FMO DATABASE

FMODB ID: 3Q65L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-645953.554003
FMO2-HF: Nuclear repulsion	609857.389994
FMO2-HF: Total energy	-36096.164009
FMO2-MP2: Total energy	-36202.300589

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.
-17.061	-23.304	30.096	-10.889	-12.964	0.005

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 : -0.020 / 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	A	3	ASP	-1	-0.891	-0.925	2.240	-10.541	-6.140	2.201	-2.949	-3.653	-0.011
4	A	4	PHE	0	0.021	0.024	3.868	2.957	3.365	0.005	-0.027	-0.386	0.000
5	A	5	ASN	0	-0.032	-0.033	2.506	-5.675	-5.390	3.702	-1.316	-2.671	0.004
6	A	6	LEU	0	0.018	-0.001	4.298	-0.211	-0.104	0.000	-0.029	-0.078	0.000
7	A	7	VAL	0	-0.014	-0.008	8.063	-0.135	-0.135	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.067	0.038	11.163	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.078	-0.039	14.564	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.017	0.005	17.338	0.009	0.009	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.817	0.891	20.579	-0.201	-0.201	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.021	0.004	24.076	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.020	-0.001	26.621	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.001	-0.014	30.325	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.012	-0.021	32.735	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.900	-0.949	35.966	0.093	0.093	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.076	-0.064	37.197	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.941	-0.948	38.459	0.062	0.062	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.043	0.004	33.938	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.053	-0.037	35.185	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.048	0.007	31.273	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.824	-0.904	30.385	0.047	0.047	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.887	-0.939	29.951	0.092	0.092	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.052	0.033	29.379	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.799	-0.879	25.790	0.082	0.082	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.910	-0.947	25.514	0.090	0.090	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.753	0.871	26.593	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.048	0.025	23.978	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.812	0.879	21.638	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.855	0.932	21.443	-0.120	-0.120	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.010	0.014	23.601	0.015	0.015	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.054	-0.015	16.964	0.044	0.044	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.032	-0.012	17.287	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.894	-0.963	16.530	0.623	0.623	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.785	0.912	11.710	-1.121	-1.121	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.012	-0.025	11.730	0.294	0.294	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.016	0.013	12.141	-0.121	-0.121	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.021	0.000	13.037	0.034	0.034	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.016	-0.007	12.777	-0.083	-0.083	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.813	0.898	14.769	-0.064	-0.064	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.026	0.024	18.219	0.045	0.045	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.843	-0.895	21.543	0.022	0.022	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.805	0.884	23.909	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.845	-0.916	26.787	0.098	0.098	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.006	-0.011	29.184	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.019	-0.012	32.726	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.025	-0.033	35.197	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.051	-0.034	37.958	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.040	0.040	38.697	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.027	0.028	34.720	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.026	-0.021	30.705	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.032	0.040	28.112	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.012	-0.005	25.679	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.832	0.914	21.744	-0.086	-0.086	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.034	0.019	19.173	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.072	-0.052	15.095	0.028	0.028	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.050	0.019	13.940	-0.051	-0.051	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.042	-0.015	9.045	0.044	0.044	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.085	0.018	8.979	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.702	0.777	2.157	-12.921	-24.537	24.190	-6.564	-6.010	0.012
61	A	61	ASP	-1	-0.826	-0.876	6.478	1.507	1.507	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.859	-0.911	5.191	7.017	7.145	-0.001	-0.003	-0.124	0.000
63	A	63	GLU	-1	-0.906	-0.972	9.245	1.012	1.012	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.044	0.040	11.305	0.233	0.233	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.083	-0.040	8.198	-0.276	-0.276	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.030	0.001	13.140	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.010	-0.008	11.072	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.859	-0.931	16.787	0.552	0.552	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.754	-0.841	17.806	0.744	0.744	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.046	-0.038	17.169	-0.050	-0.050	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.001	0.013	20.213	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.887	-0.951	22.344	0.410	0.410	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.860	0.918	20.564	-0.568	-0.568	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.074	-0.061	20.193	-0.032	-0.032	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.841	-0.919	25.267	0.242	0.242	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.970	-0.965	27.440	0.298	0.298	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.108	-0.050	27.279	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.868	-0.924	30.225	0.123	0.123	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.020	-0.032	33.073	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.033	0.002	28.256	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.932	-0.967	31.536	0.155	0.155	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.004	-0.010	29.428	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.087	-0.044	24.393	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.879	-0.918	24.292	0.317	0.317	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.018	-0.020	17.882	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.888	-0.920	20.836	0.224	0.224	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.070	-0.049	17.617	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.039	0.015	12.550	0.022	0.022	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.051	-0.017	11.805	-0.045	-0.045	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.816	0.883	8.025	-1.659	-1.659	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.037	0.001	4.603	-0.196	-0.152	-0.001	-0.001	-0.042	0.000

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