FMO DATABASE

FMODB ID: LZR59

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

Total energy (hartree)

FMO2-HF: Electronic energy	-563632.164993
FMO2-HF: Nuclear repulsion	530531.220124
FMO2-HF: Total energy	-33100.944869
FMO2-MP2: Total energy	-33197.469508

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.
-17.42	-10.24	5.702	-4.874	-8.005	0.011

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 : -0.027 / q_NPA : -0.023

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	-0.875	-0.947	3.848	-1.367	0.511	-0.018	-0.977	-0.884	0.001
4	A	55	ILE	0	-0.075	-0.015	5.065	0.125	0.125	0.000	0.000	0.000	0.000
5	A	56	ARG	1	0.943	0.969	7.941	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	57	LEU	0	0.010	-0.008	10.809	0.038	0.038	0.000	0.000	0.000	0.000
7	A	58	TRP	0	-0.012	-0.003	12.787	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	59	VAL	0	0.020	0.000	15.802	0.019	0.019	0.000	0.000	0.000	0.000
9	A	60	SER	0	0.001	0.001	18.180	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	61	VAL	0	-0.019	-0.013	21.276	0.008	0.008	0.000	0.000	0.000	0.000
11	A	62	GLU	-1	-0.793	-0.887	23.480	0.055	0.055	0.000	0.000	0.000	0.000
12	A	63	ASP	-1	-0.783	-0.898	26.270	0.024	0.024	0.000	0.000	0.000	0.000
13	A	64	ALA	0	-0.038	-0.019	28.957	0.001	0.001	0.000	0.000	0.000	0.000
14	A	65	GLN	0	-0.121	-0.061	32.098	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	66	MET	0	-0.052	-0.009	31.347	0.000	0.000	0.000	0.000	0.000	0.000
16	A	67	HIS	0	-0.009	0.016	31.693	0.001	0.001	0.000	0.000	0.000	0.000
17	A	68	THR	0	-0.017	-0.023	25.668	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	69	VAL	0	-0.021	-0.012	24.896	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	70	THR	0	-0.004	-0.003	21.718	0.006	0.006	0.000	0.000	0.000	0.000
20	A	71	ILE	0	-0.007	0.011	18.882	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	72	TRP	0	-0.029	-0.016	14.428	0.025	0.025	0.000	0.000	0.000	0.000
22	A	73	LEU	0	0.011	0.009	13.787	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	74	THR	0	0.014	0.004	10.157	0.077	0.077	0.000	0.000	0.000	0.000
24	A	75	VAL	0	-0.011	-0.010	7.549	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	76	ARG	1	0.980	0.977	3.354	1.318	2.169	0.037	-0.339	-0.548	0.002
26	A	77	PRO	0	0.025	0.007	2.169	-1.799	-0.564	3.021	-1.394	-2.861	0.004
27	A	78	ASP	-1	-0.874	-0.935	2.397	-12.761	-9.956	2.644	-2.103	-3.346	0.003
28	A	79	MET	0	0.016	0.030	3.924	-1.948	-1.703	0.019	-0.052	-0.211	0.001
29	A	80	THR	0	-0.008	0.009	6.799	0.231	0.231	0.000	0.000	0.000	0.000
30	A	81	VAL	0	0.040	0.012	10.173	0.017	0.017	0.000	0.000	0.000	0.000
31	A	82	ALA	0	0.004	0.007	13.009	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	83	SER	0	0.009	-0.008	10.577	-0.060	-0.060	0.000	0.000	0.000	0.000
33	A	84	LEU	0	-0.021	-0.003	11.523	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	85	LYS	1	0.807	0.908	12.877	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	86	ASP	-1	-0.888	-0.945	15.450	-0.125	-0.125	0.000	0.000	0.000	0.000
36	A	87	MET	0	-0.037	-0.015	12.675	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	88	VAL	0	0.032	0.014	15.877	0.005	0.005	0.000	0.000	0.000	0.000
38	A	89	PHE	0	-0.071	-0.030	18.195	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	90	LEU	0	-0.038	-0.020	17.672	0.000	0.000	0.000	0.000	0.000	0.000
