FMO DATABASE

FMODB ID: JLK89

Calculation Name: 4DBG-B-Xray372

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 4DBG

Chain ID: B

ChEMBL ID: CHEMBL4296109

UniProt ID: Q9BYM8

Base Structure: X-ray

Registration Date: 2023-06-26

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1275120.571871
FMO2-HF: Nuclear repulsion	1216352.339632
FMO2-HF: Total energy	-58768.232239
FMO2-MP2: Total energy	-58937.887642

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(B:482:ASP)

Summations of interaction energy for fragment #1(B:482: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.
55.566	61.807	0.458	-2.898	-3.802	0.018

Interaction energy analysis for fragmet #1(B:482:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.943 / q_NPA : -0.987

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	B	484	MET	0	-0.002	0.010	2.923	-15.924	-11.471	0.271	-2.242	-2.482	0.015
4	B	485	ARG	1	0.977	0.996	2.928	-44.318	-43.046	0.188	-0.546	-0.915	0.003
5	B	486	GLU	-1	-0.968	-0.985	4.385	37.540	37.834	-0.001	-0.048	-0.245	0.000
6	B	487	GLU	-1	-0.838	-0.917	6.412	22.918	22.918	0.000	0.000	0.000	0.000
7	B	488	GLY	0	0.017	0.008	7.754	-3.429	-3.429	0.000	0.000	0.000	0.000
8	B	489	LEU	0	-0.055	-0.035	7.720	-2.562	-2.562	0.000	0.000	0.000	0.000
9	B	490	GLN	0	-0.044	-0.015	10.305	-3.443	-3.443	0.000	0.000	0.000	0.000
10	B	491	LEU	0	0.038	0.027	12.072	-1.972	-1.972	0.000	0.000	0.000	0.000
11	B	492	VAL	0	-0.021	-0.016	12.922	-1.537	-1.537	0.000	0.000	0.000	0.000
12	B	493	SER	0	-0.114	-0.070	14.484	-1.387	-1.387	0.000	0.000	0.000	0.000
13	B	494	MET	0	-0.043	-0.023	16.371	-0.842	-0.842	0.000	0.000	0.000	0.000
14	B	495	ILE	0	0.031	0.004	18.775	-0.653	-0.653	0.000	0.000	0.000	0.000
15	B	496	ARG	1	0.810	0.921	16.747	-17.183	-17.183	0.000	0.000	0.000	0.000
16	B	497	GLU	-1	-0.919	-0.976	21.712	10.587	10.587	0.000	0.000	0.000	0.000
17	B	498	GLY	0	-0.019	0.008	25.493	-0.035	-0.035	0.000	0.000	0.000	0.000
18	B	499	GLU	-1	-0.863	-0.907	20.518	14.767	14.767	0.000	0.000	0.000	0.000
19	B	500	ALA	0	-0.055	-0.041	24.043	0.009	0.009	0.000	0.000	0.000	0.000
20	B	501	ALA	0	0.029	0.009	21.744	0.453	0.453	0.000	0.000	0.000	0.000
21	B	502	GLY	0	-0.004	0.003	22.983	-0.516	-0.516	0.000	0.000	0.000	0.000
22	B	503	ALA	0	0.023	0.016	20.479	0.549	0.549	0.000	0.000	0.000	0.000
23	B	504	CYS	0	0.052	0.009	20.096	-0.984	-0.984	0.000	0.000	0.000	0.000
24	B	505	PRO	0	0.073	0.031	19.607	0.782	0.782	0.000	0.000	0.000	0.000
25	B	506	GLU	-1	-0.876	-0.944	19.263	13.620	13.620	0.000	0.000	0.000	0.000
26	B	507	GLU	-1	-0.774	-0.836	15.703	17.140	17.140	0.000	0.000	0.000	0.000
27	B	508	ILE	0	0.043	0.025	14.554	1.330	1.330	0.000	0.000	0.000	0.000
28	B	509	PHE	0	0.020	0.018	15.121	0.811	0.811	0.000	0.000	0.000	0.000
29	B	510	SER	0	-0.068	-0.056	13.816	0.264	0.264	0.000	0.000	0.000	0.000
30	B	511	ALA	0	-0.010	-0.003	10.709	1.287	1.287	0.000	0.000	0.000	0.000
