FMO DATABASE

FMODB ID: N96RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1273990.160573
FMO2-HF: Nuclear repulsion	1215223.227767
FMO2-HF: Total energy	-58766.932806
FMO2-MP2: Total energy	-58936.730318

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.
53.119	59.386	0.524	-2.668	-4.124	0.022

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 : -0.942 / q_NPA : -0.969

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	-0.008	0.007	2.912	-17.539	-12.999	0.309	-2.109	-2.740	0.020
4	B	485	ARG	1	0.967	0.995	2.874	-46.037	-44.899	0.217	-0.474	-0.881	0.002
5	B	486	GLU	-1	-0.979	-0.992	4.352	35.991	36.407	-0.001	-0.068	-0.348	0.000
6	B	487	GLU	-1	-0.873	-0.938	6.228	23.065	23.065	0.000	0.000	0.000	0.000
7	B	488	GLY	0	0.022	0.010	7.724	-3.838	-3.838	0.000	0.000	0.000	0.000
8	B	489	LEU	0	-0.046	-0.031	7.897	-2.866	-2.866	0.000	0.000	0.000	0.000
9	B	490	GLN	0	0.022	0.024	10.282	-3.200	-3.200	0.000	0.000	0.000	0.000
10	B	491	LEU	0	0.022	0.018	11.943	-2.143	-2.143	0.000	0.000	0.000	0.000
11	B	492	VAL	0	-0.027	-0.016	12.878	-1.637	-1.637	0.000	0.000	0.000	0.000
12	B	493	SER	0	-0.134	-0.083	14.460	-1.520	-1.520	0.000	0.000	0.000	0.000
13	B	494	MET	0	-0.026	-0.015	16.347	-0.896	-0.896	0.000	0.000	0.000	0.000
14	B	495	ILE	0	0.038	0.013	18.750	-0.668	-0.668	0.000	0.000	0.000	0.000
15	B	496	ARG	1	0.881	0.963	16.064	-17.864	-17.864	0.000	0.000	0.000	0.000
16	B	497	GLU	-1	-0.918	-0.975	21.689	10.746	10.746	0.000	0.000	0.000	0.000
17	B	498	GLY	0	-0.020	0.006	25.470	-0.037	-0.037	0.000	0.000	0.000	0.000
18	B	499	GLU	-1	-0.937	-0.951	20.306	15.035	15.035	0.000	0.000	0.000	0.000
19	B	500	ALA	0	-0.067	-0.045	24.017	-0.016	-0.016	0.000	0.000	0.000	0.000
20	B	501	ALA	0	0.029	0.007	21.697	0.463	0.463	0.000	0.000	0.000	0.000
21	B	502	GLY	0	-0.003	0.004	22.955	-0.531	-0.531	0.000	0.000	0.000	0.000
22	B	503	ALA	0	0.035	0.020	20.462	0.551	0.551	0.000	0.000	0.000	0.000
23	B	504	CYS	0	0.055	0.010	20.094	-1.006	-1.006	0.000	0.000	0.000	0.000
24	B	505	PRO	0	0.067	0.030	19.607	0.790	0.790	0.000	0.000	0.000	0.000
25	B	506	GLU	-1	-0.887	-0.954	19.111	13.648	13.648	0.000	0.000	0.000	0.000
26	B	507	GLU	-1	-0.800	-0.875	15.625	17.467	17.467	0.000	0.000	0.000	0.000
27	B	508	ILE	0	0.026	0.019	14.554	1.332	1.332	0.000	0.000	0.000	0.000
28	B	509	PHE	0	0.024	0.018	15.121	0.808	0.808	0.000	0.000	0.000	0.000
29	B	510	SER	0	-0.049	-0.039	13.641	0.286	0.286	0.000	0.000	0.000	0.000
30	B	511	ALA	0	-0.012	-0.004	10.713	1.242	1.242	0.000	0.000	0.000	0.000
31	B	512	LEU	0	-0.013	-0.018	10.442	1.814	1.814	0.000	0.000	0.000	0.000
32	B	513	GLN	0	0.011	0.015	12.227	0.063	0.063	0.000	0.000	0.000	0.000
33	B	514	TYR	0	-0.069	-0.042	4.592	2.915	3.088	-0.001	-0.017	-0.155	0.000
34	B	515	SER	0	-0.068	-0.032	7.859	2.334	2.334	0.000	0.000	0.000	0.000
