FMO DATABASE

FMODB ID: 1NKJZ

Calculation Name: 3F2Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F2Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q5L9G5

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1432089.836394
FMO2-HF: Nuclear repulsion	1374983.612789
FMO2-HF: Total energy	-57106.223605
FMO2-MP2: Total energy	-57276.728028

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:292:ASP)

Summations of interaction energy for fragment #1(A:292:ASP)

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.
-82.828	-85.252	22.245	-10.126	-9.695	0.108

Interaction energy analysis for fragmet #1(A:292:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.865 / q_NPA : -0.934

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	294	LEU	0	-0.029	-0.016	3.866	-5.739	-4.534	0.000	-0.459	-0.746	0.002
4	A	295	SER	0	-0.015	-0.011	5.861	-1.359	-1.359	0.000	0.000	0.000	0.000
5	A	296	LYS	1	0.850	0.902	8.626	-28.570	-28.570	0.000	0.000	0.000	0.000
6	A	297	THR	0	-0.005	-0.004	11.831	-0.941	-0.941	0.000	0.000	0.000	0.000
7	A	298	ASP	-1	-0.813	-0.880	13.575	18.060	18.060	0.000	0.000	0.000	0.000
8	A	299	TRP	0	-0.007	0.013	9.869	-1.023	-1.023	0.000	0.000	0.000	0.000
9	A	300	LYS	1	0.814	0.896	15.826	-16.778	-16.778	0.000	0.000	0.000	0.000
10	A	301	ILE	0	0.012	0.014	19.273	0.328	0.328	0.000	0.000	0.000	0.000
11	A	302	VAL	0	-0.036	-0.013	21.424	-0.464	-0.464	0.000	0.000	0.000	0.000
12	A	303	SER	0	0.037	0.009	24.116	-0.579	-0.579	0.000	0.000	0.000	0.000
13	A	304	PHE	0	-0.002	-0.009	24.539	0.766	0.766	0.000	0.000	0.000	0.000
14	A	305	THR	0	-0.021	0.007	26.476	-0.256	-0.256	0.000	0.000	0.000	0.000
15	A	306	THR	0	-0.052	-0.041	27.803	-0.334	-0.334	0.000	0.000	0.000	0.000
16	A	307	GLU	-1	-0.835	-0.902	26.430	12.529	12.529	0.000	0.000	0.000	0.000
17	A	308	GLU	-1	-0.751	-0.847	27.774	9.451	9.451	0.000	0.000	0.000	0.000
18	A	309	ALA	0	0.042	0.014	29.260	0.140	0.140	0.000	0.000	0.000	0.000
19	A	310	SER	0	-0.094	-0.055	30.790	-0.302	-0.302	0.000	0.000	0.000	0.000
20	A	311	GLY	0	-0.020	-0.013	33.141	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	312	GLU	-1	-0.820	-0.917	27.862	11.345	11.345	0.000	0.000	0.000	0.000
22	A	313	GLY	0	0.018	0.017	29.460	0.157	0.157	0.000	0.000	0.000	0.000
23	A	314	SER	0	0.004	-0.019	29.426	0.248	0.248	0.000	0.000	0.000	0.000
24	A	315	ASN	0	-0.056	-0.038	26.246	0.258	0.258	0.000	0.000	0.000	0.000
25	A	316	ASN	0	0.086	0.029	23.896	0.998	0.998	0.000	0.000	0.000	0.000
26	A	317	GLY	0	0.048	0.044	24.752	-0.411	-0.411	0.000	0.000	0.000	0.000
27	A	318	HIS	0	0.002	-0.001	24.975	-0.237	-0.237	0.000	0.000	0.000	0.000
28	A	319	ALA	0	0.027	-0.009	22.439	0.645	0.645	0.000	0.000	0.000	0.000
29	A	320	LYS	1	0.796	0.902	20.641	-11.133	-11.133	0.000	0.000	0.000	0.000
30	A	321	HIS	0	-0.005	-0.003	19.596	0.435	0.435	0.000	0.000	0.000	0.000
31	A	322	LEU	0	0.033	0.030	16.788	0.287	0.287	0.000	0.000	0.000	0.000
