FMO DATABASE

FMODB ID: MVZKZ

Calculation Name: 4DBG-A-Xray372

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 4DBG

Chain ID: A

ChEMBL ID: CHEMBL4296109

UniProt ID: Q9BYM8

Base Structure: X-ray

Registration Date: 2023-06-26

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-564855.464098
FMO2-HF: Nuclear repulsion	531753.830222
FMO2-HF: Total energy	-33101.633876
FMO2-MP2: Total energy	-33198.090563

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:52:THR)

Summations of interaction energy for fragment #1(A:52:THR)

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.
-39.777	-46.359	36.368	-15.684	-14.103	-0.052

Interaction energy analysis for fragmet #1(A:52:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.076 / q_NPA : -0.071

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

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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	54	ASP	-1	-0.873	-0.947	3.870	-1.517	0.121	-0.010	-0.819	-0.808	0.002
4	A	55	ILE	0	-0.086	-0.032	4.792	-0.002	0.126	-0.001	-0.007	-0.119	0.000
5	A	56	ARG	1	0.904	0.945	7.617	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	57	LEU	0	0.008	0.003	10.691	0.054	0.054	0.000	0.000	0.000	0.000
7	A	58	TRP	0	0.004	-0.007	12.294	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	59	VAL	0	0.011	-0.011	15.303	0.029	0.029	0.000	0.000	0.000	0.000
9	A	60	SER	0	0.011	0.008	17.759	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	61	VAL	0	-0.026	-0.022	20.666	0.008	0.008	0.000	0.000	0.000	0.000
11	A	62	GLU	-1	-0.776	-0.840	22.995	0.060	0.060	0.000	0.000	0.000	0.000
12	A	63	ASP	-1	-0.775	-0.896	25.850	0.020	0.020	0.000	0.000	0.000	0.000
13	A	64	ALA	0	-0.033	-0.018	28.596	0.003	0.003	0.000	0.000	0.000	0.000
14	A	65	GLN	0	-0.104	-0.049	31.854	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	66	MET	0	-0.057	-0.009	30.924	0.000	0.000	0.000	0.000	0.000	0.000
16	A	67	HIS	0	0.000	-0.014	31.444	0.003	0.003	0.000	0.000	0.000	0.000
17	A	68	THR	0	-0.037	-0.037	25.723	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	69	VAL	0	-0.030	0.002	24.536	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	70	THR	0	-0.029	-0.019	21.878	0.008	0.008	0.000	0.000	0.000	0.000
20	A	71	ILE	0	0.007	0.011	18.403	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	72	TRP	0	-0.024	-0.013	14.209	0.029	0.029	0.000	0.000	0.000	0.000
22	A	73	LEU	0	0.018	0.019	13.344	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	74	THR	0	-0.010	-0.004	9.669	0.097	0.097	0.000	0.000	0.000	0.000
24	A	75	VAL	0	0.012	0.005	7.328	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	76	ARG	1	0.954	0.959	2.710	1.597	3.266	0.448	-0.825	-1.292	0.007
26	A	77	PRO	0	0.021	0.008	2.246	-2.585	-0.867	3.534	-1.668	-3.585	0.011
27	A	78	ASP	-1	-0.823	-0.883	1.647	-35.538	-47.839	32.375	-12.232	-7.843	-0.073
28	A	79	MET	0	0.000	0.030	3.739	-1.250	-0.893	0.023	-0.104	-0.276	0.001
29	A	80	THR	0	0.019	0.020	6.603	0.369	0.369	0.000	0.000	0.000	0.000
30	A	81	VAL	0	0.022	0.005	10.037	0.033	0.033	0.000	0.000	0.000	0.000
31	A	82	ALA	0	0.010	0.005	12.838	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	83	SER	0	-0.003	-0.011	9.971	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	84	LEU	0	-0.023	-0.006	11.065	0.005	0.005	0.000	0.000	0.000	0.000
34	A	85	LYS	1	0.772	0.883	12.538	0.009	0.009	0.000	0.000	0.000	0.000
35	A	86	ASP	-1	-0.864	-0.943	15.410	-0.161	-0.161	0.000	0.000	0.000	0.000
36	A	87	MET	0	-0.053	-0.009	12.523	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	88	VAL	0	0.032	0.008	15.366	0.015	0.015	0.000	0.000	0.000	0.000
