FMO DATABASE

FMODB ID: 72Z7K

Calculation Name: 5EB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EB9

Chain ID: A

ChEMBL ID:

UniProt ID: Q6QR64

Base Structure: X-ray

Registration Date: 2023-06-26

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-949254.235848
FMO2-HF: Nuclear repulsion	903052.240441
FMO2-HF: Total energy	-46201.995407
FMO2-MP2: Total energy	-46334.542047

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:8:THR)

Summations of interaction energy for fragment #1(A:8:THR)

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.
-2.008	0.491	-0.006	-1.038	-1.454	0.003

Interaction energy analysis for fragmet #1(A:8:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.006

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	10	GLU	-1	-0.928	-0.966	3.820	-3.322	-1.240	-0.017	-0.964	-1.101	0.003
4	A	11	ALA	0	-0.008	0.008	6.527	0.333	0.333	0.000	0.000	0.000	0.000
5	A	12	ARG	1	0.929	0.958	9.135	0.880	0.880	0.000	0.000	0.000	0.000
6	A	13	PHE	0	0.011	0.005	12.272	0.060	0.060	0.000	0.000	0.000	0.000
7	A	14	LEU	0	0.030	0.025	14.619	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	15	ASN	0	0.028	0.014	16.202	0.024	0.024	0.000	0.000	0.000	0.000
9	A	16	ARG	1	0.952	0.956	9.756	0.498	0.498	0.000	0.000	0.000	0.000
10	A	17	ASN	0	0.018	0.017	16.275	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	18	MET	0	-0.080	-0.022	19.474	0.021	0.021	0.000	0.000	0.000	0.000
12	A	19	LYS	1	0.953	0.968	18.519	0.253	0.253	0.000	0.000	0.000	0.000
13	A	20	HIS	1	0.894	0.939	19.476	0.277	0.277	0.000	0.000	0.000	0.000
14	A	21	PRO	0	0.035	0.050	21.369	0.009	0.009	0.000	0.000	0.000	0.000
15	A	22	GLN	0	0.018	-0.002	23.293	0.001	0.001	0.000	0.000	0.000	0.000
16	A	23	GLU	-1	-0.929	-0.965	27.033	-0.167	-0.167	0.000	0.000	0.000	0.000
17	A	24	GLY	0	-0.032	-0.023	29.445	0.011	0.011	0.000	0.000	0.000	0.000
18	A	25	GLN	0	-0.039	-0.024	27.501	0.000	0.000	0.000	0.000	0.000	0.000
19	A	26	PRO	0	0.034	0.022	25.425	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	27	LEU	0	-0.047	-0.016	19.920	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.860	-0.929	17.771	-0.234	-0.234	0.000	0.000	0.000	0.000
22	A	29	LEU	0	-0.055	-0.028	15.114	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	30	GLU	-1	-0.894	-0.969	10.843	-0.435	-0.435	0.000	0.000	0.000	0.000
24	A	31	CYS	0	0.002	0.002	9.622	0.000	0.000	0.000	0.000	0.000	0.000
25	A	32	MET	0	-0.010	-0.015	6.160	0.357	0.357	0.000	0.000	0.000	0.000
26	A	33	PRO	0	-0.014	-0.012	5.547	-0.986	-0.986	0.000	0.000	0.000	0.000
27	A	34	PHE	0	0.059	-0.004	3.418	-0.132	0.239	0.012	-0.074	-0.309	0.000
28	A	35	ASN	0	-0.023	0.007	5.309	0.133	0.179	-0.001	0.000	-0.044	0.000
29	A	36	ILE	0	0.057	0.018	9.010	-0.231	-0.231	0.000	0.000	0.000	0.000
30	A	37	ASP	-1	-0.954	-1.019	12.170	0.195	0.195	0.000	0.000	0.000	0.000
31	A	38	ASN	0	-0.029	-0.026	12.093	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	39	GLY	0	-0.004	0.003	13.024	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	40	VAL	0	-0.009	-0.010	10.667	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	41	SER	0	-0.032	-0.025	13.518	0.060	0.060	0.000	0.000	0.000	0.000
