FMO DATABASE

FMODB ID: YZGK2

Calculation Name: 4BGJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BGJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y5W7

Base Structure: X-ray

Registration Date: 2023-09-19

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1161267.843122
FMO2-HF: Nuclear repulsion	1110193.472977
FMO2-HF: Total energy	-51074.370146
FMO2-MP2: Total energy	-51227.270721

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:506:PRO)

Summations of interaction energy for fragment #1(A:506: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.
-3.318	-1.261	-0.022	-0.826	-1.21	0.003

Interaction energy analysis for fragmet #1(A:506:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.001

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	508	ASN	0	0.043	0.014	3.826	-0.637	1.204	-0.022	-0.771	-1.049	0.003
4	A	509	LEU	0	-0.017	-0.015	6.273	0.190	0.190	0.000	0.000	0.000	0.000
5	A	510	ALA	0	0.065	0.045	9.614	0.148	0.148	0.000	0.000	0.000	0.000
6	A	511	ALA	0	-0.087	-0.026	8.011	0.089	0.089	0.000	0.000	0.000	0.000
7	A	512	TRP	0	-0.044	-0.030	7.507	0.239	0.239	0.000	0.000	0.000	0.000
8	A	513	LYS	1	0.942	0.988	12.224	0.484	0.484	0.000	0.000	0.000	0.000
9	A	514	ILE	0	0.024	0.016	15.919	0.028	0.028	0.000	0.000	0.000	0.000
10	A	515	SER	0	-0.033	-0.026	18.377	0.002	0.002	0.000	0.000	0.000	0.000
11	A	516	ILE	0	-0.008	-0.003	22.098	0.009	0.009	0.000	0.000	0.000	0.000
12	A	517	PRO	0	-0.004	0.032	24.208	0.012	0.012	0.000	0.000	0.000	0.000
13	A	518	TYR	0	-0.016	-0.024	27.215	0.013	0.013	0.000	0.000	0.000	0.000
14	A	519	VAL	0	-0.063	-0.030	28.574	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	520	ASP	-1	-0.802	-0.911	29.723	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	521	PHE	0	-0.043	-0.035	31.659	0.001	0.001	0.000	0.000	0.000	0.000
17	A	522	PHE	0	0.049	0.024	26.787	0.002	0.002	0.000	0.000	0.000	0.000
18	A	523	GLU	-1	-0.899	-0.939	32.140	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	534	GLU	-1	-0.934	-0.953	36.183	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	535	ARG	1	0.842	0.893	36.183	0.009	0.009	0.000	0.000	0.000	0.000
21	A	536	ILE	0	-0.049	-0.022	32.666	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	537	PRO	0	-0.019	0.012	33.407	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	538	VAL	0	-0.045	-0.035	28.054	0.002	0.002	0.000	0.000	0.000	0.000
24	A	539	PHE	0	-0.002	-0.004	26.278	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	540	CYS	0	-0.003	0.019	25.119	0.002	0.002	0.000	0.000	0.000	0.000
26	A	541	ILE	0	-0.031	-0.034	19.613	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	542	ASP	-1	-0.808	-0.899	20.344	-0.190	-0.190	0.000	0.000	0.000	0.000
28	A	543	VAL	0	-0.052	-0.046	13.899	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	544	GLU	-1	-0.859	-0.936	14.731	-0.481	-0.481	0.000	0.000	0.000	0.000
30	A	545	ARG	1	0.812	0.900	5.176	1.139	1.139	0.000	0.000	0.000	0.000
31	A	546	ASN	0	-0.006	-0.018	9.942	0.075	0.075	0.000	0.000	0.000	0.000
32	A	547	ASP	-1	-0.777	-0.883	4.904	-2.917	-2.917	0.000	0.000	0.000	0.000
33	A	548	ARG	1	0.866	0.914	4.104	-0.976	-0.760	0.000	-0.055	-0.161	0.000
34	A	549	ARG	1	0.880	0.958	5.898	0.609	0.609	0.000	0.000	0.000	0.000
35	A	550	ALA	0	-0.029	-0.039	7.937	0.123	0.123	0.000	0.000	0.000	0.000
36	A	551	VAL	0	0.003	0.013	9.664	0.075	0.075	0.000	0.000	0.000	0.000
37	A	552	GLY	0	0.029	-0.022	12.821	0.041	0.041	0.000	0.000	0.000	0.000
