FMO DATABASE

FMODB ID: QYY3Y

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	OptHSide
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	-916531.124615
FMO2-HF: Nuclear repulsion	872297.08122
FMO2-HF: Total energy	-44234.043395
FMO2-MP2: Total energy	-44364.396233

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.
-3.295	-0.102	5.365	-3.99	-4.571	-0.02

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 : -0.039 / q_NPA : -0.046

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	560	VAL	0	0.036	0.019	3.790	0.148	1.779	-0.029	-0.698	-0.904	0.000
4	A	561	SER	0	-0.080	-0.049	6.918	0.369	0.369	0.000	0.000	0.000	0.000
5	A	562	GLY	0	0.015	0.005	8.491	0.132	0.132	0.000	0.000	0.000	0.000
6	A	563	VAL	0	-0.010	0.001	11.522	-0.083	-0.083	0.000	0.000	0.000	0.000
7	A	564	ALA	0	-0.008	0.009	14.197	0.045	0.045	0.000	0.000	0.000	0.000
8	A	565	SER	0	-0.007	-0.028	17.080	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	566	LEU	0	-0.031	-0.003	20.319	0.020	0.020	0.000	0.000	0.000	0.000
10	A	567	GLY	0	-0.015	-0.013	23.869	0.006	0.006	0.000	0.000	0.000	0.000
11	A	568	TYR	0	-0.086	-0.057	22.253	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	569	GLU	-1	-0.845	-0.902	22.701	-0.164	-0.164	0.000	0.000	0.000	0.000
13	A	570	GLU	-1	-0.862	-0.954	16.471	-0.336	-0.336	0.000	0.000	0.000	0.000
14	A	571	GLN	0	0.024	0.006	17.651	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	572	GLU	-1	-0.913	-0.964	18.473	-0.212	-0.212	0.000	0.000	0.000	0.000
16	A	573	VAL	0	0.008	0.005	15.861	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	574	LEU	0	0.011	0.010	11.591	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	575	LYS	1	0.881	0.943	14.771	0.220	0.220	0.000	0.000	0.000	0.000
19	A	576	MET	0	-0.007	-0.008	17.354	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	577	ALA	0	0.010	0.009	13.033	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	578	ALA	0	0.016	-0.007	12.699	-0.037	-0.037	0.000	0.000	0.000	0.000
22	A	579	ALA	0	-0.044	-0.025	13.647	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	580	VAL	0	-0.013	0.002	15.646	0.016	0.016	0.000	0.000	0.000	0.000
24	A	581	GLU	-1	-0.914	-0.970	10.376	-0.621	-0.621	0.000	0.000	0.000	0.000
25	A	582	LYS	1	0.903	0.969	12.270	0.449	0.449	0.000	0.000	0.000	0.000
26	A	583	THR	0	-0.023	-0.035	13.684	-0.041	-0.041	0.000	0.000	0.000	0.000
27	A	584	ALA	0	0.013	0.032	11.399	0.045	0.045	0.000	0.000	0.000	0.000
28	A	585	THR	0	-0.025	-0.024	11.059	-0.107	-0.107	0.000	0.000	0.000	0.000
29	A	586	HIS	0	0.020	0.016	8.379	-0.075	-0.075	0.000	0.000	0.000	0.000
30	A	587	PRO	0	0.029	-0.001	3.038	-0.633	-0.151	0.116	-0.124	-0.475	0.000
31	A	588	ILE	0	0.033	0.018	3.606	-1.606	-1.027	0.017	-0.252	-0.345	-0.001
32	A	589	ALA	0	0.065	0.043	4.506	-0.277	-0.286	-0.001	-0.005	0.015	0.000
33	A	590	LYS	1	0.880	0.918	5.892	0.927	0.927	0.000	0.000	0.000	0.000
34	A	591	ALA	0	-0.002	0.024	3.025	-0.351	-0.002	0.039	-0.125	-0.263	-0.001
35	A	592	ILE	0	0.033	0.016	5.182	0.360	0.412	-0.001	-0.004	-0.048	0.000
36	A	593	VAL	0	-0.028	-0.013	8.331	0.207	0.207	0.000	0.000	0.000	0.000
37	A	594	ASN	0	0.017	-0.008	6.582	0.416	0.416	0.000	0.000	0.000	0.000
