FMO DATABASE

FMODB ID: ZV76N

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	OptH
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	-560617.634935
FMO2-HF: Nuclear repulsion	528076.477412
FMO2-HF: Total energy	-32541.157523
FMO2-MP2: Total energy	-32637.75304

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.
-12.991	-5.34	9.488	-8.243	-8.894	-0.033

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 : 0.073 / q_NPA : 0.048

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	0.024	0.023	3.049	-2.658	1.017	0.030	-2.152	-1.552	0.014
4	D	5	ASP	-1	-0.851	-0.942	4.999	0.639	0.758	-0.001	-0.003	-0.114	0.000
5	D	6	LEU	0	-0.020	0.017	5.971	-0.214	-0.214	0.000	0.000	0.000	0.000
6	D	7	LYS	1	0.925	0.974	9.004	-0.248	-0.248	0.000	0.000	0.000	0.000
7	D	8	SER	0	-0.035	-0.038	10.349	-0.024	-0.024	0.000	0.000	0.000	0.000
8	D	9	PRO	0	0.022	-0.011	12.156	-0.088	-0.088	0.000	0.000	0.000	0.000
9	D	10	ALA	0	0.045	0.012	11.637	-0.069	-0.069	0.000	0.000	0.000	0.000
10	D	11	GLY	0	0.054	0.050	8.102	-0.239	-0.239	0.000	0.000	0.000	0.000
11	D	12	LEU	0	-0.005	-0.013	8.524	-0.295	-0.295	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.015	-0.006	11.126	0.040	0.040	0.000	0.000	0.000	0.000
13	D	14	VAL	0	0.031	0.028	6.004	-0.063	-0.063	0.000	0.000	0.000	0.000
14	D	15	LEU	0	-0.045	-0.027	7.519	-0.176	-0.176	0.000	0.000	0.000	0.000
15	D	16	ASN	0	0.015	-0.008	8.710	0.204	0.204	0.000	0.000	0.000	0.000
16	D	17	ASP	-1	-0.897	-0.954	11.174	-0.941	-0.941	0.000	0.000	0.000	0.000
17	D	18	TYR	0	-0.064	-0.012	7.293	-0.068	-0.068	0.000	0.000	0.000	0.000
18	D	19	LEU	0	-0.014	-0.020	9.875	0.170	0.170	0.000	0.000	0.000	0.000
19	D	20	ALA	0	0.024	0.001	12.663	0.156	0.156	0.000	0.000	0.000	0.000
20	D	21	ASP	-1	-0.911	-0.939	13.487	-0.717	-0.717	0.000	0.000	0.000	0.000
21	D	22	LYS	1	0.832	0.934	9.878	1.102	1.102	0.000	0.000	0.000	0.000
22	D	23	SER	0	-0.013	-0.016	14.828	0.019	0.019	0.000	0.000	0.000	0.000
23	D	24	TYR	0	-0.059	-0.059	13.734	0.044	0.044	0.000	0.000	0.000	0.000
24	D	25	ILE	0	-0.027	-0.001	7.459	-0.126	-0.126	0.000	0.000	0.000	0.000
25	D	26	GLU	-1	-0.817	-0.907	9.561	0.223	0.223	0.000	0.000	0.000	0.000
26	D	27	GLY	0	-0.014	0.006	11.750	0.067	0.067	0.000	0.000	0.000	0.000
27	D	28	TYR	0	-0.017	-0.026	15.004	-0.043	-0.043	0.000	0.000	0.000	0.000
28	D	29	VAL	0	-0.007	-0.007	17.418	0.011	0.011	0.000	0.000	0.000	0.000
29	D	30	PRO	0	0.019	0.031	16.287	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	31	SER	0	0.005	-0.016	13.591	0.057	0.057	0.000	0.000	0.000	0.000
31	D	32	GLN	0	-0.052	-0.059	14.076	0.039	0.039	0.000	0.000	0.000	0.000
32	D	33	ALA	0	-0.007	0.004	9.469	0.087	0.087	0.000	0.000	0.000	0.000
33	D	34	ASP	-1	-0.742	-0.878	9.775	-0.147	-0.147	0.000	0.000	0.000	0.000
34	D	35	VAL	0	-0.007	-0.005	12.115	-0.015	-0.015	0.000	0.000	0.000	0.000
35	D	36	ALA	0	-0.004	0.003	9.497	0.000	0.000	0.000	0.000	0.000	0.000
36	D	37	VAL	0	0.038	0.019	6.249	0.074	0.074	0.000	0.000	0.000	0.000
37	D	38	PHE	0	-0.029	-0.003	8.812	-0.078	-0.078	0.000	0.000	0.000	0.000
38	D	39	GLU	-1	-0.926	-0.980	12.461	0.309	0.309	0.000	0.000	0.000	0.000
39	D	40	ALA	0	-0.067	-0.022	9.114	0.015	0.015	0.000	0.000	0.000	0.000
40	D	41	VAL	0	0.004	0.001	10.180	-0.048	-0.048	0.000	0.000	0.000	0.000
41	D	42	SER	0	-0.063	-0.024	12.244	-0.018	-0.018	0.000	0.000	0.000	0.000
