FMO DATABASE

FMODB ID: R5798

Calculation Name: 3ONT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ONT

Chain ID: A

ChEMBL ID:

UniProt ID: Q62264

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:

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-786541.329675
FMO2-HF: Nuclear repulsion	739630.711316
FMO2-HF: Total energy	-46910.618359
FMO2-MP2: Total energy	-47043.050034

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:TYR)

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

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.
-8.069	-3.865	0.36	-1.483	-3.077	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / 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	LYS	1	1.010	0.982	3.818	-1.747	-0.469	-0.006	-0.639	-0.632	0.003
4	A	11	ASN	0	-0.033	-0.024	6.338	-0.094	-0.094	0.000	0.000	0.000	0.000
5	A	12	CYS	0	-0.043	0.021	3.197	0.159	0.948	0.189	-0.215	-0.761	0.000
6	A	13	LEU	0	0.099	0.034	6.211	-0.351	-0.351	0.000	0.000	0.000	0.000
7	A	14	LEU	0	0.066	0.020	3.491	-1.417	-0.140	0.131	-0.308	-1.100	0.003
8	A	15	THR	0	-0.001	0.002	3.198	-1.765	-0.948	0.047	-0.320	-0.543	-0.002
9	A	16	VAL	0	-0.019	-0.015	5.140	0.022	0.065	-0.001	-0.001	-0.041	0.000
10	A	17	MET	0	-0.026	-0.007	8.289	0.091	0.091	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.884	-0.940	6.741	-2.713	-2.713	0.000	0.000	0.000	0.000
12	A	19	ARG	1	0.970	0.977	9.316	0.779	0.779	0.000	0.000	0.000	0.000
13	A	20	TYR	0	-0.049	-0.023	11.031	0.131	0.131	0.000	0.000	0.000	0.000
14	A	21	SER	0	0.017	-0.019	12.379	0.080	0.080	0.000	0.000	0.000	0.000
15	A	22	ALA	0	-0.026	-0.007	13.123	0.076	0.076	0.000	0.000	0.000	0.000
16	A	23	VAL	0	-0.052	-0.032	14.835	0.097	0.097	0.000	0.000	0.000	0.000
17	A	24	VAL	0	0.014	0.013	17.080	0.067	0.067	0.000	0.000	0.000	0.000
18	A	25	ARG	1	0.930	0.965	15.920	0.821	0.821	0.000	0.000	0.000	0.000
19	A	26	ASN	0	-0.027	-0.012	18.989	0.043	0.043	0.000	0.000	0.000	0.000
20	A	27	MET	0	-0.056	-0.022	20.878	0.055	0.055	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.930	-0.989	21.585	-0.428	-0.428	0.000	0.000	0.000	0.000
22	A	29	GLN	0	-0.068	-0.017	21.912	0.045	0.045	0.000	0.000	0.000	0.000
23	A	30	VAL	0	-0.003	-0.002	24.925	0.030	0.030	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.046	-0.008	26.958	0.030	0.030	0.000	0.000	0.000	0.000
25	A	32	MET	0	-0.013	-0.014	28.889	0.004	0.004	0.000	0.000	0.000	0.000
26	A	33	ILE	0	-0.031	-0.013	31.306	0.008	0.008	0.000	0.000	0.000	0.000
27	A	34	PRO	0	0.042	0.008	30.514	0.010	0.010	0.000	0.000	0.000	0.000
28	A	35	SER	0	-0.033	-0.015	32.602	0.004	0.004	0.000	0.000	0.000	0.000
29	A	36	LEU	0	0.013	0.004	35.080	0.010	0.010	0.000	0.000	0.000	0.000
30	A	37	LEU	0	-0.026	-0.008	29.498	0.005	0.005	0.000	0.000	0.000	0.000
31	A	38	ARG	1	0.918	0.956	34.033	0.159	0.159	0.000	0.000	0.000	0.000
32	A	39	ASP	-1	-0.892	-0.940	36.650	-0.116	-0.116	0.000	0.000	0.000	0.000
33	A	40	VAL	0	-0.068	-0.014	33.853	0.007	0.007	0.000	0.000	0.000	0.000
