FMO DATABASE

FMODB ID: JQ229

Calculation Name: 1Y7Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y7Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q7X0F0

Base Structure: X-ray

Registration Date: 2023-09-22

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	69
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-417008.005113
FMO2-HF: Nuclear repulsion	390388.193309
FMO2-HF: Total energy	-26619.811804
FMO2-MP2: Total energy	-26700.136149

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:5:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
-27.625	-36.362	34.396	-9.707	-15.949	-0.061

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.040

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	7	HIS	0	0.008	0.000	2.161	-4.986	-9.236	20.561	-4.892	-11.419	0.003
4	A	8	TYR	0	-0.054	-0.024	3.719	-1.105	-1.229	0.074	0.555	-0.504	0.003
5	A	9	ALA	0	0.034	0.011	3.991	-0.131	0.059	0.000	-0.026	-0.163	0.000
6	A	10	ASP	-1	-0.829	-0.902	1.730	-31.796	-36.427	13.762	-5.340	-3.790	-0.067
7	A	11	LEU	0	-0.017	-0.015	4.992	1.462	1.540	-0.001	-0.004	-0.073	0.000
8	A	12	VAL	0	-0.025	-0.012	8.225	0.618	0.618	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.966	1.002	5.622	5.861	5.861	0.000	0.000	0.000	0.000
10	A	14	PHE	0	0.002	-0.009	8.958	0.535	0.535	0.000	0.000	0.000	0.000
11	A	15	GLY	0	0.028	0.007	10.790	0.363	0.363	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.001	-0.012	12.573	0.086	0.086	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.859	0.924	13.227	1.360	1.360	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.036	0.028	14.900	0.176	0.176	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.934	0.979	16.990	0.827	0.827	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.897	-0.933	17.113	-1.004	-1.004	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.001	-0.003	17.760	0.089	0.089	0.000	0.000	0.000	0.000
18	A	22	ARG	1	0.730	0.828	20.903	0.729	0.729	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.140	-0.105	22.335	0.073	0.073	0.000	0.000	0.000	0.000
20	A	24	ALA	0	0.044	0.033	23.655	0.049	0.049	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.869	0.936	24.912	0.606	0.606	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.008	0.028	27.331	0.030	0.030	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.021	0.021	26.139	0.024	0.024	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.107	0.040	26.766	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.064	-0.072	21.494	0.034	0.034	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.958	-0.969	25.503	-0.347	-0.347	0.000	0.000	0.000	0.000
27	A	31	THR	0	0.026	0.001	28.590	0.011	0.011	0.000	0.000	0.000	0.000
28	A	32	LEU	0	0.062	0.052	21.468	0.001	0.001	0.000	0.000	0.000	0.000
29	A	33	ALA	0	-0.069	-0.032	25.397	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	34	PHE	0	0.026	0.013	26.279	0.004	0.004	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.048	0.020	27.972	0.006	0.006	0.000	0.000	0.000	0.000
32	A	36	SER	0	-0.046	-0.011	24.160	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	37	GLY	0	-0.030	-0.025	26.185	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.079	-0.014	21.798	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	39	ASP	-1	-0.800	-0.931	25.084	-0.447	-0.447	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.980	0.970	24.537	0.376	0.376	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.009	-0.001	23.903	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	42	TYR	0	-0.003	0.008	18.159	-0.070	-0.070	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.067	0.037	19.656	-0.084	-0.084	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.012	-0.005	19.315	-0.077	-0.077	0.000	0.000	0.000	0.000
41	A	45	GLY	0	-0.078	-0.062	18.476	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.002	0.010	14.586	-0.094	-0.094	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.737	-0.845	14.521	-0.954	-0.954	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.932	0.979	15.233	0.568	0.568	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.047	0.027	11.846	0.003	0.003	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.073	-0.024	12.034	0.099	0.099	0.000	0.000	0.000	0.000
47	A	51	ARG	1	0.896	0.955	14.303	0.802	0.802	0.000	0.000	0.000	0.000
48	A	52	ASN	0	0.030	0.006	11.629	-0.357	-0.357	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.027	0.011	12.959	0.174	0.174	0.000	0.000	0.000	0.000
50	A	54	SER	0	0.016	-0.004	14.111	-0.125	-0.125	0.000	0.000	0.000	0.000
51	A	55	LEU	0	0.113	0.056	16.167	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.048	0.016	17.384	0.027	0.027	0.000	0.000	0.000	0.000
53	A	57	ASN	0	0.033	-0.006	18.886	0.078	0.078	0.000	0.000	0.000	0.000
54	A	58	ILE	0	0.010	0.017	13.571	0.026	0.026	0.000	0.000	0.000	0.000
55	A	59	LEU	0	-0.020	-0.023	17.918	0.029	0.029	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.952	0.992	21.090	0.570	0.570	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.033	-0.014	18.281	0.042	0.042	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.009	0.003	20.074	0.023	0.023	0.000	0.000	0.000	0.000
59	A	63	THR	0	0.030	0.004	21.721	0.050	0.050	0.000	0.000	0.000	0.000
60	A	64	ALA	0	-0.046	-0.011	24.802	0.036	0.036	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.065	-0.031	21.089	0.024	0.024	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.953	-0.962	25.010	-0.458	-0.458	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.079	-0.033	19.815	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.900	-0.954	21.651	-0.642	-0.642	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.042	0.000	18.326	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.964	0.987	16.392	0.591	0.591	0.000	0.000	0.000	0.000
67	A	71	GLU	-1	-0.898	-0.952	16.126	-0.838	-0.838	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.031	-0.023	14.619	-0.047	-0.047	0.000	0.000	0.000	0.000
69	A	73	PHE	0	-0.056	-0.010	10.319	-0.277	-0.277	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)