FMO DATABASE

FMODB ID: R8VG8

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	OptAll
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	-1696894.55051
FMO2-HF: Nuclear repulsion	1628408.560278
FMO2-HF: Total energy	-68485.990232
FMO2-MP2: Total energy	-68681.859732

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.
-2.589	1.168	1.816	-2.195	-3.377	-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 : 0.023 / q_NPA : 0.011

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	-0.044	-0.020	2.861	-0.533	1.742	0.260	-1.063	-1.472	0.001
4	A	2349	HIS	0	-0.051	-0.034	5.508	0.520	0.520	0.000	0.000	0.000	0.000
5	A	2350	ASN	0	-0.008	-0.025	9.178	0.033	0.033	0.000	0.000	0.000	0.000
6	A	2351	CYS	0	-0.081	-0.033	11.962	0.071	0.071	0.000	0.000	0.000	0.000
7	A	2352	VAL	0	0.078	0.046	14.556	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	2353	VAL	0	-0.025	-0.016	15.902	0.003	0.003	0.000	0.000	0.000	0.000
9	A	2354	VAL	0	-0.001	0.002	18.305	0.019	0.019	0.000	0.000	0.000	0.000
10	A	2355	GLN	0	-0.009	-0.012	21.238	0.021	0.021	0.000	0.000	0.000	0.000
11	A	2356	PHE	0	-0.023	-0.033	16.884	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	2357	ASP	-1	-0.817	-0.876	21.716	-0.132	-0.132	0.000	0.000	0.000	0.000
13	A	2358	GLY	0	0.033	0.005	21.342	0.021	0.021	0.000	0.000	0.000	0.000
14	A	2359	PRO	0	-0.028	-0.023	16.840	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	2360	MET	0	-0.068	-0.020	16.860	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	2361	SER	0	-0.028	-0.034	19.241	0.006	0.006	0.000	0.000	0.000	0.000
17	A	2362	PHE	0	0.027	0.023	13.338	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	2363	TYR	0	0.010	-0.001	18.771	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	2364	VAL	0	0.004	0.004	14.380	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	2365	GLN	0	0.024	0.009	17.703	0.009	0.009	0.000	0.000	0.000	0.000
21	A	2366	MET	0	-0.015	-0.005	11.595	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	2367	GLU	-1	-0.832	-0.923	14.969	-0.654	-0.654	0.000	0.000	0.000	0.000
23	A	2368	SER	0	-0.055	-0.053	15.262	0.012	0.012	0.000	0.000	0.000	0.000
24	A	2369	ASP	-1	-0.832	-0.882	17.103	-0.426	-0.426	0.000	0.000	0.000	0.000
25	A	2370	VAL	0	0.011	0.020	19.664	0.040	0.040	0.000	0.000	0.000	0.000
26	A	2371	PRO	0	0.051	0.025	21.309	0.030	0.030	0.000	0.000	0.000	0.000
27	A	2372	ALA	0	-0.074	-0.031	23.310	0.027	0.027	0.000	0.000	0.000	0.000
28	A	2373	LEU	0	0.013	0.012	23.517	0.021	0.021	0.000	0.000	0.000	0.000
29	A	2374	GLU	-1	-0.900	-0.946	25.595	-0.239	-0.239	0.000	0.000	0.000	0.000
30	A	2375	GLN	0	0.016	0.005	27.959	0.024	0.024	0.000	0.000	0.000	0.000
31	A	2376	MET	0	-0.039	-0.006	28.298	0.020	0.020	0.000	0.000	0.000	0.000
32	A	2377	THR	0	-0.013	-0.021	28.959	0.013	0.013	0.000	0.000	0.000	0.000
33	A	2378	ASP	-1	-0.903	-0.948	31.478	-0.149	-0.149	0.000	0.000	0.000	0.000
34	A	2379	LYS	1	0.765	0.858	32.150	0.145	0.145	0.000	0.000	0.000	0.000
35	A	2380	LEU	0	-0.051	-0.028	31.774	0.009	0.009	0.000	0.000	0.000	0.000
36	A	2381	LEU	0	0.001	0.005	35.506	0.008	0.008	0.000	0.000	0.000	0.000
37	A	2382	ASP	-1	-0.992	-0.993	37.501	-0.097	-0.097	0.000	0.000	0.000	0.000
38	A	2383	ALA	0	0.024	0.008	38.980	0.006	0.006	0.000	0.000	0.000	0.000
39	A	2384	GLU	-1	-0.827	-0.893	38.619	-0.094	-0.094	0.000	0.000	0.000	0.000
40	A	2385	GLN	0	-0.071	-0.039	40.684	0.004	0.004	0.000	0.000	0.000	0.000