40	A	91	ASP	-1	-0.919	-0.945	17.696	-0.083	-0.083	0.000	0.000	0.000	0.000
41	A	92	TYR	0	-0.077	-0.052	18.575	0.008	0.008	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.008	0.018	22.910	0.005	0.005	0.000	0.000	0.000	0.000
43	A	94	PHE	0	-0.019	-0.018	21.932	0.003	0.003	0.000	0.000	0.000	0.000
44	A	95	PRO	0	0.042	0.020	22.373	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	96	PRO	0	0.069	0.029	19.675	0.012	0.012	0.000	0.000	0.000	0.000
46	A	97	VAL	0	-0.044	-0.028	21.473	0.011	0.011	0.000	0.000	0.000	0.000
47	A	98	LEU	0	-0.024	0.002	24.505	0.004	0.004	0.000	0.000	0.000	0.000
48	A	99	GLN	0	0.014	-0.007	18.798	0.027	0.027	0.000	0.000	0.000	0.000
49	A	100	GLN	0	-0.042	-0.023	21.380	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	101	TRP	0	0.041	0.020	16.327	0.023	0.023	0.000	0.000	0.000	0.000
51	A	102	VAL	0	-0.042	-0.026	18.780	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	103	ILE	0	0.050	0.019	12.418	0.014	0.014	0.000	0.000	0.000	0.000
53	A	104	GLY	0	0.020	0.014	14.833	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	105	GLN	0	-0.045	-0.029	15.680	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	106	ARG	1	0.975	0.991	14.395	-0.186	-0.186	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.012	0.011	18.125	0.017	0.017	0.000	0.000	0.000	0.000
57	A	108	ALA	0	-0.032	-0.018	14.800	0.004	0.004	0.000	0.000	0.000	0.000
58	A	109	ARG	1	0.942	0.970	16.667	-0.081	-0.081	0.000	0.000	0.000	0.000
59	A	110	ASP	-1	-0.794	-0.886	15.349	0.025	0.025	0.000	0.000	0.000	0.000
60	A	111	GLN	0	-0.006	-0.018	14.230	0.013	0.013	0.000	0.000	0.000	0.000
61	A	112	GLU	-1	-0.868	-0.910	12.783	0.110	0.110	0.000	0.000	0.000	0.000
62	A	113	THR	0	0.052	0.035	7.184	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	114	LEU	0	0.076	0.020	7.149	-0.096	-0.096	0.000	0.000	0.000	0.000
64	A	115	HIS	0	0.011	0.014	4.622	-0.341	-0.175	-0.001	-0.009	-0.155	0.000
65	A	116	SER	0	-0.090	-0.041	6.577	-0.290	-0.290	0.000	0.000	0.000	0.000
66	A	117	HIS	1	0.709	0.830	9.844	-0.382	-0.382	0.000	0.000	0.000	0.000
67	A	118	GLY	0	0.022	0.008	9.525	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	119	VAL	0	-0.037	-0.008	7.027	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	120	ARG	1	0.869	0.927	5.852	-0.060	-0.060	0.000	0.000	0.000	0.000
70	A	121	GLN	0	-0.019	-0.001	6.483	-0.088	-0.088	0.000	0.000	0.000	0.000
71	A	122	ASN	0	0.034	0.011	8.738	0.012	0.012	0.000	0.000	0.000	0.000
72	A	123	GLY	0	-0.027	-0.014	11.124	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	124	ASP	-1	-0.769	-0.867	10.116	0.415	0.415	0.000	0.000	0.000	0.000
74	A	125	SER	0	-0.026	-0.023	12.900	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	126	ALA	0	-0.077	-0.036	14.271	0.040	0.040	0.000	0.000	0.000	0.000
76	A	127	TYR	0	-0.076	-0.041	16.294	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	128	LEU	0	-0.003	-0.008	19.141	0.006	0.006	0.000	0.000	0.000	0.000
78	A	129	TYR	0	0.028	0.017	20.737	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	130	LEU	0	-0.006	-0.015	23.239	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	131	LEU	0	-0.026	-0.002	26.004	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	132	SER	0	0.007	-0.011	28.728	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	133	ALA	0	0.001	0.006	31.401	-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)