FMO DATABASE

FMODB ID: R8Q98

Calculation Name: 5DQS-D-Xray372

Preferred Name: Elongation factor 1-beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DQS

Chain ID: D

ChEMBL ID: CHEMBL4295731

UniProt ID: P24534

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-561290.305684
FMO2-HF: Nuclear repulsion	528748.819348
FMO2-HF: Total energy	-32541.486336
FMO2-MP2: Total energy	-32638.121108

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(D:2:GLY)

Summations of interaction energy for fragment #1(D:2: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.
-10.343	-3.438	9.421	-7.726	-8.599	-0.032

Interaction energy analysis for fragmet #1(D:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.050

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	D	4	GLY	0	0.022	0.023	3.036	-2.448	1.104	0.031	-2.078	-1.505	0.013
4	D	5	ASP	-1	-0.837	-0.934	4.994	0.570	0.692	-0.001	-0.003	-0.118	0.000
5	D	6	LEU	0	-0.017	-0.001	5.816	-0.216	-0.216	0.000	0.000	0.000	0.000
6	D	7	LYS	1	0.911	0.965	9.003	-0.196	-0.196	0.000	0.000	0.000	0.000
7	D	8	SER	0	-0.047	-0.019	10.325	-0.021	-0.021	0.000	0.000	0.000	0.000
8	D	9	PRO	0	0.033	-0.009	12.154	-0.090	-0.090	0.000	0.000	0.000	0.000
9	D	10	ALA	0	0.040	0.012	11.658	-0.073	-0.073	0.000	0.000	0.000	0.000
10	D	11	GLY	0	0.051	0.046	8.103	-0.236	-0.236	0.000	0.000	0.000	0.000
11	D	12	LEU	0	-0.002	-0.013	8.524	-0.310	-0.310	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.045	-0.025	11.130	0.063	0.063	0.000	0.000	0.000	0.000
13	D	14	VAL	0	0.021	0.016	5.976	-0.067	-0.067	0.000	0.000	0.000	0.000
14	D	15	LEU	0	-0.042	-0.024	7.436	-0.185	-0.185	0.000	0.000	0.000	0.000
15	D	16	ASN	0	-0.022	-0.034	8.717	0.210	0.210	0.000	0.000	0.000	0.000
16	D	17	ASP	-1	-0.846	-0.921	11.470	-0.873	-0.873	0.000	0.000	0.000	0.000
17	D	18	TYR	0	-0.051	-0.013	7.503	-0.082	-0.082	0.000	0.000	0.000	0.000
18	D	19	LEU	0	-0.003	-0.010	9.872	0.172	0.172	0.000	0.000	0.000	0.000
19	D	20	ALA	0	0.017	0.009	12.659	0.160	0.160	0.000	0.000	0.000	0.000
20	D	21	ASP	-1	-0.893	-0.921	13.415	-0.774	-0.774	0.000	0.000	0.000	0.000
21	D	22	LYS	1	0.784	0.886	9.971	1.153	1.153	0.000	0.000	0.000	0.000
22	D	23	SER	0	-0.010	-0.013	14.824	0.000	0.000	0.000	0.000	0.000	0.000
23	D	24	TYR	0	-0.063	-0.055	13.758	0.050	0.050	0.000	0.000	0.000	0.000
24	D	25	ILE	0	-0.024	-0.007	7.401	-0.135	-0.135	0.000	0.000	0.000	0.000
25	D	26	GLU	-1	-0.795	-0.883	9.224	0.184	0.184	0.000	0.000	0.000	0.000
26	D	27	GLY	0	-0.005	0.010	11.746	0.073	0.073	0.000	0.000	0.000	0.000
27	D	28	TYR	0	-0.014	-0.026	15.001	-0.038	-0.038	0.000	0.000	0.000	0.000
28	D	29	VAL	0	-0.001	-0.001	17.442	0.015	0.015	0.000	0.000	0.000	0.000
29	D	30	PRO	0	0.011	0.028	16.258	-0.006	-0.006	0.000	0.000	0.000	0.000
30	D	31	SER	0	0.003	-0.011	13.603	0.054	0.054	0.000	0.000	0.000	0.000
31	D	32	GLN	0	-0.035	-0.057	14.060	0.028	0.028	0.000	0.000	0.000	0.000
32	D	33	ALA	0	-0.018	-0.005	9.442	0.088	0.088	0.000	0.000	0.000	0.000
33	D	34	ASP	-1	-0.742	-0.876	9.776	-0.215	-0.215	0.000	0.000	0.000	0.000
34	D	35	VAL	0	0.001	-0.001	12.116	-0.014	-0.014	0.000	0.000	0.000	0.000
35	D	36	ALA	0	-0.013	0.001	9.536	0.002	0.002	0.000	0.000	0.000	0.000
36	D	37	VAL	0	0.044	0.019	6.214	0.071	0.071	0.000	0.000	0.000	0.000
37	D	38	PHE	0	-0.029	-0.005	8.811	-0.068	-0.068	0.000	0.000	0.000	0.000
38	D	39	GLU	-1	-0.817	-0.910	12.462	0.281	0.281	0.000	0.000	0.000	0.000
39	D	40	ALA	0	-0.051	-0.014	9.105	0.019	0.019	0.000	0.000	0.000	0.000
