FMO DATABASE

FMODB ID: 39G2L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1277114.242378
FMO2-HF: Nuclear repulsion	1218345.454167
FMO2-HF: Total energy	-58768.788211
FMO2-MP2: Total energy	-58938.347566

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.
64.745	69.61	0.105	-2.075	-2.895	0.006

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 : -0.887 / q_NPA : -0.961

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	0.013	0.022	3.099	-12.647	-9.588	0.044	-1.516	-1.588	0.005
4	B	485	ARG	1	0.968	0.992	3.362	-41.610	-40.480	0.060	-0.386	-0.804	0.001
5	B	486	GLU	-1	-0.986	-0.990	4.508	40.315	40.725	-0.001	-0.101	-0.308	0.000
6	B	487	GLU	-1	-0.843	-0.929	6.460	23.001	23.001	0.000	0.000	0.000	0.000
7	B	488	GLY	0	0.003	0.000	7.724	-3.303	-3.303	0.000	0.000	0.000	0.000
8	B	489	LEU	0	-0.055	-0.033	7.494	-2.829	-2.829	0.000	0.000	0.000	0.000
9	B	490	GLN	0	-0.053	-0.023	10.474	-3.548	-3.548	0.000	0.000	0.000	0.000
10	B	491	LEU	0	0.034	0.032	12.303	-1.916	-1.916	0.000	0.000	0.000	0.000
11	B	492	VAL	0	-0.004	-0.014	13.167	-1.529	-1.529	0.000	0.000	0.000	0.000
12	B	493	SER	0	-0.110	-0.062	14.669	-1.383	-1.383	0.000	0.000	0.000	0.000
13	B	494	MET	0	-0.044	-0.022	16.522	-0.803	-0.803	0.000	0.000	0.000	0.000
14	B	495	ILE	0	0.019	-0.002	18.644	-0.682	-0.682	0.000	0.000	0.000	0.000
15	B	496	ARG	1	0.829	0.920	16.925	-17.051	-17.051	0.000	0.000	0.000	0.000
16	B	497	GLU	-1	-0.903	-0.960	22.184	10.502	10.502	0.000	0.000	0.000	0.000
17	B	498	GLY	0	-0.014	-0.004	25.890	0.118	0.118	0.000	0.000	0.000	0.000
18	B	499	GLU	-1	-0.900	-0.931	20.889	14.575	14.575	0.000	0.000	0.000	0.000
19	B	500	ALA	0	-0.011	0.004	24.353	-0.066	-0.066	0.000	0.000	0.000	0.000
20	B	501	ALA	0	-0.021	-0.015	21.497	0.222	0.222	0.000	0.000	0.000	0.000
21	B	502	GLY	0	0.016	0.004	22.990	-0.433	-0.433	0.000	0.000	0.000	0.000
22	B	503	ALA	0	0.019	0.012	20.406	0.636	0.636	0.000	0.000	0.000	0.000
23	B	504	CYS	0	0.036	0.005	20.037	-0.970	-0.970	0.000	0.000	0.000	0.000
24	B	505	PRO	0	0.060	0.034	19.607	0.815	0.815	0.000	0.000	0.000	0.000
25	B	506	GLU	-1	-0.839	-0.937	19.378	13.639	13.639	0.000	0.000	0.000	0.000
26	B	507	GLU	-1	-0.810	-0.842	15.735	17.090	17.090	0.000	0.000	0.000	0.000
27	B	508	ILE	0	0.050	0.022	14.535	1.295	1.295	0.000	0.000	0.000	0.000
28	B	509	PHE	0	-0.006	0.000	14.995	0.806	0.806	0.000	0.000	0.000	0.000
29	B	510	SER	0	-0.037	-0.040	13.363	0.385	0.385	0.000	0.000	0.000	0.000
30	B	511	ALA	0	-0.009	0.004	10.572	1.383	1.383	0.000	0.000	0.000	0.000
31	B	512	LEU	0	-0.002	-0.002	10.388	1.744	1.744	0.000	0.000	0.000	0.000
32	B	513	GLN	0	0.016	0.009	12.227	0.291	0.291	0.000	0.000	0.000	0.000
33	B	514	TYR	0	-0.056	-0.026	3.590	-0.619	-0.353	0.002	-0.072	-0.195	0.000
34	B	515	SER	0	-0.088	-0.048	8.017	2.391	2.391	0.000	0.000	0.000	0.000
