FMO DATABASE

FMODB ID: MVKQZ

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:

Apendix: None

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1401080.012257
FMO2-HF: Nuclear repulsion	1342317.282099
FMO2-HF: Total energy	-58762.730157
FMO2-MP2: Total energy	-58934.789985

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.
-14.753	-8.582	1.834	-3.187	-4.818	0.004

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 : 0.089 / q_NPA : 0.033

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	0.766	0.848	3.822	-4.554	-2.763	-0.003	-0.800	-0.988	0.004
4	D	7	LEU	0	0.008	0.026	2.366	-1.605	-0.435	1.047	-0.851	-1.367	0.000
5	D	8	MET	0	0.002	0.010	4.885	-0.391	-0.391	0.000	0.000	0.000	0.000
6	D	9	LYS	1	0.990	0.987	7.632	-1.213	-1.213	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.725	-0.846	9.188	1.353	1.353	0.000	0.000	0.000	0.000
8	D	11	LEU	0	0.052	0.044	8.214	-0.129	-0.129	0.000	0.000	0.000	0.000
9	D	12	GLU	-1	-0.894	-0.940	10.735	0.320	0.320	0.000	0.000	0.000	0.000
10	D	13	GLU	-1	-0.826	-0.894	12.713	0.308	0.308	0.000	0.000	0.000	0.000
11	D	14	ILE	0	0.023	0.007	14.123	-0.020	-0.020	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.723	0.859	16.114	-0.358	-0.358	0.000	0.000	0.000	0.000
13	D	16	LYS	1	0.839	0.912	18.525	-0.358	-0.358	0.000	0.000	0.000	0.000
14	D	17	CYS	0	-0.019	-0.023	20.221	-0.002	-0.002	0.000	0.000	0.000	0.000
15	D	18	GLY	0	0.074	0.052	21.711	0.004	0.004	0.000	0.000	0.000	0.000
16	D	19	MET	0	-0.001	-0.002	17.161	-0.020	-0.020	0.000	0.000	0.000	0.000
17	D	20	LYS	1	0.895	0.936	22.758	-0.120	-0.120	0.000	0.000	0.000	0.000
18	D	21	ASN	0	-0.027	-0.005	23.814	0.009	0.009	0.000	0.000	0.000	0.000
19	D	22	PHE	0	0.068	-0.005	15.215	-0.008	-0.008	0.000	0.000	0.000	0.000
20	D	23	ARG	1	0.931	1.009	18.672	0.052	0.052	0.000	0.000	0.000	0.000
21	D	24	ASN	0	-0.063	-0.057	14.753	-0.017	-0.017	0.000	0.000	0.000	0.000
22	D	25	ILE	0	0.077	0.034	13.466	0.012	0.012	0.000	0.000	0.000	0.000
23	D	26	GLN	0	0.031	0.001	8.945	0.114	0.114	0.000	0.000	0.000	0.000
24	D	27	VAL	0	-0.040	-0.016	12.593	0.012	0.012	0.000	0.000	0.000	0.000
25	D	28	ASP	-1	-0.894	-0.948	10.787	-0.677	-0.677	0.000	0.000	0.000	0.000
26	D	29	GLU	-1	-0.964	-0.971	11.846	-0.345	-0.345	0.000	0.000	0.000	0.000
27	D	30	ALA	0	0.082	0.021	10.477	0.005	0.005	0.000	0.000	0.000	0.000
28	D	31	ASN	0	-0.052	-0.005	4.773	-0.725	-0.523	-0.001	-0.014	-0.187	0.000
29	D	32	LEU	0	0.034	0.021	5.027	-0.141	-0.141	0.000	0.000	0.000	0.000
30	D	33	LEU	0	-0.034	-0.037	2.586	-1.486	-0.292	0.731	-0.744	-1.180	-0.003
31	D	34	THR	0	0.013	0.009	5.826	0.198	0.198	0.000	0.000	0.000	0.000
32	D	35	TRP	0	-0.063	-0.009	6.708	0.100	0.100	0.000	0.000	0.000	0.000
33	D	36	GLN	0	0.023	0.016	11.312	0.008	0.008	0.000	0.000	0.000	0.000
