FMO DATABASE

FMODB ID: 53VKZ

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	OptH
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	-361108.094395
FMO2-HF: Nuclear repulsion	334557.366588
FMO2-HF: Total energy	-26550.727807
FMO2-MP2: Total energy	-26628.501063

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.
-3.908	-1.973	3.539	-2.015	-3.46	0.004

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 : 0.039 / 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	A	4	GLU	-1	-0.853	-0.923	3.449	-1.673	0.243	0.003	-0.831	-1.088	0.002
4	A	5	VAL	0	-0.029	-0.018	2.086	-1.074	-1.362	3.537	-1.113	-2.136	0.002
5	A	6	LEU	0	0.024	0.019	4.152	0.248	0.555	-0.001	-0.071	-0.236	0.000
6	A	7	GLU	-1	-0.885	-0.961	5.657	0.835	0.835	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.875	0.952	7.742	0.695	0.695	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.903	-0.949	6.222	-2.769	-2.769	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.014	0.008	9.451	0.265	0.265	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.053	-0.035	11.462	0.202	0.202	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.943	-0.964	11.958	-0.538	-0.538	0.000	0.000	0.000	0.000
12	A	13	MET	0	-0.016	-0.009	10.799	0.109	0.109	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.015	0.008	15.154	0.104	0.104	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.845	-0.900	17.043	-0.187	-0.187	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.940	-0.965	17.391	-0.391	-0.391	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.779	-0.898	18.387	-0.422	-0.422	0.000	0.000	0.000	0.000
17	A	18	VAL	0	-0.011	-0.017	20.884	0.043	0.043	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.783	0.869	21.975	0.243	0.243	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.813	-0.899	23.361	-0.214	-0.214	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.028	-0.008	24.997	0.024	0.024	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.007	-0.014	26.940	0.021	0.021	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.003	0.010	28.135	0.019	0.019	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.023	0.017	27.583	0.013	0.013	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.060	-0.019	30.726	0.013	0.013	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.039	-0.024	32.710	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.904	-0.968	32.192	-0.137	-0.137	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.002	0.002	32.776	0.008	0.008	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.922	0.963	36.732	0.091	0.091	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.004	-0.001	38.836	0.007	0.007	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.824	-0.926	38.042	-0.105	-0.105	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.838	0.925	40.641	0.093	0.093	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.071	-0.033	42.927	0.004	0.004	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.004	-0.019	43.810	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.027	0.014	45.476	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.022	-0.006	41.141	0.002	0.002	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.017	-0.019	42.883	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.854	-0.924	37.795	-0.129	-0.129	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.911	0.948	38.400	0.099	0.099	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.008	-0.007	33.386	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.971	1.002	32.449	0.136	0.136	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.014	0.007	32.137	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.000	-0.002	32.457	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.872	0.924	26.184	0.224	0.224	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.034	0.011	27.685	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.069	-0.026	28.273	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.030	0.007	22.291	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.023	-0.014	22.224	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.007	0.007	23.253	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.012	-0.001	23.691	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.845	0.928	16.834	0.533	0.533	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.001	0.004	18.997	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.986	-0.992	19.354	-0.278	-0.278	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.017	-0.015	17.805	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.817	-0.922	14.808	-0.656	-0.656	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.028	0.013	14.692	-0.058	-0.058	0.000	0.000	0.000	0.000
56	A	57	TYR	0	-0.011	-0.001	16.520	0.033	0.033	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.028	-0.017	11.627	0.036	0.036	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.019	0.005	11.636	-0.041	-0.041	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.017	-0.006	13.068	0.101	0.101	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.895	0.940	13.189	0.399	0.399	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.098	-0.037	7.638	0.053	0.053	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.002	0.007	9.746	0.201	0.201	0.000	0.000	0.000	0.000
63	A	64	HIS	0	-0.026	-0.001	11.941	0.145	0.145	0.000	0.000	0.000	0.000
64	A	65	HIS	0	-0.036	-0.009	11.810	-0.082	-0.082	0.000	0.000	0.000	0.000

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