FMO DATABASE

FMODB ID: R9VN8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1110389.187763
FMO2-HF: Nuclear repulsion	1056031.243438
FMO2-HF: Total energy	-54357.944325
FMO2-MP2: Total energy	-54514.284898

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.
-47.593	-69.218	0.036	22.765	-1.176	-0.009

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 : 0.980 / q_NPA : 1.030

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	-0.846	-0.893	2.438	-9.371	-31.090	0.037	22.769	-1.087	-0.009
4	A	483	LYS	1	0.840	0.887	5.040	28.191	28.285	-0.001	-0.004	-0.089	0.000
5	A	484	MET	0	0.057	0.033	7.433	1.623	1.623	0.000	0.000	0.000	0.000
6	A	485	ARG	1	0.849	0.905	5.386	26.650	26.650	0.000	0.000	0.000	0.000
7	A	486	GLU	-1	-0.804	-0.884	9.531	-22.012	-22.012	0.000	0.000	0.000	0.000
8	A	487	GLU	-1	-0.917	-0.946	11.362	-17.552	-17.552	0.000	0.000	0.000	0.000
9	A	488	GLY	0	0.030	0.018	13.129	1.108	1.108	0.000	0.000	0.000	0.000
10	A	489	LEU	0	-0.042	-0.030	12.400	0.998	0.998	0.000	0.000	0.000	0.000
11	A	490	GLN	0	-0.019	-0.014	13.879	1.184	1.184	0.000	0.000	0.000	0.000
12	A	491	LEU	0	0.057	0.034	17.513	0.736	0.736	0.000	0.000	0.000	0.000
13	A	492	VAL	0	-0.009	-0.018	18.282	0.696	0.696	0.000	0.000	0.000	0.000
14	A	493	SER	0	-0.043	-0.017	19.673	0.604	0.604	0.000	0.000	0.000	0.000
15	A	494	MET	0	0.010	0.004	21.522	0.502	0.502	0.000	0.000	0.000	0.000
16	A	495	ILE	0	0.014	0.014	22.378	0.454	0.454	0.000	0.000	0.000	0.000
17	A	496	ARG	1	0.943	0.980	21.355	11.655	11.655	0.000	0.000	0.000	0.000
18	A	497	GLU	-1	-0.981	-0.992	25.691	-10.036	-10.036	0.000	0.000	0.000	0.000
19	A	498	GLY	0	0.025	-0.008	27.489	0.345	0.345	0.000	0.000	0.000	0.000
20	A	499	GLU	-1	-0.949	-0.961	28.343	-9.261	-9.261	0.000	0.000	0.000	0.000
21	A	500	ALA	0	-0.076	-0.039	30.097	0.324	0.324	0.000	0.000	0.000	0.000
22	A	501	ALA	0	-0.069	-0.033	31.965	0.275	0.275	0.000	0.000	0.000	0.000
23	A	502	GLY	0	-0.043	-0.016	33.929	0.188	0.188	0.000	0.000	0.000	0.000
24	A	503	ALA	0	-0.031	-0.005	31.547	0.116	0.116	0.000	0.000	0.000	0.000
25	A	504	CYS	0	-0.026	0.005	31.225	-0.206	-0.206	0.000	0.000	0.000	0.000
26	A	505	PRO	0	0.059	0.001	26.566	-0.147	-0.147	0.000	0.000	0.000	0.000
27	A	506	GLU	-1	-0.847	-0.932	27.585	-9.965	-9.965	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.850	-0.929	29.701	-8.439	-8.439	0.000	0.000	0.000	0.000
29	A	508	ILE	0	-0.044	-0.014	25.419	-0.104	-0.104	0.000	0.000	0.000	0.000
30	A	509	PHE	0	-0.002	-0.009	21.849	-0.306	-0.306	0.000	0.000	0.000	0.000
31	A	510	SER	0	0.020	-0.008	26.244	-0.197	-0.197	0.000	0.000	0.000	0.000