42	D	43	SER	0	-0.093	-0.046	15.686	0.002	0.002	0.000	0.000	0.000	0.000
43	D	44	PRO	0	-0.005	-0.015	16.485	-0.029	-0.029	0.000	0.000	0.000	0.000
44	D	45	PRO	0	0.017	0.024	14.367	0.005	0.005	0.000	0.000	0.000	0.000
45	D	46	PRO	0	0.039	0.022	16.859	0.030	0.030	0.000	0.000	0.000	0.000
46	D	47	ALA	0	-0.002	-0.018	18.977	-0.031	-0.031	0.000	0.000	0.000	0.000
47	D	48	ASP	-1	-0.908	-0.958	19.735	-0.367	-0.367	0.000	0.000	0.000	0.000
48	D	49	LEU	0	-0.026	0.014	14.445	-0.046	-0.046	0.000	0.000	0.000	0.000
49	D	50	CYS	0	0.007	-0.007	17.051	-0.004	-0.004	0.000	0.000	0.000	0.000
50	D	51	HIS	0	-0.006	0.007	15.148	0.083	0.083	0.000	0.000	0.000	0.000
51	D	52	ALA	0	0.061	0.024	13.218	0.008	0.008	0.000	0.000	0.000	0.000
52	D	53	LEU	0	-0.006	0.003	14.366	0.066	0.066	0.000	0.000	0.000	0.000
53	D	54	ARG	1	0.848	0.928	15.430	0.488	0.488	0.000	0.000	0.000	0.000
54	D	55	TRP	0	-0.064	-0.029	10.902	0.010	0.010	0.000	0.000	0.000	0.000
55	D	56	TYR	0	0.061	0.029	14.786	0.053	0.053	0.000	0.000	0.000	0.000
56	D	57	ASN	0	-0.006	-0.023	16.405	0.065	0.065	0.000	0.000	0.000	0.000
57	D	58	HIS	0	0.013	0.055	18.016	0.031	0.031	0.000	0.000	0.000	0.000
58	D	59	ILE	0	0.042	0.069	14.355	0.034	0.034	0.000	0.000	0.000	0.000
59	D	60	LYS	1	1.005	1.016	17.729	0.078	0.078	0.000	0.000	0.000	0.000
60	D	61	SER	0	-0.146	-0.104	19.944	0.021	0.021	0.000	0.000	0.000	0.000
61	D	62	TYR	0	0.047	-0.004	19.558	0.012	0.012	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.896	-0.933	19.756	0.104	0.104	0.000	0.000	0.000	0.000
63	D	64	LYS	1	0.781	0.857	21.266	0.014	0.014	0.000	0.000	0.000	0.000
64	D	65	GLU	-1	-0.874	-0.930	23.204	0.028	0.028	0.000	0.000	0.000	0.000
65	D	66	LYS	1	0.894	0.964	18.500	-0.160	-0.160	0.000	0.000	0.000	0.000
66	D	67	ALA	0	-0.017	-0.016	19.340	0.018	0.018	0.000	0.000	0.000	0.000
67	D	68	SER	0	-0.010	-0.002	21.140	0.014	0.014	0.000	0.000	0.000	0.000
68	D	69	LEU	0	-0.036	0.009	17.214	-0.011	-0.011	0.000	0.000	0.000	0.000
69	D	70	PRO	0	0.053	0.038	18.608	0.038	0.038	0.000	0.000	0.000	0.000
70	D	71	GLY	0	0.035	0.010	15.868	0.007	0.007	0.000	0.000	0.000	0.000
71	D	72	VAL	0	-0.001	-0.015	15.008	-0.011	-0.011	0.000	0.000	0.000	0.000
72	D	73	LYS	1	0.943	0.971	12.046	-0.398	-0.398	0.000	0.000	0.000	0.000
73	D	74	LYS	1	0.851	0.914	8.729	-0.812	-0.812	0.000	0.000	0.000	0.000
74	D	75	ALA	0	0.024	0.008	7.804	-0.074	-0.074	0.000	0.000	0.000	0.000
75	D	76	LEU	0	0.030	-0.007	4.839	0.475	0.475	0.000	0.000	0.000	0.000
76	D	77	GLY	0	0.021	0.009	2.212	-2.256	-0.848	2.697	-2.587	-1.518	-0.010
77	D	78	LYS	1	0.763	0.860	2.901	2.894	1.711	2.373	0.309	-1.499	-0.002
78	D	79	TYR	0	-0.013	0.011	3.368	-2.033	-1.770	0.007	-0.077	-0.193	0.000
79	D	80	GLY	0	0.035	0.004	2.446	-4.124	-2.960	2.007	-1.572	-1.599	-0.017
80	D	81	PRO	0	-0.043	-0.020	3.259	0.852	1.460	0.013	-0.185	-0.436	0.000
81	D	82	ALA	0	0.018	0.009	2.290	-5.035	-4.734	2.307	-1.205	-1.403	-0.014
82	D	83	ASP	-1	-0.905	-0.949	3.286	-3.831	-2.589	0.056	-0.763	-0.535	-0.004
83	D	84	VAL	0	-0.064	-0.040	4.314	0.460	0.514	-0.001	-0.008	-0.045	0.000
84	D	85	GLU	-1	-0.956	-0.956	7.545	0.534	0.534	0.000	0.000	0.000	0.000
85	D	86	ASP	-1	-0.788	-0.879	6.870	3.109	3.109	0.000	0.000	0.000	0.000
86	D	87	THR	0	-0.042	-0.014	8.443	-0.444	-0.444	0.000	0.000	0.000	0.000
87	D	88	THR	0	-0.017	-0.013	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)