38	A	595	GLU	-1	-0.900	-0.923	8.792	-0.933	-0.933	0.000	0.000	0.000	0.000
39	A	596	ALA	0	0.024	-0.003	10.426	0.212	0.212	0.000	0.000	0.000	0.000
40	A	597	GLU	-1	-1.012	-0.996	12.620	-0.654	-0.654	0.000	0.000	0.000	0.000
41	A	598	SER	0	-0.032	-0.034	11.021	0.101	0.101	0.000	0.000	0.000	0.000
42	A	599	LEU	0	-0.051	-0.020	13.493	0.118	0.118	0.000	0.000	0.000	0.000
43	A	600	ASN	0	-0.111	-0.048	16.109	0.072	0.072	0.000	0.000	0.000	0.000
44	A	601	LEU	0	-0.006	0.004	15.772	0.060	0.060	0.000	0.000	0.000	0.000
45	A	602	LYS	1	0.913	0.952	18.051	0.253	0.253	0.000	0.000	0.000	0.000
46	A	603	THR	0	0.019	0.020	16.054	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	604	PRO	0	-0.026	-0.011	19.333	0.016	0.016	0.000	0.000	0.000	0.000
48	A	605	GLU	-1	-0.915	-0.960	21.133	-0.283	-0.283	0.000	0.000	0.000	0.000
49	A	606	THR	0	0.014	0.006	20.394	0.000	0.000	0.000	0.000	0.000	0.000
50	A	607	ARG	1	0.892	0.947	23.311	0.156	0.156	0.000	0.000	0.000	0.000
51	A	608	GLY	0	0.012	0.013	23.699	0.016	0.016	0.000	0.000	0.000	0.000
52	A	609	GLN	0	0.010	-0.003	18.620	0.010	0.010	0.000	0.000	0.000	0.000
53	A	610	LEU	0	-0.036	-0.003	21.095	0.015	0.015	0.000	0.000	0.000	0.000
54	A	611	THR	0	0.012	-0.005	16.221	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	612	GLU	-1	-0.796	-0.865	18.220	-0.104	-0.104	0.000	0.000	0.000	0.000
56	A	613	PRO	0	-0.005	-0.023	16.425	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	614	GLY	0	-0.013	-0.006	14.598	0.024	0.024	0.000	0.000	0.000	0.000
58	A	615	PHE	0	-0.053	-0.010	15.629	0.026	0.026	0.000	0.000	0.000	0.000
59	A	616	GLY	0	0.039	0.005	14.709	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	617	THR	0	-0.029	-0.006	14.382	0.035	0.035	0.000	0.000	0.000	0.000
61	A	618	LEU	0	0.002	0.005	16.984	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	619	ALA	0	0.028	0.001	19.970	0.002	0.002	0.000	0.000	0.000	0.000
63	A	620	GLU	-1	-0.926	-0.952	21.611	-0.143	-0.143	0.000	0.000	0.000	0.000
64	A	621	ILE	0	-0.033	-0.036	20.060	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	622	ASP	-1	-0.966	-0.989	24.129	-0.144	-0.144	0.000	0.000	0.000	0.000
66	A	623	GLY	0	0.013	0.023	27.486	0.009	0.009	0.000	0.000	0.000	0.000
67	A	624	ARG	1	0.883	0.939	26.752	0.125	0.125	0.000	0.000	0.000	0.000
68	A	625	PHE	0	0.007	0.022	24.332	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	626	VAL	0	0.012	0.005	18.827	0.009	0.009	0.000	0.000	0.000	0.000
70	A	627	ALA	0	-0.030	-0.013	19.001	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	628	VAL	0	0.010	0.004	12.658	0.001	0.001	0.000	0.000	0.000	0.000
72	A	629	GLY	0	0.063	0.018	13.575	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	630	SER	0	-0.009	0.006	14.537	0.003	0.003	0.000	0.000	0.000	0.000
74	A	631	LEU	0	0.043	0.025	15.701	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	632	GLU	-1	-0.919	-0.961	18.408	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	633	TRP	0	0.000	-0.008	17.997	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	634	VAL	0	-0.033	-0.016	17.089	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	635	SER	0	-0.005	0.003	20.272	0.003	0.003	0.000	0.000	0.000	0.000
