FMO DATABASE

FMODB ID: GQMR1

Calculation Name: 4GF3-B-Xray313

Preferred Name: Tyrosine-protein phosphatase yopH

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4GF3

Chain ID: B

ChEMBL ID: CHEMBL4404

UniProt ID: P15273

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	29
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-78763.197645
FMO2-HF: Nuclear repulsion	68236.1124
FMO2-HF: Total energy	-10527.085245
FMO2-MP2: Total energy	-10558.436815

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(B:35:ACE )

Summations of interaction energy for fragment #1(B:35: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.
1.261	2.344	-0.004	-0.539	-0.541	-0.001

Interaction energy analysis for fragmet #1(B:35:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.022

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	B	37	THR	0	-0.053	-0.008	3.900	1.176	2.041	-0.004	-0.463	-0.398	-0.001
4	B	38	THR	0	0.021	0.011	7.151	-0.050	-0.050	0.000	0.000	0.000	0.000
5	B	39	PHE	0	-0.002	-0.017	10.850	0.097	0.097	0.000	0.000	0.000	0.000
6	B	40	GLN	0	-0.008	-0.010	12.689	-0.003	-0.003	0.000	0.000	0.000	0.000
7	B	41	GLY	0	0.011	0.010	15.843	0.007	0.007	0.000	0.000	0.000	0.000
8	B	42	LEU	0	-0.016	0.008	13.301	-0.009	-0.009	0.000	0.000	0.000	0.000
9	B	43	THR	0	0.016	0.018	9.018	0.016	0.016	0.000	0.000	0.000	0.000
10	B	44	ILE	0	-0.027	-0.016	7.409	0.091	0.091	0.000	0.000	0.000	0.000
11	B	45	ALA	0	0.070	0.028	4.333	-0.686	-0.639	0.000	-0.052	0.004	0.000
12	B	46	SER	0	-0.039	-0.011	4.317	0.686	0.857	0.000	-0.024	-0.147	0.000
13	B	47	GLY	0	0.010	0.007	5.293	-0.277	-0.277	0.000	0.000	0.000	0.000
14	B	48	ALA	0	0.032	0.008	7.936	-0.066	-0.066	0.000	0.000	0.000	0.000
15	B	49	ARG	1	0.971	0.983	10.973	0.354	0.354	0.000	0.000	0.000	0.000
16	B	50	GLU	-1	-0.844	-0.936	13.471	-0.078	-0.078	0.000	0.000	0.000	0.000
17	B	51	SER	0	0.001	-0.011	15.838	0.007	0.007	0.000	0.000	0.000	0.000
18	B	52	GLU	-1	-0.913	-0.953	15.424	-0.201	-0.201	0.000	0.000	0.000	0.000
19	B	53	LYS	1	0.925	0.968	11.264	0.132	0.132	0.000	0.000	0.000	0.000
20	B	54	VAL	0	0.010	0.015	16.765	0.020	0.020	0.000	0.000	0.000	0.000
21	B	55	PHE	0	0.010	0.007	19.640	0.015	0.015	0.000	0.000	0.000	0.000
22	B	56	ALA	0	0.032	0.004	18.384	0.011	0.011	0.000	0.000	0.000	0.000
23	B	57	GLN	0	-0.007	0.006	20.348	0.007	0.007	0.000	0.000	0.000	0.000
24	B	58	THR	0	-0.019	-0.015	21.877	0.011	0.011	0.000	0.000	0.000	0.000
25	B	59	VAL	0	-0.004	0.012	23.426	0.007	0.007	0.000	0.000	0.000	0.000
26	B	60	LEU	0	-0.018	-0.027	20.323	0.007	0.007	0.000	0.000	0.000	0.000
27	B	61	SER	0	-0.112	-0.042	24.663	0.008	0.008	0.000	0.000	0.000	0.000
28	B	62	HIS	0	-0.099	-0.064	27.240	0.006	0.006	0.000	0.000	0.000	0.000
29	B	63	VAL	-1	-0.978	-0.959	27.159	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:35:ACE )