32	A	511	ALA	0	-0.036	-0.023	28.929	0.035	0.035	0.000	0.000	0.000	0.000
33	A	512	LEU	0	-0.095	-0.036	22.571	-0.132	-0.132	0.000	0.000	0.000	0.000
34	A	513	GLN	0	-0.049	-0.028	25.426	-0.059	-0.059	0.000	0.000	0.000	0.000
35	A	514	TYR	0	-0.020	-0.004	26.348	0.087	0.087	0.000	0.000	0.000	0.000
36	A	515	DSN	0	-0.024	-0.016	27.559	0.076	0.076	0.000	0.000	0.000	0.000
37	A	516	GLY	0	0.039	0.012	24.688	0.171	0.171	0.000	0.000	0.000	0.000
38	A	517	THR	0	-0.080	-0.024	25.325	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.886	-0.946	22.209	-13.353	-13.353	0.000	0.000	0.000	0.000
40	A	519	VAL	0	-0.067	-0.031	25.058	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	520	PRO	0	0.074	0.032	25.962	0.327	0.327	0.000	0.000	0.000	0.000
42	A	521	LEU	0	0.057	0.021	28.874	0.351	0.351	0.000	0.000	0.000	0.000
43	A	522	GLN	0	-0.059	-0.049	31.439	0.097	0.097	0.000	0.000	0.000	0.000
44	A	523	TRP	0	0.079	0.044	30.994	0.316	0.316	0.000	0.000	0.000	0.000
45	A	524	LEU	0	0.013	0.013	32.053	0.245	0.245	0.000	0.000	0.000	0.000
46	A	525	ARG	1	0.901	0.944	34.659	8.401	8.401	0.000	0.000	0.000	0.000
47	A	526	SER	0	-0.102	-0.054	35.732	0.252	0.252	0.000	0.000	0.000	0.000
48	A	527	GLU	-1	-0.869	-0.931	34.365	-8.192	-8.192	0.000	0.000	0.000	0.000
49	A	528	LEU	0	-0.032	0.009	35.098	0.089	0.089	0.000	0.000	0.000	0.000
50	A	529	PRO	0	-0.008	-0.011	37.101	0.101	0.101	0.000	0.000	0.000	0.000
51	A	530	TYR	0	0.057	0.023	39.583	0.203	0.203	0.000	0.000	0.000	0.000
52	A	531	VAL	0	0.005	0.018	35.622	0.044	0.044	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.030	-0.018	38.001	0.053	0.053	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.956	-0.978	40.643	-6.633	-6.633	0.000	0.000	0.000	0.000
55	A	534	MET	0	-0.017	0.004	40.270	0.104	0.104	0.000	0.000	0.000	0.000
56	A	535	VAL	0	-0.029	-0.020	38.612	0.036	0.036	0.000	0.000	0.000	0.000
57	A	536	ALA	0	-0.013	-0.014	41.666	0.107	0.107	0.000	0.000	0.000	0.000
58	A	537	GLU	-1	-0.908	-0.938	45.233	-6.566	-6.566	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.061	0.029	41.550	0.094	0.094	0.000	0.000	0.000	0.000
60	A	539	ALA	0	0.003	0.002	44.059	0.074	0.074	0.000	0.000	0.000	0.000
61	A	540	GLY	0	-0.070	-0.053	45.725	0.119	0.119	0.000	0.000	0.000	0.000
62	A	541	GLN	0	-0.117	-0.068	47.891	0.122	0.122	0.000	0.000	0.000	0.000
63	A	542	GLN	0	-0.057	-0.021	44.056	0.071	0.071	0.000	0.000	0.000	0.000
64	A	543	ASP	-1	-0.852	-0.916	48.425	-6.148	-6.148	0.000	0.000	0.000	0.000
65	A	544	PRO	0	-0.007	0.034	50.848	0.074	0.074	0.000	0.000	0.000	0.000
66	A	545	GLY	0	-0.011	-0.037	53.705	0.060	0.060	0.000	0.000	0.000	0.000
