FMO DATABASE

FMODB ID: VRGY1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-77028.239007
FMO2-HF: Nuclear repulsion	66652.123575
FMO2-HF: Total energy	-10376.115432
FMO2-MP2: Total energy	-10407.009184

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.
-28.233	-21.889	8.811	-6.913	-8.243	-0.007

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 : -0.988 / q_NPA : -1.012

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	0.029	0.012	3.479	2.902	5.449	0.015	-1.278	-1.284	0.003
4	B	39	PHE	0	-0.009	-0.015	5.956	-3.074	-3.074	0.000	0.000	0.000	0.000
5	B	40	GLN	0	-0.008	-0.012	9.098	-0.204	-0.204	0.000	0.000	0.000	0.000
6	B	41	GLY	0	0.013	0.009	10.853	-0.780	-0.780	0.000	0.000	0.000	0.000
7	B	42	LEU	0	-0.020	0.007	8.361	0.637	0.637	0.000	0.000	0.000	0.000
8	B	43	THR	0	0.020	0.017	2.749	-8.111	-6.229	1.324	-1.333	-1.873	0.015
9	B	44	ILE	0	-0.032	-0.014	3.462	-3.816	-2.918	0.017	-0.254	-0.661	0.000
10	B	45	ALA	0	0.061	0.023	2.224	2.921	3.989	7.391	-4.274	-4.185	-0.025
11	B	46	SER	0	-0.021	-0.006	3.223	-6.973	-7.024	0.064	0.226	-0.240	0.000
12	B	47	GLY	0	0.023	0.013	5.874	2.165	2.165	0.000	0.000	0.000	0.000
13	B	48	ALA	0	0.017	0.003	8.596	0.954	0.954	0.000	0.000	0.000	0.000
14	B	49	ARG	1	0.897	0.930	10.794	-24.097	-24.097	0.000	0.000	0.000	0.000
15	B	50	GLU	-1	-0.767	-0.883	12.436	18.269	18.269	0.000	0.000	0.000	0.000
16	B	51	SER	0	0.025	0.003	15.921	-0.362	-0.362	0.000	0.000	0.000	0.000
17	B	52	GLU	-1	-0.828	-0.889	13.681	18.735	18.735	0.000	0.000	0.000	0.000
18	B	53	LYS	1	0.829	0.898	13.156	-21.039	-21.039	0.000	0.000	0.000	0.000
19	B	54	VAL	0	0.008	0.017	17.338	-0.814	-0.814	0.000	0.000	0.000	0.000
20	B	55	PHE	0	0.012	0.012	18.530	-0.901	-0.901	0.000	0.000	0.000	0.000
21	B	56	ALA	0	0.038	0.005	18.248	-0.710	-0.710	0.000	0.000	0.000	0.000
22	B	57	GLN	0	0.012	0.016	20.364	-0.348	-0.348	0.000	0.000	0.000	0.000
23	B	58	THR	0	-0.033	-0.012	22.624	-0.782	-0.782	0.000	0.000	0.000	0.000
24	B	59	VAL	0	0.006	0.013	23.076	-0.556	-0.556	0.000	0.000	0.000	0.000
25	B	60	LEU	0	-0.015	-0.022	20.426	-0.468	-0.468	0.000	0.000	0.000	0.000
26	B	61	SER	0	-0.076	-0.048	24.866	-0.504	-0.504	0.000	0.000	0.000	0.000
27	B	62	HIS	0	-0.079	-0.043	27.873	-0.735	-0.735	0.000	0.000	0.000	0.000
28	B	63	VAL	0	-0.064	-0.004	26.840	-0.542	-0.542	0.000	0.000	0.000	0.000

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