35	B	516	GLY	0	-0.026	0.005	9.046	-0.217	-0.217	0.000	0.000	0.000	0.000
36	B	517	THR	0	-0.111	-0.058	11.850	-1.249	-1.249	0.000	0.000	0.000	0.000
37	B	518	GLU	-1	-0.890	-0.953	14.858	13.472	13.472	0.000	0.000	0.000	0.000
38	B	519	VAL	0	0.003	-0.002	17.768	-0.117	-0.117	0.000	0.000	0.000	0.000
39	B	520	PRO	0	0.031	0.010	20.219	0.066	0.066	0.000	0.000	0.000	0.000
40	B	521	LEU	0	0.030	0.024	20.874	-0.077	-0.077	0.000	0.000	0.000	0.000
41	B	522	GLN	0	0.001	-0.019	23.009	0.120	0.120	0.000	0.000	0.000	0.000
42	B	523	TRP	0	-0.056	-0.017	21.347	0.037	0.037	0.000	0.000	0.000	0.000
43	B	524	LEU	0	0.031	0.011	19.183	-0.049	-0.049	0.000	0.000	0.000	0.000
44	B	525	ARG	1	0.855	0.912	23.558	-10.524	-10.524	0.000	0.000	0.000	0.000
45	B	526	SER	0	-0.068	-0.026	26.357	-0.326	-0.326	0.000	0.000	0.000	0.000
46	B	527	GLU	-1	-0.896	-0.931	25.148	10.784	10.784	0.000	0.000	0.000	0.000
47	B	528	LEU	0	-0.020	-0.006	21.939	0.042	0.042	0.000	0.000	0.000	0.000
48	B	529	PRO	0	0.006	0.017	26.412	-0.434	-0.434	0.000	0.000	0.000	0.000
49	B	530	TYR	0	-0.010	-0.049	28.900	0.215	0.215	0.000	0.000	0.000	0.000
50	B	531	VAL	0	-0.036	-0.008	30.092	-0.183	-0.183	0.000	0.000	0.000	0.000
51	B	532	LEU	0	0.047	0.009	24.989	-0.138	-0.138	0.000	0.000	0.000	0.000
52	B	533	GLU	-1	-0.853	-0.916	28.232	10.579	10.579	0.000	0.000	0.000	0.000
53	B	534	MET	0	0.025	0.012	30.468	-0.306	-0.306	0.000	0.000	0.000	0.000
54	B	535	VAL	0	-0.023	-0.006	31.185	-0.222	-0.222	0.000	0.000	0.000	0.000
55	B	536	ALA	0	0.024	0.005	29.804	-0.163	-0.163	0.000	0.000	0.000	0.000
56	B	537	GLU	-1	-0.882	-0.917	31.949	8.796	8.796	0.000	0.000	0.000	0.000
57	B	538	LEU	0	-0.012	-0.009	35.003	-0.309	-0.309	0.000	0.000	0.000	0.000
58	B	539	ALA	0	-0.005	0.002	33.931	-0.220	-0.220	0.000	0.000	0.000	0.000
59	B	540	GLY	0	-0.006	-0.013	35.377	-0.146	-0.146	0.000	0.000	0.000	0.000
60	B	541	GLN	0	-0.073	-0.051	36.638	-0.363	-0.363	0.000	0.000	0.000	0.000
61	B	542	GLN	0	-0.071	-0.036	39.353	-0.104	-0.104	0.000	0.000	0.000	0.000
62	B	543	ASP	-1	-0.824	-0.912	38.544	7.662	7.662	0.000	0.000	0.000	0.000
63	B	544	PRO	0	0.053	0.027	38.289	0.206	0.206	0.000	0.000	0.000	0.000
64	B	545	GLY	0	-0.032	0.000	38.837	0.079	0.079	0.000	0.000	0.000	0.000
65	B	546	LEU	0	-0.039	-0.014	34.924	0.112	0.112	0.000	0.000	0.000	0.000
66	B	547	GLY	0	-0.005	0.001	34.076	0.334	0.334	0.000	0.000	0.000	0.000
67	B	548	ALA	0	-0.002	-0.001	30.720	0.006	0.006	0.000	0.000	0.000	0.000
68	B	549	PHE	0	0.051	0.024	30.318	0.319	0.319	0.000	0.000	0.000	0.000
69	B	550	SER	0	-0.002	-0.017	24.684	0.203	0.203	0.000	0.000	0.000	0.000
70	B	552	GLN	0	0.003	-0.016	19.559	-0.671	-0.671	0.000	0.000	0.000	0.000
71	B	553	GLU	-1	-0.777	-0.861	23.288	10.943	10.943	0.000	0.000	0.000	0.000