32	A	323	ILE	0	-0.059	-0.053	14.704	1.498	1.498	0.000	0.000	0.000	0.000
33	A	324	ASP	-1	-0.817	-0.916	14.748	17.349	17.349	0.000	0.000	0.000	0.000
34	A	325	GLY	0	-0.006	0.006	13.415	0.353	0.353	0.000	0.000	0.000	0.000
35	A	326	ASN	0	-0.061	-0.023	14.117	0.624	0.624	0.000	0.000	0.000	0.000
36	A	327	ILE	0	0.043	0.020	12.265	-0.360	-0.360	0.000	0.000	0.000	0.000
37	A	328	GLU	-1	-0.814	-0.868	16.360	14.825	14.825	0.000	0.000	0.000	0.000
38	A	329	THR	0	-0.072	-0.011	19.395	-0.711	-0.711	0.000	0.000	0.000	0.000
39	A	330	PHE	0	0.027	-0.001	19.569	0.536	0.536	0.000	0.000	0.000	0.000
40	A	331	TRP	0	-0.057	-0.001	20.638	-0.475	-0.475	0.000	0.000	0.000	0.000
41	A	332	HIS	0	-0.033	-0.056	22.628	0.178	0.178	0.000	0.000	0.000	0.000
42	A	333	SER	0	-0.009	-0.014	25.656	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	334	ARG	1	0.822	0.919	28.207	-9.284	-9.284	0.000	0.000	0.000	0.000
44	A	335	TRP	0	-0.016	-0.016	30.553	-0.387	-0.387	0.000	0.000	0.000	0.000
45	A	336	GLN	0	0.007	0.001	34.150	-0.348	-0.348	0.000	0.000	0.000	0.000
46	A	337	GLY	0	-0.007	-0.007	36.361	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	338	GLY	0	-0.025	-0.009	38.129	-0.156	-0.156	0.000	0.000	0.000	0.000
48	A	339	SER	0	0.007	0.003	33.766	0.166	0.166	0.000	0.000	0.000	0.000
49	A	340	ASP	-1	-0.783	-0.855	32.517	9.622	9.622	0.000	0.000	0.000	0.000
50	A	341	PRO	0	-0.009	0.004	33.386	0.206	0.206	0.000	0.000	0.000	0.000
51	A	342	LEU	0	-0.018	0.015	28.747	0.298	0.298	0.000	0.000	0.000	0.000
52	A	343	PRO	0	-0.021	-0.013	28.131	-0.297	-0.297	0.000	0.000	0.000	0.000
53	A	344	TYR	0	-0.012	-0.040	26.143	0.005	0.005	0.000	0.000	0.000	0.000
54	A	345	GLU	-1	-0.829	-0.915	23.819	13.321	13.321	0.000	0.000	0.000	0.000
55	A	346	ILE	0	0.024	0.008	20.905	-0.401	-0.401	0.000	0.000	0.000	0.000
56	A	347	ILE	0	-0.016	0.011	20.714	0.951	0.951	0.000	0.000	0.000	0.000
57	A	348	ILE	0	0.001	-0.007	15.867	-0.281	-0.281	0.000	0.000	0.000	0.000
58	A	349	ASP	-1	-0.718	-0.817	18.374	15.853	15.853	0.000	0.000	0.000	0.000
59	A	350	MET	0	-0.009	-0.009	12.646	1.035	1.035	0.000	0.000	0.000	0.000
60	A	351	ASN	0	-0.080	-0.045	14.737	-0.071	-0.071	0.000	0.000	0.000	0.000
61	A	352	HIS	1	0.814	0.884	11.753	-20.381	-20.381	0.000	0.000	0.000	0.000
62	A	353	ARG	1	0.897	0.937	14.695	-16.545	-16.545	0.000	0.000	0.000	0.000
63	A	354	VAL	0	0.010	-0.007	8.977	0.931	0.931	0.000	0.000	0.000	0.000
64	A	355	LYS	1	0.961	0.997	10.210	-25.852	-25.852	0.000	0.000	0.000	0.000
65	A	356	ILE	0	-0.023	-0.011	8.479	4.004	4.004	0.000	0.000	0.000	0.000
66	A	357	ALA	0	-0.020	-0.022	5.328	-2.234	-2.234	0.000	0.000	0.000	0.000
67	A	358	GLN	0	-0.022	-0.018	5.242	4.196	4.196	0.000	0.000	0.000	0.000
68	A	359	ILE	0	0.029	0.028	7.692	1.336	1.336	0.000	0.000	0.000	0.000
69	A	360	GLU	-1	-0.808	-0.873	6.450	51.284	51.284	0.000	0.000	0.000	0.000
70	A	361	LEU	0	0.014	0.009	10.417	-1.485	-1.485	0.000	0.000	0.000	0.000
71	A	362	LEU	0	0.001	0.019	12.885	0.621	0.621	0.000	0.000	0.000	0.000
