FMO DATABASE

FMODB ID: 852RY

Calculation Name: 3LYV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYV

Chain ID: D

ChEMBL ID:

UniProt ID: Q5XAQ7

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	49
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-242574.56417
FMO2-HF: Nuclear repulsion	222599.141786
FMO2-HF: Total energy	-19975.422384
FMO2-MP2: Total energy	-20032.973394

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(D:10:THR)

Summations of interaction energy for fragment #1(D:10:THR)

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.
-3.749	-1.997	0.023	-0.854	-0.922	0.001

Interaction energy analysis for fragmet #1(D:10:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.038

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	D	12	LYS	1	0.846	0.916	3.408	-1.039	0.713	0.023	-0.854	-0.922	0.001
4	D	13	PRO	0	0.026	0.022	5.877	0.511	0.511	0.000	0.000	0.000	0.000
5	D	14	MET	0	-0.067	-0.013	8.930	-0.101	-0.101	0.000	0.000	0.000	0.000
6	D	15	ASP	-1	-0.734	-0.859	12.211	-0.470	-0.470	0.000	0.000	0.000	0.000
7	D	16	VAL	0	0.011	0.005	14.574	-0.072	-0.072	0.000	0.000	0.000	0.000
8	D	17	GLU	-1	-0.846	-0.893	16.859	-0.340	-0.340	0.000	0.000	0.000	0.000
9	D	18	GLU	-1	-0.837	-0.946	11.965	-1.103	-1.103	0.000	0.000	0.000	0.000
10	D	19	ALA	0	0.016	0.012	12.195	-0.066	-0.066	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.822	0.884	13.231	0.346	0.346	0.000	0.000	0.000	0.000
12	D	21	LEU	0	-0.022	-0.013	15.544	0.038	0.038	0.000	0.000	0.000	0.000
13	D	22	GLN	0	-0.030	-0.036	9.741	0.071	0.071	0.000	0.000	0.000	0.000
14	D	23	MET	0	-0.041	-0.004	12.695	0.051	0.051	0.000	0.000	0.000	0.000
15	D	24	GLU	-1	-0.854	-0.909	14.233	-0.193	-0.193	0.000	0.000	0.000	0.000
16	D	25	LEU	0	-0.084	-0.039	13.967	0.056	0.056	0.000	0.000	0.000	0.000
17	D	26	LEU	0	-0.052	-0.029	9.119	0.020	0.020	0.000	0.000	0.000	0.000
18	D	27	GLY	0	-0.035	-0.002	13.816	0.072	0.072	0.000	0.000	0.000	0.000
19	D	28	HIS	0	-0.006	0.011	11.105	0.064	0.064	0.000	0.000	0.000	0.000
20	D	29	ASP	-1	-0.878	-0.941	15.382	-0.039	-0.039	0.000	0.000	0.000	0.000
21	D	30	PHE	0	-0.027	-0.028	10.220	0.003	0.003	0.000	0.000	0.000	0.000
22	D	31	PHE	0	0.013	-0.004	7.524	-0.036	-0.036	0.000	0.000	0.000	0.000
23	D	32	ILE	0	-0.020	-0.010	7.411	0.140	0.140	0.000	0.000	0.000	0.000
24	D	33	TYR	0	-0.023	-0.020	7.598	-0.622	-0.622	0.000	0.000	0.000	0.000
25	D	34	THR	0	-0.026	-0.017	7.531	0.212	0.212	0.000	0.000	0.000	0.000
26	D	35	ASP	-1	-0.898	-0.952	9.772	-0.597	-0.597	0.000	0.000	0.000	0.000
27	D	36	SER	0	-0.074	-0.055	12.064	0.004	0.004	0.000	0.000	0.000	0.000
28	D	37	GLU	-1	-0.923	-0.931	12.018	-0.587	-0.587	0.000	0.000	0.000	0.000
29	D	38	ASP	-1	-0.984	-0.977	14.537	-0.272	-0.272	0.000	0.000	0.000	0.000
30	D	39	GLY	0	0.069	0.023	15.174	0.051	0.051	0.000	0.000	0.000	0.000
31	D	40	ALA	0	-0.037	-0.026	12.924	-0.091	-0.091	0.000	0.000	0.000	0.000
32	D	41	THR	0	-0.003	-0.009	9.122	-0.154	-0.154	0.000	0.000	0.000	0.000
33	D	42	ASN	0	0.012	-0.004	10.678	0.182	0.182	0.000	0.000	0.000	0.000
34	D	43	ILE	0	-0.009	0.002	11.124	-0.086	-0.086	0.000	0.000	0.000	0.000
35	D	44	LEU	0	0.023	0.034	13.316	0.054	0.054	0.000	0.000	0.000	0.000
36	D	45	TYR	0	0.000	-0.018	14.616	0.017	0.017	0.000	0.000	0.000	0.000
37	D	46	ARG	1	0.803	0.876	17.252	0.198	0.198	0.000	0.000	0.000	0.000
38	D	47	ARG	1	0.825	0.902	20.590	0.121	0.121	0.000	0.000	0.000	0.000
39	D	48	GLU	-1	-0.886	-0.944	23.664	-0.006	-0.006	0.000	0.000	0.000	0.000
40	D	49	ASP	-1	-0.867	-0.909	26.517	-0.079	-0.079	0.000	0.000	0.000	0.000
41	D	50	GLY	0	0.010	0.006	25.837	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	51	ASN	0	-0.108	-0.055	25.128	-0.022	-0.022	0.000	0.000	0.000	0.000
43	D	52	LEU	0	0.023	0.006	19.726	0.006	0.006	0.000	0.000	0.000	0.000
44	D	53	GLY	0	-0.036	-0.018	20.377	0.018	0.018	0.000	0.000	0.000	0.000
45	D	54	LEU	0	-0.010	-0.006	16.136	-0.023	-0.023	0.000	0.000	0.000	0.000
46	D	55	ILE	0	-0.035	-0.014	16.094	0.038	0.038	0.000	0.000	0.000	0.000
47	D	56	GLU	-1	-0.799	-0.864	15.340	-0.245	-0.245	0.000	0.000	0.000	0.000
48	D	57	ALA	0	-0.033	-0.013	13.436	0.062	0.062	0.000	0.000	0.000	0.000
49	D	58	LYS	1	0.819	0.880	15.502	0.162	0.162	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:THR)