FMO DATABASE

FMODB ID: YV8Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1430858.104474
FMO2-HF: Nuclear repulsion	1373752.407873
FMO2-HF: Total energy	-57105.696601
FMO2-MP2: Total energy	-57276.108485

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.
-74.126	-73.757	14.948	-7.51	-7.806	0.082

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 : -0.915 / q_NPA : -0.963

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	-0.019	-0.009	3.801	-5.802	-4.296	-0.001	-0.640	-0.865	0.003
4	A	295	SER	0	-0.012	-0.008	6.106	-1.487	-1.487	0.000	0.000	0.000	0.000
5	A	296	LYS	1	0.908	0.941	8.597	-27.429	-27.429	0.000	0.000	0.000	0.000
6	A	297	THR	0	-0.018	-0.003	11.731	-1.086	-1.086	0.000	0.000	0.000	0.000
7	A	298	ASP	-1	-0.848	-0.898	14.060	16.846	16.846	0.000	0.000	0.000	0.000
8	A	299	TRP	0	-0.046	-0.010	10.361	-0.720	-0.720	0.000	0.000	0.000	0.000
9	A	300	LYS	1	0.928	0.959	16.331	-14.770	-14.770	0.000	0.000	0.000	0.000
10	A	301	ILE	0	0.008	0.011	19.760	0.410	0.410	0.000	0.000	0.000	0.000
11	A	302	VAL	0	-0.044	-0.017	21.816	-0.534	-0.534	0.000	0.000	0.000	0.000
12	A	303	SER	0	-0.006	-0.010	24.274	-0.619	-0.619	0.000	0.000	0.000	0.000
13	A	304	PHE	0	0.028	-0.001	24.742	0.742	0.742	0.000	0.000	0.000	0.000
14	A	305	THR	0	-0.019	0.017	26.648	-0.216	-0.216	0.000	0.000	0.000	0.000
15	A	306	THR	0	-0.032	-0.034	27.979	-0.310	-0.310	0.000	0.000	0.000	0.000
16	A	307	GLU	-1	-0.851	-0.909	26.979	12.099	12.099	0.000	0.000	0.000	0.000
17	A	308	GLU	-1	-0.749	-0.847	28.033	9.239	9.239	0.000	0.000	0.000	0.000
18	A	309	ALA	0	0.017	0.002	29.175	0.186	0.186	0.000	0.000	0.000	0.000
19	A	310	SER	0	-0.067	-0.041	31.023	-0.222	-0.222	0.000	0.000	0.000	0.000
20	A	311	GLY	0	-0.016	-0.015	33.261	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	312	GLU	-1	-0.909	-0.944	27.846	10.820	10.820	0.000	0.000	0.000	0.000
22	A	313	GLY	0	-0.015	-0.004	29.454	0.180	0.180	0.000	0.000	0.000	0.000
23	A	314	SER	0	0.005	-0.021	29.888	0.134	0.134	0.000	0.000	0.000	0.000
24	A	315	ASN	0	-0.093	-0.053	25.670	0.284	0.284	0.000	0.000	0.000	0.000
25	A	316	ASN	0	0.083	0.043	23.988	0.982	0.982	0.000	0.000	0.000	0.000
26	A	317	GLY	0	0.051	0.042	24.691	-0.450	-0.450	0.000	0.000	0.000	0.000
27	A	318	HIS	0	-0.016	-0.008	25.026	-0.280	-0.280	0.000	0.000	0.000	0.000
28	A	319	ALA	0	0.031	-0.007	22.978	0.657	0.657	0.000	0.000	0.000	0.000
29	A	320	LYS	1	0.899	0.940	20.978	-11.303	-11.303	0.000	0.000	0.000	0.000
30	A	321	HIS	0	-0.006	-0.005	19.660	0.467	0.467	0.000	0.000	0.000	0.000
31	A	322	LEU	0	0.015	0.037	16.737	0.441	0.441	0.000	0.000	0.000	0.000
32	A	323	ILE	0	-0.056	-0.047	14.985	1.437	1.437	0.000	0.000	0.000	0.000
33	A	324	ASP	-1	-0.792	-0.878	15.282	16.616	16.616	0.000	0.000	0.000	0.000
34	A	325	GLY	0	-0.053	-0.016	13.129	0.046	0.046	0.000	0.000	0.000	0.000
35	A	326	ASN	0	-0.043	-0.014	13.931	0.432	0.432	0.000	0.000	0.000	0.000