35	B	516	GLY	0	0.001	0.012	8.932	0.449	0.449	0.000	0.000	0.000	0.000
36	B	517	THR	0	-0.117	-0.042	11.718	-1.262	-1.262	0.000	0.000	0.000	0.000
37	B	518	GLU	-1	-0.927	-0.977	14.889	13.820	13.820	0.000	0.000	0.000	0.000
38	B	519	VAL	0	0.020	0.015	17.348	-0.296	-0.296	0.000	0.000	0.000	0.000
39	B	520	PRO	0	0.028	0.005	19.984	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	521	LEU	0	0.065	0.029	21.420	0.076	0.076	0.000	0.000	0.000	0.000
41	B	522	GLN	0	-0.027	-0.034	23.177	0.159	0.159	0.000	0.000	0.000	0.000
42	B	523	TRP	0	0.009	0.020	22.022	-0.058	-0.058	0.000	0.000	0.000	0.000
43	B	524	LEU	0	0.052	0.021	19.306	-0.032	-0.032	0.000	0.000	0.000	0.000
44	B	525	ARG	1	0.927	0.959	23.744	-10.630	-10.630	0.000	0.000	0.000	0.000
45	B	526	SER	0	-0.068	-0.031	26.552	-0.226	-0.226	0.000	0.000	0.000	0.000
46	B	527	GLU	-1	-0.949	-0.960	24.821	11.068	11.068	0.000	0.000	0.000	0.000
47	B	528	LEU	0	-0.048	-0.013	22.243	0.090	0.090	0.000	0.000	0.000	0.000
48	B	529	PRO	0	-0.017	-0.007	26.475	-0.464	-0.464	0.000	0.000	0.000	0.000
49	B	530	TYR	0	0.035	-0.023	28.974	0.192	0.192	0.000	0.000	0.000	0.000
50	B	531	VAL	0	-0.025	-0.004	29.562	-0.031	-0.031	0.000	0.000	0.000	0.000
51	B	532	LEU	0	0.040	0.003	25.014	-0.167	-0.167	0.000	0.000	0.000	0.000
52	B	533	GLU	-1	-0.881	-0.945	28.205	10.609	10.609	0.000	0.000	0.000	0.000
53	B	534	MET	0	-0.008	0.020	30.630	-0.311	-0.311	0.000	0.000	0.000	0.000
54	B	535	VAL	0	-0.044	-0.015	31.121	-0.207	-0.207	0.000	0.000	0.000	0.000
55	B	536	ALA	0	0.022	-0.002	30.095	-0.195	-0.195	0.000	0.000	0.000	0.000
56	B	537	GLU	-1	-0.896	-0.922	32.181	8.728	8.728	0.000	0.000	0.000	0.000
57	B	538	LEU	0	-0.010	-0.012	35.282	-0.286	-0.286	0.000	0.000	0.000	0.000
58	B	539	ALA	0	-0.021	-0.009	34.198	-0.222	-0.222	0.000	0.000	0.000	0.000
59	B	540	GLY	0	-0.002	-0.008	35.655	-0.151	-0.151	0.000	0.000	0.000	0.000
60	B	541	GLN	0	-0.083	-0.050	36.902	-0.374	-0.374	0.000	0.000	0.000	0.000
61	B	542	GLN	0	-0.054	-0.017	39.555	-0.218	-0.218	0.000	0.000	0.000	0.000
62	B	543	ASP	-1	-0.839	-0.909	39.263	7.478	7.478	0.000	0.000	0.000	0.000
63	B	544	PRO	0	0.040	0.028	38.777	0.210	0.210	0.000	0.000	0.000	0.000
64	B	545	GLY	0	-0.031	0.000	39.316	0.070	0.070	0.000	0.000	0.000	0.000
65	B	546	LEU	0	-0.033	-0.028	35.467	0.108	0.108	0.000	0.000	0.000	0.000
66	B	547	GLY	0	-0.022	-0.002	34.535	0.320	0.320	0.000	0.000	0.000	0.000
67	B	548	ALA	0	0.020	0.012	31.269	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	549	PHE	0	0.037	0.010	30.223	0.234	0.234	0.000	0.000	0.000	0.000
69	B	550	SER	0	-0.001	-0.005	24.738	0.232	0.232	0.000	0.000	0.000	0.000
70	B	552	GLN	0	-0.013	-0.022	19.447	-0.699	-0.699	0.000	0.000	0.000	0.000
71	B	553	GLU	-1	-0.825	-0.886	23.321	10.917	10.917	0.000	0.000	0.000	0.000
