FMO DATABASE

FMODB ID: K3YR3

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	OptH
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	-729873.182553
FMO2-HF: Nuclear repulsion	691426.785968
FMO2-HF: Total energy	-38446.396585
FMO2-MP2: Total energy	-38560.105686

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.
-6.98	-1.677	2.587	-3.804	-4.088	-0.015

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 : 0.013 / q_NPA : -0.007

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	0.021	0.003	3.753	-1.665	-0.453	-0.006	-0.626	-0.581	0.003
4	A	21	LEU	0	-0.016	0.000	6.807	0.416	0.416	0.000	0.000	0.000	0.000
5	A	22	MET	0	-0.045	-0.028	9.369	0.163	0.163	0.000	0.000	0.000	0.000
6	A	23	ALA	0	0.030	0.008	11.863	-0.112	-0.112	0.000	0.000	0.000	0.000
7	A	24	VAL	0	-0.054	-0.015	13.633	0.071	0.071	0.000	0.000	0.000	0.000
8	A	25	HIS	0	0.012	-0.006	16.935	-0.037	-0.037	0.000	0.000	0.000	0.000
9	A	26	ALA	0	0.013	0.005	19.522	0.019	0.019	0.000	0.000	0.000	0.000
10	A	27	ALA	0	0.011	0.015	21.794	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	28	VAL	0	-0.012	-0.011	19.798	0.002	0.002	0.000	0.000	0.000	0.000
12	A	29	ARG	1	0.966	0.980	23.236	0.120	0.120	0.000	0.000	0.000	0.000
13	A	30	PRO	0	0.036	0.015	24.712	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	31	LEU	0	0.002	-0.017	25.921	0.011	0.011	0.000	0.000	0.000	0.000
15	A	32	GLY	0	-0.043	-0.009	27.726	0.008	0.008	0.000	0.000	0.000	0.000
16	A	33	ALA	0	-0.023	-0.006	29.299	0.006	0.006	0.000	0.000	0.000	0.000
17	A	34	GLY	0	0.042	0.026	31.016	0.006	0.006	0.000	0.000	0.000	0.000
18	A	35	PRO	0	-0.082	-0.056	32.854	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	36	ASP	-1	-0.880	-0.951	34.428	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	37	ALA	0	-0.043	0.012	29.320	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	38	GLU	-1	-0.912	-0.959	28.248	-0.115	-0.115	0.000	0.000	0.000	0.000
22	A	39	ALA	0	-0.063	-0.045	26.747	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.033	0.020	23.586	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	41	LEU	0	-0.014	-0.004	22.081	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	42	ARG	1	0.877	0.942	17.580	0.257	0.257	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.952	0.984	12.801	0.298	0.298	0.000	0.000	0.000	0.000
27	A	44	LEU	0	0.016	0.015	13.923	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	45	GLN	0	-0.023	-0.038	8.344	0.250	0.250	0.000	0.000	0.000	0.000
29	A	46	LEU	0	0.015	0.018	9.731	-0.040	-0.040	0.000	0.000	0.000	0.000
30	A	47	SER	0	-0.027	-0.009	4.128	-0.070	0.114	0.000	-0.072	-0.112	0.000
31	A	48	ALA	0	0.042	0.018	2.438	-0.045	0.497	0.424	-0.290	-0.677	0.001
32	A	49	ASP	-1	-0.802	-0.894	2.910	-6.043	-4.053	0.143	-1.345	-0.787	-0.014
33	A	50	PRO	0	-0.062	-0.027	2.512	-0.536	0.364	0.315	-0.354	-0.861	0.000
34	A	51	GLU	-1	-0.934	-0.962	4.213	0.068	0.107	0.001	-0.036	-0.005	0.000
35	A	52	ARG	1	0.762	0.875	7.056	0.851	0.851	0.000	0.000	0.000	0.000
36	A	53	PRO	0	0.047	0.022	7.670	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	54	GLY	0	-0.016	-0.007	7.979	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.930	0.986	8.850	0.263	0.263	0.000	0.000	0.000	0.000
39	A	56	PHE	0	0.016	0.001	7.239	-0.134	-0.134	0.000	0.000	0.000	0.000
40	A	57	ARG	1	0.914	0.959	2.514	2.318	2.754	1.710	-1.081	-1.065	-0.005
41	A	58	LEU	0	0.000	0.000	8.739	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	59	GLU	-1	-0.796	-0.887	5.884	-1.818	-1.818	0.000	0.000	0.000	0.000
43	A	60	LEU	0	-0.050	-0.020	10.663	0.081	0.081	0.000	0.000	0.000	0.000
44	A	61	LEU	0	-0.007	-0.013	10.405	0.003	0.003	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.048	0.017	13.981	0.047	0.047	0.000	0.000	0.000	0.000
46	A	63	ALA	0	-0.044	-0.033	16.901	0.006	0.006	0.000	0.000	0.000	0.000
47	A	64	GLY	0	0.043	0.029	19.436	0.021	0.021	0.000	0.000	0.000	0.000
48	A	65	PRO	0	-0.006	-0.005	16.909	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	66	GLY	0	0.001	-0.005	16.192	0.020	0.020	0.000	0.000	0.000	0.000
50	A	67	ALA	0	-0.052	-0.003	17.297	0.003	0.003	0.000	0.000	0.000	0.000
