FMO DATABASE

FMODB ID: QVKYY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-564834.593951
FMO2-HF: Nuclear repulsion	532293.031045
FMO2-HF: Total energy	-32541.562907
FMO2-MP2: Total energy	-32638.240869

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.
-12.782	-12.932	20.281	-10.522	-9.608	-0.08

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 : -0.006 / q_NPA : -0.014

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	0.026	2.948	0.089	1.637	0.049	-0.820	-0.777	0.002
4	D	5	ASP	-1	-0.855	-0.938	4.995	0.060	0.156	-0.001	-0.003	-0.091	0.000
5	D	6	LEU	0	-0.001	0.008	6.327	-0.171	-0.171	0.000	0.000	0.000	0.000
6	D	7	LYS	1	0.912	0.961	8.970	-0.117	-0.117	0.000	0.000	0.000	0.000
7	D	8	SER	0	-0.040	-0.012	10.155	0.007	0.007	0.000	0.000	0.000	0.000
8	D	9	PRO	0	0.019	-0.018	12.082	-0.081	-0.081	0.000	0.000	0.000	0.000
9	D	10	ALA	0	0.021	0.017	11.433	-0.067	-0.067	0.000	0.000	0.000	0.000
10	D	11	GLY	0	0.054	0.032	8.080	-0.108	-0.108	0.000	0.000	0.000	0.000
11	D	12	LEU	0	-0.016	-0.019	8.645	-0.336	-0.336	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.040	-0.029	11.345	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	14	VAL	0	0.002	0.002	5.793	-0.122	-0.122	0.000	0.000	0.000	0.000
14	D	15	LEU	0	-0.036	-0.021	8.006	-0.284	-0.284	0.000	0.000	0.000	0.000
15	D	16	ASN	0	-0.011	-0.028	8.974	0.071	0.071	0.000	0.000	0.000	0.000
16	D	17	ASP	-1	-0.825	-0.899	11.579	-0.482	-0.482	0.000	0.000	0.000	0.000
17	D	18	TYR	0	-0.044	-0.016	7.708	-0.100	-0.100	0.000	0.000	0.000	0.000
18	D	19	LEU	0	0.016	0.013	10.166	0.055	0.055	0.000	0.000	0.000	0.000
19	D	20	ALA	0	0.016	0.006	12.835	0.123	0.123	0.000	0.000	0.000	0.000
20	D	21	ASP	-1	-0.878	-0.914	13.506	-0.715	-0.715	0.000	0.000	0.000	0.000
21	D	22	LYS	1	0.785	0.882	10.405	1.080	1.080	0.000	0.000	0.000	0.000
22	D	23	SER	0	-0.015	-0.018	15.163	-0.005	-0.005	0.000	0.000	0.000	0.000
23	D	24	TYR	0	-0.074	-0.050	13.808	0.056	0.056	0.000	0.000	0.000	0.000
24	D	25	ILE	0	-0.005	-0.001	7.383	-0.107	-0.107	0.000	0.000	0.000	0.000
25	D	26	GLU	-1	-0.793	-0.887	9.052	-0.940	-0.940	0.000	0.000	0.000	0.000
26	D	27	GLY	0	0.000	0.017	11.677	0.109	0.109	0.000	0.000	0.000	0.000
27	D	28	TYR	0	-0.020	-0.030	15.080	-0.014	-0.014	0.000	0.000	0.000	0.000
28	D	29	VAL	0	0.010	0.002	17.298	0.045	0.045	0.000	0.000	0.000	0.000
29	D	30	PRO	0	0.000	0.028	16.445	-0.042	-0.042	0.000	0.000	0.000	0.000
30	D	31	SER	0	0.023	-0.016	13.444	0.020	0.020	0.000	0.000	0.000	0.000
31	D	32	GLN	0	-0.029	-0.059	14.285	0.002	0.002	0.000	0.000	0.000	0.000
32	D	33	ALA	0	-0.006	0.005	9.266	0.041	0.041	0.000	0.000	0.000	0.000
33	D	34	ASP	-1	-0.738	-0.854	9.927	-0.586	-0.586	0.000	0.000	0.000	0.000
34	D	35	VAL	0	0.002	0.002	12.130	0.024	0.024	0.000	0.000	0.000	0.000
35	D	36	ALA	0	-0.008	0.002	9.903	0.039	0.039	0.000	0.000	0.000	0.000
36	D	37	VAL	0	0.030	0.016	6.512	0.076	0.076	0.000	0.000	0.000	0.000
37	D	38	PHE	0	-0.035	-0.014	9.216	0.033	0.033	0.000	0.000	0.000	0.000
38	D	39	GLU	-1	-0.800	-0.895	12.865	-0.025	-0.025	0.000	0.000	0.000	0.000
39	D	40	ALA	0	-0.041	-0.013	9.489	0.050	0.050	0.000	0.000	0.000	0.000
40	D	41	VAL	0	0.016	0.002	10.293	0.033	0.033	0.000	0.000	0.000	0.000
41	D	42	SER	0	-0.084	-0.039	12.510	0.050	0.050	0.000	0.000	0.000	0.000
42	D	43	SER	0	-0.054	-0.023	15.993	0.033	0.033	0.000	0.000	0.000	0.000