72	B	554	ALA	0	0.033	0.016	26.748	-0.261	-0.261	0.000	0.000	0.000	0.000
73	B	555	ARG	1	0.853	0.900	19.086	-15.504	-15.504	0.000	0.000	0.000	0.000
74	B	556	ARG	1	0.767	0.894	23.479	-12.641	-12.641	0.000	0.000	0.000	0.000
75	B	557	ALA	0	0.067	0.028	26.385	-0.108	-0.108	0.000	0.000	0.000	0.000
76	B	558	TRP	0	0.014	-0.002	26.480	-0.133	-0.133	0.000	0.000	0.000	0.000
77	B	559	LEU	0	-0.029	-0.021	23.264	-0.108	-0.108	0.000	0.000	0.000	0.000
78	B	560	ASP	-1	-0.858	-0.913	27.793	11.404	11.404	0.000	0.000	0.000	0.000
79	B	561	ARG	1	0.771	0.882	29.812	-9.408	-9.408	0.000	0.000	0.000	0.000
80	B	562	HIS	0	0.003	0.007	30.594	-0.129	-0.129	0.000	0.000	0.000	0.000
81	B	563	GLY	0	0.008	0.009	30.961	-0.175	-0.175	0.000	0.000	0.000	0.000
82	B	564	ASN	0	-0.055	-0.027	32.069	-0.265	-0.265	0.000	0.000	0.000	0.000
83	B	565	LEU	0	0.033	-0.004	33.926	0.042	0.042	0.000	0.000	0.000	0.000
84	B	566	ASP	-1	-0.925	-0.965	36.103	7.823	7.823	0.000	0.000	0.000	0.000
85	B	567	GLU	-1	-0.842	-0.909	36.661	8.491	8.491	0.000	0.000	0.000	0.000
86	B	568	ALA	0	-0.021	-0.007	32.337	0.129	0.129	0.000	0.000	0.000	0.000
87	B	569	VAL	0	0.014	0.013	34.144	0.148	0.148	0.000	0.000	0.000	0.000
88	B	570	GLU	-1	-0.867	-0.946	36.051	8.044	8.044	0.000	0.000	0.000	0.000
89	B	571	GLU	-1	-0.967	-0.983	32.558	9.633	9.633	0.000	0.000	0.000	0.000
90	B	572	CYS	0	-0.040	-0.008	30.541	0.207	0.207	0.000	0.000	0.000	0.000
91	B	573	VAL	0	0.051	0.035	33.008	0.114	0.114	0.000	0.000	0.000	0.000
92	B	574	ARG	1	0.910	0.966	35.806	-8.430	-8.430	0.000	0.000	0.000	0.000
93	B	575	THR	0	-0.073	-0.054	29.683	0.053	0.053	0.000	0.000	0.000	0.000
94	B	576	ARG	1	0.820	0.898	29.284	-9.897	-9.897	0.000	0.000	0.000	0.000
95	B	577	ARG	1	0.901	0.924	32.858	-7.895	-7.895	0.000	0.000	0.000	0.000
96	B	578	ARG	1	0.930	0.964	30.235	-10.032	-10.032	0.000	0.000	0.000	0.000
97	B	579	LYS	1	0.874	0.920	27.068	-11.363	-11.363	0.000	0.000	0.000	0.000
98	B	580	VAL	0	0.030	0.026	32.561	0.048	0.048	0.000	0.000	0.000	0.000
99	B	581	GLN	0	-0.015	-0.016	34.658	-0.208	-0.208	0.000	0.000	0.000	0.000
100	B	582	GLU	-1	-0.917	-0.948	31.118	10.012	10.012	0.000	0.000	0.000	0.000
101	B	583	LEU	0	0.003	-0.007	29.173	0.006	0.006	0.000	0.000	0.000	0.000
102	B	584	GLN	0	0.041	0.045	33.178	-0.109	-0.109	0.000	0.000	0.000	0.000
103	B	585	SER	0	-0.122	-0.055	36.046	-0.138	-0.138	0.000	0.000	0.000	0.000
104	B	586	LEU	0	-0.054	-0.026	30.807	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	587	GLY	0	-0.068	-0.035	34.329	0.118	0.118	0.000	0.000	0.000	0.000
106	B	588	PHE	0	-0.047	-0.038	32.051	0.073	0.073	0.000	0.000	0.000	0.000
107	B	589	GLY	0	0.090	0.048	35.111	0.161	0.161	0.000	0.000	0.000	0.000
108	B	590	PRO	0	-0.053	-0.053	36.216	0.202	0.202	0.000	0.000	0.000	0.000
109	B	591	GLU	-1	-0.891	-0.948	36.953	7.765	7.765	0.000	0.000	0.000	0.000
