FMO DATABASE

FMODB ID: MNMNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1617403.947836
FMO2-HF: Nuclear repulsion	1552398.118758
FMO2-HF: Total energy	-65005.829079
FMO2-MP2: Total energy	-65195.180433

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.
-11.084	-7.045	8.08	-4.225	-7.893	0.009

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 : 0.015 / q_NPA : -0.005

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	0.981	0.990	2.247	-12.754	-10.217	5.480	-2.818	-5.199	0.008
4	B	29	ARG	1	0.906	0.948	2.187	2.500	4.002	2.600	-1.407	-2.694	0.001
5	B	30	VAL	0	0.037	0.019	5.765	-0.522	-0.522	0.000	0.000	0.000	0.000
6	B	31	SER	0	-0.009	-0.032	9.462	-0.028	-0.028	0.000	0.000	0.000	0.000
7	B	32	VAL	0	0.029	-0.001	11.141	0.098	0.098	0.000	0.000	0.000	0.000
8	B	33	ARG	1	0.915	0.958	14.189	0.409	0.409	0.000	0.000	0.000	0.000
9	B	34	ASP	-1	-0.793	-0.870	13.158	-0.326	-0.326	0.000	0.000	0.000	0.000
10	B	35	LYS	1	0.894	0.947	11.822	0.265	0.265	0.000	0.000	0.000	0.000
11	B	36	LEU	0	-0.008	0.020	15.705	0.035	0.035	0.000	0.000	0.000	0.000
12	B	37	LEU	0	0.052	0.022	18.283	0.025	0.025	0.000	0.000	0.000	0.000
13	B	38	VAL	0	-0.030	-0.006	15.762	0.023	0.023	0.000	0.000	0.000	0.000
14	B	39	LYS	1	0.811	0.903	19.039	0.039	0.039	0.000	0.000	0.000	0.000
15	B	40	GLU	-1	-0.753	-0.882	21.807	-0.111	-0.111	0.000	0.000	0.000	0.000
16	B	41	VAL	0	-0.001	-0.008	22.168	0.005	0.005	0.000	0.000	0.000	0.000
17	B	42	ALA	0	-0.047	-0.014	22.768	0.008	0.008	0.000	0.000	0.000	0.000
18	B	43	GLU	-1	-0.877	-0.927	24.607	-0.028	-0.028	0.000	0.000	0.000	0.000
19	B	44	LEU	0	0.001	0.012	27.170	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	45	GLU	-1	-0.931	-0.978	28.972	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	46	ALA	0	-0.038	-0.020	30.872	0.001	0.001	0.000	0.000	0.000	0.000
22	B	47	ASN	0	-0.077	-0.044	31.087	0.000	0.000	0.000	0.000	0.000	0.000
23	B	48	LEU	0	0.002	0.027	31.993	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	49	PRO	0	0.031	0.024	35.189	0.004	0.004	0.000	0.000	0.000	0.000
25	B	50	CYS	0	0.008	-0.006	38.380	0.002	0.002	0.000	0.000	0.000	0.000
26	B	51	THR	0	0.021	0.004	40.782	0.002	0.002	0.000	0.000	0.000	0.000
27	B	52	CYS	0	-0.066	-0.012	36.078	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	53	LYS	1	0.882	0.938	35.048	0.019	0.019	0.000	0.000	0.000	0.000
29	B	54	VAL	0	0.061	0.024	28.867	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	55	HIS	0	0.020	0.013	29.615	0.009	0.009	0.000	0.000	0.000	0.000
31	B	56	PHE	0	0.052	0.027	23.450	-0.009	-0.009	0.000	0.000	0.000	0.000
32	B	57	PRO	0	-0.049	-0.020	26.148	0.009	0.009	0.000	0.000	0.000	0.000
33	B	58	ASP	-1	-0.798	-0.894	20.558	-0.052	-0.052	0.000	0.000	0.000	0.000
34	B	59	PRO	0	0.014	0.008	21.013	-0.011	-0.011	0.000	0.000	0.000	0.000
35	B	60	ASN	0	-0.072	-0.043	16.281	0.028	0.028	0.000	0.000	0.000	0.000
36	B	61	LYS	1	0.857	0.925	17.332	0.090	0.090	0.000	0.000	0.000	0.000
37	B	62	LEU	0	0.041	0.021	17.153	0.007	0.007	0.000	0.000	0.000	0.000
38	B	63	HIS	0	-0.025	-0.015	18.985	0.010	0.010	0.000	0.000	0.000	0.000
