FMO DATABASE

FMODB ID: LNL39

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	OptHSide
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	-1374098.010306
FMO2-HF: Nuclear repulsion	1315707.763598
FMO2-HF: Total energy	-58390.246708
FMO2-MP2: Total energy	-58557.855855

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.
-105.566	-97.611	5.092	-6.749	-6.297	0.076

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 : -0.885 / q_NPA : -0.961

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	0.975	0.995	2.013	-80.789	-73.587	5.063	-6.368	-5.897	0.073
4	A	565	ALA	0	0.076	0.026	3.849	-14.819	-14.066	0.029	-0.381	-0.400	0.003
5	A	566	ASP	-1	-0.806	-0.897	6.086	32.651	32.651	0.000	0.000	0.000	0.000
6	A	567	ILE	0	-0.013	-0.002	5.811	-5.839	-5.839	0.000	0.000	0.000	0.000
7	A	568	CYS	0	-0.018	-0.012	7.679	-4.569	-4.569	0.000	0.000	0.000	0.000
8	A	569	VAL	0	0.025	0.023	10.093	-3.384	-3.384	0.000	0.000	0.000	0.000
9	A	570	HIS	0	-0.024	-0.009	11.448	-2.918	-2.918	0.000	0.000	0.000	0.000
10	A	571	LEU	0	-0.020	-0.018	11.349	-2.367	-2.367	0.000	0.000	0.000	0.000
11	A	572	ASN	0	0.047	0.038	13.733	-2.751	-2.751	0.000	0.000	0.000	0.000
12	A	573	ARG	1	0.873	0.932	16.312	-19.719	-19.719	0.000	0.000	0.000	0.000
13	A	574	LYS	1	0.938	0.966	18.121	-14.521	-14.521	0.000	0.000	0.000	0.000
14	A	575	VAL	0	0.054	0.050	19.910	-0.799	-0.799	0.000	0.000	0.000	0.000
15	A	576	PHE	0	-0.044	-0.029	14.608	-0.446	-0.446	0.000	0.000	0.000	0.000
16	A	577	LYS	1	0.927	0.959	16.027	-19.093	-19.093	0.000	0.000	0.000	0.000
17	A	578	GLU	-1	-0.874	-0.917	21.669	12.275	12.275	0.000	0.000	0.000	0.000
18	A	579	HIS	0	0.068	0.037	24.056	-0.310	-0.310	0.000	0.000	0.000	0.000
19	A	580	PRO	0	0.043	0.022	25.177	0.426	0.426	0.000	0.000	0.000	0.000
20	A	581	ALA	0	-0.017	-0.014	25.963	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	582	PHE	0	0.004	-0.020	20.398	0.359	0.359	0.000	0.000	0.000	0.000
22	A	583	ARG	1	0.952	0.993	22.388	-10.701	-10.701	0.000	0.000	0.000	0.000
23	A	584	LEU	0	-0.035	-0.026	24.256	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	585	ALA	0	-0.038	-0.004	19.080	0.122	0.122	0.000	0.000	0.000	0.000
25	A	586	SER	0	0.042	0.026	18.094	0.457	0.457	0.000	0.000	0.000	0.000
26	A	587	ASP	-1	-0.847	-0.937	13.585	20.334	20.334	0.000	0.000	0.000	0.000
27	A	588	GLY	0	-0.049	-0.027	12.659	1.732	1.732	0.000	0.000	0.000	0.000
28	A	589	CYS	0	-0.059	-0.013	13.450	0.727	0.727	0.000	0.000	0.000	0.000
29	A	590	LEU	0	0.049	0.014	14.985	0.212	0.212	0.000	0.000	0.000	0.000
30	A	591	ARG	1	0.895	0.922	8.200	-29.401	-29.401	0.000	0.000	0.000	0.000
31	A	592	ALA	0	-0.051	-0.018	11.133	1.382	1.382	0.000	0.000	0.000	0.000
32	A	593	LEU	0	0.016	0.006	12.880	-0.350	-0.350	0.000	0.000	0.000	0.000
33	A	594	ALA	0	-0.016	-0.011	11.436	-0.456	-0.456	0.000	0.000	0.000	0.000