41	A	2386	ASP	-1	-0.915	-0.950	44.040	-0.071	-0.071	0.000	0.000	0.000	0.000
42	A	2387	LEU	0	-0.058	-0.011	38.450	0.002	0.002	0.000	0.000	0.000	0.000
43	A	2388	PRO	0	-0.001	0.004	42.990	0.002	0.002	0.000	0.000	0.000	0.000
44	A	2389	ALA	0	0.046	0.014	43.768	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	2390	PHE	0	-0.017	-0.008	39.587	0.001	0.001	0.000	0.000	0.000	0.000
46	A	2391	SER	0	0.035	0.000	43.371	0.000	0.000	0.000	0.000	0.000	0.000
47	A	2392	ASP	-1	-0.872	-0.892	41.786	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	2393	LEU	0	-0.004	-0.016	41.326	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	2394	LYS	1	0.807	0.883	39.475	0.067	0.067	0.000	0.000	0.000	0.000
50	A	2395	GLU	-1	-0.832	-0.936	36.074	-0.066	-0.066	0.000	0.000	0.000	0.000
51	A	2396	GLY	0	-0.054	-0.022	33.067	0.002	0.002	0.000	0.000	0.000	0.000
52	A	2397	ALA	0	-0.016	-0.003	33.402	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	2398	LEU	0	-0.020	-0.013	30.820	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	2399	CYS	0	-0.076	-0.026	34.393	0.005	0.005	0.000	0.000	0.000	0.000
55	A	2400	VAL	0	0.062	0.030	34.443	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	2401	ALA	0	-0.002	-0.014	35.453	0.007	0.007	0.000	0.000	0.000	0.000
57	A	2402	GLN	0	-0.017	0.002	35.856	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	2403	PHE	0	0.051	0.023	32.027	0.005	0.005	0.000	0.000	0.000	0.000
59	A	2404	PRO	0	-0.034	-0.042	36.029	0.000	0.000	0.000	0.000	0.000	0.000
60	A	2405	GLU	-1	-0.991	-0.982	33.254	-0.110	-0.110	0.000	0.000	0.000	0.000
61	A	2406	ASP	-1	-0.850	-0.915	33.975	-0.132	-0.132	0.000	0.000	0.000	0.000
62	A	2407	GLU	-1	-0.992	-0.984	36.520	-0.082	-0.082	0.000	0.000	0.000	0.000
63	A	2408	VAL	0	0.044	0.038	34.368	0.004	0.004	0.000	0.000	0.000	0.000
64	A	2409	PHE	0	-0.038	-0.028	36.389	0.003	0.003	0.000	0.000	0.000	0.000
65	A	2410	TYR	0	-0.031	-0.032	30.895	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	2411	ARG	1	0.708	0.795	26.131	0.188	0.188	0.000	0.000	0.000	0.000
67	A	2412	ALA	0	0.003	-0.003	30.519	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	2413	GLN	0	-0.011	0.003	29.418	0.000	0.000	0.000	0.000	0.000	0.000
69	A	2414	ILE	0	0.017	0.012	32.364	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	2415	ARG	1	0.807	0.890	26.813	0.120	0.120	0.000	0.000	0.000	0.000
71	A	2416	LYS	1	0.877	0.926	34.178	0.074	0.074	0.000	0.000	0.000	0.000
72	A	2417	VAL	0	0.021	0.014	37.701	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	2418	LEU	0	-0.069	-0.035	39.713	0.002	0.002	0.000	0.000	0.000	0.000
74	A	2419	ASP	-1	-0.872	-0.934	43.461	-0.046	-0.046	0.000	0.000	0.000	0.000
75	A	2420	ASP	-1	-0.891	-0.939	46.281	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	2421	GLY	0	0.005	0.008	46.303	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	2422	LYS	1	0.849	0.915	42.485	0.051	0.051	0.000	0.000	0.000	0.000
78	A	2423	CYS	0	-0.032	-0.002	38.495	0.002	0.002	0.000	0.000	0.000	0.000
79	A	2424	GLU	-1	-0.832	-0.875	33.057	-0.088	-0.088	0.000	0.000	0.000	0.000
80	A	2425	VAL	0	0.008	-0.006	34.035	0.002	0.002	0.000	0.000	0.000	0.000
81	A	2426	HIS	0	0.017	0.007	25.217	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	2427	PHE	0	0.077	0.039	29.041	0.001	0.001	0.000	0.000	0.000	0.000