72	B	554	ALA	0	0.041	0.017	26.733	-0.211	-0.211	0.000	0.000	0.000	0.000
73	B	555	ARG	1	0.811	0.873	18.994	-15.411	-15.411	0.000	0.000	0.000	0.000
74	B	556	ARG	1	0.767	0.860	23.930	-12.396	-12.396	0.000	0.000	0.000	0.000
75	B	557	ALA	0	0.059	0.030	26.246	-0.089	-0.089	0.000	0.000	0.000	0.000
76	B	558	TRP	0	0.007	-0.009	26.638	-0.084	-0.084	0.000	0.000	0.000	0.000
77	B	559	LEU	0	-0.033	-0.016	23.637	-0.087	-0.087	0.000	0.000	0.000	0.000
78	B	560	ASP	-1	-0.835	-0.882	28.152	11.349	11.349	0.000	0.000	0.000	0.000
79	B	561	ARG	1	0.730	0.840	30.348	-9.308	-9.308	0.000	0.000	0.000	0.000
80	B	562	HIS	0	-0.028	-0.014	30.808	-0.170	-0.170	0.000	0.000	0.000	0.000
81	B	563	GLY	0	0.053	0.035	31.600	-0.120	-0.120	0.000	0.000	0.000	0.000
82	B	564	ASN	0	-0.086	-0.062	32.394	-0.227	-0.227	0.000	0.000	0.000	0.000
83	B	565	LEU	0	0.013	-0.005	34.017	0.063	0.063	0.000	0.000	0.000	0.000
84	B	566	ASP	-1	-0.917	-0.953	36.019	7.820	7.820	0.000	0.000	0.000	0.000
85	B	567	GLU	-1	-0.780	-0.875	37.023	8.588	8.588	0.000	0.000	0.000	0.000
86	B	568	ALA	0	-0.029	-0.003	32.448	0.126	0.126	0.000	0.000	0.000	0.000
87	B	569	VAL	0	0.015	0.013	33.655	0.205	0.205	0.000	0.000	0.000	0.000
88	B	570	GLU	-1	-0.765	-0.856	35.730	8.092	8.092	0.000	0.000	0.000	0.000
89	B	571	GLU	-1	-0.807	-0.880	33.338	9.104	9.104	0.000	0.000	0.000	0.000
90	B	572	CYS	0	-0.051	-0.009	30.028	0.226	0.226	0.000	0.000	0.000	0.000
91	B	573	VAL	0	0.011	0.013	32.777	0.099	0.099	0.000	0.000	0.000	0.000
92	B	574	ARG	1	0.749	0.850	35.710	-8.505	-8.505	0.000	0.000	0.000	0.000
93	B	575	THR	0	-0.065	-0.045	29.625	0.085	0.085	0.000	0.000	0.000	0.000
94	B	576	ARG	1	0.792	0.887	29.153	-9.884	-9.884	0.000	0.000	0.000	0.000
95	B	577	ARG	1	0.878	0.913	32.622	-7.986	-7.986	0.000	0.000	0.000	0.000
96	B	578	ARG	1	0.801	0.865	29.736	-10.288	-10.288	0.000	0.000	0.000	0.000
97	B	579	LYS	1	0.848	0.919	26.796	-11.352	-11.352	0.000	0.000	0.000	0.000
98	B	580	VAL	0	0.007	0.017	32.232	0.051	0.051	0.000	0.000	0.000	0.000
99	B	581	GLN	0	-0.012	-0.007	34.534	-0.232	-0.232	0.000	0.000	0.000	0.000
100	B	582	GLU	-1	-0.812	-0.867	31.062	10.129	10.129	0.000	0.000	0.000	0.000
101	B	583	LEU	0	-0.003	0.010	28.885	-0.006	-0.006	0.000	0.000	0.000	0.000
102	B	584	GLN	0	0.025	0.024	32.962	-0.049	-0.049	0.000	0.000	0.000	0.000
103	B	585	SER	0	-0.112	-0.067	35.368	-0.127	-0.127	0.000	0.000	0.000	0.000
104	B	586	LEU	0	-0.048	-0.023	30.552	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	587	GLY	0	-0.023	-0.001	34.032	0.125	0.125	0.000	0.000	0.000	0.000
106	B	588	PHE	0	-0.001	-0.020	31.678	0.100	0.100	0.000	0.000	0.000	0.000
107	B	589	GLY	0	0.069	0.035	34.699	0.149	0.149	0.000	0.000	0.000	0.000
108	B	590	PRO	0	-0.045	-0.043	35.884	0.197	0.197	0.000	0.000	0.000	0.000
109	B	591	GLU	-1	-0.894	-0.950	36.504	7.835	7.835	0.000	0.000	0.000	0.000
