FMO DATABASE

FMODB ID: K9963

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	OptAll
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	-919993.079013
FMO2-HF: Nuclear repulsion	875758.691513
FMO2-HF: Total energy	-44234.3875
FMO2-MP2: Total energy	-44364.717155

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.
-5.54	-0.4	2.374	-2.948	-4.563	-0.015

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 : -0.055 / q_NPA : -0.050

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	0.035	0.022	3.870	-0.082	1.504	-0.020	-0.759	-0.806	0.000
4	A	561	SER	0	-0.088	-0.050	6.970	0.362	0.362	0.000	0.000	0.000	0.000
5	A	562	GLY	0	0.020	0.010	8.631	0.117	0.117	0.000	0.000	0.000	0.000
6	A	563	VAL	0	-0.019	-0.004	11.625	-0.075	-0.075	0.000	0.000	0.000	0.000
7	A	564	ALA	0	0.005	0.013	14.366	0.043	0.043	0.000	0.000	0.000	0.000
8	A	565	SER	0	-0.022	-0.039	17.503	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	566	LEU	0	-0.024	-0.010	20.702	0.017	0.017	0.000	0.000	0.000	0.000
10	A	567	GLY	0	-0.036	-0.020	24.374	0.011	0.011	0.000	0.000	0.000	0.000
11	A	568	TYR	0	-0.053	-0.043	22.615	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	569	GLU	-1	-0.857	-0.911	22.637	-0.140	-0.140	0.000	0.000	0.000	0.000
13	A	570	GLU	-1	-0.868	-0.963	16.356	-0.294	-0.294	0.000	0.000	0.000	0.000
14	A	571	GLN	0	0.028	0.016	17.724	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	572	GLU	-1	-0.908	-0.950	18.827	-0.177	-0.177	0.000	0.000	0.000	0.000
16	A	573	VAL	0	0.025	0.009	16.106	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	574	LEU	0	0.008	0.010	11.607	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	575	LYS	1	0.873	0.935	14.737	0.193	0.193	0.000	0.000	0.000	0.000
19	A	576	MET	0	-0.008	-0.012	17.239	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	577	ALA	0	0.025	0.012	13.100	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	578	ALA	0	-0.005	-0.009	12.568	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	579	ALA	0	-0.017	-0.012	13.532	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	580	VAL	0	-0.034	-0.012	15.916	0.014	0.014	0.000	0.000	0.000	0.000
24	A	581	GLU	-1	-0.847	-0.932	10.801	-0.498	-0.498	0.000	0.000	0.000	0.000
25	A	582	LYS	1	0.880	0.953	12.227	0.421	0.421	0.000	0.000	0.000	0.000
26	A	583	THR	0	-0.031	-0.035	13.405	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	584	ALA	0	0.020	0.036	11.268	0.018	0.018	0.000	0.000	0.000	0.000
28	A	585	THR	0	-0.019	-0.021	10.400	-0.113	-0.113	0.000	0.000	0.000	0.000
29	A	586	HIS	0	0.035	0.020	8.036	-0.110	-0.110	0.000	0.000	0.000	0.000
30	A	587	PRO	0	0.024	-0.002	2.698	-0.826	-0.257	0.701	-0.269	-1.001	0.001
31	A	588	ILE	0	0.034	0.025	3.084	-2.446	-1.213	0.173	-0.615	-0.791	-0.005
32	A	589	ALA	0	0.063	0.041	4.605	-0.232	-0.239	-0.001	-0.007	0.015	0.000
33	A	590	LYS	1	0.892	0.927	5.382	0.889	0.889	0.000	0.000	0.000	0.000
34	A	591	ALA	0	-0.009	0.011	2.676	-0.497	-0.031	0.170	-0.182	-0.453	0.000
35	A	592	ILE	0	0.031	0.012	4.690	0.395	0.464	-0.001	-0.013	-0.054	0.000
36	A	593	VAL	0	-0.037	-0.018	8.224	0.181	0.181	0.000	0.000	0.000	0.000
37	A	594	ASN	0	0.019	-0.003	7.069	0.318	0.318	0.000	0.000	0.000	0.000
