FMO DATABASE

FMODB ID: 6Y8VZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1694210.552473
FMO2-HF: Nuclear repulsion	1625725.553518
FMO2-HF: Total energy	-68484.998956
FMO2-MP2: Total energy	-68680.893359

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.
-5.7	-1.707	2.358	-2.647	-3.7	-0.019

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 : -0.014 / q_NPA : -0.017

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	-0.013	3.137	-0.893	1.215	0.103	-0.866	-1.344	0.000
4	A	2349	HIS	0	-0.002	0.008	5.640	0.727	0.727	0.000	0.000	0.000	0.000
5	A	2350	ASN	0	0.011	0.003	9.246	-0.091	-0.091	0.000	0.000	0.000	0.000
6	A	2351	CYS	0	-0.036	-0.012	12.127	0.056	0.056	0.000	0.000	0.000	0.000
7	A	2352	VAL	0	0.075	0.053	14.560	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	2353	VAL	0	-0.011	-0.012	16.229	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	2354	VAL	0	-0.007	-0.006	18.449	0.029	0.029	0.000	0.000	0.000	0.000
10	A	2355	GLN	0	0.066	0.037	21.084	0.024	0.024	0.000	0.000	0.000	0.000
11	A	2356	PHE	0	-0.025	-0.029	17.193	-0.041	-0.041	0.000	0.000	0.000	0.000
12	A	2357	ASP	-1	-0.889	-0.926	21.873	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	2358	GLY	0	0.019	-0.014	21.526	0.024	0.024	0.000	0.000	0.000	0.000
14	A	2359	PRO	0	-0.016	-0.014	16.932	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	2360	MET	0	-0.066	-0.016	16.982	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	2361	SER	0	-0.023	-0.023	19.143	0.016	0.016	0.000	0.000	0.000	0.000
17	A	2362	PHE	0	0.017	0.022	13.427	0.001	0.001	0.000	0.000	0.000	0.000
18	A	2363	TYR	0	0.007	-0.011	18.617	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	2364	VAL	0	-0.008	-0.001	14.309	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	2365	GLN	0	0.014	0.001	17.529	0.014	0.014	0.000	0.000	0.000	0.000
21	A	2366	MET	0	-0.019	-0.012	11.196	-0.039	-0.039	0.000	0.000	0.000	0.000
22	A	2367	GLU	-1	-0.835	-0.935	14.807	-0.619	-0.619	0.000	0.000	0.000	0.000
23	A	2368	SER	0	-0.038	-0.029	15.090	0.033	0.033	0.000	0.000	0.000	0.000
24	A	2369	ASP	-1	-0.862	-0.926	17.030	-0.407	-0.407	0.000	0.000	0.000	0.000
25	A	2370	VAL	0	0.005	0.020	19.520	0.039	0.039	0.000	0.000	0.000	0.000
26	A	2371	PRO	0	0.026	0.016	21.083	0.034	0.034	0.000	0.000	0.000	0.000
27	A	2372	ALA	0	-0.017	-0.006	23.150	0.026	0.026	0.000	0.000	0.000	0.000
28	A	2373	LEU	0	0.002	0.004	23.463	0.023	0.023	0.000	0.000	0.000	0.000
29	A	2374	GLU	-1	-0.914	-0.963	25.454	-0.231	-0.231	0.000	0.000	0.000	0.000
30	A	2375	GLN	0	0.003	0.012	27.626	0.024	0.024	0.000	0.000	0.000	0.000
31	A	2376	MET	0	-0.071	-0.031	28.208	0.021	0.021	0.000	0.000	0.000	0.000
32	A	2377	THR	0	-0.006	-0.022	28.689	0.012	0.012	0.000	0.000	0.000	0.000
33	A	2378	ASP	-1	-0.899	-0.940	31.278	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	2379	LYS	1	0.870	0.925	32.161	0.148	0.148	0.000	0.000	0.000	0.000
35	A	2380	LEU	0	-0.040	-0.024	32.188	0.009	0.009	0.000	0.000	0.000	0.000
36	A	2381	LEU	0	0.013	0.015	35.544	0.007	0.007	0.000	0.000	0.000	0.000
37	A	2382	ASP	-1	-0.998	-0.993	37.415	-0.097	-0.097	0.000	0.000	0.000	0.000
38	A	2383	ALA	0	0.018	0.006	38.851	0.006	0.006	0.000	0.000	0.000	0.000
39	A	2384	GLU	-1	-0.893	-0.946	38.860	-0.114	-0.114	0.000	0.000	0.000	0.000
40	A	2385	GLN	0	-0.074	-0.040	40.693	0.002	0.002	0.000	0.000	0.000	0.000
