FMO DATABASE

FMODB ID: MNMQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1431974.495987
FMO2-HF: Nuclear repulsion	1372849.088888
FMO2-HF: Total energy	-59125.407099
FMO2-MP2: Total energy	-59299.450547

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.
-4.134	-1.446	0.187	-1.213	-1.662	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 : 0.036 / q_NPA : -0.001

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	-0.007	-0.002	3.254	-2.332	-0.393	-0.003	-0.955	-0.982	0.001
4	B	5	PRO	0	0.078	0.038	3.083	-0.896	-0.147	0.190	-0.258	-0.680	0.000
5	B	6	ARG	1	0.977	0.971	5.757	-0.286	-0.286	0.000	0.000	0.000	0.000
6	B	7	ARG	1	0.788	0.883	7.771	-0.603	-0.603	0.000	0.000	0.000	0.000
7	B	8	ILE	0	0.037	0.027	7.970	-0.057	-0.057	0.000	0.000	0.000	0.000
8	B	9	ILE	0	0.022	0.023	8.907	-0.024	-0.024	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.814	0.895	11.832	-0.130	-0.130	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.747	-0.856	13.355	0.279	0.279	0.000	0.000	0.000	0.000
11	B	12	THR	0	0.037	0.016	13.926	-0.021	-0.021	0.000	0.000	0.000	0.000
12	B	13	GLN	0	0.011	0.005	15.858	0.016	0.016	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.818	0.878	16.863	-0.210	-0.210	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.043	-0.025	19.535	0.005	0.005	0.000	0.000	0.000	0.000
15	B	16	LEU	0	0.017	0.000	19.196	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	17	ALA	0	-0.032	-0.001	21.821	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	18	GLU	-1	-0.836	-0.898	20.494	0.097	0.097	0.000	0.000	0.000	0.000
18	B	19	PRO	0	0.024	0.032	24.027	0.015	0.015	0.000	0.000	0.000	0.000
19	B	20	VAL	0	-0.014	-0.007	24.751	0.005	0.005	0.000	0.000	0.000	0.000
20	B	21	PRO	0	0.039	0.020	27.113	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	GLY	0	0.060	0.027	30.874	0.002	0.002	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.041	-0.014	26.367	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.832	0.900	26.711	0.005	0.005	0.000	0.000	0.000	0.000
24	B	25	ALA	0	0.012	-0.003	23.336	0.001	0.001	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.802	-0.869	24.067	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	27	PRO	0	-0.045	-0.026	19.797	0.003	0.003	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.783	-0.870	21.301	-0.091	-0.091	0.000	0.000	0.000	0.000
28	B	29	GLU	-1	-0.946	-0.971	21.518	-0.086	-0.086	0.000	0.000	0.000	0.000
29	B	30	SER	0	-0.103	-0.060	22.901	-0.011	-0.011	0.000	0.000	0.000	0.000
30	B	31	ASN	0	0.003	-0.009	17.859	-0.044	-0.044	0.000	0.000	0.000	0.000
31	B	32	ALA	0	0.056	0.022	15.546	0.015	0.015	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.809	0.917	8.955	0.355	0.355	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.029	-0.013	16.147	0.028	0.028	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.027	-0.015	16.162	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	36	HIS	0	-0.011	-0.004	21.894	0.017	0.017	0.000	0.000	0.000	0.000
36	B	37	VAL	0	-0.012	-0.014	23.939	0.004	0.004	0.000	0.000	0.000	0.000
37	B	38	VAL	0	0.000	-0.011	26.578	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	39	ILE	0	-0.023	-0.010	28.120	0.005	0.005	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.022	-0.013	31.509	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	41	GLY	0	0.004	-0.008	34.924	0.004	0.004	0.000	0.000	0.000	0.000
41	B	42	PRO	0	-0.025	-0.014	35.554	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	43	GLN	0	-0.036	-0.014	38.139	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.904	-0.948	41.312	0.033	0.033	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.066	-0.035	40.102	0.000	0.000	0.000	0.000	0.000	0.000
45	B	46	PRO	0	-0.051	-0.042	41.957	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	47	PHE	0	-0.019	-0.025	39.128	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.816	-0.886	40.326	0.023	0.023	0.000	0.000	0.000	0.000
