FMO DATABASE

FMODB ID: R99J8

Calculation Name: 5LBK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LBK

Chain ID: A

ChEMBL ID:

UniProt ID: B9DFX7

Base Structure: X-ray

Registration Date: 2023-06-21

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-915927.825484
FMO2-HF: Nuclear repulsion	871694.378091
FMO2-HF: Total energy	-44233.447392
FMO2-MP2: Total energy	-44363.779209

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:558:PRO)

Summations of interaction energy for fragment #1(A:558:PRO)

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.
-3.78	-0.305	5.012	-3.936	-4.552	-0.018

Interaction energy analysis for fragmet #1(A:558:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.032

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

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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	560	VAL	0	0.048	0.019	3.790	0.275	2.070	-0.028	-0.803	-0.964	0.001
4	A	561	SER	0	-0.080	-0.051	6.905	0.326	0.326	0.000	0.000	0.000	0.000
5	A	562	GLY	0	0.016	0.010	8.498	0.165	0.165	0.000	0.000	0.000	0.000
6	A	563	VAL	0	-0.002	0.007	11.497	-0.080	-0.080	0.000	0.000	0.000	0.000
7	A	564	ALA	0	-0.009	0.008	14.172	0.049	0.049	0.000	0.000	0.000	0.000
8	A	565	SER	0	-0.022	-0.046	17.051	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	566	LEU	0	-0.007	0.004	20.284	0.021	0.021	0.000	0.000	0.000	0.000
10	A	567	GLY	0	-0.010	-0.008	23.832	0.005	0.005	0.000	0.000	0.000	0.000
11	A	568	TYR	0	-0.081	-0.070	22.198	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	569	GLU	-1	-0.860	-0.905	22.679	-0.210	-0.210	0.000	0.000	0.000	0.000
13	A	570	GLU	-1	-0.891	-0.954	16.541	-0.438	-0.438	0.000	0.000	0.000	0.000
14	A	571	GLN	0	0.013	-0.010	17.633	-0.066	-0.066	0.000	0.000	0.000	0.000
15	A	572	GLU	-1	-0.918	-0.969	18.464	-0.252	-0.252	0.000	0.000	0.000	0.000
16	A	573	VAL	0	0.016	0.011	15.733	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	574	LEU	0	0.018	0.012	11.444	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	575	LYS	1	0.914	0.959	14.765	0.283	0.283	0.000	0.000	0.000	0.000
19	A	576	MET	0	-0.009	-0.008	17.352	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	577	ALA	0	0.012	0.011	13.005	0.002	0.002	0.000	0.000	0.000	0.000
21	A	578	ALA	0	0.019	-0.007	12.703	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	579	ALA	0	-0.049	-0.026	13.649	0.001	0.001	0.000	0.000	0.000	0.000
23	A	580	VAL	0	-0.022	-0.003	15.616	0.023	0.023	0.000	0.000	0.000	0.000
24	A	581	GLU	-1	-0.914	-0.970	10.363	-0.620	-0.620	0.000	0.000	0.000	0.000
25	A	582	LYS	1	0.908	0.981	12.284	0.508	0.508	0.000	0.000	0.000	0.000
26	A	583	THR	0	-0.033	-0.037	13.709	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	584	ALA	0	0.028	0.039	11.334	0.056	0.056	0.000	0.000	0.000	0.000
28	A	585	THR	0	-0.026	-0.042	11.007	-0.099	-0.099	0.000	0.000	0.000	0.000
29	A	586	HIS	0	-0.003	0.002	8.280	-0.066	-0.066	0.000	0.000	0.000	0.000
30	A	587	PRO	0	0.023	-0.001	2.866	-0.660	-0.199	0.136	-0.129	-0.468	0.000
31	A	588	ILE	0	0.043	0.022	3.587	-1.668	-1.114	0.016	-0.233	-0.337	-0.001
32	A	589	ALA	0	0.069	0.047	4.493	-0.337	-0.347	-0.001	-0.005	0.016	0.000
33	A	590	LYS	1	0.895	0.942	5.663	0.912	0.912	0.000	0.000	0.000	0.000
34	A	591	ALA	0	-0.007	0.021	3.053	-0.395	-0.053	0.036	-0.116	-0.261	-0.001