41	A	2386	ASP	-1	-0.917	-0.957	43.801	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	2387	LEU	0	-0.100	-0.030	38.713	0.002	0.002	0.000	0.000	0.000	0.000
43	A	2388	PRO	0	-0.009	-0.003	43.329	0.001	0.001	0.000	0.000	0.000	0.000
44	A	2389	ALA	0	0.047	0.014	43.884	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	2390	PHE	0	-0.002	-0.008	39.762	0.002	0.002	0.000	0.000	0.000	0.000
46	A	2391	SER	0	-0.003	-0.021	43.414	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	2392	ASP	-1	-0.950	-0.959	41.784	-0.081	-0.081	0.000	0.000	0.000	0.000
48	A	2393	LEU	0	-0.030	-0.022	41.042	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	2394	LYS	1	0.959	0.980	38.574	0.093	0.093	0.000	0.000	0.000	0.000
50	A	2395	GLU	-1	-0.902	-0.961	35.952	-0.108	-0.108	0.000	0.000	0.000	0.000
51	A	2396	GLY	0	-0.053	-0.031	33.262	0.003	0.003	0.000	0.000	0.000	0.000
52	A	2397	ALA	0	-0.036	-0.014	33.818	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	2398	LEU	0	-0.001	-0.004	30.303	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	2399	CYS	0	-0.076	-0.030	34.382	0.008	0.008	0.000	0.000	0.000	0.000
55	A	2400	VAL	0	0.040	0.038	34.539	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	2401	ALA	0	0.008	-0.004	35.587	0.009	0.009	0.000	0.000	0.000	0.000
57	A	2402	GLN	0	-0.002	0.005	36.057	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	2403	PHE	0	0.037	0.022	32.128	0.005	0.005	0.000	0.000	0.000	0.000
59	A	2404	PRO	0	-0.034	-0.035	36.082	0.001	0.001	0.000	0.000	0.000	0.000
60	A	2405	GLU	-1	-0.982	-0.985	33.636	-0.157	-0.157	0.000	0.000	0.000	0.000
61	A	2406	ASP	-1	-0.831	-0.918	33.850	-0.164	-0.164	0.000	0.000	0.000	0.000
62	A	2407	GLU	-1	-1.027	-1.007	36.442	-0.101	-0.101	0.000	0.000	0.000	0.000
63	A	2408	VAL	0	0.024	0.036	34.162	0.006	0.006	0.000	0.000	0.000	0.000
64	A	2409	PHE	0	-0.063	-0.039	36.156	0.000	0.000	0.000	0.000	0.000	0.000
65	A	2410	TYR	0	-0.025	-0.012	30.860	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	2411	ARG	1	0.736	0.835	26.203	0.214	0.214	0.000	0.000	0.000	0.000
67	A	2412	ALA	0	-0.004	-0.016	30.858	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	2413	GLN	0	-0.032	-0.010	29.430	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	2414	ILE	0	-0.012	-0.002	32.369	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	2415	ARG	1	0.875	0.940	26.954	0.180	0.180	0.000	0.000	0.000	0.000
71	A	2416	LYS	1	0.977	0.997	34.276	0.111	0.111	0.000	0.000	0.000	0.000
72	A	2417	VAL	0	0.023	0.017	37.763	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	2418	LEU	0	-0.088	-0.044	40.064	0.002	0.002	0.000	0.000	0.000	0.000
74	A	2419	ASP	-1	-0.876	-0.941	43.411	-0.071	-0.071	0.000	0.000	0.000	0.000
75	A	2420	ASP	-1	-0.952	-0.986	46.369	-0.074	-0.074	0.000	0.000	0.000	0.000
76	A	2421	GLY	0	-0.006	-0.007	46.275	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	2422	LYS	1	0.937	0.981	42.587	0.084	0.084	0.000	0.000	0.000	0.000
78	A	2423	CYS	0	0.002	0.011	38.700	0.004	0.004	0.000	0.000	0.000	0.000
79	A	2424	GLU	-1	-0.906	-0.940	33.387	-0.142	-0.142	0.000	0.000	0.000	0.000
80	A	2425	VAL	0	0.002	-0.008	33.581	0.002	0.002	0.000	0.000	0.000	0.000
81	A	2426	HIS	0	-0.015	-0.011	25.321	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	2427	PHE	0	0.069	0.025	29.049	0.006	0.006	0.000	0.000	0.000	0.000