48	B	49	GLY	0	-0.011	-0.010	40.867	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	50	GLY	0	-0.014	0.004	39.405	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.045	-0.029	35.469	0.003	0.003	0.000	0.000	0.000	0.000
51	B	52	PHE	0	0.013	-0.002	33.762	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	53	LYS	1	0.935	0.972	31.044	0.016	0.016	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.038	-0.024	27.498	0.003	0.003	0.000	0.000	0.000	0.000
54	B	55	GLU	-1	-0.787	-0.850	23.860	-0.037	-0.037	0.000	0.000	0.000	0.000
55	B	56	LEU	0	-0.010	-0.008	19.152	0.014	0.014	0.000	0.000	0.000	0.000
56	B	57	PHE	0	0.033	0.010	16.835	-0.011	-0.011	0.000	0.000	0.000	0.000
57	B	58	LEU	0	-0.003	0.003	13.920	0.036	0.036	0.000	0.000	0.000	0.000
58	B	59	PRO	0	0.025	0.011	14.293	-0.062	-0.062	0.000	0.000	0.000	0.000
59	B	60	GLU	-1	-0.901	-0.953	10.546	-0.336	-0.336	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.911	-0.964	8.807	-0.062	-0.062	0.000	0.000	0.000	0.000
61	B	62	TYR	0	-0.071	-0.023	9.884	0.214	0.214	0.000	0.000	0.000	0.000
62	B	63	PRO	0	-0.051	-0.043	8.881	0.019	0.019	0.000	0.000	0.000	0.000
63	B	64	MET	0	-0.003	-0.014	6.880	0.099	0.099	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.016	0.020	11.746	-0.061	-0.061	0.000	0.000	0.000	0.000
65	B	66	ALA	0	0.030	0.005	14.047	0.016	0.016	0.000	0.000	0.000	0.000
66	B	67	PRO	0	-0.031	-0.009	16.938	-0.037	-0.037	0.000	0.000	0.000	0.000
67	B	68	LYS	1	0.903	0.945	18.085	-0.012	-0.012	0.000	0.000	0.000	0.000
68	B	69	VAL	0	0.030	0.011	21.176	-0.009	-0.009	0.000	0.000	0.000	0.000
69	B	70	ARG	1	0.796	0.877	24.217	0.025	0.025	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.051	0.019	27.816	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.049	-0.025	28.133	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	73	THR	0	-0.036	-0.024	31.847	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	74	LYS	1	0.895	0.960	35.280	0.006	0.006	0.000	0.000	0.000	0.000
74	B	75	ILE	0	0.042	0.022	35.464	0.000	0.000	0.000	0.000	0.000	0.000
75	B	76	TYR	0	0.015	0.015	38.670	0.000	0.000	0.000	0.000	0.000	0.000
76	B	77	HIS	0	0.033	-0.013	35.844	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	78	PRO	0	0.031	0.028	38.328	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	79	ASN	0	-0.009	-0.022	34.096	0.001	0.001	0.000	0.000	0.000	0.000
79	B	80	VAL	0	-0.013	-0.006	32.787	0.003	0.003	0.000	0.000	0.000	0.000
80	B	81	ASP	-1	-0.736	-0.849	33.478	0.007	0.007	0.000	0.000	0.000	0.000
81	B	82	LYS	1	0.835	0.887	35.459	-0.012	-0.012	0.000	0.000	0.000	0.000
82	B	83	LEU	0	-0.105	-0.057	32.659	-0.004	-0.004	0.000	0.000	0.000	0.000
83	B	84	GLY	0	0.023	0.031	31.924	-0.004	-0.004	0.000	0.000	0.000	0.000
84	B	85	ARG	1	0.848	0.901	29.322	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	86	ILE	0	0.050	0.028	27.411	0.000	0.000	0.000	0.000	0.000	0.000
86	B	87	CYS	0	-0.121	-0.070	28.739	0.006	0.006	0.000	0.000	0.000	0.000
87	B	88	LEU	0	0.055	0.025	26.911	0.002	0.002	0.000	0.000	0.000	0.000
88	B	89	ASP	-1	-0.793	-0.899	26.835	0.112	0.112	0.000	0.000	0.000	0.000
89	B	90	ILE	0	-0.028	-0.022	22.994	0.009	0.009	0.000	0.000	0.000	0.000
90	B	91	LEU	0	-0.057	-0.028	22.004	0.012	0.012	0.000	0.000	0.000	0.000
91	B	92	LYS	1	0.859	0.935	23.096	-0.072	-0.072	0.000	0.000	0.000	0.000
92	B	93	ASP	-1	-0.852	-0.910	22.224	0.117	0.117	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.854	0.910	23.400	-0.117	-0.117	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.014	0.006	15.031	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	96	SER	0	0.029	0.001	17.360	0.028	0.028	0.000	0.000	0.000	0.000
96	B	97	PRO	0	0.032	0.027	12.377	-0.010	-0.010	0.000	0.000	0.000	0.000
97	B	98	ALA	0	-0.018	-0.003	13.581	0.062	0.062	0.000	0.000	0.000	0.000
98	B	99	LEU	0	-0.015	0.014	15.897	-0.029	-0.029	0.000	0.000	0.000	0.000
99	B	100	GLN	0	0.032	0.015	15.626	0.017	0.017	0.000	0.000	0.000	0.000
100	B	101	ILE	0	0.064	0.035	15.322	-0.027	-0.027	0.000	0.000	0.000	0.000
