FMO DATABASE

FMODB ID: 2J87R

Calculation Name: 5X0W-H-Xray372

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 5X0W

Chain ID: H

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455464.502658
FMO2-HF: Nuclear repulsion	426126.524601
FMO2-HF: Total energy	-29337.978057
FMO2-MP2: Total energy	-29423.301302

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(H:218:PRO)

Summations of interaction energy for fragment #1(H:218:PRO)

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.
-9.36	-4.342	14.932	-6.045	-13.905	-0.037

Interaction energy analysis for fragmet #1(H:218:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.006

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

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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	H	220	ARG	0	0.001	-0.019	3.828	-0.718	1.368	-0.016	-0.892	-1.178	0.005
4	H	221	LEU	0	0.042	0.020	5.451	-0.651	-0.651	0.000	0.000	0.000	0.000
5	H	222	GLN	0	-0.016	-0.019	8.371	0.010	0.010	0.000	0.000	0.000	0.000
6	H	223	VAL	0	-0.009	0.017	11.546	-0.061	-0.061	0.000	0.000	0.000	0.000
7	H	224	THR	0	0.017	-0.002	13.454	-0.036	-0.036	0.000	0.000	0.000	0.000
8	H	225	LEU	0	-0.027	-0.013	16.330	-0.006	-0.006	0.000	0.000	0.000	0.000
9	H	226	GLU	-1	-0.790	-0.882	19.355	0.103	0.103	0.000	0.000	0.000	0.000
10	H	227	ASP	-1	-0.790	-0.891	22.773	0.055	0.055	0.000	0.000	0.000	0.000
11	H	228	ALA	0	-0.053	-0.036	26.044	0.002	0.002	0.000	0.000	0.000	0.000
12	H	229	ALA	0	-0.065	-0.035	29.354	-0.002	-0.002	0.000	0.000	0.000	0.000
13	H	230	SER	0	-0.055	-0.055	24.580	0.001	0.001	0.000	0.000	0.000	0.000
14	H	231	ALA	0	0.015	0.008	25.706	0.000	0.000	0.000	0.000	0.000	0.000
15	H	232	ALA	0	0.007	0.030	25.515	-0.005	-0.005	0.000	0.000	0.000	0.000
16	H	233	SER	0	0.004	-0.011	26.791	-0.005	-0.005	0.000	0.000	0.000	0.000
17	H	234	ALA	0	-0.057	-0.026	30.514	0.001	0.001	0.000	0.000	0.000	0.000
18	H	235	ALA	0	-0.046	-0.033	28.581	-0.003	-0.003	0.000	0.000	0.000	0.000
19	H	236	SER	0	0.005	-0.001	23.040	0.004	0.004	0.000	0.000	0.000	0.000
20	H	237	SER	0	-0.024	-0.012	21.702	-0.007	-0.007	0.000	0.000	0.000	0.000
21	H	238	ALA	0	0.008	0.011	20.623	0.006	0.006	0.000	0.000	0.000	0.000
22	H	239	HIS	0	-0.032	-0.023	15.794	0.029	0.029	0.000	0.000	0.000	0.000
23	H	240	VAL	0	0.027	0.010	12.026	-0.030	-0.030	0.000	0.000	0.000	0.000
24	H	241	ALA	0	-0.034	-0.005	9.287	0.043	0.043	0.000	0.000	0.000	0.000
25	H	242	LEU	0	0.003	-0.014	7.218	-0.134	-0.134	0.000	0.000	0.000	0.000
26	H	243	GLN	0	0.002	-0.055	2.394	-2.788	-1.176	5.762	-2.740	-4.635	-0.011
27	H	244	VAL	0	0.010	0.038	3.354	-1.606	-0.749	0.052	-0.294	-0.615	-0.002
28	H	245	HIS	0	0.074	0.006	3.215	-0.889	0.069	0.160	-0.330	-0.788	-0.003
29	H	246	PRO	0	-0.082	-0.023	3.054	-1.857	-0.500	0.144	-0.411	-1.090	-0.002
30	H	247	HIS	0	0.014	0.004	1.973	-5.122	-3.976	8.847	-4.982	-5.011	-0.020
31	H	248	CYM	-1	-0.752	-0.809	2.774	4.406	1.362	-0.016	3.632	-0.571	-0.004
32	H	249	THR	0	-0.102	-0.068	4.781	0.155	0.201	-0.001	-0.028	-0.017	0.000
33	H	250	DVA	0	-0.016	-0.016	8.302	-0.140	-0.140	0.000	0.000	0.000	0.000
34	H	251	ALA	0	0.018	0.027	10.213	0.066	0.066	0.000	0.000	0.000	0.000