67	A	546	LEU	0	-0.007	0.046	52.347	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	547	GLY	0	0.206	0.144	50.483	-0.108	-0.108	0.000	0.000	0.000	0.000
69	A	548	ALA	0	-0.151	-0.164	51.803	0.117	0.117	0.000	0.000	0.000	0.000
70	A	549	PHE	0	0.008	0.009	46.776	0.043	0.043	0.000	0.000	0.000	0.000
71	A	550	SER	0	-0.032	-0.045	47.705	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	551	CYS	0	0.025	-0.002	43.646	-0.149	-0.149	0.000	0.000	0.000	0.000
73	A	552	GLN	0	0.038	0.011	42.388	-0.297	-0.297	0.000	0.000	0.000	0.000
74	A	553	GLU	-1	-0.806	-0.859	42.650	-6.582	-6.582	0.000	0.000	0.000	0.000
75	A	554	ALA	0	0.062	0.029	41.914	-0.147	-0.147	0.000	0.000	0.000	0.000
76	A	555	ARG	1	0.928	0.964	37.853	7.519	7.519	0.000	0.000	0.000	0.000
77	A	556	ARG	1	0.911	0.963	37.869	6.895	6.895	0.000	0.000	0.000	0.000
78	A	557	ALA	0	0.030	0.023	37.714	-0.159	-0.159	0.000	0.000	0.000	0.000
79	A	558	TRP	0	0.038	-0.004	32.257	-0.198	-0.198	0.000	0.000	0.000	0.000
80	A	559	LEU	0	-0.046	-0.019	33.066	-0.261	-0.261	0.000	0.000	0.000	0.000
81	A	560	ASP	-1	-0.915	-0.944	32.720	-8.409	-8.409	0.000	0.000	0.000	0.000
82	A	561	ARG	1	0.727	0.840	31.182	9.215	9.215	0.000	0.000	0.000	0.000
83	A	562	HIS	0	-0.027	-0.009	26.477	-0.106	-0.106	0.000	0.000	0.000	0.000
84	A	563	GLY	0	0.078	0.041	29.105	-0.341	-0.341	0.000	0.000	0.000	0.000
85	A	564	ASN	0	-0.051	-0.014	28.954	-0.149	-0.149	0.000	0.000	0.000	0.000
86	A	565	LEU	0	0.037	0.014	32.466	0.242	0.242	0.000	0.000	0.000	0.000
87	A	566	ASP	-1	-0.899	-0.953	35.609	-8.086	-8.086	0.000	0.000	0.000	0.000
88	A	567	GLU	-1	-0.805	-0.893	32.710	-9.420	-9.420	0.000	0.000	0.000	0.000
89	A	568	ALA	0	-0.039	-0.010	36.082	0.192	0.192	0.000	0.000	0.000	0.000
90	A	569	VAL	0	0.012	0.004	37.659	0.224	0.224	0.000	0.000	0.000	0.000
91	A	570	GLU	-1	-0.885	-0.925	39.800	-7.084	-7.084	0.000	0.000	0.000	0.000
92	A	571	GLU	-1	-0.782	-0.868	38.887	-7.285	-7.285	0.000	0.000	0.000	0.000
93	A	572	CYS	0	-0.038	-0.003	40.872	0.234	0.234	0.000	0.000	0.000	0.000
94	A	573	VAL	0	0.053	0.018	43.087	0.211	0.211	0.000	0.000	0.000	0.000
95	A	574	ARG	1	0.857	0.949	43.303	6.913	6.913	0.000	0.000	0.000	0.000
96	A	575	THR	0	-0.011	-0.043	42.645	0.189	0.189	0.000	0.000	0.000	0.000
97	A	576	ARG	1	0.816	0.902	45.288	6.292	6.292	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.846	0.904	46.997	6.692	6.692	0.000	0.000	0.000	0.000
99	A	578	ARG	1	0.783	0.867	42.711	7.164	7.164	0.000	0.000	0.000	0.000
100	A	579	LYS	1	0.827	0.897	47.183	6.513	6.513	0.000	0.000	0.000	0.000
101	A	580	VAL	0	0.003	-0.005	50.731	0.118	0.118	0.000	0.000	0.000	0.000
102	A	581	GLN	0	-0.057	-0.034	51.107	0.000	0.000	0.000	0.000	0.000	0.000
