FMO DATABASE

FMODB ID: 82J2Y

Calculation Name: 4EMO-A-Xray321

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMO

Chain ID: A

ChEMBL ID: CHEMBL4296109

UniProt ID: Q9H0F6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	106
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-735397.93942
FMO2-HF: Nuclear repulsion	696780.663114
FMO2-HF: Total energy	-38617.276306
FMO2-MP2: Total energy	-38731.524773

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:17:ACE )

Summations of interaction energy for fragment #1(A:17:ACE )

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.
5.87	0.9	6.932	0.306	-2.267	-0.009

Interaction energy analysis for fragmet #1(A:17:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.017

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	19	ALA	0	-0.018	0.008	3.813	0.653	1.697	-0.006	-0.477	-0.560	-0.001
4	A	20	VAL	0	0.030	0.008	5.991	0.167	0.167	0.000	0.000	0.000	0.000
5	A	21	LEU	0	-0.019	-0.001	9.502	0.090	0.090	0.000	0.000	0.000	0.000
6	A	22	MET	0	-0.046	-0.028	10.964	0.031	0.031	0.000	0.000	0.000	0.000
7	A	23	ALA	0	0.028	0.007	14.238	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	24	VAL	0	-0.048	-0.013	16.476	0.028	0.028	0.000	0.000	0.000	0.000
9	A	25	HIS	0	0.010	-0.007	20.093	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	26	ALA	0	0.009	0.003	22.848	0.013	0.013	0.000	0.000	0.000	0.000
11	A	27	ALA	0	0.012	0.015	25.138	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	28	VAL	0	-0.009	-0.009	23.186	0.006	0.006	0.000	0.000	0.000	0.000
13	A	29	ARG	1	0.966	0.979	26.617	0.048	0.048	0.000	0.000	0.000	0.000
14	A	30	PRO	0	0.038	0.015	27.985	0.002	0.002	0.000	0.000	0.000	0.000
15	A	31	LEU	0	-0.002	-0.017	29.103	0.004	0.004	0.000	0.000	0.000	0.000
16	A	32	GLY	0	-0.043	-0.009	30.621	0.004	0.004	0.000	0.000	0.000	0.000
17	A	33	ALA	0	-0.023	-0.006	32.120	0.002	0.002	0.000	0.000	0.000	0.000
18	A	34	GLY	0	0.043	0.026	34.190	0.001	0.001	0.000	0.000	0.000	0.000
19	A	35	PRO	0	-0.084	-0.057	36.066	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	36	ASP	-1	-0.879	-0.950	37.756	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	37	ALA	0	-0.042	0.012	32.868	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	38	GLU	-1	-0.911	-0.959	32.225	-0.071	-0.071	0.000	0.000	0.000	0.000
23	A	39	ALA	0	-0.064	-0.045	30.362	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	40	GLN	0	0.033	0.020	27.526	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	41	LEU	0	-0.016	-0.003	25.889	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	42	ARG	1	0.880	0.944	21.498	0.133	0.133	0.000	0.000	0.000	0.000
27	A	43	ARG	1	0.947	0.982	16.904	0.196	0.196	0.000	0.000	0.000	0.000
28	A	44	LEU	0	0.017	0.015	17.298	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	45	GLN	0	-0.026	-0.039	12.316	0.081	0.081	0.000	0.000	0.000	0.000
30	A	46	LEU	0	0.016	0.019	11.640	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	47	SER	0	-0.023	-0.008	6.797	0.008	0.008	0.000	0.000	0.000	0.000
32	A	48	ALA	0	0.028	0.010	3.411	-0.023	0.173	0.029	-0.087	-0.138	0.000
33	A	49	ASP	-1	-0.804	-0.892	4.342	-0.871	-0.926	0.001	-0.041	0.095	0.000
34	A	50	PRO	0	-0.070	-0.021	2.211	4.339	-0.199	6.725	-0.788	-1.399	-0.005
35	A	51	GLU	-1	-0.937	-0.956	2.954	1.668	0.051	0.183	1.699	-0.265	-0.003
36	A	52	ARG	1	0.763	0.875	5.901	-0.153	-0.153	0.000	0.000	0.000	0.000
37	A	53	PRO	0	0.044	0.020	5.998	0.049	0.049	0.000	0.000	0.000	0.000
38	A	54	GLY	0	-0.016	-0.007	6.780	-0.247	-0.247	0.000	0.000	0.000	0.000
39	A	55	ARG	1	0.930	0.986	8.088	-0.328	-0.328	0.000	0.000	0.000	0.000
40	A	56	PHE	0	0.011	-0.001	7.328	0.081	0.081	0.000	0.000	0.000	0.000
41	A	57	ARG	1	0.917	0.961	6.079	1.263	1.263	0.000	0.000	0.000	0.000
42	A	58	LEU	0	0.004	0.001	10.109	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.796	-0.887	9.626	-0.718	-0.718	0.000	0.000	0.000	0.000
44	A	60	LEU	0	-0.048	-0.020	13.908	0.040	0.040	0.000	0.000	0.000	0.000
45	A	61	LEU	0	-0.011	-0.014	14.589	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.052	0.020	18.091	0.032	0.032	0.000	0.000	0.000	0.000
47	A	63	ALA	0	-0.045	-0.033	21.136	0.003	0.003	0.000	0.000	0.000	0.000
48	A	64	GLY	0	0.043	0.028	23.950	0.013	0.013	0.000	0.000	0.000	0.000
49	A	65	PRO	0	-0.005	-0.005	21.912	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	66	GLY	0	0.001	-0.005	21.165	0.013	0.013	0.000	0.000	0.000	0.000