34	D	37	GLY	0	0.013	-0.006	15.087	0.040	0.040	0.000	0.000	0.000	0.000
35	D	38	LEU	0	-0.083	-0.020	17.651	-0.024	-0.024	0.000	0.000	0.000	0.000
36	D	39	ILE	0	0.025	0.031	20.337	0.019	0.019	0.000	0.000	0.000	0.000
37	D	40	VAL	0	-0.048	-0.043	22.694	-0.013	-0.013	0.000	0.000	0.000	0.000
38	D	41	PRO	0	-0.016	-0.010	25.989	0.008	0.008	0.000	0.000	0.000	0.000
39	D	42	ASP	-1	-0.816	-0.924	28.332	0.047	0.047	0.000	0.000	0.000	0.000
40	D	43	ASN	0	-0.033	-0.004	31.421	0.000	0.000	0.000	0.000	0.000	0.000
41	D	44	PRO	0	0.008	0.033	31.461	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	45	PRO	0	0.043	0.007	34.116	-0.001	-0.001	0.000	0.000	0.000	0.000
43	D	46	TYR	0	-0.086	-0.027	30.119	-0.003	-0.003	0.000	0.000	0.000	0.000
44	D	47	ASP	-1	-0.803	-0.917	31.512	0.022	0.022	0.000	0.000	0.000	0.000
45	D	48	LYS	1	0.735	0.872	31.402	-0.028	-0.028	0.000	0.000	0.000	0.000
46	D	49	GLY	0	0.098	0.036	30.722	-0.004	-0.004	0.000	0.000	0.000	0.000
47	D	50	ALA	0	-0.097	-0.032	25.779	0.000	0.000	0.000	0.000	0.000	0.000
48	D	51	PHE	0	0.040	0.017	24.268	-0.010	-0.010	0.000	0.000	0.000	0.000
49	D	52	ARG	1	0.870	0.910	19.602	0.140	0.140	0.000	0.000	0.000	0.000
50	D	53	ILE	0	-0.020	-0.024	16.547	-0.011	-0.011	0.000	0.000	0.000	0.000
51	D	54	GLU	-1	-0.820	-0.912	13.857	-0.324	-0.324	0.000	0.000	0.000	0.000
52	D	55	ILE	0	-0.045	-0.012	10.285	0.002	0.002	0.000	0.000	0.000	0.000
53	D	56	ASN	0	-0.001	-0.014	9.554	-0.153	-0.153	0.000	0.000	0.000	0.000
54	D	57	PHE	0	0.039	0.019	5.458	0.286	0.286	0.000	0.000	0.000	0.000
55	D	58	PRO	0	-0.014	0.007	5.680	-0.438	-0.438	0.000	0.000	0.000	0.000
56	D	59	ALA	0	0.088	0.033	3.517	-0.339	-0.127	0.002	-0.049	-0.165	0.000
57	D	60	GLU	-1	-0.845	-0.902	3.745	-4.278	-3.837	0.005	-0.213	-0.233	-0.001
58	D	61	TYR	0	-0.023	0.008	3.343	-0.390	0.544	0.050	-0.429	-0.555	0.004
59	D	62	PRO	0	-0.066	-0.055	3.791	-0.398	-0.171	0.003	-0.087	-0.143	0.000
60	D	63	PHE	0	0.004	-0.015	6.786	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	64	LYS	1	0.848	0.922	8.290	0.669	0.669	0.000	0.000	0.000	0.000
62	D	65	PRO	0	0.003	0.022	8.779	0.166	0.166	0.000	0.000	0.000	0.000
63	D	66	PRO	0	0.020	-0.012	8.929	-0.151	-0.151	0.000	0.000	0.000	0.000
64	D	67	LYS	1	0.882	0.949	10.239	0.304	0.304	0.000	0.000	0.000	0.000
65	D	68	ILE	0	-0.010	-0.017	13.205	-0.017	-0.017	0.000	0.000	0.000	0.000
66	D	69	THR	0	0.031	0.019	15.682	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	70	PHE	0	-0.013	-0.009	18.162	0.006	0.006	0.000	0.000	0.000	0.000
68	D	71	LYS	1	0.969	0.998	19.920	0.103	0.103	0.000	0.000	0.000	0.000
69	D	72	THR	0	-0.097	-0.050	21.812	-0.006	-0.006	0.000	0.000	0.000	0.000
70	D	73	LYS	1	0.948	0.977	25.055	0.085	0.085	0.000	0.000	0.000	0.000
