	-0.300	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.831	-0.907	18.774	-0.481	-0.481	0.000	0.000	0.000	0.000
48	A	54	TYR	0	-0.027	-0.017	18.436	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.004	-0.011	20.361	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	56	SER	0	0.007	0.023	21.272	0.019	0.019	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.007	0.001	15.059	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	58	GLU	-1	-0.795	-0.876	19.295	-0.333	-0.333	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.856	-0.935	21.100	-0.221	-0.221	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.047	-0.033	19.680	0.023	0.023	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.021	-0.019	18.213	0.011	0.011	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.054	-0.009	19.985	0.030	0.030	0.000	0.000	0.000	0.000
57	A	63	LEU	0	-0.006	0.004	23.606	0.023	0.023	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.028	-0.021	19.633	0.024	0.024	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.785	0.873	20.222	0.310	0.310	0.000	0.000	0.000	0.000
60	A	66	SER	0	0.008	0.011	22.760	0.023	0.023	0.000	0.000	0.000	0.000
61	A	67	PRO	0	0.045	0.006	23.628	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.002	0.004	25.545	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	ASN	0	-0.046	-0.033	27.184	0.018	0.018	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.039	0.024	23.356	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.857	0.915	25.452	0.114	0.114	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.946	0.974	27.217	0.124	0.124	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.029	0.025	25.392	0.006	0.006	0.000	0.000	0.000	0.000
68	A	74	MET	0	0.008	0.003	23.670	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.809	-0.894	26.991	-0.132	-0.132	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.008	0.004	30.330	0.011	0.011	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.011	-0.004	26.564	0.005	0.005	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.779	-0.887	26.747	-0.218	-0.218	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.033	-0.012	29.700	0.012	0.012	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.002	-0.009	32.207	0.007	0.007	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.814	0.895	24.653	0.246	0.246	0.000	0.000	0.000	0.000
76	A	82	SER	0	-0.084	-0.051	31.567	0.007	0.007	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.031	0.021	34.078	0.009	0.009	0.000	0.000	0.000	0.000
78	A	84	LYS	1	0.843	0.926	34.385	0.125	0.125	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.010	0.018	38.183	0.002	0.002	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.049	-0.033	38.889	0.007	0.007	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.916	-0.948	42.489	-0.092	-0.092	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.839	0.896	44.378	0.086	0.086	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.818	-0.884	45.140	-0.086	-0.086	0.000	0.000	0.000	0.000
84	A	90	ILE	0	-0.046	-0.032	44.635	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	91	ILE	0	-0.066	-0.034	47.065	0.004	0.004	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.966	-0.973	49.207	-0.072	-0.072	0.000	0.000	0.000	0.000

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