103	A	582	GLU	-1	-0.826	-0.889	49.026	-6.232	-6.232	0.000	0.000	0.000	0.000
104	A	583	LEU	0	-0.027	0.000	53.699	0.076	0.076	0.000	0.000	0.000	0.000
105	A	584	GLN	0	-0.008	0.002	56.466	0.052	0.052	0.000	0.000	0.000	0.000
106	A	585	SER	0	-0.076	-0.038	60.021	0.102	0.102	0.000	0.000	0.000	0.000
107	A	586	LEU	0	0.038	0.022	59.063	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	587	GLY	0	0.054	0.012	62.858	0.058	0.058	0.000	0.000	0.000	0.000
109	A	588	PHE	0	-0.046	-0.018	62.788	0.076	0.076	0.000	0.000	0.000	0.000
110	A	589	GLY	0	0.040	0.025	65.038	-0.055	-0.055	0.000	0.000	0.000	0.000
111	A	590	PRO	0	-0.066	-0.048	66.951	0.002	0.002	0.000	0.000	0.000	0.000
112	A	591	GLU	-1	-0.845	-0.924	65.624	-4.590	-4.590	0.000	0.000	0.000	0.000
113	A	592	GLU	-1	-0.899	-0.957	61.528	-5.161	-5.161	0.000	0.000	0.000	0.000
114	A	593	GLY	0	0.013	0.019	62.090	-0.074	-0.074	0.000	0.000	0.000	0.000
115	A	594	SER	0	-0.062	-0.041	59.878	-0.071	-0.071	0.000	0.000	0.000	0.000
116	A	595	LEU	0	-0.018	0.005	54.378	-0.096	-0.096	0.000	0.000	0.000	0.000
117	A	596	GLN	0	0.024	-0.005	55.869	-0.139	-0.139	0.000	0.000	0.000	0.000
118	A	597	ALA	0	0.047	0.045	56.757	-0.065	-0.065	0.000	0.000	0.000	0.000
119	A	598	LEU	0	0.012	-0.010	51.798	-0.084	-0.084	0.000	0.000	0.000	0.000
120	A	599	PHE	0	-0.032	-0.004	51.067	-0.106	-0.106	0.000	0.000	0.000	0.000
121	A	600	GLN	0	-0.027	-0.010	52.285	-0.053	-0.053	0.000	0.000	0.000	0.000
122	A	601	HIS	0	-0.024	-0.020	52.678	-0.076	-0.076	0.000	0.000	0.000	0.000
123	A	602	GLY	0	-0.004	0.000	48.664	-0.078	-0.078	0.000	0.000	0.000	0.000
124	A	603	GLY	0	-0.010	-0.016	47.638	-0.146	-0.146	0.000	0.000	0.000	0.000
125	A	604	ASP	-1	-0.862	-0.922	48.603	-6.105	-6.105	0.000	0.000	0.000	0.000
126	A	605	VAL	0	0.045	0.004	50.046	0.120	0.120	0.000	0.000	0.000	0.000
127	A	606	SER	0	-0.033	-0.015	51.972	0.137	0.137	0.000	0.000	0.000	0.000
128	A	607	ARG	1	0.906	0.964	51.140	5.909	5.909	0.000	0.000	0.000	0.000
129	A	608	ALA	0	0.026	0.014	53.998	0.107	0.107	0.000	0.000	0.000	0.000
130	A	609	LEU	0	0.000	0.005	55.705	0.099	0.099	0.000	0.000	0.000	0.000
131	A	610	THR	0	-0.047	-0.044	57.173	0.112	0.112	0.000	0.000	0.000	0.000
132	A	611	GLU	-1	-0.919	-0.946	58.412	-4.977	-4.977	0.000	0.000	0.000	0.000
133	A	612	LEU	0	-0.076	-0.023	58.502	0.085	0.085	0.000	0.000	0.000	0.000
134	A	613	GLN	0	-0.053	-0.011	61.589	0.098	0.098	0.000	0.000	0.000	0.000
135	A	614	ARG	1	0.865	0.935	63.282	4.861	4.861	0.000	0.000	0.000	0.000
136	A	615	GLN	0	-0.058	-0.032	66.487	0.053	0.053	0.000	0.000	0.000	0.000

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