FMO DATABASE

FMODB ID: LNLK9

Calculation Name: 4IP3-B-Xray372

Preferred Name: Ubiquitin-conjugating enzyme E2 N

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4IP3

Chain ID: B

ChEMBL ID: CHEMBL6089

UniProt ID: P61088

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1429333.603329
FMO2-HF: Nuclear repulsion	1370209.456913
FMO2-HF: Total energy	-59124.146415
FMO2-MP2: Total energy	-59298.255405

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:2:ALA)

Summations of interaction energy for fragment #1(B:2:ALA)

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.
-4.703	-2.101	1.008	-1.429	-2.179	-0.001

Interaction energy analysis for fragmet #1(B:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.006

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	4	LEU	0	-0.005	-0.007	3.192	-2.305	-0.298	0.003	-0.974	-1.036	0.000
4	B	5	PRO	0	0.086	0.044	2.494	-1.000	-0.468	1.006	-0.453	-1.085	-0.001
5	B	6	ARG	1	0.990	0.973	5.195	-0.579	-0.516	-0.001	-0.002	-0.058	0.000
6	B	7	ARG	1	0.798	0.886	7.550	-0.548	-0.548	0.000	0.000	0.000	0.000
7	B	8	ILE	0	0.054	0.033	8.095	-0.068	-0.068	0.000	0.000	0.000	0.000
8	B	9	ILE	0	0.020	0.018	8.782	-0.014	-0.014	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.965	0.984	11.327	-0.200	-0.200	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.834	-0.902	13.149	0.232	0.232	0.000	0.000	0.000	0.000
11	B	12	THR	0	0.028	0.014	13.626	-0.023	-0.023	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.007	-0.006	15.374	0.012	0.012	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.939	0.974	17.064	-0.181	-0.181	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.059	-0.012	18.913	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	16	LEU	0	0.022	-0.008	18.683	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	17	ALA	0	-0.032	0.009	21.298	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	18	GLU	-1	-0.982	-0.981	22.409	0.080	0.080	0.000	0.000	0.000	0.000
18	B	19	PRO	0	-0.015	0.003	23.839	0.015	0.015	0.000	0.000	0.000	0.000
19	B	20	VAL	0	-0.017	-0.009	24.751	0.003	0.003	0.000	0.000	0.000	0.000
20	B	21	PRO	0	0.053	0.031	27.015	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	GLY	0	0.045	0.010	30.688	0.002	0.002	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.031	-0.016	26.055	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.960	0.984	26.869	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.034	-0.034	23.105	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.892	-0.931	24.175	-0.021	-0.021	0.000	0.000	0.000	0.000
26	B	27	PRO	0	-0.034	-0.027	19.780	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.816	-0.895	20.934	-0.094	-0.094	0.000	0.000	0.000	0.000
28	B	29	GLU	-1	-0.932	-0.976	21.478	-0.092	-0.092	0.000	0.000	0.000	0.000
29	B	30	SER	0	-0.090	-0.031	22.680	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	31	ASN	0	0.004	-0.001	17.925	-0.038	-0.038	0.000	0.000	0.000	0.000
31	B	32	ALA	0	0.072	0.023	15.350	0.015	0.015	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.818	0.911	9.885	0.339	0.339	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.019	-0.005	16.516	0.030	0.030	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.012	-0.009	16.227	0.003	0.003	0.000	0.000	0.000	0.000
35	B	36	HIS	0	0.027	0.023	21.740	0.015	0.015	0.000	0.000	0.000	0.000
36	B	37	VAL	0	-0.021	-0.014	23.972	0.006	0.006	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.019	-0.014	26.470	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	39	ILE	0	-0.015	-0.009	28.310	0.005	0.005	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.023	-0.012	31.478	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	41	GLY	0	-0.004	-0.008	34.942	0.003	0.003	0.000	0.000	0.000	0.000
41	B	42	PRO	0	-0.044	-0.024	35.532	0.000	0.000	0.000	0.000	0.000	0.000
42	B	43	GLN	0	0.005	0.015	38.045	0.000	0.000	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.892	-0.953	41.353	0.030	0.030	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.056	-0.025	40.157	0.000	0.000	0.000	0.000	0.000	0.000
