FMO DATABASE

FMODB ID: 34JVL

Calculation Name: 4EMO-D-Xray549

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4EMO

Chain ID: D

ChEMBL ID: CHEMBL4296109

UniProt ID: Q9H0F6

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-755049.730689
FMO2-HF: Nuclear repulsion	715712.229099
FMO2-HF: Total energy	-39337.50159
FMO2-MP2: Total energy	-39453.788825

3D Structure Molmil

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(D:15:LEU)

Summations of interaction energy for fragment #1(D:15:LEU)

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.
-50.515	-48.075	0.298	-1.134	-1.602	-0.009

Interaction energy analysis for fragmet #1(D:15:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.906

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	D	17	SER	0	-0.029	-0.021	2.867	-0.874	1.548	0.299	-1.132	-1.588	-0.009
4	D	18	ALA	0	0.036	0.017	5.082	1.810	1.828	-0.001	-0.002	-0.014	0.000
5	D	19	ALA	0	0.023	0.019	8.795	1.624	1.624	0.000	0.000	0.000	0.000
6	D	20	VAL	0	-0.004	-0.012	11.335	0.399	0.399	0.000	0.000	0.000	0.000
7	D	21	LEU	0	-0.022	0.006	14.979	0.477	0.477	0.000	0.000	0.000	0.000
8	D	22	MET	0	-0.014	-0.013	17.562	1.002	1.002	0.000	0.000	0.000	0.000
9	D	23	ALA	0	0.014	0.003	20.114	-0.499	-0.499	0.000	0.000	0.000	0.000
10	D	24	VAL	0	-0.029	-0.003	21.862	0.530	0.530	0.000	0.000	0.000	0.000
11	D	25	HIS	0	0.041	0.021	25.239	-0.706	-0.706	0.000	0.000	0.000	0.000
12	D	26	ALA	0	0.019	0.016	27.960	0.300	0.300	0.000	0.000	0.000	0.000
13	D	27	ALA	0	0.020	0.012	30.307	-0.222	-0.222	0.000	0.000	0.000	0.000
14	D	28	VAL	0	-0.008	-0.011	28.029	0.151	0.151	0.000	0.000	0.000	0.000
15	D	29	ARG	1	0.936	0.978	31.298	8.656	8.656	0.000	0.000	0.000	0.000
16	D	30	PRO	0	0.017	0.014	31.657	-0.112	-0.112	0.000	0.000	0.000	0.000
17	D	31	LEU	0	0.015	-0.016	33.070	0.282	0.282	0.000	0.000	0.000	0.000
18	D	32	GLY	0	-0.039	-0.004	34.492	0.224	0.224	0.000	0.000	0.000	0.000
19	D	33	ALA	0	-0.024	-0.014	35.792	-0.009	-0.009	0.000	0.000	0.000	0.000
20	D	34	GLY	0	0.018	0.014	38.524	-0.017	-0.017	0.000	0.000	0.000	0.000
21	D	35	PRO	0	-0.082	-0.045	41.117	-0.112	-0.112	0.000	0.000	0.000	0.000
22	D	36	ASP	-1	-0.851	-0.927	41.026	-7.708	-7.708	0.000	0.000	0.000	0.000
23	D	37	ALA	0	-0.015	0.002	37.137	-0.176	-0.176	0.000	0.000	0.000	0.000
24	D	38	GLU	-1	-0.854	-0.911	34.967	-8.928	-8.928	0.000	0.000	0.000	0.000
25	D	39	ALA	0	-0.045	-0.034	34.591	-0.248	-0.248	0.000	0.000	0.000	0.000
26	D	40	GLN	0	-0.010	-0.012	30.855	-0.294	-0.294	0.000	0.000	0.000	0.000
27	D	41	LEU	0	-0.048	-0.022	29.956	-0.201	-0.201	0.000	0.000	0.000	0.000
28	D	42	ARG	1	0.869	0.914	25.489	11.247	11.247	0.000	0.000	0.000	0.000
29	D	43	ARG	1	0.889	0.941	20.613	13.641	13.641	0.000	0.000	0.000	0.000
30	D	44	LEU	0	-0.003	0.004	22.908	-0.345	-0.345	0.000	0.000	0.000	0.000
