FMO DATABASE

FMODB ID: 76J6K

Calculation Name: 3FN1-B-Xray372

Preferred Name: NEDD8-activating enzyme E1 catalytic subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3FN1

Chain ID: B

ChEMBL ID: CHEMBL2016430

UniProt ID: Q8TBC4

Base Structure: X-ray

Registration Date: 2023-09-20

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1621628.78075
FMO2-HF: Nuclear repulsion	1556622.425501
FMO2-HF: Total energy	-65006.355249
FMO2-MP2: Total energy	-65195.676579

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(B:26:SER)

Summations of interaction energy for fragment #1(B:26:SER)

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.
-21.077	-16.157	7.992	-4.974	-7.939	0.021

Interaction energy analysis for fragmet #1(B:26:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.015

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

Sort

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	B	28	ARG	1	0.957	0.978	2.170	-18.155	-15.057	6.738	-3.987	-5.849	0.017
4	B	29	ARG	1	0.916	0.949	2.690	-2.536	-0.714	1.254	-0.987	-2.090	0.004
5	B	30	VAL	0	0.060	0.038	6.036	-0.250	-0.250	0.000	0.000	0.000	0.000
6	B	31	SER	0	0.021	-0.022	9.861	0.049	0.049	0.000	0.000	0.000	0.000
7	B	32	VAL	0	0.023	0.011	11.999	0.064	0.064	0.000	0.000	0.000	0.000
8	B	33	ARG	1	0.884	0.926	14.852	0.217	0.217	0.000	0.000	0.000	0.000
9	B	34	ASP	-1	-0.777	-0.842	13.538	-0.146	-0.146	0.000	0.000	0.000	0.000
10	B	35	LYS	1	0.821	0.894	11.844	0.034	0.034	0.000	0.000	0.000	0.000
11	B	36	LEU	0	-0.004	0.024	15.830	0.017	0.017	0.000	0.000	0.000	0.000
12	B	37	LEU	0	0.046	0.025	18.380	0.010	0.010	0.000	0.000	0.000	0.000
13	B	38	VAL	0	-0.028	-0.010	15.881	0.012	0.012	0.000	0.000	0.000	0.000
14	B	39	LYS	1	0.807	0.909	19.171	-0.012	-0.012	0.000	0.000	0.000	0.000
15	B	40	GLU	-1	-0.741	-0.876	21.785	-0.031	-0.031	0.000	0.000	0.000	0.000
16	B	41	VAL	0	0.005	-0.010	22.341	0.001	0.001	0.000	0.000	0.000	0.000
17	B	42	ALA	0	-0.045	-0.015	23.014	0.003	0.003	0.000	0.000	0.000	0.000
18	B	43	GLU	-1	-0.871	-0.926	24.898	0.017	0.017	0.000	0.000	0.000	0.000
19	B	44	LEU	0	-0.008	0.007	27.405	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	45	GLU	-1	-0.900	-0.958	29.197	0.023	0.023	0.000	0.000	0.000	0.000
21	B	46	ALA	0	-0.051	-0.028	30.960	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.074	-0.044	31.293	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	48	LEU	0	0.000	0.024	32.090	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	49	PRO	0	0.026	0.021	35.320	0.002	0.002	0.000	0.000	0.000	0.000
25	B	50	CYS	0	-0.003	-0.004	38.727	0.002	0.002	0.000	0.000	0.000	0.000
26	B	51	THR	0	0.044	0.011	40.965	0.002	0.002	0.000	0.000	0.000	0.000
27	B	52	CYS	0	-0.059	-0.001	36.329	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	53	LYS	1	0.868	0.928	35.233	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	54	VAL	0	0.042	0.015	29.091	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	55	HIS	0	0.021	0.016	29.307	0.006	0.006	0.000	0.000	0.000	0.000
31	B	56	PHE	0	0.045	0.016	23.444	-0.006	-0.006	0.000	0.000	0.000	0.000
32	B	57	PRO	0	-0.040	-0.016	26.213	0.007	0.007	0.000	0.000	0.000	0.000
33	B	58	ASP	-1	-0.790	-0.883	20.537	0.022	0.022	0.000	0.000	0.000	0.000
