FMO DATABASE

FMODB ID: 4J5VN

Calculation Name: 1JY2-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: N

ChEMBL ID:

UniProt ID: P02672

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-162336.660209
FMO2-HF: Nuclear repulsion	143905.042245
FMO2-HF: Total energy	-18431.617964
FMO2-MP2: Total energy	-18482.34412

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(N:35:GLY)

Summations of interaction energy for fragment #1(N:35: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.
-0.903	0.221	-0.012	-0.531	-0.58	0.002

Interaction energy analysis for fragmet #1(N:35:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.015

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

Sort

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	N	37	PRO	0	0.011	0.015	3.782	-0.773	0.351	-0.012	-0.531	-0.580	0.002
4	N	38	PHE	0	0.000	-0.011	6.621	0.453	0.453	0.000	0.000	0.000	0.000
5	N	39	CYS	0	-0.072	-0.031	8.627	-0.004	-0.004	0.000	0.000	0.000	0.000
6	N	40	SER	0	0.013	-0.005	11.626	0.006	0.006	0.000	0.000	0.000	0.000
7	N	41	ASP	-1	-0.894	-0.970	14.974	0.012	0.012	0.000	0.000	0.000	0.000
8	N	42	GLU	-1	-0.963	-0.987	18.238	-0.083	-0.083	0.000	0.000	0.000	0.000
9	N	43	ASP	-1	-0.812	-0.862	14.073	-0.157	-0.157	0.000	0.000	0.000	0.000
10	N	44	TRP	0	0.033	0.012	16.534	0.047	0.047	0.000	0.000	0.000	0.000
11	N	45	ASN	0	-0.041	-0.031	18.482	-0.007	-0.007	0.000	0.000	0.000	0.000
12	N	46	THR	0	-0.013	0.013	18.049	-0.005	-0.005	0.000	0.000	0.000	0.000
13	N	47	LYS	1	0.802	0.889	12.120	0.183	0.183	0.000	0.000	0.000	0.000
14	N	48	CYS	0	-0.011	-0.011	15.814	-0.006	-0.006	0.000	0.000	0.000	0.000
15	N	49	PRO	0	0.030	0.017	14.638	0.057	0.057	0.000	0.000	0.000	0.000
16	N	50	SER	0	0.010	0.009	14.172	-0.060	-0.060	0.000	0.000	0.000	0.000
17	N	51	GLY	0	0.098	0.037	15.938	-0.018	-0.018	0.000	0.000	0.000	0.000
18	N	52	CYS	0	-0.004	-0.005	17.449	-0.019	-0.019	0.000	0.000	0.000	0.000
19	N	53	ARG	1	0.933	0.974	13.543	-0.585	-0.585	0.000	0.000	0.000	0.000
20	N	54	MET	0	0.047	0.020	17.985	-0.012	-0.012	0.000	0.000	0.000	0.000
21	N	55	LYS	1	0.822	0.892	20.799	-0.188	-0.188	0.000	0.000	0.000	0.000
22	N	56	GLY	0	0.019	0.013	21.434	-0.016	-0.016	0.000	0.000	0.000	0.000
23	N	57	LEU	0	0.000	-0.010	18.789	-0.008	-0.008	0.000	0.000	0.000	0.000
24	N	58	ILE	0	-0.024	-0.013	22.944	-0.019	-0.019	0.000	0.000	0.000	0.000
25	N	59	ASP	-1	-0.798	-0.874	25.723	0.157	0.157	0.000	0.000	0.000	0.000
26	N	60	GLU	-1	-0.963	-0.977	23.283	0.213	0.213	0.000	0.000	0.000	0.000
27	N	61	VAL	0	0.004	-0.001	26.214	-0.013	-0.013	0.000	0.000	0.000	0.000
28	N	62	ASP	-1	-0.913	-0.954	28.651	0.096	0.096	0.000	0.000	0.000	0.000
29	N	63	GLN	0	-0.003	0.000	30.348	-0.008	-0.008	0.000	0.000	0.000	0.000
30	N	64	ASP	-1	-0.797	-0.892	30.233	0.102	0.102	0.000	0.000	0.000	0.000
31	N	65	PHE	0	-0.021	-0.029	31.543	-0.009	-0.009	0.000	0.000	0.000	0.000
32	N	66	THR	0	0.010	0.018	34.668	-0.010	-0.010	0.000	0.000	0.000	0.000
33	N	67	SER	0	-0.063	-0.029	35.118	-0.009	-0.009	0.000	0.000	0.000	0.000
34	N	68	ARG	1	0.818	0.885	32.551	-0.101	-0.101	0.000	0.000	0.000	0.000
35	N	69	ILE	0	0.008	0.006	37.984	-0.006	-0.006	0.000	0.000	0.000	0.000
36	N	70	ASN	0	-0.006	-0.013	40.092	-0.007	-0.007	0.000	0.000	0.000	0.000
37	N	71	LYS	1	0.990	1.006	36.851	-0.089	-0.089	0.000	0.000	0.000	0.000
38	N	72	LEU	0	-0.009	0.000	41.039	-0.003	-0.003	0.000	0.000	0.000	0.000
39	N	73	ARG	1	0.916	0.964	43.001	-0.066	-0.066	0.000	0.000	0.000	0.000
40	N	74	ASP	-1	-0.878	-0.941	44.935	0.058	0.058	0.000	0.000	0.000	0.000
41	N	75	SER	0	-0.153	-0.071	46.348	-0.002	-0.002	0.000	0.000	0.000	0.000
42	N	76	LEU	0	-0.040	-0.020	47.867	-0.002	-0.002	0.000	0.000	0.000	0.000
43	N	77	PHE	0	-0.051	-0.011	49.054	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(N:35:GLY)