39	B	64	CYS	0	-0.009	-0.018	21.060	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	65	PHE	0	0.003	0.014	23.961	0.014	0.014	0.000	0.000	0.000	0.000
41	B	66	GLN	0	-0.050	-0.042	27.083	0.001	0.001	0.000	0.000	0.000	0.000
42	B	67	LEU	0	0.006	0.008	30.840	0.006	0.006	0.000	0.000	0.000	0.000
43	B	68	THR	0	-0.036	-0.022	33.468	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	69	VAL	0	0.046	0.020	37.064	0.003	0.003	0.000	0.000	0.000	0.000
45	B	70	THR	0	-0.072	-0.048	39.716	0.001	0.001	0.000	0.000	0.000	0.000
46	B	71	PRO	0	-0.006	0.004	43.075	0.002	0.002	0.000	0.000	0.000	0.000
47	B	72	ASP	-1	-0.856	-0.942	45.462	-0.020	-0.020	0.000	0.000	0.000	0.000
48	B	73	GLU	-1	-0.948	-0.962	48.150	-0.024	-0.024	0.000	0.000	0.000	0.000
49	B	74	GLY	0	0.055	0.028	49.384	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	75	TYR	0	-0.074	-0.072	51.188	0.002	0.002	0.000	0.000	0.000	0.000
51	B	76	TYR	0	0.002	-0.019	47.052	0.000	0.000	0.000	0.000	0.000	0.000
52	B	77	GLN	0	-0.037	-0.004	47.871	0.000	0.000	0.000	0.000	0.000	0.000
53	B	78	GLY	0	-0.003	0.006	48.110	0.001	0.001	0.000	0.000	0.000	0.000
54	B	79	GLY	0	-0.028	-0.007	46.793	0.001	0.001	0.000	0.000	0.000	0.000
55	B	80	LYS	1	0.899	0.954	41.865	0.019	0.019	0.000	0.000	0.000	0.000
56	B	81	PHE	0	0.043	0.001	40.900	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	82	GLN	0	-0.007	0.003	36.316	0.000	0.000	0.000	0.000	0.000	0.000
58	B	83	PHE	0	0.030	0.011	34.148	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	84	GLU	-1	-0.832	-0.898	29.558	-0.084	-0.084	0.000	0.000	0.000	0.000
60	B	85	THR	0	-0.022	-0.001	27.519	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	86	GLU	-1	-0.937	-0.967	23.520	-0.185	-0.185	0.000	0.000	0.000	0.000
62	B	87	VAL	0	-0.020	-0.008	21.105	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	88	PRO	0	0.034	0.014	21.341	-0.022	-0.022	0.000	0.000	0.000	0.000
64	B	89	ASP	-1	-0.854	-0.946	16.309	-0.433	-0.433	0.000	0.000	0.000	0.000
65	B	90	ALA	0	-0.080	-0.033	16.981	-0.035	-0.035	0.000	0.000	0.000	0.000
66	B	91	TYR	0	-0.054	-0.054	19.070	0.022	0.022	0.000	0.000	0.000	0.000
67	B	92	ASN	0	0.008	0.002	20.198	-0.031	-0.031	0.000	0.000	0.000	0.000
68	B	93	MET	0	-0.026	0.000	20.454	0.018	0.018	0.000	0.000	0.000	0.000
69	B	94	VAL	0	-0.024	-0.004	23.338	0.010	0.010	0.000	0.000	0.000	0.000
70	B	95	PRO	0	0.014	0.019	24.566	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	96	PRO	0	-0.025	-0.027	25.733	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	97	LYS	1	0.956	0.991	26.792	0.172	0.172	0.000	0.000	0.000	0.000
73	B	98	VAL	0	-0.006	-0.018	28.814	0.003	0.003	0.000	0.000	0.000	0.000
74	B	99	LYS	1	0.914	0.971	31.772	0.095	0.095	0.000	0.000	0.000	0.000
75	B	100	CYS	0	-0.030	-0.012	34.221	0.005	0.005	0.000	0.000	0.000	0.000
76	B	101	LEU	0	-0.027	-0.030	33.573	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	102	THR	0	-0.035	-0.001	37.788	0.003	0.003	0.000	0.000	0.000	0.000
78	B	103	LYS	1	0.864	0.947	41.305	0.043	0.043	0.000	0.000	0.000	0.000
79	B	104	ILE	0	-0.031	-0.019	43.520	0.004	0.004	0.000	0.000	0.000	0.000
