FMO DATABASE

FMODB ID: 14L9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-76726.214293
FMO2-HF: Nuclear repulsion	66350.001711
FMO2-HF: Total energy	-10376.212582
FMO2-MP2: Total energy	-10407.081274

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.
-30.664	-23.177	6.226	-5.829	-7.885	0.004

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 : -0.985 / q_NPA : -1.005

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	0.032	0.002	3.564	4.069	6.095	0.022	-1.003	-1.045	0.003
4	B	39	PHE	0	-0.005	-0.003	6.109	-3.577	-3.577	0.000	0.000	0.000	0.000
5	B	40	GLN	0	-0.024	-0.021	9.432	0.373	0.373	0.000	0.000	0.000	0.000
6	B	41	GLY	0	0.026	0.022	10.939	-1.126	-1.126	0.000	0.000	0.000	0.000
7	B	42	LEU	0	-0.016	0.002	8.523	0.845	0.845	0.000	0.000	0.000	0.000
8	B	43	THR	0	0.013	0.000	2.606	-8.864	-7.120	1.821	-1.466	-2.099	0.017
9	B	44	ILE	0	-0.030	-0.005	3.459	-2.776	-2.010	0.014	-0.173	-0.608	0.000
10	B	45	ALA	0	0.061	0.021	2.443	0.394	3.409	4.306	-3.422	-3.899	-0.016
11	B	46	SER	0	-0.028	-0.003	3.228	-7.353	-7.417	0.063	0.235	-0.234	0.000
12	B	47	GLY	0	0.030	0.006	6.448	1.075	1.075	0.000	0.000	0.000	0.000
13	B	48	ALA	0	-0.007	-0.005	9.002	0.637	0.637	0.000	0.000	0.000	0.000
14	B	49	ARG	1	0.867	0.911	10.480	-24.043	-24.043	0.000	0.000	0.000	0.000
15	B	50	GLU	-1	-0.783	-0.892	12.200	19.060	19.060	0.000	0.000	0.000	0.000
16	B	51	SER	0	0.011	-0.015	15.751	-0.600	-0.600	0.000	0.000	0.000	0.000
17	B	52	GLU	-1	-0.774	-0.848	13.302	19.444	19.444	0.000	0.000	0.000	0.000
18	B	53	LYS	1	0.830	0.915	13.397	-21.853	-21.853	0.000	0.000	0.000	0.000
19	B	54	VAL	0	0.046	0.028	17.329	-0.837	-0.837	0.000	0.000	0.000	0.000
20	B	55	PHE	0	0.001	0.012	18.516	-0.866	-0.866	0.000	0.000	0.000	0.000
21	B	56	ALA	0	0.028	0.006	18.447	-0.691	-0.691	0.000	0.000	0.000	0.000
22	B	57	GLN	0	0.004	0.001	20.479	-0.350	-0.350	0.000	0.000	0.000	0.000
23	B	58	THR	0	-0.030	-0.007	22.939	-0.820	-0.820	0.000	0.000	0.000	0.000
24	B	59	VAL	0	-0.001	-0.003	23.168	-0.532	-0.532	0.000	0.000	0.000	0.000
25	B	60	LEU	0	-0.022	-0.023	20.803	-0.462	-0.462	0.000	0.000	0.000	0.000
26	B	61	SER	0	-0.054	-0.039	25.264	-0.513	-0.513	0.000	0.000	0.000	0.000
27	B	62	HIS	0	-0.066	-0.030	28.303	-0.709	-0.709	0.000	0.000	0.000	0.000
28	B	63	VAL	0	-0.078	-0.015	27.011	-0.589	-0.589	0.000	0.000	0.000	0.000

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