FMO DATABASE

FMODB ID: 98YV2

Calculation Name: 4F8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4F8A

Chain ID: A

ChEMBL ID:

UniProt ID: Q60603

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1374773.910172
FMO2-HF: Nuclear repulsion	1316383.347875
FMO2-HF: Total energy	-58390.562297
FMO2-MP2: Total energy	-58558.168379

3D Structure Molmil

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:562:ASP)

Summations of interaction energy for fragment #1(A:562: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.
-113.776	-108.347	11.592	-8.9	-8.121	0.098

Interaction energy analysis for fragmet #1(A:562:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.838 / q_NPA : -0.930

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	564	ARG	1	0.955	0.983	1.874	-84.081	-80.016	11.523	-8.212	-7.376	0.091
4	A	565	ALA	0	0.059	0.026	3.696	-17.395	-16.112	0.070	-0.687	-0.666	0.007
5	A	566	ASP	-1	-0.795	-0.888	5.977	32.079	32.079	0.000	0.000	0.000	0.000
6	A	567	ILE	0	-0.007	-0.002	5.060	-6.182	-6.101	-0.001	-0.001	-0.079	0.000
7	A	568	CYS	0	-0.010	-0.004	7.507	-5.020	-5.020	0.000	0.000	0.000	0.000
8	A	569	VAL	0	-0.005	0.007	9.953	-3.766	-3.766	0.000	0.000	0.000	0.000
9	A	570	HIS	0	-0.033	-0.014	11.290	-3.023	-3.023	0.000	0.000	0.000	0.000
10	A	571	LEU	0	-0.004	-0.002	11.110	-2.335	-2.335	0.000	0.000	0.000	0.000
11	A	572	ASN	0	0.038	0.024	13.246	-3.160	-3.160	0.000	0.000	0.000	0.000
12	A	573	ARG	1	0.873	0.934	15.921	-20.393	-20.393	0.000	0.000	0.000	0.000
13	A	574	LYS	1	0.876	0.923	17.764	-14.766	-14.766	0.000	0.000	0.000	0.000
14	A	575	VAL	0	0.037	0.037	19.568	-0.778	-0.778	0.000	0.000	0.000	0.000
15	A	576	PHE	0	-0.019	-0.028	13.828	-0.456	-0.456	0.000	0.000	0.000	0.000
16	A	577	LYS	1	0.908	0.958	15.337	-20.025	-20.025	0.000	0.000	0.000	0.000
17	A	578	GLU	-1	-0.841	-0.894	21.266	12.833	12.833	0.000	0.000	0.000	0.000
18	A	579	HIS	0	0.065	0.050	23.677	-0.293	-0.293	0.000	0.000	0.000	0.000
19	A	580	PRO	0	0.023	0.005	24.587	0.445	0.445	0.000	0.000	0.000	0.000
20	A	581	ALA	0	-0.018	-0.012	24.739	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	582	PHE	0	0.034	0.002	19.349	0.282	0.282	0.000	0.000	0.000	0.000
22	A	583	ARG	1	0.930	0.978	21.716	-10.862	-10.862	0.000	0.000	0.000	0.000
23	A	584	LEU	0	-0.047	-0.026	23.207	-0.357	-0.357	0.000	0.000	0.000	0.000
24	A	585	ALA	0	-0.010	0.006	18.187	0.028	0.028	0.000	0.000	0.000	0.000
25	A	586	SER	0	0.033	0.018	17.731	0.486	0.486	0.000	0.000	0.000	0.000
26	A	587	ASP	-1	-0.841	-0.934	13.082	20.969	20.969	0.000	0.000	0.000	0.000
27	A	588	GLY	0	-0.056	-0.025	12.331	2.061	2.061	0.000	0.000	0.000	0.000
28	A	589	CYS	0	-0.039	0.002	13.095	0.644	0.644	0.000	0.000	0.000	0.000
29	A	590	LEU	0	0.029	0.004	14.138	0.548	0.548	0.000	0.000	0.000	0.000
30	A	591	ARG	1	0.899	0.913	7.948	-29.427	-29.427	0.000	0.000	0.000	0.000
31	A	592	ALA	0	-0.044	-0.011	10.440	1.507	1.507	0.000	0.000	0.000	0.000
