FMO DATABASE

FMODB ID: 94M52

Calculation Name: 4UED-B-Xray372

Preferred Name: Eukaryotic translation initiation factor 4E-binding protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UED

Chain ID: B

ChEMBL ID: CHEMBL3351214

UniProt ID: Q13541

Base Structure: X-ray

Registration Date: 2023-06-22

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	35
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-117218.505616
FMO2-HF: Nuclear repulsion	102610.124699
FMO2-HF: Total energy	-14608.380917
FMO2-MP2: Total energy	-14648.968545

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(B:49:MET)

Summations of interaction energy for fragment #1(B:49: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.
-0.257	1.394	-0.018	-0.918	-0.715	0.002

Interaction energy analysis for fragmet #1(B:49:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.004

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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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	B	51	ARG	1	0.958	0.974	3.634	-0.893	0.758	-0.018	-0.918	-0.715	0.002
4	B	52	ILE	0	0.033	0.018	5.368	0.457	0.457	0.000	0.000	0.000	0.000
5	B	53	ILE	0	-0.038	-0.017	7.410	-0.023	-0.023	0.000	0.000	0.000	0.000
6	B	54	TYR	0	0.027	0.013	10.340	0.099	0.099	0.000	0.000	0.000	0.000
7	B	55	ASP	-1	-0.846	-0.915	13.788	-0.066	-0.066	0.000	0.000	0.000	0.000
8	B	56	ARG	1	1.009	0.977	17.194	0.073	0.073	0.000	0.000	0.000	0.000
9	B	57	LYS	1	0.956	0.975	20.452	0.003	0.003	0.000	0.000	0.000	0.000
10	B	58	PHE	0	0.084	0.045	14.599	0.002	0.002	0.000	0.000	0.000	0.000
11	B	59	LEU	0	0.013	0.002	15.634	0.000	0.000	0.000	0.000	0.000	0.000
12	B	60	MET	0	-0.081	-0.050	18.857	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	61	GLU	-1	-0.943	-0.955	20.415	0.005	0.005	0.000	0.000	0.000	0.000
14	B	62	CYS	0	0.007	-0.001	17.639	0.003	0.003	0.000	0.000	0.000	0.000
15	B	63	ARG	1	0.929	0.969	20.437	0.064	0.064	0.000	0.000	0.000	0.000
16	B	64	ASN	0	-0.039	-0.024	23.573	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	65	SER	0	0.021	0.024	21.565	0.009	0.009	0.000	0.000	0.000	0.000
18	B	66	PRO	0	0.041	0.004	24.107	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	67	VAL	0	0.033	0.020	21.344	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	68	THR	0	-0.055	-0.032	22.387	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	69	LYS	1	0.900	0.955	24.906	0.042	0.042	0.000	0.000	0.000	0.000
22	B	70	THR	0	-0.028	0.004	27.013	0.005	0.005	0.000	0.000	0.000	0.000
23	B	71	PRO	0	0.012	0.011	27.213	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	72	PRO	0	0.050	0.014	25.504	0.002	0.002	0.000	0.000	0.000	0.000
25	B	73	ARG	1	0.880	0.932	26.879	0.064	0.064	0.000	0.000	0.000	0.000
26	B	74	ASP	-1	-0.871	-0.929	26.992	-0.079	-0.079	0.000	0.000	0.000	0.000
27	B	75	LEU	0	-0.064	-0.023	28.532	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	76	PRO	0	0.040	0.032	30.072	0.006	0.006	0.000	0.000	0.000	0.000
29	B	77	THR	0	0.000	0.017	33.007	0.001	0.001	0.000	0.000	0.000	0.000
30	B	78	ILE	0	0.031	0.008	33.706	0.001	0.001	0.000	0.000	0.000	0.000
31	B	79	PRO	0	0.040	0.028	37.338	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	80	GLY	0	0.007	0.002	39.169	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	81	VAL	0	-0.053	-0.018	32.875	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	82	THR	0	-0.037	-0.058	32.225	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	83	SER	0	-0.037	-0.009	34.952	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:49:MET)