FMO DATABASE

FMODB ID: JM8M9

Calculation Name: 3FN1-A-Xray312

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-645491.515914
FMO2-HF: Nuclear repulsion	609776.969948
FMO2-HF: Total energy	-35714.545966
FMO2-MP2: Total energy	-35819.477768

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:349:ACE )

Summations of interaction energy for fragment #1(A:349:ACE )

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.
0.954	1.723	0.001	-0.236	-0.534	0

Interaction energy analysis for fragmet #1(A:349:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.010

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].
3	A	351	GLN	0	0.043	0.030	3.851	1.270	1.982	0.001	-0.230	-0.483
4	A	352	ASN	0	-0.033	-0.011	5.971	0.448	0.505	0.000	-0.006	-0.051
5	A	353	ILE	0	0.006	0.017	9.591	0.085	0.085	0.000	0.000	0.000
6	A	354	GLN	0	0.004	0.006	12.951	-0.039	-0.039	0.000	0.000	0.000
7	A	355	PHE	0	0.049	0.021	15.815	0.026	0.026	0.000	0.000	0.000
8	A	356	SER	0	0.033	0.028	19.302	0.002	0.002	0.000	0.000	0.000
9	A	357	PRO	0	0.051	0.015	22.473	-0.003	-0.003	0.000	0.000	0.000
10	A	358	SER	0	-0.061	-0.031	23.666	0.008	0.008	0.000	0.000	0.000
11	A	359	ALA	0	0.024	0.022	22.310	0.011	0.011	0.000	0.000	0.000
12	A	360	LYS	1	0.920	0.956	23.912	0.122	0.122	0.000	0.000	0.000
13	A	361	LEU	0	0.017	0.007	19.991	-0.015	-0.015	0.000	0.000	0.000
14	A	362	GLN	0	-0.017	-0.017	21.479	-0.017	-0.017	0.000	0.000	0.000
15	A	363	GLU	-1	-0.813	-0.916	22.306	-0.176	-0.176	0.000	0.000	0.000
16	A	364	VAL	0	-0.008	0.005	16.300	-0.015	-0.015	0.000	0.000	0.000
17	A	365	LEU	0	-0.025	-0.016	17.782	-0.024	-0.024	0.000	0.000	0.000
18	A	366	ASP	-1	-0.912	-0.941	19.616	-0.159	-0.159	0.000	0.000	0.000
19	A	367	TYR	0	0.021	0.017	11.964	0.034	0.034	0.000	0.000	0.000
20	A	368	LEU	0	-0.030	-0.026	13.125	-0.006	-0.006	0.000	0.000	0.000
21	A	369	THR	0	-0.027	-0.007	16.016	0.013	0.013	0.000	0.000	0.000
22	A	370	ASN	0	-0.048	-0.044	19.033	0.031	0.031	0.000	0.000	0.000
23	A	371	SER	0	-0.032	0.004	14.266	0.032	0.032	0.000	0.000	0.000
24	A	372	ALA	0	0.022	-0.003	16.957	0.006	0.006	0.000	0.000	0.000
25	A	373	SER	0	-0.069	-0.026	11.822	0.015	0.015	0.000	0.000	0.000
26	A	374	LEU	0	-0.048	-0.019	10.081	-0.008	-0.008	0.000	0.000	0.000
27	A	375	GLN	0	-0.015	0.004	13.403	0.037	0.037	0.000	0.000	0.000
28	A	376	MET	0	-0.049	-0.010	13.105	0.006	0.006	0.000	0.000	0.000
29	A	377	LYS	1	0.913	0.950	16.555	0.098	0.098	0.000	0.000	0.000
30	A	378	SER	0	-0.033	-0.032	19.191	0.013	0.013	0.000	0.000	0.000
31	A	379	PRO	0	0.003	0.026	16.408	0.003	0.003	0.000	0.000	0.000
32	A	380	ALA	0	-0.039	-0.037	16.861	0.022	0.022	0.000	0.000	0.000
33	A	381	ILE	0	0.009	0.001	15.908	-0.049	-0.049	0.000	0.000	0.000
34	A	382	THR	0	-0.073	-0.039	15.683	0.051	0.051	0.000	0.000	0.000
35	A	383	ALA	0	0.091	0.037	15.626	-0.060	-0.060	0.000	0.000	0.000
36	A	384	THR	0	-0.011	0.005	16.190	0.049	0.049	0.000	0.000	0.000
37	A	385	LEU	0	-0.015	-0.004	18.328	-0.012	-0.012	0.000	0.000	0.000
38	A	386	GLU	-1	-0.931	-0.967	21.440	-0.099	-0.099	0.000	0.000	0.000
39	A	387	GLY	0	-0.022	-0.005	21.479	0.014	0.014	0.000	0.000	0.000
40	A	388	LYS	1	0.946	0.970	21.506	0.086	0.086	0.000	0.000	0.000
41	A	389	ASN	0	0.050	0.017	18.733	-0.038	-0.038	0.000	0.000	0.000
42	A	390	ARG	1	0.940	0.970	20.223	0.156	0.156	0.000	0.000	0.000
43	A	391	THR	0	-0.003	-0.010	20.210	-0.026	-0.026	0.000	0.000	0.000
44	A	392	LEU	0	-0.017	-0.001	18.242	0.019	0.019	0.000	0.000	0.000