31	B	512	LEU	0	0.003	-0.009	10.581	1.827	1.827	0.000	0.000	0.000	0.000
32	B	513	GLN	0	-0.005	0.008	12.512	0.187	0.187	0.000	0.000	0.000	0.000
33	B	514	TYR	0	-0.063	-0.035	4.082	-0.476	-0.254	0.000	-0.062	-0.160	0.000
34	B	515	SER	0	-0.064	-0.033	8.139	2.164	2.164	0.000	0.000	0.000	0.000
35	B	516	GLY	0	-0.027	-0.003	9.216	0.587	0.587	0.000	0.000	0.000	0.000
36	B	517	THR	0	-0.115	-0.049	11.967	-1.353	-1.353	0.000	0.000	0.000	0.000
37	B	518	GLU	-1	-0.904	-0.961	15.163	13.729	13.729	0.000	0.000	0.000	0.000
38	B	519	VAL	0	0.005	0.011	17.633	-0.274	-0.274	0.000	0.000	0.000	0.000
39	B	520	PRO	0	0.031	0.009	20.208	0.001	0.001	0.000	0.000	0.000	0.000
40	B	521	LEU	0	0.045	0.023	21.211	0.053	0.053	0.000	0.000	0.000	0.000
41	B	522	GLN	0	-0.019	-0.031	23.283	0.127	0.127	0.000	0.000	0.000	0.000
42	B	523	TRP	0	-0.036	0.004	21.417	0.041	0.041	0.000	0.000	0.000	0.000
43	B	524	LEU	0	0.060	0.025	19.354	-0.040	-0.040	0.000	0.000	0.000	0.000
44	B	525	ARG	1	0.857	0.911	23.760	-10.626	-10.626	0.000	0.000	0.000	0.000
45	B	526	SER	0	-0.073	-0.031	26.552	-0.236	-0.236	0.000	0.000	0.000	0.000
46	B	527	GLU	-1	-0.928	-0.955	24.773	10.931	10.931	0.000	0.000	0.000	0.000
47	B	528	LEU	0	-0.029	-0.001	22.213	0.064	0.064	0.000	0.000	0.000	0.000
48	B	529	PRO	0	-0.017	-0.012	26.516	-0.444	-0.444	0.000	0.000	0.000	0.000
49	B	530	TYR	0	0.018	-0.021	28.995	0.188	0.188	0.000	0.000	0.000	0.000
50	B	531	VAL	0	-0.035	-0.010	29.786	-0.014	-0.014	0.000	0.000	0.000	0.000
51	B	532	LEU	0	0.046	0.009	24.997	-0.157	-0.157	0.000	0.000	0.000	0.000
52	B	533	GLU	-1	-0.835	-0.910	28.277	10.535	10.535	0.000	0.000	0.000	0.000
53	B	534	MET	0	0.025	0.023	30.630	-0.311	-0.311	0.000	0.000	0.000	0.000
54	B	535	VAL	0	-0.032	-0.009	31.145	-0.202	-0.202	0.000	0.000	0.000	0.000
55	B	536	ALA	0	0.016	-0.001	30.040	-0.193	-0.193	0.000	0.000	0.000	0.000
56	B	537	GLU	-1	-0.902	-0.924	32.181	8.686	8.686	0.000	0.000	0.000	0.000
57	B	538	LEU	0	0.001	-0.007	35.282	-0.288	-0.288	0.000	0.000	0.000	0.000
58	B	539	ALA	0	-0.018	-0.005	34.164	-0.220	-0.220	0.000	0.000	0.000	0.000
59	B	540	GLY	0	0.002	-0.009	35.655	-0.147	-0.147	0.000	0.000	0.000	0.000
60	B	541	GLN	0	-0.089	-0.059	36.902	-0.365	-0.365	0.000	0.000	0.000	0.000
61	B	542	GLN	0	-0.068	-0.029	39.568	-0.152	-0.152	0.000	0.000	0.000	0.000
62	B	543	ASP	-1	-0.822	-0.906	39.139	7.572	7.572	0.000	0.000	0.000	0.000
63	B	544	PRO	0	0.039	0.026	38.740	0.203	0.203	0.000	0.000	0.000	0.000
64	B	545	GLY	0	-0.027	0.001	39.266	0.070	0.070	0.000	0.000	0.000	0.000
65	B	546	LEU	0	-0.037	-0.025	35.459	0.119	0.119	0.000	0.000	0.000	0.000
66	B	547	GLY	0	0.001	0.009	34.432	0.332	0.332	0.000	0.000	0.000	0.000
67	B	548	ALA	0	0.011	0.013	31.224	-0.020	-0.020	0.000	0.000	0.000	0.000
68	B	549	PHE	0	0.040	0.010	30.228	0.247	0.247	0.000	0.000	0.000	0.000