36	A	327	ILE	0	0.061	0.028	12.684	-0.168	-0.168	0.000	0.000	0.000	0.000
37	A	328	GLU	-1	-0.831	-0.910	16.474	14.292	14.292	0.000	0.000	0.000	0.000
38	A	329	THR	0	-0.106	-0.048	19.393	-0.703	-0.703	0.000	0.000	0.000	0.000
39	A	330	PHE	0	0.029	-0.009	19.357	0.685	0.685	0.000	0.000	0.000	0.000
40	A	331	TRP	0	-0.055	-0.008	20.786	-0.382	-0.382	0.000	0.000	0.000	0.000
41	A	332	HIS	0	-0.064	-0.082	22.721	0.295	0.295	0.000	0.000	0.000	0.000
42	A	333	SER	0	-0.004	-0.016	25.803	-0.081	-0.081	0.000	0.000	0.000	0.000
43	A	334	ARG	1	0.937	0.993	28.270	-9.117	-9.117	0.000	0.000	0.000	0.000
44	A	335	TRP	0	-0.070	-0.053	30.832	-0.397	-0.397	0.000	0.000	0.000	0.000
45	A	336	GLN	0	-0.005	-0.002	33.998	-0.343	-0.343	0.000	0.000	0.000	0.000
46	A	337	GLY	0	-0.042	-0.029	36.327	0.027	0.027	0.000	0.000	0.000	0.000
47	A	338	GLY	0	-0.027	-0.005	37.961	-0.164	-0.164	0.000	0.000	0.000	0.000
48	A	339	SER	0	-0.009	-0.003	34.378	0.148	0.148	0.000	0.000	0.000	0.000
49	A	340	ASP	-1	-0.804	-0.877	32.461	9.376	9.376	0.000	0.000	0.000	0.000
50	A	341	PRO	0	-0.035	-0.004	33.290	0.228	0.228	0.000	0.000	0.000	0.000
51	A	342	LEU	0	-0.028	0.012	28.548	0.256	0.256	0.000	0.000	0.000	0.000
52	A	343	PRO	0	-0.014	-0.014	28.136	-0.285	-0.285	0.000	0.000	0.000	0.000
53	A	344	TYR	0	-0.036	-0.057	25.940	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	345	GLU	-1	-0.900	-0.962	23.941	12.669	12.669	0.000	0.000	0.000	0.000
55	A	346	ILE	0	0.015	0.004	20.872	-0.322	-0.322	0.000	0.000	0.000	0.000
56	A	347	ILE	0	-0.019	0.003	20.897	0.838	0.838	0.000	0.000	0.000	0.000
57	A	348	ILE	0	0.003	-0.001	15.817	-0.301	-0.301	0.000	0.000	0.000	0.000
58	A	349	ASP	-1	-0.769	-0.870	18.651	15.399	15.399	0.000	0.000	0.000	0.000
59	A	350	MET	0	0.004	-0.005	13.026	0.836	0.836	0.000	0.000	0.000	0.000
60	A	351	ASN	0	-0.081	-0.043	15.059	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	352	HIS	1	0.811	0.885	12.867	-19.682	-19.682	0.000	0.000	0.000	0.000
62	A	353	ARG	1	0.856	0.919	14.810	-16.574	-16.574	0.000	0.000	0.000	0.000
63	A	354	VAL	0	0.006	-0.006	9.192	0.946	0.946	0.000	0.000	0.000	0.000
64	A	355	LYS	1	0.976	0.996	10.741	-25.298	-25.298	0.000	0.000	0.000	0.000
65	A	356	ILE	0	-0.015	-0.017	9.462	4.101	4.101	0.000	0.000	0.000	0.000
66	A	357	ALA	0	-0.030	-0.017	6.361	-1.870	-1.870	0.000	0.000	0.000	0.000
67	A	358	GLN	0	-0.038	-0.036	5.416	5.439	5.475	-0.001	0.000	-0.034	0.000
68	A	359	ILE	0	0.020	0.025	8.002	1.767	1.767	0.000	0.000	0.000	0.000
69	A	360	GLU	-1	-0.795	-0.885	6.834	44.564	44.564	0.000	0.000	0.000	0.000
70	A	361	LEU	0	0.014	0.014	10.544	-1.164	-1.164	0.000	0.000	0.000	0.000
71	A	362	LEU	0	0.006	0.016	12.873	0.314	0.314	0.000	0.000	0.000	0.000
72	A	363	PRO	0	0.011	0.008	14.699	-1.057	-1.057	0.000	0.000	0.000	0.000
73	A	364	ARG	1	0.982	1.004	18.398	-11.951	-11.951	0.000	0.000	0.000	0.000
