FMO DATABASE

FMODB ID: YYGR2

Calculation Name: 4GF3-B-Xray372

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: 2023-06-19

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	28
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-77130.42016
FMO2-HF: Nuclear repulsion	66754.460301
FMO2-HF: Total energy	-10375.95986
FMO2-MP2: Total energy	-10406.870368

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:36:GLU)

Summations of interaction energy for fragment #1(B:36:GLU)

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.
-23.898	-18.644	8.22	-6.248	-7.223	-0.017

Interaction energy analysis for fragmet #1(B:36:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.982 / q_NPA : -1.007

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	38	THR	0	0.016	0.008	3.419	2.002	4.570	0.026	-1.256	-1.337	0.003
4	B	39	PHE	0	-0.003	-0.017	6.078	-3.035	-3.035	0.000	0.000	0.000	0.000
5	B	40	GLN	0	-0.005	-0.009	8.960	-0.363	-0.363	0.000	0.000	0.000	0.000
6	B	41	GLY	0	0.013	0.010	10.856	-0.764	-0.764	0.000	0.000	0.000	0.000
7	B	42	LEU	0	-0.017	0.007	8.285	0.734	0.734	0.000	0.000	0.000	0.000
8	B	43	THR	0	0.019	0.020	2.540	-1.876	-0.754	0.917	-0.712	-1.327	0.006
9	B	44	ILE	0	-0.028	-0.016	3.312	-3.724	-2.804	0.021	-0.288	-0.653	-0.001
10	B	45	ALA	0	0.062	0.021	2.209	3.477	4.175	7.197	-4.197	-3.697	-0.025
11	B	46	SER	0	-0.015	-0.002	3.239	-7.058	-7.112	0.059	0.205	-0.209	0.000
12	B	47	GLY	0	0.008	0.006	5.974	1.989	1.989	0.000	0.000	0.000	0.000
13	B	48	ALA	0	0.027	0.007	8.697	0.888	0.888	0.000	0.000	0.000	0.000
14	B	49	ARG	1	0.977	0.987	10.841	-23.745	-23.745	0.000	0.000	0.000	0.000
15	B	50	GLU	-1	-0.842	-0.935	12.803	17.249	17.249	0.000	0.000	0.000	0.000
16	B	51	SER	0	0.004	-0.010	16.235	-0.343	-0.343	0.000	0.000	0.000	0.000
17	B	52	GLU	-1	-0.912	-0.952	14.206	18.283	18.283	0.000	0.000	0.000	0.000
18	B	53	LYS	1	0.927	0.969	12.737	-21.559	-21.559	0.000	0.000	0.000	0.000
19	B	54	VAL	0	0.013	0.016	17.294	-0.785	-0.785	0.000	0.000	0.000	0.000
20	B	55	PHE	0	0.013	0.009	19.085	-0.894	-0.894	0.000	0.000	0.000	0.000
21	B	56	ALA	0	0.034	0.005	18.262	-0.688	-0.688	0.000	0.000	0.000	0.000
22	B	57	GLN	0	-0.005	0.006	20.380	-0.314	-0.314	0.000	0.000	0.000	0.000
23	B	58	THR	0	-0.013	-0.011	22.658	-0.761	-0.761	0.000	0.000	0.000	0.000
24	B	59	VAL	0	0.007	0.018	23.011	-0.593	-0.593	0.000	0.000	0.000	0.000
25	B	60	LEU	0	-0.018	-0.028	20.472	-0.446	-0.446	0.000	0.000	0.000	0.000
26	B	61	SER	0	-0.108	-0.041	24.882	-0.482	-0.482	0.000	0.000	0.000	0.000
27	B	62	HIS	0	-0.058	-0.040	27.890	-0.691	-0.691	0.000	0.000	0.000	0.000
28	B	63	VAL	0	-0.059	-0.003	26.976	-0.399	-0.399	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:36:GLU)