FMO DATABASE

FMODB ID: 94Q52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-564024.085192
FMO2-HF: Nuclear repulsion	530922.754777
FMO2-HF: Total energy	-33101.330414
FMO2-MP2: Total energy	-33197.828244

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.
-34.571	-32.312	20.864	-11.57	-11.554	-0.046

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 : -0.079 / q_NPA : -0.065

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	-0.876	-0.946	3.848	-0.889	1.078	-0.019	-1.051	-0.897	0.002
4	A	55	ILE	0	-0.087	-0.021	5.182	0.081	0.081	0.000	0.000	0.000	0.000
5	A	56	ARG	1	0.925	0.970	7.981	-0.358	-0.358	0.000	0.000	0.000	0.000
6	A	57	LEU	0	-0.003	-0.011	10.708	0.040	0.040	0.000	0.000	0.000	0.000
7	A	58	TRP	0	0.000	0.001	12.849	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	59	VAL	0	0.018	-0.002	15.779	0.010	0.010	0.000	0.000	0.000	0.000
9	A	60	SER	0	0.003	0.007	18.225	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	61	VAL	0	-0.028	-0.020	21.029	0.002	0.002	0.000	0.000	0.000	0.000
11	A	62	GLU	-1	-0.790	-0.859	23.328	0.063	0.063	0.000	0.000	0.000	0.000
12	A	63	ASP	-1	-0.772	-0.889	26.144	0.021	0.021	0.000	0.000	0.000	0.000
13	A	64	ALA	0	-0.044	-0.028	28.833	0.002	0.002	0.000	0.000	0.000	0.000
14	A	65	GLN	0	-0.128	-0.061	31.987	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	66	MET	0	-0.055	-0.017	31.159	0.001	0.001	0.000	0.000	0.000	0.000
16	A	67	HIS	0	-0.001	0.020	31.539	0.001	0.001	0.000	0.000	0.000	0.000
17	A	68	THR	0	-0.019	-0.037	25.649	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	69	VAL	0	-0.029	-0.007	24.676	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	70	THR	0	-0.012	-0.006	21.912	0.003	0.003	0.000	0.000	0.000	0.000
20	A	71	ILE	0	0.008	0.013	18.758	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	72	TRP	0	-0.031	-0.012	14.544	0.033	0.033	0.000	0.000	0.000	0.000
22	A	73	LEU	0	0.011	0.009	13.713	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	74	THR	0	0.014	0.002	9.924	0.094	0.094	0.000	0.000	0.000	0.000
24	A	75	VAL	0	-0.005	-0.009	7.539	-0.084	-0.084	0.000	0.000	0.000	0.000
25	A	76	ARG	1	0.991	0.978	3.095	1.329	2.527	0.108	-0.517	-0.790	0.004
26	A	77	PRO	0	0.024	0.009	2.374	-2.457	-0.542	2.176	-1.296	-2.794	0.007
27	A	78	ASP	-1	-0.833	-0.896	1.723	-30.774	-34.025	18.586	-8.629	-6.706	-0.059
28	A	79	MET	0	0.008	0.032	3.850	-1.387	-1.122	0.014	-0.066	-0.214	0.000
29	A	80	THR	0	0.007	0.015	6.662	0.269	0.269	0.000	0.000	0.000	0.000
30	A	81	VAL	0	0.033	0.009	10.045	0.069	0.069	0.000	0.000	0.000	0.000
31	A	82	ALA	0	-0.008	0.004	12.985	0.008	0.008	0.000	0.000	0.000	0.000
32	A	83	SER	0	0.008	-0.010	10.441	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	84	LEU	0	-0.021	-0.009	11.373	0.029	0.029	0.000	0.000	0.000	0.000
34	A	85	LYS	1	0.784	0.890	12.789	0.065	0.065	0.000	0.000	0.000	0.000
35	A	86	ASP	-1	-0.889	-0.949	15.415	-0.186	-0.186	0.000	0.000	0.000	0.000
36	A	87	MET	0	-0.039	-0.011	12.480	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	88	VAL	0	0.041	0.017	15.753	0.018	0.018	0.000	0.000	0.000	0.000
38	A	89	PHE	0	-0.060	-0.030	18.064	0.004	0.004	0.000	0.000	0.000	0.000
39	A	90	LEU	0	-0.031	-0.012	17.746	0.004	0.004	0.000	0.000	0.000	0.000
40	A	91	ASP	-1	-0.935	-0.954	17.346	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	92	TYR	0	-0.060	-0.047	18.460	0.014	0.014	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.006	0.019	22.764	0.004	0.004	0.000	0.000	0.000	0.000
43	A	94	PHE	0	-0.025	-0.022	21.840	0.001	0.001	0.000	0.000	0.000	0.000
44	A	95	PRO	0	0.029	0.015	22.274	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	96	PRO	0	0.074	0.029	19.656	0.013	0.013	0.000	0.000	0.000	0.000
46	A	97	VAL	0	-0.052	-0.031	21.365	0.008	0.008	0.000	0.000	0.000	0.000
47	A	98	LEU	0	-0.035	-0.002	24.432	0.004	0.004	0.000	0.000	0.000	0.000
48	A	99	GLN	0	0.010	-0.001	18.617	0.028	0.028	0.000	0.000	0.000	0.000
49	A	100	GLN	0	-0.036	-0.017	21.346	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	101	TRP	0	0.045	0.016	16.009	0.031	0.031	0.000	0.000	0.000	0.000
51	A	102	VAL	0	-0.042	-0.025	18.704	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	103	ILE	0	0.052	0.016	12.366	0.023	0.023	0.000	0.000	0.000	0.000
53	A	104	GLY	0	0.035	0.032	14.794	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	105	GLN	0	-0.045	-0.027	15.637	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	106	ARG	1	0.929	0.975	13.853	-0.098	-0.098	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.009	0.004	17.990	0.015	0.015	0.000	0.000	0.000	0.000
57	A	108	ALA	0	-0.056	-0.029	14.744	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	109	ARG	1	0.963	0.969	16.614	0.001	0.001	0.000	0.000	0.000	0.000
59	A	110	ASP	-1	-0.785	-0.877	15.371	-0.089	-0.089	0.000	0.000	0.000	0.000
60	A	111	GLN	0	0.023	-0.005	14.132	0.000	0.000	0.000	0.000	0.000	0.000
61	A	112	GLU	-1	-0.823	-0.874	12.612	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	113	THR	0	0.046	0.023	7.111	0.069	0.069	0.000	0.000	0.000	0.000
63	A	114	LEU	0	0.068	0.028	7.157	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	115	HIS	0	0.023	0.020	4.411	-0.184	-0.019	-0.001	-0.011	-0.153	0.000
65	A	116	SER	0	-0.085	-0.040	6.471	-0.174	-0.174	0.000	0.000	0.000	0.000
66	A	117	HIS	1	0.705	0.813	9.753	-0.219	-0.219	0.000	0.000	0.000	0.000
67	A	118	GLY	0	0.013	0.007	9.572	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	119	VAL	0	-0.047	-0.015	7.133	0.012	0.012	0.000	0.000	0.000	0.000
69	A	120	ARG	1	0.857	0.911	5.878	-0.177	-0.177	0.000	0.000	0.000	0.000
70	A	121	GLN	0	0.002	0.008	6.487	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	122	ASN	0	0.036	0.003	8.753	-0.049	-0.049	0.000	0.000	0.000	0.000
72	A	123	GLY	0	-0.003	-0.002	11.146	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	124	ASP	-1	-0.778	-0.860	9.938	0.590	0.590	0.000	0.000	0.000	0.000
74	A	125	SER	0	-0.027	-0.022	12.947	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	126	ALA	0	-0.067	-0.033	14.225	0.032	0.032	0.000	0.000	0.000	0.000
76	A	127	TYR	0	-0.067	-0.056	16.328	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	128	LEU	0	-0.009	-0.007	18.932	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	129	TYR	0	0.036	0.022	20.616	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	130	LEU	0	-0.007	-0.015	22.814	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	131	LEU	0	-0.015	0.005	25.898	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	132	SER	0	0.035	0.009	28.640	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	133	ALA	0	-0.036	-0.021	31.308	-0.004	-0.004	0.000	0.000	0.000	0.000

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