FMO DATABASE

FMODB ID: 7GK4K

Calculation Name: 3FN1-A-Xray372

Preferred Name: NEDD8-activating enzyme E1 catalytic subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3FN1

Chain ID: A

ChEMBL ID: CHEMBL2016430

UniProt ID: Q8TBC4

Base Structure: X-ray

Registration Date: 2023-03-14

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-639916.362776
FMO2-HF: Nuclear repulsion	604372.753732
FMO2-HF: Total energy	-35543.609045
FMO2-MP2: Total energy	-35647.995953

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:350:PRO)

Summations of interaction energy for fragment #1(A:350: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.
-4.009	1.041	0.203	-2.289	-2.964	-0.006

Interaction energy analysis for fragmet #1(A:350:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.002

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	352	ASN	0	-0.024	-0.007	3.831	-1.383	0.459	-0.019	-0.854	-0.969	0.004
4	A	353	ILE	0	0.008	0.019	6.585	0.460	0.460	0.000	0.000	0.000	0.000
5	A	354	GLN	0	0.004	0.006	9.836	-0.229	-0.229	0.000	0.000	0.000	0.000
6	A	355	PHE	0	0.054	0.024	12.678	0.093	0.093	0.000	0.000	0.000	0.000
7	A	356	SER	0	0.033	0.028	15.313	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	357	PRO	0	0.058	0.018	17.747	0.022	0.022	0.000	0.000	0.000	0.000
9	A	358	SER	0	-0.059	-0.031	18.850	0.029	0.029	0.000	0.000	0.000	0.000
10	A	359	ALA	0	0.018	0.020	18.389	0.022	0.022	0.000	0.000	0.000	0.000
11	A	360	LYS	1	0.918	0.956	19.937	0.090	0.090	0.000	0.000	0.000	0.000
12	A	361	LEU	0	0.018	0.007	16.255	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	362	GLN	0	-0.017	-0.017	18.007	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	363	GLU	-1	-0.815	-0.917	19.062	-0.125	-0.125	0.000	0.000	0.000	0.000
15	A	364	VAL	0	-0.008	0.005	12.937	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	365	LEU	0	-0.019	-0.015	15.076	0.024	0.024	0.000	0.000	0.000	0.000
17	A	366	ASP	-1	-0.917	-0.943	16.993	0.011	0.011	0.000	0.000	0.000	0.000
18	A	367	TYR	0	0.022	0.018	10.572	0.029	0.029	0.000	0.000	0.000	0.000
19	A	368	LEU	0	-0.029	-0.026	10.652	0.030	0.030	0.000	0.000	0.000	0.000
20	A	369	THR	0	-0.027	-0.009	14.306	0.057	0.057	0.000	0.000	0.000	0.000
21	A	370	ASN	0	-0.047	-0.044	17.807	0.027	0.027	0.000	0.000	0.000	0.000
22	A	371	SER	0	-0.031	0.005	13.774	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	372	ALA	0	0.021	-0.004	16.672	0.039	0.039	0.000	0.000	0.000	0.000
24	A	373	SER	0	-0.068	-0.026	11.956	0.027	0.027	0.000	0.000	0.000	0.000
25	A	374	LEU	0	-0.051	-0.020	9.635	0.089	0.089	0.000	0.000	0.000	0.000
26	A	375	GLN	0	-0.013	0.004	13.585	0.051	0.051	0.000	0.000	0.000	0.000
27	A	376	MET	0	-0.053	-0.011	11.383	0.077	0.077	0.000	0.000	0.000	0.000
28	A	377	LYS	1	0.918	0.951	16.050	-0.273	-0.273	0.000	0.000	0.000	0.000
29	A	378	SER	0	-0.034	-0.032	18.353	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	379	PRO	0	0.008	0.028	14.640	0.024	0.024	0.000	0.000	0.000	0.000
31	A	380	ALA	0	-0.044	-0.039	14.924	-0.057	-0.057	0.000	0.000	0.000	0.000
32	A	381	ILE	0	0.008	0.001	12.395	0.059	0.059	0.000	0.000	0.000	0.000
33	A	382	THR	0	-0.071	-0.039	12.524	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	383	ALA	0	0.090	0.037	11.944	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	384	THR	0	-0.009	0.005	12.488	0.030	0.030	0.000	0.000	0.000	0.000
36	A	385	LEU	0	-0.018	-0.005	14.220	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	386	GLU	-1	-0.929	-0.966	17.038	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	387	GLY	0	-0.022	-0.005	17.439	0.015	0.015	0.000	0.000	0.000	0.000
39	A	388	LYS	1	0.946	0.970	17.993	0.007	0.007	0.000	0.000	0.000	0.000
40	A	389	ASN	0	0.049	0.016	15.766	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	390	ARG	1	0.939	0.969	16.647	0.018	0.018	0.000	0.000	0.000	0.000
42	A	391	THR	0	-0.003	-0.009	16.701	0.014	0.014	0.000	0.000	0.000	0.000
