FMO DATABASE

FMODB ID: 2M4NR

Calculation Name: 2EKK-A-Other547

Preferred Name: E3 ubiquitin-protein ligase HUWE1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EKK

Chain ID: A

ChEMBL ID: CHEMBL4295881

UniProt ID: Q7Z6Z7

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	47
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-211510.217319
FMO2-HF: Nuclear repulsion	192401.319254
FMO2-HF: Total energy	-19108.898065
FMO2-MP2: Total energy	-19161.373993

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-31.518	-30.831	0	-0.284	-0.403	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.919

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].	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	3	SER	0	0.012	-0.005	3.826	-1.671	-0.984	-0.284	-0.403	-0.001
4	A	4	GLY	0	0.032	0.022	6.405	1.116	1.116	0.000	0.000	0.000
5	A	5	SER	0	0.012	0.016	10.042	0.718	0.718	0.000	0.000	0.000
6	A	6	SER	0	-0.035	-0.027	13.249	0.157	0.157	0.000	0.000	0.000
7	A	7	GLY	0	0.019	0.020	15.157	0.421	0.421	0.000	0.000	0.000
8	A	8	VAL	0	0.036	0.020	18.922	-0.223	-0.223	0.000	0.000	0.000
9	A	9	ASN	0	0.002	-0.009	16.754	-0.838	-0.838	0.000	0.000	0.000
10	A	10	GLN	0	0.019	-0.004	18.989	0.888	0.888	0.000	0.000	0.000
11	A	11	GLN	0	-0.004	0.014	19.339	1.130	1.130	0.000	0.000	0.000
12	A	12	GLN	0	0.104	0.027	21.227	0.106	0.106	0.000	0.000	0.000
13	A	13	LEU	0	0.004	0.014	23.556	0.502	0.502	0.000	0.000	0.000
14	A	14	GLN	0	-0.049	-0.041	23.950	0.607	0.607	0.000	0.000	0.000
15	A	15	GLN	0	-0.003	0.000	24.947	0.718	0.718	0.000	0.000	0.000
16	A	16	LEU	0	-0.009	0.005	27.260	0.427	0.427	0.000	0.000	0.000
17	A	17	MET	0	-0.050	-0.015	27.552	0.439	0.439	0.000	0.000	0.000
18	A	18	ASP	-1	-0.850	-0.919	29.308	-10.577	-10.577	0.000	0.000	0.000
19	A	19	MET	0	-0.105	-0.044	31.400	0.349	0.349	0.000	0.000	0.000
20	A	20	GLY	0	-0.023	0.011	33.975	0.329	0.329	0.000	0.000	0.000
21	A	21	PHE	0	0.019	0.006	33.002	0.167	0.167	0.000	0.000	0.000
22	A	22	THR	0	-0.001	-0.006	33.585	-0.125	-0.125	0.000	0.000	0.000
23	A	23	ARG	1	1.011	0.967	23.755	12.226	12.226	0.000	0.000	0.000
24	A	24	GLU	-1	-0.985	-0.981	30.008	-9.389	-9.389	0.000	0.000	0.000
25	A	25	HIS	1	0.945	0.973	31.397	8.827	8.827	0.000	0.000	0.000
26	A	26	ALA	0	0.049	0.024	29.329	-0.096	-0.096	0.000	0.000	0.000
27	A	27	MET	0	-0.064	-0.041	23.224	-0.540	-0.540	0.000	0.000	0.000
28	A	28	GLU	-1	-0.883	-0.942	27.568	-10.654	-10.654	0.000	0.000	0.000
29	A	29	ALA	0	0.007	0.007	29.662	0.009	0.009	0.000	0.000	0.000
30	A	30	LEU	0	-0.062	-0.016	24.042	-0.154	-0.154	0.000	0.000	0.000
31	A	31	LEU	0	-0.073	-0.030	24.091	-0.368	-0.368	0.000	0.000	0.000
32	A	32	ASN	0	0.012	0.011	26.736	-0.198	-0.198	0.000	0.000	0.000
33	A	33	THR	0	-0.092	-0.051	28.541	0.078	0.078	0.000	0.000	0.000
34	A	34	SER	0	-0.012	-0.026	24.956	-0.370	-0.370	0.000	0.000	0.000
35	A	35	THR	0	-0.067	-0.047	24.240	-0.480	-0.480	0.000	0.000	0.000
36	A	36	MET	0	0.017	0.000	25.241	0.025	0.025	0.000	0.000	0.000
37	A	37	GLU	-1	-0.887	-0.923	26.938	-9.678	-9.678	0.000	0.000	0.000
38	A	38	GLN	0	0.074	0.052	29.303	-0.078	-0.078	0.000	0.000	0.000
39	A	39	ALA	0	0.006	0.012	28.032	0.277	0.277	0.000	0.000	0.000
40	A	40	THR	0	0.019	-0.017	30.123	0.188	0.188	0.000	0.000	0.000
41	A	41	GLU	-1	-0.923	-0.959	32.335	-8.572	-8.572	0.000	0.000	0.000
42	A	42	TYR	0	-0.022	0.013	32.750	0.329	0.329	0.000	0.000	0.000
43	A	43	LEU	0	-0.033	-0.012	31.219	0.078	0.078	0.000	0.000	0.000
44	A	44	LEU	0	-0.007	-0.002	35.436	0.245	0.245	0.000	0.000	0.000
45	A	45	THR	0	-0.084	-0.057	37.674	0.254	0.254	0.000	0.000	0.000
46	A	46	HIS	0	-0.118	-0.062	37.861	0.097	0.097	0.000	0.000	0.000
47	A	47	PRO	-1	-0.907	-0.937	38.211	-8.214	-8.214	0.000	0.000	0.000

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