FMO DATABASE

FMODB ID: 98Y12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1430148.045579
FMO2-HF: Nuclear repulsion	1371022.985854
FMO2-HF: Total energy	-59125.059725
FMO2-MP2: Total energy	-59299.102639

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.
-4.648	-1.944	0.877	-1.393	-2.188	0

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 : 0.016 / q_NPA : -0.007

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	-0.008	-0.008	3.245	-2.236	-0.267	-0.003	-0.953	-1.013	0.001
4	B	5	PRO	0	0.090	0.039	2.569	-1.043	-0.370	0.881	-0.438	-1.116	-0.001
5	B	6	ARG	1	0.980	0.975	5.258	-0.601	-0.539	-0.001	-0.002	-0.059	0.000
6	B	7	ARG	1	0.809	0.889	7.605	-0.543	-0.543	0.000	0.000	0.000	0.000
7	B	8	ILE	0	0.036	0.027	8.066	-0.065	-0.065	0.000	0.000	0.000	0.000
8	B	9	ILE	0	0.023	0.023	8.532	-0.018	-0.018	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.923	0.960	11.382	-0.177	-0.177	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.777	-0.872	13.210	0.224	0.224	0.000	0.000	0.000	0.000
11	B	12	THR	0	0.024	0.001	13.617	-0.024	-0.024	0.000	0.000	0.000	0.000
12	B	13	GLN	0	0.037	0.020	15.434	0.015	0.015	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.834	0.899	16.913	-0.195	-0.195	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.039	-0.013	18.974	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	16	LEU	0	0.013	-0.008	18.931	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	17	ALA	0	-0.043	0.001	21.367	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	18	GLU	-1	-0.972	-0.977	21.753	0.092	0.092	0.000	0.000	0.000	0.000
18	B	19	PRO	0	0.015	0.023	23.902	0.016	0.016	0.000	0.000	0.000	0.000
19	B	20	VAL	0	-0.023	-0.013	24.723	0.003	0.003	0.000	0.000	0.000	0.000
20	B	21	PRO	0	0.066	0.033	27.074	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	GLY	0	0.047	0.021	30.747	0.001	0.001	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.045	-0.020	26.292	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.875	0.930	26.877	0.005	0.005	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.025	-0.026	23.206	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.814	-0.885	24.243	-0.015	-0.015	0.000	0.000	0.000	0.000
26	B	27	PRO	0	-0.026	-0.017	19.920	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.775	-0.861	20.986	-0.097	-0.097	0.000	0.000	0.000	0.000
28	B	29	GLU	-1	-0.953	-0.977	21.537	-0.090	-0.090	0.000	0.000	0.000	0.000
29	B	30	SER	0	-0.100	-0.041	22.733	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	31	ASN	0	0.005	-0.013	17.912	-0.045	-0.045	0.000	0.000	0.000	0.000
31	B	32	ALA	0	0.061	0.021	15.443	0.016	0.016	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.831	0.925	9.301	0.406	0.406	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.014	-0.002	16.581	0.020	0.020	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.013	-0.012	16.166	0.003	0.003	0.000	0.000	0.000	0.000
35	B	36	HIS	0	-0.009	-0.008	21.807	0.015	0.015	0.000	0.000	0.000	0.000
36	B	37	VAL	0	-0.029	-0.023	23.910	0.006	0.006	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.003	-0.004	26.539	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	39	ILE	0	-0.017	-0.007	28.056	0.005	0.005	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.013	-0.006	31.546	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	41	GLY	0	0.001	-0.006	35.008	0.003	0.003	0.000	0.000	0.000	0.000
41	B	42	PRO	0	-0.033	-0.022	35.576	0.000	0.000	0.000	0.000	0.000	0.000
42	B	43	GLN	0	-0.033	-0.009	38.108	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.908	-0.954	41.415	0.030	0.030	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.055	-0.032	40.244	0.000	0.000	0.000	0.000	0.000	0.000
45	B	46	PRO	0	-0.052	-0.042	41.884	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	47	PHE	0	0.004	-0.021	39.084	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.823	-0.874	40.376	0.020	0.020	0.000	0.000	0.000	0.000
