FMO DATABASE

FMODB ID: ZV15N

Calculation Name: 3NTK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NTK

Chain ID: A

ChEMBL ID:

UniProt ID: P25823

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1695059.653163
FMO2-HF: Nuclear repulsion	1626573.848035
FMO2-HF: Total energy	-68485.805128
FMO2-MP2: Total energy	-68681.700577

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:2346:ALA)

Summations of interaction energy for fragment #1(A:2346:ALA)

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.
-3.963	0.321	1.134	-2.325	-3.093	-0.01

Interaction energy analysis for fragmet #1(A:2346:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.002

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	2348	LEU	0	-0.037	-0.012	3.126	-1.019	1.371	0.082	-1.058	-1.414	0.002
4	A	2349	HIS	0	-0.056	-0.028	5.732	0.570	0.570	0.000	0.000	0.000	0.000
5	A	2350	ASN	0	-0.006	-0.016	9.341	-0.019	-0.019	0.000	0.000	0.000	0.000
6	A	2351	CYS	0	-0.063	-0.019	12.214	0.074	0.074	0.000	0.000	0.000	0.000
7	A	2352	VAL	0	0.081	0.049	14.644	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	2353	VAL	0	-0.011	-0.011	16.228	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	2354	VAL	0	0.001	-0.001	18.515	0.022	0.022	0.000	0.000	0.000	0.000
10	A	2355	GLN	0	-0.017	-0.010	21.148	0.023	0.023	0.000	0.000	0.000	0.000
11	A	2356	PHE	0	-0.017	-0.029	17.183	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	2357	ASP	-1	-0.828	-0.888	21.920	-0.149	-0.149	0.000	0.000	0.000	0.000
13	A	2358	GLY	0	0.033	0.004	21.560	0.021	0.021	0.000	0.000	0.000	0.000
14	A	2359	PRO	0	-0.008	-0.011	16.910	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	2360	MET	0	-0.071	-0.023	17.006	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	2361	SER	0	-0.034	-0.037	19.165	0.009	0.009	0.000	0.000	0.000	0.000
17	A	2362	PHE	0	0.024	0.024	13.357	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	2363	TYR	0	0.015	-0.010	18.675	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	2364	VAL	0	-0.007	0.001	14.287	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	2365	GLN	0	0.021	0.004	17.605	0.014	0.014	0.000	0.000	0.000	0.000
21	A	2366	MET	0	-0.022	-0.010	11.502	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	2367	GLU	-1	-0.818	-0.913	15.101	-0.694	-0.694	0.000	0.000	0.000	0.000
23	A	2368	SER	0	-0.044	-0.039	15.216	0.023	0.023	0.000	0.000	0.000	0.000
24	A	2369	ASP	-1	-0.851	-0.910	17.120	-0.436	-0.436	0.000	0.000	0.000	0.000
25	A	2370	VAL	0	0.010	0.024	19.680	0.040	0.040	0.000	0.000	0.000	0.000
26	A	2371	PRO	0	0.040	0.026	21.278	0.033	0.033	0.000	0.000	0.000	0.000
27	A	2372	ALA	0	-0.047	-0.022	23.187	0.027	0.027	0.000	0.000	0.000	0.000
28	A	2373	LEU	0	0.015	0.014	23.509	0.024	0.024	0.000	0.000	0.000	0.000
29	A	2374	GLU	-1	-0.892	-0.950	25.538	-0.250	-0.250	0.000	0.000	0.000	0.000
30	A	2375	GLN	0	-0.012	0.000	27.709	0.025	0.025	0.000	0.000	0.000	0.000
31	A	2376	MET	0	-0.058	-0.017	28.253	0.021	0.021	0.000	0.000	0.000	0.000
32	A	2377	THR	0	-0.012	-0.031	28.777	0.014	0.014	0.000	0.000	0.000	0.000
33	A	2378	ASP	-1	-0.892	-0.937	31.374	-0.158	-0.158	0.000	0.000	0.000	0.000
34	A	2379	LYS	1	0.783	0.875	32.246	0.152	0.152	0.000	0.000	0.000	0.000
35	A	2380	LEU	0	-0.051	-0.029	31.964	0.009	0.009	0.000	0.000	0.000	0.000
36	A	2381	LEU	0	0.004	0.008	35.639	0.008	0.008	0.000	0.000	0.000	0.000
37	A	2382	ASP	-1	-0.997	-0.989	37.510	-0.102	-0.102	0.000	0.000	0.000	0.000