38	A	553	HIS	0	-0.106	-0.038	13.851	0.038	0.038	0.000	0.000	0.000	0.000
39	A	554	GLU	-1	-0.835	-0.891	13.532	-0.395	-0.395	0.000	0.000	0.000	0.000
40	A	555	PRO	0	0.032	0.028	11.911	0.002	0.002	0.000	0.000	0.000	0.000
41	A	556	GLU	-1	-0.948	-0.968	9.115	-0.252	-0.252	0.000	0.000	0.000	0.000
42	A	557	HIS	0	0.020	0.003	13.006	-0.073	-0.073	0.000	0.000	0.000	0.000
43	A	558	TRP	0	-0.083	-0.029	11.126	0.051	0.051	0.000	0.000	0.000	0.000
44	A	559	SER	0	0.054	0.024	17.943	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	560	VAL	0	-0.068	-0.029	18.036	0.028	0.028	0.000	0.000	0.000	0.000
46	A	561	TYR	0	0.012	0.013	21.167	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	562	ARG	1	0.830	0.919	19.422	0.080	0.080	0.000	0.000	0.000	0.000
48	A	563	ARG	1	0.966	0.975	25.314	0.016	0.016	0.000	0.000	0.000	0.000
49	A	564	TYR	0	0.075	0.025	27.803	0.000	0.000	0.000	0.000	0.000	0.000
50	A	565	LEU	0	-0.032	-0.034	29.228	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	566	GLU	-1	-0.783	-0.871	24.767	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	567	PHE	0	0.054	0.025	24.055	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	568	TYR	0	-0.003	-0.038	25.246	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	569	VAL	0	-0.055	-0.005	24.442	0.003	0.003	0.000	0.000	0.000	0.000
55	A	570	LEU	0	0.003	0.003	18.750	0.008	0.008	0.000	0.000	0.000	0.000
56	A	571	GLU	-1	-0.831	-0.915	22.101	-0.111	-0.111	0.000	0.000	0.000	0.000
57	A	572	SER	0	-0.050	-0.027	24.203	0.002	0.002	0.000	0.000	0.000	0.000
58	A	573	LYS	1	0.967	0.982	21.475	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	574	LEU	0	-0.034	-0.014	17.174	0.005	0.005	0.000	0.000	0.000	0.000
60	A	575	THR	0	-0.050	-0.024	20.606	0.004	0.004	0.000	0.000	0.000	0.000
61	A	576	GLU	-1	-0.975	-0.967	23.431	0.012	0.012	0.000	0.000	0.000	0.000
62	A	577	PHE	0	-0.076	-0.034	16.357	0.015	0.015	0.000	0.000	0.000	0.000
63	A	578	HIS	0	-0.027	-0.031	14.702	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	579	GLY	0	0.023	0.029	20.056	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	580	ALA	0	-0.044	-0.035	22.576	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	581	PHE	0	0.077	0.027	18.483	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	582	PRO	0	-0.018	-0.006	23.529	0.003	0.003	0.000	0.000	0.000	0.000
68	A	583	ASP	-1	-0.861	-0.910	22.256	-0.245	-0.245	0.000	0.000	0.000	0.000
69	A	584	ALA	0	-0.014	-0.013	22.470	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	585	GLN	0	-0.034	-0.025	24.450	0.016	0.016	0.000	0.000	0.000	0.000
71	A	586	LEU	0	-0.036	-0.004	26.114	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	587	PRO	0	0.026	0.026	28.880	0.009	0.009	0.000	0.000	0.000	0.000
73	A	588	SER	0	0.022	0.008	32.481	0.003	0.003	0.000	0.000	0.000	0.000
74	A	589	LYS	1	0.950	1.000	32.636	0.042	0.042	0.000	0.000	0.000	0.000
75	A	590	ARG	1	0.913	0.964	34.832	0.061	0.061	0.000	0.000	0.000	0.000
76	A	591	ILE	0	-0.040	-0.024	37.320	0.003	0.003	0.000	0.000	0.000	0.000
77	A	592	ILE	0	0.035	0.020	40.105	0.003	0.003	0.000	0.000	0.000	0.000
78	A	593	GLY	0	0.036	0.015	42.840	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	594	PRO	0	-0.032	-0.011	41.367	0.001	0.001	0.000	0.000	0.000	0.000
80	A	595	LYS	1	0.943	0.965	35.650	0.035	0.035	0.000	0.000	0.000	0.000