48	B	49	GLY	0	-0.018	-0.016	40.941	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	50	GLY	0	-0.018	-0.005	39.535	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.047	-0.020	35.270	0.003	0.003	0.000	0.000	0.000	0.000
51	B	52	PHE	0	-0.001	-0.020	33.619	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	53	LYS	1	0.951	0.971	30.970	0.021	0.021	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.021	-0.014	27.441	0.002	0.002	0.000	0.000	0.000	0.000
54	B	55	GLU	-1	-0.785	-0.850	24.067	-0.056	-0.056	0.000	0.000	0.000	0.000
55	B	56	LEU	0	-0.023	-0.011	19.202	0.010	0.010	0.000	0.000	0.000	0.000
56	B	57	PHE	0	0.023	0.001	17.348	-0.012	-0.012	0.000	0.000	0.000	0.000
57	B	58	LEU	0	-0.014	-0.003	14.001	0.029	0.029	0.000	0.000	0.000	0.000
58	B	59	PRO	0	0.015	-0.003	14.769	-0.056	-0.056	0.000	0.000	0.000	0.000
59	B	60	GLU	-1	-0.927	-0.969	11.128	-0.412	-0.412	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.916	-0.965	9.706	-0.177	-0.177	0.000	0.000	0.000	0.000
61	B	62	TYR	0	-0.058	0.004	10.776	0.179	0.179	0.000	0.000	0.000	0.000
62	B	63	PRO	0	-0.058	-0.052	9.192	-0.024	-0.024	0.000	0.000	0.000	0.000
63	B	64	MET	0	0.008	-0.010	7.777	0.128	0.128	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.009	0.025	12.382	-0.032	-0.032	0.000	0.000	0.000	0.000
65	B	66	ALA	0	0.023	-0.001	14.783	0.014	0.014	0.000	0.000	0.000	0.000
66	B	67	PRO	0	-0.032	-0.013	17.303	-0.036	-0.036	0.000	0.000	0.000	0.000
67	B	68	LYS	1	0.919	0.953	18.363	0.039	0.039	0.000	0.000	0.000	0.000
68	B	69	VAL	0	0.040	0.015	21.482	-0.006	-0.006	0.000	0.000	0.000	0.000
69	B	70	ARG	1	0.791	0.876	24.402	0.043	0.043	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.048	0.016	27.963	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.044	-0.027	28.521	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	73	THR	0	-0.069	-0.018	32.032	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	74	LYS	1	0.941	0.971	35.296	0.016	0.016	0.000	0.000	0.000	0.000
74	B	75	ILE	0	0.040	0.016	35.676	0.000	0.000	0.000	0.000	0.000	0.000
75	B	76	TYR	0	0.004	0.014	38.839	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	77	HIS	0	0.031	-0.016	36.134	0.000	0.000	0.000	0.000	0.000	0.000
77	B	78	PRO	0	0.035	0.030	38.871	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	79	ASN	0	0.000	-0.014	34.252	0.001	0.001	0.000	0.000	0.000	0.000
79	B	80	VAL	0	-0.008	-0.003	33.162	0.001	0.001	0.000	0.000	0.000	0.000
80	B	81	ASP	-1	-0.765	-0.864	34.192	-0.004	-0.004	0.000	0.000	0.000	0.000
81	B	82	LYS	1	0.887	0.911	35.974	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	83	LEU	0	-0.115	-0.054	32.858	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	84	GLY	0	0.018	0.021	32.259	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	85	ARG	1	0.852	0.916	29.669	0.012	0.012	0.000	0.000	0.000	0.000
85	B	86	ILE	0	0.047	0.019	27.849	0.001	0.001	0.000	0.000	0.000	0.000
86	B	87	CYS	0	-0.130	-0.065	29.338	0.004	0.004	0.000	0.000	0.000	0.000
87	B	88	LEU	0	0.070	0.022	27.015	0.002	0.002	0.000	0.000	0.000	0.000
88	B	89	ASP	-1	-0.796	-0.898	27.323	0.092	0.092	0.000	0.000	0.000	0.000
89	B	90	ILE	0	-0.040	-0.022	23.081	0.005	0.005	0.000	0.000	0.000	0.000
90	B	91	LEU	0	-0.053	-0.029	22.202	0.011	0.011	0.000	0.000	0.000	0.000
91	B	92	LYS	1	0.849	0.919	23.084	-0.048	-0.048	0.000	0.000	0.000	0.000
92	B	93	ASP	-1	-0.858	-0.915	22.664	0.092	0.092	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.894	0.939	23.834	-0.086	-0.086	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.017	0.007	15.237	0.003	0.003	0.000	0.000	0.000	0.000
95	B	96	SER	0	0.036	0.001	18.041	0.027	0.027	0.000	0.000	0.000	0.000
96	B	97	PRO	0	0.023	0.026	12.689	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	98	ALA	0	-0.029	-0.012	13.897	0.055	0.055	0.000	0.000	0.000	0.000
98	B	99	LEU	0	-0.017	0.007	16.054	-0.016	-0.016	0.000	0.000	0.000	0.000
99	B	100	GLN	0	0.031	0.017	15.790	0.015	0.015	0.000	0.000	0.000	0.000
100	B	101	ILE	0	0.059	0.027	15.372	-0.024	-0.024	0.000	0.000	0.000	0.000
101	B	102	ARG	1	0.837	0.897	18.740	-0.120	-0.120	0.000	0.000	0.000	0.000