32	A	593	LEU	0	0.000	0.003	12.580	-0.515	-0.515	0.000	0.000	0.000	0.000
33	A	594	ALA	0	-0.008	-0.017	10.274	-0.255	-0.255	0.000	0.000	0.000	0.000
34	A	595	MET	0	-0.075	-0.035	6.656	3.623	3.623	0.000	0.000	0.000	0.000
35	A	596	GLU	-1	-0.862	-0.908	10.478	19.728	19.728	0.000	0.000	0.000	0.000
36	A	597	PHE	0	-0.053	-0.032	14.266	-1.566	-1.566	0.000	0.000	0.000	0.000
37	A	598	GLN	0	-0.044	-0.015	14.633	0.963	0.963	0.000	0.000	0.000	0.000
38	A	599	THR	0	-0.017	-0.014	16.867	-0.493	-0.493	0.000	0.000	0.000	0.000
39	A	600	VAL	0	-0.010	-0.011	18.755	0.157	0.157	0.000	0.000	0.000	0.000
40	A	601	HIS	0	-0.048	-0.037	19.838	0.263	0.263	0.000	0.000	0.000	0.000
41	A	602	CYS	0	-0.033	-0.005	23.888	-0.161	-0.161	0.000	0.000	0.000	0.000
42	A	603	ALA	0	0.000	-0.016	27.702	0.039	0.039	0.000	0.000	0.000	0.000
43	A	604	PRO	0	-0.026	-0.018	30.886	-0.096	-0.096	0.000	0.000	0.000	0.000
44	A	605	GLY	0	0.010	0.009	34.479	-0.154	-0.154	0.000	0.000	0.000	0.000
45	A	606	ASP	-1	-0.834	-0.902	29.974	10.693	10.693	0.000	0.000	0.000	0.000
46	A	607	LEU	0	-0.036	-0.031	33.076	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	608	ILE	0	0.000	0.000	28.112	0.139	0.139	0.000	0.000	0.000	0.000
48	A	609	TYR	0	0.013	-0.003	27.551	0.174	0.174	0.000	0.000	0.000	0.000
49	A	610	HIS	1	0.768	0.863	32.047	-10.126	-10.126	0.000	0.000	0.000	0.000
50	A	611	ALA	0	0.055	0.028	35.775	0.095	0.095	0.000	0.000	0.000	0.000
51	A	612	GLY	0	-0.016	-0.009	38.689	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	613	GLU	-1	-0.817	-0.879	32.116	10.086	10.086	0.000	0.000	0.000	0.000
53	A	614	SER	0	-0.001	-0.008	30.568	-0.119	-0.119	0.000	0.000	0.000	0.000
54	A	615	VAL	0	0.027	0.015	30.397	0.382	0.382	0.000	0.000	0.000	0.000
55	A	616	ASP	-1	-0.841	-0.903	25.462	12.741	12.741	0.000	0.000	0.000	0.000
56	A	617	SER	0	-0.003	-0.016	23.945	0.428	0.428	0.000	0.000	0.000	0.000
57	A	618	LEU	0	-0.072	-0.010	23.238	-0.498	-0.498	0.000	0.000	0.000	0.000
58	A	619	CYS	0	-0.026	-0.014	23.460	0.846	0.846	0.000	0.000	0.000	0.000
59	A	620	PHE	0	0.063	0.011	22.729	-0.476	-0.476	0.000	0.000	0.000	0.000
60	A	621	VAL	0	0.045	0.029	24.639	0.452	0.452	0.000	0.000	0.000	0.000
61	A	622	VAL	0	-0.059	-0.033	21.591	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	623	SER	0	-0.084	-0.058	24.856	-0.299	-0.299	0.000	0.000	0.000	0.000
63	A	624	GLY	0	0.066	0.033	26.880	0.034	0.034	0.000	0.000	0.000	0.000
64	A	625	SER	0	-0.066	-0.047	30.238	-0.171	-0.171	0.000	0.000	0.000	0.000
65	A	626	LEU	0	0.007	0.004	29.744	0.057	0.057	0.000	0.000	0.000	0.000
66	A	627	GLU	-1	-0.792	-0.875	34.081	8.131	8.131	0.000	0.000	0.000	0.000
67	A	628	VAL	0	-0.011	-0.008	35.288	0.248	0.248	0.000	0.000	0.000	0.000
68	A	629	ILE	0	-0.003	0.001	37.804	-0.212	-0.212	0.000	0.000	0.000	0.000
69	A	630	GLN	0	-0.019	-0.008	40.514	0.281	0.281	0.000	0.000	0.000	0.000
