FMO DATABASE

FMODB ID: 746YK

Calculation Name: 4V6X-A-Other547

Preferred Name: Elongation factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V6X

Chain ID: A

ChEMBL ID: CHEMBL1795108

UniProt ID: P13639

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1075510.026892
FMO2-HF: Nuclear repulsion	1026093.628272
FMO2-HF: Total energy	-49416.39862
FMO2-MP2: Total energy	-49559.961556

3D Structure Molmil

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:8:GLY)

Summations of interaction energy for fragment #1(A:8: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.
133.517	135.335	7.418	-4.574	-4.662	-0.041

Interaction energy analysis for fragmet #1(A:8:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.892

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

Sort

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	A	10	SER	0	0.040	0.018	3.669	-9.896	-8.793	-0.002	-0.642	-0.459	-0.002
53	A	60	MET	0	-0.019	0.004	3.739	-1.021	-0.869	0.001	-0.040	-0.113	0.000
102	A	109	LYS	1	0.927	0.974	3.247	18.277	19.529	0.102	-0.560	-0.793	-0.004
103	A	110	GLY	0	0.027	-0.019	2.553	-16.075	-14.049	1.279	-1.884	-1.421	-0.019
104	A	111	GLU	-1	-0.837	-0.898	4.256	-24.954	-24.998	0.001	-0.032	0.075	0.000
122	A	129	TRP	0	0.007	0.019	2.168	-17.047	-19.718	6.037	-1.416	-1.951	-0.016
4	A	11	GLY	0	0.026	0.025	6.311	3.862	3.862	0.000	0.000	0.000	0.000
5	A	12	ALA	0	0.004	-0.006	8.734	-1.485	-1.485	0.000	0.000	0.000	0.000
6	A	13	LYS	1	0.846	0.918	9.915	26.222	26.222	0.000	0.000	0.000	0.000
7	A	14	PHE	0	0.050	0.021	11.599	0.853	0.853	0.000	0.000	0.000	0.000
8	A	15	ARG	1	0.897	0.936	14.743	15.843	15.843	0.000	0.000	0.000	0.000
9	A	16	ILE	0	0.069	0.053	15.066	0.926	0.926	0.000	0.000	0.000	0.000
10	A	17	SER	0	-0.045	-0.035	17.855	-0.161	-0.161	0.000	0.000	0.000	0.000
11	A	18	LEU	0	-0.033	-0.008	15.708	-0.311	-0.311	0.000	0.000	0.000	0.000
12	A	19	GLY	0	0.000	-0.015	18.793	0.939	0.939	0.000	0.000	0.000	0.000
13	A	20	LEU	0	-0.055	-0.012	16.291	0.653	0.653	0.000	0.000	0.000	0.000
14	A	21	PRO	0	0.033	0.007	18.058	-1.043	-1.043	0.000	0.000	0.000	0.000
15	A	22	VAL	0	0.009	0.004	17.800	-0.144	-0.144	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.004	0.013	19.887	0.740	0.740	0.000	0.000	0.000	0.000
17	A	24	ALA	0	-0.022	-0.004	19.872	0.607	0.607	0.000	0.000	0.000	0.000
18	A	25	VAL	0	-0.051	-0.031	20.349	-0.532	-0.532	0.000	0.000	0.000	0.000
19	A	26	ILE	0	-0.009	0.004	15.192	0.302	0.302	0.000	0.000	0.000	0.000
20	A	27	ASN	0	-0.033	-0.037	19.916	0.381	0.381	0.000	0.000	0.000	0.000
21	A	28	CYS	0	-0.081	-0.038	17.119	-1.239	-1.239	0.000	0.000	0.000	0.000