43	A	392	LEU	0	-0.016	-0.001	14.335	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	393	TYR	0	0.018	-0.033	17.257	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	394	MET	0	0.033	0.014	17.311	0.027	0.027	0.000	0.000	0.000	0.000
46	A	395	GLN	0	0.019	0.007	19.258	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	396	SER	0	0.024	0.022	19.974	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	397	VAL	0	0.005	0.012	21.825	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	398	THR	0	0.072	0.035	24.096	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	399	SER	0	0.029	0.011	27.355	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	400	ILE	0	0.011	-0.001	21.370	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	401	GLU	-1	-0.786	-0.834	23.565	0.066	0.066	0.000	0.000	0.000	0.000
53	A	402	GLU	-1	-0.924	-0.970	24.519	0.057	0.057	0.000	0.000	0.000	0.000
54	A	403	ARG	1	0.890	0.945	26.402	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	404	THR	0	-0.058	-0.051	21.610	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	405	ARG	1	0.889	0.944	23.307	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	406	PRO	0	-0.002	-0.007	25.138	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	407	ASN	0	-0.053	-0.041	21.408	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	408	LEU	0	0.017	0.018	20.624	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	409	SER	0	-0.041	-0.015	22.765	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	410	LYS	1	0.937	0.984	22.770	0.018	0.018	0.000	0.000	0.000	0.000
62	A	411	THR	0	0.018	0.021	21.471	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	412	LEU	0	0.039	0.005	14.854	0.009	0.009	0.000	0.000	0.000	0.000
64	A	413	LYS	1	0.994	0.993	18.253	0.135	0.135	0.000	0.000	0.000	0.000
65	A	414	GLU	-1	-1.011	-1.020	20.061	-0.077	-0.077	0.000	0.000	0.000	0.000
66	A	415	LEU	0	-0.054	-0.019	18.383	0.016	0.016	0.000	0.000	0.000	0.000
67	A	416	GLY	0	-0.037	-0.002	19.536	0.016	0.016	0.000	0.000	0.000	0.000
68	A	417	LEU	0	-0.057	-0.018	13.686	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	418	VAL	0	0.006	-0.001	13.220	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	419	ASP	-1	-0.843	-0.947	12.575	-0.673	-0.673	0.000	0.000	0.000	0.000
71	A	420	GLY	0	-0.046	-0.017	8.901	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	421	GLN	0	-0.006	0.001	7.845	-0.193	-0.193	0.000	0.000	0.000	0.000
73	A	422	GLU	-1	-0.917	-0.968	3.367	-2.937	-1.876	0.059	-0.463	-0.657	-0.003
74	A	423	LEU	0	-0.048	-0.022	7.247	0.196	0.196	0.000	0.000	0.000	0.000
75	A	424	ALA	0	0.012	0.003	7.303	0.186	0.186	0.000	0.000	0.000	0.000
76	A	425	VAL	0	-0.009	0.002	8.401	-0.153	-0.153	0.000	0.000	0.000	0.000
77	A	426	ALA	0	0.010	0.003	9.642	0.251	0.251	0.000	0.000	0.000	0.000
78	A	427	ASP	-1	-0.689	-0.837	12.382	0.248	0.248	0.000	0.000	0.000	0.000
79	A	428	VAL	0	-0.017	-0.013	15.056	0.046	0.046	0.000	0.000	0.000	0.000
80	A	429	THR	0	-0.058	-0.055	15.178	0.028	0.028	0.000	0.000	0.000	0.000
81	A	430	THR	0	-0.036	0.002	10.677	0.058	0.058	0.000	0.000	0.000	0.000
82	A	431	PRO	0	0.002	0.000	11.727	-0.059	-0.059	0.000	0.000	0.000	0.000
83	A	432	GLN	0	0.003	0.004	8.492	-0.474	-0.474	0.000	0.000	0.000	0.000
84	A	433	THR	0	-0.018	-0.024	8.367	0.056	0.056	0.000	0.000	0.000	0.000
85	A	434	VAL	0	0.001	0.013	4.911	0.564	0.564	0.000	0.000	0.000	0.000
86	A	435	LEU	0	-0.015	-0.008	3.251	-1.064	-0.624	0.025	-0.104	-0.362	0.000
87	A	436	PHE	0	-0.030	-0.017	3.123	-1.053	0.264	0.130	-0.790	-0.657	-0.007
88	A	437	LYS	1	0.957	0.976	3.366	1.704	2.112	0.009	-0.077	-0.340	0.000
89	A	438	LEU	0	-0.019	-0.008	5.236	0.115	0.097	-0.001	-0.001	0.021	0.000
90	A	439	HIS	0	-0.002	-0.005	8.991	0.028	0.028	0.000	0.000	0.000	0.000
91	A	440	PHE	0	0.022	-0.006	10.832	0.100	0.100	0.000	0.000	0.000	0.000
92	A	441	THR	0	-0.039	-0.008	14.463	0.041	0.041	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:350:PRO)