38	A	2383	ALA	0	0.016	0.002	38.934	0.006	0.006	0.000	0.000	0.000	0.000
39	A	2384	GLU	-1	-0.844	-0.907	38.800	-0.100	-0.100	0.000	0.000	0.000	0.000
40	A	2385	GLN	0	-0.062	-0.034	40.771	0.004	0.004	0.000	0.000	0.000	0.000
41	A	2386	ASP	-1	-0.916	-0.949	43.890	-0.075	-0.075	0.000	0.000	0.000	0.000
42	A	2387	LEU	0	-0.087	-0.020	38.781	0.002	0.002	0.000	0.000	0.000	0.000
43	A	2388	PRO	0	0.001	0.000	43.406	0.002	0.002	0.000	0.000	0.000	0.000
44	A	2389	ALA	0	0.048	0.017	43.956	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	2390	PHE	0	0.003	-0.002	40.015	0.001	0.001	0.000	0.000	0.000	0.000
46	A	2391	SER	0	0.022	-0.008	43.481	0.000	0.000	0.000	0.000	0.000	0.000
47	A	2392	ASP	-1	-0.902	-0.913	42.012	-0.067	-0.067	0.000	0.000	0.000	0.000
48	A	2393	LEU	0	-0.005	-0.013	41.247	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	2394	LYS	1	0.847	0.903	39.286	0.074	0.074	0.000	0.000	0.000	0.000
50	A	2395	GLU	-1	-0.869	-0.945	36.046	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	2396	GLY	0	-0.059	-0.034	33.312	0.003	0.003	0.000	0.000	0.000	0.000
52	A	2397	ALA	0	-0.045	-0.015	33.874	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	2398	LEU	0	-0.014	-0.009	30.561	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	2399	CYS	0	-0.068	-0.032	34.446	0.006	0.006	0.000	0.000	0.000	0.000
55	A	2400	VAL	0	0.045	0.036	34.607	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	2401	ALA	0	0.005	-0.004	35.652	0.008	0.008	0.000	0.000	0.000	0.000
57	A	2402	GLN	0	0.003	0.010	36.142	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	2403	PHE	0	0.040	0.029	32.151	0.006	0.006	0.000	0.000	0.000	0.000
59	A	2404	PRO	0	-0.020	-0.025	36.160	0.000	0.000	0.000	0.000	0.000	0.000
60	A	2405	GLU	-1	-0.984	-0.986	33.604	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	2406	ASP	-1	-0.841	-0.913	33.795	-0.145	-0.145	0.000	0.000	0.000	0.000
62	A	2407	GLU	-1	-1.015	-0.998	36.519	-0.088	-0.088	0.000	0.000	0.000	0.000
63	A	2408	VAL	0	0.026	0.039	34.204	0.004	0.004	0.000	0.000	0.000	0.000
64	A	2409	PHE	0	-0.043	-0.035	36.241	0.002	0.002	0.000	0.000	0.000	0.000
65	A	2410	TYR	0	-0.025	-0.028	30.620	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	2411	ARG	1	0.729	0.820	26.240	0.200	0.200	0.000	0.000	0.000	0.000
67	A	2412	ALA	0	-0.004	-0.016	30.923	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	2413	GLN	0	0.016	0.019	29.425	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	2414	ILE	0	0.007	0.005	32.426	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	2415	ARG	1	0.835	0.913	26.892	0.135	0.135	0.000	0.000	0.000	0.000
71	A	2416	LYS	1	0.906	0.945	34.318	0.084	0.084	0.000	0.000	0.000	0.000
72	A	2417	VAL	0	0.008	0.004	37.802	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	2418	LEU	0	-0.070	-0.036	39.927	0.003	0.003	0.000	0.000	0.000	0.000
74	A	2419	ASP	-1	-0.876	-0.937	43.450	-0.051	-0.051	0.000	0.000	0.000	0.000
75	A	2420	ASP	-1	-0.883	-0.944	46.425	-0.056	-0.056	0.000	0.000	0.000	0.000
76	A	2421	GLY	0	0.012	0.005	46.325	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	2422	LYS	1	0.856	0.934	42.683	0.058	0.058	0.000	0.000	0.000	0.000
78	A	2423	CYS	0	-0.019	0.008	38.744	0.003	0.003	0.000	0.000	0.000	0.000
79	A	2424	GLU	-1	-0.842	-0.887	33.420	-0.100	-0.100	0.000	0.000	0.000	0.000
80	A	2425	VAL	0	-0.006	-0.013	33.782	0.002	0.002	0.000	0.000	0.000	0.000