34	A	41	GLN	0	0.080	0.004	34.893	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	42	LEU	0	-0.012	0.009	29.994	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	43	SER	0	-0.021	-0.017	32.217	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	44	GLY	0	0.030	0.035	33.916	0.005	0.005	0.000	0.000	0.000	0.000
38	A	45	PRO	0	-0.010	-0.004	34.537	0.008	0.008	0.000	0.000	0.000	0.000
39	A	46	GLY	0	0.000	0.004	37.859	0.004	0.004	0.000	0.000	0.000	0.000
40	A	47	GLY	0	0.032	0.022	40.334	0.001	0.001	0.000	0.000	0.000	0.000
41	A	48	SER	0	-0.131	-0.081	40.726	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.007	0.003	37.620	0.001	0.001	0.000	0.000	0.000	0.000
43	A	50	GLN	0	-0.010	0.003	40.970	0.003	0.003	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.896	-0.950	41.670	-0.099	-0.099	0.000	0.000	0.000	0.000
45	A	52	GLY	0	-0.011	-0.012	41.533	0.004	0.004	0.000	0.000	0.000	0.000
46	A	53	ALA	0	-0.077	-0.035	38.168	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	54	PRO	0	-0.011	-0.014	33.220	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	55	ASP	-1	-0.747	-0.863	34.323	-0.143	-0.143	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.011	-0.009	28.920	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	57	TYR	0	-0.014	-0.001	30.010	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	58	THR	0	0.006	-0.010	30.402	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	59	TYR	0	-0.057	-0.051	24.148	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	60	PHE	0	0.031	-0.006	25.964	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	61	THR	0	-0.055	-0.033	25.514	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	62	MET	0	0.000	0.026	23.455	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	63	LEU	0	-0.004	0.002	20.884	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	64	LYS	1	0.914	0.957	20.962	0.268	0.268	0.000	0.000	0.000	0.000
58	A	65	SER	0	-0.062	-0.039	21.521	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	66	ILE	0	0.063	0.035	17.904	-0.024	-0.024	0.000	0.000	0.000	0.000
60	A	67	CYS	0	-0.059	-0.027	17.041	-0.063	-0.063	0.000	0.000	0.000	0.000
61	A	68	VAL	0	0.010	0.013	16.885	-0.081	-0.081	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.869	-0.937	17.497	-0.366	-0.366	0.000	0.000	0.000	0.000
63	A	70	VAL	0	-0.061	-0.040	12.225	-0.047	-0.047	0.000	0.000	0.000	0.000
64	A	71	ASP	-1	-0.786	-0.872	12.457	-1.065	-1.065	0.000	0.000	0.000	0.000
65	A	72	HIS	0	-0.146	-0.074	13.761	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	73	GLY	0	-0.048	-0.022	11.136	0.006	0.006	0.000	0.000	0.000	0.000
67	A	74	LEU	0	-0.050	-0.011	11.954	0.077	0.077	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.005	0.002	14.669	0.039	0.039	0.000	0.000	0.000	0.000
69	A	76	PRO	0	-0.029	-0.005	16.791	0.022	0.022	0.000	0.000	0.000	0.000
70	A	105	ASP	-1	-0.924	-0.971	35.614	-0.043	-0.043	0.000	0.000	0.000	0.000
71	A	106	ARG	1	0.893	0.946	32.634	0.020	0.020	0.000	0.000	0.000	0.000
72	A	107	ILE	0	0.057	0.030	30.501	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	108	SER	0	-0.024	-0.027	30.676	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	109	GLU	-1	-0.879	-0.947	28.280	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	110	GLU	-1	-0.893	-0.917	24.632	-0.151	-0.151	0.000	0.000	0.000	0.000