45	B	46	PRO	0	-0.059	-0.048	41.778	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	47	PHE	0	0.017	-0.020	39.013	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.862	-0.892	40.309	0.019	0.019	0.000	0.000	0.000	0.000
48	B	49	GLY	0	-0.023	-0.017	40.868	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	50	GLY	0	-0.023	-0.006	39.463	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.051	-0.021	35.228	0.003	0.003	0.000	0.000	0.000	0.000
51	B	52	PHE	0	-0.002	-0.023	33.473	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	53	LYS	1	0.962	0.983	30.898	0.023	0.023	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.011	-0.010	27.273	0.002	0.002	0.000	0.000	0.000	0.000
54	B	55	GLU	-1	-0.814	-0.896	23.958	-0.055	-0.055	0.000	0.000	0.000	0.000
55	B	56	LEU	0	-0.025	-0.007	19.058	0.011	0.011	0.000	0.000	0.000	0.000
56	B	57	PHE	0	0.027	0.000	17.619	-0.013	-0.013	0.000	0.000	0.000	0.000
57	B	58	LEU	0	-0.016	-0.004	13.890	0.029	0.029	0.000	0.000	0.000	0.000
58	B	59	PRO	0	0.005	-0.007	14.867	-0.058	-0.058	0.000	0.000	0.000	0.000
59	B	60	GLU	-1	-0.921	-0.970	11.168	-0.388	-0.388	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.918	-0.961	9.740	-0.141	-0.141	0.000	0.000	0.000	0.000
61	B	62	TYR	0	-0.083	-0.011	10.813	0.172	0.172	0.000	0.000	0.000	0.000
62	B	63	PRO	0	-0.063	-0.058	9.076	-0.021	-0.021	0.000	0.000	0.000	0.000
63	B	64	MET	0	0.014	-0.010	8.250	0.118	0.118	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.010	0.026	12.425	-0.036	-0.036	0.000	0.000	0.000	0.000
65	B	66	ALA	0	0.024	-0.007	14.825	0.015	0.015	0.000	0.000	0.000	0.000
66	B	67	PRO	0	-0.040	-0.017	17.000	-0.036	-0.036	0.000	0.000	0.000	0.000
67	B	68	LYS	1	0.931	0.963	18.363	0.042	0.042	0.000	0.000	0.000	0.000
68	B	69	VAL	0	0.045	0.018	21.482	-0.006	-0.006	0.000	0.000	0.000	0.000
69	B	70	ARG	1	0.826	0.922	24.402	0.041	0.041	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.044	0.015	27.963	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.028	-0.025	29.045	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	73	THR	0	-0.050	-0.011	32.032	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	74	LYS	1	0.935	0.966	35.227	0.015	0.015	0.000	0.000	0.000	0.000
74	B	75	ILE	0	0.047	0.021	35.667	0.000	0.000	0.000	0.000	0.000	0.000
75	B	76	TYR	0	0.002	0.010	38.839	0.000	0.000	0.000	0.000	0.000	0.000
76	B	77	HIS	0	0.020	-0.012	36.076	0.000	0.000	0.000	0.000	0.000	0.000
77	B	78	PRO	0	0.041	0.028	38.849	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	79	ASN	0	0.033	0.012	34.167	0.002	0.002	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.005	0.007	33.238	0.001	0.001	0.000	0.000	0.000	0.000
80	B	81	ASP	-1	-0.778	-0.873	33.987	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	82	LYS	1	0.975	0.957	35.974	-0.002	-0.002	0.000	0.000	0.000	0.000
82	B	83	LEU	0	-0.110	-0.052	32.760	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	84	GLY	0	0.017	0.023	32.259	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	85	ARG	1	0.881	0.937	29.678	0.010	0.010	0.000	0.000	0.000	0.000
85	B	86	ILE	0	0.035	0.016	27.684	0.001	0.001	0.000	0.000	0.000	0.000
86	B	87	CYS	0	-0.129	-0.063	29.374	0.004	0.004	0.000	0.000	0.000	0.000
87	B	88	LEU	0	0.053	0.012	26.116	0.002	0.002	0.000	0.000	0.000	0.000
88	B	89	ASP	-1	-0.771	-0.880	27.293	0.090	0.090	0.000	0.000	0.000	0.000
89	B	90	ILE	0	-0.056	-0.037	22.994	0.006	0.006	0.000	0.000	0.000	0.000
90	B	91	LEU	0	-0.051	-0.029	22.277	0.011	0.011	0.000	0.000	0.000	0.000
91	B	92	LYS	1	0.879	0.937	23.126	-0.048	-0.048	0.000	0.000	0.000	0.000
92	B	93	ASP	-1	-0.906	-0.953	22.707	0.096	0.096	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.951	0.979	23.877	-0.097	-0.097	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.021	0.004	15.309	0.004	0.004	0.000	0.000	0.000	0.000
95	B	96	SER	0	0.044	0.011	18.032	0.027	0.027	0.000	0.000	0.000	0.000
96	B	97	PRO	0	0.036	0.033	12.666	-0.005	-0.005	0.000	0.000	0.000	0.000
97	B	98	ALA	0	-0.025	-0.014	13.848	0.056	0.056	0.000	0.000	0.000	0.000
98	B	99	LEU	0	-0.018	0.007	16.011	-0.018	-0.018	0.000	0.000	0.000	0.000
99	B	100	GLN	0	-0.038	-0.027	15.915	0.004	0.004	0.000	0.000	0.000	0.000