38	A	89	PHE	0	-0.055	-0.023	17.727	0.006	0.006	0.000	0.000	0.000	0.000
39	A	90	LEU	0	-0.048	-0.023	17.682	0.004	0.004	0.000	0.000	0.000	0.000
40	A	91	ASP	-1	-0.919	-0.958	16.837	-0.099	-0.099	0.000	0.000	0.000	0.000
41	A	92	TYR	0	-0.059	-0.042	18.338	0.014	0.014	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.007	0.021	22.696	0.007	0.007	0.000	0.000	0.000	0.000
43	A	94	PHE	0	-0.001	-0.010	21.311	0.002	0.002	0.000	0.000	0.000	0.000
44	A	95	PRO	0	0.045	0.023	21.993	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	96	PRO	0	0.063	0.029	19.508	0.015	0.015	0.000	0.000	0.000	0.000
46	A	97	VAL	0	-0.047	-0.026	21.133	0.009	0.009	0.000	0.000	0.000	0.000
47	A	98	LEU	0	-0.021	-0.012	24.190	0.005	0.005	0.000	0.000	0.000	0.000
48	A	99	GLN	0	0.004	0.005	18.368	0.030	0.030	0.000	0.000	0.000	0.000
49	A	100	GLN	0	-0.030	-0.019	21.107	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	101	TRP	0	0.045	0.019	15.586	0.032	0.032	0.000	0.000	0.000	0.000
51	A	102	VAL	0	-0.021	-0.015	18.261	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	103	ILE	0	0.055	0.022	11.893	0.020	0.020	0.000	0.000	0.000	0.000
53	A	104	GLY	0	0.045	0.041	14.306	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	105	GLN	0	-0.064	-0.037	15.124	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	106	ARG	1	0.848	0.914	13.406	-0.233	-0.233	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.035	0.006	17.488	0.019	0.019	0.000	0.000	0.000	0.000
57	A	108	ALA	0	-0.041	-0.018	14.778	0.006	0.006	0.000	0.000	0.000	0.000
58	A	109	ARG	1	0.930	0.956	16.144	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	110	ASP	-1	-0.790	-0.883	15.287	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	111	GLN	0	0.025	0.006	14.132	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	112	GLU	-1	-0.801	-0.858	12.697	0.102	0.102	0.000	0.000	0.000	0.000
62	A	113	THR	0	0.034	0.016	7.097	0.020	0.020	0.000	0.000	0.000	0.000
63	A	114	LEU	0	0.066	0.036	6.822	-0.023	-0.023	0.000	0.000	0.000	0.000
64	A	115	HIS	0	0.033	0.018	4.373	-0.185	0.024	-0.001	-0.029	-0.180	0.000
65	A	116	SER	0	-0.101	-0.050	6.351	-0.278	-0.278	0.000	0.000	0.000	0.000
66	A	117	HIS	1	0.735	0.839	9.635	-0.415	-0.415	0.000	0.000	0.000	0.000
67	A	118	GLY	0	0.013	0.008	9.458	-0.052	-0.052	0.000	0.000	0.000	0.000
68	A	119	VAL	0	-0.033	-0.003	6.759	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	120	ARG	1	0.859	0.907	5.396	0.053	0.053	0.000	0.000	0.000	0.000
70	A	121	GLN	0	0.014	0.010	6.185	-0.170	-0.170	0.000	0.000	0.000	0.000
71	A	122	ASN	0	0.023	0.018	8.478	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	123	GLY	0	0.020	0.011	10.705	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	124	ASP	-1	-0.778	-0.866	9.386	0.644	0.644	0.000	0.000	0.000	0.000
74	A	125	SER	0	-0.041	-0.028	12.530	-0.039	-0.039	0.000	0.000	0.000	0.000
75	A	126	ALA	0	-0.050	-0.026	14.098	0.041	0.041	0.000	0.000	0.000	0.000
76	A	127	TYR	0	-0.059	-0.049	16.161	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	128	LEU	0	-0.015	-0.002	18.621	0.007	0.007	0.000	0.000	0.000	0.000
78	A	129	TYR	0	-0.006	0.001	20.313	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	130	LEU	0	0.000	-0.007	22.666	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	131	LEU	0	-0.001	0.004	25.630	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	132	SER	0	0.028	0.012	28.320	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	133	ALA	0	-0.040	-0.023	31.225	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:52:THR)