FMO DATABASE

FMODB ID: VRG71

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

Total energy (hartree)

FMO2-HF: Electronic energy	-361978.1408
FMO2-HF: Nuclear repulsion	335426.326947
FMO2-HF: Total energy	-26551.813854
FMO2-MP2: Total energy	-26629.544813

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.
-2.815	-0.767	2.574	-1.61	-3.011	0.002

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 : 0.019 / q_NPA : -0.008

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	4	GLU	-1	-0.871	-0.927	3.884	-1.733	-0.387	-0.001	-0.536	-0.809	0.001
4	A	5	VAL	0	0.000	-0.011	2.273	-1.110	-0.817	2.577	-0.997	-1.873	0.001
5	A	6	LEU	0	0.030	0.027	3.771	0.686	0.976	-0.001	-0.072	-0.217	0.000
6	A	7	GLU	-1	-0.845	-0.917	5.214	0.471	0.590	-0.001	-0.005	-0.112	0.000
7	A	8	LYS	1	0.766	0.884	7.614	0.901	0.901	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.902	-0.960	6.190	-1.932	-1.932	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.013	-0.003	9.193	0.266	0.266	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.023	-0.020	11.194	0.216	0.216	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.828	-0.896	11.760	-0.409	-0.409	0.000	0.000	0.000	0.000
12	A	13	MET	0	0.009	0.014	10.860	0.123	0.123	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.005	-0.001	14.925	0.094	0.094	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.836	-0.879	16.873	-0.185	-0.185	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.936	-0.966	17.917	-0.262	-0.262	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.769	-0.881	17.983	-0.352	-0.352	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.019	0.007	20.724	0.037	0.037	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.777	0.853	21.515	0.238	0.238	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.771	-0.852	23.059	-0.164	-0.164	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.013	0.003	24.769	0.022	0.022	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.014	-0.022	26.681	0.019	0.019	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.021	-0.027	27.784	0.019	0.019	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.020	-0.002	27.738	0.013	0.013	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.042	-0.014	30.668	0.011	0.011	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.007	-0.004	32.376	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.837	-0.907	32.775	-0.105	-0.105	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.024	0.015	32.684	0.008	0.008	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.921	0.970	36.599	0.083	0.083	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.037	0.017	38.675	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.822	-0.896	37.337	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.854	0.919	40.053	0.083	0.083	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.040	-0.018	42.414	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.042	-0.036	43.469	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.015	0.006	45.218	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.027	-0.020	39.999	0.004	0.004	0.000	0.000	0.000	0.000
36	A	37	MET	0	0.045	0.019	43.202	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.791	-0.868	37.483	-0.102	-0.102	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.792	0.864	37.987	0.084	0.084	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.048	-0.038	33.429	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.848	0.922	32.113	0.097	0.097	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.020	0.012	31.691	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.004	0.000	31.889	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.832	0.890	26.558	0.167	0.167	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.028	0.011	27.221	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.027	-0.016	27.627	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.009	0.002	21.597	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.037	-0.027	21.549	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.023	-0.013	22.714	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.015	0.010	23.343	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.775	0.881	16.537	0.448	0.448	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.018	0.002	18.584	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.959	-0.977	19.038	-0.291	-0.291	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.013	-0.011	17.958	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.814	-0.910	14.195	-0.639	-0.639	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.016	0.017	14.388	-0.092	-0.092	0.000	0.000	0.000	0.000
56	A	57	TYR	0	-0.012	-0.013	16.263	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.032	-0.019	11.935	0.017	0.017	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.035	0.022	11.252	-0.098	-0.098	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.022	-0.006	12.642	0.027	0.027	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.858	0.937	12.240	0.527	0.527	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.064	-0.023	7.163	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	63	SER	0	0.054	0.003	8.911	0.146	0.146	0.000	0.000	0.000	0.000
63	A	64	HIS	0	-0.048	-0.008	11.335	0.163	0.163	0.000	0.000	0.000	0.000
64	A	65	HIS	0	-0.038	-0.019	10.802	-0.019	-0.019	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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