74	A	365	GLY	0	0.048	0.035	21.058	0.036	0.036	0.000	0.000	0.000	0.000
75	A	366	ARG	1	0.787	0.856	18.988	-15.495	-15.495	0.000	0.000	0.000	0.000
76	A	367	GLY	0	-0.004	0.009	24.162	-0.496	-0.496	0.000	0.000	0.000	0.000
77	A	368	SER	0	-0.066	-0.033	24.668	-0.436	-0.436	0.000	0.000	0.000	0.000
78	A	369	ASN	0	0.010	-0.007	27.262	0.245	0.245	0.000	0.000	0.000	0.000
79	A	370	ASN	0	0.022	-0.011	22.035	-0.319	-0.319	0.000	0.000	0.000	0.000
80	A	371	PRO	0	-0.026	0.003	25.029	0.540	0.540	0.000	0.000	0.000	0.000
81	A	372	ILE	0	-0.005	0.011	22.095	-0.305	-0.305	0.000	0.000	0.000	0.000
82	A	373	LYS	1	0.948	0.968	24.273	-10.525	-10.525	0.000	0.000	0.000	0.000
83	A	374	VAL	0	-0.037	-0.021	22.771	0.473	0.473	0.000	0.000	0.000	0.000
84	A	375	VAL	0	0.033	0.025	17.881	-0.352	-0.352	0.000	0.000	0.000	0.000
85	A	376	ARG	1	0.922	0.941	20.061	-13.125	-13.125	0.000	0.000	0.000	0.000
86	A	377	PHE	0	0.020	0.017	15.343	0.339	0.339	0.000	0.000	0.000	0.000
87	A	378	GLU	-1	-0.880	-0.932	18.379	12.920	12.920	0.000	0.000	0.000	0.000
88	A	379	ALA	0	-0.004	-0.003	16.688	0.831	0.831	0.000	0.000	0.000	0.000
89	A	380	SER	0	0.056	0.019	18.596	-0.878	-0.878	0.000	0.000	0.000	0.000
90	A	381	GLU	-1	-0.737	-0.871	18.944	17.250	17.250	0.000	0.000	0.000	0.000
91	A	382	ASP	-1	-0.826	-0.901	20.739	12.434	12.434	0.000	0.000	0.000	0.000
92	A	383	GLY	0	-0.001	0.006	23.280	-0.307	-0.307	0.000	0.000	0.000	0.000
93	A	384	THR	0	-0.073	-0.032	24.244	-0.435	-0.435	0.000	0.000	0.000	0.000
94	A	385	ASN	0	-0.088	-0.063	26.166	-0.486	-0.486	0.000	0.000	0.000	0.000
95	A	386	TRP	0	-0.008	0.006	20.014	0.909	0.909	0.000	0.000	0.000	0.000
96	A	387	GLU	-1	-0.946	-0.964	19.300	15.830	15.830	0.000	0.000	0.000	0.000
97	A	388	SER	0	0.001	-0.009	20.817	0.668	0.668	0.000	0.000	0.000	0.000
98	A	389	ILE	0	-0.028	-0.021	14.390	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	390	GLY	0	0.019	0.003	16.857	1.105	1.105	0.000	0.000	0.000	0.000
100	A	391	GLN	0	-0.015	0.001	18.940	-0.296	-0.296	0.000	0.000	0.000	0.000
101	A	392	PHE	0	-0.003	-0.002	15.553	0.313	0.313	0.000	0.000	0.000	0.000
102	A	393	GLY	0	0.044	0.028	19.389	-0.735	-0.735	0.000	0.000	0.000	0.000
103	A	394	PHE	0	-0.008	0.004	18.428	1.199	1.199	0.000	0.000	0.000	0.000
104	A	395	THR	0	0.030	0.007	19.767	-0.985	-0.985	0.000	0.000	0.000	0.000
105	A	396	ASN	0	0.023	0.026	20.012	1.440	1.440	0.000	0.000	0.000	0.000
106	A	397	GLN	0	-0.055	-0.032	15.557	-1.342	-1.342	0.000	0.000	0.000	0.000
107	A	398	ASP	-1	-0.804	-0.919	18.377	15.185	15.185	0.000	0.000	0.000	0.000
108	A	399	ALA	0	-0.037	-0.006	13.594	0.875	0.875	0.000	0.000	0.000	0.000
109	A	400	ALA	0	0.041	0.014	10.470	-0.827	-0.827	0.000	0.000	0.000	0.000
110	A	401	LEU	0	-0.049	-0.004	12.576	0.139	0.139	0.000	0.000	0.000	0.000
111	A	402	LYS	1	0.862	0.912	6.140	-42.046	-42.046	0.000	0.000	0.000	0.000
