FMO DATABASE

FMODB ID: 432NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-729944.025984
FMO2-HF: Nuclear repulsion	691497.136121
FMO2-HF: Total energy	-38446.889864
FMO2-MP2: Total energy	-38560.548734

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.
-7.554	-1.824	1.431	-3.272	-3.889	-0.016

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 : 0.014 / 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	0.015	-0.004	3.753	-1.694	-0.547	-0.011	-0.567	-0.569	0.003
4	A	21	LEU	0	-0.017	0.004	6.807	0.433	0.433	0.000	0.000	0.000	0.000
5	A	22	MET	0	-0.046	-0.028	9.369	0.174	0.174	0.000	0.000	0.000	0.000
6	A	23	ALA	0	0.022	0.002	11.777	-0.125	-0.125	0.000	0.000	0.000	0.000
7	A	24	VAL	0	-0.049	-0.013	13.642	0.074	0.074	0.000	0.000	0.000	0.000
8	A	25	HIS	0	0.010	-0.004	16.945	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	26	ALA	0	0.018	0.009	19.533	0.020	0.020	0.000	0.000	0.000	0.000
10	A	27	ALA	0	0.007	0.013	21.803	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	28	VAL	0	-0.005	-0.009	19.765	0.001	0.001	0.000	0.000	0.000	0.000
12	A	29	ARG	1	0.904	0.950	23.242	0.128	0.128	0.000	0.000	0.000	0.000
13	A	30	PRO	0	0.024	0.018	24.593	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	31	LEU	0	0.023	-0.011	25.922	0.012	0.012	0.000	0.000	0.000	0.000
15	A	32	GLY	0	-0.041	-0.007	27.728	0.009	0.009	0.000	0.000	0.000	0.000
16	A	33	ALA	0	-0.024	-0.012	29.289	0.006	0.006	0.000	0.000	0.000	0.000
17	A	34	GLY	0	0.051	0.037	31.017	0.006	0.006	0.000	0.000	0.000	0.000
18	A	35	PRO	0	-0.054	-0.046	32.856	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	36	ASP	-1	-0.884	-0.948	34.432	-0.084	-0.084	0.000	0.000	0.000	0.000
20	A	37	ALA	0	-0.035	0.013	29.374	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	38	GLU	-1	-0.854	-0.921	27.995	-0.124	-0.124	0.000	0.000	0.000	0.000
22	A	39	ALA	0	-0.057	-0.045	26.756	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.003	-0.008	23.400	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	41	LEU	0	0.002	0.007	22.003	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	42	ARG	1	0.810	0.917	17.630	0.269	0.269	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.976	0.990	12.794	0.310	0.310	0.000	0.000	0.000	0.000
27	A	44	LEU	0	-0.004	0.006	13.902	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	45	GLN	0	-0.026	-0.052	8.125	0.276	0.276	0.000	0.000	0.000	0.000
29	A	46	LEU	0	0.022	0.026	9.723	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	47	SER	0	-0.062	-0.046	4.336	-0.236	-0.081	-0.001	-0.061	-0.093	0.000
31	A	48	ALA	0	0.062	0.025	2.523	-0.072	0.495	0.296	-0.257	-0.606	0.001
32	A	49	ASP	-1	-0.782	-0.870	2.911	-6.268	-4.329	0.146	-1.302	-0.783	-0.014
33	A	50	PRO	0	-0.050	-0.026	2.456	-0.472	0.469	0.398	-0.398	-0.941	0.000
34	A	51	GLU	-1	-0.925	-0.957	4.238	-0.012	0.059	0.001	-0.037	-0.035	0.000
35	A	52	ARG	1	0.675	0.809	7.075	0.951	0.951	0.000	0.000	0.000	0.000
36	A	53	PRO	0	0.048	0.018	7.664	-0.035	-0.035	0.000	0.000	0.000	0.000
37	A	54	GLY	0	-0.023	-0.010	7.973	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.871	0.946	8.863	0.285	0.285	0.000	0.000	0.000	0.000
39	A	56	PHE	0	0.012	0.001	7.236	-0.140	-0.140	0.000	0.000	0.000	0.000
40	A	57	ARG	1	0.830	0.917	2.743	2.596	3.506	0.602	-0.650	-0.862	-0.006
41	A	58	LEU	0	-0.004	-0.001	8.741	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	59	GLU	-1	-0.790	-0.868	5.754	-2.067	-2.067	0.000	0.000	0.000	0.000
43	A	60	LEU	0	-0.030	-0.010	10.664	0.090	0.090	0.000	0.000	0.000	0.000
44	A	61	LEU	0	-0.006	-0.013	10.307	0.002	0.002	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.057	0.029	13.994	0.050	0.050	0.000	0.000	0.000	0.000
46	A	63	ALA	0	-0.040	-0.040	16.916	0.008	0.008	0.000	0.000	0.000	0.000
47	A	64	GLY	0	0.043	0.030	19.525	0.022	0.022	0.000	0.000	0.000	0.000
48	A	65	PRO	0	-0.008	-0.007	16.987	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	66	GLY	0	0.003	-0.003	16.249	0.020	0.020	0.000	0.000	0.000	0.000
50	A	67	ALA	0	-0.053	-0.006	17.342	0.002	0.002	0.000	0.000	0.000	0.000
51	A	68	VAL	0	0.014	0.000	14.567	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	69	ASN	0	0.020	0.014	10.580	0.082	0.082	0.000	0.000	0.000	0.000