80	B	105	TRP	0	0.028	0.019	46.164	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	106	HIS	0	0.048	0.012	44.901	0.001	0.001	0.000	0.000	0.000	0.000
82	B	107	PRO	0	0.041	0.034	46.947	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	108	ASN	0	0.039	0.002	42.982	0.000	0.000	0.000	0.000	0.000	0.000
84	B	109	ILE	0	0.018	0.017	40.444	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	110	THR	0	0.007	0.011	41.824	0.004	0.004	0.000	0.000	0.000	0.000
86	B	111	GLU	-1	-0.759	-0.868	42.835	-0.045	-0.045	0.000	0.000	0.000	0.000
87	B	112	THR	0	-0.062	-0.048	40.709	0.002	0.002	0.000	0.000	0.000	0.000
88	B	113	GLY	0	0.032	0.026	38.891	-0.003	-0.003	0.000	0.000	0.000	0.000
89	B	114	GLU	-1	-0.897	-0.928	35.464	-0.106	-0.106	0.000	0.000	0.000	0.000
90	B	115	ILE	0	-0.033	-0.034	35.367	0.007	0.007	0.000	0.000	0.000	0.000
91	B	116	CYS	0	-0.030	-0.009	37.768	-0.007	-0.007	0.000	0.000	0.000	0.000
92	B	117	LEU	0	0.062	0.029	35.229	0.004	0.004	0.000	0.000	0.000	0.000
93	B	118	SER	0	0.041	0.017	36.300	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	119	LEU	0	0.005	0.000	32.320	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	120	LEU	0	-0.027	-0.030	30.901	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	121	ARG	1	0.931	0.991	32.036	0.079	0.079	0.000	0.000	0.000	0.000
97	B	122	GLU	-1	-0.879	-0.953	29.689	-0.155	-0.155	0.000	0.000	0.000	0.000
98	B	123	HIS	0	-0.068	-0.016	31.180	0.011	0.011	0.000	0.000	0.000	0.000
99	B	124	SER	0	0.012	0.017	34.334	-0.003	-0.003	0.000	0.000	0.000	0.000
100	B	125	ILE	0	0.013	0.000	36.879	0.001	0.001	0.000	0.000	0.000	0.000
101	B	126	ASP	-1	-0.833	-0.905	39.518	-0.077	-0.077	0.000	0.000	0.000	0.000
102	B	127	GLY	0	-0.008	0.002	36.757	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	128	THR	0	-0.089	-0.072	36.553	0.000	0.000	0.000	0.000	0.000	0.000
104	B	129	GLY	0	0.020	0.005	34.537	0.001	0.001	0.000	0.000	0.000	0.000
105	B	130	TRP	0	-0.018	-0.021	25.685	0.008	0.008	0.000	0.000	0.000	0.000
106	B	131	ALA	0	-0.001	-0.011	29.116	-0.002	-0.002	0.000	0.000	0.000	0.000
107	B	132	PRO	0	0.033	0.010	24.160	0.005	0.005	0.000	0.000	0.000	0.000
108	B	133	THR	0	-0.084	-0.041	25.691	0.000	0.000	0.000	0.000	0.000	0.000
109	B	134	ARG	1	0.826	0.937	28.185	0.108	0.108	0.000	0.000	0.000	0.000
110	B	135	THR	0	0.000	-0.010	26.283	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	136	LEU	0	0.014	-0.019	24.124	0.002	0.002	0.000	0.000	0.000	0.000
112	B	137	LYS	1	0.932	0.968	28.131	0.053	0.053	0.000	0.000	0.000	0.000
113	B	138	ASP	-1	-0.839	-0.920	30.847	-0.066	-0.066	0.000	0.000	0.000	0.000
114	B	139	VAL	0	0.014	0.014	29.360	0.002	0.002	0.000	0.000	0.000	0.000
115	B	140	VAL	0	0.001	0.009	31.304	0.003	0.003	0.000	0.000	0.000	0.000
116	B	141	TRP	0	-0.036	-0.032	33.965	0.004	0.004	0.000	0.000	0.000	0.000
117	B	142	GLY	0	0.016	0.020	35.844	0.002	0.002	0.000	0.000	0.000	0.000
118	B	143	LEU	0	-0.003	-0.022	33.452	0.002	0.002	0.000	0.000	0.000	0.000
119	B	144	ASN	0	0.018	0.007	37.720	0.005	0.005	0.000	0.000	0.000	0.000
120	B	145	SER	0	0.040	0.000	39.855	0.002	0.002	0.000	0.000	0.000	0.000
