FMO DATABASE

FMODB ID: 5379Z

Calculation Name: 4EMO-A-Xray372

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: 2023-06-20

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-729701.242683
FMO2-HF: Nuclear repulsion	691253.991041
FMO2-HF: Total energy	-38447.251642
FMO2-MP2: Total energy	-38560.843919

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:18:ALA)

Summations of interaction energy for fragment #1(A:18:ALA)

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.
-12.161	-8.016	7.754	-5.653	-6.245	-0.045

Interaction energy analysis for fragmet #1(A:18:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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

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	20	VAL	0	-0.019	-0.014	3.856	-1.801	-0.599	-0.012	-0.606	-0.583	0.002
4	A	21	LEU	0	-0.017	0.005	6.751	0.467	0.467	0.000	0.000	0.000	0.000
5	A	22	MET	0	-0.038	-0.023	8.985	0.175	0.175	0.000	0.000	0.000	0.000
6	A	23	ALA	0	0.011	-0.006	11.416	-0.150	-0.150	0.000	0.000	0.000	0.000
7	A	24	VAL	0	-0.043	-0.008	13.574	0.075	0.075	0.000	0.000	0.000	0.000
8	A	25	HIS	0	0.028	0.002	16.694	-0.048	-0.048	0.000	0.000	0.000	0.000
9	A	26	ALA	0	0.023	0.010	19.459	0.016	0.016	0.000	0.000	0.000	0.000
10	A	27	ALA	0	0.020	0.014	21.877	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	28	VAL	0	-0.010	-0.009	19.432	0.002	0.002	0.000	0.000	0.000	0.000
12	A	29	ARG	1	0.888	0.939	22.894	0.139	0.139	0.000	0.000	0.000	0.000
13	A	30	PRO	0	0.009	0.012	24.279	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	31	LEU	0	0.023	-0.008	25.626	0.014	0.014	0.000	0.000	0.000	0.000
15	A	32	GLY	0	-0.036	-0.012	27.391	0.010	0.010	0.000	0.000	0.000	0.000
16	A	33	ALA	0	-0.019	-0.002	28.537	0.005	0.005	0.000	0.000	0.000	0.000
17	A	34	GLY	0	0.024	0.027	30.305	0.008	0.008	0.000	0.000	0.000	0.000
18	A	35	PRO	0	-0.040	-0.041	32.366	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	36	ASP	-1	-0.869	-0.940	33.738	-0.091	-0.091	0.000	0.000	0.000	0.000
20	A	37	ALA	0	-0.034	0.012	29.334	0.000	0.000	0.000	0.000	0.000	0.000
21	A	38	GLU	-1	-0.841	-0.919	27.671	-0.132	-0.132	0.000	0.000	0.000	0.000
22	A	39	ALA	0	-0.040	-0.031	26.698	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.001	0.002	23.063	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	41	LEU	0	-0.027	-0.012	22.249	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	42	ARG	1	0.805	0.895	17.551	0.277	0.277	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.936	0.967	12.077	0.346	0.346	0.000	0.000	0.000	0.000
27	A	44	LEU	0	0.001	0.006	13.811	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	45	GLN	0	-0.042	-0.050	8.241	0.299	0.299	0.000	0.000	0.000	0.000
29	A	46	LEU	0	0.032	0.024	9.265	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	47	SER	0	-0.034	-0.039	4.139	-0.296	-0.101	0.000	-0.062	-0.133	0.000
31	A	48	ALA	0	0.033	0.016	2.431	-0.495	0.350	0.524	-0.512	-0.857	0.004
32	A	49	ASP	-1	-0.781	-0.878	1.989	-10.508	-10.785	6.190	-3.309	-2.604	-0.045
33	A	50	PRO	0	-0.037	-0.021	2.480	-0.778	0.457	0.307	-0.450	-1.092	0.000
34	A	51	GLU	-1	-0.924	-0.954	3.882	0.138	0.225	0.004	-0.052	-0.039	0.000
35	A	52	ARG	1	0.671	0.819	7.119	1.229	1.229	0.000	0.000	0.000	0.000
36	A	53	PRO	0	0.069	0.017	7.262	-0.060	-0.060	0.000	0.000	0.000	0.000
37	A	54	GLY	0	-0.031	-0.009	7.724	0.000	0.000	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.861	0.936	8.282	0.417	0.417	0.000	0.000	0.000	0.000
39	A	56	PHE	0	0.031	0.009	6.552	-0.245	-0.245	0.000	0.000	0.000	0.000
40	A	57	ARG	1	0.821	0.917	2.779	2.814	3.672	0.741	-0.662	-0.937	-0.006
41	A	58	LEU	0	-0.017	-0.012	8.218	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	59	GLU	-1	-0.782	-0.857	5.672	-2.134	-2.134	0.000	0.000	0.000	0.000
43	A	60	LEU	0	-0.021	-0.016	10.409	0.101	0.101	0.000	0.000	0.000	0.000
44	A	61	LEU	0	0.012	0.010	10.439	0.013	0.013	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.081	0.043	13.997	0.044	0.044	0.000	0.000	0.000	0.000
46	A	63	ALA	0	-0.054	-0.039	16.838	0.009	0.009	0.000	0.000	0.000	0.000
47	A	64	GLY	0	0.043	0.025	19.175	0.023	0.023	0.000	0.000	0.000	0.000
48	A	65	PRO	0	-0.022	-0.010	17.167	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	66	GLY	0	0.024	0.009	16.380	0.020	0.020	0.000	0.000	0.000	0.000