34	A	595	MET	0	-0.089	-0.041	7.604	3.038	3.038	0.000	0.000	0.000	0.000
35	A	596	GLU	-1	-0.882	-0.935	11.354	19.992	19.992	0.000	0.000	0.000	0.000
36	A	597	PHE	0	-0.079	-0.037	15.025	-1.415	-1.415	0.000	0.000	0.000	0.000
37	A	598	GLN	0	-0.033	-0.005	15.409	0.843	0.843	0.000	0.000	0.000	0.000
38	A	599	THR	0	-0.010	-0.006	17.383	-0.425	-0.425	0.000	0.000	0.000	0.000
39	A	600	VAL	0	-0.003	-0.004	19.124	0.139	0.139	0.000	0.000	0.000	0.000
40	A	601	HIS	0	-0.061	-0.049	20.372	0.465	0.465	0.000	0.000	0.000	0.000
41	A	602	CYS	0	-0.026	0.001	24.463	-0.173	-0.173	0.000	0.000	0.000	0.000
42	A	603	ALA	0	0.011	-0.014	28.236	0.059	0.059	0.000	0.000	0.000	0.000
43	A	604	PRO	0	-0.007	-0.011	31.196	-0.080	-0.080	0.000	0.000	0.000	0.000
44	A	605	GLY	0	-0.026	-0.014	34.570	-0.101	-0.101	0.000	0.000	0.000	0.000
45	A	606	ASP	-1	-0.831	-0.901	30.382	10.466	10.466	0.000	0.000	0.000	0.000
46	A	607	LEU	0	-0.066	-0.047	33.423	-0.065	-0.065	0.000	0.000	0.000	0.000
47	A	608	ILE	0	-0.052	-0.023	28.569	0.243	0.243	0.000	0.000	0.000	0.000
48	A	609	TYR	0	0.009	-0.009	28.196	0.157	0.157	0.000	0.000	0.000	0.000
49	A	610	HIS	1	0.838	0.901	33.039	-9.859	-9.859	0.000	0.000	0.000	0.000
50	A	611	ALA	0	0.047	0.018	36.602	0.124	0.124	0.000	0.000	0.000	0.000
51	A	612	GLY	0	-0.020	-0.016	39.001	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	613	GLU	-1	-0.843	-0.893	32.627	10.012	10.012	0.000	0.000	0.000	0.000
53	A	614	SER	0	0.012	0.002	31.269	-0.141	-0.141	0.000	0.000	0.000	0.000
54	A	615	VAL	0	0.016	0.013	31.037	0.343	0.343	0.000	0.000	0.000	0.000
55	A	616	ASP	-1	-0.858	-0.927	26.368	12.371	12.371	0.000	0.000	0.000	0.000
56	A	617	SER	0	0.012	0.008	24.602	0.560	0.560	0.000	0.000	0.000	0.000
57	A	618	LEU	0	-0.073	-0.010	24.208	-0.514	-0.514	0.000	0.000	0.000	0.000
58	A	619	CYS	0	-0.020	-0.011	24.253	0.810	0.810	0.000	0.000	0.000	0.000
59	A	620	PHE	0	0.056	0.008	23.361	-0.463	-0.463	0.000	0.000	0.000	0.000
60	A	621	VAL	0	0.053	0.040	24.694	0.534	0.534	0.000	0.000	0.000	0.000
61	A	622	VAL	0	-0.053	-0.034	22.060	-0.090	-0.090	0.000	0.000	0.000	0.000
62	A	623	SER	0	-0.083	-0.041	25.302	-0.360	-0.360	0.000	0.000	0.000	0.000
63	A	624	GLY	0	0.055	0.023	27.384	0.052	0.052	0.000	0.000	0.000	0.000
64	A	625	SER	0	-0.037	-0.023	30.739	-0.120	-0.120	0.000	0.000	0.000	0.000
65	A	626	LEU	0	0.014	-0.002	30.168	0.105	0.105	0.000	0.000	0.000	0.000
66	A	627	GLU	-1	-0.769	-0.857	34.489	8.022	8.022	0.000	0.000	0.000	0.000
67	A	628	VAL	0	-0.023	-0.020	35.957	0.193	0.193	0.000	0.000	0.000	0.000
68	A	629	ILE	0	-0.005	0.000	38.354	-0.224	-0.224	0.000	0.000	0.000	0.000
69	A	630	GLN	0	-0.009	0.006	41.081	0.306	0.306	0.000	0.000	0.000	0.000
70	A	631	ASP	-1	-0.830	-0.911	43.412	6.977	6.977	0.000	0.000	0.000	0.000
71	A	632	ASP	-1	-0.960	-0.973	45.179	7.035	7.035	0.000	0.000	0.000	0.000
