FMO DATABASE

FMODB ID: KGZJ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-644066.361121
FMO2-HF: Nuclear repulsion	608616.770004
FMO2-HF: Total energy	-35449.591116
FMO2-MP2: Total energy	-35554.43696

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.
-29.558	-19.509	11.738	-5.708	-16.078	-0.055

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 : 0.015 / q_NPA : 0.028

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	-0.023	-0.018	2.588	-2.274	0.172	0.925	-1.443	-1.928	-0.010
4	E	4	ILE	0	-0.006	-0.001	5.211	-0.304	-0.231	-0.001	-0.005	-0.067	0.000
5	E	5	TRP	0	-0.005	-0.012	7.882	0.395	0.395	0.000	0.000	0.000	0.000
6	E	6	SER	0	-0.011	-0.022	11.122	-0.097	-0.097	0.000	0.000	0.000	0.000
7	E	7	GLU	-1	-0.891	-0.957	14.566	0.055	0.055	0.000	0.000	0.000	0.000
8	E	8	GLU	-1	-0.804	-0.879	17.837	0.133	0.133	0.000	0.000	0.000	0.000
9	E	9	SER	0	-0.056	-0.038	12.584	0.025	0.025	0.000	0.000	0.000	0.000
10	E	10	TRP	0	-0.012	-0.007	13.542	0.106	0.106	0.000	0.000	0.000	0.000
11	E	11	ASP	-1	-0.824	-0.917	15.671	0.198	0.198	0.000	0.000	0.000	0.000
12	E	12	ASP	-1	-0.822	-0.919	16.853	0.369	0.369	0.000	0.000	0.000	0.000
13	E	13	TYR	0	-0.066	-0.075	14.399	0.024	0.024	0.000	0.000	0.000	0.000
14	E	14	LEU	0	-0.002	-0.006	16.848	0.019	0.019	0.000	0.000	0.000	0.000
15	E	15	TYR	0	0.046	0.026	19.669	-0.004	-0.004	0.000	0.000	0.000	0.000
16	E	16	TRP	0	-0.016	-0.044	18.044	-0.021	-0.021	0.000	0.000	0.000	0.000
17	E	17	GLN	0	-0.046	-0.021	17.154	0.005	0.005	0.000	0.000	0.000	0.000
18	E	18	GLU	-1	-0.966	-0.967	21.038	0.208	0.208	0.000	0.000	0.000	0.000
19	E	19	THR	0	-0.035	0.001	24.066	-0.028	-0.028	0.000	0.000	0.000	0.000
20	E	20	ASP	-1	-0.795	-0.903	23.760	0.351	0.351	0.000	0.000	0.000	0.000
21	E	21	LYS	1	0.947	0.965	20.522	-0.381	-0.381	0.000	0.000	0.000	0.000
22	E	22	ARG	1	0.850	0.907	21.343	-0.295	-0.295	0.000	0.000	0.000	0.000
23	E	23	ILE	0	-0.018	-0.003	19.393	0.059	0.059	0.000	0.000	0.000	0.000
24	E	24	VAL	0	0.030	0.034	16.971	0.081	0.081	0.000	0.000	0.000	0.000
25	E	25	LYS	1	0.915	0.961	16.478	-0.496	-0.496	0.000	0.000	0.000	0.000
26	E	26	LYS	1	0.882	0.938	16.302	-0.464	-0.464	0.000	0.000	0.000	0.000
27	E	27	ILE	0	0.060	0.040	13.086	0.112	0.112	0.000	0.000	0.000	0.000
28	E	28	ASN	0	0.041	0.036	12.183	0.202	0.202	0.000	0.000	0.000	0.000
29	E	29	GLU	-1	-0.824	-0.899	11.477	1.374	1.374	0.000	0.000	0.000	0.000
30	E	30	LEU	0	0.013	0.021	12.002	0.155	0.155	0.000	0.000	0.000	0.000
31	E	31	ILE	0	0.032	0.040	7.052	0.342	0.342	0.000	0.000	0.000	0.000
32	E	32	LYS	1	0.810	0.881	7.066	-0.497	-0.497	0.000	0.000	0.000	0.000
33	E	33	ASP	-1	-0.850	-0.920	7.620	1.777	1.777	0.000	0.000	0.000	0.000
34	E	34	THR	0	-0.005	-0.011	5.240	-0.291	-0.197	-0.001	-0.009	-0.084	0.000
35	E	35	ARG	1	0.859	0.917	2.450	-6.913	-4.787	0.878	-0.919	-2.084	0.004
36	E	36	ARG	1	0.908	0.974	4.184	-1.353	-1.096	0.000	-0.010	-0.247	0.000
37	E	37	THR	0	0.017	-0.001	7.036	-0.583	-0.583	0.000	0.000	0.000	0.000
38	E	38	PRO	0	0.044	0.026	3.362	-0.712	-0.182	0.051	-0.114	-0.466	0.000
39	E	39	PHE	0	0.005	-0.002	5.857	-0.046	-0.046	0.000	0.000	0.000	0.000
40	E	40	GLU	-1	-0.917	-0.949	9.146	0.240	0.240	0.000	0.000	0.000	0.000
41	E	41	GLY	0	0.033	0.021	11.157	0.249	0.249	0.000	0.000	0.000	0.000
