FMO DATABASE

FMODB ID: Z61RN

Calculation Name: 5X0W-A-Xray372

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 5X0W

Chain ID: A

ChEMBL ID: CHEMBL4296109

UniProt ID: Q96EP0

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1109775.317585
FMO2-HF: Nuclear repulsion	1055417.880768
FMO2-HF: Total energy	-54357.436816
FMO2-MP2: Total energy	-54513.767976

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:480:ARG)

Summations of interaction energy for fragment #1(A:480:ARG)

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.
-45.763	-68.074	0.133	23.4	-1.222	-0.008

Interaction energy analysis for fragmet #1(A:480:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 1.002

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	482	ASP	-1	-0.854	-0.910	2.403	-3.838	-26.235	0.134	23.403	-1.140	-0.008
4	A	483	LYS	1	0.826	0.876	5.306	27.831	27.917	-0.001	-0.003	-0.082	0.000
5	A	484	MET	0	0.051	0.029	7.401	1.546	1.546	0.000	0.000	0.000	0.000
6	A	485	ARG	1	0.886	0.941	6.425	23.600	23.600	0.000	0.000	0.000	0.000
7	A	486	GLU	-1	-0.807	-0.877	9.494	-22.414	-22.414	0.000	0.000	0.000	0.000
8	A	487	GLU	-1	-0.918	-0.950	11.331	-16.964	-16.964	0.000	0.000	0.000	0.000
9	A	488	GLY	0	0.032	0.014	13.262	1.059	1.059	0.000	0.000	0.000	0.000
10	A	489	LEU	0	-0.043	-0.033	12.752	0.926	0.926	0.000	0.000	0.000	0.000
11	A	490	GLN	0	-0.021	-0.014	13.668	1.100	1.100	0.000	0.000	0.000	0.000
12	A	491	LEU	0	0.062	0.037	17.483	0.698	0.698	0.000	0.000	0.000	0.000
13	A	492	VAL	0	-0.007	-0.018	18.690	0.678	0.678	0.000	0.000	0.000	0.000
14	A	493	SER	0	-0.071	-0.030	19.885	0.726	0.726	0.000	0.000	0.000	0.000
15	A	494	MET	0	0.040	0.017	21.696	0.482	0.482	0.000	0.000	0.000	0.000
16	A	495	ILE	0	0.009	0.012	22.567	0.442	0.442	0.000	0.000	0.000	0.000
17	A	496	ARG	1	0.941	0.977	21.737	11.656	11.656	0.000	0.000	0.000	0.000
18	A	497	GLU	-1	-0.980	-0.992	25.888	-10.059	-10.059	0.000	0.000	0.000	0.000
19	A	498	GLY	0	0.019	-0.008	27.602	0.336	0.336	0.000	0.000	0.000	0.000
20	A	499	GLU	-1	-0.942	-0.957	29.033	-9.027	-9.027	0.000	0.000	0.000	0.000
21	A	500	ALA	0	-0.075	-0.038	30.431	0.317	0.317	0.000	0.000	0.000	0.000
22	A	501	ALA	0	-0.075	-0.036	32.287	0.268	0.268	0.000	0.000	0.000	0.000
23	A	502	GLY	0	-0.046	-0.020	34.181	0.185	0.185	0.000	0.000	0.000	0.000
24	A	503	ALA	0	-0.031	-0.002	31.568	0.114	0.114	0.000	0.000	0.000	0.000
25	A	504	CYS	0	-0.036	0.002	31.489	-0.213	-0.213	0.000	0.000	0.000	0.000
26	A	505	PRO	0	0.052	-0.005	26.999	-0.156	-0.156	0.000	0.000	0.000	0.000
27	A	506	GLU	-1	-0.838	-0.929	27.724	-9.806	-9.806	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.888	-0.948	29.871	-8.440	-8.440	0.000	0.000	0.000	0.000