72	A	633	GLU	-1	-0.883	-0.940	45.751	6.718	6.718	0.000	0.000	0.000	0.000
73	A	634	VAL	0	-0.043	-0.024	41.698	0.221	0.221	0.000	0.000	0.000	0.000
74	A	635	VAL	0	-0.037	-0.023	40.963	-0.113	-0.113	0.000	0.000	0.000	0.000
75	A	636	ALA	0	-0.026	-0.021	38.828	0.014	0.014	0.000	0.000	0.000	0.000
76	A	637	ILE	0	-0.018	-0.006	37.185	0.042	0.042	0.000	0.000	0.000	0.000
77	A	638	LEU	0	-0.035	0.002	32.461	0.033	0.033	0.000	0.000	0.000	0.000
78	A	639	GLY	0	0.028	-0.005	32.361	-0.057	-0.057	0.000	0.000	0.000	0.000
79	A	640	LYS	1	0.813	0.895	26.834	-11.492	-11.492	0.000	0.000	0.000	0.000
80	A	641	GLY	0	-0.034	-0.024	27.884	-0.246	-0.246	0.000	0.000	0.000	0.000
81	A	642	ASP	-1	-0.788	-0.857	28.890	9.781	9.781	0.000	0.000	0.000	0.000
82	A	643	VAL	0	-0.051	-0.043	27.143	0.516	0.516	0.000	0.000	0.000	0.000
83	A	644	PHE	0	0.029	0.019	29.064	-0.452	-0.452	0.000	0.000	0.000	0.000
84	A	645	GLY	0	0.059	0.027	29.124	0.551	0.551	0.000	0.000	0.000	0.000
85	A	646	ASP	-1	-0.737	-0.857	30.128	9.105	9.105	0.000	0.000	0.000	0.000
86	A	647	VAL	0	-0.063	-0.028	30.115	0.404	0.404	0.000	0.000	0.000	0.000
87	A	648	PHE	0	0.050	0.010	26.591	-0.096	-0.096	0.000	0.000	0.000	0.000
88	A	649	TRP	0	0.008	-0.006	27.316	0.056	0.056	0.000	0.000	0.000	0.000
89	A	650	LYS	1	0.856	0.922	29.607	-9.731	-9.731	0.000	0.000	0.000	0.000
90	A	651	GLU	-1	-0.870	-0.901	32.479	8.455	8.455	0.000	0.000	0.000	0.000
91	A	652	ALA	0	-0.029	-0.004	32.552	0.275	0.275	0.000	0.000	0.000	0.000
92	A	653	THR	0	-0.002	-0.002	33.314	0.130	0.130	0.000	0.000	0.000	0.000
93	A	654	LEU	0	-0.022	-0.003	30.598	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	655	ALA	0	0.037	0.012	33.398	-0.284	-0.284	0.000	0.000	0.000	0.000
95	A	656	GLN	0	-0.040	-0.026	34.990	0.109	0.109	0.000	0.000	0.000	0.000
96	A	657	SER	0	-0.008	0.001	35.200	-0.097	-0.097	0.000	0.000	0.000	0.000
97	A	658	CYS	0	-0.027	-0.012	37.101	-0.263	-0.263	0.000	0.000	0.000	0.000
98	A	659	ALA	0	-0.017	-0.010	38.361	-0.214	-0.214	0.000	0.000	0.000	0.000
99	A	660	ASN	0	-0.015	-0.014	37.267	0.370	0.370	0.000	0.000	0.000	0.000
100	A	661	VAL	0	0.013	0.017	32.430	-0.109	-0.109	0.000	0.000	0.000	0.000
101	A	662	ARG	1	0.845	0.908	34.165	-7.996	-7.996	0.000	0.000	0.000	0.000
102	A	663	ALA	0	0.015	0.013	31.678	-0.062	-0.062	0.000	0.000	0.000	0.000
103	A	664	LEU	0	-0.014	0.004	33.663	-0.232	-0.232	0.000	0.000	0.000	0.000
104	A	665	THR	0	-0.008	-0.022	31.942	-0.220	-0.220	0.000	0.000	0.000	0.000
105	A	666	TYR	0	0.018	0.005	28.928	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	667	CYS	0	-0.068	-0.011	28.196	-0.194	-0.194	0.000	0.000	0.000	0.000
107	A	668	ASP	-1	-0.822	-0.893	22.605	13.927	13.927	0.000	0.000	0.000	0.000
108	A	669	LEU	0	0.005	0.000	23.835	-0.297	-0.297	0.000	0.000	0.000	0.000
109	A	670	HIS	0	-0.051	-0.027	17.616	0.270	0.270	0.000	0.000	0.000	0.000
