FMO DATABASE

FMODB ID: QLMZY

Calculation Name: 2KQ0-A-Other547

Preferred Name: E3 ubiquitin-protein ligase NEDD4

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KQ0

Chain ID: A

ChEMBL ID: CHEMBL3621023

UniProt ID: P46934

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	35
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-152720.561545
FMO2-HF: Nuclear repulsion	138427.682517
FMO2-HF: Total energy	-14292.879028
FMO2-MP2: Total energy	-14336.132728

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:12:PHE)

Summations of interaction energy for fragment #1(A:12:PHE)

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.
27.693	32.066	1.745	-1.75	-4.368	-0.001

Interaction energy analysis for fragmet #1(A:12:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.900

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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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	14	PRO	0	0.035	0.030	3.845	-0.422	1.667	-0.021	-0.781	-1.287	0.000
8	A	19	VAL	0	-0.031	-0.020	4.745	-0.386	-0.343	-0.001	-0.003	-0.039	0.000
32	A	43	ARG	1	0.801	0.874	2.575	47.354	49.595	1.767	-0.966	-3.042	-0.001
4	A	15	LYS	1	0.986	0.983	6.596	25.759	25.759	0.000	0.000	0.000	0.000
5	A	16	GLY	0	0.027	0.014	7.936	1.961	1.961	0.000	0.000	0.000	0.000
6	A	17	TRP	0	0.012	0.008	8.003	1.419	1.419	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.797	-0.846	7.573	-27.922	-27.922	0.000	0.000	0.000	0.000
9	A	20	ARG	1	0.872	0.906	7.544	22.112	22.112	0.000	0.000	0.000	0.000
10	A	21	HIS	0	-0.009	-0.008	10.825	1.264	1.264	0.000	0.000	0.000	0.000
11	A	22	ALA	0	0.032	0.022	12.503	1.342	1.342	0.000	0.000	0.000	0.000
12	A	23	PRO	0	0.008	-0.019	15.946	-0.253	-0.253	0.000	0.000	0.000	0.000
13	A	24	ASN	0	-0.059	-0.027	17.515	0.435	0.435	0.000	0.000	0.000	0.000
14	A	25	GLY	0	0.048	0.039	16.741	0.137	0.137	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.882	0.931	12.070	22.831	22.831	0.000	0.000	0.000	0.000
16	A	27	PRO	0	-0.021	-0.009	8.756	0.489	0.489	0.000	0.000	0.000	0.000
17	A	28	PHE	0	-0.002	0.002	10.663	0.231	0.231	0.000	0.000	0.000	0.000
18	A	29	PHE	0	-0.001	-0.008	5.627	-2.936	-2.936	0.000	0.000	0.000	0.000
19	A	30	ILE	0	0.002	-0.006	10.081	2.647	2.647	0.000	0.000	0.000	0.000
20	A	31	ASP	-1	-0.765	-0.839	11.570	-23.332	-23.332	0.000	0.000	0.000	0.000
21	A	32	HIS	0	-0.012	-0.022	12.459	2.910	2.910	0.000	0.000	0.000	0.000
22	A	33	ASN	0	-0.123	-0.073	14.312	2.377	2.377	0.000	0.000	0.000	0.000
23	A	34	THR	0	-0.007	-0.025	15.749	1.371	1.371	0.000	0.000	0.000	0.000
24	A	35	LYS	1	0.813	0.911	17.333	16.669	16.669	0.000	0.000	0.000	0.000
25	A	36	THR	0	0.042	0.033	14.903	0.860	0.860	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.013	-0.021	14.447	-1.621	-1.621	0.000	0.000	0.000	0.000
27	A	38	THR	0	0.001	-0.003	11.911	0.929	0.929	0.000	0.000	0.000	0.000
28	A	39	TRP	0	0.055	0.027	12.848	-1.691	-1.691	0.000	0.000	0.000	0.000
29	A	40	GLU	-1	-0.818	-0.882	11.917	-21.635	-21.635	0.000	0.000	0.000	0.000
30	A	41	ASP	-1	-0.761	-0.863	5.440	-49.223	-49.223	0.000	0.000	0.000	0.000
31	A	42	PRO	0	0.044	0.018	8.289	1.246	1.246	0.000	0.000	0.000	0.000
33	A	44	LEU	0	-0.069	-0.033	7.059	1.447	1.447	0.000	0.000	0.000	0.000
34	A	45	LYS	1	0.791	0.877	10.151	20.602	20.602	0.000	0.000	0.000	0.000
35	A	46	ILE	-1	-0.885	-0.919	10.398	-19.278	-19.278	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PHE)