70	A	631	ASP	-1	-0.794	-0.886	42.838	7.006	7.006	0.000	0.000	0.000	0.000
71	A	632	ASP	-1	-0.953	-0.972	44.566	7.155	7.155	0.000	0.000	0.000	0.000
72	A	633	GLU	-1	-0.878	-0.919	45.749	6.849	6.849	0.000	0.000	0.000	0.000
73	A	634	VAL	0	-0.043	-0.042	41.203	0.218	0.218	0.000	0.000	0.000	0.000
74	A	635	VAL	0	-0.036	-0.010	40.384	-0.069	-0.069	0.000	0.000	0.000	0.000
75	A	636	ALA	0	-0.025	-0.015	38.217	0.012	0.012	0.000	0.000	0.000	0.000
76	A	637	ILE	0	-0.010	-0.008	37.338	0.035	0.035	0.000	0.000	0.000	0.000
77	A	638	LEU	0	-0.025	0.000	32.177	0.029	0.029	0.000	0.000	0.000	0.000
78	A	639	GLY	0	0.034	0.004	31.886	-0.059	-0.059	0.000	0.000	0.000	0.000
79	A	640	LYS	1	0.829	0.910	26.467	-11.767	-11.767	0.000	0.000	0.000	0.000
80	A	641	GLY	0	-0.031	-0.022	27.901	-0.265	-0.265	0.000	0.000	0.000	0.000
81	A	642	ASP	-1	-0.770	-0.847	28.745	10.088	10.088	0.000	0.000	0.000	0.000
82	A	643	VAL	0	-0.053	-0.037	26.340	0.553	0.553	0.000	0.000	0.000	0.000
83	A	644	PHE	0	0.033	0.018	28.396	-0.437	-0.437	0.000	0.000	0.000	0.000
84	A	645	GLY	0	0.074	0.029	28.226	0.568	0.568	0.000	0.000	0.000	0.000
85	A	646	ASP	-1	-0.732	-0.839	29.378	9.157	9.157	0.000	0.000	0.000	0.000
86	A	647	VAL	0	-0.036	-0.019	29.372	0.430	0.430	0.000	0.000	0.000	0.000
87	A	648	PHE	0	0.040	0.002	26.347	-0.092	-0.092	0.000	0.000	0.000	0.000
88	A	649	TRP	0	0.011	0.003	26.739	0.032	0.032	0.000	0.000	0.000	0.000
89	A	650	LYS	1	0.797	0.893	28.953	-9.861	-9.861	0.000	0.000	0.000	0.000
90	A	651	GLU	-1	-0.867	-0.918	31.905	8.539	8.539	0.000	0.000	0.000	0.000
91	A	652	ALA	0	-0.021	0.001	32.033	0.281	0.281	0.000	0.000	0.000	0.000
92	A	653	THR	0	-0.017	-0.005	33.138	0.046	0.046	0.000	0.000	0.000	0.000
93	A	654	LEU	0	-0.019	0.001	29.765	-0.019	-0.019	0.000	0.000	0.000	0.000
94	A	655	ALA	0	0.040	0.015	32.681	-0.298	-0.298	0.000	0.000	0.000	0.000
95	A	656	GLN	0	-0.060	-0.038	34.357	0.105	0.105	0.000	0.000	0.000	0.000
96	A	657	SER	0	-0.007	-0.014	34.536	-0.092	-0.092	0.000	0.000	0.000	0.000
97	A	658	CYS	0	-0.064	-0.029	36.421	-0.268	-0.268	0.000	0.000	0.000	0.000
98	A	659	ALA	0	-0.025	-0.004	37.671	-0.223	-0.223	0.000	0.000	0.000	0.000
99	A	660	ASN	0	0.013	0.014	36.683	0.387	0.387	0.000	0.000	0.000	0.000
100	A	661	VAL	0	-0.001	0.001	31.999	-0.076	-0.076	0.000	0.000	0.000	0.000
101	A	662	ARG	1	0.821	0.886	34.028	-8.166	-8.166	0.000	0.000	0.000	0.000
102	A	663	ALA	0	0.018	0.017	31.423	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	664	LEU	0	-0.007	0.000	33.423	-0.227	-0.227	0.000	0.000	0.000	0.000
104	A	665	THR	0	-0.028	-0.040	31.623	-0.229	-0.229	0.000	0.000	0.000	0.000
105	A	666	TYR	0	0.032	0.012	28.873	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	667	CYS	0	-0.069	-0.003	28.056	-0.270	-0.270	0.000	0.000	0.000	0.000
107	A	668	ASP	-1	-0.825	-0.880	22.451	14.133	14.133	0.000	0.000	0.000	0.000
108	A	669	LEU	0	0.009	0.008	23.882	-0.230	-0.230	0.000	0.000	0.000	0.000