83	A	2428	ILE	0	-0.005	-0.003	26.145	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	2429	ASP	-1	-0.727	-0.822	24.504	-0.215	-0.215	0.000	0.000	0.000	0.000
85	A	2430	PHE	0	0.049	0.017	24.472	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	2431	GLY	0	-0.010	0.001	23.668	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	2432	ASN	0	0.043	0.030	24.556	0.002	0.002	0.000	0.000	0.000	0.000
88	A	2433	ASN	0	-0.053	-0.044	27.719	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	2434	ALA	0	0.032	0.022	30.844	0.001	0.001	0.000	0.000	0.000	0.000
90	A	2435	VAL	0	-0.030	-0.012	34.507	0.002	0.002	0.000	0.000	0.000	0.000
91	A	2436	THR	0	-0.001	-0.006	37.670	0.001	0.001	0.000	0.000	0.000	0.000
92	A	2437	GLN	0	-0.031	-0.035	39.934	0.003	0.003	0.000	0.000	0.000	0.000
93	A	2438	GLN	0	-0.037	0.000	41.352	0.003	0.003	0.000	0.000	0.000	0.000
94	A	2439	PHE	0	0.033	0.012	38.808	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	2440	ARG	1	0.816	0.889	39.893	0.092	0.092	0.000	0.000	0.000	0.000
96	A	2441	GLN	0	-0.056	-0.046	39.341	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	2442	LEU	0	0.029	0.029	32.426	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	2443	PRO	0	0.034	0.017	36.647	0.002	0.002	0.000	0.000	0.000	0.000
99	A	2444	GLU	-1	-0.872	-0.948	35.744	-0.092	-0.092	0.000	0.000	0.000	0.000
100	A	2445	GLU	-1	-0.901	-0.930	33.713	-0.128	-0.128	0.000	0.000	0.000	0.000
101	A	2446	LEU	0	0.083	0.027	32.142	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	2447	ALA	0	0.000	0.004	31.164	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	2448	LYS	1	0.818	0.912	30.116	0.108	0.108	0.000	0.000	0.000	0.000
104	A	2449	PRO	0	-0.008	0.007	26.413	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	2450	ALA	0	0.024	0.020	22.125	0.008	0.008	0.000	0.000	0.000	0.000
106	A	2451	ARG	1	0.769	0.881	21.811	0.206	0.206	0.000	0.000	0.000	0.000
107	A	2452	TYR	0	0.056	0.012	21.626	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	2453	SER	0	-0.016	0.007	20.491	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	2454	ARG	1	0.823	0.873	13.786	0.529	0.529	0.000	0.000	0.000	0.000
110	A	2455	HIS	0	0.040	0.031	17.868	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	2456	CYS	0	-0.071	-0.033	14.067	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	2457	GLU	-1	-0.771	-0.857	14.627	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	2458	LEU	0	-0.002	-0.011	11.720	-0.041	-0.041	0.000	0.000	0.000	0.000
114	A	2459	ASP	-1	-0.779	-0.862	9.752	0.214	0.214	0.000	0.000	0.000	0.000
115	A	2460	ALA	0	-0.001	0.000	12.132	0.010	0.010	0.000	0.000	0.000	0.000
116	A	2461	SER	0	-0.105	-0.067	12.042	0.032	0.032	0.000	0.000	0.000	0.000
117	A	2462	THR	0	-0.059	-0.051	9.331	0.015	0.015	0.000	0.000	0.000	0.000
118	A	2463	ILE	0	0.011	0.009	12.122	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	2464	SER	0	-0.014	-0.029	15.476	0.019	0.019	0.000	0.000	0.000	0.000
120	A	2465	LYS	1	0.960	0.952	19.106	-0.028	-0.028	0.000	0.000	0.000	0.000
121	A	2514	CYS	0	-0.104	-0.017	20.276	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	2467	ASP	-1	-0.740	-0.833	17.156	-0.021	-0.021	0.000	0.000	0.000	0.000
123	A	2468	ALA	0	0.001	-0.010	19.143	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	2469	ALA	0	-0.048	-0.015	19.998	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	2470	LEU	0	0.007	0.004	20.749	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	2471	LEU	0	0.014	-0.002	15.340	-0.015	-0.015	0.000	0.000	0.000	0.000