31	D	45	GLN	0	-0.057	-0.060	15.852	1.066	1.066	0.000	0.000	0.000	0.000
32	D	46	LEU	0	0.017	0.018	18.535	-0.225	-0.225	0.000	0.000	0.000	0.000
33	D	47	SER	0	-0.023	-0.034	13.194	-0.155	-0.155	0.000	0.000	0.000	0.000
34	D	48	ALA	0	0.044	0.020	10.915	0.393	0.393	0.000	0.000	0.000	0.000
35	D	49	ASP	-1	-0.772	-0.886	11.293	-26.455	-26.455	0.000	0.000	0.000	0.000
36	D	50	PRO	0	-0.063	-0.028	6.565	-0.799	-0.799	0.000	0.000	0.000	0.000
37	D	51	GLU	-1	-0.927	-0.959	6.256	-48.577	-48.577	0.000	0.000	0.000	0.000
38	D	52	ARG	1	0.695	0.832	8.595	22.073	22.073	0.000	0.000	0.000	0.000
39	D	53	PRO	0	0.060	0.013	8.894	1.876	1.876	0.000	0.000	0.000	0.000
40	D	54	GLY	0	-0.023	-0.006	11.411	1.354	1.354	0.000	0.000	0.000	0.000
41	D	55	ARG	1	0.888	0.961	13.887	17.280	17.280	0.000	0.000	0.000	0.000
42	D	56	PHE	0	0.023	0.009	13.944	-1.337	-1.337	0.000	0.000	0.000	0.000
43	D	57	ARG	1	0.803	0.905	12.078	23.460	23.460	0.000	0.000	0.000	0.000
44	D	58	LEU	0	-0.020	-0.009	16.421	0.453	0.453	0.000	0.000	0.000	0.000
45	D	59	GLU	-1	-0.792	-0.876	14.566	-20.596	-20.596	0.000	0.000	0.000	0.000
46	D	60	LEU	0	-0.023	-0.020	18.885	0.777	0.777	0.000	0.000	0.000	0.000
47	D	61	LEU	0	-0.017	-0.015	18.250	-0.119	-0.119	0.000	0.000	0.000	0.000
48	D	62	GLY	0	0.040	0.017	20.637	0.700	0.700	0.000	0.000	0.000	0.000
49	D	63	ALA	0	-0.042	-0.010	22.512	0.653	0.653	0.000	0.000	0.000	0.000
50	D	64	GLY	0	0.029	0.014	22.183	0.306	0.306	0.000	0.000	0.000	0.000
51	D	65	PRO	0	-0.008	-0.026	22.328	0.156	0.156	0.000	0.000	0.000	0.000
52	D	66	GLY	0	0.000	0.008	22.635	0.435	0.435	0.000	0.000	0.000	0.000
53	D	67	ALA	0	0.015	0.010	22.496	-0.262	-0.262	0.000	0.000	0.000	0.000
54	D	68	VAL	0	-0.002	0.016	18.235	-0.392	-0.392	0.000	0.000	0.000	0.000
55	D	69	ASN	0	0.006	-0.013	15.623	1.536	1.536	0.000	0.000	0.000	0.000
56	D	70	LEU	0	-0.009	0.017	18.760	-0.211	-0.211	0.000	0.000	0.000	0.000
57	D	71	GLU	-1	-0.840	-0.920	13.106	-23.401	-23.401	0.000	0.000	0.000	0.000
58	D	72	TRP	0	0.011	-0.002	17.882	0.333	0.333	0.000	0.000	0.000	0.000
59	D	73	PRO	0	0.058	0.022	15.553	-0.172	-0.172	0.000	0.000	0.000	0.000
60	D	74	LEU	0	-0.017	0.008	17.585	0.863	0.863	0.000	0.000	0.000	0.000
61	D	75	GLU	-1	-0.788	-0.894	19.074	-16.009	-16.009	0.000	0.000	0.000	0.000
62	D	76	SER	0	-0.075	-0.038	20.464	0.208	0.208	0.000	0.000	0.000	0.000
63	D	77	VAL	0	-0.030	-0.010	22.363	0.334	0.334	0.000	0.000	0.000	0.000
64	D	78	SER	0	-0.016	0.012	24.655	0.301	0.301	0.000	0.000	0.000	0.000
65	D	79	TYR	0	-0.003	-0.032	26.595	-0.049	-0.049	0.000	0.000	0.000	0.000
66	D	80	THR	0	-0.047	-0.020	29.214	0.318	0.318	0.000	0.000	0.000	0.000
67	D	81	ILE	0	-0.011	-0.012	32.775	-0.091	-0.091	0.000	0.000	0.000	0.000
68	D	82	ARG	1	0.843	0.917	34.853	8.808	8.808	0.000	0.000	0.000	0.000
69	D	83	GLY	0	0.046	0.016	37.470	0.291	0.291	0.000	0.000	0.000	0.000