83	A	2428	ILE	0	0.012	-0.011	26.002	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	2429	ASP	-1	-0.736	-0.827	24.452	-0.258	-0.258	0.000	0.000	0.000	0.000
85	A	2430	PHE	0	0.033	0.004	24.245	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	2431	GLY	0	-0.022	0.002	23.628	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	2432	ASN	0	0.052	0.047	24.596	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	2433	ASN	0	-0.017	-0.006	27.782	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	2434	ALA	0	0.020	0.016	30.930	0.001	0.001	0.000	0.000	0.000	0.000
90	A	2435	VAL	0	-0.014	-0.002	34.506	0.002	0.002	0.000	0.000	0.000	0.000
91	A	2436	THR	0	-0.001	-0.011	37.635	0.003	0.003	0.000	0.000	0.000	0.000
92	A	2437	GLN	0	-0.037	-0.041	39.942	0.003	0.003	0.000	0.000	0.000	0.000
93	A	2438	GLN	0	-0.032	0.011	41.492	0.006	0.006	0.000	0.000	0.000	0.000
94	A	2439	PHE	0	0.038	0.006	38.493	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	2440	ARG	1	0.916	0.957	39.885	0.104	0.104	0.000	0.000	0.000	0.000
96	A	2441	GLN	0	-0.041	-0.033	39.454	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	2442	LEU	0	0.018	0.023	32.628	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	2443	PRO	0	0.037	0.020	36.827	0.003	0.003	0.000	0.000	0.000	0.000
99	A	2444	GLU	-1	-0.857	-0.942	35.795	-0.100	-0.100	0.000	0.000	0.000	0.000
100	A	2445	GLU	-1	-1.023	-1.018	34.085	-0.118	-0.118	0.000	0.000	0.000	0.000
101	A	2446	LEU	0	0.029	0.006	32.259	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	2447	ALA	0	0.019	0.007	31.331	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	2448	LYS	1	0.860	0.939	29.945	0.108	0.108	0.000	0.000	0.000	0.000
104	A	2449	PRO	0	-0.024	0.006	26.377	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	2450	ALA	0	0.043	0.030	22.247	0.005	0.005	0.000	0.000	0.000	0.000
106	A	2451	ARG	1	0.769	0.861	21.593	0.285	0.285	0.000	0.000	0.000	0.000
107	A	2452	TYR	0	0.066	0.013	21.422	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	2453	SER	0	-0.013	0.013	20.407	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	2454	ARG	1	0.828	0.898	13.796	0.586	0.586	0.000	0.000	0.000	0.000
110	A	2455	HIS	0	0.041	0.028	18.030	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	2456	CYS	0	-0.058	-0.033	14.069	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	2457	GLU	-1	-0.770	-0.861	14.845	-0.244	-0.244	0.000	0.000	0.000	0.000
113	A	2458	LEU	0	-0.012	-0.023	11.864	-0.057	-0.057	0.000	0.000	0.000	0.000
114	A	2459	ASP	-1	-0.831	-0.885	10.663	-0.295	-0.295	0.000	0.000	0.000	0.000
115	A	2460	ALA	0	0.003	-0.017	12.720	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	2461	SER	0	-0.110	-0.058	12.693	0.030	0.030	0.000	0.000	0.000	0.000
117	A	2462	THR	0	-0.065	-0.049	9.205	0.000	0.000	0.000	0.000	0.000	0.000
118	A	2463	ILE	0	0.008	0.016	12.389	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	2464	SER	0	-0.027	-0.008	15.527	0.046	0.046	0.000	0.000	0.000	0.000
120	A	2465	LYS	1	0.961	0.957	19.115	0.094	0.094	0.000	0.000	0.000	0.000
121	A	2514	CYS	0	-0.079	-0.016	20.603	0.011	0.011	0.000	0.000	0.000	0.000
122	A	2467	ASP	-1	-0.718	-0.869	17.240	-0.271	-0.271	0.000	0.000	0.000	0.000
123	A	2468	ALA	0	-0.029	-0.021	19.513	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	2469	ALA	0	-0.058	-0.028	20.345	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	2470	LEU	0	0.025	0.013	21.560	0.004	0.004	0.000	0.000	0.000	0.000
