FMO DATABASE

FMODB ID: YY4K2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-96664.170978
FMO2-HF: Nuclear repulsion	85209.723715
FMO2-HF: Total energy	-11454.447264
FMO2-MP2: Total energy	-11488.718732

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.
-282.231	-293.177	43.889	-16.816	-16.129	0.191

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 : -0.684 / q_NPA : -0.812

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	-0.066	-0.074	1.614	-53.775	-64.740	32.739	-13.383	-8.392	0.119
4	D	42	GLU	-1	-0.776	-0.845	1.953	13.019	11.901	11.133	-3.000	-7.015	0.070
5	D	43	ARG	1	1.007	1.007	3.756	-51.753	-50.768	0.018	-0.430	-0.574	0.002
6	D	44	ARG	1	0.942	0.979	5.668	-50.273	-50.273	0.000	0.000	0.000	0.000
7	D	45	ARG	1	0.906	0.937	5.128	-53.663	-53.511	-0.001	-0.003	-0.148	0.000
8	D	46	ARG	1	0.834	0.883	6.562	-38.959	-38.959	0.000	0.000	0.000	0.000
9	D	47	LEU	0	0.013	0.012	9.098	-3.234	-3.234	0.000	0.000	0.000	0.000
10	D	48	LEU	0	0.024	-0.003	11.312	-2.579	-2.579	0.000	0.000	0.000	0.000
11	D	49	GLU	-1	-0.892	-0.929	11.452	25.867	25.867	0.000	0.000	0.000	0.000
12	D	50	LEU	0	0.042	0.036	13.540	-1.976	-1.976	0.000	0.000	0.000	0.000
13	D	51	GLN	0	-0.002	-0.010	15.465	-1.469	-1.469	0.000	0.000	0.000	0.000
14	D	52	LYS	1	0.892	0.941	15.411	-19.764	-19.764	0.000	0.000	0.000	0.000
15	D	53	SER	0	0.016	0.003	17.174	-1.132	-1.132	0.000	0.000	0.000	0.000
16	D	54	LYS	1	0.891	0.931	19.579	-15.135	-15.135	0.000	0.000	0.000	0.000
17	D	55	ARG	1	0.941	0.974	19.306	-16.176	-16.176	0.000	0.000	0.000	0.000
18	D	56	LEU	0	0.014	0.000	22.441	-0.716	-0.716	0.000	0.000	0.000	0.000
19	D	57	ASP	-1	-0.838	-0.902	23.399	12.894	12.894	0.000	0.000	0.000	0.000
20	D	58	TYR	0	0.004	0.005	25.913	-0.532	-0.532	0.000	0.000	0.000	0.000
21	D	59	VAL	0	0.029	0.002	26.993	-0.475	-0.475	0.000	0.000	0.000	0.000
22	D	60	ASN	0	-0.012	0.007	27.188	-0.682	-0.682	0.000	0.000	0.000	0.000
23	D	61	HIS	0	0.049	0.035	30.275	-0.259	-0.259	0.000	0.000	0.000	0.000
24	D	62	ALA	0	-0.013	-0.011	31.913	-0.325	-0.325	0.000	0.000	0.000	0.000
25	D	63	ARG	1	0.861	0.928	28.548	-10.944	-10.944	0.000	0.000	0.000	0.000
26	D	64	ARG	1	0.880	0.956	31.410	-10.190	-10.190	0.000	0.000	0.000	0.000

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