110	B	592	GLU	-1	-0.900	-0.941	35.740	7.928	7.928	0.000	0.000	0.000	0.000
111	B	593	GLY	0	-0.026	-0.009	32.911	0.231	0.231	0.000	0.000	0.000	0.000
112	B	594	SER	0	-0.034	-0.016	31.531	0.415	0.415	0.000	0.000	0.000	0.000
113	B	595	LEU	0	0.031	0.005	30.985	0.350	0.350	0.000	0.000	0.000	0.000
114	B	596	GLN	0	0.004	0.004	29.954	0.199	0.199	0.000	0.000	0.000	0.000
115	B	597	ALA	0	0.026	0.022	26.986	0.419	0.419	0.000	0.000	0.000	0.000
116	B	598	LEU	0	0.038	0.003	25.908	0.555	0.555	0.000	0.000	0.000	0.000
117	B	599	PHE	0	-0.056	-0.004	26.199	0.434	0.434	0.000	0.000	0.000	0.000
118	B	600	GLN	0	-0.029	-0.019	23.099	0.828	0.828	0.000	0.000	0.000	0.000
119	B	601	HIS	0	-0.034	-0.020	21.208	1.091	1.091	0.000	0.000	0.000	0.000
120	B	602	GLY	0	0.020	0.011	22.139	0.415	0.415	0.000	0.000	0.000	0.000
121	B	603	GLY	0	0.019	0.006	23.142	0.064	0.064	0.000	0.000	0.000	0.000
122	B	604	ASP	-1	-0.883	-0.926	20.899	13.946	13.946	0.000	0.000	0.000	0.000
123	B	605	VAL	0	0.073	0.020	23.912	-0.012	-0.012	0.000	0.000	0.000	0.000
124	B	606	SER	0	0.037	0.023	22.323	-0.367	-0.367	0.000	0.000	0.000	0.000
125	B	607	ARG	1	0.886	0.943	17.604	-15.650	-15.650	0.000	0.000	0.000	0.000
126	B	608	ALA	0	0.048	0.031	22.287	-0.115	-0.115	0.000	0.000	0.000	0.000
127	B	609	LEU	0	0.010	0.002	25.523	-0.266	-0.266	0.000	0.000	0.000	0.000
128	B	610	THR	0	-0.026	-0.008	21.468	-0.145	-0.145	0.000	0.000	0.000	0.000
129	B	611	GLU	-1	-0.884	-0.915	23.374	11.959	11.959	0.000	0.000	0.000	0.000
130	B	612	LEU	0	0.038	0.001	24.844	-0.212	-0.212	0.000	0.000	0.000	0.000
131	B	613	GLN	0	-0.074	-0.036	27.617	-0.035	-0.035	0.000	0.000	0.000	0.000
132	B	614	ARG	1	0.875	0.939	20.299	-13.382	-13.382	0.000	0.000	0.000	0.000
133	B	615	GLN	0	-0.063	-0.040	26.757	-0.497	-0.497	0.000	0.000	0.000	0.000
134	B	616	ARG	1	0.993	0.994	29.103	-9.005	-9.005	0.000	0.000	0.000	0.000
135	B	617	LEU	0	-0.035	-0.021	28.172	-0.281	-0.281	0.000	0.000	0.000	0.000
136	B	618	GLU	-1	-0.751	-0.855	27.386	10.641	10.641	0.000	0.000	0.000	0.000
137	B	619	PRO	0	-0.012	-0.007	29.867	-0.046	-0.046	0.000	0.000	0.000	0.000
138	B	620	PHE	0	-0.063	-0.035	31.269	-0.156	-0.156	0.000	0.000	0.000	0.000
139	B	621	ARG	1	0.904	0.942	24.487	-11.035	-11.035	0.000	0.000	0.000	0.000
140	B	622	GLN	0	-0.058	-0.047	28.820	-0.186	-0.186	0.000	0.000	0.000	0.000
141	B	623	ARG	1	0.980	0.981	30.740	-8.443	-8.443	0.000	0.000	0.000	0.000
142	B	624	LEU	0	-0.084	-0.021	27.290	-0.137	-0.137	0.000	0.000	0.000	0.000
143	B	625	TRP	0	-0.062	-0.041	24.929	0.137	0.137	0.000	0.000	0.000	0.000
144	B	626	ASP	-1	-0.964	-0.957	30.917	8.324	8.324	0.000	0.000	0.000	0.000
145	B	627	SER	0	-0.027	0.004	34.493	-0.174	-0.174	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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