FMO DATABASE

FMODB ID: 22MGR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-640720.028222
FMO2-HF: Nuclear repulsion	605175.844596
FMO2-HF: Total energy	-35544.183626
FMO2-MP2: Total energy	-35648.534102

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.
-3.733	0.789	0.204	-1.926	-2.8	-0.005

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 : 0.016 / q_NPA : -0.018

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	-0.020	-0.005	3.831	-1.669	-0.039	-0.020	-0.744	-0.867	0.003
4	A	353	ILE	0	0.008	0.017	6.630	0.439	0.439	0.000	0.000	0.000	0.000
5	A	354	GLN	0	0.012	0.010	9.891	-0.192	-0.192	0.000	0.000	0.000	0.000
6	A	355	PHE	0	0.039	0.019	12.872	0.085	0.085	0.000	0.000	0.000	0.000
7	A	356	SER	0	0.039	0.033	15.369	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	357	PRO	0	0.055	0.020	17.841	0.020	0.020	0.000	0.000	0.000	0.000
9	A	358	SER	0	0.002	-0.002	18.908	0.017	0.017	0.000	0.000	0.000	0.000
10	A	359	ALA	0	-0.028	-0.005	18.429	0.023	0.023	0.000	0.000	0.000	0.000
11	A	360	LYS	1	0.863	0.920	20.000	0.075	0.075	0.000	0.000	0.000	0.000
12	A	361	LEU	0	0.011	0.003	16.385	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	362	GLN	0	-0.017	-0.017	18.033	0.003	0.003	0.000	0.000	0.000	0.000
14	A	363	GLU	-1	-0.804	-0.897	19.018	-0.077	-0.077	0.000	0.000	0.000	0.000
15	A	364	VAL	0	-0.005	0.001	12.948	0.004	0.004	0.000	0.000	0.000	0.000
16	A	365	LEU	0	-0.013	-0.010	15.077	0.033	0.033	0.000	0.000	0.000	0.000
17	A	366	ASP	-1	-0.894	-0.926	16.994	0.069	0.069	0.000	0.000	0.000	0.000
18	A	367	TYR	0	0.028	0.012	10.595	0.024	0.024	0.000	0.000	0.000	0.000
19	A	368	LEU	0	-0.036	-0.029	10.573	0.041	0.041	0.000	0.000	0.000	0.000
20	A	369	THR	0	-0.036	-0.017	14.279	0.057	0.057	0.000	0.000	0.000	0.000
21	A	370	ASN	0	-0.044	-0.039	17.772	0.029	0.029	0.000	0.000	0.000	0.000
22	A	371	SER	0	-0.038	0.001	13.738	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	372	ALA	0	0.021	-0.003	16.623	0.035	0.035	0.000	0.000	0.000	0.000
24	A	373	SER	0	-0.060	-0.023	12.587	0.016	0.016	0.000	0.000	0.000	0.000
25	A	374	LEU	0	-0.065	-0.029	9.667	0.096	0.096	0.000	0.000	0.000	0.000
26	A	375	GLN	0	0.002	0.013	13.518	0.039	0.039	0.000	0.000	0.000	0.000
27	A	376	MET	0	-0.040	-0.006	11.220	0.061	0.061	0.000	0.000	0.000	0.000
28	A	377	LYS	1	0.909	0.946	15.979	-0.295	-0.295	0.000	0.000	0.000	0.000
29	A	378	SER	0	-0.032	-0.034	18.371	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	379	PRO	0	0.010	0.020	14.523	0.012	0.012	0.000	0.000	0.000	0.000
31	A	380	ALA	0	-0.033	-0.028	14.930	-0.058	-0.058	0.000	0.000	0.000	0.000
32	A	381	ILE	0	0.008	-0.002	12.490	0.054	0.054	0.000	0.000	0.000	0.000
33	A	382	THR	0	-0.070	-0.044	12.556	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	383	ALA	0	0.087	0.038	11.842	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	384	THR	0	-0.003	0.005	12.135	0.034	0.034	0.000	0.000	0.000	0.000
36	A	385	LEU	0	-0.005	0.006	13.919	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	386	GLU	-1	-0.864	-0.930	16.739	-0.068	-0.068	0.000	0.000	0.000	0.000
38	A	387	GLY	0	-0.022	-0.011	17.218	0.018	0.018	0.000	0.000	0.000	0.000
39	A	388	LYS	1	0.934	0.966	17.787	0.061	0.061	0.000	0.000	0.000	0.000
40	A	389	ASN	0	0.029	0.010	15.480	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	390	ARG	1	0.883	0.941	16.306	0.065	0.065	0.000	0.000	0.000	0.000
42	A	391	THR	0	0.007	-0.004	16.446	0.009	0.009	0.000	0.000	0.000	0.000
43	A	392	LEU	0	-0.013	0.001	14.565	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	393	TYR	0	0.017	-0.036	17.289	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	394	MET	0	0.041	0.019	17.328	0.026	0.026	0.000	0.000	0.000	0.000
