FMO DATABASE

FMODB ID: 3JZYL

Calculation Name: 2BSK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BSK

Chain ID: B

ChEMBL ID:

UniProt ID: P62072

Base Structure: X-ray

Registration Date: 2023-09-23

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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-342001.521268
FMO2-HF: Nuclear repulsion	313017.051652
FMO2-HF: Total energy	-28984.469615
FMO2-MP2: Total energy	-29060.456071

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:13:LEU)

Summations of interaction energy for fragment #1(B:13:LEU)

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.
-6.771	1.316	4.221	-4.639	-7.668	-0.029

Interaction energy analysis for fragmet #1(B:13:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.011

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	15	VAL	0	-0.019	-0.022	2.873	-0.450	1.328	0.017	-0.781	-1.014	0.002
4	B	16	GLU	-1	-0.923	-0.961	2.264	-9.087	-4.388	3.176	-3.356	-4.519	-0.033
5	B	17	MET	0	-0.005	-0.004	2.472	-0.006	1.495	1.029	-0.496	-2.034	0.002
6	B	18	MET	0	-0.010	-0.003	5.247	0.672	0.781	-0.001	-0.006	-0.101	0.000
7	B	19	ALA	0	0.025	0.007	7.660	0.372	0.372	0.000	0.000	0.000	0.000
8	B	20	ASP	-1	-0.773	-0.836	7.906	-0.226	-0.226	0.000	0.000	0.000	0.000
9	B	21	MET	0	-0.026	-0.007	9.432	0.203	0.203	0.000	0.000	0.000	0.000
10	B	22	TYR	0	0.052	0.023	11.421	0.125	0.125	0.000	0.000	0.000	0.000
11	B	23	ASN	0	-0.016	-0.008	11.988	0.158	0.158	0.000	0.000	0.000	0.000
12	B	24	ARG	1	0.756	0.843	10.437	0.411	0.411	0.000	0.000	0.000	0.000
13	B	25	MET	0	0.002	0.016	15.416	0.065	0.065	0.000	0.000	0.000	0.000
14	B	26	THR	0	-0.023	-0.017	17.233	0.044	0.044	0.000	0.000	0.000	0.000
15	B	27	SER	0	-0.018	-0.007	18.498	0.043	0.043	0.000	0.000	0.000	0.000
16	B	28	ALA	0	-0.037	-0.024	19.679	0.029	0.029	0.000	0.000	0.000	0.000
17	B	29	CYS	0	-0.085	-0.053	21.384	0.035	0.035	0.000	0.000	0.000	0.000
18	B	30	HIS	0	0.058	0.040	23.087	0.011	0.011	0.000	0.000	0.000	0.000
19	B	31	ARG	1	0.908	0.948	23.625	0.131	0.131	0.000	0.000	0.000	0.000
20	B	32	LYS	1	0.880	0.935	24.726	0.093	0.093	0.000	0.000	0.000	0.000
21	B	33	CYS	0	-0.129	-0.049	27.435	0.016	0.016	0.000	0.000	0.000	0.000
22	B	34	VAL	0	0.058	0.040	28.108	0.001	0.001	0.000	0.000	0.000	0.000
23	B	35	PRO	0	-0.005	-0.001	29.976	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	36	PRO	0	-0.006	-0.013	30.743	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	37	HIS	0	-0.020	-0.009	32.838	0.000	0.000	0.000	0.000	0.000	0.000
26	B	38	TYR	0	-0.026	-0.017	28.710	0.004	0.004	0.000	0.000	0.000	0.000
27	B	39	LYS	1	0.805	0.886	35.384	0.074	0.074	0.000	0.000	0.000	0.000