29	A	508	ILE	0	-0.039	-0.010	25.374	-0.106	-0.106	0.000	0.000	0.000	0.000
30	A	509	PHE	0	-0.013	-0.012	22.099	-0.309	-0.309	0.000	0.000	0.000	0.000
31	A	510	SER	0	0.022	-0.005	26.207	-0.194	-0.194	0.000	0.000	0.000	0.000
32	A	511	ALA	0	-0.038	-0.020	28.808	0.028	0.028	0.000	0.000	0.000	0.000
33	A	512	LEU	0	-0.099	-0.039	22.527	-0.136	-0.136	0.000	0.000	0.000	0.000
34	A	513	GLN	0	-0.042	-0.024	25.398	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	514	TYR	0	-0.029	-0.010	26.316	0.076	0.076	0.000	0.000	0.000	0.000
36	A	515	DSN	0	-0.028	-0.016	27.451	0.077	0.077	0.000	0.000	0.000	0.000
37	A	516	GLY	0	0.045	0.016	24.665	0.180	0.180	0.000	0.000	0.000	0.000
38	A	517	THR	0	-0.070	-0.013	25.306	-0.077	-0.077	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.896	-0.954	21.985	-13.428	-13.428	0.000	0.000	0.000	0.000
40	A	519	VAL	0	-0.068	-0.032	25.038	0.016	0.016	0.000	0.000	0.000	0.000
41	A	520	PRO	0	0.088	0.034	25.835	0.321	0.321	0.000	0.000	0.000	0.000
42	A	521	LEU	0	0.055	0.021	28.847	0.338	0.338	0.000	0.000	0.000	0.000
43	A	522	GLN	0	-0.059	-0.051	31.409	0.111	0.111	0.000	0.000	0.000	0.000
44	A	523	TRP	0	0.088	0.045	30.983	0.340	0.340	0.000	0.000	0.000	0.000
45	A	524	LEU	0	0.020	0.019	32.133	0.235	0.235	0.000	0.000	0.000	0.000
46	A	525	ARG	1	0.899	0.946	34.630	8.427	8.427	0.000	0.000	0.000	0.000
47	A	526	SER	0	-0.054	-0.037	35.742	0.199	0.199	0.000	0.000	0.000	0.000
48	A	527	GLU	-1	-0.943	-0.979	34.510	-8.192	-8.192	0.000	0.000	0.000	0.000
49	A	528	LEU	0	-0.033	0.026	34.904	0.091	0.091	0.000	0.000	0.000	0.000
50	A	529	PRO	0	-0.023	-0.019	37.072	0.105	0.105	0.000	0.000	0.000	0.000
51	A	530	TYR	0	0.070	0.028	39.830	0.209	0.209	0.000	0.000	0.000	0.000
52	A	531	VAL	0	0.018	0.025	35.604	0.054	0.054	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.030	-0.022	38.007	0.060	0.060	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.960	-0.977	40.611	-6.630	-6.630	0.000	0.000	0.000	0.000
55	A	534	MET	0	-0.013	0.005	40.231	0.104	0.104	0.000	0.000	0.000	0.000
56	A	535	VAL	0	-0.031	-0.022	38.616	0.035	0.035	0.000	0.000	0.000	0.000
57	A	536	ALA	0	-0.020	-0.019	41.632	0.110	0.110	0.000	0.000	0.000	0.000
58	A	537	GLU	-1	-0.903	-0.933	45.199	-6.552	-6.552	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.066	0.031	41.518	0.096	0.096	0.000	0.000	0.000	0.000
60	A	539	ALA	0	-0.011	-0.013	44.040	0.074	0.074	0.000	0.000	0.000	0.000
61	A	540	GLY	0	-0.063	-0.048	45.690	0.118	0.118	0.000	0.000	0.000	0.000
62	A	541	GLN	0	-0.099	-0.064	48.138	0.125	0.125	0.000	0.000	0.000	0.000
63	A	542	GLN	0	-0.025	0.004	43.369	0.080	0.080	0.000	0.000	0.000	0.000
64	A	543	ASP	-1	-0.848	-0.910	48.391	-6.109	-6.109	0.000	0.000	0.000	0.000