110	B	592	GLU	-1	-0.896	-0.947	35.587	8.253	8.253	0.000	0.000	0.000	0.000
111	B	593	GLY	0	-0.002	0.003	32.624	0.239	0.239	0.000	0.000	0.000	0.000
112	B	594	SER	0	-0.028	-0.010	31.277	0.424	0.424	0.000	0.000	0.000	0.000
113	B	595	LEU	0	0.031	0.012	30.505	0.350	0.350	0.000	0.000	0.000	0.000
114	B	596	GLN	0	0.035	0.013	29.886	0.307	0.307	0.000	0.000	0.000	0.000
115	B	597	ALA	0	0.017	0.016	26.797	0.400	0.400	0.000	0.000	0.000	0.000
116	B	598	LEU	0	0.010	-0.008	25.658	0.561	0.561	0.000	0.000	0.000	0.000
117	B	599	PHE	0	-0.071	-0.025	25.923	0.431	0.431	0.000	0.000	0.000	0.000
118	B	600	GLN	0	0.006	0.007	22.561	0.663	0.663	0.000	0.000	0.000	0.000
119	B	601	HIS	0	-0.010	-0.008	20.271	1.111	1.111	0.000	0.000	0.000	0.000
120	B	602	GLY	0	0.020	0.012	21.372	0.601	0.601	0.000	0.000	0.000	0.000
121	B	603	GLY	0	0.011	-0.007	22.807	0.082	0.082	0.000	0.000	0.000	0.000
122	B	604	ASP	-1	-0.805	-0.858	20.200	14.469	14.469	0.000	0.000	0.000	0.000
123	B	605	VAL	0	0.062	0.019	23.524	-0.038	-0.038	0.000	0.000	0.000	0.000
124	B	606	SER	0	0.005	-0.014	22.592	-0.269	-0.269	0.000	0.000	0.000	0.000
125	B	607	ARG	1	0.815	0.899	17.640	-15.557	-15.557	0.000	0.000	0.000	0.000
126	B	608	ALA	0	0.020	0.021	22.163	-0.126	-0.126	0.000	0.000	0.000	0.000
127	B	609	LEU	0	0.024	0.020	25.247	-0.288	-0.288	0.000	0.000	0.000	0.000
128	B	610	THR	0	-0.053	-0.047	21.575	-0.106	-0.106	0.000	0.000	0.000	0.000
129	B	611	GLU	-1	-0.838	-0.879	22.951	12.330	12.330	0.000	0.000	0.000	0.000
130	B	612	LEU	0	0.034	0.015	24.764	-0.241	-0.241	0.000	0.000	0.000	0.000
131	B	613	GLN	0	-0.026	-0.016	27.551	-0.145	-0.145	0.000	0.000	0.000	0.000
132	B	614	ARG	1	0.850	0.906	20.687	-13.513	-13.513	0.000	0.000	0.000	0.000
133	B	615	GLN	0	-0.065	-0.054	26.435	-0.539	-0.539	0.000	0.000	0.000	0.000
134	B	616	ARG	1	0.848	0.940	28.966	-9.097	-9.097	0.000	0.000	0.000	0.000
135	B	617	LEU	0	-0.016	-0.009	28.666	-0.298	-0.298	0.000	0.000	0.000	0.000
136	B	618	GLU	-1	-0.756	-0.843	27.271	10.682	10.682	0.000	0.000	0.000	0.000
137	B	619	PRO	0	-0.001	-0.012	29.530	-0.032	-0.032	0.000	0.000	0.000	0.000
138	B	620	PHE	0	-0.037	-0.034	31.540	-0.240	-0.240	0.000	0.000	0.000	0.000
139	B	621	ARG	1	0.881	0.933	24.227	-11.235	-11.235	0.000	0.000	0.000	0.000
140	B	622	GLN	0	-0.056	-0.037	28.661	-0.085	-0.085	0.000	0.000	0.000	0.000
141	B	623	ARG	1	0.984	0.989	30.811	-8.544	-8.544	0.000	0.000	0.000	0.000
142	B	624	LEU	0	-0.086	-0.029	27.482	-0.137	-0.137	0.000	0.000	0.000	0.000
143	B	625	TRP	0	-0.096	-0.050	25.081	0.226	0.226	0.000	0.000	0.000	0.000
144	B	626	ASP	-1	-0.904	-0.937	31.439	8.636	8.636	0.000	0.000	0.000	0.000
145	B	627	SER	0	-0.067	-0.021	34.751	-0.310	-0.310	0.000	0.000	0.000	0.000

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