FMO DATABASE

FMODB ID: 6645Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-641954.903607
FMO2-HF: Nuclear repulsion	606410.49448
FMO2-HF: Total energy	-35544.409128
FMO2-MP2: Total energy	-35648.765875

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.
-7.439	-0.754	1.255	-3.318	-4.624	-0.017

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 : 0.003 / q_NPA : -0.019

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	-0.021	-0.014	3.748	-1.949	-0.314	-0.002	-0.779	-0.856	0.003
4	A	353	ILE	0	0.008	0.007	6.174	0.433	0.433	0.000	0.000	0.000	0.000
5	A	354	GLN	0	0.001	0.004	9.636	-0.163	-0.163	0.000	0.000	0.000	0.000
6	A	355	PHE	0	0.038	0.014	12.541	0.082	0.082	0.000	0.000	0.000	0.000
7	A	356	SER	0	0.054	0.044	15.225	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	357	PRO	0	0.037	0.012	17.693	0.011	0.011	0.000	0.000	0.000	0.000
9	A	358	SER	0	0.001	-0.011	18.580	0.017	0.017	0.000	0.000	0.000	0.000
10	A	359	ALA	0	-0.007	0.011	17.805	0.025	0.025	0.000	0.000	0.000	0.000
11	A	360	LYS	1	0.832	0.903	19.793	0.118	0.118	0.000	0.000	0.000	0.000
12	A	361	LEU	0	0.016	0.011	16.194	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	362	GLN	0	-0.008	-0.010	17.856	0.000	0.000	0.000	0.000	0.000	0.000
14	A	363	GLU	-1	-0.798	-0.890	18.816	-0.132	-0.132	0.000	0.000	0.000	0.000
15	A	364	VAL	0	-0.016	-0.003	12.707	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	365	LEU	0	-0.008	-0.007	14.655	0.023	0.023	0.000	0.000	0.000	0.000
17	A	366	ASP	-1	-0.896	-0.919	16.650	0.017	0.017	0.000	0.000	0.000	0.000
18	A	367	TYR	0	0.042	0.014	10.290	0.037	0.037	0.000	0.000	0.000	0.000
19	A	368	LEU	0	-0.022	-0.022	10.141	0.036	0.036	0.000	0.000	0.000	0.000
20	A	369	THR	0	-0.043	-0.019	13.864	0.067	0.067	0.000	0.000	0.000	0.000
21	A	370	ASN	0	-0.058	-0.051	17.418	0.034	0.034	0.000	0.000	0.000	0.000
22	A	371	SER	0	-0.012	0.013	13.835	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	372	ALA	0	0.018	-0.003	16.241	0.047	0.047	0.000	0.000	0.000	0.000
24	A	373	SER	0	-0.047	-0.017	12.422	0.016	0.016	0.000	0.000	0.000	0.000
25	A	374	LEU	0	-0.077	-0.040	9.587	0.108	0.108	0.000	0.000	0.000	0.000
26	A	375	GLN	0	-0.034	-0.014	13.557	0.042	0.042	0.000	0.000	0.000	0.000
27	A	376	MET	0	-0.019	0.005	11.348	0.051	0.051	0.000	0.000	0.000	0.000
28	A	377	LYS	1	0.914	0.940	15.858	-0.240	-0.240	0.000	0.000	0.000	0.000
29	A	378	SER	0	-0.044	-0.033	18.276	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	379	PRO	0	0.023	0.023	14.389	0.010	0.010	0.000	0.000	0.000	0.000
31	A	380	ALA	0	-0.053	-0.028	14.714	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	381	ILE	0	0.021	0.006	12.113	0.041	0.041	0.000	0.000	0.000	0.000
33	A	382	THR	0	-0.065	-0.043	11.955	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	383	ALA	0	0.084	0.039	11.246	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	384	THR	0	-0.011	0.000	11.754	0.049	0.049	0.000	0.000	0.000	0.000
36	A	385	LEU	0	0.012	0.006	13.630	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	386	GLU	-1	-0.832	-0.920	16.497	-0.094	-0.094	0.000	0.000	0.000	0.000
38	A	387	GLY	0	0.016	0.017	16.939	0.020	0.020	0.000	0.000	0.000	0.000
39	A	388	LYS	1	0.881	0.939	17.824	0.097	0.097	0.000	0.000	0.000	0.000
40	A	389	ASN	0	0.028	0.003	15.491	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	390	ARG	1	0.849	0.927	15.937	0.117	0.117	0.000	0.000	0.000	0.000
42	A	391	THR	0	0.017	-0.001	16.013	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	392	LEU	0	-0.007	0.012	13.969	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	393	TYR	0	0.011	-0.037	17.144	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	394	MET	0	0.011	-0.002	17.122	0.019	0.019	0.000	0.000	0.000	0.000
