FMO DATABASE

FMODB ID: 94512

Calculation Name: 1C4Z-D-Xray372

Preferred Name: Ubiquitin-conjugating enzyme E2 L3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1C4Z

Chain ID: D

ChEMBL ID: CHEMBL4105871

UniProt ID: P68036

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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1403036.993669
FMO2-HF: Nuclear repulsion	1344276.267065
FMO2-HF: Total energy	-58760.726604
FMO2-MP2: Total energy	-58933.057964

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(D:4:SER)

Summations of interaction energy for fragment #1(D:4: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.
-16.155	-9.628	2.15	-3.52	-5.157	0.008

Interaction energy analysis for fragmet #1(D:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.087 / q_NPA : 0.039

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	D	6	ARG	1	0.789	0.880	3.822	-6.570	-4.511	0.010	-0.992	-1.077	0.006
4	D	7	LEU	0	0.011	0.031	2.326	-2.196	-0.812	1.317	-1.061	-1.640	0.001
5	D	8	MET	0	-0.021	-0.003	5.213	-0.629	-0.629	0.000	0.000	0.000	0.000
6	D	9	LYS	1	0.999	0.990	7.654	-1.836	-1.836	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.782	-0.902	8.701	1.878	1.878	0.000	0.000	0.000	0.000
8	D	11	LEU	0	0.050	0.043	7.980	-0.171	-0.171	0.000	0.000	0.000	0.000
9	D	12	GLU	-1	-0.968	-0.981	10.765	0.546	0.546	0.000	0.000	0.000	0.000
10	D	13	GLU	-1	-0.842	-0.902	12.738	0.429	0.429	0.000	0.000	0.000	0.000
11	D	14	ILE	0	0.031	0.013	14.032	-0.032	-0.032	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.806	0.904	16.237	-0.491	-0.491	0.000	0.000	0.000	0.000
13	D	16	LYS	1	0.842	0.917	18.604	-0.524	-0.524	0.000	0.000	0.000	0.000
14	D	17	CYS	0	-0.013	-0.016	20.259	0.003	0.003	0.000	0.000	0.000	0.000
15	D	18	GLY	0	0.061	0.039	21.751	0.009	0.009	0.000	0.000	0.000	0.000
16	D	19	MET	0	0.004	0.000	17.451	-0.028	-0.028	0.000	0.000	0.000	0.000
17	D	20	LYS	1	0.883	0.932	22.804	-0.207	-0.207	0.000	0.000	0.000	0.000
18	D	21	ASN	0	-0.017	-0.014	23.862	0.023	0.023	0.000	0.000	0.000	0.000
19	D	22	PHE	0	0.054	-0.013	15.307	-0.007	-0.007	0.000	0.000	0.000	0.000
20	D	23	ARG	1	0.926	1.029	18.496	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	24	ASN	0	-0.062	-0.079	14.064	-0.010	-0.010	0.000	0.000	0.000	0.000
22	D	25	ILE	0	0.073	0.035	13.353	0.002	0.002	0.000	0.000	0.000	0.000
23	D	26	GLN	0	0.027	0.001	9.301	0.159	0.159	0.000	0.000	0.000	0.000
24	D	27	VAL	0	-0.033	-0.018	12.603	-0.001	-0.001	0.000	0.000	0.000	0.000
25	D	28	ASP	-1	-0.884	-0.943	10.974	-0.707	-0.707	0.000	0.000	0.000	0.000
26	D	29	GLU	-1	-0.985	-0.969	12.095	-0.383	-0.383	0.000	0.000	0.000	0.000
27	D	30	ALA	0	0.083	0.016	10.460	-0.020	-0.020	0.000	0.000	0.000	0.000
28	D	31	ASN	0	-0.054	-0.006	4.844	-0.823	-0.618	-0.001	-0.014	-0.190	0.000
29	D	32	LEU	0	0.030	0.019	4.949	-0.063	-0.063	0.000	0.000	0.000	0.000