42	E	42	LYS	1	0.754	0.862	12.833	-1.423	-1.423	0.000	0.000	0.000	0.000
43	E	43	GLY	0	0.041	0.007	13.926	0.085	0.085	0.000	0.000	0.000	0.000
44	E	44	LYS	1	0.839	0.924	16.347	-0.375	-0.375	0.000	0.000	0.000	0.000
45	E	45	PRO	0	0.014	0.021	11.846	-0.043	-0.043	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.865	-0.921	13.955	0.194	0.194	0.000	0.000	0.000	0.000
47	E	47	PRO	0	-0.003	0.017	13.575	0.036	0.036	0.000	0.000	0.000	0.000
48	E	48	LEU	0	-0.019	-0.010	14.452	-0.041	-0.041	0.000	0.000	0.000	0.000
49	E	49	LYS	1	0.921	0.944	16.349	-0.138	-0.138	0.000	0.000	0.000	0.000
50	E	50	HIS	0	0.053	0.027	18.953	0.006	0.006	0.000	0.000	0.000	0.000
51	E	51	ASN	0	0.036	0.018	19.766	-0.031	-0.031	0.000	0.000	0.000	0.000
52	E	52	LEU	0	0.013	0.015	16.869	-0.001	-0.001	0.000	0.000	0.000	0.000
53	E	53	SER	0	-0.026	-0.032	15.530	0.039	0.039	0.000	0.000	0.000	0.000
54	E	54	GLY	0	-0.007	0.006	12.083	-0.053	-0.053	0.000	0.000	0.000	0.000
55	E	55	PHE	0	-0.024	-0.007	10.465	0.015	0.015	0.000	0.000	0.000	0.000
56	E	56	TRP	0	-0.004	-0.008	9.852	-0.004	-0.004	0.000	0.000	0.000	0.000
57	E	57	SER	0	0.011	0.002	12.082	0.084	0.084	0.000	0.000	0.000	0.000
58	E	58	ARG	1	0.834	0.914	8.940	-1.538	-1.538	0.000	0.000	0.000	0.000
59	E	59	ARG	1	0.920	0.959	14.711	-0.392	-0.392	0.000	0.000	0.000	0.000
60	E	60	ILE	0	0.003	0.019	15.734	0.067	0.067	0.000	0.000	0.000	0.000
61	E	61	THR	0	-0.080	-0.072	18.212	-0.006	-0.006	0.000	0.000	0.000	0.000
62	E	62	GLU	-1	-0.790	-0.887	21.551	0.348	0.348	0.000	0.000	0.000	0.000
63	E	63	GLU	-1	-0.856	-0.874	23.986	0.243	0.243	0.000	0.000	0.000	0.000
64	E	64	HIS	0	0.028	0.006	20.051	0.034	0.034	0.000	0.000	0.000	0.000
65	E	65	ARG	1	0.832	0.895	16.823	-0.369	-0.369	0.000	0.000	0.000	0.000
66	E	66	LEU	0	0.015	0.022	9.789	-0.020	-0.020	0.000	0.000	0.000	0.000
67	E	67	VAL	0	-0.023	-0.016	13.038	0.022	0.022	0.000	0.000	0.000	0.000
68	E	68	TYR	0	-0.002	-0.008	7.115	0.070	0.070	0.000	0.000	0.000	0.000
69	E	69	ALA	0	0.061	0.041	8.650	-0.168	-0.168	0.000	0.000	0.000	0.000
70	E	70	VAL	0	-0.023	-0.023	2.570	0.161	0.520	1.479	-0.334	-1.504	0.000
71	E	71	THR	0	0.015	0.011	3.430	-0.976	-0.669	0.003	-0.061	-0.249	0.000
72	E	72	ASP	-1	-0.898	-0.955	2.658	-7.369	-6.249	0.578	-0.682	-1.016	-0.010
73	E	73	ASP	-1	-0.771	-0.847	3.961	-4.186	-3.515	0.005	-0.233	-0.443	-0.001
74	E	74	SER	0	-0.086	-0.078	2.255	-6.225	-3.203	4.581	-3.660	-3.943	-0.031
75	E	75	LEU	0	-0.003	0.005	2.482	2.134	1.489	3.178	1.339	-3.872	-0.008
76	E	76	LEU	0	-0.025	-0.014	3.850	-1.174	-1.485	0.062	0.423	-0.175	0.001
77	E	77	ILE	0	0.005	-0.005	7.511	0.133	0.133	0.000	0.000	0.000	0.000
78	E	78	ALA	0	0.034	0.024	9.724	-0.183	-0.183	0.000	0.000	0.000	0.000
79	E	79	ALA	0	0.026	0.014	13.326	-0.077	-0.077	0.000	0.000	0.000	0.000
80	E	80	CYS	0	-0.117	-0.050	13.688	0.151	0.151	0.000	0.000	0.000	0.000
81	E	81	ARG	1	0.927	0.990	15.624	-0.267	-0.267	0.000	0.000	0.000	0.000
82	E	82	TYR	0	-0.032	-0.009	19.468	-0.002	-0.002	0.000	0.000	0.000	0.000
83	E	83	HIS	0	-0.016	-0.029	20.745	-0.024	-0.024	0.000	0.000	0.000	0.000
84	E	84	TYR	0	-0.048	-0.041	25.134	-0.015	-0.015	0.000	0.000	0.000	0.000

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