69	B	550	SER	0	-0.001	-0.025	24.670	0.223	0.223	0.000	0.000	0.000	0.000
70	B	552	GLN	0	-0.011	-0.021	19.488	-0.687	-0.687	0.000	0.000	0.000	0.000
71	B	553	GLU	-1	-0.811	-0.868	23.321	10.882	10.882	0.000	0.000	0.000	0.000
72	B	554	ALA	0	0.035	0.010	26.735	-0.266	-0.266	0.000	0.000	0.000	0.000
73	B	555	ARG	1	0.824	0.879	18.987	-15.444	-15.444	0.000	0.000	0.000	0.000
74	B	556	ARG	1	0.759	0.870	24.319	-12.417	-12.417	0.000	0.000	0.000	0.000
75	B	557	ALA	0	0.048	0.023	26.385	-0.119	-0.119	0.000	0.000	0.000	0.000
76	B	558	TRP	0	0.019	0.000	26.513	-0.133	-0.133	0.000	0.000	0.000	0.000
77	B	559	LEU	0	-0.033	-0.022	23.558	-0.126	-0.126	0.000	0.000	0.000	0.000
78	B	560	ASP	-1	-0.840	-0.892	28.146	11.356	11.356	0.000	0.000	0.000	0.000
79	B	561	ARG	1	0.750	0.857	30.279	-9.310	-9.310	0.000	0.000	0.000	0.000
80	B	562	HIS	0	-0.005	0.004	31.195	-0.165	-0.165	0.000	0.000	0.000	0.000
81	B	563	GLY	0	0.005	0.008	31.317	-0.178	-0.178	0.000	0.000	0.000	0.000
82	B	564	ASN	0	-0.091	-0.058	32.381	-0.257	-0.257	0.000	0.000	0.000	0.000
83	B	565	LEU	0	0.030	-0.001	33.929	0.062	0.062	0.000	0.000	0.000	0.000
84	B	566	ASP	-1	-0.917	-0.958	36.103	7.770	7.770	0.000	0.000	0.000	0.000
85	B	567	GLU	-1	-0.810	-0.888	36.906	8.498	8.498	0.000	0.000	0.000	0.000
86	B	568	ALA	0	-0.026	-0.006	32.419	0.129	0.129	0.000	0.000	0.000	0.000
87	B	569	VAL	0	0.015	0.012	34.144	0.146	0.146	0.000	0.000	0.000	0.000
88	B	570	GLU	-1	-0.786	-0.879	36.051	8.027	8.027	0.000	0.000	0.000	0.000
89	B	571	GLU	-1	-0.822	-0.893	32.981	9.137	9.137	0.000	0.000	0.000	0.000
90	B	572	CYS	0	-0.054	-0.018	30.321	0.225	0.225	0.000	0.000	0.000	0.000
91	B	573	VAL	0	0.043	0.031	32.982	0.118	0.118	0.000	0.000	0.000	0.000
92	B	574	ARG	1	0.772	0.873	35.671	-8.474	-8.474	0.000	0.000	0.000	0.000
93	B	575	THR	0	-0.073	-0.052	29.470	0.082	0.082	0.000	0.000	0.000	0.000
94	B	576	ARG	1	0.782	0.882	29.488	-9.837	-9.837	0.000	0.000	0.000	0.000
95	B	577	ARG	1	0.907	0.925	32.681	-7.929	-7.929	0.000	0.000	0.000	0.000
96	B	578	ARG	1	0.815	0.889	29.643	-10.131	-10.131	0.000	0.000	0.000	0.000
97	B	579	LYS	1	0.885	0.935	26.746	-11.370	-11.370	0.000	0.000	0.000	0.000
98	B	580	VAL	0	0.016	0.015	32.289	0.049	0.049	0.000	0.000	0.000	0.000
99	B	581	GLN	0	-0.011	-0.011	34.396	-0.222	-0.222	0.000	0.000	0.000	0.000
100	B	582	GLU	-1	-0.794	-0.863	30.757	10.048	10.048	0.000	0.000	0.000	0.000
101	B	583	LEU	0	0.003	0.002	28.885	0.014	0.014	0.000	0.000	0.000	0.000
102	B	584	GLN	0	0.056	0.049	32.932	-0.062	-0.062	0.000	0.000	0.000	0.000
103	B	585	SER	0	-0.128	-0.064	35.605	-0.121	-0.121	0.000	0.000	0.000	0.000
104	B	586	LEU	0	-0.061	-0.031	30.598	0.001	0.001	0.000	0.000	0.000	0.000
105	B	587	GLY	0	-0.063	-0.032	34.111	0.127	0.127	0.000	0.000	0.000	0.000
106	B	588	PHE	0	-0.041	-0.036	31.816	0.086	0.086	0.000	0.000	0.000	0.000
107	B	589	GLY	0	0.069	0.039	34.876	0.149	0.149	0.000	0.000	0.000	0.000