81	A	596	ASN	0	0.055	0.028	36.804	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	597	TYR	0	0.110	0.040	34.777	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	598	GLU	-1	-0.908	-0.953	36.329	-0.066	-0.066	0.000	0.000	0.000	0.000
84	A	599	PHE	0	-0.031	-0.008	35.342	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	600	LEU	0	0.016	0.016	31.109	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	601	LYS	1	0.957	0.979	32.815	0.085	0.085	0.000	0.000	0.000	0.000
87	A	602	SER	0	-0.099	-0.067	34.051	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	603	LYS	1	0.878	0.943	31.721	0.093	0.093	0.000	0.000	0.000	0.000
89	A	604	ARG	1	0.913	0.956	28.343	0.145	0.145	0.000	0.000	0.000	0.000
90	A	605	GLU	-1	-0.946	-0.975	28.070	-0.156	-0.156	0.000	0.000	0.000	0.000
91	A	606	GLU	-1	-0.788	-0.901	28.025	-0.130	-0.130	0.000	0.000	0.000	0.000
92	A	607	PHE	0	-0.015	-0.018	26.363	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	608	GLN	0	0.028	0.023	23.547	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	609	GLU	-1	-0.912	-0.958	23.031	-0.233	-0.233	0.000	0.000	0.000	0.000
95	A	610	TYR	0	-0.013	-0.015	23.062	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	611	LEU	0	0.027	0.001	19.592	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	612	GLN	0	-0.049	-0.032	18.697	-0.035	-0.035	0.000	0.000	0.000	0.000
98	A	613	LYS	1	0.917	0.967	18.250	0.169	0.169	0.000	0.000	0.000	0.000
99	A	614	LEU	0	-0.018	-0.004	17.723	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	615	LEU	0	-0.046	-0.019	13.597	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	616	GLN	0	-0.017	-0.005	13.314	-0.156	-0.156	0.000	0.000	0.000	0.000
102	A	617	HIS	1	0.762	0.864	15.115	0.317	0.317	0.000	0.000	0.000	0.000
103	A	618	PRO	0	0.026	0.010	11.993	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	619	GLU	-1	-0.826	-0.900	11.641	-0.370	-0.370	0.000	0.000	0.000	0.000
105	A	620	LEU	0	-0.044	-0.018	13.116	0.056	0.056	0.000	0.000	0.000	0.000
106	A	621	SER	0	-0.008	0.014	8.133	-0.072	-0.072	0.000	0.000	0.000	0.000
107	A	622	ASN	0	0.078	0.030	6.263	-0.414	-0.414	0.000	0.000	0.000	0.000
108	A	623	SER	0	0.006	0.015	8.457	0.289	0.289	0.000	0.000	0.000	0.000
109	A	624	GLN	0	0.032	0.008	11.056	0.025	0.025	0.000	0.000	0.000	0.000
110	A	625	LEU	0	0.049	0.025	12.562	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	626	LEU	0	0.034	0.019	13.909	0.011	0.011	0.000	0.000	0.000	0.000
112	A	627	ALA	0	0.037	0.011	10.924	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	628	ASP	-1	-0.853	-0.910	12.958	0.140	0.140	0.000	0.000	0.000	0.000
114	A	629	PHE	0	-0.048	-0.034	15.717	0.003	0.003	0.000	0.000	0.000	0.000
115	A	630	LEU	0	-0.033	-0.014	14.550	0.007	0.007	0.000	0.000	0.000	0.000
116	A	631	SER	0	0.013	-0.009	13.425	-0.042	-0.042	0.000	0.000	0.000	0.000
117	A	632	PRO	0	-0.006	0.004	15.379	0.023	0.023	0.000	0.000	0.000	0.000
118	A	633	ASN	0	-0.020	-0.018	18.122	0.017	0.017	0.000	0.000	0.000	0.000
119	A	634	GLY	0	0.007	0.013	19.785	0.006	0.006	0.000	0.000	0.000	0.000
120	A	635	GLY	0	0.037	0.018	20.801	0.016	0.016	0.000	0.000	0.000	0.000
121	A	636	GLU	-1	-0.902	-0.961	21.607	0.100	0.100	0.000	0.000	0.000	0.000
122	A	637	THR	0	-0.028	-0.013	25.263	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	639	GLN	0	-0.029	0.005	18.566	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	640	PHE	0	-0.017	-0.025	18.752	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	641	LEU	0	-0.042	-0.018	24.735	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:506:PRO)