FMO DATABASE

FMODB ID: 98Y82

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1615890.92463
FMO2-HF: Nuclear repulsion	1550886.034744
FMO2-HF: Total energy	-65004.889885
FMO2-MP2: Total energy	-65194.213226

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.
-10.269	-6.97	9.283	-4.442	-8.14	0.01

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 : 0.020 / q_NPA : -0.004

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	0.979	0.990	2.199	-13.046	-11.069	6.296	-2.940	-5.334	0.010
4	B	29	ARG	1	0.906	0.948	2.120	3.672	4.994	2.987	-1.502	-2.806	0.000
5	B	30	VAL	0	0.035	0.020	5.800	-0.506	-0.506	0.000	0.000	0.000	0.000
6	B	31	SER	0	0.015	0.017	9.493	-0.028	-0.028	0.000	0.000	0.000	0.000
7	B	32	VAL	0	0.041	0.008	11.037	0.107	0.107	0.000	0.000	0.000	0.000
8	B	33	ARG	1	0.930	0.983	14.093	0.447	0.447	0.000	0.000	0.000	0.000
9	B	34	ASP	-1	-0.838	-0.932	13.070	-0.347	-0.347	0.000	0.000	0.000	0.000
10	B	35	LYS	1	0.910	0.946	12.096	0.308	0.308	0.000	0.000	0.000	0.000
11	B	36	LEU	0	-0.035	0.007	15.597	0.043	0.043	0.000	0.000	0.000	0.000
12	B	37	LEU	0	0.058	0.023	18.387	0.031	0.031	0.000	0.000	0.000	0.000
13	B	38	VAL	0	-0.020	0.003	15.916	0.027	0.027	0.000	0.000	0.000	0.000
14	B	39	LYS	1	0.907	0.959	19.066	0.049	0.049	0.000	0.000	0.000	0.000
15	B	40	GLU	-1	-0.764	-0.895	21.839	-0.135	-0.135	0.000	0.000	0.000	0.000
16	B	41	VAL	0	0.014	0.000	22.165	0.007	0.007	0.000	0.000	0.000	0.000
17	B	42	ALA	0	-0.057	-0.019	22.813	0.011	0.011	0.000	0.000	0.000	0.000
18	B	43	GLU	-1	-0.981	-0.985	24.633	-0.046	-0.046	0.000	0.000	0.000	0.000
19	B	44	LEU	0	0.002	0.004	27.189	0.001	0.001	0.000	0.000	0.000	0.000
20	B	45	GLU	-1	-0.925	-0.976	28.996	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	46	ALA	0	-0.054	-0.023	30.897	0.002	0.002	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.077	-0.039	31.144	0.002	0.002	0.000	0.000	0.000	0.000
23	B	48	LEU	0	0.014	0.024	32.272	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	49	PRO	0	0.018	0.020	35.213	0.005	0.005	0.000	0.000	0.000	0.000
25	B	50	CYS	0	0.007	-0.006	38.401	0.002	0.002	0.000	0.000	0.000	0.000
26	B	51	THR	0	-0.011	-0.008	40.804	0.002	0.002	0.000	0.000	0.000	0.000
27	B	52	CYS	0	-0.049	-0.005	36.026	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	53	LYS	1	0.912	0.952	35.074	0.024	0.024	0.000	0.000	0.000	0.000
29	B	54	VAL	0	0.051	0.023	29.016	-0.007	-0.007	0.000	0.000	0.000	0.000
30	B	55	HIS	0	0.013	0.010	29.842	0.011	0.011	0.000	0.000	0.000	0.000
31	B	56	PHE	0	0.052	0.027	23.482	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	57	PRO	0	-0.060	-0.028	26.151	0.010	0.010	0.000	0.000	0.000	0.000
33	B	58	ASP	-1	-0.872	-0.950	20.713	-0.067	-0.067	0.000	0.000	0.000	0.000
34	B	59	PRO	0	0.008	0.008	21.040	-0.013	-0.013	0.000	0.000	0.000	0.000
35	B	60	ASN	0	-0.028	-0.015	16.248	0.025	0.025	0.000	0.000	0.000	0.000
36	B	61	LYS	1	0.898	0.960	17.339	0.130	0.130	0.000	0.000	0.000	0.000
37	B	62	LEU	0	0.057	0.027	17.373	0.009	0.009	0.000	0.000	0.000	0.000
38	B	63	HIS	0	-0.024	-0.016	18.252	0.006	0.006	0.000	0.000	0.000	0.000
