FMO DATABASE

FMODB ID: 534LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-96544.20492
FMO2-HF: Nuclear repulsion	85089.931771
FMO2-HF: Total energy	-11454.273149
FMO2-MP2: Total energy	-11488.552337

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.
-240.43	-243.429	34.217	-17.188	-14.032	0.135

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 : -0.729 / q_NPA : -0.842

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	-0.106	-0.100	1.569	-40.600	-48.765	29.042	-13.573	-7.304	0.094
4	D	42	GLU	-1	-0.769	-0.843	2.271	37.195	41.147	5.113	-3.230	-5.836	0.037
5	D	43	ARG	1	1.016	1.001	3.692	-49.147	-48.231	0.063	-0.320	-0.659	0.004
6	D	44	ARG	1	0.950	0.977	5.854	-42.784	-42.784	0.000	0.000	0.000	0.000
7	D	45	ARG	1	0.924	0.949	4.087	-58.552	-58.254	-0.001	-0.065	-0.233	0.000
8	D	46	ARG	1	0.929	0.956	6.592	-40.027	-40.027	0.000	0.000	0.000	0.000
9	D	47	LEU	0	-0.008	0.007	9.668	-2.882	-2.882	0.000	0.000	0.000	0.000
10	D	48	LEU	0	0.014	-0.009	11.446	-2.316	-2.316	0.000	0.000	0.000	0.000
11	D	49	GLU	-1	-0.942	-0.962	12.117	24.019	24.019	0.000	0.000	0.000	0.000
12	D	50	LEU	0	0.050	0.044	14.024	-1.853	-1.853	0.000	0.000	0.000	0.000
13	D	51	GLN	0	0.014	-0.005	15.747	-1.054	-1.054	0.000	0.000	0.000	0.000
14	D	52	LYS	1	0.894	0.936	15.488	-19.417	-19.417	0.000	0.000	0.000	0.000
15	D	53	SER	0	0.009	-0.004	17.646	-1.008	-1.008	0.000	0.000	0.000	0.000
16	D	54	LYS	1	0.883	0.943	20.083	-14.924	-14.924	0.000	0.000	0.000	0.000
17	D	55	ARG	1	0.942	0.980	18.983	-15.882	-15.882	0.000	0.000	0.000	0.000
18	D	56	LEU	0	0.009	-0.006	22.430	-0.731	-0.731	0.000	0.000	0.000	0.000
19	D	57	ASP	-1	-0.853	-0.919	23.902	12.780	12.780	0.000	0.000	0.000	0.000
20	D	58	TYR	0	0.001	0.010	26.124	-0.495	-0.495	0.000	0.000	0.000	0.000
21	D	59	VAL	0	0.015	-0.012	26.972	-0.463	-0.463	0.000	0.000	0.000	0.000
22	D	60	ASN	0	-0.020	-0.016	27.485	-0.658	-0.658	0.000	0.000	0.000	0.000
23	D	61	HIS	0	0.023	0.021	30.459	-0.207	-0.207	0.000	0.000	0.000	0.000
24	D	62	ALA	0	-0.013	0.002	32.172	-0.300	-0.300	0.000	0.000	0.000	0.000
25	D	63	ARG	1	0.866	0.935	27.863	-10.979	-10.979	0.000	0.000	0.000	0.000
26	D	64	ARG	1	0.934	0.989	31.262	-10.145	-10.145	0.000	0.000	0.000	0.000

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