100	B	101	ILE	0	0.068	0.033	15.394	-0.024	-0.024	0.000	0.000	0.000	0.000
101	B	102	ARG	1	0.849	0.904	18.677	-0.121	-0.121	0.000	0.000	0.000	0.000
102	B	103	THR	0	0.054	0.024	20.807	-0.007	-0.007	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.031	0.025	21.021	-0.010	-0.010	0.000	0.000	0.000	0.000
104	B	105	LEU	0	0.011	0.001	22.556	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	106	LEU	0	0.014	0.011	24.974	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	107	SER	0	-0.001	0.008	26.408	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	108	ILE	0	0.001	0.005	26.170	-0.006	-0.006	0.000	0.000	0.000	0.000
108	B	109	GLN	0	-0.022	-0.019	29.283	0.000	0.000	0.000	0.000	0.000	0.000
109	B	110	ALA	0	-0.008	-0.009	30.969	-0.004	-0.004	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.029	0.009	30.943	-0.003	-0.003	0.000	0.000	0.000	0.000
111	B	112	LEU	0	-0.080	-0.025	33.539	-0.004	-0.004	0.000	0.000	0.000	0.000
112	B	113	SER	0	-0.003	-0.011	35.868	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	114	ALA	0	-0.035	-0.010	36.892	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	115	PRO	0	-0.029	-0.002	36.971	0.003	0.003	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.011	0.003	34.626	0.002	0.002	0.000	0.000	0.000	0.000
116	B	117	PRO	0	-0.029	-0.014	37.248	-0.003	-0.003	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.956	-0.970	36.920	0.049	0.049	0.000	0.000	0.000	0.000
118	B	119	ASP	-1	-0.777	-0.893	35.681	0.038	0.038	0.000	0.000	0.000	0.000
119	B	120	PRO	0	-0.036	-0.010	34.766	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	121	LEU	0	-0.080	-0.046	33.199	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	122	ALA	0	0.055	0.038	37.574	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	123	ASN	0	-0.014	-0.017	39.367	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	124	ASP	-1	-0.879	-0.947	41.988	0.007	0.007	0.000	0.000	0.000	0.000
124	B	125	VAL	0	-0.059	-0.026	41.643	0.000	0.000	0.000	0.000	0.000	0.000
125	B	126	ALA	0	0.002	-0.010	40.952	0.001	0.001	0.000	0.000	0.000	0.000
126	B	127	GLU	-1	-0.905	-0.944	42.901	0.020	0.020	0.000	0.000	0.000	0.000
127	B	128	GLN	0	0.009	0.006	46.381	0.000	0.000	0.000	0.000	0.000	0.000
128	B	129	TRP	0	0.001	0.006	42.550	0.001	0.001	0.000	0.000	0.000	0.000
129	B	130	LYS	1	0.938	0.979	45.558	-0.025	-0.025	0.000	0.000	0.000	0.000
130	B	131	THR	0	-0.057	-0.030	47.108	0.000	0.000	0.000	0.000	0.000	0.000
131	B	132	ASN	0	-0.093	-0.056	49.867	0.000	0.000	0.000	0.000	0.000	0.000
132	B	133	GLU	-1	-0.847	-0.915	47.197	0.024	0.024	0.000	0.000	0.000	0.000
133	B	134	ALA	0	0.021	-0.001	48.859	0.000	0.000	0.000	0.000	0.000	0.000
134	B	135	GLN	0	0.014	-0.001	51.071	-0.001	-0.001	0.000	0.000	0.000	0.000
135	B	136	ALA	0	-0.002	0.012	46.154	-0.001	-0.001	0.000	0.000	0.000	0.000
136	B	137	ILE	0	0.052	0.014	46.042	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	138	GLU	-1	-0.893	-0.932	47.373	0.011	0.011	0.000	0.000	0.000	0.000
138	B	139	THR	0	-0.056	-0.031	46.241	-0.002	-0.002	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.008	-0.005	43.005	-0.002	-0.002	0.000	0.000	0.000	0.000
140	B	141	ARG	1	0.897	0.958	43.931	-0.016	-0.016	0.000	0.000	0.000	0.000
141	B	142	ALA	0	-0.059	-0.033	45.891	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	143	TRP	0	-0.004	-0.016	41.343	-0.002	-0.002	0.000	0.000	0.000	0.000
143	B	144	THR	0	0.020	0.012	40.993	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	145	ARG	1	0.939	0.954	42.434	-0.007	-0.007	0.000	0.000	0.000	0.000
145	B	146	LEU	0	-0.048	-0.004	44.265	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	147	TYR	0	-0.024	-0.031	39.580	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	148	ALA	0	-0.040	-0.006	38.291	-0.002	-0.002	0.000	0.000	0.000	0.000
148	B	149	MET	0	0.053	0.054	39.489	0.001	0.001	0.000	0.000	0.000	0.000
149	B	150	ASN	0	-0.046	-0.017	41.624	-0.002	-0.002	0.000	0.000	0.000	0.000
150	B	151	ASN	0	0.044	0.030	36.422	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	152	ILE	0	-0.061	-0.027	33.505	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ALA)