110	A	671	VAL	0	0.019	-0.005	20.656	-0.591	-0.591	0.000	0.000	0.000	0.000
111	A	672	ILE	0	0.012	0.020	18.107	0.941	0.941	0.000	0.000	0.000	0.000
112	A	673	LYS	1	0.885	0.928	20.612	-14.142	-14.142	0.000	0.000	0.000	0.000
113	A	674	ARG	1	0.859	0.916	22.190	-11.378	-11.378	0.000	0.000	0.000	0.000
114	A	675	ASP	-1	-0.847	-0.916	22.375	12.852	12.852	0.000	0.000	0.000	0.000
115	A	676	ALA	0	0.031	0.016	17.879	0.131	0.131	0.000	0.000	0.000	0.000
116	A	677	LEU	0	-0.010	-0.005	19.241	0.475	0.475	0.000	0.000	0.000	0.000
117	A	678	GLN	0	0.021	0.001	21.293	-0.058	-0.058	0.000	0.000	0.000	0.000
118	A	679	LYS	1	0.932	0.979	14.772	-19.693	-19.693	0.000	0.000	0.000	0.000
119	A	680	VAL	0	-0.028	-0.020	16.706	0.140	0.140	0.000	0.000	0.000	0.000
120	A	681	LEU	0	-0.050	-0.024	19.351	-0.176	-0.176	0.000	0.000	0.000	0.000
121	A	682	GLU	-1	-0.898	-0.958	22.958	12.250	12.250	0.000	0.000	0.000	0.000
122	A	683	PHE	0	-0.032	0.002	18.487	-0.150	-0.150	0.000	0.000	0.000	0.000
123	A	684	TYR	0	0.016	0.010	15.019	-0.402	-0.402	0.000	0.000	0.000	0.000
124	A	685	THR	0	0.035	0.004	21.843	-0.365	-0.365	0.000	0.000	0.000	0.000
125	A	686	ALA	0	-0.007	-0.005	25.040	-0.400	-0.400	0.000	0.000	0.000	0.000
126	A	687	PHE	0	0.021	-0.001	21.317	-0.334	-0.334	0.000	0.000	0.000	0.000
127	A	688	SER	0	0.085	0.038	24.527	-0.229	-0.229	0.000	0.000	0.000	0.000
128	A	689	HIS	0	0.017	0.016	25.907	-0.377	-0.377	0.000	0.000	0.000	0.000
129	A	690	SER	0	-0.056	-0.023	27.050	-0.498	-0.498	0.000	0.000	0.000	0.000
130	A	691	PHE	0	0.038	0.029	23.640	-0.232	-0.232	0.000	0.000	0.000	0.000
131	A	692	SER	0	-0.010	-0.003	27.129	-0.351	-0.351	0.000	0.000	0.000	0.000
132	A	693	ARG	1	0.850	0.897	30.136	-10.214	-10.214	0.000	0.000	0.000	0.000
133	A	694	ASN	0	-0.048	-0.022	29.169	-0.338	-0.338	0.000	0.000	0.000	0.000
134	A	695	LEU	0	-0.024	0.009	26.295	0.008	0.008	0.000	0.000	0.000	0.000
135	A	696	ILE	0	-0.039	-0.013	30.064	-0.200	-0.200	0.000	0.000	0.000	0.000
136	A	697	LEU	0	-0.057	-0.026	30.293	0.106	0.106	0.000	0.000	0.000	0.000
137	A	698	THR	0	-0.013	-0.017	32.586	-0.166	-0.166	0.000	0.000	0.000	0.000
138	A	699	TYR	0	0.037	0.009	33.839	-0.324	-0.324	0.000	0.000	0.000	0.000
139	A	700	ASN	0	-0.027	-0.028	34.028	0.361	0.361	0.000	0.000	0.000	0.000
140	A	701	LEU	0	0.019	-0.004	32.409	-0.253	-0.253	0.000	0.000	0.000	0.000
141	A	702	ARG	1	0.814	0.896	34.641	-9.230	-9.230	0.000	0.000	0.000	0.000
142	A	703	LYN	0	-0.048	-0.008	37.836	-0.168	-0.168	0.000	0.000	0.000	0.000
143	A	704	ARG	1	0.868	0.913	40.754	-7.188	-7.188	0.000	0.000	0.000	0.000
144	A	705	ILE	0	-0.013	-0.005	42.499	-0.119	-0.119	0.000	0.000	0.000	0.000
145	A	706	VAL	0	-0.018	-0.009	45.610	-0.080	-0.080	0.000	0.000	0.000	0.000
146	A	707	PHE	0	0.000	0.008	46.512	-0.094	-0.094	0.000	0.000	0.000	0.000

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