FMO DATABASE

FMODB ID: 72M8K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-117297.218564
FMO2-HF: Nuclear repulsion	102688.613494
FMO2-HF: Total energy	-14608.605069
FMO2-MP2: Total energy	-14649.188989

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.
0.376	1.778	-0.006	-0.735	-0.66	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 : 0.001

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	0.938	0.960	3.648	-0.234	1.168	-0.006	-0.735	-0.660	0.002
4	B	52	ILE	0	0.032	0.024	5.190	0.499	0.499	0.000	0.000	0.000	0.000
5	B	53	ILE	0	-0.016	-0.013	7.260	-0.054	-0.054	0.000	0.000	0.000	0.000
6	B	54	TYR	0	0.010	0.007	10.450	0.050	0.050	0.000	0.000	0.000	0.000
7	B	55	ASP	-1	-0.752	-0.871	13.924	-0.094	-0.094	0.000	0.000	0.000	0.000
8	B	56	ARG	1	0.983	0.986	17.553	0.084	0.084	0.000	0.000	0.000	0.000
9	B	57	LYS	1	0.810	0.884	20.925	0.009	0.009	0.000	0.000	0.000	0.000
10	B	58	PHE	0	0.054	0.016	14.423	0.004	0.004	0.000	0.000	0.000	0.000
11	B	59	LEU	0	0.016	0.010	15.978	0.002	0.002	0.000	0.000	0.000	0.000
12	B	60	MET	0	-0.054	-0.036	19.210	0.001	0.001	0.000	0.000	0.000	0.000
13	B	61	GLU	-1	-0.835	-0.888	20.414	0.002	0.002	0.000	0.000	0.000	0.000
14	B	62	CYS	0	0.038	0.018	17.763	0.006	0.006	0.000	0.000	0.000	0.000
15	B	63	ARG	1	0.943	0.989	20.447	0.074	0.074	0.000	0.000	0.000	0.000
16	B	64	ASN	0	-0.030	-0.028	23.507	0.001	0.001	0.000	0.000	0.000	0.000
17	B	65	SER	0	-0.008	-0.003	21.472	0.009	0.009	0.000	0.000	0.000	0.000
18	B	66	PRO	0	0.033	0.016	23.927	-0.009	-0.009	0.000	0.000	0.000	0.000
19	B	67	VAL	0	0.050	0.029	21.211	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	68	THR	0	-0.037	-0.032	22.421	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	69	LYS	1	0.834	0.918	24.932	0.048	0.048	0.000	0.000	0.000	0.000
22	B	70	THR	0	-0.012	0.009	26.828	0.005	0.005	0.000	0.000	0.000	0.000
23	B	71	PRO	0	0.007	0.005	27.030	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	72	PRO	0	0.040	0.011	25.258	0.004	0.004	0.000	0.000	0.000	0.000
25	B	73	ARG	1	0.867	0.924	26.989	0.067	0.067	0.000	0.000	0.000	0.000
26	B	74	ASP	-1	-0.865	-0.927	26.627	-0.085	-0.085	0.000	0.000	0.000	0.000
27	B	75	LEU	0	-0.062	-0.019	28.913	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	76	PRO	0	0.027	0.028	30.085	0.006	0.006	0.000	0.000	0.000	0.000
29	B	77	THR	0	0.007	0.010	33.047	0.001	0.001	0.000	0.000	0.000	0.000
30	B	78	ILE	0	0.035	0.012	33.363	0.001	0.001	0.000	0.000	0.000	0.000
31	B	79	PRO	0	0.020	0.015	37.221	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	80	GLY	0	0.012	0.001	39.107	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	81	VAL	0	-0.063	-0.026	32.638	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	82	THR	0	-0.044	-0.047	32.209	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	83	SER	0	-0.008	0.009	34.966	0.004	0.004	0.000	0.000	0.000	0.000

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