39	B	64	CYS	0	-0.001	-0.023	21.071	-0.011	-0.011	0.000	0.000	0.000	0.000
40	B	65	PHE	0	-0.016	0.013	23.968	0.016	0.016	0.000	0.000	0.000	0.000
41	B	66	GLN	0	-0.046	-0.040	27.091	0.002	0.002	0.000	0.000	0.000	0.000
42	B	67	LEU	0	0.011	0.006	30.848	0.007	0.007	0.000	0.000	0.000	0.000
43	B	68	THR	0	-0.044	-0.026	33.480	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	69	VAL	0	0.041	0.021	37.075	0.003	0.003	0.000	0.000	0.000	0.000
45	B	70	THR	0	-0.073	-0.047	39.730	0.001	0.001	0.000	0.000	0.000	0.000
46	B	71	PRO	0	-0.006	0.003	43.089	0.002	0.002	0.000	0.000	0.000	0.000
47	B	72	ASP	-1	-0.896	-0.959	45.479	-0.026	-0.026	0.000	0.000	0.000	0.000
48	B	73	GLU	-1	-0.948	-0.967	48.168	-0.030	-0.030	0.000	0.000	0.000	0.000
49	B	74	GLY	0	0.036	0.017	49.401	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	75	TYR	0	-0.092	-0.079	51.179	0.003	0.003	0.000	0.000	0.000	0.000
51	B	76	TYR	0	0.018	-0.016	47.087	0.000	0.000	0.000	0.000	0.000	0.000
52	B	77	GLN	0	0.030	0.034	47.884	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	78	GLY	0	-0.020	-0.007	48.126	0.001	0.001	0.000	0.000	0.000	0.000
54	B	79	GLY	0	-0.048	-0.015	46.801	0.001	0.001	0.000	0.000	0.000	0.000
55	B	80	LYS	1	0.901	0.955	41.803	0.026	0.026	0.000	0.000	0.000	0.000
56	B	81	PHE	0	0.038	-0.004	40.909	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	82	GLN	0	-0.011	-0.003	36.242	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	83	PHE	0	0.025	0.009	34.194	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	84	GLU	-1	-0.903	-0.937	29.391	-0.101	-0.101	0.000	0.000	0.000	0.000
60	B	85	THR	0	-0.035	-0.004	27.708	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	86	GLU	-1	-0.918	-0.961	23.666	-0.222	-0.222	0.000	0.000	0.000	0.000
62	B	87	VAL	0	-0.023	-0.007	20.933	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	88	PRO	0	0.054	0.019	21.243	-0.027	-0.027	0.000	0.000	0.000	0.000
64	B	89	ASP	-1	-0.877	-0.963	16.283	-0.505	-0.505	0.000	0.000	0.000	0.000
65	B	90	ALA	0	-0.083	-0.036	16.893	-0.043	-0.043	0.000	0.000	0.000	0.000
66	B	91	TYR	0	-0.047	-0.047	18.992	0.026	0.026	0.000	0.000	0.000	0.000
67	B	92	ASN	0	0.012	0.007	20.106	-0.037	-0.037	0.000	0.000	0.000	0.000
68	B	93	MET	0	-0.034	-0.008	20.435	0.019	0.019	0.000	0.000	0.000	0.000
69	B	94	VAL	0	-0.017	0.001	23.248	0.012	0.012	0.000	0.000	0.000	0.000
70	B	95	PRO	0	0.004	0.015	24.475	-0.008	-0.008	0.000	0.000	0.000	0.000
71	B	96	PRO	0	-0.022	-0.030	25.666	-0.014	-0.014	0.000	0.000	0.000	0.000
72	B	97	LYS	1	0.963	0.996	26.694	0.202	0.202	0.000	0.000	0.000	0.000
73	B	98	VAL	0	0.003	-0.015	28.720	0.003	0.003	0.000	0.000	0.000	0.000
74	B	99	LYS	1	0.990	1.018	31.674	0.112	0.112	0.000	0.000	0.000	0.000
75	B	100	CYS	0	-0.031	-0.004	34.228	0.005	0.005	0.000	0.000	0.000	0.000
76	B	101	LEU	0	-0.029	-0.038	33.482	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	102	THR	0	-0.027	0.007	37.790	0.003	0.003	0.000	0.000	0.000	0.000
78	B	103	LYS	1	0.947	0.985	41.309	0.049	0.049	0.000	0.000	0.000	0.000
79	B	104	ILE	0	-0.022	-0.015	43.578	0.004	0.004	0.000	0.000	0.000	0.000
