FMO DATABASE

FMODB ID: 435MN

Calculation Name: 3LWW-D-Xray372

Preferred Name: Importin subunit beta-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3LWW

Chain ID: D

ChEMBL ID: CHEMBL1741199

UniProt ID: Q14974

Base Structure: X-ray

Registration Date: 2023-06-19

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	26
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-96394.780107
FMO2-HF: Nuclear repulsion	84940.796686
FMO2-HF: Total energy	-11453.983421
FMO2-MP2: Total energy	-11488.281016

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(D:39:GLU)

Summations of interaction energy for fragment #1(D:39:GLU)

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.
-173.703	-169.026	8.453	-5.071	-8.061	0.014

Interaction energy analysis for fragmet #1(D:39:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.822 / q_NPA : -0.920

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	D	41	SER	0	-0.046	-0.044	2.684	-7.220	-4.055	1.510	-1.648	-3.027	0.001
4	D	42	GLU	-1	-0.852	-0.924	1.844	38.305	39.313	6.920	-3.426	-4.502	0.013
5	D	43	ARG	1	1.062	1.024	3.524	-43.286	-42.782	0.023	0.003	-0.532	0.000
6	D	44	ARG	1	0.931	0.970	5.996	-35.509	-35.509	0.000	0.000	0.000	0.000
7	D	45	ARG	1	0.971	0.990	5.167	-44.967	-44.967	0.000	0.000	0.000	0.000
8	D	46	ARG	1	0.971	1.001	7.200	-37.858	-37.858	0.000	0.000	0.000	0.000
9	D	47	LEU	0	-0.015	0.004	9.629	-2.201	-2.201	0.000	0.000	0.000	0.000
10	D	48	LEU	0	0.021	-0.007	11.616	-1.933	-1.933	0.000	0.000	0.000	0.000
11	D	49	GLU	-1	-0.914	-0.961	12.458	22.100	22.100	0.000	0.000	0.000	0.000
12	D	50	LEU	0	0.029	0.040	14.170	-1.635	-1.635	0.000	0.000	0.000	0.000
13	D	51	GLN	0	-0.001	-0.011	15.336	-0.607	-0.607	0.000	0.000	0.000	0.000
14	D	52	LYS	1	0.875	0.928	16.084	-17.886	-17.886	0.000	0.000	0.000	0.000
15	D	53	SER	0	0.024	0.006	17.704	-0.821	-0.821	0.000	0.000	0.000	0.000
16	D	54	LYS	1	0.960	0.985	20.116	-14.876	-14.876	0.000	0.000	0.000	0.000
17	D	55	ARG	1	0.928	0.973	19.325	-14.693	-14.693	0.000	0.000	0.000	0.000
18	D	56	LEU	0	-0.008	-0.014	23.139	-0.627	-0.627	0.000	0.000	0.000	0.000
19	D	57	ASP	-1	-0.872	-0.932	24.251	12.147	12.147	0.000	0.000	0.000	0.000
20	D	58	TYR	0	-0.012	0.006	26.267	-0.448	-0.448	0.000	0.000	0.000	0.000
21	D	59	VAL	0	-0.012	-0.025	27.005	-0.421	-0.421	0.000	0.000	0.000	0.000
22	D	60	ASN	0	-0.029	-0.034	28.131	-0.519	-0.519	0.000	0.000	0.000	0.000
23	D	61	HIS	0	0.007	0.015	30.883	-0.201	-0.201	0.000	0.000	0.000	0.000
24	D	62	ALA	0	-0.023	-0.006	32.522	-0.280	-0.280	0.000	0.000	0.000	0.000
25	D	63	ARG	1	0.879	0.953	28.528	-10.507	-10.507	0.000	0.000	0.000	0.000
26	D	64	ARG	1	0.981	1.012	32.111	-9.760	-9.760	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:39:GLU)