30	D	33	LEU	0	-0.023	-0.041	2.388	-1.245	-0.142	0.742	-0.709	-1.136	-0.002
31	D	34	THR	0	0.033	0.017	5.838	0.246	0.246	0.000	0.000	0.000	0.000
32	D	35	TRP	0	-0.039	0.004	6.977	0.050	0.050	0.000	0.000	0.000	0.000
33	D	36	GLN	0	0.045	0.025	11.338	-0.026	-0.026	0.000	0.000	0.000	0.000
34	D	37	GLY	0	0.018	-0.011	15.111	0.043	0.043	0.000	0.000	0.000	0.000
35	D	38	LEU	0	-0.093	-0.018	17.683	-0.032	-0.032	0.000	0.000	0.000	0.000
36	D	39	ILE	0	0.026	0.037	20.466	0.020	0.020	0.000	0.000	0.000	0.000
37	D	40	VAL	0	-0.053	-0.039	22.736	-0.021	-0.021	0.000	0.000	0.000	0.000
38	D	41	PRO	0	-0.027	-0.014	26.195	0.011	0.011	0.000	0.000	0.000	0.000
39	D	42	ASP	-1	-0.854	-0.932	28.320	0.113	0.113	0.000	0.000	0.000	0.000
40	D	43	ASN	0	-0.040	-0.014	31.440	-0.003	-0.003	0.000	0.000	0.000	0.000
41	D	44	PRO	0	0.017	0.032	31.417	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	45	PRO	0	0.051	0.022	33.745	-0.001	-0.001	0.000	0.000	0.000	0.000
43	D	46	TYR	0	-0.081	-0.039	30.009	-0.003	-0.003	0.000	0.000	0.000	0.000
44	D	47	ASP	-1	-0.893	-0.956	31.442	0.068	0.068	0.000	0.000	0.000	0.000
45	D	48	LYS	1	0.908	0.947	30.454	-0.076	-0.076	0.000	0.000	0.000	0.000
46	D	49	GLY	0	0.103	0.037	30.762	-0.007	-0.007	0.000	0.000	0.000	0.000
47	D	50	ALA	0	-0.104	-0.036	25.787	0.003	0.003	0.000	0.000	0.000	0.000
48	D	51	PHE	0	0.057	0.022	24.310	-0.012	-0.012	0.000	0.000	0.000	0.000
49	D	52	ARG	1	0.812	0.886	19.520	0.098	0.098	0.000	0.000	0.000	0.000
50	D	53	ILE	0	0.006	-0.020	16.351	-0.015	-0.015	0.000	0.000	0.000	0.000
51	D	54	GLU	-1	-0.874	-0.926	13.785	-0.242	-0.242	0.000	0.000	0.000	0.000
52	D	55	ILE	0	-0.033	-0.003	9.987	0.010	0.010	0.000	0.000	0.000	0.000
53	D	56	ASN	0	0.000	-0.024	9.451	-0.147	-0.147	0.000	0.000	0.000	0.000
54	D	57	PHE	0	0.003	0.005	4.838	0.300	0.300	0.000	0.000	0.000	0.000
55	D	58	PRO	0	-0.007	0.003	5.629	-0.450	-0.450	0.000	0.000	0.000	0.000
56	D	59	ALA	0	0.097	0.038	3.577	-0.077	0.119	0.002	-0.045	-0.153	0.000
57	D	60	GLU	-1	-0.878	-0.940	3.836	-2.345	-2.029	0.004	-0.136	-0.184	-0.001
58	D	61	TYR	0	-0.033	-0.002	3.234	-0.982	0.073	0.074	-0.489	-0.639	0.004
59	D	62	PRO	0	-0.066	-0.056	3.821	0.381	0.590	0.002	-0.074	-0.138	0.000
60	D	63	PHE	0	0.005	-0.019	6.990	-0.223	-0.223	0.000	0.000	0.000	0.000
61	D	64	LYS	1	0.882	0.964	8.307	0.287	0.287	0.000	0.000	0.000	0.000
62	D	65	PRO	0	-0.007	0.013	8.761	0.262	0.262	0.000	0.000	0.000	0.000
63	D	66	PRO	0	0.031	-0.009	8.401	-0.156	-0.156	0.000	0.000	0.000	0.000
64	D	67	LYS	1	0.918	0.980	10.177	0.152	0.152	0.000	0.000	0.000	0.000
65	D	68	ILE	0	-0.005	-0.012	13.129	-0.019	-0.019	0.000	0.000	0.000	0.000
66	D	69	THR	0	0.028	0.017	15.599	-0.005	-0.005	0.000	0.000	0.000	0.000
67	D	70	PHE	0	-0.011	-0.011	18.081	0.005	0.005	0.000	0.000	0.000	0.000
68	D	71	LYS	1	0.980	0.997	20.012	0.048	0.048	0.000	0.000	0.000	0.000