101	B	102	ARG	1	0.832	0.904	18.755	-0.121	-0.121	0.000	0.000	0.000	0.000
102	B	103	THR	0	0.052	0.022	20.801	-0.011	-0.011	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.028	0.035	20.914	-0.011	-0.011	0.000	0.000	0.000	0.000
104	B	105	LEU	0	0.003	0.000	22.246	-0.012	-0.012	0.000	0.000	0.000	0.000
105	B	106	LEU	0	0.007	0.004	24.467	-0.007	-0.007	0.000	0.000	0.000	0.000
106	B	107	SER	0	-0.020	-0.015	25.899	-0.005	-0.005	0.000	0.000	0.000	0.000
107	B	108	ILE	0	-0.009	-0.009	25.884	-0.007	-0.007	0.000	0.000	0.000	0.000
108	B	109	GLN	0	-0.022	-0.024	29.153	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	110	ALA	0	-0.004	-0.004	30.871	-0.005	-0.005	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.016	0.008	31.574	-0.004	-0.004	0.000	0.000	0.000	0.000
111	B	112	LEU	0	-0.036	-0.001	33.523	-0.005	-0.005	0.000	0.000	0.000	0.000
112	B	113	SER	0	0.018	-0.005	35.974	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	114	ALA	0	-0.041	-0.015	36.742	-0.002	-0.002	0.000	0.000	0.000	0.000
114	B	115	PRO	0	-0.025	-0.003	36.549	0.004	0.004	0.000	0.000	0.000	0.000
115	B	116	ASN	0	0.004	-0.004	34.676	0.001	0.001	0.000	0.000	0.000	0.000
116	B	117	PRO	0	-0.020	-0.006	37.165	-0.003	-0.003	0.000	0.000	0.000	0.000
117	B	118	ASP	-1	-0.943	-0.961	37.324	0.056	0.056	0.000	0.000	0.000	0.000
118	B	119	ASP	-1	-0.743	-0.851	35.144	0.052	0.052	0.000	0.000	0.000	0.000
119	B	120	PRO	0	0.002	0.003	34.343	-0.004	-0.004	0.000	0.000	0.000	0.000
120	B	121	LEU	0	-0.065	-0.036	32.320	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	122	ALA	0	0.010	0.008	36.690	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	123	ASN	0	-0.043	-0.028	38.475	-0.005	-0.005	0.000	0.000	0.000	0.000
123	B	124	ASP	-1	-0.774	-0.876	41.401	0.014	0.014	0.000	0.000	0.000	0.000
124	B	125	VAL	0	0.002	0.010	40.953	0.000	0.000	0.000	0.000	0.000	0.000
125	B	126	ALA	0	0.006	-0.009	40.284	0.001	0.001	0.000	0.000	0.000	0.000
126	B	127	GLU	-1	-0.877	-0.906	42.299	0.025	0.025	0.000	0.000	0.000	0.000
127	B	128	GLN	0	0.016	0.000	45.814	0.000	0.000	0.000	0.000	0.000	0.000
128	B	129	TRP	0	-0.028	-0.025	42.150	0.001	0.001	0.000	0.000	0.000	0.000
129	B	130	LYS	1	0.916	0.976	45.097	-0.029	-0.029	0.000	0.000	0.000	0.000
130	B	131	THR	0	-0.063	-0.066	46.654	0.001	0.001	0.000	0.000	0.000	0.000
131	B	132	ASN	0	-0.063	-0.031	49.552	-0.001	-0.001	0.000	0.000	0.000	0.000
132	B	133	GLU	-1	-0.885	-0.930	46.813	0.027	0.027	0.000	0.000	0.000	0.000
133	B	134	ALA	0	0.037	0.010	48.663	0.000	0.000	0.000	0.000	0.000	0.000
134	B	135	GLN	0	0.010	-0.002	50.863	-0.001	-0.001	0.000	0.000	0.000	0.000
135	B	136	ALA	0	-0.011	0.016	45.898	-0.001	-0.001	0.000	0.000	0.000	0.000
136	B	137	ILE	0	0.056	0.028	45.948	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	138	GLU	-1	-0.788	-0.867	46.992	0.015	0.015	0.000	0.000	0.000	0.000
138	B	139	THR	0	-0.081	-0.043	45.931	-0.002	-0.002	0.000	0.000	0.000	0.000
139	B	140	ALA	0	-0.014	-0.001	42.907	-0.002	-0.002	0.000	0.000	0.000	0.000
140	B	141	ARG	1	0.871	0.918	43.871	-0.020	-0.020	0.000	0.000	0.000	0.000
141	B	142	ALA	0	-0.079	-0.047	46.126	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	143	TRP	0	0.000	-0.016	40.387	-0.002	-0.002	0.000	0.000	0.000	0.000
143	B	144	THR	0	0.003	-0.008	40.861	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	145	ARG	1	0.949	0.961	42.555	-0.012	-0.012	0.000	0.000	0.000	0.000
145	B	146	LEU	0	-0.063	0.001	44.439	-0.002	-0.002	0.000	0.000	0.000	0.000
146	B	147	TYR	0	-0.023	-0.030	39.501	-0.003	-0.003	0.000	0.000	0.000	0.000
147	B	148	ALA	0	-0.016	-0.007	38.392	-0.002	-0.002	0.000	0.000	0.000	0.000
148	B	149	MET	0	0.033	0.039	39.556	0.001	0.001	0.000	0.000	0.000	0.000
149	B	150	ASN	0	-0.029	-0.019	41.902	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	151	ASN	0	0.032	0.033	36.430	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	152	ILE	0	-0.021	-0.005	33.369	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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