34	B	59	PRO	0	0.010	0.010	21.157	-0.009	-0.009	0.000	0.000	0.000	0.000
35	B	60	ASN	0	-0.069	-0.050	16.451	0.021	0.021	0.000	0.000	0.000	0.000
36	B	61	LYS	1	0.851	0.929	17.190	0.008	0.008	0.000	0.000	0.000	0.000
37	B	62	LEU	0	0.032	0.012	17.068	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	63	HIS	0	-0.060	-0.041	18.843	0.006	0.006	0.000	0.000	0.000	0.000
39	B	64	CYS	0	-0.029	-0.013	20.840	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	65	PHE	0	0.010	0.007	23.803	0.010	0.010	0.000	0.000	0.000	0.000
41	B	66	GLN	0	-0.028	-0.036	26.869	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	67	LEU	0	0.013	0.005	30.639	0.004	0.004	0.000	0.000	0.000	0.000
43	B	68	THR	0	-0.040	-0.024	33.513	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	69	VAL	0	0.047	0.025	37.191	0.002	0.002	0.000	0.000	0.000	0.000
45	B	70	THR	0	-0.068	-0.039	39.882	0.000	0.000	0.000	0.000	0.000	0.000
46	B	71	PRO	0	0.004	0.009	43.219	0.001	0.001	0.000	0.000	0.000	0.000
47	B	72	ASP	-1	-0.855	-0.931	45.459	0.001	0.001	0.000	0.000	0.000	0.000
48	B	73	GLU	-1	-0.914	-0.949	48.022	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	74	GLY	0	0.069	0.035	49.476	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	75	TYR	0	-0.087	-0.074	51.143	0.001	0.001	0.000	0.000	0.000	0.000
51	B	76	TYR	0	-0.029	-0.035	47.070	0.000	0.000	0.000	0.000	0.000	0.000
52	B	77	GLN	0	-0.025	-0.001	48.070	0.001	0.001	0.000	0.000	0.000	0.000
53	B	78	GLY	0	-0.014	-0.005	48.277	0.000	0.000	0.000	0.000	0.000	0.000
54	B	79	GLY	0	-0.012	0.005	47.019	0.001	0.001	0.000	0.000	0.000	0.000
55	B	80	LYS	1	0.863	0.918	42.272	-0.004	-0.004	0.000	0.000	0.000	0.000
56	B	81	PHE	0	0.054	0.014	41.150	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	82	GLN	0	-0.005	0.007	36.633	0.000	0.000	0.000	0.000	0.000	0.000
58	B	83	PHE	0	0.036	0.003	34.295	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	84	GLU	-1	-0.835	-0.900	29.604	-0.026	-0.026	0.000	0.000	0.000	0.000
60	B	85	THR	0	-0.026	-0.008	27.535	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	86	GLU	-1	-0.874	-0.921	23.033	-0.088	-0.088	0.000	0.000	0.000	0.000
62	B	87	VAL	0	-0.018	-0.005	21.266	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	88	PRO	0	0.043	0.021	21.553	-0.012	-0.012	0.000	0.000	0.000	0.000
64	B	89	ASP	-1	-0.848	-0.939	16.049	-0.243	-0.243	0.000	0.000	0.000	0.000
65	B	90	ALA	0	-0.064	-0.031	17.405	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	91	TYR	0	-0.025	-0.034	19.661	0.010	0.010	0.000	0.000	0.000	0.000
67	B	92	ASN	0	-0.028	-0.009	20.862	-0.013	-0.013	0.000	0.000	0.000	0.000
68	B	93	MET	0	-0.019	-0.012	20.862	0.007	0.007	0.000	0.000	0.000	0.000
69	B	94	VAL	0	-0.039	-0.006	23.369	0.002	0.002	0.000	0.000	0.000	0.000
70	B	95	PRO	0	0.000	0.010	25.023	0.001	0.001	0.000	0.000	0.000	0.000
71	B	96	PRO	0	-0.024	-0.025	26.293	-0.008	-0.008	0.000	0.000	0.000	0.000
72	B	97	LYS	1	0.870	0.940	27.421	0.082	0.082	0.000	0.000	0.000	0.000
73	B	98	VAL	0	-0.003	-0.016	29.109	0.002	0.002	0.000	0.000	0.000	0.000
74	B	99	LYS	1	0.913	0.967	31.868	0.037	0.037	0.000	0.000	0.000	0.000
75	B	100	CYS	0	-0.047	-0.014	34.458	0.004	0.004	0.000	0.000	0.000	0.000