40	D	41	VAL	0	0.017	0.004	10.105	-0.041	-0.041	0.000	0.000	0.000	0.000
41	D	42	SER	0	-0.076	-0.026	12.244	0.005	0.005	0.000	0.000	0.000	0.000
42	D	43	SER	0	-0.053	-0.031	15.685	0.019	0.019	0.000	0.000	0.000	0.000
43	D	44	PRO	0	-0.030	-0.025	16.486	-0.030	-0.030	0.000	0.000	0.000	0.000
44	D	45	PRO	0	0.008	0.020	14.326	0.009	0.009	0.000	0.000	0.000	0.000
45	D	46	PRO	0	0.050	0.025	16.862	0.027	0.027	0.000	0.000	0.000	0.000
46	D	47	ALA	0	0.003	-0.014	18.982	-0.032	-0.032	0.000	0.000	0.000	0.000
47	D	48	ASP	-1	-0.924	-0.960	19.952	-0.346	-0.346	0.000	0.000	0.000	0.000
48	D	49	LEU	0	-0.025	0.007	14.250	-0.043	-0.043	0.000	0.000	0.000	0.000
49	D	50	CYS	0	0.008	-0.003	17.057	-0.006	-0.006	0.000	0.000	0.000	0.000
50	D	51	HIS	0	0.016	0.013	15.080	0.080	0.080	0.000	0.000	0.000	0.000
51	D	52	ALA	0	0.056	0.022	13.197	0.004	0.004	0.000	0.000	0.000	0.000
52	D	53	LEU	0	-0.008	0.004	14.372	0.064	0.064	0.000	0.000	0.000	0.000
53	D	54	ARG	1	0.849	0.926	15.384	0.529	0.529	0.000	0.000	0.000	0.000
54	D	55	TRP	0	-0.058	-0.028	10.959	0.008	0.008	0.000	0.000	0.000	0.000
55	D	56	TYR	0	0.061	0.029	14.769	0.050	0.050	0.000	0.000	0.000	0.000
56	D	57	ASN	0	-0.017	-0.028	16.409	0.069	0.069	0.000	0.000	0.000	0.000
57	D	58	HIS	0	0.007	0.046	18.183	0.031	0.031	0.000	0.000	0.000	0.000
58	D	59	ILE	0	0.037	0.036	14.378	0.034	0.034	0.000	0.000	0.000	0.000
59	D	60	LYS	1	1.002	1.019	17.732	0.098	0.098	0.000	0.000	0.000	0.000
60	D	61	SER	0	-0.118	-0.062	19.946	0.024	0.024	0.000	0.000	0.000	0.000
61	D	62	TYR	0	0.041	-0.003	19.558	0.016	0.016	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.893	-0.926	19.480	0.084	0.084	0.000	0.000	0.000	0.000
63	D	64	LYS	1	0.794	0.857	21.266	0.027	0.027	0.000	0.000	0.000	0.000
64	D	65	GLU	-1	-0.914	-0.934	23.014	0.014	0.014	0.000	0.000	0.000	0.000
65	D	66	LYS	1	0.869	0.920	17.725	-0.141	-0.141	0.000	0.000	0.000	0.000
66	D	67	ALA	0	-0.008	-0.007	19.339	0.016	0.016	0.000	0.000	0.000	0.000
67	D	68	SER	0	-0.004	0.002	21.138	0.015	0.015	0.000	0.000	0.000	0.000
68	D	69	LEU	0	-0.035	0.008	17.386	-0.011	-0.011	0.000	0.000	0.000	0.000
69	D	70	PRO	0	0.049	0.041	18.630	0.037	0.037	0.000	0.000	0.000	0.000
70	D	71	GLY	0	0.031	0.007	15.868	0.003	0.003	0.000	0.000	0.000	0.000
71	D	72	VAL	0	-0.001	-0.016	14.732	-0.009	-0.009	0.000	0.000	0.000	0.000
72	D	73	LYS	1	0.854	0.928	12.038	-0.355	-0.355	0.000	0.000	0.000	0.000
73	D	74	LYS	1	0.846	0.906	8.591	-0.663	-0.663	0.000	0.000	0.000	0.000
74	D	75	ALA	0	0.022	0.008	7.878	-0.068	-0.068	0.000	0.000	0.000	0.000
75	D	76	LEU	0	0.034	-0.004	4.863	0.458	0.458	0.000	0.000	0.000	0.000
76	D	77	GLY	0	0.015	0.005	2.219	-2.429	-0.990	2.697	-2.610	-1.525	-0.011
77	D	78	LYS	1	0.746	0.847	2.901	3.003	1.833	2.369	0.283	-1.481	-0.003
78	D	79	TYR	0	-0.021	0.008	3.382	-1.920	-1.655	0.007	-0.078	-0.194	0.000
79	D	80	GLY	0	0.033	0.009	2.440	-4.525	-3.281	1.981	-1.605	-1.621	-0.018
80	D	81	PRO	0	-0.050	-0.026	3.446	0.749	1.281	0.007	-0.151	-0.387	0.000
81	D	82	ALA	0	0.016	0.009	2.294	-5.141	-4.783	2.274	-1.223	-1.409	-0.014
82	D	83	ASP	-1	-0.889	-0.947	2.998	-1.100	-0.594	0.057	-0.249	-0.314	0.001
83	D	84	VAL	0	-0.056	-0.031	4.320	0.340	0.397	-0.001	-0.012	-0.045	0.000
84	D	85	GLU	-1	-0.972	-0.966	7.558	0.583	0.583	0.000	0.000	0.000	0.000
85	D	86	ASP	-1	-0.784	-0.878	6.832	3.263	3.263	0.000	0.000	0.000	0.000
86	D	87	THR	0	-0.047	-0.009	8.451	-0.451	-0.451	0.000	0.000	0.000	0.000
87	D	88	THR	0	-0.004	-0.005	10.483	0.163	0.163	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:GLY)