35	A	592	ILE	0	0.038	0.021	5.198	0.319	0.372	-0.001	-0.004	-0.049	0.000
36	A	593	VAL	0	-0.032	-0.015	8.329	0.204	0.204	0.000	0.000	0.000	0.000
37	A	594	ASN	0	0.018	-0.010	5.769	0.517	0.517	0.000	0.000	0.000	0.000
38	A	595	GLU	-1	-0.899	-0.937	8.860	-1.126	-1.126	0.000	0.000	0.000	0.000
39	A	596	ALA	0	0.016	-0.004	10.437	0.236	0.236	0.000	0.000	0.000	0.000
40	A	597	GLU	-1	-1.009	-0.997	12.282	-0.808	-0.808	0.000	0.000	0.000	0.000
41	A	598	SER	0	-0.034	-0.022	11.082	0.110	0.110	0.000	0.000	0.000	0.000
42	A	599	LEU	0	-0.055	-0.015	13.467	0.131	0.131	0.000	0.000	0.000	0.000
43	A	600	ASN	0	-0.093	-0.040	16.032	0.062	0.062	0.000	0.000	0.000	0.000
44	A	601	LEU	0	-0.012	0.002	15.592	0.078	0.078	0.000	0.000	0.000	0.000
45	A	602	LYS	1	0.902	0.943	18.066	0.306	0.306	0.000	0.000	0.000	0.000
46	A	603	THR	0	0.009	0.004	16.003	0.001	0.001	0.000	0.000	0.000	0.000
47	A	604	PRO	0	-0.022	-0.007	19.343	0.019	0.019	0.000	0.000	0.000	0.000
48	A	605	GLU	-1	-0.909	-0.957	21.142	-0.304	-0.304	0.000	0.000	0.000	0.000
49	A	606	THR	0	0.015	0.005	20.642	0.000	0.000	0.000	0.000	0.000	0.000
50	A	607	ARG	1	0.897	0.951	23.320	0.164	0.164	0.000	0.000	0.000	0.000
51	A	608	GLY	0	-0.003	0.002	23.692	0.017	0.017	0.000	0.000	0.000	0.000
52	A	609	GLN	0	0.022	0.004	18.790	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	610	LEU	0	-0.039	-0.007	21.079	0.017	0.017	0.000	0.000	0.000	0.000
54	A	611	THR	0	0.007	-0.005	16.292	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	612	GLU	-1	-0.863	-0.922	18.216	-0.072	-0.072	0.000	0.000	0.000	0.000
56	A	613	PRO	0	-0.015	-0.027	16.418	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	614	GLY	0	-0.015	-0.008	14.736	0.024	0.024	0.000	0.000	0.000	0.000
58	A	615	PHE	0	-0.047	-0.004	15.771	0.029	0.029	0.000	0.000	0.000	0.000
59	A	616	GLY	0	0.035	0.001	14.688	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	617	THR	0	-0.027	-0.004	14.403	0.040	0.040	0.000	0.000	0.000	0.000
61	A	618	LEU	0	-0.004	0.005	16.972	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	619	ALA	0	0.032	0.004	19.958	0.004	0.004	0.000	0.000	0.000	0.000
63	A	620	GLU	-1	-0.939	-0.960	21.606	-0.148	-0.148	0.000	0.000	0.000	0.000
64	A	621	ILE	0	-0.028	-0.032	20.180	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	622	ASP	-1	-0.975	-0.994	24.124	-0.162	-0.162	0.000	0.000	0.000	0.000
66	A	623	GLY	0	0.013	0.026	27.483	0.010	0.010	0.000	0.000	0.000	0.000
67	A	624	ARG	1	0.906	0.949	26.729	0.137	0.137	0.000	0.000	0.000	0.000
68	A	625	PHE	0	0.018	0.028	24.278	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	626	VAL	0	0.011	0.004	18.769	0.009	0.009	0.000	0.000	0.000	0.000
70	A	627	ALA	0	-0.029	-0.015	18.975	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	628	VAL	0	0.020	0.008	12.581	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	629	GLY	0	0.053	0.014	13.544	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	630	SER	0	-0.005	0.008	14.506	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	631	LEU	0	0.036	0.023	15.804	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	632	GLU	-1	-0.926	-0.968	18.532	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	633	TRP	0	0.012	0.003	18.038	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	634	VAL	0	-0.030	-0.015	17.088	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	635	SER	0	-0.013	-0.007	20.238	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	636	ASP	-1	-0.952	-0.986	23.243	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	637	ARG	1	0.824	0.934	21.830	0.108	0.108	0.000	0.000	0.000	0.000