108	B	590	PRO	0	-0.038	-0.044	35.959	0.185	0.185	0.000	0.000	0.000	0.000
109	B	591	GLU	-1	-0.901	-0.951	36.732	7.791	7.791	0.000	0.000	0.000	0.000
110	B	592	GLU	-1	-0.912	-0.952	35.612	8.012	8.012	0.000	0.000	0.000	0.000
111	B	593	GLY	0	-0.032	-0.010	32.709	0.233	0.233	0.000	0.000	0.000	0.000
112	B	594	SER	0	-0.018	-0.014	31.312	0.429	0.429	0.000	0.000	0.000	0.000
113	B	595	LEU	0	0.021	0.006	30.748	0.338	0.338	0.000	0.000	0.000	0.000
114	B	596	GLN	0	0.014	0.004	29.812	0.246	0.246	0.000	0.000	0.000	0.000
115	B	597	ALA	0	0.029	0.026	26.770	0.417	0.417	0.000	0.000	0.000	0.000
116	B	598	LEU	0	0.022	0.002	25.686	0.570	0.570	0.000	0.000	0.000	0.000
117	B	599	PHE	0	-0.051	-0.006	26.042	0.437	0.437	0.000	0.000	0.000	0.000
118	B	600	GLN	0	-0.018	-0.006	22.926	0.707	0.707	0.000	0.000	0.000	0.000
119	B	601	HIS	0	-0.007	-0.014	20.317	1.157	1.157	0.000	0.000	0.000	0.000
120	B	602	GLY	0	0.025	0.010	21.955	0.437	0.437	0.000	0.000	0.000	0.000
121	B	603	GLY	0	0.023	0.001	23.047	0.060	0.060	0.000	0.000	0.000	0.000
122	B	604	ASP	-1	-0.826	-0.879	20.278	14.185	14.185	0.000	0.000	0.000	0.000
123	B	605	VAL	0	0.069	0.018	23.643	-0.011	-0.011	0.000	0.000	0.000	0.000
124	B	606	SER	0	-0.002	-0.007	22.234	-0.226	-0.226	0.000	0.000	0.000	0.000
125	B	607	ARG	1	0.830	0.923	17.809	-15.414	-15.414	0.000	0.000	0.000	0.000
126	B	608	ALA	0	0.038	0.022	22.051	-0.104	-0.104	0.000	0.000	0.000	0.000
127	B	609	LEU	0	-0.005	0.006	25.290	-0.252	-0.252	0.000	0.000	0.000	0.000
128	B	610	THR	0	-0.025	-0.028	21.343	-0.152	-0.152	0.000	0.000	0.000	0.000
129	B	611	GLU	-1	-0.847	-0.876	23.088	12.172	12.172	0.000	0.000	0.000	0.000
130	B	612	LEU	0	0.047	0.006	24.652	-0.224	-0.224	0.000	0.000	0.000	0.000
131	B	613	GLN	0	-0.072	-0.039	27.454	-0.140	-0.140	0.000	0.000	0.000	0.000
132	B	614	ARG	1	0.853	0.907	20.184	-13.536	-13.536	0.000	0.000	0.000	0.000
133	B	615	GLN	0	-0.070	-0.043	26.602	-0.502	-0.502	0.000	0.000	0.000	0.000
134	B	616	ARG	1	0.963	0.989	28.952	-9.093	-9.093	0.000	0.000	0.000	0.000
135	B	617	LEU	0	-0.036	-0.025	28.129	-0.287	-0.287	0.000	0.000	0.000	0.000
136	B	618	GLU	-1	-0.740	-0.839	27.468	10.708	10.708	0.000	0.000	0.000	0.000
137	B	619	PRO	0	0.005	0.000	29.760	-0.039	-0.039	0.000	0.000	0.000	0.000
138	B	620	PHE	0	-0.042	-0.030	31.232	-0.159	-0.159	0.000	0.000	0.000	0.000
139	B	621	ARG	1	0.890	0.934	24.104	-11.282	-11.282	0.000	0.000	0.000	0.000
140	B	622	GLN	0	-0.062	-0.055	28.748	-0.188	-0.188	0.000	0.000	0.000	0.000
141	B	623	ARG	1	0.967	0.983	30.689	-8.546	-8.546	0.000	0.000	0.000	0.000
142	B	624	LEU	0	-0.103	-0.034	27.377	-0.131	-0.131	0.000	0.000	0.000	0.000
143	B	625	TRP	0	-0.076	-0.042	24.894	0.167	0.167	0.000	0.000	0.000	0.000
144	B	626	ASP	-1	-0.923	-0.944	30.917	8.494	8.494	0.000	0.000	0.000	0.000
145	B	627	SER	0	-0.039	-0.002	34.487	-0.191	-0.191	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:482:ASP)