46	A	395	GLN	0	0.062	0.020	19.330	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	396	SER	0	-0.017	0.016	19.444	0.007	0.007	0.000	0.000	0.000	0.000
48	A	397	VAL	0	0.000	-0.003	21.238	0.003	0.003	0.000	0.000	0.000	0.000
49	A	398	THR	0	0.074	0.043	23.704	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	399	SER	0	0.025	0.016	26.895	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	400	ILE	0	-0.018	-0.016	21.390	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	401	GLU	-1	-0.765	-0.794	23.229	0.030	0.030	0.000	0.000	0.000	0.000
53	A	402	GLU	-1	-0.867	-0.944	24.161	0.027	0.027	0.000	0.000	0.000	0.000
54	A	403	ARG	1	0.868	0.943	25.620	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	404	THR	0	-0.047	-0.055	21.129	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	405	ARG	1	0.848	0.907	23.167	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	406	PRO	0	-0.005	-0.009	25.163	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	407	ASN	0	-0.022	-0.029	20.810	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	408	LEU	0	-0.001	0.013	20.507	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	409	SER	0	0.010	-0.001	22.565	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	410	LYS	1	0.853	0.937	22.091	0.052	0.052	0.000	0.000	0.000	0.000
62	A	411	THR	0	-0.033	-0.047	21.190	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	412	LEU	0	0.017	0.002	14.420	0.005	0.005	0.000	0.000	0.000	0.000
64	A	413	LYS	1	0.924	0.948	17.843	0.136	0.136	0.000	0.000	0.000	0.000
65	A	414	GLU	-1	-0.859	-0.897	19.976	-0.114	-0.114	0.000	0.000	0.000	0.000
66	A	415	LEU	0	-0.055	-0.020	17.556	0.014	0.014	0.000	0.000	0.000	0.000
67	A	416	GLY	0	-0.038	-0.010	18.691	0.007	0.007	0.000	0.000	0.000	0.000
68	A	417	LEU	0	-0.040	-0.010	12.941	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	418	VAL	0	-0.018	-0.018	12.974	0.020	0.020	0.000	0.000	0.000	0.000
70	A	419	ASP	-1	-0.803	-0.908	12.275	-0.680	-0.680	0.000	0.000	0.000	0.000
71	A	420	GLY	0	0.007	0.012	8.527	0.013	0.013	0.000	0.000	0.000	0.000
72	A	421	GLN	0	-0.009	0.007	7.759	-0.185	-0.185	0.000	0.000	0.000	0.000
73	A	422	GLU	-1	-0.876	-0.929	3.172	-4.533	-2.895	0.133	-0.831	-0.940	-0.007
74	A	423	LEU	0	-0.026	-0.004	6.199	0.212	0.212	0.000	0.000	0.000	0.000
75	A	424	ALA	0	0.009	0.006	6.667	0.038	0.038	0.000	0.000	0.000	0.000
76	A	425	VAL	0	-0.019	-0.002	7.902	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	426	ALA	0	0.017	0.005	9.598	0.206	0.206	0.000	0.000	0.000	0.000
78	A	427	ASP	-1	-0.687	-0.830	12.239	0.210	0.210	0.000	0.000	0.000	0.000
79	A	428	VAL	0	-0.011	0.000	15.058	0.049	0.049	0.000	0.000	0.000	0.000
80	A	429	THR	0	-0.042	-0.044	14.519	0.033	0.033	0.000	0.000	0.000	0.000
81	A	430	THR	0	-0.032	-0.008	10.569	0.061	0.061	0.000	0.000	0.000	0.000
82	A	431	PRO	0	-0.008	-0.008	12.001	-0.042	-0.042	0.000	0.000	0.000	0.000
83	A	432	GLN	0	-0.040	-0.010	7.880	-0.198	-0.198	0.000	0.000	0.000	0.000
84	A	433	THR	0	-0.001	-0.009	8.613	0.080	0.080	0.000	0.000	0.000	0.000
85	A	434	VAL	0	-0.006	0.006	4.777	0.375	0.448	-0.001	-0.003	-0.069	0.000
86	A	435	LEU	0	0.004	0.005	2.591	-1.828	-0.659	0.538	-0.426	-1.282	-0.001
87	A	436	PHE	0	-0.002	-0.017	2.811	-1.696	-0.039	0.562	-1.167	-1.053	-0.012
88	A	437	LYS	1	0.828	0.892	3.264	1.683	2.215	0.026	-0.110	-0.447	0.000
89	A	438	LEU	0	-0.020	-0.005	5.231	0.103	0.084	-0.001	-0.002	0.023	0.000
90	A	439	HIS	0	0.016	0.009	8.984	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	440	PHE	0	0.028	-0.003	10.878	0.088	0.088	0.000	0.000	0.000	0.000
92	A	441	THR	0	-0.059	-0.031	14.470	0.082	0.082	0.000	0.000	0.000	0.000

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