51	A	67	ALA	0	-0.051	-0.003	22.030	0.002	0.002	0.000	0.000	0.000	0.000
52	A	68	VAL	0	0.013	0.001	18.363	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	69	ASN	0	0.020	0.010	14.768	0.066	0.066	0.000	0.000	0.000	0.000
54	A	70	LEU	0	-0.021	-0.005	16.355	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	71	GLU	-1	-0.874	-0.948	10.477	-0.700	-0.700	0.000	0.000	0.000	0.000
56	A	72	TRP	0	-0.026	-0.022	13.624	0.025	0.025	0.000	0.000	0.000	0.000
57	A	73	PRO	0	0.034	0.015	11.644	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	74	LEU	0	-0.010	-0.002	12.349	0.003	0.003	0.000	0.000	0.000	0.000
59	A	75	GLU	-1	-0.803	-0.936	13.760	0.082	0.082	0.000	0.000	0.000	0.000
60	A	76	SER	0	-0.109	-0.037	16.045	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	77	VAL	0	-0.014	-0.001	17.295	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	78	SER	0	-0.027	0.004	19.535	0.016	0.016	0.000	0.000	0.000	0.000
63	A	79	TYR	0	-0.019	-0.040	20.327	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	80	THR	0	-0.021	-0.018	22.604	0.010	0.010	0.000	0.000	0.000	0.000
65	A	81	ILE	0	-0.002	-0.011	24.585	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	82	ARG	1	0.948	0.979	27.694	0.027	0.027	0.000	0.000	0.000	0.000
67	A	83	GLY	0	0.021	0.004	30.358	0.002	0.002	0.000	0.000	0.000	0.000
68	A	84	PRO	0	-0.012	-0.009	30.175	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	85	THR	0	0.001	0.001	29.393	0.001	0.001	0.000	0.000	0.000	0.000
70	A	86	GLN	0	0.029	0.022	29.198	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	87	HIS	0	0.012	0.044	23.924	0.001	0.001	0.000	0.000	0.000	0.000
72	A	88	GLU	-1	-0.940	-0.971	26.011	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	89	LEU	0	0.024	0.021	19.136	0.004	0.004	0.000	0.000	0.000	0.000
74	A	90	GLN	0	0.006	-0.006	23.371	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	91	PRO	0	0.009	0.008	20.568	0.003	0.003	0.000	0.000	0.000	0.000
76	A	92	PRO	0	0.022	0.010	19.132	0.009	0.009	0.000	0.000	0.000	0.000
77	A	93	PRO	0	-0.002	-0.019	22.235	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	94	GLY	0	0.006	0.010	23.778	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	95	GLY	0	-0.004	0.015	22.624	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	96	PRO	0	-0.030	-0.020	22.165	0.006	0.006	0.000	0.000	0.000	0.000
81	A	97	GLY	0	0.029	0.021	25.064	0.008	0.008	0.000	0.000	0.000	0.000
82	A	98	THR	0	0.004	-0.019	25.430	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	99	LEU	0	-0.023	0.005	22.543	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	100	SER	0	0.028	0.031	26.336	0.005	0.005	0.000	0.000	0.000	0.000
85	A	101	MET	0	-0.010	-0.023	21.078	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	102	HIS	0	0.010	0.013	26.522	0.009	0.009	0.000	0.000	0.000	0.000
87	A	103	PHE	0	-0.018	-0.025	22.636	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	104	LEU	0	0.063	0.024	27.388	0.004	0.004	0.000	0.000	0.000	0.000
89	A	105	ASN	0	-0.050	-0.035	28.507	0.008	0.008	0.000	0.000	0.000	0.000
90	A	106	PRO	0	0.058	0.011	28.650	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	107	GLN	0	0.019	0.022	27.065	0.003	0.003	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.914	-0.942	24.366	-0.045	-0.045	0.000	0.000	0.000	0.000
93	A	109	ALA	0	0.042	0.022	23.577	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	110	GLN	0	-0.004	0.000	24.263	0.001	0.001	0.000	0.000	0.000	0.000
95	A	111	ARG	1	0.957	0.981	20.736	0.022	0.022	0.000	0.000	0.000	0.000
96	A	112	TRP	0	0.027	0.004	15.608	0.010	0.010	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.014	0.007	19.657	0.004	0.004	0.000	0.000	0.000	0.000
98	A	114	VAL	0	-0.092	-0.050	20.993	0.008	0.008	0.000	0.000	0.000	0.000
99	A	115	LEU	0	0.022	0.023	14.466	0.013	0.013	0.000	0.000	0.000	0.000
100	A	116	VAL	0	0.015	0.004	16.479	0.016	0.016	0.000	0.000	0.000	0.000
101	A	117	ARG	1	0.925	0.953	17.187	-0.021	-0.021	0.000	0.000	0.000	0.000
102	A	118	GLY	0	-0.027	-0.009	17.529	0.010	0.010	0.000	0.000	0.000	0.000
103	A	119	ALA	0	-0.033	-0.021	12.710	0.026	0.026	0.000	0.000	0.000	0.000
104	A	120	THR	0	-0.046	-0.008	13.580	0.011	0.011	0.000	0.000	0.000	0.000
105	A	121	VAL	0	-0.031	-0.017	13.695	0.018	0.018	0.000	0.000	0.000	0.000
106	A	122	NME	0	-0.022	-0.008	16.634	-0.017	-0.017	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:17:ACE )