22	A	29	ALA	0	0.030	0.019	17.270	0.826	0.826	0.000	0.000	0.000	0.000
23	A	30	ASP	-1	-0.699	-0.822	15.073	-18.562	-18.562	0.000	0.000	0.000	0.000
24	A	31	ASN	0	0.047	0.027	17.724	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.029	-0.038	15.878	0.681	0.681	0.000	0.000	0.000	0.000
26	A	33	GLY	0	0.006	-0.004	19.219	0.557	0.557	0.000	0.000	0.000	0.000
27	A	34	ALA	0	0.004	0.012	18.729	0.564	0.564	0.000	0.000	0.000	0.000
28	A	35	LYS	1	0.985	0.992	20.802	11.692	11.692	0.000	0.000	0.000	0.000
29	A	36	ASN	0	-0.069	-0.050	20.910	0.513	0.513	0.000	0.000	0.000	0.000
30	A	37	LEU	0	0.041	0.021	14.258	-0.230	-0.230	0.000	0.000	0.000	0.000
31	A	38	TYR	0	-0.052	-0.026	18.029	0.373	0.373	0.000	0.000	0.000	0.000
32	A	39	ILE	0	0.023	0.013	15.478	-0.805	-0.805	0.000	0.000	0.000	0.000
33	A	40	ILE	0	0.037	0.008	16.118	0.907	0.907	0.000	0.000	0.000	0.000
34	A	41	SER	0	-0.012	-0.004	13.985	-0.184	-0.184	0.000	0.000	0.000	0.000
35	A	42	VAL	0	0.008	0.001	11.497	-0.996	-0.996	0.000	0.000	0.000	0.000
36	A	43	LYS	1	0.945	0.957	6.886	34.676	34.676	0.000	0.000	0.000	0.000
37	A	44	GLY	0	-0.002	0.016	8.786	-1.357	-1.357	0.000	0.000	0.000	0.000
38	A	45	ILE	0	-0.056	-0.035	10.000	0.956	0.956	0.000	0.000	0.000	0.000
39	A	46	LYS	1	1.026	1.021	13.729	19.393	19.393	0.000	0.000	0.000	0.000
40	A	47	GLY	0	0.018	0.020	16.072	0.473	0.473	0.000	0.000	0.000	0.000
41	A	48	ARG	1	0.924	0.959	19.252	11.837	11.837	0.000	0.000	0.000	0.000
42	A	49	LEU	0	0.083	0.044	23.062	-0.220	-0.220	0.000	0.000	0.000	0.000
43	A	50	ASN	0	0.048	0.005	26.071	0.018	0.018	0.000	0.000	0.000	0.000
44	A	51	ARG	1	0.914	0.975	20.640	13.901	13.901	0.000	0.000	0.000	0.000
45	A	52	LEU	0	0.062	0.029	21.936	-0.546	-0.546	0.000	0.000	0.000	0.000
46	A	53	PRO	0	-0.014	-0.006	16.595	-0.341	-0.341	0.000	0.000	0.000	0.000
47	A	54	ALA	0	0.019	0.006	17.197	0.311	0.311	0.000	0.000	0.000	0.000
48	A	55	ALA	0	0.022	0.012	13.687	-0.863	-0.863	0.000	0.000	0.000	0.000
49	A	56	GLY	0	0.011	-0.014	14.098	1.908	1.908	0.000	0.000	0.000	0.000
50	A	57	VAL	0	0.028	0.011	13.400	-1.544	-1.544	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.064	0.026	10.306	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	59	ASP	-1	-0.846	-0.904	8.490	-30.607	-30.607	0.000	0.000	0.000	0.000
54	A	61	VAL	0	-0.023	-0.024	7.704	1.563	1.563	0.000	0.000	0.000	0.000
55	A	62	MET	0	-0.038	0.001	10.349	-2.390	-2.390	0.000	0.000	0.000	0.000
56	A	63	ALA	0	0.029	0.000	12.289	1.438	1.438	0.000	0.000	0.000	0.000
57	A	64	THR	0	0.024	0.016	15.076	0.370	0.370	0.000	0.000	0.000	0.000
58	A	65	VAL	0	0.056	0.031	17.947	0.296	0.296	0.000	0.000	0.000	0.000
59	A	66	LYS	1	0.970	0.992	20.060	12.704	12.704	0.000	0.000	0.000	0.000