46	A	395	GLN	0	0.005	0.008	19.285	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	396	SER	0	0.017	0.020	20.066	0.004	0.004	0.000	0.000	0.000	0.000
48	A	397	VAL	0	-0.008	0.000	21.750	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	398	THR	0	0.076	0.039	24.093	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	399	SER	0	0.036	0.015	27.355	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	400	ILE	0	-0.001	-0.010	21.488	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	401	GLU	-1	-0.766	-0.791	23.580	0.067	0.067	0.000	0.000	0.000	0.000
53	A	402	GLU	-1	-0.913	-0.963	24.532	0.053	0.053	0.000	0.000	0.000	0.000
54	A	403	ARG	1	0.882	0.945	26.297	-0.048	-0.048	0.000	0.000	0.000	0.000
55	A	404	THR	0	-0.056	-0.058	21.667	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	405	ARG	1	0.875	0.914	23.341	-0.069	-0.069	0.000	0.000	0.000	0.000
57	A	406	PRO	0	-0.001	-0.011	25.167	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	407	ASN	0	-0.035	-0.025	21.442	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	408	LEU	0	0.022	0.024	20.593	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	409	SER	0	-0.007	-0.005	22.797	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	410	LYS	1	0.875	0.948	22.625	0.015	0.015	0.000	0.000	0.000	0.000
62	A	411	THR	0	-0.046	-0.045	21.518	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	412	LEU	0	0.038	0.013	14.702	0.004	0.004	0.000	0.000	0.000	0.000
64	A	413	LYS	1	0.982	0.989	18.315	0.116	0.116	0.000	0.000	0.000	0.000
65	A	414	GLU	-1	-0.929	-0.947	20.119	-0.076	-0.076	0.000	0.000	0.000	0.000
66	A	415	LEU	0	-0.051	-0.018	18.448	0.012	0.012	0.000	0.000	0.000	0.000
67	A	416	GLY	0	-0.043	-0.008	19.325	0.010	0.010	0.000	0.000	0.000	0.000
68	A	417	LEU	0	-0.052	-0.020	13.524	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	418	VAL	0	-0.003	-0.007	13.286	0.006	0.006	0.000	0.000	0.000	0.000
70	A	419	ASP	-1	-0.839	-0.938	12.660	-0.607	-0.607	0.000	0.000	0.000	0.000
71	A	420	GLY	0	0.020	0.021	8.936	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	421	GLN	0	-0.027	-0.006	7.886	-0.189	-0.189	0.000	0.000	0.000	0.000
73	A	422	GLU	-1	-0.874	-0.931	3.896	-2.448	-1.995	0.005	-0.142	-0.317	-0.001
74	A	423	LEU	0	-0.045	-0.018	6.876	0.156	0.156	0.000	0.000	0.000	0.000
75	A	424	ALA	0	0.004	-0.003	7.351	0.151	0.151	0.000	0.000	0.000	0.000
76	A	425	VAL	0	-0.010	0.004	8.297	-0.114	-0.114	0.000	0.000	0.000	0.000
77	A	426	ALA	0	0.008	0.004	9.625	0.219	0.219	0.000	0.000	0.000	0.000
78	A	427	ASP	-1	-0.676	-0.831	12.359	0.285	0.285	0.000	0.000	0.000	0.000
79	A	428	VAL	0	-0.027	-0.015	15.015	0.040	0.040	0.000	0.000	0.000	0.000
80	A	429	THR	0	-0.055	-0.045	15.021	0.030	0.030	0.000	0.000	0.000	0.000
81	A	430	THR	0	-0.037	0.001	10.526	0.071	0.071	0.000	0.000	0.000	0.000
82	A	431	PRO	0	0.001	-0.003	11.790	-0.062	-0.062	0.000	0.000	0.000	0.000
83	A	432	GLN	0	-0.008	0.000	7.759	-0.334	-0.334	0.000	0.000	0.000	0.000
84	A	433	THR	0	-0.012	-0.022	8.563	0.094	0.094	0.000	0.000	0.000	0.000
85	A	434	VAL	0	-0.003	0.014	4.963	0.447	0.447	0.000	0.000	0.000	0.000
86	A	435	LEU	0	-0.002	-0.001	3.078	-1.261	-0.604	0.066	-0.158	-0.564	0.000
87	A	436	PHE	0	-0.020	-0.019	3.122	-0.765	0.553	0.138	-0.783	-0.672	-0.007
88	A	437	LYS	1	0.843	0.893	3.311	1.491	1.970	0.016	-0.098	-0.398	0.000
89	A	438	LEU	0	-0.020	-0.006	5.297	0.122	0.107	-0.001	-0.001	0.018	0.000
90	A	439	HIS	0	0.017	0.004	9.050	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	440	PHE	0	0.010	-0.018	10.880	0.096	0.096	0.000	0.000	0.000	0.000
92	A	441	THR	0	-0.024	0.000	14.513	0.032	0.032	0.000	0.000	0.000	0.000

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