38	A	595	GLU	-1	-0.894	-0.927	8.567	-0.795	-0.795	0.000	0.000	0.000	0.000
39	A	596	ALA	0	0.016	-0.001	10.110	0.190	0.190	0.000	0.000	0.000	0.000
40	A	597	GLU	-1	-1.004	-0.992	12.240	-0.576	-0.576	0.000	0.000	0.000	0.000
41	A	598	SER	0	-0.019	-0.023	11.080	0.102	0.102	0.000	0.000	0.000	0.000
42	A	599	LEU	0	-0.045	-0.023	13.679	0.106	0.106	0.000	0.000	0.000	0.000
43	A	600	ASN	0	-0.101	-0.049	15.967	0.073	0.073	0.000	0.000	0.000	0.000
44	A	601	LEU	0	-0.024	-0.001	15.690	0.050	0.050	0.000	0.000	0.000	0.000
45	A	602	LYS	1	0.855	0.918	17.612	0.220	0.220	0.000	0.000	0.000	0.000
46	A	603	THR	0	0.007	0.021	15.709	0.001	0.001	0.000	0.000	0.000	0.000
47	A	604	PRO	0	-0.019	-0.007	18.979	0.015	0.015	0.000	0.000	0.000	0.000
48	A	605	GLU	-1	-0.861	-0.927	20.769	-0.267	-0.267	0.000	0.000	0.000	0.000
49	A	606	THR	0	0.003	0.001	20.241	0.015	0.015	0.000	0.000	0.000	0.000
50	A	607	ARG	1	0.902	0.939	23.139	0.144	0.144	0.000	0.000	0.000	0.000
51	A	608	GLY	0	0.032	0.018	23.215	0.017	0.017	0.000	0.000	0.000	0.000
52	A	609	GLN	0	-0.010	-0.005	18.134	0.014	0.014	0.000	0.000	0.000	0.000
53	A	610	LEU	0	-0.025	-0.005	20.726	0.013	0.013	0.000	0.000	0.000	0.000
54	A	611	THR	0	0.003	-0.001	15.540	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	612	GLU	-1	-0.791	-0.862	17.838	-0.096	-0.096	0.000	0.000	0.000	0.000
56	A	613	PRO	0	-0.023	-0.035	15.805	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	614	GLY	0	-0.005	0.004	14.393	0.022	0.022	0.000	0.000	0.000	0.000
58	A	615	PHE	0	-0.058	-0.016	15.139	0.019	0.019	0.000	0.000	0.000	0.000
59	A	616	GLY	0	0.039	0.008	14.217	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	617	THR	0	-0.050	-0.022	13.945	0.031	0.031	0.000	0.000	0.000	0.000
61	A	618	LEU	0	0.000	0.005	16.691	0.000	0.000	0.000	0.000	0.000	0.000
62	A	619	ALA	0	0.028	0.002	19.820	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	620	GLU	-1	-0.927	-0.951	21.487	-0.125	-0.125	0.000	0.000	0.000	0.000
64	A	621	ILE	0	-0.056	-0.044	20.000	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	622	ASP	-1	-0.956	-0.985	24.025	-0.127	-0.127	0.000	0.000	0.000	0.000
66	A	623	GLY	0	0.030	0.025	27.433	0.007	0.007	0.000	0.000	0.000	0.000
67	A	624	ARG	1	0.870	0.930	26.959	0.110	0.110	0.000	0.000	0.000	0.000
68	A	625	PHE	0	-0.001	0.006	24.301	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	626	VAL	0	-0.006	-0.009	19.157	0.007	0.007	0.000	0.000	0.000	0.000
70	A	627	ALA	0	-0.022	-0.004	19.003	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	628	VAL	0	0.011	0.009	12.677	0.000	0.000	0.000	0.000	0.000	0.000
72	A	629	GLY	0	0.058	0.017	13.407	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	630	SER	0	0.003	0.010	14.239	0.001	0.001	0.000	0.000	0.000	0.000
74	A	631	LEU	0	0.030	0.015	15.585	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	632	GLU	-1	-0.924	-0.963	18.377	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	633	TRP	0	-0.014	-0.019	17.778	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	634	VAL	0	-0.049	-0.024	16.810	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	635	SER	0	-0.013	-0.016	20.007	0.001	0.001	0.000	0.000	0.000	0.000