43	D	44	PRO	0	-0.012	-0.020	16.777	-0.027	-0.027	0.000	0.000	0.000	0.000
44	D	45	PRO	0	0.004	0.017	14.633	0.020	0.020	0.000	0.000	0.000	0.000
45	D	46	PRO	0	0.035	0.015	16.901	0.013	0.013	0.000	0.000	0.000	0.000
46	D	47	ALA	0	-0.006	-0.011	19.145	-0.027	-0.027	0.000	0.000	0.000	0.000
47	D	48	ASP	-1	-0.891	-0.950	19.833	-0.183	-0.183	0.000	0.000	0.000	0.000
48	D	49	LEU	0	-0.020	0.012	14.338	-0.028	-0.028	0.000	0.000	0.000	0.000
49	D	50	CYS	0	0.016	-0.002	17.059	-0.027	-0.027	0.000	0.000	0.000	0.000
50	D	51	HIS	0	-0.010	-0.002	15.195	0.026	0.026	0.000	0.000	0.000	0.000
51	D	52	ALA	0	0.061	0.033	13.183	-0.025	-0.025	0.000	0.000	0.000	0.000
52	D	53	LEU	0	-0.009	0.001	14.524	0.022	0.022	0.000	0.000	0.000	0.000
53	D	54	ARG	1	0.835	0.919	15.579	0.489	0.489	0.000	0.000	0.000	0.000
54	D	55	TRP	0	-0.066	-0.033	11.329	0.014	0.014	0.000	0.000	0.000	0.000
55	D	56	TYR	0	0.056	0.027	15.298	0.037	0.037	0.000	0.000	0.000	0.000
56	D	57	ASN	0	-0.039	-0.035	16.564	0.049	0.049	0.000	0.000	0.000	0.000
57	D	58	HIS	0	0.013	0.044	18.546	0.013	0.013	0.000	0.000	0.000	0.000
58	D	59	ILE	0	0.005	0.018	14.432	0.024	0.024	0.000	0.000	0.000	0.000
59	D	60	LYS	1	0.992	1.005	17.840	0.151	0.151	0.000	0.000	0.000	0.000
60	D	61	SER	0	-0.097	-0.059	20.387	0.024	0.024	0.000	0.000	0.000	0.000
61	D	62	TYR	0	0.042	0.011	19.539	0.021	0.021	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.859	-0.926	19.979	-0.104	-0.104	0.000	0.000	0.000	0.000
63	D	64	LYS	1	0.793	0.851	21.580	0.139	0.139	0.000	0.000	0.000	0.000
64	D	65	GLU	-1	-0.892	-0.925	23.058	-0.125	-0.125	0.000	0.000	0.000	0.000
65	D	66	LYS	1	0.840	0.921	17.922	0.092	0.092	0.000	0.000	0.000	0.000
66	D	67	ALA	0	-0.008	-0.006	19.398	-0.009	-0.009	0.000	0.000	0.000	0.000
67	D	68	SER	0	-0.003	-0.001	21.639	0.007	0.007	0.000	0.000	0.000	0.000
68	D	69	LEU	0	-0.038	0.009	17.702	-0.007	-0.007	0.000	0.000	0.000	0.000
69	D	70	PRO	0	0.043	0.034	18.472	0.013	0.013	0.000	0.000	0.000	0.000
70	D	71	GLY	0	0.020	0.006	15.740	-0.036	-0.036	0.000	0.000	0.000	0.000
71	D	72	VAL	0	-0.004	-0.015	14.129	0.034	0.034	0.000	0.000	0.000	0.000
72	D	73	LYS	1	0.833	0.917	11.983	0.023	0.023	0.000	0.000	0.000	0.000
73	D	74	LYS	1	0.829	0.897	8.367	0.583	0.583	0.000	0.000	0.000	0.000
74	D	75	ALA	0	0.032	0.013	7.981	0.016	0.016	0.000	0.000	0.000	0.000
75	D	76	LEU	0	0.025	-0.009	5.024	-0.147	-0.147	0.000	0.000	0.000	0.000
76	D	77	GLY	0	0.031	0.024	2.159	0.264	0.943	3.196	-2.328	-1.547	-0.008
77	D	78	LYS	1	0.739	0.842	2.045	-5.970	-7.840	5.158	-1.027	-2.262	-0.025
78	D	79	TYR	0	0.007	0.009	2.833	-0.154	0.249	0.047	-0.159	-0.290	0.000
79	D	80	GLY	0	0.065	0.024	2.310	-2.792	-2.648	3.353	-2.163	-1.334	-0.018
80	D	81	PRO	0	-0.035	-0.027	3.519	0.243	0.896	0.002	-0.236	-0.419	0.000
81	D	82	ALA	0	-0.003	0.013	1.891	-7.434	-10.300	8.259	-3.201	-2.193	-0.033
82	D	83	ASP	-1	-0.853	-0.928	3.094	4.890	5.879	0.216	-0.547	-0.658	0.002
83	D	84	VAL	0	-0.061	-0.038	4.455	-1.336	-1.262	0.002	-0.038	-0.037	0.000
84	D	85	GLU	-1	-0.963	-0.970	7.650	0.443	0.443	0.000	0.000	0.000	0.000
85	D	86	ASP	-1	-0.804	-0.866	6.006	0.620	0.620	0.000	0.000	0.000	0.000
86	D	87	THR	0	-0.002	0.002	7.351	-0.296	-0.296	0.000	0.000	0.000	0.000
87	D	88	THR	0	-0.085	-0.050	9.033	-0.105	-0.105	0.000	0.000	0.000	0.000

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