FMO DATABASE

FMODB ID: QYJ7Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1113627.226761
FMO2-HF: Nuclear repulsion	1059268.361669
FMO2-HF: Total energy	-54358.865092
FMO2-MP2: Total energy	-54515.083582

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.
-59.526	-66.266	0.254	7.588	-1.101	-0.003

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 : 1.016 / q_NPA : 1.022

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	-0.821	-0.861	2.680	-21.885	-28.734	0.255	7.591	-0.997	-0.003
4	A	483	LYS	1	0.813	0.864	5.212	28.813	28.922	-0.001	-0.003	-0.104	0.000
5	A	484	MET	0	0.076	0.043	7.491	1.569	1.569	0.000	0.000	0.000	0.000
6	A	485	ARG	1	0.832	0.894	5.262	27.094	27.094	0.000	0.000	0.000	0.000
7	A	486	GLU	-1	-0.804	-0.885	9.576	-21.802	-21.802	0.000	0.000	0.000	0.000
8	A	487	GLU	-1	-0.914	-0.939	11.339	-18.196	-18.196	0.000	0.000	0.000	0.000
9	A	488	GLY	0	0.039	0.019	13.227	1.112	1.112	0.000	0.000	0.000	0.000
10	A	489	LEU	0	-0.047	-0.032	12.183	0.963	0.963	0.000	0.000	0.000	0.000
11	A	490	GLN	0	-0.018	-0.017	14.055	1.215	1.215	0.000	0.000	0.000	0.000
12	A	491	LEU	0	0.049	0.034	17.545	0.719	0.719	0.000	0.000	0.000	0.000
13	A	492	VAL	0	-0.010	-0.020	18.383	0.696	0.696	0.000	0.000	0.000	0.000
14	A	493	SER	0	-0.031	-0.010	19.642	0.573	0.573	0.000	0.000	0.000	0.000
15	A	494	MET	0	0.013	0.009	21.448	0.490	0.490	0.000	0.000	0.000	0.000
16	A	495	ILE	0	0.012	0.008	22.242	0.465	0.465	0.000	0.000	0.000	0.000
17	A	496	ARG	1	0.883	0.948	21.997	11.354	11.354	0.000	0.000	0.000	0.000
18	A	497	GLU	-1	-0.977	-0.988	25.611	-10.014	-10.014	0.000	0.000	0.000	0.000
19	A	498	GLY	0	0.014	0.000	27.538	0.339	0.339	0.000	0.000	0.000	0.000
20	A	499	GLU	-1	-0.906	-0.957	27.478	-9.578	-9.578	0.000	0.000	0.000	0.000
21	A	500	ALA	0	-0.071	-0.041	29.702	0.322	0.322	0.000	0.000	0.000	0.000
22	A	501	ALA	0	-0.051	-0.025	31.515	0.249	0.249	0.000	0.000	0.000	0.000
23	A	502	GLY	0	-0.046	-0.014	33.556	0.209	0.209	0.000	0.000	0.000	0.000
24	A	503	ALA	0	-0.030	0.006	31.746	0.111	0.111	0.000	0.000	0.000	0.000
25	A	504	CYS	0	-0.046	-0.008	31.219	-0.228	-0.228	0.000	0.000	0.000	0.000
26	A	505	PRO	0	0.044	-0.001	26.467	-0.166	-0.166	0.000	0.000	0.000	0.000
27	A	506	GLU	-1	-0.847	-0.926	27.414	-10.083	-10.083	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.799	-0.895	29.644	-8.504	-8.504	0.000	0.000	0.000	0.000
29	A	508	ILE	0	-0.040	-0.017	25.339	-0.110	-0.110	0.000	0.000	0.000	0.000
30	A	509	PHE	0	-0.013	-0.010	21.986	-0.322	-0.322	0.000	0.000	0.000	0.000
31	A	510	SER	0	0.014	-0.018	26.267	-0.204	-0.204	0.000	0.000	0.000	0.000
32	A	511	ALA	0	-0.016	-0.015	29.027	0.051	0.051	0.000	0.000	0.000	0.000