35	A	42	TRP	0	0.006	0.011	13.169	-0.107	-0.107	0.000	0.000	0.000	0.000
36	A	43	ILE	0	-0.030	-0.025	14.552	0.071	0.071	0.000	0.000	0.000	0.000
37	A	44	ARG	1	0.900	0.951	16.289	0.235	0.235	0.000	0.000	0.000	0.000
38	A	45	GLN	0	-0.082	-0.058	16.651	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	46	ASP	-1	-0.785	-0.895	18.962	-0.280	-0.280	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.971	0.952	21.078	0.246	0.246	0.000	0.000	0.000	0.000
41	A	48	ASP	-1	-0.951	-0.963	22.872	-0.233	-0.233	0.000	0.000	0.000	0.000
42	A	49	GLY	0	0.014	0.029	20.571	0.006	0.006	0.000	0.000	0.000	0.000
43	A	50	LYS	1	0.946	0.978	20.622	0.180	0.180	0.000	0.000	0.000	0.000
44	A	51	LEU	0	0.008	0.006	16.777	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	52	HIS	0	-0.043	-0.009	20.067	0.057	0.057	0.000	0.000	0.000	0.000
46	A	53	PHE	0	0.006	0.011	19.108	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	54	ILE	0	-0.038	-0.016	18.943	0.023	0.023	0.000	0.000	0.000	0.000
48	A	55	VAL	0	0.034	0.006	19.214	0.029	0.029	0.000	0.000	0.000	0.000
49	A	56	TYR	0	-0.010	0.013	16.258	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	57	ILE	0	-0.033	-0.011	16.505	0.030	0.030	0.000	0.000	0.000	0.000
51	A	58	SER	0	0.031	0.013	16.758	0.003	0.003	0.000	0.000	0.000	0.000
52	A	59	PRO	0	0.049	0.042	16.114	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	60	LEU	0	-0.032	-0.034	17.562	0.009	0.009	0.000	0.000	0.000	0.000
54	A	61	SER	0	0.024	0.017	19.723	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	62	ARG	1	0.927	0.984	20.976	0.003	0.003	0.000	0.000	0.000	0.000
56	A	63	THR	0	0.019	0.018	21.410	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	64	ALA	0	-0.013	0.006	22.331	0.016	0.016	0.000	0.000	0.000	0.000
58	A	65	PHE	0	0.037	0.012	22.932	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	66	PRO	0	-0.061	-0.028	24.275	0.014	0.014	0.000	0.000	0.000	0.000
60	A	67	ARG	1	1.015	1.009	26.795	0.106	0.106	0.000	0.000	0.000	0.000
61	A	68	ASN	0	-0.027	-0.020	30.470	0.013	0.013	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.719	-0.869	28.831	-0.153	-0.153	0.000	0.000	0.000	0.000
63	A	70	ARG	1	0.993	1.001	30.234	0.131	0.131	0.000	0.000	0.000	0.000
64	A	71	THR	0	-0.038	-0.032	24.548	0.000	0.000	0.000	0.000	0.000	0.000
65	A	72	SER	0	-0.023	0.031	26.920	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	73	SER	0	-0.069	-0.058	28.166	0.008	0.008	0.000	0.000	0.000	0.000
67	A	74	GLN	0	-0.084	-0.051	27.576	0.013	0.013	0.000	0.000	0.000	0.000
68	A	75	PHE	0	0.003	-0.002	22.237	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	76	GLU	-1	-0.867	-0.930	23.363	-0.130	-0.130	0.000	0.000	0.000	0.000
70	A	77	GLY	0	0.001	0.003	19.894	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	78	SER	0	-0.006	-0.010	18.768	0.032	0.032	0.000	0.000	0.000	0.000
72	A	79	LYS	1	0.952	0.992	14.017	-0.066	-0.066	0.000	0.000	0.000	0.000