76	B	101	LEU	0	-0.033	-0.033	33.676	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	102	THR	0	-0.016	0.003	37.835	0.001	0.001	0.000	0.000	0.000	0.000
78	B	103	LYS	1	0.843	0.934	41.416	0.016	0.016	0.000	0.000	0.000	0.000
79	B	104	ILE	0	-0.021	-0.010	43.467	0.002	0.002	0.000	0.000	0.000	0.000
80	B	105	TRP	0	-0.002	0.003	45.936	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	106	HIS	0	0.043	0.009	45.144	0.000	0.000	0.000	0.000	0.000	0.000
82	B	107	PRO	0	0.037	0.035	47.323	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	108	ASN	0	0.040	0.001	43.385	0.000	0.000	0.000	0.000	0.000	0.000
84	B	109	ILE	0	0.007	0.010	40.536	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	110	THR	0	0.000	0.002	41.777	0.002	0.002	0.000	0.000	0.000	0.000
86	B	111	GLU	-1	-0.758	-0.867	43.019	-0.018	-0.018	0.000	0.000	0.000	0.000
87	B	112	THR	0	-0.045	-0.027	40.350	0.002	0.002	0.000	0.000	0.000	0.000
88	B	113	GLY	0	0.009	0.021	38.758	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	114	GLU	-1	-0.872	-0.923	36.027	-0.051	-0.051	0.000	0.000	0.000	0.000
90	B	115	ILE	0	-0.016	-0.032	35.392	0.004	0.004	0.000	0.000	0.000	0.000
91	B	116	CYS	0	-0.027	-0.007	37.930	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	117	LEU	0	0.024	0.021	35.419	0.002	0.002	0.000	0.000	0.000	0.000
93	B	118	SER	0	0.023	0.001	36.869	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	119	LEU	0	0.007	0.003	32.582	-0.004	-0.004	0.000	0.000	0.000	0.000
95	B	120	LEU	0	-0.024	-0.026	31.104	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	121	ARG	1	0.860	0.945	32.771	0.036	0.036	0.000	0.000	0.000	0.000
97	B	122	GLU	-1	-0.836	-0.925	29.800	-0.079	-0.079	0.000	0.000	0.000	0.000
98	B	123	HIS	0	-0.056	-0.004	31.491	0.005	0.005	0.000	0.000	0.000	0.000
99	B	124	SER	0	-0.006	-0.009	34.231	-0.003	-0.003	0.000	0.000	0.000	0.000
100	B	125	ILE	0	-0.009	-0.004	37.038	0.001	0.001	0.000	0.000	0.000	0.000
101	B	126	ASP	-1	-0.833	-0.907	39.246	-0.039	-0.039	0.000	0.000	0.000	0.000
102	B	127	GLY	0	0.000	-0.006	36.961	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	128	THR	0	-0.026	-0.024	36.771	0.000	0.000	0.000	0.000	0.000	0.000
104	B	129	GLY	0	0.059	0.034	35.059	0.001	0.001	0.000	0.000	0.000	0.000
105	B	130	TRP	0	-0.042	-0.042	26.253	0.005	0.005	0.000	0.000	0.000	0.000
106	B	131	ALA	0	0.013	-0.001	29.393	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	132	PRO	0	0.000	-0.007	24.897	0.004	0.004	0.000	0.000	0.000	0.000
108	B	133	THR	0	-0.039	-0.020	26.457	0.003	0.003	0.000	0.000	0.000	0.000
109	B	134	ARG	1	0.816	0.935	28.860	0.047	0.047	0.000	0.000	0.000	0.000
110	B	135	THR	0	-0.015	-0.026	26.830	-0.002	-0.002	0.000	0.000	0.000	0.000
111	B	136	LEU	0	0.017	-0.010	24.140	0.000	0.000	0.000	0.000	0.000	0.000
112	B	137	LYS	1	0.930	0.968	28.262	0.009	0.009	0.000	0.000	0.000	0.000
113	B	138	ASP	-1	-0.818	-0.896	31.282	-0.018	-0.018	0.000	0.000	0.000	0.000
114	B	139	VAL	0	0.002	0.009	29.814	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	140	VAL	0	0.013	0.007	31.389	0.001	0.001	0.000	0.000	0.000	0.000
116	B	141	TRP	0	-0.043	-0.034	34.054	0.001	0.001	0.000	0.000	0.000	0.000
117	B	142	GLY	0	0.017	0.014	36.179	0.000	0.000	0.000	0.000	0.000	0.000