126	A	2471	LEU	0	0.019	-0.006	15.773	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	2472	GLN	0	0.012	0.025	20.177	-0.027	-0.027	0.000	0.000	0.000	0.000
128	A	2473	SER	0	0.008	0.009	22.977	0.001	0.001	0.000	0.000	0.000	0.000
129	A	2474	PHE	0	-0.027	-0.017	17.035	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	2475	ILE	0	0.007	-0.003	16.951	-0.020	-0.020	0.000	0.000	0.000	0.000
131	A	2476	ASP	-1	-0.860	-0.929	20.718	-0.248	-0.248	0.000	0.000	0.000	0.000
132	A	2477	THR	0	-0.110	-0.052	23.811	0.019	0.019	0.000	0.000	0.000	0.000
133	A	2478	ARG	1	0.845	0.904	19.471	0.331	0.331	0.000	0.000	0.000	0.000
134	A	2479	PHE	0	0.039	0.031	20.662	-0.036	-0.036	0.000	0.000	0.000	0.000
135	A	2480	SER	0	-0.024	-0.003	21.494	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	2481	GLU	-1	-0.862	-0.867	19.073	-0.378	-0.378	0.000	0.000	0.000	0.000
137	A	2482	THR	0	-0.031	-0.014	14.094	-0.025	-0.025	0.000	0.000	0.000	0.000
138	A	2483	PHE	0	-0.055	-0.025	12.683	0.000	0.000	0.000	0.000	0.000	0.000
139	A	2484	GLN	0	0.023	-0.003	8.043	-0.050	-0.050	0.000	0.000	0.000	0.000
140	A	2485	VAL	0	0.014	0.001	8.140	0.080	0.080	0.000	0.000	0.000	0.000
141	A	2486	GLU	-1	-0.832	-0.919	2.661	-5.109	-3.391	2.257	-1.773	-2.201	-0.019
142	A	2487	ILE	0	-0.014	-0.024	5.408	0.503	0.503	0.000	0.000	0.000	0.000
143	A	2488	LEU	0	-0.032	-0.007	5.581	0.044	0.044	0.000	0.000	0.000	0.000
144	A	2489	ALA	0	-0.004	-0.014	7.899	0.182	0.182	0.000	0.000	0.000	0.000
145	A	2490	THR	0	0.007	0.017	11.300	-0.088	-0.088	0.000	0.000	0.000	0.000
146	A	2491	LYS	1	0.794	0.886	14.437	0.332	0.332	0.000	0.000	0.000	0.000
147	A	2492	GLY	0	0.019	0.008	17.625	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	2493	THR	0	-0.017	-0.020	20.720	0.002	0.002	0.000	0.000	0.000	0.000
149	A	2494	GLY	0	0.011	0.006	18.984	0.003	0.003	0.000	0.000	0.000	0.000
150	A	2495	THR	0	-0.041	0.009	16.617	-0.027	-0.027	0.000	0.000	0.000	0.000
151	A	2496	HIS	0	0.010	0.008	12.065	0.005	0.005	0.000	0.000	0.000	0.000
152	A	2497	VAL	0	0.007	0.007	11.418	0.015	0.015	0.000	0.000	0.000	0.000
153	A	2498	VAL	0	-0.007	-0.013	9.031	-0.082	-0.082	0.000	0.000	0.000	0.000
154	A	2499	ARG	1	0.874	0.960	4.410	0.989	1.074	-0.001	-0.004	-0.079	0.000
155	A	2500	LEU	0	0.047	0.021	7.617	-0.283	-0.283	0.000	0.000	0.000	0.000
156	A	2501	PHE	0	-0.024	-0.021	4.478	-0.180	-0.098	-0.001	-0.004	-0.076	0.000
157	A	2502	TYR	0	-0.019	-0.071	9.485	0.087	0.087	0.000	0.000	0.000	0.000
158	A	2503	GLN	0	-0.022	-0.015	12.635	0.070	0.070	0.000	0.000	0.000	0.000
159	A	2504	SER	0	-0.017	-0.020	7.690	0.032	0.032	0.000	0.000	0.000	0.000
160	A	2505	LYS	1	0.882	0.957	7.897	0.483	0.483	0.000	0.000	0.000	0.000
161	A	2506	ASN	0	0.054	0.024	7.307	-0.235	-0.235	0.000	0.000	0.000	0.000
162	A	2507	ILE	0	0.063	0.022	9.674	0.154	0.154	0.000	0.000	0.000	0.000
163	A	2508	SER	0	-0.019	-0.012	12.667	0.087	0.087	0.000	0.000	0.000	0.000
164	A	2509	GLU	-1	-0.977	-0.982	12.507	-0.239	-0.239	0.000	0.000	0.000	0.000
165	A	2510	LYS	1	0.855	0.928	13.857	0.454	0.454	0.000	0.000	0.000	0.000
166	A	2511	LEU	0	-0.037	0.007	16.543	0.025	0.025	0.000	0.000	0.000	0.000
167	A	2512	GLN	0	-0.002	-0.017	18.882	0.033	0.033	0.000	0.000	0.000	0.000
168	A	2513	GLU	-1	-0.941	-0.960	21.503	-0.176	-0.176	0.000	0.000	0.000	0.000

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