35	H	252	ALA	0	0.064	0.037	13.208	-0.020	-0.020	0.000	0.000	0.000	0.000
36	H	253	LEU	0	-0.025	0.003	7.425	-0.001	-0.001	0.000	0.000	0.000	0.000
37	H	254	GLN	0	0.007	-0.021	7.309	-0.098	-0.098	0.000	0.000	0.000	0.000
38	H	255	GLU	-1	-0.886	-0.950	10.824	0.057	0.057	0.000	0.000	0.000	0.000
39	H	256	GLN	0	-0.054	-0.036	12.762	-0.030	-0.030	0.000	0.000	0.000	0.000
40	H	257	DVA	0	-0.019	-0.008	10.076	-0.023	-0.023	0.000	0.000	0.000	0.000
41	H	258	PHE	0	-0.018	0.000	12.690	0.006	0.006	0.000	0.000	0.000	0.000
42	H	259	DSN	0	-0.065	-0.043	15.354	-0.006	-0.006	0.000	0.000	0.000	0.000
43	H	260	GLU	-1	-0.951	-0.964	11.412	0.171	0.171	0.000	0.000	0.000	0.000
44	H	261	LEU	0	-0.019	-0.009	14.977	-0.012	-0.012	0.000	0.000	0.000	0.000
45	H	262	GLY	0	0.061	0.056	17.313	-0.001	-0.001	0.000	0.000	0.000	0.000
46	H	263	PHE	0	-0.037	-0.037	18.035	-0.007	-0.007	0.000	0.000	0.000	0.000
47	H	264	PRO	0	0.019	0.005	19.112	0.001	0.001	0.000	0.000	0.000	0.000
48	H	265	PRO	0	0.065	0.020	17.814	0.008	0.008	0.000	0.000	0.000	0.000
49	H	266	ALA	0	-0.050	-0.013	19.719	0.004	0.004	0.000	0.000	0.000	0.000
50	H	267	VAL	0	-0.004	0.000	22.356	0.000	0.000	0.000	0.000	0.000	0.000
51	H	268	GLN	0	0.006	0.011	16.119	0.028	0.028	0.000	0.000	0.000	0.000
52	H	269	ARG	1	0.905	0.962	19.893	-0.094	-0.094	0.000	0.000	0.000	0.000
53	H	270	TRP	0	0.037	0.014	12.083	0.028	0.028	0.000	0.000	0.000	0.000
54	H	271	VAL	0	-0.021	-0.027	17.179	-0.024	-0.024	0.000	0.000	0.000	0.000
55	H	272	ILE	0	0.104	0.044	11.753	0.024	0.024	0.000	0.000	0.000	0.000
56	H	273	GLY	0	0.048	0.090	15.799	-0.022	-0.022	0.000	0.000	0.000	0.000
57	H	274	ARG	1	0.913	0.949	18.127	-0.087	-0.087	0.000	0.000	0.000	0.000
58	H	275	CYS	0	-0.063	-0.047	18.693	-0.019	-0.019	0.000	0.000	0.000	0.000
59	H	276	LEU	0	0.004	0.001	19.229	0.013	0.013	0.000	0.000	0.000	0.000
60	H	277	CYS	0	-0.030	0.010	16.228	0.002	0.002	0.000	0.000	0.000	0.000
61	H	278	VAL	0	0.012	0.005	18.554	-0.007	-0.007	0.000	0.000	0.000	0.000
62	H	279	PRO	0	0.030	0.019	16.648	0.003	0.003	0.000	0.000	0.000	0.000
63	H	280	GLU	-1	-0.932	-0.976	16.129	-0.069	-0.069	0.000	0.000	0.000	0.000
64	H	281	ARG	0	0.027	0.008	15.579	0.007	0.007	0.000	0.000	0.000	0.000
65	H	282	SER	0	-0.060	-0.011	12.351	0.015	0.015	0.000	0.000	0.000	0.000
66	H	283	LEU	0	0.074	0.034	7.591	0.016	0.016	0.000	0.000	0.000	0.000
67	H	284	DAL	0	0.054	0.004	8.985	0.023	0.023	0.000	0.000	0.000	0.000
68	H	285	SER	0	-0.174	-0.079	10.746	-0.032	-0.032	0.000	0.000	0.000	0.000
69	H	286	TYR	0	-0.094	-0.097	13.556	-0.003	-0.003	0.000	0.000	0.000	0.000
70	H	294	PRO	0	-0.012	-0.030	11.717	0.040	0.040	0.000	0.000	0.000	0.000
71	H	295	ALA	0	-0.033	0.015	13.332	-0.048	-0.048	0.000	0.000	0.000	0.000
72	H	296	PHE	0	-0.030	-0.020	15.097	0.003	0.003	0.000	0.000	0.000	0.000
73	H	297	LEU	0	0.011	0.017	15.606	0.000	0.000	0.000	0.000	0.000	0.000
74	H	298	TYR	0	-0.026	-0.023	17.650	-0.011	-0.011	0.000	0.000	0.000	0.000
75	H	299	LEU	0	0.034	0.016	19.794	-0.003	-0.003	0.000	0.000	0.000	0.000
76	H	300	LEU	0	-0.083	-0.041	23.087	-0.003	-0.003	0.000	0.000	0.000	0.000
77	H	301	SER	0	0.019	0.022	26.293	-0.007	-0.007	0.000	0.000	0.000	0.000
78	H	302	ALA	0	-0.049	-0.024	28.626	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:218:PRO)