79	A	636	ASP	-1	-0.873	-0.932	23.187	-0.051	-0.051	0.000	0.000	0.000	0.000
80	A	637	ARG	1	0.778	0.889	21.515	0.120	0.120	0.000	0.000	0.000	0.000
81	A	638	PHE	0	0.001	0.004	22.210	0.000	0.000	0.000	0.000	0.000	0.000
82	A	639	LEU	0	0.003	0.002	27.234	0.006	0.006	0.000	0.000	0.000	0.000
83	A	640	LYS	1	0.791	0.892	29.062	0.060	0.060	0.000	0.000	0.000	0.000
84	A	641	LYS	1	0.881	0.948	26.879	0.055	0.055	0.000	0.000	0.000	0.000
85	A	642	ASN	0	-0.005	-0.019	24.442	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	643	ASP	-1	-0.811	-0.886	27.597	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	644	SER	0	0.003	-0.018	28.608	0.001	0.001	0.000	0.000	0.000	0.000
88	A	645	SER	0	-0.048	-0.038	28.985	0.005	0.005	0.000	0.000	0.000	0.000
89	A	646	ASP	-1	-0.849	-0.911	26.363	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	647	MET	0	0.027	0.020	22.546	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	648	VAL	0	0.029	0.020	23.541	0.004	0.004	0.000	0.000	0.000	0.000
92	A	649	LYS	1	0.909	0.963	24.287	0.010	0.010	0.000	0.000	0.000	0.000
93	A	650	LEU	0	0.028	0.014	18.403	0.003	0.003	0.000	0.000	0.000	0.000
94	A	651	GLU	-1	-0.782	-0.886	19.002	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	652	SER	0	-0.056	-0.046	19.759	0.018	0.018	0.000	0.000	0.000	0.000
96	A	653	LEU	0	-0.063	-0.022	18.822	0.011	0.011	0.000	0.000	0.000	0.000
97	A	654	LEU	0	-0.049	-0.019	14.131	0.008	0.008	0.000	0.000	0.000	0.000
98	A	655	ASP	-1	-0.897	-0.940	15.537	0.131	0.131	0.000	0.000	0.000	0.000
99	A	656	HIS	0	-0.195	-0.088	13.351	0.023	0.023	0.000	0.000	0.000	0.000
100	A	669	LYS	1	0.976	0.989	6.918	-0.531	-0.531	0.000	0.000	0.000	0.000
101	A	670	THR	0	-0.096	-0.053	6.954	-0.058	-0.058	0.000	0.000	0.000	0.000
102	A	671	VAL	0	0.031	0.019	8.776	-0.047	-0.047	0.000	0.000	0.000	0.000
103	A	672	VAL	0	-0.033	-0.002	8.708	0.007	0.007	0.000	0.000	0.000	0.000
104	A	673	TYR	0	-0.016	-0.044	11.575	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	674	VAL	0	0.031	0.000	14.839	-0.031	-0.031	0.000	0.000	0.000	0.000
106	A	675	GLY	0	0.011	0.007	17.191	0.026	0.026	0.000	0.000	0.000	0.000
107	A	676	ARG	1	0.874	0.943	20.896	0.123	0.123	0.000	0.000	0.000	0.000
108	A	677	GLU	-1	-0.813	-0.912	23.950	-0.093	-0.093	0.000	0.000	0.000	0.000
109	A	678	GLY	0	-0.053	-0.026	27.144	0.001	0.001	0.000	0.000	0.000	0.000
110	A	679	GLU	-1	-0.864	-0.893	26.455	-0.110	-0.110	0.000	0.000	0.000	0.000
111	A	680	GLY	0	0.044	0.030	25.469	0.009	0.009	0.000	0.000	0.000	0.000
112	A	681	ILE	0	-0.052	-0.036	19.434	-0.016	-0.016	0.000	0.000	0.000	0.000
113	A	682	ILE	0	0.007	0.009	20.277	0.012	0.012	0.000	0.000	0.000	0.000
114	A	683	GLY	0	0.029	-0.004	18.806	0.007	0.007	0.000	0.000	0.000	0.000
115	A	684	ALA	0	-0.048	-0.005	14.670	0.002	0.002	0.000	0.000	0.000	0.000
116	A	685	ILE	0	0.009	0.009	9.553	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	686	ALA	0	0.033	0.030	10.057	0.014	0.014	0.000	0.000	0.000	0.000
118	A	687	ILE	0	-0.008	-0.005	3.914	-0.377	-0.182	0.003	-0.041	-0.157	0.000
119	A	688	SER	0	0.026	0.000	2.563	-1.089	-0.060	1.349	-1.062	-1.316	-0.011

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