80	B	105	TRP	0	-0.002	0.004	46.170	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	106	HIS	0	0.059	0.025	44.883	0.001	0.001	0.000	0.000	0.000	0.000
82	B	107	PRO	0	0.024	0.032	46.851	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	108	ASN	0	0.031	0.000	42.855	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	109	ILE	0	0.020	0.019	40.517	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	110	THR	0	0.010	0.011	41.588	0.004	0.004	0.000	0.000	0.000	0.000
86	B	111	GLU	-1	-0.839	-0.911	42.841	-0.054	-0.054	0.000	0.000	0.000	0.000
87	B	112	THR	0	-0.072	-0.051	40.724	0.002	0.002	0.000	0.000	0.000	0.000
88	B	113	GLY	0	0.030	0.022	38.895	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	114	GLU	-1	-0.870	-0.903	34.973	-0.122	-0.122	0.000	0.000	0.000	0.000
90	B	115	ILE	0	-0.049	-0.051	35.555	0.008	0.008	0.000	0.000	0.000	0.000
91	B	116	CYS	0	-0.031	-0.011	37.676	-0.007	-0.007	0.000	0.000	0.000	0.000
92	B	117	LEU	0	0.060	0.028	34.974	0.005	0.005	0.000	0.000	0.000	0.000
93	B	118	SER	0	0.020	-0.005	36.207	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	119	LEU	0	0.020	0.013	32.568	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	120	LEU	0	-0.036	-0.034	30.859	-0.008	-0.008	0.000	0.000	0.000	0.000
96	B	121	ARG	1	0.962	1.007	31.947	0.092	0.092	0.000	0.000	0.000	0.000
97	B	122	GLU	-1	-0.855	-0.942	29.166	-0.182	-0.182	0.000	0.000	0.000	0.000
98	B	123	HIS	0	-0.079	-0.018	30.913	0.012	0.012	0.000	0.000	0.000	0.000
99	B	124	SER	0	0.018	0.017	34.262	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	125	ILE	0	0.003	-0.005	36.808	0.001	0.001	0.000	0.000	0.000	0.000
101	B	126	ASP	-1	-0.866	-0.918	39.564	-0.088	-0.088	0.000	0.000	0.000	0.000
102	B	127	GLY	0	-0.018	-0.001	36.680	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	128	THR	0	-0.074	-0.067	36.469	-0.001	-0.001	0.000	0.000	0.000	0.000
104	B	129	GLY	0	0.010	0.001	34.449	0.001	0.001	0.000	0.000	0.000	0.000
105	B	130	TRP	0	-0.016	-0.018	25.613	0.010	0.010	0.000	0.000	0.000	0.000
106	B	131	ALA	0	0.014	-0.004	29.033	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	132	PRO	0	0.020	0.006	24.190	0.004	0.004	0.000	0.000	0.000	0.000
108	B	133	THR	0	-0.100	-0.049	25.598	0.000	0.000	0.000	0.000	0.000	0.000
109	B	134	ARG	1	0.848	0.950	28.079	0.125	0.125	0.000	0.000	0.000	0.000
110	B	135	THR	0	0.011	0.017	26.116	-0.008	-0.008	0.000	0.000	0.000	0.000
111	B	136	LEU	0	0.015	-0.018	24.069	0.004	0.004	0.000	0.000	0.000	0.000
112	B	137	LYS	1	0.968	0.989	28.033	0.059	0.059	0.000	0.000	0.000	0.000
113	B	138	ASP	-1	-0.868	-0.947	30.784	-0.085	-0.085	0.000	0.000	0.000	0.000
114	B	139	VAL	0	-0.004	-0.003	29.203	0.003	0.003	0.000	0.000	0.000	0.000
115	B	140	VAL	0	-0.006	0.006	31.334	0.004	0.004	0.000	0.000	0.000	0.000
116	B	141	TRP	0	-0.046	-0.036	33.986	0.005	0.005	0.000	0.000	0.000	0.000
117	B	142	GLY	0	0.019	0.020	35.739	0.003	0.003	0.000	0.000	0.000	0.000
118	B	143	LEU	0	-0.002	-0.020	33.512	0.002	0.002	0.000	0.000	0.000	0.000
119	B	144	ASN	0	0.035	0.010	37.673	0.005	0.005	0.000	0.000	0.000	0.000
120	B	145	SER	0	0.025	-0.003	39.874	0.003	0.003	0.000	0.000	0.000	0.000