33	A	512	LEU	0	-0.079	-0.021	22.531	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	513	GLN	0	-0.045	-0.026	25.525	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	514	TYR	0	-0.027	-0.014	26.603	0.040	0.040	0.000	0.000	0.000	0.000
36	A	515	DSN	0	-0.009	-0.019	27.985	0.168	0.168	0.000	0.000	0.000	0.000
37	A	516	GLY	0	0.009	0.021	24.748	0.080	0.080	0.000	0.000	0.000	0.000
38	A	517	THR	0	-0.056	-0.026	25.068	-0.043	-0.043	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.907	-0.964	22.193	-13.082	-13.082	0.000	0.000	0.000	0.000
40	A	519	VAL	0	-0.028	-0.012	25.069	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	520	PRO	0	0.090	0.046	26.059	0.432	0.432	0.000	0.000	0.000	0.000
42	A	521	LEU	0	0.036	0.017	28.969	0.362	0.362	0.000	0.000	0.000	0.000
43	A	522	GLN	0	-0.084	-0.048	31.333	0.122	0.122	0.000	0.000	0.000	0.000
44	A	523	TRP	0	0.094	0.044	31.035	0.350	0.350	0.000	0.000	0.000	0.000
45	A	524	LEU	0	0.015	-0.004	31.408	0.274	0.274	0.000	0.000	0.000	0.000
46	A	525	ARG	1	0.833	0.923	34.571	8.479	8.479	0.000	0.000	0.000	0.000
47	A	526	SER	0	-0.088	-0.058	35.846	0.247	0.247	0.000	0.000	0.000	0.000
48	A	527	GLU	-1	-0.848	-0.909	34.295	-8.221	-8.221	0.000	0.000	0.000	0.000
49	A	528	LEU	0	-0.037	-0.001	35.285	0.115	0.115	0.000	0.000	0.000	0.000
50	A	529	PRO	0	-0.011	-0.013	37.091	0.099	0.099	0.000	0.000	0.000	0.000
51	A	530	TYR	0	0.058	0.027	39.395	0.194	0.194	0.000	0.000	0.000	0.000
52	A	531	VAL	0	-0.015	0.010	35.530	0.036	0.036	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.021	-0.016	38.107	0.045	0.045	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.967	-0.978	40.819	-6.637	-6.637	0.000	0.000	0.000	0.000
55	A	534	MET	0	-0.011	0.001	40.337	0.092	0.092	0.000	0.000	0.000	0.000
56	A	535	VAL	0	-0.017	-0.010	38.787	0.046	0.046	0.000	0.000	0.000	0.000
57	A	536	ALA	0	-0.014	-0.018	41.872	0.099	0.099	0.000	0.000	0.000	0.000
58	A	537	GLU	-1	-0.895	-0.934	45.405	-6.578	-6.578	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.055	0.032	41.780	0.104	0.104	0.000	0.000	0.000	0.000
60	A	539	ALA	0	0.019	0.009	44.342	0.072	0.072	0.000	0.000	0.000	0.000
61	A	540	GLY	0	-0.056	-0.041	46.029	0.129	0.129	0.000	0.000	0.000	0.000
62	A	541	GLN	0	-0.129	-0.083	47.640	0.123	0.123	0.000	0.000	0.000	0.000
63	A	542	GLN	0	-0.060	-0.028	44.658	0.041	0.041	0.000	0.000	0.000	0.000
64	A	543	ASP	-1	-0.839	-0.907	48.659	-6.224	-6.224	0.000	0.000	0.000	0.000
65	A	544	PRO	0	-0.003	0.028	51.127	0.079	0.079	0.000	0.000	0.000	0.000
66	A	545	GLY	0	-0.016	-0.029	54.099	0.066	0.066	0.000	0.000	0.000	0.000