81	A	638	PHE	0	0.021	0.017	22.223	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	639	LEU	0	0.000	0.002	27.263	0.008	0.008	0.000	0.000	0.000	0.000
83	A	640	LYS	1	0.908	0.963	29.118	0.076	0.076	0.000	0.000	0.000	0.000
84	A	641	LYS	1	0.924	0.964	27.682	0.053	0.053	0.000	0.000	0.000	0.000
85	A	642	ASN	0	0.017	0.002	24.849	0.000	0.000	0.000	0.000	0.000	0.000
86	A	643	ASP	-1	-0.860	-0.913	27.951	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	644	SER	0	-0.008	-0.023	28.465	0.001	0.001	0.000	0.000	0.000	0.000
88	A	645	SER	0	-0.001	-0.010	28.328	0.005	0.005	0.000	0.000	0.000	0.000
89	A	646	ASP	-1	-0.877	-0.938	25.922	-0.061	-0.061	0.000	0.000	0.000	0.000
90	A	647	MET	0	-0.005	-0.002	23.145	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	648	VAL	0	0.015	0.013	23.333	0.008	0.008	0.000	0.000	0.000	0.000
92	A	649	LYS	1	0.922	0.962	23.890	0.025	0.025	0.000	0.000	0.000	0.000
93	A	650	LEU	0	0.023	0.012	18.593	0.002	0.002	0.000	0.000	0.000	0.000
94	A	651	GLU	-1	-0.789	-0.881	18.904	0.012	0.012	0.000	0.000	0.000	0.000
95	A	652	SER	0	-0.057	-0.016	19.825	0.024	0.024	0.000	0.000	0.000	0.000
96	A	653	LEU	0	-0.065	-0.033	18.675	0.012	0.012	0.000	0.000	0.000	0.000
97	A	654	LEU	0	-0.036	-0.018	13.865	0.003	0.003	0.000	0.000	0.000	0.000
98	A	655	ASP	-1	-0.962	-0.968	15.633	0.166	0.166	0.000	0.000	0.000	0.000
99	A	656	HIS	0	-0.145	-0.061	12.637	0.018	0.018	0.000	0.000	0.000	0.000
100	A	669	LYS	1	0.936	0.945	6.801	-0.608	-0.608	0.000	0.000	0.000	0.000
101	A	670	THR	0	-0.029	0.005	6.948	-0.070	-0.070	0.000	0.000	0.000	0.000
102	A	671	VAL	0	0.042	0.029	8.576	-0.121	-0.121	0.000	0.000	0.000	0.000
103	A	672	VAL	0	-0.035	-0.005	8.715	0.035	0.035	0.000	0.000	0.000	0.000
104	A	673	TYR	0	-0.041	-0.067	11.678	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	674	VAL	0	0.047	0.009	14.852	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	675	GLY	0	0.019	0.012	17.149	0.031	0.031	0.000	0.000	0.000	0.000
107	A	676	ARG	1	0.931	0.965	20.787	0.153	0.153	0.000	0.000	0.000	0.000
108	A	677	GLU	-1	-0.886	-0.953	23.692	-0.095	-0.095	0.000	0.000	0.000	0.000
109	A	678	GLY	0	-0.070	-0.048	26.995	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	679	GLU	-1	-0.877	-0.906	26.085	-0.143	-0.143	0.000	0.000	0.000	0.000
111	A	680	GLY	0	0.013	0.022	25.409	0.009	0.009	0.000	0.000	0.000	0.000
112	A	681	ILE	0	-0.040	-0.041	19.764	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	682	ILE	0	-0.004	0.007	19.984	0.011	0.011	0.000	0.000	0.000	0.000
114	A	683	GLY	0	0.026	-0.006	18.283	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	684	ALA	0	-0.044	-0.010	14.653	0.013	0.013	0.000	0.000	0.000	0.000
116	A	685	ILE	0	0.013	0.013	9.221	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	686	ALA	0	0.025	0.025	9.565	0.051	0.051	0.000	0.000	0.000	0.000
118	A	687	ILE	0	-0.005	-0.002	3.467	-0.610	-0.260	0.023	-0.098	-0.276	0.000
119	A	688	SER	0	-0.001	-0.007	2.214	0.048	-0.022	4.831	-2.548	-2.213	-0.017

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Interactive mode: IFIE and PIEDA for fragment #1(A:558:PRO)