28	B	40	GLU	-1	-0.800	-0.871	37.608	-0.074	-0.074	0.000	0.000	0.000	0.000
29	B	41	ALA	0	-0.033	-0.021	35.032	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	42	GLU	-1	-0.888	-0.940	33.693	-0.128	-0.128	0.000	0.000	0.000	0.000
31	B	43	LEU	0	-0.027	0.003	28.793	0.005	0.005	0.000	0.000	0.000	0.000
32	B	44	SER	0	0.055	0.027	33.388	0.008	0.008	0.000	0.000	0.000	0.000
33	B	45	LYS	1	0.971	0.977	34.304	0.058	0.058	0.000	0.000	0.000	0.000
34	B	46	GLY	0	-0.030	-0.017	34.841	0.000	0.000	0.000	0.000	0.000	0.000
35	B	47	GLU	-1	-0.824	-0.920	31.441	-0.101	-0.101	0.000	0.000	0.000	0.000
36	B	48	SER	0	0.014	-0.001	30.191	-0.009	-0.009	0.000	0.000	0.000	0.000
37	B	49	VAL	0	0.010	0.003	29.482	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	51	LEU	0	0.046	0.013	25.041	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	52	ASP	-1	-0.849	-0.908	24.911	-0.134	-0.134	0.000	0.000	0.000	0.000
40	B	53	ARG	1	0.902	0.949	25.120	0.065	0.065	0.000	0.000	0.000	0.000
41	B	55	VAL	0	0.072	0.022	19.737	0.002	0.002	0.000	0.000	0.000	0.000
42	B	56	SER	0	-0.027	-0.025	20.324	0.000	0.000	0.000	0.000	0.000	0.000
43	B	57	LYS	1	0.916	0.950	21.522	0.074	0.074	0.000	0.000	0.000	0.000
44	B	58	TYR	0	0.018	0.010	14.374	0.022	0.022	0.000	0.000	0.000	0.000
45	B	59	LEU	0	0.027	0.014	15.575	0.004	0.004	0.000	0.000	0.000	0.000
46	B	60	ASP	-1	-0.819	-0.881	17.220	0.031	0.031	0.000	0.000	0.000	0.000
47	B	61	ILE	0	-0.027	-0.027	18.254	0.027	0.027	0.000	0.000	0.000	0.000
48	B	62	HIS	0	-0.010	-0.007	10.490	0.015	0.015	0.000	0.000	0.000	0.000
49	B	63	GLU	-1	-0.907	-0.947	14.524	0.079	0.079	0.000	0.000	0.000	0.000
50	B	64	ARG	1	0.809	0.887	15.714	0.015	0.015	0.000	0.000	0.000	0.000
51	B	65	MET	0	-0.040	-0.019	15.832	0.022	0.022	0.000	0.000	0.000	0.000
52	B	66	GLY	0	0.061	0.040	13.265	0.031	0.031	0.000	0.000	0.000	0.000
53	B	67	LYS	1	0.841	0.915	13.871	-0.111	-0.111	0.000	0.000	0.000	0.000
54	B	68	LYS	1	0.828	0.900	16.703	-0.153	-0.153	0.000	0.000	0.000	0.000
55	B	69	LEU	0	0.031	0.012	12.013	0.000	0.000	0.000	0.000	0.000	0.000
56	B	70	THR	0	0.014	0.002	13.312	0.058	0.058	0.000	0.000	0.000	0.000
57	B	71	GLU	-1	-0.829	-0.887	14.783	0.191	0.191	0.000	0.000	0.000	0.000
58	B	72	LEU	0	-0.046	-0.024	18.137	-0.007	-0.007	0.000	0.000	0.000	0.000
59	B	73	SER	0	-0.010	-0.004	14.037	0.020	0.020	0.000	0.000	0.000	0.000
60	B	74	MET	0	-0.070	-0.046	16.063	0.039	0.039	0.000	0.000	0.000	0.000
61	B	75	GLN	0	-0.060	-0.029	18.697	-0.020	-0.020	0.000	0.000	0.000	0.000
62	B	76	ASP	-1	-0.913	-0.959	20.275	0.202	0.202	0.000	0.000	0.000	0.000
63	B	77	GLU	-1	-1.006	-0.979	18.672	0.292	0.292	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:13:LEU)