65	A	544	PRO	0	-0.021	0.018	50.811	0.079	0.079	0.000	0.000	0.000	0.000
66	A	545	GLY	0	-0.020	-0.035	53.669	0.060	0.060	0.000	0.000	0.000	0.000
67	A	546	LEU	0	0.010	0.059	52.315	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	547	GLY	0	0.206	0.135	50.497	-0.109	-0.109	0.000	0.000	0.000	0.000
69	A	548	ALA	0	-0.157	-0.166	51.768	0.112	0.112	0.000	0.000	0.000	0.000
70	A	549	PHE	0	0.040	0.024	46.728	0.045	0.045	0.000	0.000	0.000	0.000
71	A	550	SER	0	-0.009	0.006	47.827	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	551	CYS	0	0.027	0.002	43.190	-0.140	-0.140	0.000	0.000	0.000	0.000
73	A	552	GLN	0	0.023	0.004	42.358	-0.293	-0.293	0.000	0.000	0.000	0.000
74	A	553	GLU	-1	-0.825	-0.896	42.652	-6.548	-6.548	0.000	0.000	0.000	0.000
75	A	554	ALA	0	0.064	0.033	41.795	-0.139	-0.139	0.000	0.000	0.000	0.000
76	A	555	ARG	1	0.950	0.969	38.413	7.336	7.336	0.000	0.000	0.000	0.000
77	A	556	ARG	1	0.935	0.972	37.830	6.868	6.868	0.000	0.000	0.000	0.000
78	A	557	ALA	0	0.035	0.028	37.802	-0.155	-0.155	0.000	0.000	0.000	0.000
79	A	558	TRP	0	0.022	-0.009	32.377	-0.191	-0.191	0.000	0.000	0.000	0.000
80	A	559	LEU	0	-0.038	-0.017	32.936	-0.260	-0.260	0.000	0.000	0.000	0.000
81	A	560	ASP	-1	-0.901	-0.939	32.814	-8.348	-8.348	0.000	0.000	0.000	0.000
82	A	561	ARG	1	0.738	0.852	31.386	9.092	9.092	0.000	0.000	0.000	0.000
83	A	562	HIS	0	-0.018	-0.003	26.727	-0.136	-0.136	0.000	0.000	0.000	0.000
84	A	563	GLY	0	0.084	0.043	29.068	-0.334	-0.334	0.000	0.000	0.000	0.000
85	A	564	ASN	0	-0.042	-0.010	28.972	-0.152	-0.152	0.000	0.000	0.000	0.000
86	A	565	LEU	0	0.035	0.014	32.431	0.237	0.237	0.000	0.000	0.000	0.000
87	A	566	ASP	-1	-0.897	-0.955	35.578	-8.013	-8.013	0.000	0.000	0.000	0.000
88	A	567	GLU	-1	-0.833	-0.912	32.592	-9.382	-9.382	0.000	0.000	0.000	0.000
89	A	568	ALA	0	-0.035	-0.009	36.060	0.192	0.192	0.000	0.000	0.000	0.000
90	A	569	VAL	0	0.005	0.004	37.621	0.233	0.233	0.000	0.000	0.000	0.000
91	A	570	GLU	-1	-0.924	-0.944	39.614	-7.113	-7.113	0.000	0.000	0.000	0.000
92	A	571	GLU	-1	-0.788	-0.883	38.754	-7.284	-7.284	0.000	0.000	0.000	0.000
93	A	572	CYS	0	-0.033	-0.007	40.836	0.225	0.225	0.000	0.000	0.000	0.000
94	A	573	VAL	0	0.038	0.017	43.047	0.207	0.207	0.000	0.000	0.000	0.000
95	A	574	ARG	1	0.867	0.952	43.320	6.922	6.922	0.000	0.000	0.000	0.000
96	A	575	THR	0	-0.018	-0.047	42.730	0.193	0.193	0.000	0.000	0.000	0.000
97	A	576	ARG	1	0.806	0.896	45.429	6.268	6.268	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.859	0.908	47.408	6.593	6.593	0.000	0.000	0.000	0.000
99	A	578	ARG	1	0.780	0.876	43.001	7.097	7.097	0.000	0.000	0.000	0.000
100	A	579	LYS	1	0.841	0.906	47.549	6.459	6.459	0.000	0.000	0.000	0.000
