FMO DATABASE

FMODB ID: YYGL2

Calculation Name: 1SKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SKV

Chain ID: A

ChEMBL ID:

UniProt ID: P20215

Base Structure: X-ray

Registration Date: 2023-06-20

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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361354.926582
FMO2-HF: Nuclear repulsion	334803.406598
FMO2-HF: Total energy	-26551.519984
FMO2-MP2: Total energy	-26629.273067

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(A:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-2.712	-0.771	3.895	-2.072	-3.762	0.003

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : -0.003

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	A	4	GLU	-1	-0.862	-0.927	3.437	-1.396	0.524	0.005	-0.817	-1.107	0.001
4	A	5	VAL	0	-0.032	-0.025	2.255	-0.496	-0.966	3.892	-1.154	-2.268	0.002
5	A	6	LEU	0	0.026	0.026	3.761	0.363	0.717	-0.001	-0.096	-0.257	0.000
6	A	7	GLU	-1	-0.853	-0.921	5.227	0.636	0.773	-0.001	-0.005	-0.130	0.000
7	A	8	LYS	1	0.758	0.873	7.539	0.712	0.712	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.906	-0.954	5.878	-2.455	-2.455	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.008	0.006	9.098	0.263	0.263	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.034	-0.030	11.092	0.205	0.205	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.833	-0.888	11.740	-0.336	-0.336	0.000	0.000	0.000	0.000
12	A	13	MET	0	0.002	-0.002	10.475	0.105	0.105	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.014	0.007	14.865	0.096	0.096	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.826	-0.873	16.758	-0.158	-0.158	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.942	-0.967	17.482	-0.283	-0.283	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.754	-0.869	17.982	-0.358	-0.358	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.009	-0.001	20.582	0.037	0.037	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.760	0.848	21.441	0.212	0.212	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.769	-0.872	23.058	-0.172	-0.172	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.021	0.002	24.692	0.022	0.022	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.003	-0.013	26.621	0.018	0.018	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.007	-0.006	27.766	0.017	0.017	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.006	0.017	27.505	0.012	0.012	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.048	-0.018	30.538	0.012	0.012	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.025	-0.017	32.661	0.011	0.011	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.845	-0.918	32.323	-0.109	-0.109	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.009	0.004	32.524	0.007	0.007	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.924	0.962	36.428	0.079	0.079	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.011	0.008	38.555	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.793	-0.888	37.498	-0.087	-0.087	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.862	0.936	40.257	0.082	0.082	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.058	-0.026	42.613	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.022	-0.029	43.611	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.033	0.005	45.179	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.048	-0.035	40.015	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.003	-0.022	42.589	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.819	-0.891	37.435	-0.107	-0.107	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.878	0.941	38.089	0.083	0.083	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.032	-0.034	33.145	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.868	0.932	32.155	0.102	0.102	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.008	0.004	31.816	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.005	-0.003	32.105	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.850	0.905	26.209	0.177	0.177	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.028	0.009	27.344	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.069	-0.026	27.895	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.023	0.005	21.866	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.037	-0.035	21.622	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.006	-0.005	22.864	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.000	0.011	23.379	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.793	0.881	17.031	0.443	0.443	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.007	-0.003	18.633	-0.047	-0.047	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.972	-0.986	19.054	-0.288	-0.288	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.025	-0.014	17.919	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.813	-0.902	14.273	-0.629	-0.629	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.020	0.014	14.572	-0.076	-0.076	0.000	0.000	0.000	0.000
56	A	57	TYR	0	0.012	0.005	16.615	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.036	-0.019	11.811	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.026	0.009	11.704	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.016	-0.004	13.068	0.075	0.075	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.870	0.933	12.992	0.456	0.456	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.100	-0.044	7.528	0.011	0.011	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.008	-0.010	9.628	0.155	0.155	0.000	0.000	0.000	0.000
63	A	64	HIS	0	-0.056	-0.014	11.941	0.141	0.141	0.000	0.000	0.000	0.000
64	A	65	HIS	0	-0.030	-0.007	11.654	-0.057	-0.057	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)