FMO DATABASE

FMODB ID: Q172Y

Calculation Name: 2YY3-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YY3

Chain ID: A

ChEMBL ID:

UniProt ID: P58748

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-645138.074525
FMO2-HF: Nuclear repulsion	609043.415676
FMO2-HF: Total energy	-36094.658849
FMO2-MP2: Total energy	-36200.792398

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:MET )

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

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.
-12.87	-23.631	35.733	-11.48	-13.492	0.006

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

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 : 0.023

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	A	3	ASP	-1	-0.865	-0.910	2.015	-7.437	-4.327	3.306	-2.837	-3.579	-0.014
4	A	4	PHE	0	-0.033	-0.002	3.421	2.547	2.745	0.009	0.183	-0.390	0.000
5	A	5	ASN	0	0.020	0.002	2.235	-3.986	-3.692	3.381	-1.171	-2.504	-0.008
6	A	6	LEU	0	0.012	-0.008	3.952	0.321	0.476	0.004	-0.047	-0.112	0.000
7	A	7	VAL	0	-0.018	-0.001	7.702	-0.206	-0.206	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.050	0.027	10.885	0.076	0.076	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.076	-0.043	14.228	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.030	0.008	17.048	0.021	0.021	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.849	0.930	20.265	-0.127	-0.127	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.042	0.011	23.786	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.022	-0.014	26.328	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.013	-0.016	30.029	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.013	0.004	32.463	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.906	-0.963	35.668	0.044	0.044	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.076	-0.066	36.958	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.934	-0.943	38.263	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.057	-0.002	33.650	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.010	-0.001	34.574	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.059	0.004	31.034	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.851	-0.900	30.289	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.992	-1.004	29.828	0.015	0.015	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.043	0.025	28.758	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.837	-0.921	25.511	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.862	-0.928	25.351	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.790	0.884	26.439	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.024	0.012	23.767	0.014	0.014	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.852	0.912	21.462	0.081	0.081	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.864	0.941	21.271	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.008	0.011	22.838	0.016	0.016	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.055	-0.019	16.742	0.041	0.041	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.041	-0.019	17.132	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.884	-0.953	16.533	0.351	0.351	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.861	0.950	11.548	-1.052	-1.052	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.015	0.003	11.408	0.163	0.163	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.021	0.015	12.024	-0.110	-0.110	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.015	0.003	12.894	0.051	0.051	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.012	-0.005	12.719	-0.092	-0.092	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.880	0.933	14.737	0.118	0.118	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.029	0.031	18.170	0.036	0.036	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.943	-0.980	21.446	-0.081	-0.081	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.825	0.891	23.808	0.053	0.053	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.926	-0.967	27.080	0.025	0.025	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.003	-0.009	29.035	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.002	-0.001	32.727	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.039	-0.040	35.009	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.053	-0.041	37.732	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.040	0.041	38.514	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.034	0.029	34.558	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.013	-0.013	30.485	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.025	0.033	27.829	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.029	-0.002	25.448	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.906	0.966	21.535	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.040	0.021	18.917	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.069	-0.026	14.799	0.032	0.032	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.042	0.015	13.554	-0.077	-0.077	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.043	-0.014	8.854	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.082	0.009	8.662	0.047	0.047	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.760	0.811	2.122	-10.927	-25.478	29.033	-7.607	-6.874	0.028
61	A	61	ASP	-1	-0.892	-0.942	6.480	1.720	1.720	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.906	-0.938	5.622	6.282	6.282	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.930	-0.980	9.469	0.860	0.860	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.042	0.027	11.521	0.183	0.183	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.095	-0.049	8.816	-0.055	-0.055	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.040	0.007	13.202	0.029	0.029	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.009	-0.012	10.663	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.859	-0.925	16.352	0.395	0.395	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.907	-0.951	18.090	0.574	0.574	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.023	-0.023	16.563	-0.048	-0.048	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.005	0.010	19.830	-0.050	-0.050	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.883	-0.949	21.957	0.323	0.323	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.927	0.961	20.770	-0.384	-0.384	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.076	-0.059	20.129	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.848	-0.926	24.932	0.171	0.171	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.974	-0.965	27.166	0.212	0.212	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.110	-0.048	27.127	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.874	-0.925	29.919	0.063	0.063	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.009	-0.025	32.804	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.038	0.008	28.067	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.967	-0.989	31.228	0.105	0.105	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.007	-0.004	29.243	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.061	-0.035	24.029	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.872	-0.917	23.867	0.243	0.243	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.010	-0.014	17.609	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.938	-0.953	20.451	0.156	0.156	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.091	-0.057	17.432	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.051	0.015	12.084	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.075	-0.039	11.341	0.010	0.010	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.862	0.936	7.850	-1.465	-1.465	0.000	0.000	0.000	0.000
91	A	91	ILE	-1	-0.933	-0.948	5.114	-1.754	-1.721	0.000	-0.001	-0.033	0.000

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