101	A	580	VAL	0	0.001	-0.005	50.985	0.117	0.117	0.000	0.000	0.000	0.000
102	A	581	GLN	0	-0.076	-0.044	51.471	0.004	0.004	0.000	0.000	0.000	0.000
103	A	582	GLU	-1	-0.829	-0.892	49.407	-6.181	-6.181	0.000	0.000	0.000	0.000
104	A	583	LEU	0	-0.022	0.002	54.103	0.076	0.076	0.000	0.000	0.000	0.000
105	A	584	GLN	0	-0.012	-0.001	56.985	0.050	0.050	0.000	0.000	0.000	0.000
106	A	585	SER	0	-0.076	-0.038	60.454	0.100	0.100	0.000	0.000	0.000	0.000
107	A	586	LEU	0	0.036	0.022	59.240	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	587	GLY	0	0.039	0.006	63.065	0.056	0.056	0.000	0.000	0.000	0.000
109	A	588	PHE	0	-0.065	-0.023	62.985	0.072	0.072	0.000	0.000	0.000	0.000
110	A	589	GLY	0	0.053	0.032	65.195	-0.058	-0.058	0.000	0.000	0.000	0.000
111	A	590	PRO	0	-0.057	-0.043	67.396	0.002	0.002	0.000	0.000	0.000	0.000
112	A	591	GLU	-1	-0.855	-0.930	65.826	-4.601	-4.601	0.000	0.000	0.000	0.000
113	A	592	GLU	-1	-0.925	-0.972	61.809	-5.113	-5.113	0.000	0.000	0.000	0.000
114	A	593	GLY	0	0.026	0.025	62.092	-0.073	-0.073	0.000	0.000	0.000	0.000
115	A	594	SER	0	-0.049	-0.028	60.009	-0.061	-0.061	0.000	0.000	0.000	0.000
116	A	595	LEU	0	-0.025	-0.003	54.323	-0.090	-0.090	0.000	0.000	0.000	0.000
117	A	596	GLN	0	0.023	-0.006	55.829	-0.153	-0.153	0.000	0.000	0.000	0.000
118	A	597	ALA	0	0.055	0.046	56.726	-0.064	-0.064	0.000	0.000	0.000	0.000
119	A	598	LEU	0	0.004	-0.012	51.707	-0.078	-0.078	0.000	0.000	0.000	0.000
120	A	599	PHE	0	-0.040	-0.005	50.925	-0.106	-0.106	0.000	0.000	0.000	0.000
121	A	600	GLN	0	-0.018	-0.012	52.247	-0.065	-0.065	0.000	0.000	0.000	0.000
122	A	601	HIS	0	-0.025	-0.018	52.791	-0.083	-0.083	0.000	0.000	0.000	0.000
123	A	602	GLY	0	-0.016	-0.009	48.738	-0.077	-0.077	0.000	0.000	0.000	0.000
124	A	603	GLY	0	-0.001	-0.013	47.773	-0.141	-0.141	0.000	0.000	0.000	0.000
125	A	604	ASP	-1	-0.941	-0.971	48.859	-6.116	-6.116	0.000	0.000	0.000	0.000
126	A	605	VAL	0	0.028	0.001	50.354	0.124	0.124	0.000	0.000	0.000	0.000
127	A	606	SER	0	-0.007	-0.007	52.437	0.138	0.138	0.000	0.000	0.000	0.000
128	A	607	ARG	1	0.954	1.000	52.234	5.830	5.830	0.000	0.000	0.000	0.000
129	A	608	ALA	0	0.033	0.018	54.299	0.103	0.103	0.000	0.000	0.000	0.000
130	A	609	LEU	0	-0.004	0.000	56.061	0.096	0.096	0.000	0.000	0.000	0.000
131	A	610	THR	0	-0.050	-0.045	57.659	0.110	0.110	0.000	0.000	0.000	0.000
132	A	611	GLU	-1	-0.957	-0.972	58.739	-5.003	-5.003	0.000	0.000	0.000	0.000
133	A	612	LEU	0	-0.075	-0.024	58.738	0.086	0.086	0.000	0.000	0.000	0.000
134	A	613	GLN	0	-0.040	-0.005	61.827	0.071	0.071	0.000	0.000	0.000	0.000
135	A	614	ARG	1	0.914	0.965	63.851	4.789	4.789	0.000	0.000	0.000	0.000
136	A	615	GLN	0	-0.042	-0.024	66.755	0.048	0.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:480:ARG)