67	A	546	LEU	0	-0.066	-0.028	52.397	0.035	0.035	0.000	0.000	0.000	0.000
68	A	547	GLY	0	0.059	0.032	50.339	-0.116	-0.116	0.000	0.000	0.000	0.000
69	A	548	ALA	0	0.009	-0.004	51.794	0.077	0.077	0.000	0.000	0.000	0.000
70	A	549	PHE	0	0.041	0.015	46.817	0.046	0.046	0.000	0.000	0.000	0.000
71	A	550	SER	0	-0.006	-0.031	47.754	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	551	CYS	0	0.017	-0.005	43.560	-0.154	-0.154	0.000	0.000	0.000	0.000
73	A	552	GLN	0	0.032	0.011	42.299	-0.296	-0.296	0.000	0.000	0.000	0.000
74	A	553	GLU	-1	-0.797	-0.865	42.705	-6.566	-6.566	0.000	0.000	0.000	0.000
75	A	554	ALA	0	0.049	0.035	41.765	-0.133	-0.133	0.000	0.000	0.000	0.000
76	A	555	ARG	1	0.901	0.935	37.404	7.621	7.621	0.000	0.000	0.000	0.000
77	A	556	ARG	1	0.865	0.944	37.760	6.862	6.862	0.000	0.000	0.000	0.000
78	A	557	ALA	0	0.067	0.041	37.528	-0.190	-0.190	0.000	0.000	0.000	0.000
79	A	558	TRP	0	0.021	-0.009	32.386	-0.188	-0.188	0.000	0.000	0.000	0.000
80	A	559	LEU	0	-0.031	-0.008	32.830	-0.289	-0.289	0.000	0.000	0.000	0.000
81	A	560	ASP	-1	-0.924	-0.955	32.734	-8.394	-8.394	0.000	0.000	0.000	0.000
82	A	561	ARG	1	0.755	0.848	31.483	9.272	9.272	0.000	0.000	0.000	0.000
83	A	562	HIS	0	-0.018	-0.005	27.006	-0.173	-0.173	0.000	0.000	0.000	0.000
84	A	563	GLY	0	0.082	0.037	29.017	-0.381	-0.381	0.000	0.000	0.000	0.000
85	A	564	ASN	0	-0.049	-0.021	28.952	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	565	LEU	0	0.006	-0.002	32.486	0.229	0.229	0.000	0.000	0.000	0.000
87	A	566	ASP	-1	-0.905	-0.949	35.612	-8.165	-8.165	0.000	0.000	0.000	0.000
88	A	567	GLU	-1	-0.804	-0.893	32.770	-9.413	-9.413	0.000	0.000	0.000	0.000
89	A	568	ALA	0	-0.028	-0.004	36.139	0.198	0.198	0.000	0.000	0.000	0.000
90	A	569	VAL	0	0.007	0.014	37.848	0.228	0.228	0.000	0.000	0.000	0.000
91	A	570	GLU	-1	-0.773	-0.870	40.407	-6.967	-6.967	0.000	0.000	0.000	0.000
92	A	571	GLU	-1	-0.775	-0.866	39.277	-7.222	-7.222	0.000	0.000	0.000	0.000
93	A	572	CYS	0	-0.043	-0.014	41.248	0.234	0.234	0.000	0.000	0.000	0.000
94	A	573	VAL	0	0.035	0.013	43.158	0.203	0.203	0.000	0.000	0.000	0.000
95	A	574	ARG	1	0.803	0.912	43.604	6.875	6.875	0.000	0.000	0.000	0.000
96	A	575	THR	0	-0.003	-0.037	42.977	0.166	0.166	0.000	0.000	0.000	0.000
97	A	576	ARG	1	0.781	0.900	45.579	6.252	6.252	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.801	0.872	46.381	6.804	6.804	0.000	0.000	0.000	0.000
99	A	578	ARG	1	0.739	0.860	42.902	7.188	7.188	0.000	0.000	0.000	0.000
100	A	579	LYS	1	0.824	0.880	47.136	6.555	6.555	0.000	0.000	0.000	0.000
101	A	580	VAL	0	0.002	0.001	50.839	0.121	0.121	0.000	0.000	0.000	0.000