121	B	146	LEU	0	-0.049	0.002	38.884	0.001	0.001	0.000	0.000	0.000	0.000
122	B	147	PHE	0	-0.061	-0.034	40.586	0.001	0.001	0.000	0.000	0.000	0.000
123	B	148	THR	0	0.006	-0.007	45.128	0.002	0.002	0.000	0.000	0.000	0.000
124	B	149	ASP	-1	-0.864	-0.913	44.033	-0.043	-0.043	0.000	0.000	0.000	0.000
125	B	150	LEU	0	-0.063	-0.035	40.644	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	151	LEU	0	-0.065	0.003	44.582	-0.003	-0.003	0.000	0.000	0.000	0.000
127	B	152	ASN	0	-0.069	-0.070	46.487	0.000	0.000	0.000	0.000	0.000	0.000
128	B	153	PHE	0	0.037	-0.004	48.154	-0.002	-0.002	0.000	0.000	0.000	0.000
129	B	154	ASP	-1	-0.899	-0.934	50.231	-0.045	-0.045	0.000	0.000	0.000	0.000
130	B	155	ASP	-1	-0.965	-0.973	45.665	-0.067	-0.067	0.000	0.000	0.000	0.000
131	B	156	PRO	0	-0.035	-0.001	46.249	-0.002	-0.002	0.000	0.000	0.000	0.000
132	B	157	LEU	0	-0.014	-0.015	40.763	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	158	ASN	0	-0.080	-0.035	44.988	0.000	0.000	0.000	0.000	0.000	0.000
134	B	159	ILE	0	0.056	0.006	47.506	0.002	0.002	0.000	0.000	0.000	0.000
135	B	160	GLU	-1	-0.887	-0.939	50.677	-0.041	-0.041	0.000	0.000	0.000	0.000
136	B	161	ALA	0	0.001	-0.001	50.095	0.003	0.003	0.000	0.000	0.000	0.000
137	B	162	ALA	0	0.033	0.014	51.340	0.002	0.002	0.000	0.000	0.000	0.000
138	B	163	GLU	-1	-0.881	-0.924	53.103	-0.040	-0.040	0.000	0.000	0.000	0.000
139	B	164	HIS	0	-0.066	-0.046	55.237	0.000	0.000	0.000	0.000	0.000	0.000
140	B	165	HIS	0	0.013	0.020	54.709	0.004	0.004	0.000	0.000	0.000	0.000
141	B	166	LEU	0	-0.050	-0.024	56.721	0.002	0.002	0.000	0.000	0.000	0.000
142	B	167	ARG	1	0.802	0.881	58.847	0.037	0.037	0.000	0.000	0.000	0.000
143	B	168	ASP	-1	-0.832	-0.910	60.473	-0.025	-0.025	0.000	0.000	0.000	0.000
144	B	169	LYS	1	0.907	0.947	58.127	0.029	0.029	0.000	0.000	0.000	0.000
145	B	170	GLU	-1	-0.961	-0.968	58.992	-0.021	-0.021	0.000	0.000	0.000	0.000
146	B	171	ASP	-1	-0.809	-0.896	60.297	-0.028	-0.028	0.000	0.000	0.000	0.000
147	B	172	PHE	0	-0.047	-0.020	51.676	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	173	ARG	1	0.867	0.915	54.441	0.024	0.024	0.000	0.000	0.000	0.000
149	B	174	ASN	0	0.006	0.020	55.579	0.000	0.000	0.000	0.000	0.000	0.000
150	B	175	LYS	1	0.908	0.978	52.759	0.039	0.039	0.000	0.000	0.000	0.000
151	B	176	VAL	0	-0.018	-0.008	50.462	-0.001	-0.001	0.000	0.000	0.000	0.000
152	B	177	ASP	-1	-0.854	-0.927	51.404	-0.025	-0.025	0.000	0.000	0.000	0.000
153	B	178	ASP	-1	-0.849	-0.889	53.079	-0.026	-0.026	0.000	0.000	0.000	0.000
154	B	179	TYR	0	-0.035	-0.061	48.338	0.001	0.001	0.000	0.000	0.000	0.000
155	B	180	ILE	0	-0.007	0.009	48.013	0.000	0.000	0.000	0.000	0.000	0.000
156	B	181	LYS	1	0.890	0.936	48.766	0.019	0.019	0.000	0.000	0.000	0.000
157	B	182	ARG	1	0.760	0.855	49.985	0.028	0.028	0.000	0.000	0.000	0.000
158	B	183	TYR	0	-0.028	-0.024	45.068	0.000	0.000	0.000	0.000	0.000	0.000
159	B	184	ALA	0	0.020	0.039	44.247	-0.001	-0.001	0.000	0.000	0.000	0.000
160	B	185	ARG	1	0.823	0.913	45.412	0.023	0.023	0.000	0.000	0.000	0.000

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