FMO DATABASE

FMODB ID: YYG22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-164056.319135
FMO2-HF: Nuclear repulsion	146800.265888
FMO2-HF: Total energy	-17256.053247
FMO2-MP2: Total energy	-17306.550314

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.
-5.867	-3.526	-0.01	-1.093	-1.238	0.006

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 : -0.012 / 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

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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	340	ASP	-1	-0.806	-0.906	3.708	-4.846	-2.505	-0.010	-1.093	-1.238	0.006
4	A	341	TYR	0	-0.013	-0.027	6.272	0.776	0.776	0.000	0.000	0.000	0.000
5	A	342	SER	0	-0.040	-0.024	9.415	0.436	0.436	0.000	0.000	0.000	0.000
6	A	343	ASP	-1	-0.808	-0.908	6.093	-5.005	-5.005	0.000	0.000	0.000	0.000
7	A	344	LEU	0	-0.035	-0.021	8.706	0.489	0.489	0.000	0.000	0.000	0.000
8	A	345	GLN	0	-0.046	-0.019	11.036	0.347	0.347	0.000	0.000	0.000	0.000
9	A	346	ARG	1	0.992	0.999	11.638	1.535	1.535	0.000	0.000	0.000	0.000
10	A	347	VAL	0	0.083	0.039	10.756	0.169	0.169	0.000	0.000	0.000	0.000
11	A	348	LYS	1	0.902	0.967	13.747	0.796	0.796	0.000	0.000	0.000	0.000
12	A	349	GLN	0	-0.056	-0.047	16.416	0.039	0.039	0.000	0.000	0.000	0.000
13	A	350	GLU	-1	-0.911	-0.945	15.207	-0.822	-0.822	0.000	0.000	0.000	0.000
14	A	351	LEU	0	0.066	0.022	17.178	0.087	0.087	0.000	0.000	0.000	0.000
15	A	352	MET	0	-0.080	-0.043	19.253	0.075	0.075	0.000	0.000	0.000	0.000
16	A	353	GLU	-1	-0.912	-0.954	21.707	-0.345	-0.345	0.000	0.000	0.000	0.000
17	A	354	GLU	-1	-0.928	-0.963	19.586	-0.349	-0.349	0.000	0.000	0.000	0.000
18	A	355	VAL	0	0.012	-0.006	22.766	0.042	0.042	0.000	0.000	0.000	0.000
19	A	356	LYS	1	0.893	0.950	25.158	0.375	0.375	0.000	0.000	0.000	0.000
20	A	357	LYS	1	0.877	0.940	24.609	0.283	0.283	0.000	0.000	0.000	0.000
21	A	358	GLU	-1	-0.831	-0.901	26.360	-0.169	-0.169	0.000	0.000	0.000	0.000
22	A	359	LEU	0	-0.024	-0.013	28.824	0.020	0.020	0.000	0.000	0.000	0.000
23	A	360	GLN	0	-0.031	-0.017	31.193	0.023	0.023	0.000	0.000	0.000	0.000
24	A	361	LYS	1	0.956	0.984	29.889	0.166	0.166	0.000	0.000	0.000	0.000
25	A	362	VAL	0	0.035	0.011	33.209	0.011	0.011	0.000	0.000	0.000	0.000
26	A	363	LYS	1	0.886	0.954	35.009	0.156	0.156	0.000	0.000	0.000	0.000
27	A	364	GLU	-1	-0.994	-1.002	37.011	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	365	GLU	-1	-0.882	-0.950	36.189	-0.103	-0.103	0.000	0.000	0.000	0.000
29	A	366	ILE	0	-0.040	-0.011	37.447	0.009	0.009	0.000	0.000	0.000	0.000
30	A	367	ILE	0	-0.032	-0.020	40.942	0.006	0.006	0.000	0.000	0.000	0.000
31	A	368	GLU	-1	-0.890	-0.941	42.672	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	369	ALA	0	-0.012	-0.016	43.590	0.006	0.006	0.000	0.000	0.000	0.000
33	A	370	PHE	0	-0.009	0.000	45.295	0.006	0.006	0.000	0.000	0.000	0.000
34	A	371	VAL	0	0.010	0.000	47.151	0.004	0.004	0.000	0.000	0.000	0.000
35	A	372	GLN	0	0.036	0.020	48.066	0.003	0.003	0.000	0.000	0.000	0.000
36	A	373	GLU	-1	-0.831	-0.892	49.343	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	374	LEU	0	-0.004	-0.011	51.104	0.003	0.003	0.000	0.000	0.000	0.000
38	A	375	ARG	1	0.844	0.914	49.939	0.070	0.070	0.000	0.000	0.000	0.000
39	A	376	LYS	1	0.834	0.933	50.685	0.050	0.050	0.000	0.000	0.000	0.000
40	A	377	ARG	1	0.846	0.897	53.208	0.043	0.043	0.000	0.000	0.000	0.000
41	A	378	GLY	0	-0.012	0.022	57.195	0.002	0.002	0.000	0.000	0.000	0.000

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