FMO DATABASE

FMODB ID: V5YG1

Calculation Name: 5TOH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TOH

Chain ID: A

ChEMBL ID:

UniProt ID: P35259

Base Structure: X-ray

Registration Date: 2023-06-22

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	52
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-207735.736532
FMO2-HF: Nuclear repulsion	187144.048323
FMO2-HF: Total energy	-20591.688209
FMO2-MP2: Total energy	-20653.402415

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:1:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-6.379	-3.275	2.434	-2.056	-3.481	0.016

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / 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	A	3	ILE	0	0.049	0.009	3.741	1.329	2.454	0.007	-0.482	-0.649	0.001
4	A	4	ILE	0	-0.006	-0.006	2.629	-3.492	-2.108	2.412	-1.393	-2.403	0.014
5	A	5	TRP	0	0.003	0.005	3.659	-2.618	-2.091	0.016	-0.175	-0.368	0.001
6	A	6	ASP	-1	-0.853	-0.931	4.993	-0.486	-0.418	-0.001	-0.006	-0.061	0.000
7	A	7	GLN	0	-0.041	-0.033	7.117	0.248	0.248	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.039	-0.006	7.636	-0.264	-0.264	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.033	0.015	9.363	-0.185	-0.185	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.007	0.002	11.280	-0.077	-0.077	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.939	0.968	12.740	-0.579	-0.579	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.882	0.944	13.527	-0.271	-0.271	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.018	0.008	15.262	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.022	0.020	17.247	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.033	-0.033	18.168	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.856	-0.932	19.266	0.154	0.154	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.026	-0.017	21.372	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.023	-0.011	21.844	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.007	0.021	23.391	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.001	-0.011	26.052	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.042	0.036	27.456	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.005	-0.019	24.672	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.908	0.969	29.099	-0.074	-0.074	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.028	0.000	31.911	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.001	0.006	29.919	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.036	-0.010	32.772	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.877	-0.949	34.574	0.066	0.066	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.020	-0.006	35.882	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.007	-0.015	33.081	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.025	0.000	38.231	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.051	0.020	40.635	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.011	-0.003	40.183	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.017	-0.003	41.793	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.905	-0.953	43.689	0.043	0.043	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.031	-0.027	46.274	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.010	-0.014	45.351	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.005	0.009	47.431	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.899	0.945	49.817	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.010	0.000	50.886	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	HIS	0	0.049	0.031	51.337	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.876	-0.933	53.311	0.035	0.035	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.027	-0.012	55.088	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.938	-0.968	54.041	0.037	0.037	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.806	0.897	54.818	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.011	-0.001	59.498	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.027	-0.020	60.386	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.001	-0.005	61.406	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.944	-0.975	63.341	0.027	0.027	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.080	-0.042	65.915	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.044	0.005	64.300	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.042	-0.020	66.995	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.021	0.003	69.877	-0.001	-0.001	0.000	0.000	0.000	0.000

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