109	A	670	HIS	0	-0.035	-0.023	16.802	0.555	0.555	0.000	0.000	0.000	0.000
110	A	671	VAL	0	0.007	0.005	20.112	-0.612	-0.612	0.000	0.000	0.000	0.000
111	A	672	ILE	0	0.009	0.010	17.325	1.088	1.088	0.000	0.000	0.000	0.000
112	A	673	LYS	1	0.862	0.918	20.047	-14.409	-14.409	0.000	0.000	0.000	0.000
113	A	674	ARG	1	0.874	0.921	21.481	-11.478	-11.478	0.000	0.000	0.000	0.000
114	A	675	ASP	-1	-0.812	-0.890	21.821	13.051	13.051	0.000	0.000	0.000	0.000
115	A	676	ALA	0	0.025	0.022	17.387	0.116	0.116	0.000	0.000	0.000	0.000
116	A	677	LEU	0	-0.003	-0.006	18.831	0.415	0.415	0.000	0.000	0.000	0.000
117	A	678	GLN	0	-0.018	-0.020	20.756	-0.102	-0.102	0.000	0.000	0.000	0.000
118	A	679	LYS	1	0.905	0.947	14.266	-19.981	-19.981	0.000	0.000	0.000	0.000
119	A	680	VAL	0	-0.049	-0.019	15.971	0.355	0.355	0.000	0.000	0.000	0.000
120	A	681	LEU	0	-0.033	-0.019	18.773	-0.149	-0.149	0.000	0.000	0.000	0.000
121	A	682	GLU	-1	-0.876	-0.947	22.288	12.194	12.194	0.000	0.000	0.000	0.000
122	A	683	PHE	0	-0.023	0.007	18.131	-0.193	-0.193	0.000	0.000	0.000	0.000
123	A	684	TYR	0	0.002	-0.002	14.623	-0.388	-0.388	0.000	0.000	0.000	0.000
124	A	685	THR	0	0.034	0.012	21.215	-0.308	-0.308	0.000	0.000	0.000	0.000
125	A	686	ALA	0	0.005	-0.002	24.639	-0.373	-0.373	0.000	0.000	0.000	0.000
126	A	687	PHE	0	0.030	0.009	20.524	-0.293	-0.293	0.000	0.000	0.000	0.000
127	A	688	SER	0	0.051	0.029	23.810	-0.254	-0.254	0.000	0.000	0.000	0.000
128	A	689	HIS	0	0.034	0.012	25.234	-0.401	-0.401	0.000	0.000	0.000	0.000
129	A	690	SER	0	-0.048	-0.006	26.091	-0.558	-0.558	0.000	0.000	0.000	0.000
130	A	691	PHE	0	0.044	0.024	22.577	-0.367	-0.367	0.000	0.000	0.000	0.000
131	A	692	SER	0	0.016	0.003	26.485	-0.411	-0.411	0.000	0.000	0.000	0.000
132	A	693	ARG	1	0.840	0.894	29.488	-10.382	-10.382	0.000	0.000	0.000	0.000
133	A	694	ASN	0	-0.054	-0.028	28.302	-0.290	-0.290	0.000	0.000	0.000	0.000
134	A	695	LEU	0	-0.028	0.000	25.401	0.069	0.069	0.000	0.000	0.000	0.000
135	A	696	ILE	0	-0.024	-0.004	29.234	-0.166	-0.166	0.000	0.000	0.000	0.000
136	A	697	LEU	0	-0.047	-0.014	29.176	0.212	0.212	0.000	0.000	0.000	0.000
137	A	698	THR	0	-0.031	-0.040	32.121	-0.219	-0.219	0.000	0.000	0.000	0.000
138	A	699	TYR	0	0.028	0.008	33.308	-0.327	-0.327	0.000	0.000	0.000	0.000
139	A	700	ASN	0	-0.041	-0.038	33.192	0.413	0.413	0.000	0.000	0.000	0.000
140	A	701	LEU	0	0.037	-0.001	31.444	-0.268	-0.268	0.000	0.000	0.000	0.000
141	A	702	ARG	1	0.804	0.891	34.148	-9.304	-9.304	0.000	0.000	0.000	0.000
142	A	703	LYN	0	-0.029	0.009	37.079	-0.177	-0.177	0.000	0.000	0.000	0.000
143	A	704	ARG	1	0.834	0.884	40.057	-7.225	-7.225	0.000	0.000	0.000	0.000
144	A	705	ILE	0	-0.001	-0.001	42.127	-0.128	-0.128	0.000	0.000	0.000	0.000
145	A	706	VAL	0	-0.007	-0.005	45.032	-0.062	-0.062	0.000	0.000	0.000	0.000
146	A	707	PHE	0	0.002	0.008	46.016	-0.155	-0.155	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:562:ASP)