60	A	67	LYS	1	0.940	0.963	23.399	11.541	11.541	0.000	0.000	0.000	0.000
61	A	68	GLY	0	0.066	0.025	23.381	-0.529	-0.529	0.000	0.000	0.000	0.000
62	A	69	LYS	1	0.920	0.957	22.587	13.405	13.405	0.000	0.000	0.000	0.000
63	A	70	PRO	0	0.031	0.004	23.781	-0.513	-0.513	0.000	0.000	0.000	0.000
64	A	71	GLU	-1	-0.844	-0.920	23.127	-12.275	-12.275	0.000	0.000	0.000	0.000
65	A	72	LEU	0	-0.046	-0.003	18.112	-0.781	-0.781	0.000	0.000	0.000	0.000
66	A	73	ARG	1	0.832	0.922	19.485	11.274	11.274	0.000	0.000	0.000	0.000
67	A	74	LYS	1	0.936	0.954	21.829	11.315	11.315	0.000	0.000	0.000	0.000
68	A	75	LYS	0	0.031	0.020	18.112	0.037	0.037	0.000	0.000	0.000	0.000
69	A	76	VAL	0	-0.013	-0.007	14.219	-0.473	-0.473	0.000	0.000	0.000	0.000
70	A	77	HIS	0	-0.021	-0.002	12.681	-0.350	-0.350	0.000	0.000	0.000	0.000
71	A	78	PRO	0	-0.011	-0.014	7.783	0.457	0.457	0.000	0.000	0.000	0.000
72	A	79	ALA	0	0.028	0.019	9.675	1.559	1.559	0.000	0.000	0.000	0.000
73	A	80	VAL	0	-0.002	0.003	6.525	-2.570	-2.570	0.000	0.000	0.000	0.000
74	A	81	VAL	0	-0.033	-0.001	9.487	2.594	2.594	0.000	0.000	0.000	0.000
75	A	82	ILE	0	0.022	-0.015	12.044	-1.317	-1.317	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.802	0.890	14.338	15.523	15.523	0.000	0.000	0.000	0.000
77	A	84	GLN	0	-0.041	-0.035	17.933	-0.243	-0.243	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.985	0.985	20.056	11.618	11.618	0.000	0.000	0.000	0.000
79	A	86	LYS	1	0.814	0.923	21.822	13.088	13.088	0.000	0.000	0.000	0.000
80	A	87	SER	0	0.042	0.030	22.681	-0.529	-0.529	0.000	0.000	0.000	0.000
81	A	88	TYR	0	-0.068	-0.057	19.137	0.198	0.198	0.000	0.000	0.000	0.000
82	A	89	ARG	1	0.927	0.990	22.380	12.644	12.644	0.000	0.000	0.000	0.000
83	A	90	ARG	1	0.909	0.957	20.468	13.281	13.281	0.000	0.000	0.000	0.000
84	A	91	LYS	1	0.898	0.939	19.061	16.605	16.605	0.000	0.000	0.000	0.000
85	A	92	ASP	-1	-0.765	-0.873	23.200	-13.077	-13.077	0.000	0.000	0.000	0.000
86	A	93	GLY	0	-0.021	-0.005	26.226	0.344	0.344	0.000	0.000	0.000	0.000
87	A	94	VAL	0	0.001	-0.001	25.045	0.134	0.134	0.000	0.000	0.000	0.000
88	A	95	PHE	0	0.012	-0.008	25.372	-0.656	-0.656	0.000	0.000	0.000	0.000
89	A	96	LEU	0	-0.006	0.002	22.416	0.339	0.339	0.000	0.000	0.000	0.000
90	A	97	TYR	0	-0.021	-0.022	23.105	-0.493	-0.493	0.000	0.000	0.000	0.000
91	A	98	PHE	0	0.045	0.020	19.592	0.099	0.099	0.000	0.000	0.000	0.000
92	A	99	GLU	-1	-0.845	-0.922	23.846	-10.670	-10.670	0.000	0.000	0.000	0.000
93	A	100	ASP	-1	-0.836	-0.892	22.159	-13.709	-13.709	0.000	0.000	0.000	0.000
94	A	101	ASN	0	0.030	0.014	19.938	-0.434	-0.434	0.000	0.000	0.000	0.000
