FMO DATABASE

FMODB ID: MV9KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-117454.864148
FMO2-HF: Nuclear repulsion	102846.324648
FMO2-HF: Total energy	-14608.539501
FMO2-MP2: Total energy	-14649.131388

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.
-0.178	1.444	-0.018	-0.894	-0.711	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 : 0.025 / q_NPA : 0.002

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	0.940	0.961	3.660	-0.730	0.892	-0.018	-0.894	-0.711	0.002
4	B	52	ILE	0	0.021	0.013	5.372	0.460	0.460	0.000	0.000	0.000	0.000
5	B	53	ILE	0	-0.023	-0.008	7.431	-0.040	-0.040	0.000	0.000	0.000	0.000
6	B	54	TYR	0	0.019	0.007	10.328	0.047	0.047	0.000	0.000	0.000	0.000
7	B	55	ASP	-1	-0.777	-0.889	13.810	-0.057	-0.057	0.000	0.000	0.000	0.000
8	B	56	ARG	1	0.995	0.983	17.220	0.064	0.064	0.000	0.000	0.000	0.000
9	B	57	LYS	1	0.842	0.907	20.475	-0.016	-0.016	0.000	0.000	0.000	0.000
10	B	58	PHE	0	0.052	0.021	14.314	0.005	0.005	0.000	0.000	0.000	0.000
11	B	59	LEU	0	0.023	0.011	15.742	0.000	0.000	0.000	0.000	0.000	0.000
12	B	60	MET	0	-0.068	-0.042	18.873	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	61	GLU	-1	-0.860	-0.901	20.414	0.021	0.021	0.000	0.000	0.000	0.000
14	B	62	CYS	0	0.027	0.010	17.746	0.004	0.004	0.000	0.000	0.000	0.000
15	B	63	ARG	1	0.952	0.985	20.448	0.056	0.056	0.000	0.000	0.000	0.000
16	B	64	ASN	0	-0.045	-0.030	23.582	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	65	SER	0	0.018	0.016	21.548	0.009	0.009	0.000	0.000	0.000	0.000
18	B	66	PRO	0	0.044	0.012	24.111	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	67	VAL	0	0.035	0.020	21.329	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	68	THR	0	-0.039	-0.027	22.426	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	69	LYS	1	0.834	0.922	24.906	0.036	0.036	0.000	0.000	0.000	0.000
22	B	70	THR	0	-0.022	0.007	26.947	0.004	0.004	0.000	0.000	0.000	0.000
23	B	71	PRO	0	0.009	0.007	27.208	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	72	PRO	0	0.050	0.016	25.463	0.002	0.002	0.000	0.000	0.000	0.000
25	B	73	ARG	1	0.877	0.930	26.868	0.059	0.059	0.000	0.000	0.000	0.000
26	B	74	ASP	-1	-0.873	-0.930	26.927	-0.076	-0.076	0.000	0.000	0.000	0.000
27	B	75	LEU	0	-0.062	-0.018	28.795	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	76	PRO	0	0.036	0.027	30.057	0.005	0.005	0.000	0.000	0.000	0.000
29	B	77	THR	0	-0.001	0.020	32.998	0.002	0.002	0.000	0.000	0.000	0.000
30	B	78	ILE	0	0.030	0.006	33.666	0.001	0.001	0.000	0.000	0.000	0.000
31	B	79	PRO	0	0.040	0.030	37.332	0.000	0.000	0.000	0.000	0.000	0.000
32	B	80	GLY	0	0.006	-0.001	39.170	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	81	VAL	0	-0.059	-0.024	32.803	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	82	THR	0	-0.028	-0.058	32.154	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	83	SER	0	-0.033	0.000	34.949	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)