FMO DATABASE

FMODB ID: VRG41

Calculation Name: 1USD-A-Xray372

Preferred Name: Vasodilator-stimulated phosphoprotein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1USD

Chain ID: A

ChEMBL ID: CHEMBL4295774

UniProt ID: P50552

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	41
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-164267.171244
FMO2-HF: Nuclear repulsion	147010.578281
FMO2-HF: Total energy	-17256.592963
FMO2-MP2: Total energy	-17307.095755

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:338:SER)

Summations of interaction energy for fragment #1(A:338: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.
-2.885	-1.478	-0.006	-0.508	-0.892	0.002

Interaction energy analysis for fragmet #1(A:338: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 : -0.036

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	340	ASP	-1	-0.769	-0.881	3.738	-4.031	-2.624	-0.006	-0.508	-0.892	0.002
4	A	341	TYR	0	-0.023	-0.019	6.120	0.864	0.864	0.000	0.000	0.000	0.000
5	A	342	SER	0	-0.055	-0.054	9.359	0.449	0.449	0.000	0.000	0.000	0.000
6	A	343	ASP	-1	-0.821	-0.914	6.165	-2.041	-2.041	0.000	0.000	0.000	0.000
7	A	344	LEU	0	-0.033	-0.019	8.485	0.390	0.390	0.000	0.000	0.000	0.000
8	A	345	GLN	0	-0.021	-0.007	11.069	0.288	0.288	0.000	0.000	0.000	0.000
9	A	346	ARG	1	0.950	0.984	11.679	0.536	0.536	0.000	0.000	0.000	0.000
10	A	347	VAL	0	0.072	0.037	10.694	0.103	0.103	0.000	0.000	0.000	0.000
11	A	348	LYS	1	0.846	0.930	13.763	0.465	0.465	0.000	0.000	0.000	0.000
12	A	349	GLN	0	0.003	-0.010	16.437	0.017	0.017	0.000	0.000	0.000	0.000
13	A	350	GLU	-1	-0.890	-0.948	14.937	-0.097	-0.097	0.000	0.000	0.000	0.000
14	A	351	LEU	0	0.024	0.007	16.476	0.034	0.034	0.000	0.000	0.000	0.000
15	A	352	MET	0	-0.038	-0.023	19.270	0.025	0.025	0.000	0.000	0.000	0.000
16	A	353	GLU	-1	-0.830	-0.887	21.731	-0.107	-0.107	0.000	0.000	0.000	0.000
17	A	354	GLU	-1	-0.841	-0.907	20.864	0.061	0.061	0.000	0.000	0.000	0.000
18	A	355	VAL	0	0.003	-0.009	22.774	0.012	0.012	0.000	0.000	0.000	0.000
19	A	356	LYS	1	0.809	0.882	25.176	0.123	0.123	0.000	0.000	0.000	0.000
20	A	357	LYS	1	0.797	0.892	24.749	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	358	GLU	-1	-0.804	-0.891	26.562	0.040	0.040	0.000	0.000	0.000	0.000
22	A	359	LEU	0	-0.023	-0.012	28.861	0.003	0.003	0.000	0.000	0.000	0.000
23	A	360	GLN	0	-0.010	0.005	31.211	0.004	0.004	0.000	0.000	0.000	0.000
24	A	361	LYS	1	0.928	0.964	29.605	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	362	VAL	0	0.036	0.012	33.194	0.001	0.001	0.000	0.000	0.000	0.000
26	A	363	LYS	1	0.761	0.865	35.025	0.020	0.020	0.000	0.000	0.000	0.000
27	A	364	GLU	-1	-0.876	-0.931	37.021	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	365	GLU	-1	-0.905	-0.959	35.963	0.027	0.027	0.000	0.000	0.000	0.000
29	A	366	ILE	0	-0.039	-0.008	37.423	0.001	0.001	0.000	0.000	0.000	0.000
30	A	367	ILE	0	-0.022	-0.013	40.960	0.000	0.000	0.000	0.000	0.000	0.000
31	A	368	GLU	-1	-0.811	-0.898	42.686	0.006	0.006	0.000	0.000	0.000	0.000
32	A	369	ALA	0	-0.017	-0.016	43.598	0.001	0.001	0.000	0.000	0.000	0.000
33	A	370	PHE	0	-0.005	0.002	45.314	0.000	0.000	0.000	0.000	0.000	0.000
34	A	371	VAL	0	0.002	-0.007	47.169	0.000	0.000	0.000	0.000	0.000	0.000
35	A	372	GLN	0	0.039	0.029	47.760	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	373	GLU	-1	-0.781	-0.847	49.423	0.016	0.016	0.000	0.000	0.000	0.000
37	A	374	LEU	0	-0.022	-0.019	51.261	0.000	0.000	0.000	0.000	0.000	0.000
38	A	375	ARG	1	0.779	0.871	49.027	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	376	LYS	1	0.809	0.893	51.154	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	377	ARG	1	0.825	0.894	52.891	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	378	GLY	0	-0.014	0.020	57.212	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:338:SER)