69	D	72	THR	0	-0.088	-0.041	21.789	-0.009	-0.009	0.000	0.000	0.000	0.000
70	D	73	LYS	1	0.978	0.987	25.083	0.051	0.051	0.000	0.000	0.000	0.000
71	D	74	ILE	0	0.054	0.028	25.728	0.006	0.006	0.000	0.000	0.000	0.000
72	D	75	TYR	0	-0.069	-0.054	28.655	-0.007	-0.007	0.000	0.000	0.000	0.000
73	D	76	HIS	1	0.864	0.942	27.045	-0.063	-0.063	0.000	0.000	0.000	0.000
74	D	77	PRO	0	0.066	0.037	29.636	-0.006	-0.006	0.000	0.000	0.000	0.000
75	D	78	ASN	0	-0.026	-0.039	26.098	-0.001	-0.001	0.000	0.000	0.000	0.000
76	D	79	ILE	0	-0.047	-0.020	23.619	0.010	0.010	0.000	0.000	0.000	0.000
77	D	80	ASP	-1	-0.741	-0.844	25.154	-0.022	-0.022	0.000	0.000	0.000	0.000
78	D	81	GLU	-1	-0.830	-0.920	26.242	-0.046	-0.046	0.000	0.000	0.000	0.000
79	D	82	LYS	1	0.734	0.836	23.586	0.051	0.051	0.000	0.000	0.000	0.000
80	D	83	GLY	0	0.016	0.008	22.485	-0.014	-0.014	0.000	0.000	0.000	0.000
81	D	84	GLN	0	-0.042	-0.029	17.703	-0.021	-0.021	0.000	0.000	0.000	0.000
82	D	85	VAL	0	0.020	0.006	19.097	0.011	0.011	0.000	0.000	0.000	0.000
83	D	86	CYS	0	0.037	0.012	20.022	-0.007	-0.007	0.000	0.000	0.000	0.000
84	D	87	LEU	0	0.006	0.021	17.486	0.000	0.000	0.000	0.000	0.000	0.000
85	D	88	PRO	0	0.095	0.019	19.025	0.025	0.025	0.000	0.000	0.000	0.000
86	D	89	VAL	0	-0.021	-0.004	16.870	0.013	0.013	0.000	0.000	0.000	0.000
87	D	90	ILE	0	-0.046	-0.026	13.582	0.071	0.071	0.000	0.000	0.000	0.000
88	D	91	SER	0	-0.035	-0.024	15.423	-0.023	-0.023	0.000	0.000	0.000	0.000
89	D	92	ALA	0	-0.016	-0.025	16.540	0.006	0.006	0.000	0.000	0.000	0.000
90	D	93	GLU	-1	-0.890	-0.915	17.659	0.121	0.121	0.000	0.000	0.000	0.000
91	D	94	ASN	0	-0.003	-0.016	18.832	0.006	0.006	0.000	0.000	0.000	0.000
92	D	95	TRP	0	-0.042	0.000	9.783	0.001	0.001	0.000	0.000	0.000	0.000
93	D	96	LYS	1	0.969	0.977	14.837	-0.390	-0.390	0.000	0.000	0.000	0.000
94	D	97	PRO	0	0.029	0.029	11.205	0.091	0.091	0.000	0.000	0.000	0.000
95	D	98	ALA	0	0.010	0.002	10.923	0.293	0.293	0.000	0.000	0.000	0.000
96	D	99	THR	0	-0.017	0.003	13.358	0.003	0.003	0.000	0.000	0.000	0.000
97	D	100	LYS	1	0.940	0.972	11.462	-0.752	-0.752	0.000	0.000	0.000	0.000
98	D	101	THR	0	-0.004	-0.032	9.464	-0.297	-0.297	0.000	0.000	0.000	0.000
99	D	102	ASP	-1	-0.876	-0.940	12.434	0.559	0.559	0.000	0.000	0.000	0.000
100	D	103	GLN	0	0.006	-0.012	15.533	0.000	0.000	0.000	0.000	0.000	0.000
101	D	104	VAL	0	-0.010	0.063	12.628	-0.061	-0.061	0.000	0.000	0.000	0.000
102	D	105	ILE	0	0.056	0.028	14.158	-0.086	-0.086	0.000	0.000	0.000	0.000
103	D	106	GLN	0	0.039	0.022	17.473	0.040	0.040	0.000	0.000	0.000	0.000
104	D	107	SER	0	-0.054	-0.061	19.213	-0.041	-0.041	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.025	-0.003	18.934	-0.032	-0.032	0.000	0.000	0.000	0.000
106	D	109	ILE	0	0.000	0.003	21.343	-0.026	-0.026	0.000	0.000	0.000	0.000
107	D	110	ALA	0	0.034	0.018	23.577	-0.023	-0.023	0.000	0.000	0.000	0.000