72	A	363	PRO	0	-0.008	0.006	14.824	-1.075	-1.075	0.000	0.000	0.000	0.000
73	A	364	ARG	1	0.873	0.941	18.599	-12.033	-12.033	0.000	0.000	0.000	0.000
74	A	365	GLY	0	0.019	0.027	20.868	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	366	ARG	1	0.799	0.854	18.959	-16.011	-16.011	0.000	0.000	0.000	0.000
76	A	367	GLY	0	-0.007	0.007	24.310	-0.508	-0.508	0.000	0.000	0.000	0.000
77	A	368	SER	0	-0.042	-0.020	24.780	-0.415	-0.415	0.000	0.000	0.000	0.000
78	A	369	ASN	0	-0.004	-0.018	27.049	0.375	0.375	0.000	0.000	0.000	0.000
79	A	370	ASN	0	0.011	-0.014	22.179	-0.247	-0.247	0.000	0.000	0.000	0.000
80	A	371	PRO	0	-0.025	0.008	25.196	0.507	0.507	0.000	0.000	0.000	0.000
81	A	372	ILE	0	-0.009	0.005	21.999	-0.296	-0.296	0.000	0.000	0.000	0.000
82	A	373	LYS	1	0.866	0.924	24.086	-10.673	-10.673	0.000	0.000	0.000	0.000
83	A	374	VAL	0	-0.030	-0.019	22.672	0.421	0.421	0.000	0.000	0.000	0.000
84	A	375	VAL	0	0.014	0.022	17.864	-0.384	-0.384	0.000	0.000	0.000	0.000
85	A	376	ARG	1	0.847	0.891	19.940	-13.789	-13.789	0.000	0.000	0.000	0.000
86	A	377	PHE	0	0.022	0.018	15.363	0.467	0.467	0.000	0.000	0.000	0.000
87	A	378	GLU	-1	-0.819	-0.899	17.788	13.243	13.243	0.000	0.000	0.000	0.000
88	A	379	ALA	0	-0.004	-0.005	15.890	0.841	0.841	0.000	0.000	0.000	0.000
89	A	380	SER	0	0.052	0.007	17.908	-0.905	-0.905	0.000	0.000	0.000	0.000
90	A	381	GLU	-1	-0.748	-0.873	18.116	17.830	17.830	0.000	0.000	0.000	0.000
91	A	382	ASP	-1	-0.824	-0.886	20.194	12.570	12.570	0.000	0.000	0.000	0.000
92	A	383	GLY	0	0.019	0.017	22.406	-0.400	-0.400	0.000	0.000	0.000	0.000
93	A	384	THR	0	-0.057	-0.013	23.565	-0.429	-0.429	0.000	0.000	0.000	0.000
94	A	385	ASN	0	-0.067	-0.060	25.196	-0.501	-0.501	0.000	0.000	0.000	0.000
95	A	386	TRP	0	-0.057	-0.016	19.239	1.028	1.028	0.000	0.000	0.000	0.000
96	A	387	GLU	-1	-0.822	-0.894	18.274	15.931	15.931	0.000	0.000	0.000	0.000
97	A	388	SER	0	-0.028	-0.018	20.154	0.519	0.519	0.000	0.000	0.000	0.000
98	A	389	ILE	0	-0.019	-0.019	13.520	-0.090	-0.090	0.000	0.000	0.000	0.000
99	A	390	GLY	0	0.019	0.002	16.015	1.228	1.228	0.000	0.000	0.000	0.000
100	A	391	GLN	0	-0.006	0.009	17.894	-0.425	-0.425	0.000	0.000	0.000	0.000
101	A	392	PHE	0	-0.007	0.007	15.000	0.187	0.187	0.000	0.000	0.000	0.000
102	A	393	GLY	0	0.070	0.039	19.518	-0.665	-0.665	0.000	0.000	0.000	0.000
103	A	394	PHE	0	-0.005	-0.004	17.923	1.228	1.228	0.000	0.000	0.000	0.000
104	A	395	THR	0	0.039	0.012	19.658	-0.953	-0.953	0.000	0.000	0.000	0.000
105	A	396	ASN	0	0.029	0.032	19.965	1.514	1.514	0.000	0.000	0.000	0.000
106	A	397	GLN	0	-0.043	-0.026	15.299	-1.334	-1.334	0.000	0.000	0.000	0.000
107	A	398	ASP	-1	-0.772	-0.912	18.190	15.742	15.742	0.000	0.000	0.000	0.000
108	A	399	ALA	0	-0.030	0.006	13.877	0.892	0.892	0.000	0.000	0.000	0.000
109	A	400	ALA	0	0.032	0.010	10.234	-0.745	-0.745	0.000	0.000	0.000	0.000
110	A	401	LEU	0	-0.034	0.001	12.074	0.490	0.490	0.000	0.000	0.000	0.000
