FMO DATABASE

FMODB ID: J31Z9

Calculation Name: 2YY3-A-Xray372

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: 2023-06-20

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	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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-645314.591145
FMO2-HF: Nuclear repulsion	609219.090298
FMO2-HF: Total energy	-36095.500847
FMO2-MP2: Total energy	-36201.640367

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.
-11.865	-22.901	35.781	-11.23	-13.515	0.002

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 : -0.013 / q_NPA : 0.024

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	ASP	-1	-0.870	-0.913	2.083	-7.036	-4.104	3.820	-2.982	-3.770	-0.016
4	A	4	PHE	0	-0.004	0.016	3.328	2.320	2.441	0.015	0.290	-0.426	-0.001
5	A	5	ASN	0	-0.018	-0.027	2.404	-4.731	-4.149	2.721	-0.993	-2.310	-0.006
6	A	6	LEU	0	0.024	-0.004	4.055	0.160	0.298	0.002	-0.038	-0.101	0.000
7	A	7	VAL	0	-0.020	-0.003	7.785	-0.225	-0.225	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.056	0.031	10.940	0.070	0.070	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.073	-0.041	14.277	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.033	0.010	17.043	0.017	0.017	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.852	0.931	20.287	-0.163	-0.163	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.042	0.011	23.815	0.012	0.012	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.022	-0.014	26.328	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.011	-0.017	30.037	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.014	0.004	32.446	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.905	-0.961	35.650	0.058	0.058	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.079	-0.067	36.938	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.932	-0.942	38.244	0.034	0.034	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.059	-0.003	33.604	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.008	0.001	34.497	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.059	0.004	30.993	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.849	-0.900	30.215	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.993	-1.004	29.739	0.027	0.027	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.045	0.026	28.692	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.837	-0.922	25.438	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.864	-0.928	25.256	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.789	0.883	26.314	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.026	0.013	23.694	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.850	0.910	21.355	0.053	0.053	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.863	0.941	21.137	-0.050	-0.050	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.006	0.013	22.737	0.011	0.011	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.055	-0.020	16.624	0.040	0.040	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.038	-0.017	17.042	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.881	-0.952	16.410	0.338	0.338	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.863	0.950	11.554	-1.018	-1.018	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.018	0.000	11.269	0.170	0.170	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.018	0.013	11.886	-0.115	-0.115	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.010	0.005	12.759	0.062	0.062	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.018	-0.009	12.684	-0.087	-0.087	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.881	0.934	14.687	0.032	0.032	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.034	0.033	18.144	0.035	0.035	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.943	-0.980	21.419	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.827	0.892	23.815	0.022	0.022	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.926	-0.967	27.126	0.067	0.067	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.006	-0.007	29.075	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.007	-0.003	32.779	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.033	-0.037	35.060	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.052	-0.041	37.788	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.040	0.042	38.547	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.036	0.029	34.571	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.016	-0.013	30.496	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.024	0.033	27.866	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.023	0.000	25.427	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.905	0.965	21.572	-0.054	-0.054	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.042	0.023	18.881	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.075	-0.029	14.818	0.038	0.038	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.045	0.018	13.491	-0.074	-0.074	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.052	-0.020	8.814	0.056	0.056	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.092	0.014	8.628	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.748	0.801	2.127	-10.465	-25.274	29.223	-7.507	-6.908	0.025
61	A	61	ASP	-1	-0.886	-0.940	6.514	1.815	1.815	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.901	-0.934	5.625	5.990	5.990	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.923	-0.976	9.477	0.850	0.850	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.046	0.030	11.522	0.170	0.170	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.097	-0.053	8.822	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.042	0.009	13.215	0.044	0.044	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.005	-0.014	10.663	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.858	-0.924	16.344	0.436	0.436	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.904	-0.950	18.102	0.571	0.571	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.027	-0.025	16.489	-0.048	-0.048	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.002	0.010	19.767	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.883	-0.948	21.931	0.334	0.334	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.925	0.961	20.779	-0.384	-0.384	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.081	-0.061	20.062	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.842	-0.925	24.870	0.191	0.191	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.973	-0.964	27.067	0.216	0.216	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.110	-0.048	27.037	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.870	-0.922	29.835	0.073	0.073	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.007	-0.023	32.732	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.040	0.006	28.030	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.963	-0.988	31.190	0.121	0.121	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.003	-0.003	29.259	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.064	-0.037	24.016	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.871	-0.915	23.898	0.271	0.271	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.012	-0.016	17.669	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.932	-0.950	20.504	0.206	0.206	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.087	-0.056	17.573	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.060	0.021	12.210	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.058	-0.028	11.515	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.878	0.947	8.079	-1.711	-1.711	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.036	0.003	4.830	-0.151	-0.151	0.000	0.000	0.000	0.000

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