53	A	70	LEU	0	-0.020	-0.004	12.631	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	71	GLU	-1	-0.808	-0.907	7.107	-1.565	-1.565	0.000	0.000	0.000	0.000
55	A	72	TRP	0	-0.022	-0.020	10.977	0.092	0.092	0.000	0.000	0.000	0.000
56	A	73	PRO	0	0.058	0.027	10.803	-0.088	-0.088	0.000	0.000	0.000	0.000
57	A	74	LEU	0	-0.013	0.002	11.538	0.081	0.081	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.728	-0.879	13.221	-0.330	-0.330	0.000	0.000	0.000	0.000
59	A	76	SER	0	-0.109	-0.038	15.319	0.023	0.023	0.000	0.000	0.000	0.000
60	A	77	VAL	0	-0.009	-0.003	15.722	0.018	0.018	0.000	0.000	0.000	0.000
61	A	78	SER	0	-0.025	0.003	18.431	0.027	0.027	0.000	0.000	0.000	0.000
62	A	79	TYR	0	-0.003	-0.020	18.271	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	80	THR	0	-0.012	-0.011	21.263	0.021	0.021	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.014	-0.013	23.707	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	82	ARG	1	0.844	0.887	26.222	0.135	0.135	0.000	0.000	0.000	0.000
66	A	83	GLY	0	0.025	0.009	28.650	0.010	0.010	0.000	0.000	0.000	0.000
67	A	84	PRO	0	-0.015	-0.012	28.428	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	85	THR	0	0.002	0.001	27.212	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	86	GLN	0	0.044	0.027	26.799	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	87	HIS	0	-0.008	0.024	22.188	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.826	-0.882	24.173	-0.142	-0.142	0.000	0.000	0.000	0.000
72	A	89	LEU	0	0.006	0.015	16.870	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	90	GLN	0	0.009	-0.006	21.383	0.017	0.017	0.000	0.000	0.000	0.000
74	A	91	PRO	0	0.013	0.018	18.450	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	92	PRO	0	0.028	0.010	17.725	0.026	0.026	0.000	0.000	0.000	0.000
76	A	93	PRO	0	-0.004	-0.012	20.771	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	94	GLY	0	0.003	0.003	21.979	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	95	GLY	0	-0.003	0.015	20.071	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	96	PRO	0	-0.032	-0.020	19.143	0.018	0.018	0.000	0.000	0.000	0.000
80	A	97	GLY	0	0.029	0.021	22.088	0.020	0.020	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.005	-0.017	22.818	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	99	LEU	0	-0.022	-0.001	19.589	0.008	0.008	0.000	0.000	0.000	0.000
83	A	100	SER	0	0.006	0.021	23.669	0.001	0.001	0.000	0.000	0.000	0.000
84	A	101	MET	0	-0.003	-0.019	18.595	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	102	HIS	0	-0.003	0.008	23.710	0.012	0.012	0.000	0.000	0.000	0.000
86	A	103	PHE	0	-0.014	-0.021	20.163	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	104	LEU	0	0.050	0.020	24.069	0.009	0.009	0.000	0.000	0.000	0.000
88	A	105	ASN	0	-0.039	-0.031	25.849	0.012	0.012	0.000	0.000	0.000	0.000
89	A	106	PRO	0	0.062	0.010	26.382	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	107	GLN	0	0.018	0.024	25.425	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.907	-0.948	21.824	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	109	ALA	0	0.029	0.027	21.675	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	110	GLN	0	0.004	0.000	22.614	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	111	ARG	1	0.945	0.975	19.303	0.079	0.079	0.000	0.000	0.000	0.000
95	A	112	TRP	0	0.032	0.011	13.387	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.008	0.004	18.181	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	114	VAL	0	-0.093	-0.049	19.822	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	115	LEU	0	0.025	0.022	13.111	0.007	0.007	0.000	0.000	0.000	0.000
99	A	116	VAL	0	0.038	0.015	15.250	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	117	ARG	1	0.916	0.958	16.261	0.097	0.097	0.000	0.000	0.000	0.000
101	A	118	GLY	0	-0.027	-0.009	16.939	0.008	0.008	0.000	0.000	0.000	0.000
102	A	119	ALA	0	-0.025	-0.016	11.924	0.014	0.014	0.000	0.000	0.000	0.000
103	A	120	THR	0	-0.045	-0.025	13.192	-0.048	-0.048	0.000	0.000	0.000	0.000
104	A	121	VAL	0	-0.032	-0.007	13.998	0.036	0.036	0.000	0.000	0.000	0.000

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