81	A	2426	HIS	0	0.019	0.014	25.390	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	2427	PHE	0	0.075	0.029	29.128	0.003	0.003	0.000	0.000	0.000	0.000
83	A	2428	ILE	0	0.001	-0.011	26.111	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	2429	ASP	-1	-0.735	-0.821	24.517	-0.231	-0.231	0.000	0.000	0.000	0.000
85	A	2430	PHE	0	0.048	0.014	24.332	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	2431	GLY	0	-0.030	0.000	23.700	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	2432	ASN	0	0.057	0.045	24.670	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	2433	ASN	0	-0.033	-0.029	27.851	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	2434	ALA	0	0.018	0.016	30.997	0.001	0.001	0.000	0.000	0.000	0.000
90	A	2435	VAL	0	-0.021	-0.010	34.573	0.002	0.002	0.000	0.000	0.000	0.000
91	A	2436	THR	0	-0.006	-0.023	37.701	0.002	0.002	0.000	0.000	0.000	0.000
92	A	2437	GLN	0	-0.035	-0.043	40.016	0.003	0.003	0.000	0.000	0.000	0.000
93	A	2438	GLN	0	-0.041	0.010	41.583	0.003	0.003	0.000	0.000	0.000	0.000
94	A	2439	PHE	0	0.037	0.005	38.875	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	2440	ARG	1	0.829	0.895	39.954	0.097	0.097	0.000	0.000	0.000	0.000
96	A	2441	GLN	0	-0.072	-0.053	39.524	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	2442	LEU	0	0.022	0.025	32.691	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	2443	PRO	0	0.041	0.021	36.883	0.002	0.002	0.000	0.000	0.000	0.000
99	A	2444	GLU	-1	-0.857	-0.941	35.875	-0.097	-0.097	0.000	0.000	0.000	0.000
100	A	2445	GLU	-1	-0.947	-0.978	33.940	-0.135	-0.135	0.000	0.000	0.000	0.000
101	A	2446	LEU	0	0.057	0.019	32.366	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	2447	ALA	0	0.019	0.009	31.411	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	2448	LYS	1	0.854	0.936	30.047	0.111	0.111	0.000	0.000	0.000	0.000
104	A	2449	PRO	0	-0.009	0.013	26.400	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	2450	ALA	0	0.029	0.025	22.340	0.008	0.008	0.000	0.000	0.000	0.000
106	A	2451	ARG	1	0.768	0.870	21.698	0.228	0.228	0.000	0.000	0.000	0.000
107	A	2452	TYR	0	0.054	0.007	21.521	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	2453	SER	0	-0.001	0.013	20.471	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	2454	ARG	1	0.803	0.870	14.087	0.534	0.534	0.000	0.000	0.000	0.000
110	A	2455	HIS	0	0.046	0.042	18.103	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	2456	CYS	0	-0.059	-0.031	14.098	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	2457	GLU	-1	-0.773	-0.858	14.864	-0.104	-0.104	0.000	0.000	0.000	0.000
113	A	2458	LEU	0	-0.013	-0.019	11.835	-0.031	-0.031	0.000	0.000	0.000	0.000
114	A	2459	ASP	-1	-0.797	-0.866	10.294	0.111	0.111	0.000	0.000	0.000	0.000
115	A	2460	ALA	0	0.005	-0.019	12.714	0.008	0.008	0.000	0.000	0.000	0.000
116	A	2461	SER	0	-0.114	-0.067	12.669	0.032	0.032	0.000	0.000	0.000	0.000
117	A	2462	THR	0	-0.061	-0.045	9.446	0.014	0.014	0.000	0.000	0.000	0.000
118	A	2463	ILE	0	0.008	0.013	12.351	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	2464	SER	0	-0.019	-0.042	15.496	0.024	0.024	0.000	0.000	0.000	0.000
120	A	2465	LYS	1	0.965	0.961	19.077	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	2514	CYS	0	-0.069	-0.009	20.598	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	2467	ASP	-1	-0.732	-0.820	17.302	-0.059	-0.059	0.000	0.000	0.000	0.000
123	A	2468	ALA	0	-0.008	-0.010	19.510	-0.023	-0.023	0.000	0.000	0.000	0.000