71	D	74	ILE	0	0.036	0.022	25.852	0.007	0.007	0.000	0.000	0.000	0.000
72	D	75	TYR	0	-0.049	-0.027	28.748	-0.007	-0.007	0.000	0.000	0.000	0.000
73	D	76	HIS	1	0.873	0.926	26.912	0.009	0.009	0.000	0.000	0.000	0.000
74	D	77	PRO	0	0.079	0.041	29.718	-0.007	-0.007	0.000	0.000	0.000	0.000
75	D	78	ASN	0	-0.054	-0.041	26.034	-0.003	-0.003	0.000	0.000	0.000	0.000
76	D	79	ILE	0	-0.024	-0.012	23.721	0.001	0.001	0.000	0.000	0.000	0.000
77	D	80	ASP	-1	-0.751	-0.832	25.211	-0.091	-0.091	0.000	0.000	0.000	0.000
78	D	81	GLU	-1	-0.830	-0.916	26.316	-0.102	-0.102	0.000	0.000	0.000	0.000
79	D	82	LYS	1	0.739	0.841	23.479	0.111	0.111	0.000	0.000	0.000	0.000
80	D	83	GLY	0	0.013	0.010	22.562	-0.017	-0.017	0.000	0.000	0.000	0.000
81	D	84	GLN	0	-0.016	-0.011	17.811	-0.032	-0.032	0.000	0.000	0.000	0.000
82	D	85	VAL	0	0.016	0.005	19.155	0.018	0.018	0.000	0.000	0.000	0.000
83	D	86	CYS	0	0.030	0.008	20.087	-0.017	-0.017	0.000	0.000	0.000	0.000
84	D	87	LEU	0	0.023	0.024	17.407	0.007	0.007	0.000	0.000	0.000	0.000
85	D	88	PRO	0	0.094	0.024	19.088	0.006	0.006	0.000	0.000	0.000	0.000
86	D	89	VAL	0	-0.030	-0.007	16.939	0.003	0.003	0.000	0.000	0.000	0.000
87	D	90	ILE	0	-0.048	-0.024	13.807	0.046	0.046	0.000	0.000	0.000	0.000
88	D	91	SER	0	-0.021	-0.022	15.463	-0.030	-0.030	0.000	0.000	0.000	0.000
89	D	92	ALA	0	-0.006	-0.020	16.578	0.015	0.015	0.000	0.000	0.000	0.000
90	D	93	GLU	-1	-0.883	-0.915	17.677	0.004	0.004	0.000	0.000	0.000	0.000
91	D	94	ASN	0	-0.003	-0.004	18.847	0.020	0.020	0.000	0.000	0.000	0.000
92	D	95	TRP	0	-0.024	0.012	9.775	0.018	0.018	0.000	0.000	0.000	0.000
93	D	96	LYS	1	0.914	0.936	14.849	-0.188	-0.188	0.000	0.000	0.000	0.000
94	D	97	PRO	0	0.046	0.035	11.145	0.061	0.061	0.000	0.000	0.000	0.000
95	D	98	ALA	0	-0.012	-0.003	10.812	0.215	0.215	0.000	0.000	0.000	0.000
96	D	99	THR	0	-0.027	-0.003	13.237	0.017	0.017	0.000	0.000	0.000	0.000
97	D	100	LYS	1	0.962	0.984	11.458	-0.497	-0.497	0.000	0.000	0.000	0.000
98	D	101	THR	0	-0.032	-0.028	9.532	-0.222	-0.222	0.000	0.000	0.000	0.000
99	D	102	ASP	-1	-0.861	-0.935	12.434	0.430	0.430	0.000	0.000	0.000	0.000
100	D	103	GLN	0	-0.014	-0.026	15.528	-0.010	-0.010	0.000	0.000	0.000	0.000
101	D	104	VAL	0	0.023	0.043	12.803	-0.049	-0.049	0.000	0.000	0.000	0.000
102	D	105	ILE	0	0.052	0.023	14.159	-0.063	-0.063	0.000	0.000	0.000	0.000
103	D	106	GLN	0	0.026	0.018	17.579	0.021	0.021	0.000	0.000	0.000	0.000
104	D	107	SER	0	-0.039	-0.044	19.371	-0.026	-0.026	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.041	-0.005	18.774	-0.022	-0.022	0.000	0.000	0.000	0.000
106	D	109	ILE	0	0.000	-0.008	21.299	-0.017	-0.017	0.000	0.000	0.000	0.000
107	D	110	ALA	0	0.034	0.021	23.682	-0.013	-0.013	0.000	0.000	0.000	0.000
108	D	111	LEU	0	0.019	0.030	22.954	-0.009	-0.009	0.000	0.000	0.000	0.000