112	A	403	TYR	0	-0.010	-0.025	10.822	-1.662	-1.662	0.000	0.000	0.000	0.000
113	A	404	TYR	0	0.000	-0.014	8.954	2.046	2.046	0.000	0.000	0.000	0.000
114	A	405	VAL	0	-0.009	0.007	11.311	-1.957	-1.957	0.000	0.000	0.000	0.000
115	A	406	LYS	1	0.956	0.984	13.423	-14.843	-14.843	0.000	0.000	0.000	0.000
116	A	407	SER	0	-0.037	-0.021	13.266	0.951	0.951	0.000	0.000	0.000	0.000
117	A	408	SER	0	0.046	0.023	13.627	-1.482	-1.482	0.000	0.000	0.000	0.000
118	A	409	THR	0	-0.058	-0.033	13.772	2.236	2.236	0.000	0.000	0.000	0.000
119	A	410	ALA	0	0.016	0.024	14.835	-1.187	-1.187	0.000	0.000	0.000	0.000
120	A	411	ARG	1	0.847	0.916	15.021	-13.356	-13.356	0.000	0.000	0.000	0.000
121	A	412	TYR	0	-0.021	0.000	16.899	0.308	0.308	0.000	0.000	0.000	0.000
122	A	413	ILE	0	0.004	-0.005	13.443	0.406	0.406	0.000	0.000	0.000	0.000
123	A	414	LYS	1	0.879	0.949	17.359	-13.698	-13.698	0.000	0.000	0.000	0.000
124	A	415	LEU	0	0.009	0.016	17.914	0.600	0.600	0.000	0.000	0.000	0.000
125	A	416	VAL	0	0.022	-0.002	19.524	-0.788	-0.788	0.000	0.000	0.000	0.000
126	A	417	ILE	0	-0.008	-0.009	22.237	0.476	0.476	0.000	0.000	0.000	0.000
127	A	418	PRO	0	-0.034	-0.018	24.234	-0.494	-0.494	0.000	0.000	0.000	0.000
128	A	419	ASP	-1	-0.752	-0.880	27.259	9.684	9.684	0.000	0.000	0.000	0.000
129	A	420	GLY	0	-0.055	-0.035	30.502	0.167	0.167	0.000	0.000	0.000	0.000
130	A	421	VAL	0	-0.038	-0.024	27.062	-0.061	-0.061	0.000	0.000	0.000	0.000
131	A	422	GLY	0	-0.046	-0.021	29.431	0.213	0.213	0.000	0.000	0.000	0.000
132	A	423	ASN	0	-0.008	0.011	25.540	0.284	0.284	0.000	0.000	0.000	0.000
133	A	424	GLY	0	0.048	0.013	28.992	-0.405	-0.405	0.000	0.000	0.000	0.000
134	A	425	THR	0	0.031	0.005	29.858	0.254	0.254	0.000	0.000	0.000	0.000
135	A	426	VAL	0	-0.059	0.005	28.353	0.006	0.006	0.000	0.000	0.000	0.000
136	A	427	ALA	0	0.021	0.003	24.477	0.238	0.238	0.000	0.000	0.000	0.000
137	A	428	ALA	0	-0.001	0.004	23.361	-0.202	-0.202	0.000	0.000	0.000	0.000
138	A	429	ILE	0	-0.076	-0.042	17.109	0.388	0.388	0.000	0.000	0.000	0.000
139	A	430	ARG	1	0.810	0.898	16.555	-15.940	-15.940	0.000	0.000	0.000	0.000
140	A	431	GLU	-1	-0.852	-0.919	10.830	25.315	25.315	0.000	0.000	0.000	0.000
141	A	432	LEU	0	-0.006	0.008	12.277	0.109	0.109	0.000	0.000	0.000	0.000
142	A	433	ASP	-1	-0.823	-0.915	7.895	31.935	31.935	0.000	0.000	0.000	0.000
143	A	434	VAL	0	0.027	0.003	8.099	-0.465	-0.465	0.000	0.000	0.000	0.000
144	A	435	ARG	1	0.786	0.889	1.949	-97.601	-99.030	14.952	-6.852	-6.671	0.079
145	A	436	GLY	0	0.071	0.018	4.736	-6.639	-6.419	-0.001	-0.013	-0.207	0.000
146	A	437	THR	0	-0.022	0.002	5.025	2.889	2.925	-0.001	-0.005	-0.029	0.000
147	A	438	VAL	0	0.016	0.004	7.469	-2.438	-2.438	0.000	0.000	0.000	0.000
148	A	439	VAL	0	-0.050	-0.018	10.114	-0.091	-0.091	0.000	0.000	0.000	0.000
149	A	440	ASN	0	0.005	0.002	13.218	-1.607	-1.607	0.000	0.000	0.000	0.000

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