124	A	2469	ALA	0	-0.064	-0.030	20.337	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	2470	LEU	0	0.009	0.010	21.353	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	2471	LEU	0	0.025	-0.005	15.788	-0.015	-0.015	0.000	0.000	0.000	0.000
127	A	2472	GLN	0	-0.041	-0.006	20.186	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	2473	SER	0	0.013	0.015	22.997	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	2474	PHE	0	-0.024	-0.009	17.261	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	2475	ILE	0	0.013	-0.008	16.737	-0.023	-0.023	0.000	0.000	0.000	0.000
131	A	2476	ASP	-1	-0.834	-0.916	20.752	-0.175	-0.175	0.000	0.000	0.000	0.000
132	A	2477	THR	0	-0.112	-0.059	23.777	0.010	0.010	0.000	0.000	0.000	0.000
133	A	2478	ARG	1	0.839	0.919	19.347	0.238	0.238	0.000	0.000	0.000	0.000
134	A	2479	PHE	0	0.035	0.033	20.713	-0.034	-0.034	0.000	0.000	0.000	0.000
135	A	2480	SER	0	0.000	0.008	21.557	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	2481	GLU	-1	-0.902	-0.926	18.988	-0.324	-0.324	0.000	0.000	0.000	0.000
137	A	2482	THR	0	-0.010	-0.006	14.274	0.001	0.001	0.000	0.000	0.000	0.000
138	A	2483	PHE	0	-0.052	-0.023	12.822	0.010	0.010	0.000	0.000	0.000	0.000
139	A	2484	GLN	0	-0.011	-0.026	8.153	-0.041	-0.041	0.000	0.000	0.000	0.000
140	A	2485	VAL	0	0.022	0.003	8.160	0.129	0.129	0.000	0.000	0.000	0.000
141	A	2486	GLU	-1	-0.824	-0.893	2.704	-2.889	-1.099	1.053	-1.256	-1.587	-0.012
142	A	2487	ILE	0	-0.002	-0.022	5.479	0.459	0.459	0.000	0.000	0.000	0.000
143	A	2488	LEU	0	-0.044	-0.009	5.606	0.042	0.042	0.000	0.000	0.000	0.000
144	A	2489	ALA	0	-0.013	-0.015	7.907	0.131	0.131	0.000	0.000	0.000	0.000
145	A	2490	THR	0	0.007	0.013	11.321	-0.072	-0.072	0.000	0.000	0.000	0.000
146	A	2491	LYS	1	0.796	0.879	14.472	0.170	0.170	0.000	0.000	0.000	0.000
147	A	2492	GLY	0	0.020	0.007	17.648	-0.011	-0.011	0.000	0.000	0.000	0.000
148	A	2493	THR	0	-0.019	-0.020	20.743	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	2494	GLY	0	0.006	0.003	19.031	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	2495	THR	0	-0.047	0.005	16.768	-0.027	-0.027	0.000	0.000	0.000	0.000
151	A	2496	HIS	0	0.019	0.007	12.134	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	2497	VAL	0	0.005	0.008	11.590	0.014	0.014	0.000	0.000	0.000	0.000
153	A	2498	VAL	0	0.002	-0.012	9.042	-0.056	-0.056	0.000	0.000	0.000	0.000
154	A	2499	ARG	1	0.848	0.934	4.830	0.048	0.048	0.000	0.000	0.000	0.000
155	A	2500	LEU	0	0.033	0.017	7.654	-0.267	-0.267	0.000	0.000	0.000	0.000
156	A	2501	PHE	0	-0.020	-0.024	4.227	-0.202	-0.098	-0.001	-0.011	-0.092	0.000
157	A	2502	TYR	0	-0.008	-0.036	9.508	0.029	0.029	0.000	0.000	0.000	0.000
158	A	2503	GLN	0	0.033	0.022	12.320	0.077	0.077	0.000	0.000	0.000	0.000
159	A	2504	SER	0	0.021	0.000	7.565	0.171	0.171	0.000	0.000	0.000	0.000
160	A	2505	LYS	1	0.817	0.931	7.614	0.487	0.487	0.000	0.000	0.000	0.000
161	A	2506	ASN	0	0.037	0.019	7.539	-0.179	-0.179	0.000	0.000	0.000	0.000
162	A	2507	ILE	0	0.063	0.018	9.651	0.089	0.089	0.000	0.000	0.000	0.000
163	A	2508	SER	0	-0.027	-0.036	12.661	0.052	0.052	0.000	0.000	0.000	0.000
164	A	2509	GLU	-1	-0.960	-0.982	11.917	-0.076	-0.076	0.000	0.000	0.000	0.000
165	A	2510	LYS	1	0.831	0.913	13.680	0.295	0.295	0.000	0.000	0.000	0.000
166	A	2511	LEU	0	-0.031	0.012	16.411	0.001	0.001	0.000	0.000	0.000	0.000
167	A	2512	GLN	0	-0.002	-0.013	18.866	0.030	0.030	0.000	0.000	0.000	0.000
168	A	2513	GLU	-1	-0.938	-0.965	21.412	-0.084	-0.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2346:ALA)