79	A	636	ASP	-1	-0.945	-0.987	23.281	-0.052	-0.052	0.000	0.000	0.000	0.000
80	A	637	ARG	1	0.753	0.882	21.812	0.129	0.129	0.000	0.000	0.000	0.000
81	A	638	PHE	0	0.014	0.008	22.234	0.001	0.001	0.000	0.000	0.000	0.000
82	A	639	LEU	0	0.014	0.014	27.293	0.007	0.007	0.000	0.000	0.000	0.000
83	A	640	LYS	1	0.839	0.936	29.073	0.070	0.070	0.000	0.000	0.000	0.000
84	A	641	LYS	1	0.906	0.949	27.072	0.063	0.063	0.000	0.000	0.000	0.000
85	A	642	ASN	0	0.022	0.006	24.847	0.000	0.000	0.000	0.000	0.000	0.000
86	A	643	ASP	-1	-0.862	-0.927	27.994	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	644	SER	0	0.036	0.003	28.514	0.001	0.001	0.000	0.000	0.000	0.000
88	A	645	SER	0	-0.032	-0.020	28.372	0.005	0.005	0.000	0.000	0.000	0.000
89	A	646	ASP	-1	-0.866	-0.939	25.969	-0.049	-0.049	0.000	0.000	0.000	0.000
90	A	647	MET	0	0.009	0.008	22.894	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	648	VAL	0	0.023	0.015	23.375	0.006	0.006	0.000	0.000	0.000	0.000
92	A	649	LYS	1	0.928	0.979	23.922	0.013	0.013	0.000	0.000	0.000	0.000
93	A	650	LEU	0	0.021	0.013	18.243	0.004	0.004	0.000	0.000	0.000	0.000
94	A	651	GLU	-1	-0.783	-0.890	18.890	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	652	SER	0	-0.058	-0.032	19.853	0.022	0.022	0.000	0.000	0.000	0.000
96	A	653	LEU	0	-0.065	-0.032	18.752	0.014	0.014	0.000	0.000	0.000	0.000
97	A	654	LEU	0	-0.035	-0.016	13.836	0.010	0.010	0.000	0.000	0.000	0.000
98	A	655	ASP	-1	-0.940	-0.964	15.650	0.150	0.150	0.000	0.000	0.000	0.000
99	A	656	HIS	0	-0.181	-0.076	12.903	0.026	0.026	0.000	0.000	0.000	0.000
100	A	669	LYS	1	0.952	0.971	6.812	-0.600	-0.600	0.000	0.000	0.000	0.000
101	A	670	THR	0	-0.047	-0.018	6.970	-0.050	-0.050	0.000	0.000	0.000	0.000
102	A	671	VAL	0	0.036	0.023	8.538	-0.086	-0.086	0.000	0.000	0.000	0.000
103	A	672	VAL	0	-0.041	-0.010	8.725	0.018	0.018	0.000	0.000	0.000	0.000
104	A	673	TYR	0	-0.030	-0.052	11.720	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	674	VAL	0	0.048	0.011	14.840	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	675	GLY	0	0.014	0.009	17.180	0.032	0.032	0.000	0.000	0.000	0.000
107	A	676	ARG	1	0.920	0.949	20.818	0.137	0.137	0.000	0.000	0.000	0.000
108	A	677	GLU	-1	-0.869	-0.940	23.717	-0.097	-0.097	0.000	0.000	0.000	0.000
109	A	678	GLY	0	-0.053	-0.037	27.020	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	679	GLU	-1	-0.858	-0.898	26.182	-0.125	-0.125	0.000	0.000	0.000	0.000
111	A	680	GLY	0	0.007	0.018	25.442	0.009	0.009	0.000	0.000	0.000	0.000
112	A	681	ILE	0	-0.049	-0.040	19.780	-0.017	-0.017	0.000	0.000	0.000	0.000
113	A	682	ILE	0	0.008	0.004	20.045	0.013	0.013	0.000	0.000	0.000	0.000
114	A	683	GLY	0	0.029	-0.005	18.319	0.002	0.002	0.000	0.000	0.000	0.000
115	A	684	ALA	0	-0.047	-0.009	14.746	0.005	0.005	0.000	0.000	0.000	0.000
116	A	685	ILE	0	0.010	0.010	9.261	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	686	ALA	0	0.018	0.022	9.600	0.023	0.023	0.000	0.000	0.000	0.000
118	A	687	ILE	0	-0.003	-0.003	3.465	-0.575	-0.211	0.025	-0.098	-0.291	0.000
119	A	688	SER	0	0.018	0.003	2.186	0.189	-0.066	5.199	-2.684	-2.260	-0.018

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