127	A	2472	GLN	0	-0.062	-0.024	19.678	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	2473	SER	0	0.019	0.016	22.524	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	2474	PHE	0	-0.034	-0.014	16.772	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	2475	ILE	0	0.031	0.008	16.462	-0.024	-0.024	0.000	0.000	0.000	0.000
131	A	2476	ASP	-1	-0.804	-0.906	20.482	-0.144	-0.144	0.000	0.000	0.000	0.000
132	A	2477	THR	0	-0.125	-0.075	23.147	0.006	0.006	0.000	0.000	0.000	0.000
133	A	2478	ARG	1	0.829	0.916	18.892	0.209	0.209	0.000	0.000	0.000	0.000
134	A	2479	PHE	0	0.006	0.013	20.500	-0.031	-0.031	0.000	0.000	0.000	0.000
135	A	2480	SER	0	-0.004	0.011	22.199	0.002	0.002	0.000	0.000	0.000	0.000
136	A	2481	GLU	-1	-0.879	-0.912	18.571	-0.281	-0.281	0.000	0.000	0.000	0.000
137	A	2482	THR	0	-0.012	-0.010	14.050	0.009	0.009	0.000	0.000	0.000	0.000
138	A	2483	PHE	0	-0.028	-0.007	12.695	-0.013	-0.013	0.000	0.000	0.000	0.000
139	A	2484	GLN	0	-0.017	-0.019	7.856	-0.020	-0.020	0.000	0.000	0.000	0.000
140	A	2485	VAL	0	0.019	-0.003	7.807	0.125	0.125	0.000	0.000	0.000	0.000
141	A	2486	GLU	-1	-0.844	-0.895	2.353	-1.851	-0.647	1.557	-1.096	-1.664	-0.011
142	A	2487	ILE	0	0.014	-0.011	5.035	0.435	0.490	-0.001	-0.001	-0.052	0.000
143	A	2488	LEU	0	-0.052	-0.008	5.421	0.040	0.040	0.000	0.000	0.000	0.000
144	A	2489	ALA	0	-0.005	-0.010	7.806	0.117	0.117	0.000	0.000	0.000	0.000
145	A	2490	THR	0	-0.006	0.006	11.429	-0.080	-0.080	0.000	0.000	0.000	0.000
146	A	2491	LYS	1	0.802	0.890	14.596	0.136	0.136	0.000	0.000	0.000	0.000
147	A	2492	GLY	0	0.017	0.000	17.855	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	2493	THR	0	-0.017	-0.016	20.846	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	2494	GLY	0	0.010	0.008	19.077	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	2495	THR	0	-0.042	0.010	16.624	-0.024	-0.024	0.000	0.000	0.000	0.000
151	A	2496	HIS	0	0.021	0.006	12.003	-0.020	-0.020	0.000	0.000	0.000	0.000
152	A	2497	VAL	0	0.003	0.002	11.488	0.027	0.027	0.000	0.000	0.000	0.000
153	A	2498	VAL	0	0.007	-0.004	8.572	-0.045	-0.045	0.000	0.000	0.000	0.000
154	A	2499	ARG	1	0.804	0.904	4.761	-0.189	-0.121	-0.001	-0.003	-0.065	0.000
155	A	2500	LEU	0	0.041	0.021	7.702	-0.230	-0.230	0.000	0.000	0.000	0.000
156	A	2501	PHE	0	-0.039	-0.033	3.890	-0.211	-0.056	0.001	-0.032	-0.124	0.000
157	A	2502	TYR	0	-0.003	-0.031	9.194	0.002	0.002	0.000	0.000	0.000	0.000
158	A	2503	GLN	0	0.016	0.007	12.065	0.059	0.059	0.000	0.000	0.000	0.000
159	A	2504	SER	0	0.011	0.001	7.647	0.050	0.050	0.000	0.000	0.000	0.000
160	A	2505	LYS	1	0.800	0.914	8.213	0.533	0.533	0.000	0.000	0.000	0.000
161	A	2506	ASN	0	0.046	0.020	7.224	-0.099	-0.099	0.000	0.000	0.000	0.000
162	A	2507	ILE	0	0.059	0.022	9.220	0.064	0.064	0.000	0.000	0.000	0.000
163	A	2508	SER	0	-0.005	-0.019	12.255	0.035	0.035	0.000	0.000	0.000	0.000
164	A	2509	GLU	-1	-0.895	-0.953	12.201	-0.107	-0.107	0.000	0.000	0.000	0.000
165	A	2510	LYS	1	0.806	0.900	13.447	0.226	0.226	0.000	0.000	0.000	0.000
166	A	2511	LEU	0	-0.034	0.011	16.381	-0.003	-0.003	0.000	0.000	0.000	0.000
167	A	2512	GLN	0	0.002	-0.004	18.604	0.025	0.025	0.000	0.000	0.000	0.000
168	A	2513	GLU	-1	-0.925	-0.963	20.857	-0.065	-0.065	0.000	0.000	0.000	0.000

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