FMO DATABASE

FMODB ID: 63JKZ

Calculation Name: 1SKV-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	66
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-364554.046528
FMO2-HF: Nuclear repulsion	337832.377501
FMO2-HF: Total energy	-26721.669027
FMO2-MP2: Total energy	-26799.981042

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:1:ACE )

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

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.
-0.087	1.258	-0.001	-0.653	-0.69	-0.001

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.013

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

Sort

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	3	LYS	1	0.937	0.960	3.783	0.268	1.613	-0.001	-0.653	-0.690	-0.001
4	A	4	GLU	-1	-0.851	-0.920	5.477	-0.428	-0.428	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.021	-0.013	7.069	0.139	0.139	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.023	0.018	8.146	0.184	0.184	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.883	-0.960	9.466	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.876	0.953	11.145	0.448	0.448	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.903	-0.949	12.173	-0.471	-0.471	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.013	0.009	13.176	0.064	0.064	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.052	-0.035	14.688	0.049	0.049	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.943	-0.964	17.011	-0.285	-0.285	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.020	-0.010	16.035	0.031	0.031	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.016	0.009	18.564	0.026	0.026	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.847	-0.900	21.451	-0.099	-0.099	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.939	-0.964	23.093	-0.139	-0.139	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.777	-0.898	23.350	-0.106	-0.106	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.013	-0.017	25.339	0.014	0.014	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.787	0.870	26.183	0.111	0.111	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.815	-0.899	28.620	-0.068	-0.068	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.028	-0.008	29.852	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.006	-0.013	31.662	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.002	0.009	33.321	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.022	0.017	32.653	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.060	-0.019	35.122	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	HIS	0	-0.039	-0.024	37.200	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.904	-0.969	37.695	-0.051	-0.051	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.002	0.001	37.589	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.925	0.964	41.698	0.030	0.030	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.003	-0.001	43.854	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.823	-0.926	43.347	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.837	0.925	45.349	0.026	0.026	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.073	-0.033	47.772	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.005	-0.018	49.165	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.028	0.014	50.505	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.021	-0.006	46.686	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.018	-0.020	47.958	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.855	-0.923	43.222	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.911	0.948	43.312	0.026	0.026	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.010	-0.007	38.689	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.972	1.001	37.591	0.048	0.048	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.015	0.008	37.024	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.000	-0.002	36.883	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.872	0.924	31.475	0.070	0.070	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.033	0.010	32.390	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.069	-0.026	32.540	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.031	0.007	27.002	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.021	-0.013	27.326	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.003	0.006	27.448	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.011	0.000	27.281	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.838	0.925	21.904	0.127	0.127	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.010	0.007	22.867	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.986	-0.992	22.789	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.016	-0.015	21.169	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.820	-0.924	18.500	-0.127	-0.127	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.031	0.013	17.879	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.012	-0.001	18.835	0.020	0.020	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.029	-0.018	14.588	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.022	0.005	13.835	0.011	0.011	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.020	-0.006	14.636	0.018	0.018	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.895	0.941	14.235	-0.038	-0.038	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.099	-0.038	9.078	0.065	0.065	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.001	0.006	10.309	0.031	0.031	0.000	0.000	0.000	0.000
64	A	64	HIS	0	-0.027	-0.004	12.504	0.026	0.026	0.000	0.000	0.000	0.000
65	A	65	HIS	0	-0.042	-0.014	11.224	0.009	0.009	0.000	0.000	0.000	0.000
66	A	66	NME	0	0.004	0.007	12.328	-0.043	-0.043	0.000	0.000	0.000	0.000

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