95	A	102	ALA	0	0.015	0.014	18.109	0.378	0.378	0.000	0.000	0.000	0.000
96	A	103	GLY	0	0.051	0.022	14.163	-0.970	-0.970	0.000	0.000	0.000	0.000
97	A	104	VAL	0	-0.006	0.010	10.951	1.305	1.305	0.000	0.000	0.000	0.000
98	A	105	ILE	0	0.033	0.006	11.464	-1.814	-1.814	0.000	0.000	0.000	0.000
99	A	106	VAL	0	-0.040	-0.008	5.957	-0.137	-0.137	0.000	0.000	0.000	0.000
100	A	107	ASN	0	0.016	0.002	6.806	-3.724	-3.724	0.000	0.000	0.000	0.000
101	A	108	ASN	0	0.013	-0.023	5.193	-4.821	-4.821	0.000	0.000	0.000	0.000
105	A	112	MET	0	-0.028	0.018	7.928	0.392	0.392	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.928	0.976	10.396	18.006	18.006	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.001	-0.005	13.149	1.325	1.325	0.000	0.000	0.000	0.000
108	A	115	SER	0	-0.039	-0.038	14.451	-0.811	-0.811	0.000	0.000	0.000	0.000
109	A	116	ALA	0	0.029	0.021	16.874	0.414	0.414	0.000	0.000	0.000	0.000
110	A	117	ILE	0	-0.022	-0.014	13.642	-0.528	-0.528	0.000	0.000	0.000	0.000
111	A	118	THR	0	-0.046	-0.007	17.955	0.873	0.873	0.000	0.000	0.000	0.000
112	A	119	GLY	0	0.045	0.013	20.526	-0.305	-0.305	0.000	0.000	0.000	0.000
113	A	120	PRO	0	0.022	0.018	20.939	-0.380	-0.380	0.000	0.000	0.000	0.000
114	A	121	VAL	0	-0.013	-0.028	14.608	-0.589	-0.589	0.000	0.000	0.000	0.000
115	A	122	ALA	0	0.061	0.037	16.058	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	123	LYS	1	0.948	0.952	15.133	16.641	16.641	0.000	0.000	0.000	0.000
117	A	124	GLU	-1	-0.854	-0.906	14.074	-19.803	-19.803	0.000	0.000	0.000	0.000
118	A	125	CYS	0	-0.084	-0.016	10.844	-1.824	-1.824	0.000	0.000	0.000	0.000
119	A	126	ALA	0	0.007	0.003	10.201	-2.780	-2.780	0.000	0.000	0.000	0.000
120	A	127	ASP	-1	-0.844	-0.926	11.328	-22.074	-22.074	0.000	0.000	0.000	0.000
121	A	128	LEU	0	-0.058	-0.004	7.089	-1.726	-1.726	0.000	0.000	0.000	0.000
123	A	130	PRO	0	0.105	0.049	6.840	3.244	3.244	0.000	0.000	0.000	0.000
124	A	131	ARG	1	0.888	0.920	7.589	29.151	29.151	0.000	0.000	0.000	0.000
125	A	132	ILE	0	-0.025	-0.014	8.088	1.807	1.807	0.000	0.000	0.000	0.000
126	A	133	ALA	0	0.002	-0.005	10.940	1.984	1.984	0.000	0.000	0.000	0.000
127	A	134	SER	0	-0.018	0.000	12.860	1.557	1.557	0.000	0.000	0.000	0.000
128	A	135	ASN	0	-0.029	-0.029	13.590	1.595	1.595	0.000	0.000	0.000	0.000
129	A	136	ALA	0	-0.018	-0.011	15.407	0.670	0.670	0.000	0.000	0.000	0.000
130	A	137	GLY	0	0.053	0.039	17.147	0.422	0.422	0.000	0.000	0.000	0.000
131	A	138	SER	0	-0.001	-0.008	20.514	-0.184	-0.184	0.000	0.000	0.000	0.000
132	A	139	ILE	0	-0.024	-0.010	17.315	-0.447	-0.447	0.000	0.000	0.000	0.000
133	A	140	ALA	-1	-0.941	-0.967	19.887	-13.598	-13.598	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLY)