FMO DATABASE

FMODB ID: 6N8LZ

Calculation Name: 5X0W-H-Xray372

Preferred Name: Sharpin/RBCK1/RNF31

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 5X0W

Chain ID: H

ChEMBL ID: CHEMBL4296109

UniProt ID: Q96EP0

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455033.551748
FMO2-HF: Nuclear repulsion	425694.877577
FMO2-HF: Total energy	-29338.674171
FMO2-MP2: Total energy	-29423.873048

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(H:218:PRO)

Summations of interaction energy for fragment #1(H:218:PRO)

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.
-13.356	-4.45	7.879	-6.002	-10.781	-0.034

Interaction energy analysis for fragmet #1(H:218:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.008

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	H	220	ARG	0	-0.009	-0.017	3.894	-0.322	1.685	-0.012	-0.909	-1.085	0.003
4	H	221	LEU	0	0.057	0.034	5.643	-0.939	-0.833	-0.001	-0.007	-0.097	0.000
5	H	222	GLN	0	-0.016	-0.015	8.521	0.114	0.114	0.000	0.000	0.000	0.000
6	H	223	VAL	0	-0.009	0.013	11.844	-0.088	-0.088	0.000	0.000	0.000	0.000
7	H	224	THR	0	0.014	-0.003	13.830	-0.024	-0.024	0.000	0.000	0.000	0.000
8	H	225	LEU	0	-0.032	-0.021	16.422	-0.009	-0.009	0.000	0.000	0.000	0.000
9	H	226	GLU	-1	-0.767	-0.854	19.586	0.131	0.131	0.000	0.000	0.000	0.000
10	H	227	ASP	-1	-0.753	-0.871	22.962	0.082	0.082	0.000	0.000	0.000	0.000
11	H	228	ALA	0	-0.037	-0.017	26.202	-0.001	-0.001	0.000	0.000	0.000	0.000
12	H	229	ALA	0	-0.070	-0.037	29.418	-0.003	-0.003	0.000	0.000	0.000	0.000
13	H	230	SER	0	-0.055	-0.046	24.587	0.003	0.003	0.000	0.000	0.000	0.000
14	H	231	ALA	0	-0.011	-0.009	25.907	-0.006	-0.006	0.000	0.000	0.000	0.000
15	H	232	ALA	0	0.015	0.019	25.714	-0.007	-0.007	0.000	0.000	0.000	0.000
16	H	233	SER	0	0.006	0.000	26.879	-0.005	-0.005	0.000	0.000	0.000	0.000
17	H	234	ALA	0	-0.061	-0.031	30.699	0.001	0.001	0.000	0.000	0.000	0.000
18	H	235	ALA	0	-0.044	-0.031	28.645	-0.003	-0.003	0.000	0.000	0.000	0.000
19	H	236	SER	0	-0.005	0.001	22.946	0.003	0.003	0.000	0.000	0.000	0.000
20	H	237	SER	0	-0.032	-0.034	21.917	-0.008	-0.008	0.000	0.000	0.000	0.000
21	H	238	ALA	0	0.011	0.011	20.481	0.009	0.009	0.000	0.000	0.000	0.000
22	H	239	HIS	0	-0.026	-0.017	15.926	0.037	0.037	0.000	0.000	0.000	0.000
23	H	240	VAL	0	0.020	0.011	11.822	-0.030	-0.030	0.000	0.000	0.000	0.000
24	H	241	ALA	0	-0.009	0.009	9.254	0.036	0.036	0.000	0.000	0.000	0.000
25	H	242	LEU	0	-0.004	-0.021	7.435	-0.106	-0.106	0.000	0.000	0.000	0.000
26	H	243	GLN	0	-0.006	-0.055	2.503	-4.134	-1.770	3.857	-2.285	-3.936	-0.008
27	H	244	VAL	0	0.001	0.024	4.039	-1.555	-1.149	0.002	-0.070	-0.338	0.000
28	H	245	HIS	0	0.079	0.015	3.349	-1.013	-0.070	0.105	-0.358	-0.691	-0.003
29	H	246	PRO	0	-0.060	-0.010	3.340	-0.720	-0.231	0.011	-0.123	-0.377	0.000
30	H	247	HIS	0	0.003	-0.007	2.265	-6.182	-3.492	3.844	-2.864	-3.670	-0.022
31	H	248	CYM	-1	-0.907	-0.890	3.257	1.235	1.114	0.074	0.615	-0.568	-0.004
32	H	249	THR	0	-0.016	-0.034	5.399	0.189	0.211	-0.001	-0.001	-0.019	0.000
33	H	250	DVA	0	-0.017	-0.004	8.132	-0.158	-0.158	0.000	0.000	0.000	0.000
34	H	251	ALA	0	0.057	0.033	10.503	0.065	0.065	0.000	0.000	0.000	0.000
35	H	252	ALA	0	0.049	0.022	13.189	-0.026	-0.026	0.000	0.000	0.000	0.000
36	H	253	LEU	0	-0.047	0.002	7.503	0.014	0.014	0.000	0.000	0.000	0.000
37	H	254	GLN	0	0.019	-0.024	7.647	-0.104	-0.104	0.000	0.000	0.000	0.000
38	H	255	GLU	-1	-0.900	-0.951	11.223	0.073	0.073	0.000	0.000	0.000	0.000
39	H	256	GLN	0	-0.047	-0.039	13.342	-0.017	-0.017	0.000	0.000	0.000	0.000
40	H	257	DVA	0	0.014	0.013	10.106	-0.011	-0.011	0.000	0.000	0.000	0.000
41	H	258	PHE	0	0.003	0.003	13.006	0.011	0.011	0.000	0.000	0.000	0.000
42	H	259	DSN	0	-0.092	-0.052	15.196	-0.012	-0.012	0.000	0.000	0.000	0.000
43	H	260	GLU	-1	-0.976	-0.975	11.315	0.382	0.382	0.000	0.000	0.000	0.000
44	H	261	LEU	0	-0.005	0.001	14.802	-0.015	-0.015	0.000	0.000	0.000	0.000
45	H	262	GLY	0	0.037	0.037	17.196	-0.007	-0.007	0.000	0.000	0.000	0.000
46	H	263	PHE	0	-0.010	-0.030	18.536	-0.016	-0.016	0.000	0.000	0.000	0.000
47	H	264	PRO	0	0.018	0.007	19.805	0.003	0.003	0.000	0.000	0.000	0.000
48	H	265	PRO	0	0.043	0.012	18.289	0.005	0.005	0.000	0.000	0.000	0.000
49	H	266	ALA	0	-0.030	-0.007	20.342	0.003	0.003	0.000	0.000	0.000	0.000
50	H	267	VAL	0	-0.012	0.002	23.099	-0.003	-0.003	0.000	0.000	0.000	0.000
51	H	268	GLN	0	0.003	0.009	16.726	0.029	0.029	0.000	0.000	0.000	0.000
52	H	269	ARG	1	0.898	0.959	20.479	-0.109	-0.109	0.000	0.000	0.000	0.000
53	H	270	TRP	0	0.042	0.010	12.241	0.025	0.025	0.000	0.000	0.000	0.000
54	H	271	VAL	0	-0.029	-0.036	17.388	-0.032	-0.032	0.000	0.000	0.000	0.000
55	H	272	ILE	0	0.089	0.049	11.697	0.036	0.036	0.000	0.000	0.000	0.000
56	H	273	GLY	0	0.024	0.035	15.827	-0.034	-0.034	0.000	0.000	0.000	0.000
57	H	274	ARG	1	0.908	0.947	18.173	-0.061	-0.061	0.000	0.000	0.000	0.000
58	H	275	CYS	0	-0.078	-0.055	19.302	-0.019	-0.019	0.000	0.000	0.000	0.000
59	H	276	LEU	0	0.007	0.009	19.753	0.016	0.016	0.000	0.000	0.000	0.000
60	H	277	CYS	0	-0.034	-0.002	16.154	0.000	0.000	0.000	0.000	0.000	0.000
61	H	278	VAL	0	0.005	0.014	18.555	-0.004	-0.004	0.000	0.000	0.000	0.000
62	H	279	PRO	0	0.051	0.044	16.931	-0.002	-0.002	0.000	0.000	0.000	0.000
63	H	280	GLU	-1	-0.925	-0.973	16.082	-0.092	-0.092	0.000	0.000	0.000	0.000
64	H	281	ARG	0	-0.018	-0.008	16.163	0.007	0.007	0.000	0.000	0.000	0.000
65	H	282	SER	0	-0.011	0.010	12.693	-0.003	-0.003	0.000	0.000	0.000	0.000
66	H	283	LEU	0	0.063	0.023	8.025	0.020	0.020	0.000	0.000	0.000	0.000
67	H	284	DAL	0	0.015	0.002	9.330	0.039	0.039	0.000	0.000	0.000	0.000
68	H	285	SER	0	-0.088	-0.039	11.114	-0.020	-0.020	0.000	0.000	0.000	0.000
69	H	286	TYR	0	-0.042	-0.036	13.896	0.015	0.015	0.000	0.000	0.000	0.000
70	H	294	PRO	0	-0.007	-0.022	11.147	0.046	0.046	0.000	0.000	0.000	0.000
71	H	295	ALA	0	-0.038	0.002	13.097	-0.053	-0.053	0.000	0.000	0.000	0.000
72	H	296	PHE	0	-0.007	-0.004	14.875	0.009	0.009	0.000	0.000	0.000	0.000
73	H	297	LEU	0	0.014	0.016	16.001	-0.009	-0.009	0.000	0.000	0.000	0.000
74	H	298	TYR	0	-0.033	-0.024	17.904	-0.008	-0.008	0.000	0.000	0.000	0.000
75	H	299	LEU	0	0.025	0.011	20.359	-0.004	-0.004	0.000	0.000	0.000	0.000
76	H	300	LEU	0	-0.086	-0.042	23.533	-0.006	-0.006	0.000	0.000	0.000	0.000
77	H	301	SER	0	-0.022	-0.024	26.651	-0.008	-0.008	0.000	0.000	0.000	0.000
78	H	302	ALA	0	-0.050	-0.016	28.711	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:218:PRO)