FMO DATABASE

FMODB ID: ZYKYN

Calculation Name: 2P8Q-B-Xray372

Preferred Name: Importin subunit beta-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2P8Q

Chain ID: B

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:

Apendix: None

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	39
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-160580.641774
FMO2-HF: Nuclear repulsion	143877.94627
FMO2-HF: Total energy	-16702.695504
FMO2-MP2: Total energy	-16752.676126

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(B:26:PRO)

Summations of interaction energy for fragment #1(B:26:PRO)

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.
-7.198	-4.158	-0.007	-1.484	-1.548	0.004

Interaction energy analysis for fragmet #1(B:26:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.002

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	B	28	LEU	0	0.049	0.033	3.605	-3.433	-0.494	-0.006	-1.477	-1.456	0.004
4	B	29	SER	0	-0.004	-0.005	5.458	-1.077	-0.976	-0.001	-0.007	-0.092	0.000
5	B	30	GLN	0	0.017	0.007	7.346	-0.647	-0.647	0.000	0.000	0.000	0.000
6	B	31	TYR	0	0.031	0.025	7.486	-0.303	-0.303	0.000	0.000	0.000	0.000
7	B	32	LYS	1	0.922	0.958	9.197	-0.672	-0.672	0.000	0.000	0.000	0.000
8	B	33	SER	0	0.004	0.012	12.125	-0.030	-0.030	0.000	0.000	0.000	0.000
9	B	34	LYS	1	0.955	0.982	13.309	-0.649	-0.649	0.000	0.000	0.000	0.000
10	B	35	TYR	0	-0.003	-0.020	15.863	-0.004	-0.004	0.000	0.000	0.000	0.000
11	B	36	SER	0	0.026	0.012	17.891	-0.005	-0.005	0.000	0.000	0.000	0.000
12	B	37	SER	0	0.050	0.021	19.604	-0.014	-0.014	0.000	0.000	0.000	0.000
13	B	38	LEU	0	-0.046	-0.028	20.520	-0.024	-0.024	0.000	0.000	0.000	0.000
14	B	39	GLU	-1	-0.742	-0.839	14.705	0.281	0.281	0.000	0.000	0.000	0.000
15	B	40	GLN	0	0.057	0.009	15.339	-0.070	-0.070	0.000	0.000	0.000	0.000
16	B	41	SER	0	-0.015	-0.007	15.421	-0.023	-0.023	0.000	0.000	0.000	0.000
17	B	42	GLU	-1	-0.704	-0.815	18.286	0.095	0.095	0.000	0.000	0.000	0.000
18	B	43	ARG	1	0.882	0.931	19.991	-0.212	-0.212	0.000	0.000	0.000	0.000
19	B	44	ARG	1	0.875	0.933	19.473	-0.129	-0.129	0.000	0.000	0.000	0.000
20	B	45	ARG	1	0.898	0.938	18.789	-0.083	-0.083	0.000	0.000	0.000	0.000
21	B	46	ARG	1	0.936	0.950	22.769	-0.142	-0.142	0.000	0.000	0.000	0.000
22	B	47	LEU	0	0.018	0.026	25.725	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	48	LEU	0	-0.008	-0.013	24.254	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	49	GLU	-1	-0.972	-0.979	25.823	0.046	0.046	0.000	0.000	0.000	0.000
25	B	50	LEU	0	0.036	0.022	28.537	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	51	GLN	0	0.013	-0.003	30.929	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	52	LYS	1	0.917	0.963	27.214	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	53	SER	0	0.009	0.013	32.770	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	54	LYS	1	0.875	0.921	34.711	-0.038	-0.038	0.000	0.000	0.000	0.000
30	B	55	ARG	1	0.970	0.983	32.411	-0.019	-0.019	0.000	0.000	0.000	0.000
31	B	56	LEU	0	-0.007	0.000	35.880	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	57	ASP	-1	-0.829	-0.914	38.406	0.025	0.025	0.000	0.000	0.000	0.000
33	B	58	TYR	0	0.006	0.005	40.762	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	59	VAL	0	0.032	0.002	41.069	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	60	ASN	0	-0.016	-0.002	40.611	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	61	HIS	0	-0.007	0.000	44.081	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	62	ALA	0	-0.019	0.002	46.193	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	63	ARG	1	0.873	0.930	41.269	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	64	ARG	1	0.917	0.981	44.086	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:PRO)