45	A	393	TYR	0	0.014	-0.034	20.725	0.018	0.018	0.000	0.000	0.000
46	A	394	MET	0	0.036	0.015	19.691	-0.017	-0.017	0.000	0.000	0.000
47	A	395	GLN	0	0.024	0.009	21.751	0.004	0.004	0.000	0.000	0.000
48	A	396	SER	0	0.022	0.022	21.480	0.015	0.015	0.000	0.000	0.000
49	A	397	VAL	0	0.002	0.010	23.594	0.012	0.012	0.000	0.000	0.000
50	A	398	THR	0	0.073	0.035	25.999	-0.005	-0.005	0.000	0.000	0.000
51	A	399	SER	0	0.030	0.012	29.444	-0.005	-0.005	0.000	0.000	0.000
52	A	400	ILE	0	0.010	-0.003	24.166	-0.001	-0.001	0.000	0.000	0.000
53	A	401	GLU	-1	-0.784	-0.832	26.161	-0.108	-0.108	0.000	0.000	0.000
54	A	402	GLU	-1	-0.925	-0.971	27.204	-0.070	-0.070	0.000	0.000	0.000
55	A	403	ARG	1	0.890	0.946	29.599	0.076	0.076	0.000	0.000	0.000
56	A	404	THR	0	-0.059	-0.052	24.932	-0.005	-0.005	0.000	0.000	0.000
57	A	405	ARG	1	0.889	0.944	26.832	0.080	0.080	0.000	0.000	0.000
58	A	406	PRO	0	-0.004	-0.008	28.460	-0.004	-0.004	0.000	0.000	0.000
59	A	407	ASN	0	-0.053	-0.041	25.248	0.009	0.009	0.000	0.000	0.000
60	A	408	LEU	0	0.017	0.018	23.988	-0.010	-0.010	0.000	0.000	0.000
61	A	409	SER	0	-0.040	-0.015	26.360	-0.004	-0.004	0.000	0.000	0.000
62	A	410	LYS	1	0.938	0.984	26.745	0.121	0.121	0.000	0.000	0.000
63	A	411	THR	0	0.017	0.020	25.521	-0.015	-0.015	0.000	0.000	0.000
64	A	412	LEU	0	0.037	0.005	19.189	-0.001	-0.001	0.000	0.000	0.000
65	A	413	LYS	1	0.998	0.995	22.671	0.127	0.127	0.000	0.000	0.000
66	A	414	GLU	-1	-1.014	-1.020	24.968	-0.113	-0.113	0.000	0.000	0.000
67	A	415	LEU	0	-0.057	-0.020	22.413	0.009	0.009	0.000	0.000	0.000
68	A	416	GLY	0	-0.037	-0.002	24.257	0.000	0.000	0.000	0.000	0.000
69	A	417	LEU	0	-0.055	-0.017	18.172	-0.007	-0.007	0.000	0.000	0.000
70	A	418	VAL	0	0.007	-0.002	18.665	0.015	0.015	0.000	0.000	0.000
71	A	419	ASP	-1	-0.844	-0.947	17.986	-0.315	-0.315	0.000	0.000	0.000
72	A	420	GLY	0	-0.045	-0.017	14.505	0.013	0.013	0.000	0.000	0.000
73	A	421	GLN	0	-0.010	0.000	13.465	-0.047	-0.047	0.000	0.000	0.000
74	A	422	GLU	-1	-0.914	-0.967	8.401	-1.039	-1.039	0.000	0.000	0.000
75	A	423	LEU	0	-0.051	-0.024	11.627	0.130	0.130	0.000	0.000	0.000
76	A	424	ALA	0	0.014	0.004	11.081	-0.153	-0.153	0.000	0.000	0.000
77	A	425	VAL	0	-0.010	0.003	10.993	0.101	0.101	0.000	0.000	0.000
78	A	426	ALA	0	0.013	0.004	11.535	-0.040	-0.040	0.000	0.000	0.000
79	A	427	ASP	-1	-0.691	-0.838	13.830	-0.167	-0.167	0.000	0.000	0.000
80	A	428	VAL	0	-0.017	-0.013	15.445	0.017	0.017	0.000	0.000	0.000
81	A	429	THR	0	-0.059	-0.055	14.790	0.015	0.015	0.000	0.000	0.000
82	A	430	THR	0	-0.033	0.003	10.618	-0.011	-0.011	0.000	0.000	0.000
83	A	431	PRO	0	0.001	-0.001	9.935	0.015	0.015	0.000	0.000	0.000
84	A	432	GLN	0	0.000	0.003	7.173	-0.002	-0.002	0.000	0.000	0.000
85	A	433	THR	0	-0.020	-0.025	10.105	-0.036	-0.036	0.000	0.000	0.000
86	A	434	VAL	0	0.002	0.013	5.454	0.004	0.004	0.000	0.000	0.000
87	A	435	LEU	0	-0.020	-0.011	6.215	0.136	0.136	0.000	0.000	0.000
88	A	436	PHE	0	-0.022	-0.012	6.556	-0.698	-0.698	0.000	0.000	0.000
89	A	437	LYS	1	0.954	0.974	8.539	0.844	0.844	0.000	0.000	0.000
90	A	438	LEU	0	-0.017	-0.007	10.158	0.045	0.045	0.000	0.000	0.000
91	A	439	HIS	0	-0.001	-0.005	13.840	0.045	0.045	0.000	0.000	0.000
92	A	440	PHE	0	0.043	0.000	15.613	0.024	0.024	0.000	0.000	0.000
93	A	441	THR	0	-0.049	-0.008	18.998	0.020	0.020	0.000	0.000	0.000
94	A	442	NME	0	-0.010	-0.007	21.259	0.021	0.021	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:349:ACE )