70	D	84	PRO	0	-0.022	-0.018	37.099	-0.247	-0.247	0.000	0.000	0.000	0.000
71	D	85	THR	0	0.000	0.002	35.961	-0.147	-0.147	0.000	0.000	0.000	0.000
72	D	86	GLN	0	0.012	0.022	35.695	0.067	0.067	0.000	0.000	0.000	0.000
73	D	87	HIS	0	-0.003	0.022	30.768	-0.211	-0.211	0.000	0.000	0.000	0.000
74	D	88	GLU	-1	-0.796	-0.899	32.554	-8.691	-8.691	0.000	0.000	0.000	0.000
75	D	89	LEU	0	-0.020	0.005	24.840	-0.088	-0.088	0.000	0.000	0.000	0.000
76	D	90	GLN	0	0.040	0.023	29.037	0.511	0.511	0.000	0.000	0.000	0.000
77	D	91	PRO	0	0.001	-0.001	24.677	-0.344	-0.344	0.000	0.000	0.000	0.000
78	D	92	PRO	0	0.042	0.038	21.659	0.488	0.488	0.000	0.000	0.000	0.000
79	D	93	PRO	0	0.007	-0.022	24.888	0.075	0.075	0.000	0.000	0.000	0.000
80	D	94	GLY	0	0.006	0.012	24.129	-0.511	-0.511	0.000	0.000	0.000	0.000
81	D	95	GLY	0	-0.014	0.010	24.450	-0.269	-0.269	0.000	0.000	0.000	0.000
82	D	96	PRO	0	-0.030	-0.017	25.210	0.345	0.345	0.000	0.000	0.000	0.000
83	D	97	GLY	0	0.014	0.011	28.210	0.430	0.430	0.000	0.000	0.000	0.000
84	D	98	THR	0	-0.028	-0.035	29.532	-0.243	-0.243	0.000	0.000	0.000	0.000
85	D	99	LEU	0	0.001	0.011	26.823	0.156	0.156	0.000	0.000	0.000	0.000
86	D	100	SER	0	-0.009	0.003	31.121	0.143	0.143	0.000	0.000	0.000	0.000
87	D	101	MET	0	0.017	0.002	27.750	-0.150	-0.150	0.000	0.000	0.000	0.000
88	D	102	HIS	0	-0.011	0.005	32.512	0.072	0.072	0.000	0.000	0.000	0.000
89	D	103	PHE	0	-0.004	-0.018	28.660	-0.201	-0.201	0.000	0.000	0.000	0.000
90	D	104	LEU	0	0.031	0.012	31.398	0.335	0.335	0.000	0.000	0.000	0.000
91	D	105	ASN	0	-0.027	-0.031	33.355	0.285	0.285	0.000	0.000	0.000	0.000
92	D	106	PRO	0	0.059	0.018	34.470	-0.255	-0.255	0.000	0.000	0.000	0.000
93	D	107	GLN	0	-0.003	0.002	34.462	-0.282	-0.282	0.000	0.000	0.000	0.000
94	D	108	GLU	-1	-0.894	-0.939	30.069	-10.152	-10.152	0.000	0.000	0.000	0.000
95	D	109	ALA	0	0.023	0.023	29.852	-0.341	-0.341	0.000	0.000	0.000	0.000
96	D	110	GLN	0	-0.017	-0.017	31.007	-0.150	-0.150	0.000	0.000	0.000	0.000
97	D	111	ARG	1	0.948	0.972	28.097	9.618	9.618	0.000	0.000	0.000	0.000
98	D	112	TRP	0	0.035	0.016	21.889	-0.344	-0.344	0.000	0.000	0.000	0.000
99	D	113	ALA	0	0.020	0.006	26.503	-0.318	-0.318	0.000	0.000	0.000	0.000
100	D	114	VAL	0	-0.079	-0.035	28.377	0.016	0.016	0.000	0.000	0.000	0.000
101	D	115	LEU	0	0.020	0.009	21.253	-0.104	-0.104	0.000	0.000	0.000	0.000
102	D	116	VAL	0	0.038	0.017	23.448	-0.404	-0.404	0.000	0.000	0.000	0.000
103	D	117	ARG	1	0.913	0.969	24.381	9.720	9.720	0.000	0.000	0.000	0.000
104	D	118	GLY	0	-0.002	-0.005	25.314	-0.039	-0.039	0.000	0.000	0.000	0.000
105	D	119	ALA	0	-0.013	-0.008	19.958	-0.173	-0.173	0.000	0.000	0.000	0.000
106	D	120	THR	0	-0.047	-0.040	20.817	-0.721	-0.721	0.000	0.000	0.000	0.000
107	D	121	VAL	-1	-0.988	-0.967	22.545	-13.407	-13.407	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:15:LEU)