73	A	80	GLN	0	-0.019	-0.007	15.838	0.048	0.048	0.000	0.000	0.000	0.000
74	A	81	GLY	0	0.019	0.006	15.268	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	82	SER	0	-0.014	-0.021	11.101	0.006	0.006	0.000	0.000	0.000	0.000
76	A	83	SER	0	0.016	0.034	10.752	-0.056	-0.056	0.000	0.000	0.000	0.000
77	A	84	PHE	0	0.002	-0.010	11.508	0.089	0.089	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.867	0.941	13.387	0.190	0.190	0.000	0.000	0.000	0.000
79	A	86	LEU	0	-0.013	-0.006	16.161	0.031	0.031	0.000	0.000	0.000	0.000
80	A	87	VAL	0	0.042	0.015	18.406	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	88	VAL	0	-0.012	0.002	21.610	0.011	0.011	0.000	0.000	0.000	0.000
82	A	89	LYS	1	0.945	0.980	23.996	0.134	0.134	0.000	0.000	0.000	0.000
83	A	90	ASN	0	-0.068	-0.048	27.240	0.017	0.017	0.000	0.000	0.000	0.000
84	A	91	PHE	0	0.021	0.025	22.126	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	92	ARG	1	0.977	0.989	27.092	0.153	0.153	0.000	0.000	0.000	0.000
86	A	93	ALA	0	0.070	0.034	27.383	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	94	GLN	0	-0.010	-0.017	27.492	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	95	ASP	-1	-0.836	-0.912	24.090	-0.228	-0.228	0.000	0.000	0.000	0.000
89	A	96	GLN	0	-0.009	0.016	22.725	-0.042	-0.042	0.000	0.000	0.000	0.000
90	A	97	GLY	0	0.018	-0.003	20.555	0.016	0.016	0.000	0.000	0.000	0.000
91	A	98	THR	0	-0.048	-0.016	14.150	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	99	TYR	0	-0.039	-0.039	15.255	0.024	0.024	0.000	0.000	0.000	0.000
93	A	100	PHE	0	0.001	0.003	10.199	-0.103	-0.103	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.015	-0.003	9.793	-0.135	-0.135	0.000	0.000	0.000	0.000
95	A	103	ALA	0	0.036	0.018	9.211	0.088	0.088	0.000	0.000	0.000	0.000
96	A	104	ASN	0	-0.020	-0.017	11.122	0.030	0.030	0.000	0.000	0.000	0.000
97	A	105	ILE	0	0.042	0.018	9.990	0.030	0.030	0.000	0.000	0.000	0.000
98	A	106	ASN	0	0.002	-0.010	13.841	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	107	GLN	0	-0.020	-0.014	16.857	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	108	MET	0	0.003	0.033	12.854	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	109	LEU	0	-0.029	-0.019	12.463	0.008	0.008	0.000	0.000	0.000	0.000
102	A	110	TYR	0	-0.003	0.001	6.953	0.042	0.042	0.000	0.000	0.000	0.000
103	A	111	PHE	0	0.025	0.005	7.570	0.030	0.030	0.000	0.000	0.000	0.000
104	A	112	SER	0	-0.022	0.013	5.479	-0.261	-0.261	0.000	0.000	0.000	0.000
105	A	113	SER	0	0.025	0.005	5.816	0.337	0.337	0.000	0.000	0.000	0.000
106	A	114	GLY	0	0.025	0.005	7.374	0.147	0.147	0.000	0.000	0.000	0.000
107	A	115	GLN	0	-0.021	-0.024	11.103	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	116	PRO	0	-0.034	-0.017	13.519	0.086	0.086	0.000	0.000	0.000	0.000
109	A	117	ALA	0	0.006	0.002	16.708	0.014	0.014	0.000	0.000	0.000	0.000
110	A	118	PHE	0	0.015	0.012	19.370	0.020	0.020	0.000	0.000	0.000	0.000
111	A	119	PHE	0	0.016	0.002	22.892	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:THR)