109	D	112	VAL	0	-0.071	-0.046	24.630	-0.014	-0.014	0.000	0.000	0.000	0.000
110	D	113	ASN	0	-0.045	-0.076	27.140	-0.012	-0.012	0.000	0.000	0.000	0.000
111	D	114	ASP	-1	-0.868	-0.926	29.039	0.033	0.033	0.000	0.000	0.000	0.000
112	D	115	PRO	0	-0.089	-0.023	29.276	0.001	0.001	0.000	0.000	0.000	0.000
113	D	116	GLN	0	0.061	0.045	26.191	-0.001	-0.001	0.000	0.000	0.000	0.000
114	D	117	PRO	0	-0.080	-0.048	29.868	-0.005	-0.005	0.000	0.000	0.000	0.000
115	D	118	GLU	-1	-0.872	-0.925	30.181	0.023	0.023	0.000	0.000	0.000	0.000
116	D	119	HIS	0	0.008	0.013	26.729	-0.007	-0.007	0.000	0.000	0.000	0.000
117	D	120	PRO	0	-0.046	-0.007	28.805	-0.002	-0.002	0.000	0.000	0.000	0.000
118	D	121	LEU	0	-0.061	-0.025	24.347	-0.003	-0.003	0.000	0.000	0.000	0.000
119	D	122	ARG	1	0.923	0.917	28.485	0.048	0.048	0.000	0.000	0.000	0.000
120	D	123	ALA	0	0.028	0.008	31.790	0.005	0.005	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.900	-0.949	35.037	-0.036	-0.036	0.000	0.000	0.000	0.000
122	D	125	LEU	0	-0.011	-0.010	32.342	0.004	0.004	0.000	0.000	0.000	0.000
123	D	126	ALA	0	-0.007	0.005	33.989	0.005	0.005	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.786	-0.857	35.507	-0.011	-0.011	0.000	0.000	0.000	0.000
125	D	128	GLU	-1	-0.822	-0.873	38.452	-0.022	-0.022	0.000	0.000	0.000	0.000
126	D	129	TYR	0	0.014	0.008	34.145	0.002	0.002	0.000	0.000	0.000	0.000
127	D	130	SER	0	-0.039	-0.038	37.948	0.003	0.003	0.000	0.000	0.000	0.000
128	D	131	LYS	1	0.807	0.885	39.491	0.017	0.017	0.000	0.000	0.000	0.000
129	D	132	ASP	-1	-0.747	-0.895	41.972	-0.007	-0.007	0.000	0.000	0.000	0.000
130	D	133	ARG	1	0.911	0.995	37.075	-0.011	-0.011	0.000	0.000	0.000	0.000
131	D	134	LYS	1	0.941	0.942	41.172	-0.001	-0.001	0.000	0.000	0.000	0.000
132	D	135	LYS	1	0.692	0.855	42.065	0.022	0.022	0.000	0.000	0.000	0.000
133	D	136	PHE	0	0.081	0.030	33.330	-0.002	-0.002	0.000	0.000	0.000	0.000
134	D	137	CYS	0	-0.005	-0.029	37.643	-0.001	-0.001	0.000	0.000	0.000	0.000
135	D	138	LYS	1	1.059	1.036	38.631	0.008	0.008	0.000	0.000	0.000	0.000
136	D	139	ASN	0	-0.032	-0.011	38.599	-0.001	-0.001	0.000	0.000	0.000	0.000
137	D	140	ALA	0	0.070	0.043	34.436	-0.004	-0.004	0.000	0.000	0.000	0.000
138	D	141	GLU	-1	-0.880	-0.916	35.239	-0.006	-0.006	0.000	0.000	0.000	0.000
139	D	142	GLU	-1	-0.787	-0.880	36.806	-0.025	-0.025	0.000	0.000	0.000	0.000
140	D	143	PHE	0	-0.102	-0.054	32.398	-0.006	-0.006	0.000	0.000	0.000	0.000
141	D	144	THR	0	-0.048	-0.026	31.575	-0.005	-0.005	0.000	0.000	0.000	0.000
142	D	145	LYS	1	0.852	0.914	33.042	0.020	0.020	0.000	0.000	0.000	0.000
143	D	146	LYS	1	0.812	0.910	35.509	0.034	0.034	0.000	0.000	0.000	0.000
144	D	147	TYR	0	0.017	0.010	30.179	-0.010	-0.010	0.000	0.000	0.000	0.000

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