108	D	111	LEU	0	0.003	0.024	22.907	-0.014	-0.014	0.000	0.000	0.000	0.000
109	D	112	VAL	0	-0.094	-0.060	24.453	-0.021	-0.021	0.000	0.000	0.000	0.000
110	D	113	ASN	0	-0.076	-0.088	27.041	-0.016	-0.016	0.000	0.000	0.000	0.000
111	D	114	ASP	-1	-0.890	-0.928	28.934	0.096	0.096	0.000	0.000	0.000	0.000
112	D	115	PRO	0	-0.070	-0.024	29.192	0.005	0.005	0.000	0.000	0.000	0.000
113	D	116	GLN	0	0.092	0.060	25.973	-0.006	-0.006	0.000	0.000	0.000	0.000
114	D	117	PRO	0	-0.091	-0.060	29.798	-0.003	-0.003	0.000	0.000	0.000	0.000
115	D	118	GLU	-1	-0.888	-0.929	29.707	0.097	0.097	0.000	0.000	0.000	0.000
116	D	119	HIS	0	-0.009	0.003	26.910	-0.016	-0.016	0.000	0.000	0.000	0.000
117	D	120	PRO	0	-0.052	-0.017	28.747	0.002	0.002	0.000	0.000	0.000	0.000
118	D	121	LEU	0	-0.079	-0.017	24.309	-0.004	-0.004	0.000	0.000	0.000	0.000
119	D	122	ARG	1	0.979	0.963	28.426	-0.004	-0.004	0.000	0.000	0.000	0.000
120	D	123	ALA	0	0.031	0.012	31.727	0.004	0.004	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.903	-0.942	34.976	0.001	0.001	0.000	0.000	0.000	0.000
122	D	125	LEU	0	-0.009	-0.024	32.106	0.003	0.003	0.000	0.000	0.000	0.000
123	D	126	ALA	0	0.006	0.018	34.087	0.005	0.005	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.876	-0.935	35.433	0.028	0.028	0.000	0.000	0.000	0.000
125	D	128	GLU	-1	-0.877	-0.903	38.342	0.012	0.012	0.000	0.000	0.000	0.000
126	D	129	TYR	0	0.021	0.013	33.888	0.002	0.002	0.000	0.000	0.000	0.000
127	D	130	SER	0	-0.056	-0.042	37.864	0.002	0.002	0.000	0.000	0.000	0.000
128	D	131	LYS	1	0.906	0.964	39.412	-0.017	-0.017	0.000	0.000	0.000	0.000
129	D	132	ASP	-1	-0.738	-0.885	41.887	0.022	0.022	0.000	0.000	0.000	0.000
130	D	133	ARG	1	0.922	1.001	36.964	-0.057	-0.057	0.000	0.000	0.000	0.000
131	D	134	LYS	1	0.949	0.943	41.080	-0.033	-0.033	0.000	0.000	0.000	0.000
132	D	135	LYS	1	0.730	0.891	42.073	-0.009	-0.009	0.000	0.000	0.000	0.000
133	D	136	PHE	0	0.078	0.033	33.167	-0.002	-0.002	0.000	0.000	0.000	0.000
134	D	137	CYS	0	-0.005	-0.029	37.540	0.000	0.000	0.000	0.000	0.000	0.000
135	D	138	LYS	1	1.050	1.030	38.529	-0.020	-0.020	0.000	0.000	0.000	0.000
136	D	139	ASN	0	-0.022	-0.012	38.475	-0.003	-0.003	0.000	0.000	0.000	0.000
137	D	140	ALA	0	0.058	0.036	34.311	-0.004	-0.004	0.000	0.000	0.000	0.000
138	D	141	GLU	-1	-0.878	-0.916	35.139	0.032	0.032	0.000	0.000	0.000	0.000
139	D	142	GLU	-1	-0.892	-0.946	36.702	0.003	0.003	0.000	0.000	0.000	0.000
140	D	143	PHE	0	-0.128	-0.121	33.358	-0.008	-0.008	0.000	0.000	0.000	0.000
141	D	144	THR	0	-0.054	-0.025	31.487	-0.003	-0.003	0.000	0.000	0.000	0.000
142	D	145	LYS	1	0.950	0.981	33.075	-0.007	-0.007	0.000	0.000	0.000	0.000
143	D	146	LYS	1	0.853	0.985	35.333	0.006	0.006	0.000	0.000	0.000	0.000
144	D	147	TYR	0	-0.006	-0.002	30.079	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:4:SER)