50	A	67	ALA	0	-0.053	-0.008	17.444	0.000	0.000	0.000	0.000	0.000	0.000
51	A	68	VAL	0	0.013	-0.003	14.857	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	69	ASN	0	0.014	0.007	10.616	0.057	0.057	0.000	0.000	0.000	0.000
53	A	70	LEU	0	-0.024	-0.005	12.872	0.002	0.002	0.000	0.000	0.000	0.000
54	A	71	GLU	-1	-0.818	-0.909	6.829	-1.630	-1.630	0.000	0.000	0.000	0.000
55	A	72	TRP	0	0.013	-0.006	10.557	0.120	0.120	0.000	0.000	0.000	0.000
56	A	73	PRO	0	0.057	0.023	10.178	-0.137	-0.137	0.000	0.000	0.000	0.000
57	A	74	LEU	0	-0.014	0.007	10.781	0.108	0.108	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.748	-0.872	12.598	-0.462	-0.462	0.000	0.000	0.000	0.000
59	A	76	SER	0	-0.090	-0.037	14.786	0.044	0.044	0.000	0.000	0.000	0.000
60	A	77	VAL	0	-0.034	-0.020	14.995	0.022	0.022	0.000	0.000	0.000	0.000
61	A	78	SER	0	-0.016	0.013	17.660	0.022	0.022	0.000	0.000	0.000	0.000
62	A	79	TYR	0	0.012	-0.024	17.655	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	80	THR	0	-0.037	-0.015	20.822	0.024	0.024	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.004	-0.012	23.451	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	82	ARG	1	0.833	0.881	25.787	0.156	0.156	0.000	0.000	0.000	0.000
66	A	83	GLY	0	0.030	0.012	28.257	0.012	0.012	0.000	0.000	0.000	0.000
67	A	84	PRO	0	-0.016	-0.016	28.024	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	85	THR	0	0.016	0.011	26.968	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	86	GLN	0	0.038	0.029	26.154	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	87	HIS	0	-0.007	0.025	21.260	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.820	-0.880	23.572	-0.158	-0.158	0.000	0.000	0.000	0.000
72	A	89	LEU	0	-0.008	0.008	16.448	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	90	GLN	0	0.049	0.011	20.921	0.019	0.019	0.000	0.000	0.000	0.000
74	A	91	PRO	0	0.008	0.016	17.693	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	92	PRO	0	0.024	0.005	16.892	0.031	0.031	0.000	0.000	0.000	0.000
76	A	93	PRO	0	-0.005	0.001	19.980	0.001	0.001	0.000	0.000	0.000	0.000
77	A	94	GLY	0	0.005	0.002	21.728	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	95	GLY	0	0.007	0.019	19.624	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	96	PRO	0	-0.032	-0.024	18.965	0.023	0.023	0.000	0.000	0.000	0.000
80	A	97	GLY	0	0.013	0.008	21.893	0.018	0.018	0.000	0.000	0.000	0.000
81	A	98	THR	0	-0.011	-0.015	22.405	-0.023	-0.023	0.000	0.000	0.000	0.000
82	A	99	LEU	0	-0.012	0.003	19.359	0.013	0.013	0.000	0.000	0.000	0.000
83	A	100	SER	0	-0.007	0.014	23.430	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	101	MET	0	-0.006	-0.015	18.485	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	102	HIS	0	0.002	0.008	23.552	0.011	0.011	0.000	0.000	0.000	0.000
86	A	103	PHE	0	0.000	-0.012	19.585	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	104	LEU	0	0.028	0.010	23.496	0.012	0.012	0.000	0.000	0.000	0.000
88	A	105	ASN	0	-0.040	-0.032	25.394	0.013	0.013	0.000	0.000	0.000	0.000
89	A	106	PRO	0	0.061	0.017	26.004	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	107	GLN	0	0.004	0.019	24.765	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.891	-0.950	21.301	-0.125	-0.125	0.000	0.000	0.000	0.000
92	A	109	ALA	0	0.029	0.029	21.194	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	110	GLN	0	-0.007	-0.012	22.060	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	111	ARG	1	0.941	0.973	18.704	0.104	0.104	0.000	0.000	0.000	0.000
95	A	112	TRP	0	0.009	0.000	12.755	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.026	0.010	17.424	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	114	VAL	0	-0.086	-0.048	19.246	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	115	LEU	0	0.012	0.007	12.418	0.006	0.006	0.000	0.000	0.000	0.000
99	A	116	VAL	0	0.057	0.025	14.532	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	117	ARG	1	0.895	0.961	15.590	0.128	0.128	0.000	0.000	0.000	0.000
101	A	118	GLY	0	-0.019	-0.002	16.228	0.013	0.013	0.000	0.000	0.000	0.000
102	A	119	ALA	0	-0.008	0.004	11.101	0.018	0.018	0.000	0.000	0.000	0.000
103	A	120	THR	0	-0.027	-0.028	12.425	-0.076	-0.076	0.000	0.000	0.000	0.000
104	A	121	VAL	0	-0.036	-0.009	13.297	0.044	0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ALA)