111	A	402	LYS	1	0.832	0.902	5.704	-47.631	-47.631	0.000	0.000	0.000	0.000
112	A	403	TYR	0	-0.002	-0.023	10.620	-2.110	-2.110	0.000	0.000	0.000	0.000
113	A	404	TYR	0	0.018	0.003	8.185	1.934	1.934	0.000	0.000	0.000	0.000
114	A	405	VAL	0	-0.025	-0.014	10.697	-2.092	-2.092	0.000	0.000	0.000	0.000
115	A	406	LYS	1	0.855	0.921	12.178	-15.300	-15.300	0.000	0.000	0.000	0.000
116	A	407	SER	0	-0.013	-0.004	11.933	1.213	1.213	0.000	0.000	0.000	0.000
117	A	408	SER	0	0.012	0.011	12.473	-1.626	-1.626	0.000	0.000	0.000	0.000
118	A	409	THR	0	-0.085	-0.068	12.733	1.857	1.857	0.000	0.000	0.000	0.000
119	A	410	ALA	0	0.028	0.034	14.432	-1.189	-1.189	0.000	0.000	0.000	0.000
120	A	411	ARG	1	0.847	0.913	14.954	-13.604	-13.604	0.000	0.000	0.000	0.000
121	A	412	TYR	0	-0.060	-0.026	16.752	0.285	0.285	0.000	0.000	0.000	0.000
122	A	413	ILE	0	0.014	-0.006	13.025	0.476	0.476	0.000	0.000	0.000	0.000
123	A	414	LYS	1	0.798	0.892	16.721	-14.086	-14.086	0.000	0.000	0.000	0.000
124	A	415	LEU	0	0.006	0.018	17.726	0.783	0.783	0.000	0.000	0.000	0.000
125	A	416	VAL	0	0.010	-0.015	19.165	-0.870	-0.870	0.000	0.000	0.000	0.000
126	A	417	ILE	0	0.011	0.000	21.933	0.524	0.524	0.000	0.000	0.000	0.000
127	A	418	PRO	0	-0.021	-0.013	24.186	-0.522	-0.522	0.000	0.000	0.000	0.000
128	A	419	ASP	-1	-0.752	-0.883	27.188	9.888	9.888	0.000	0.000	0.000	0.000
129	A	420	GLY	0	-0.036	-0.009	30.244	0.225	0.225	0.000	0.000	0.000	0.000
130	A	421	VAL	0	-0.073	-0.050	26.785	-0.153	-0.153	0.000	0.000	0.000	0.000
131	A	422	GLY	0	0.005	0.011	29.378	0.183	0.183	0.000	0.000	0.000	0.000
132	A	423	ASN	0	-0.015	-0.012	25.371	0.229	0.229	0.000	0.000	0.000	0.000
133	A	424	GLY	0	0.051	0.013	29.019	-0.445	-0.445	0.000	0.000	0.000	0.000
134	A	425	THR	0	-0.017	-0.009	29.500	0.390	0.390	0.000	0.000	0.000	0.000
135	A	426	VAL	0	-0.034	0.009	28.623	-0.031	-0.031	0.000	0.000	0.000	0.000
136	A	427	ALA	0	0.019	0.002	24.473	0.226	0.226	0.000	0.000	0.000	0.000
137	A	428	ALA	0	0.007	0.009	23.330	-0.205	-0.205	0.000	0.000	0.000	0.000
138	A	429	ILE	0	-0.068	-0.038	17.006	0.396	0.396	0.000	0.000	0.000	0.000
139	A	430	ARG	1	0.802	0.878	16.610	-16.194	-16.194	0.000	0.000	0.000	0.000
140	A	431	GLU	-1	-0.800	-0.882	10.840	28.375	28.375	0.000	0.000	0.000	0.000
141	A	432	LEU	0	0.009	0.013	12.687	-0.131	-0.131	0.000	0.000	0.000	0.000
142	A	433	ASP	-1	-0.798	-0.884	7.810	33.291	33.291	0.000	0.000	0.000	0.000
143	A	434	VAL	0	0.034	0.006	7.298	-1.159	-1.159	0.000	0.000	0.000	0.000
144	A	435	ARG	1	0.782	0.871	1.664	-104.376	-108.740	22.241	-9.443	-8.434	0.104
145	A	436	GLY	0	0.042	0.004	3.628	-9.543	-8.907	0.005	-0.218	-0.423	0.002
146	A	437	THR	0	-0.022	-0.008	4.722	2.370	2.469	-0.001	-0.006	-0.092	0.000
147	A	438	VAL	0	0.019	0.008	7.369	-2.477	-2.477	0.000	0.000	0.000	0.000
148	A	439	VAL	0	-0.050	-0.022	9.958	-0.467	-0.467	0.000	0.000	0.000	0.000
149	A	440	ASN	0	0.002	0.005	12.905	-1.605	-1.605	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:292:ASP)