76	A	111	LEU	0	-0.014	-0.035	26.165	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	112	ASP	-1	-0.879	-0.914	27.908	-0.092	-0.092	0.000	0.000	0.000	0.000
78	A	113	LEU	0	-0.049	-0.029	21.713	0.002	0.002	0.000	0.000	0.000	0.000
79	A	114	GLU	-1	-0.826	-0.898	22.656	-0.244	-0.244	0.000	0.000	0.000	0.000
80	A	115	ALA	0	0.021	0.011	23.328	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	116	GLN	0	-0.035	-0.024	23.242	0.013	0.013	0.000	0.000	0.000	0.000
82	A	117	PHE	0	-0.015	-0.003	15.564	0.021	0.021	0.000	0.000	0.000	0.000
83	A	118	HIS	0	0.049	0.018	19.406	0.027	0.027	0.000	0.000	0.000	0.000
84	A	119	LEU	0	0.002	0.008	20.577	0.011	0.011	0.000	0.000	0.000	0.000
85	A	120	HIS	0	-0.008	-0.011	17.952	0.033	0.033	0.000	0.000	0.000	0.000
86	A	121	PHE	0	-0.025	0.001	15.079	0.034	0.034	0.000	0.000	0.000	0.000
87	A	122	CYS	0	0.052	0.029	16.150	0.000	0.000	0.000	0.000	0.000	0.000
88	A	123	SER	0	-0.048	-0.041	18.699	0.027	0.027	0.000	0.000	0.000	0.000
89	A	124	LEU	0	-0.026	-0.006	12.357	0.051	0.051	0.000	0.000	0.000	0.000
90	A	125	HIS	0	0.003	0.016	14.474	0.084	0.084	0.000	0.000	0.000	0.000
91	A	126	HIS	0	0.024	-0.001	15.477	0.019	0.019	0.000	0.000	0.000	0.000
92	A	127	ILE	0	0.002	-0.004	16.089	0.023	0.023	0.000	0.000	0.000	0.000
93	A	128	LEU	0	0.023	0.003	10.609	0.034	0.034	0.000	0.000	0.000	0.000
94	A	129	THR	0	0.026	0.046	14.700	0.002	0.002	0.000	0.000	0.000	0.000
95	A	130	HIS	0	-0.013	-0.008	16.849	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	131	LEU	0	-0.028	-0.039	16.083	0.005	0.005	0.000	0.000	0.000	0.000
97	A	132	THR	0	-0.024	-0.010	14.407	0.037	0.037	0.000	0.000	0.000	0.000
98	A	133	ARG	1	0.947	0.985	16.480	-0.061	-0.061	0.000	0.000	0.000	0.000
99	A	134	LYS	1	0.864	0.940	20.120	-0.130	-0.130	0.000	0.000	0.000	0.000
100	A	135	ALA	0	0.052	0.023	17.227	0.004	0.004	0.000	0.000	0.000	0.000
101	A	136	GLN	0	0.002	-0.006	18.616	0.000	0.000	0.000	0.000	0.000	0.000
102	A	137	GLU	-1	-0.862	-0.943	20.708	0.096	0.096	0.000	0.000	0.000	0.000
103	A	138	VAL	0	-0.042	-0.018	21.615	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	139	THR	0	-0.028	-0.008	20.353	0.010	0.010	0.000	0.000	0.000	0.000
105	A	140	ARG	1	0.975	0.991	22.892	-0.088	-0.088	0.000	0.000	0.000	0.000
106	A	141	LYS	1	0.933	0.980	25.948	-0.137	-0.137	0.000	0.000	0.000	0.000
107	A	142	TYR	0	0.011	0.005	25.546	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	143	GLN	0	0.009	-0.001	24.316	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	144	GLU	-1	-0.936	-0.964	28.385	0.090	0.090	0.000	0.000	0.000	0.000
110	A	145	MET	0	-0.054	-0.042	30.720	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	146	THR	0	-0.064	-0.023	29.891	0.002	0.002	0.000	0.000	0.000	0.000
112	A	147	GLY	0	-0.006	-0.001	32.499	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	148	GLN	0	-0.004	-0.006	27.616	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	149	VAL	0	-0.060	-0.016	29.517	-0.010	-0.010	0.000	0.000	0.000	0.000

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