118	B	143	LEU	0	-0.002	-0.017	33.489	0.000	0.000	0.000	0.000	0.000	0.000
119	B	144	ASN	0	0.016	0.013	37.757	0.002	0.002	0.000	0.000	0.000	0.000
120	B	145	SER	0	0.016	-0.018	40.152	0.001	0.001	0.000	0.000	0.000	0.000
121	B	146	LEU	0	-0.029	0.007	39.191	0.000	0.000	0.000	0.000	0.000	0.000
122	B	147	PHE	0	-0.057	-0.036	40.542	0.000	0.000	0.000	0.000	0.000	0.000
123	B	148	THR	0	-0.017	-0.027	45.337	0.001	0.001	0.000	0.000	0.000	0.000
124	B	149	ASP	-1	-0.842	-0.889	44.295	-0.013	-0.013	0.000	0.000	0.000	0.000
125	B	150	LEU	0	-0.054	-0.036	41.009	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	151	LEU	0	-0.056	0.005	44.965	-0.002	-0.002	0.000	0.000	0.000	0.000
127	B	152	ASN	0	-0.077	-0.069	46.882	0.000	0.000	0.000	0.000	0.000	0.000
128	B	153	PHE	0	0.013	-0.013	48.805	-0.001	-0.001	0.000	0.000	0.000	0.000
129	B	154	ASP	-1	-0.867	-0.919	50.060	-0.020	-0.020	0.000	0.000	0.000	0.000
130	B	155	ASP	-1	-0.905	-0.947	44.896	-0.035	-0.035	0.000	0.000	0.000	0.000
131	B	156	PRO	0	-0.032	0.005	46.134	-0.001	-0.001	0.000	0.000	0.000	0.000
132	B	157	LEU	0	0.010	-0.001	40.997	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	158	ASN	0	-0.089	-0.035	45.158	-0.001	-0.001	0.000	0.000	0.000	0.000
134	B	159	ILE	0	0.058	0.016	47.771	0.002	0.002	0.000	0.000	0.000	0.000
135	B	160	GLU	-1	-0.844	-0.919	50.969	-0.018	-0.018	0.000	0.000	0.000	0.000
136	B	161	ALA	0	0.013	0.002	49.996	0.001	0.001	0.000	0.000	0.000	0.000
137	B	162	ALA	0	0.014	0.000	51.350	0.001	0.001	0.000	0.000	0.000	0.000
138	B	163	GLU	-1	-0.858	-0.921	53.162	-0.019	-0.019	0.000	0.000	0.000	0.000
139	B	164	HIS	0	-0.066	-0.043	55.148	0.000	0.000	0.000	0.000	0.000	0.000
140	B	165	HIS	0	0.050	0.038	54.661	0.002	0.002	0.000	0.000	0.000	0.000
141	B	166	LEU	0	-0.061	-0.019	56.702	0.001	0.001	0.000	0.000	0.000	0.000
142	B	167	ARG	1	0.771	0.866	59.163	0.017	0.017	0.000	0.000	0.000	0.000
143	B	168	ASP	-1	-0.837	-0.912	60.420	-0.009	-0.009	0.000	0.000	0.000	0.000
144	B	169	LYS	1	0.880	0.932	57.887	0.011	0.011	0.000	0.000	0.000	0.000
145	B	170	GLU	-1	-0.967	-0.968	59.153	-0.006	-0.006	0.000	0.000	0.000	0.000
146	B	171	ASP	-1	-0.811	-0.903	59.956	-0.010	-0.010	0.000	0.000	0.000	0.000
147	B	172	PHE	0	-0.045	-0.010	51.727	0.000	0.000	0.000	0.000	0.000	0.000
148	B	173	ARG	1	0.852	0.908	53.560	0.006	0.006	0.000	0.000	0.000	0.000
149	B	174	ASN	0	-0.013	-0.009	55.484	0.000	0.000	0.000	0.000	0.000	0.000
150	B	175	LYS	1	0.881	0.954	52.887	0.016	0.016	0.000	0.000	0.000	0.000
151	B	176	VAL	0	-0.012	-0.003	50.363	0.000	0.000	0.000	0.000	0.000	0.000
152	B	177	ASP	-1	-0.825	-0.900	51.447	-0.005	-0.005	0.000	0.000	0.000	0.000
153	B	178	ASP	-1	-0.851	-0.907	53.065	-0.006	-0.006	0.000	0.000	0.000	0.000
154	B	179	TYR	0	-0.030	-0.055	48.386	0.001	0.001	0.000	0.000	0.000	0.000
155	B	180	ILE	0	-0.021	-0.010	48.135	0.000	0.000	0.000	0.000	0.000	0.000
156	B	181	LYS	1	0.876	0.934	48.896	0.003	0.003	0.000	0.000	0.000	0.000
157	B	182	ARG	1	0.783	0.872	49.680	0.008	0.008	0.000	0.000	0.000	0.000
158	B	183	TYR	0	-0.017	-0.010	44.872	0.000	0.000	0.000	0.000	0.000	0.000
159	B	184	ALA	0	0.022	0.044	44.105	0.000	0.000	0.000	0.000	0.000	0.000
160	B	185	ARG	1	0.818	0.900	45.217	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:SER)