102	B	103	THR	0	0.044	0.024	20.864	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.031	0.029	21.109	-0.010	-0.010	0.000	0.000	0.000	0.000
104	B	105	LEU	0	0.011	0.002	22.513	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	106	LEU	0	0.014	0.014	24.753	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	107	SER	0	-0.012	-0.012	26.167	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	108	ILE	0	0.002	0.001	26.131	-0.006	-0.006	0.000	0.000	0.000	0.000
108	B	109	GLN	0	-0.030	-0.027	29.347	0.000	0.000	0.000	0.000	0.000	0.000
109	B	110	ALA	0	-0.004	-0.005	31.030	-0.004	-0.004	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.031	0.010	31.437	-0.003	-0.003	0.000	0.000	0.000	0.000
111	B	112	LEU	0	-0.074	-0.018	33.438	-0.004	-0.004	0.000	0.000	0.000	0.000
112	B	113	SER	0	0.010	-0.004	35.923	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	114	ALA	0	-0.044	-0.015	36.957	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	115	PRO	0	-0.031	-0.003	37.031	0.003	0.003	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.011	-0.002	34.959	0.002	0.002	0.000	0.000	0.000	0.000
116	B	117	PRO	0	-0.029	-0.011	37.306	-0.003	-0.003	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.942	-0.961	37.430	0.047	0.047	0.000	0.000	0.000	0.000
118	B	119	ASP	-1	-0.755	-0.864	35.741	0.038	0.038	0.000	0.000	0.000	0.000
119	B	120	PRO	0	-0.011	-0.007	35.011	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	121	LEU	0	-0.074	-0.037	33.213	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	122	ALA	0	0.034	0.026	37.532	0.000	0.000	0.000	0.000	0.000	0.000
122	B	123	ASN	0	-0.038	-0.030	39.072	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	124	ASP	-1	-0.798	-0.894	41.947	0.006	0.006	0.000	0.000	0.000	0.000
124	B	125	VAL	0	-0.011	-0.003	41.652	0.000	0.000	0.000	0.000	0.000	0.000
125	B	126	ALA	0	0.017	-0.002	40.874	0.001	0.001	0.000	0.000	0.000	0.000
126	B	127	GLU	-1	-0.892	-0.926	42.919	0.019	0.019	0.000	0.000	0.000	0.000
127	B	128	GLN	0	0.028	0.016	46.339	0.000	0.000	0.000	0.000	0.000	0.000
128	B	129	TRP	0	-0.012	-0.001	42.422	0.001	0.001	0.000	0.000	0.000	0.000
129	B	130	LYS	1	0.934	0.981	45.625	-0.024	-0.024	0.000	0.000	0.000	0.000
130	B	131	THR	0	-0.079	-0.059	47.167	0.001	0.001	0.000	0.000	0.000	0.000
131	B	132	ASN	0	-0.091	-0.053	49.929	0.000	0.000	0.000	0.000	0.000	0.000
132	B	133	GLU	-1	-0.858	-0.925	46.980	0.023	0.023	0.000	0.000	0.000	0.000
133	B	134	ALA	0	0.032	0.007	48.921	0.000	0.000	0.000	0.000	0.000	0.000
134	B	135	GLN	0	0.009	-0.006	51.134	-0.001	-0.001	0.000	0.000	0.000	0.000
135	B	136	ALA	0	-0.021	0.003	46.243	-0.001	-0.001	0.000	0.000	0.000	0.000
136	B	137	ILE	0	0.063	0.022	45.952	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	138	GLU	-1	-0.819	-0.883	47.437	0.011	0.011	0.000	0.000	0.000	0.000
138	B	139	THR	0	-0.080	-0.041	46.408	-0.002	-0.002	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.002	-0.001	43.097	-0.002	-0.002	0.000	0.000	0.000	0.000
140	B	141	ARG	1	0.868	0.930	43.995	-0.016	-0.016	0.000	0.000	0.000	0.000
141	B	142	ALA	0	-0.064	-0.036	45.959	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	143	TRP	0	-0.001	-0.014	40.997	-0.002	-0.002	0.000	0.000	0.000	0.000
143	B	144	THR	0	0.008	0.002	40.841	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	145	ARG	1	0.947	0.959	42.503	-0.007	-0.007	0.000	0.000	0.000	0.000
145	B	146	LEU	0	-0.056	-0.007	44.528	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	147	TYR	0	-0.021	-0.027	39.655	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	148	ALA	0	-0.036	-0.012	38.382	-0.002	-0.002	0.000	0.000	0.000	0.000
148	B	149	MET	0	0.053	0.056	39.558	0.001	0.001	0.000	0.000	0.000	0.000
149	B	150	ASN	0	-0.045	-0.020	41.701	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	151	ASN	0	0.045	0.035	36.699	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	152	ILE	0	-0.033	-0.008	33.367	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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