121	B	146	LEU	0	-0.044	0.006	38.888	0.001	0.001	0.000	0.000	0.000	0.000
122	B	147	PHE	0	-0.065	-0.039	40.657	0.001	0.001	0.000	0.000	0.000	0.000
123	B	148	THR	0	0.005	0.004	45.079	0.002	0.002	0.000	0.000	0.000	0.000
124	B	149	ASP	-1	-0.871	-0.931	44.142	-0.052	-0.052	0.000	0.000	0.000	0.000
125	B	150	LEU	0	-0.061	-0.034	40.485	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	151	LEU	0	-0.047	0.007	44.482	-0.003	-0.003	0.000	0.000	0.000	0.000
127	B	152	ASN	0	-0.027	-0.037	46.545	0.001	0.001	0.000	0.000	0.000	0.000
128	B	153	PHE	0	0.020	-0.010	48.058	-0.002	-0.002	0.000	0.000	0.000	0.000
129	B	154	ASP	-1	-0.930	-0.947	50.102	-0.051	-0.051	0.000	0.000	0.000	0.000
130	B	155	ASP	-1	-0.988	-0.995	45.650	-0.077	-0.077	0.000	0.000	0.000	0.000
131	B	156	PRO	0	-0.026	0.000	46.159	-0.002	-0.002	0.000	0.000	0.000	0.000
132	B	157	LEU	0	-0.020	-0.016	40.586	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	158	ASN	0	-0.065	-0.025	44.899	0.000	0.000	0.000	0.000	0.000	0.000
134	B	159	ILE	0	0.059	0.005	47.415	0.003	0.003	0.000	0.000	0.000	0.000
135	B	160	GLU	-1	-0.866	-0.929	50.588	-0.048	-0.048	0.000	0.000	0.000	0.000
136	B	161	ALA	0	-0.014	-0.006	50.029	0.003	0.003	0.000	0.000	0.000	0.000
137	B	162	ALA	0	0.029	0.014	51.308	0.003	0.003	0.000	0.000	0.000	0.000
138	B	163	GLU	-1	-0.963	-0.983	53.009	-0.047	-0.047	0.000	0.000	0.000	0.000
139	B	164	HIS	0	-0.069	-0.053	55.193	0.000	0.000	0.000	0.000	0.000	0.000
140	B	165	HIS	0	0.000	-0.002	54.591	0.004	0.004	0.000	0.000	0.000	0.000
141	B	166	LEU	0	-0.049	-0.028	56.623	0.002	0.002	0.000	0.000	0.000	0.000
142	B	167	ARG	1	0.869	0.930	58.424	0.043	0.043	0.000	0.000	0.000	0.000
143	B	168	ASP	-1	-0.837	-0.919	60.377	-0.029	-0.029	0.000	0.000	0.000	0.000
144	B	169	LYS	1	0.925	0.964	58.367	0.034	0.034	0.000	0.000	0.000	0.000
145	B	170	GLU	-1	-0.967	-0.977	59.004	-0.026	-0.026	0.000	0.000	0.000	0.000
146	B	171	ASP	-1	-0.777	-0.858	60.264	-0.033	-0.033	0.000	0.000	0.000	0.000
147	B	172	PHE	0	-0.043	-0.020	51.649	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	173	ARG	1	0.932	0.958	55.053	0.029	0.029	0.000	0.000	0.000	0.000
149	B	174	ASN	0	0.028	0.027	55.588	0.000	0.000	0.000	0.000	0.000	0.000
150	B	175	LYS	1	0.940	0.999	52.358	0.045	0.045	0.000	0.000	0.000	0.000
151	B	176	VAL	0	-0.022	-0.015	50.540	-0.001	-0.001	0.000	0.000	0.000	0.000
152	B	177	ASP	-1	-0.908	-0.959	51.412	-0.030	-0.030	0.000	0.000	0.000	0.000
153	B	178	ASP	-1	-0.912	-0.943	53.085	-0.032	-0.032	0.000	0.000	0.000	0.000
154	B	179	TYR	0	-0.072	-0.078	48.296	0.001	0.001	0.000	0.000	0.000	0.000
155	B	180	ILE	0	0.001	0.015	48.011	-0.001	-0.001	0.000	0.000	0.000	0.000
156	B	181	LYS	1	0.888	0.933	48.770	0.024	0.024	0.000	0.000	0.000	0.000
157	B	182	ARG	1	0.805	0.895	50.099	0.034	0.034	0.000	0.000	0.000	0.000
158	B	183	TYR	0	-0.025	-0.023	45.063	0.000	0.000	0.000	0.000	0.000	0.000
159	B	184	ALA	0	0.026	0.042	44.249	-0.002	-0.002	0.000	0.000	0.000	0.000
160	B	185	ARG	1	0.863	0.936	45.417	0.029	0.029	0.000	0.000	0.000	0.000

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