102	A	581	GLN	0	-0.002	0.002	51.010	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	582	GLU	-1	-0.841	-0.901	48.992	-6.275	-6.275	0.000	0.000	0.000	0.000
104	A	583	LEU	0	-0.025	0.003	53.585	0.066	0.066	0.000	0.000	0.000	0.000
105	A	584	GLN	0	0.004	-0.002	56.196	0.063	0.063	0.000	0.000	0.000	0.000
106	A	585	SER	0	-0.073	-0.047	59.930	0.134	0.134	0.000	0.000	0.000	0.000
107	A	586	LEU	0	0.019	0.026	58.870	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	587	GLY	0	0.042	0.014	62.686	0.055	0.055	0.000	0.000	0.000	0.000
109	A	588	PHE	0	-0.023	-0.004	63.020	0.078	0.078	0.000	0.000	0.000	0.000
110	A	589	GLY	0	0.033	0.016	65.303	-0.051	-0.051	0.000	0.000	0.000	0.000
111	A	590	PRO	0	-0.063	-0.044	66.986	0.003	0.003	0.000	0.000	0.000	0.000
112	A	591	GLU	-1	-0.843	-0.917	65.914	-4.571	-4.571	0.000	0.000	0.000	0.000
113	A	592	GLU	-1	-0.871	-0.942	61.296	-5.184	-5.184	0.000	0.000	0.000	0.000
114	A	593	GLY	0	0.005	0.017	62.317	-0.076	-0.076	0.000	0.000	0.000	0.000
115	A	594	SER	0	-0.053	-0.048	59.838	-0.060	-0.060	0.000	0.000	0.000	0.000
116	A	595	LEU	0	-0.030	-0.001	54.894	-0.095	-0.095	0.000	0.000	0.000	0.000
117	A	596	GLN	0	0.029	0.001	55.896	-0.144	-0.144	0.000	0.000	0.000	0.000
118	A	597	ALA	0	0.031	0.032	56.313	-0.085	-0.085	0.000	0.000	0.000	0.000
119	A	598	LEU	0	0.001	-0.017	51.893	-0.086	-0.086	0.000	0.000	0.000	0.000
120	A	599	PHE	0	-0.031	-0.003	51.075	-0.107	-0.107	0.000	0.000	0.000	0.000
121	A	600	GLN	0	-0.038	-0.021	51.973	-0.057	-0.057	0.000	0.000	0.000	0.000
122	A	601	HIS	0	0.004	0.001	52.222	-0.070	-0.070	0.000	0.000	0.000	0.000
123	A	602	GLY	0	0.001	0.012	48.183	-0.080	-0.080	0.000	0.000	0.000	0.000
124	A	603	GLY	0	0.026	0.006	47.062	-0.179	-0.179	0.000	0.000	0.000	0.000
125	A	604	ASP	-1	-0.817	-0.875	48.820	-6.061	-6.061	0.000	0.000	0.000	0.000
126	A	605	VAL	0	0.045	0.006	49.909	0.123	0.123	0.000	0.000	0.000	0.000
127	A	606	SER	0	-0.052	-0.030	51.807	0.138	0.138	0.000	0.000	0.000	0.000
128	A	607	ARG	1	0.875	0.927	50.611	5.982	5.982	0.000	0.000	0.000	0.000
129	A	608	ALA	0	0.020	0.014	54.105	0.112	0.112	0.000	0.000	0.000	0.000
130	A	609	LEU	0	0.018	-0.002	55.894	0.102	0.102	0.000	0.000	0.000	0.000
131	A	610	THR	0	-0.041	-0.024	57.231	0.116	0.116	0.000	0.000	0.000	0.000
132	A	611	GLU	-1	-0.863	-0.916	58.609	-4.970	-4.970	0.000	0.000	0.000	0.000
133	A	612	LEU	0	-0.056	-0.009	58.549	0.078	0.078	0.000	0.000	0.000	0.000
134	A	613	GLN	0	-0.096	-0.034	61.150	0.147	0.147	0.000	0.000	0.000	0.000
135	A	614	ARG	1	0.802	0.893	63.292	4.917	4.917	0.000	0.000	0.000	0.000
136	A	615	GLN	0	-0.063	-0.042	66.503	0.059	0.059	0.000	0.000	0.000	0.000

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