51	A	68	VAL	0	0.014	0.002	14.599	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	69	ASN	0	0.020	0.011	10.479	0.081	0.081	0.000	0.000	0.000	0.000
53	A	70	LEU	0	-0.019	-0.004	12.625	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	71	GLU	-1	-0.878	-0.949	7.445	-1.291	-1.291	0.000	0.000	0.000	0.000
55	A	72	TRP	0	-0.025	-0.022	10.982	0.085	0.085	0.000	0.000	0.000	0.000
56	A	73	PRO	0	0.035	0.016	10.796	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	74	LEU	0	-0.008	-0.001	11.514	0.071	0.071	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.807	-0.938	13.350	-0.278	-0.278	0.000	0.000	0.000	0.000
59	A	76	SER	0	-0.111	-0.037	15.317	0.022	0.022	0.000	0.000	0.000	0.000
60	A	77	VAL	0	-0.015	0.000	15.852	0.017	0.017	0.000	0.000	0.000	0.000
61	A	78	SER	0	-0.025	0.005	18.427	0.024	0.024	0.000	0.000	0.000	0.000
62	A	79	TYR	0	-0.020	-0.041	18.663	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	80	THR	0	-0.021	-0.017	21.268	0.020	0.020	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.001	-0.011	23.299	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	82	ARG	1	0.950	0.979	26.233	0.125	0.125	0.000	0.000	0.000	0.000
66	A	83	GLY	0	0.019	0.004	28.656	0.009	0.009	0.000	0.000	0.000	0.000
67	A	84	PRO	0	-0.010	-0.009	28.432	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	85	THR	0	0.004	0.001	27.200	0.000	0.000	0.000	0.000	0.000	0.000
69	A	86	GLN	0	0.023	0.021	26.823	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	87	HIS	0	0.014	0.044	22.248	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.936	-0.970	24.166	-0.134	-0.134	0.000	0.000	0.000	0.000
72	A	89	LEU	0	0.020	0.021	16.738	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	90	GLN	0	0.006	-0.005	21.391	0.014	0.014	0.000	0.000	0.000	0.000
74	A	91	PRO	0	0.010	0.008	18.351	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	92	PRO	0	0.023	0.010	17.766	0.024	0.024	0.000	0.000	0.000	0.000
76	A	93	PRO	0	-0.001	-0.019	20.785	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	94	GLY	0	0.003	0.008	21.990	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	95	GLY	0	-0.002	0.015	20.077	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	96	PRO	0	-0.032	-0.020	19.156	0.017	0.017	0.000	0.000	0.000	0.000
80	A	97	GLY	0	0.030	0.022	22.090	0.018	0.018	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.007	-0.018	22.822	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	99	LEU	0	-0.024	0.004	19.655	0.007	0.007	0.000	0.000	0.000	0.000
83	A	100	SER	0	0.027	0.031	23.672	0.002	0.002	0.000	0.000	0.000	0.000
84	A	101	MET	0	-0.011	-0.024	18.614	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	102	HIS	0	0.009	0.012	23.718	0.011	0.011	0.000	0.000	0.000	0.000
86	A	103	PHE	0	-0.016	-0.024	20.130	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	104	LEU	0	0.063	0.024	24.221	0.009	0.009	0.000	0.000	0.000	0.000
88	A	105	ASN	0	-0.050	-0.035	25.943	0.011	0.011	0.000	0.000	0.000	0.000
89	A	106	PRO	0	0.057	0.011	26.379	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	107	GLN	0	0.019	0.022	25.368	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.915	-0.942	21.985	-0.106	-0.106	0.000	0.000	0.000	0.000
92	A	109	ALA	0	0.038	0.021	21.674	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	110	GLN	0	-0.004	0.000	22.633	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	111	ARG	1	0.959	0.982	19.244	0.075	0.075	0.000	0.000	0.000	0.000
95	A	112	TRP	0	0.028	0.004	13.312	0.000	0.000	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.014	0.007	18.201	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	114	VAL	0	-0.093	-0.051	19.839	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	115	LEU	0	0.022	0.023	13.076	0.007	0.007	0.000	0.000	0.000	0.000
99	A	116	VAL	0	0.038	0.012	15.270	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	117	ARG	1	0.902	0.944	16.275	0.091	0.091	0.000	0.000	0.000	0.000
101	A	118	GLY	0	-0.027	-0.009	16.960	0.008	0.008	0.000	0.000	0.000	0.000
102	A	119	ALA	0	-0.030	-0.019	11.905	0.014	0.014	0.000	0.000	0.000	0.000
103	A	120	THR	0	-0.043	-0.007	13.202	-0.044	-0.044	0.000	0.000	0.000	0.000
104	A	121	VAL	0	-0.053	-0.024	14.040	0.034	0.034	0.000	0.000	0.000	0.000

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