FMO DATABASE

FMODB ID: 7281K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1401140.387264
FMO2-HF: Nuclear repulsion	1342376.134555
FMO2-HF: Total energy	-58764.252709
FMO2-MP2: Total energy	-58936.060243

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.
-22.557	-13.72	2.242	-4.694	-6.385	-0.003

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 : 0.102 / q_NPA : 0.042

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	0.745	0.837	3.390	-5.260	-3.151	0.010	-1.019	-1.100	0.005
4	D	7	LEU	0	0.042	0.027	2.349	-2.893	-1.435	1.147	-1.017	-1.589	0.002
5	D	8	MET	0	0.051	0.046	4.916	-0.721	-0.721	0.000	0.000	0.000	0.000
6	D	9	LYS	1	0.985	0.988	7.147	-1.365	-1.365	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.754	-0.834	7.599	1.964	1.964	0.000	0.000	0.000	0.000
8	D	11	LEU	0	0.019	0.021	7.922	-0.178	-0.178	0.000	0.000	0.000	0.000
9	D	12	GLU	-1	-0.870	-0.928	10.307	0.407	0.407	0.000	0.000	0.000	0.000
10	D	13	GLU	-1	-0.794	-0.882	12.576	0.362	0.362	0.000	0.000	0.000	0.000
11	D	14	ILE	0	-0.019	-0.015	13.620	-0.053	-0.053	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.789	0.891	15.817	-0.479	-0.479	0.000	0.000	0.000	0.000
13	D	16	LYS	1	0.828	0.924	18.376	-0.422	-0.422	0.000	0.000	0.000	0.000
14	D	17	CYS	0	-0.023	-0.031	20.090	-0.008	-0.008	0.000	0.000	0.000	0.000
15	D	18	GLY	0	0.065	0.043	21.756	0.007	0.007	0.000	0.000	0.000	0.000
16	D	19	MET	0	0.022	0.014	16.932	-0.025	-0.025	0.000	0.000	0.000	0.000
17	D	20	LYS	1	0.849	0.915	22.636	-0.140	-0.140	0.000	0.000	0.000	0.000
18	D	21	ASN	0	-0.033	-0.029	22.784	0.018	0.018	0.000	0.000	0.000	0.000
19	D	22	PHE	0	0.054	0.010	14.996	-0.010	-0.010	0.000	0.000	0.000	0.000
20	D	23	ARG	1	0.935	0.990	18.433	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	24	ASN	0	-0.049	-0.031	14.538	-0.023	-0.023	0.000	0.000	0.000	0.000
22	D	25	ILE	0	0.052	0.021	13.895	0.014	0.014	0.000	0.000	0.000	0.000
23	D	26	GLN	0	0.056	0.022	8.873	0.091	0.091	0.000	0.000	0.000	0.000
24	D	27	VAL	0	-0.052	-0.027	12.497	0.027	0.027	0.000	0.000	0.000	0.000
25	D	28	ASP	-1	-0.817	-0.903	10.612	-0.570	-0.570	0.000	0.000	0.000	0.000
26	D	29	GLU	-1	-0.975	-0.991	11.991	-0.170	-0.170	0.000	0.000	0.000	0.000
27	D	30	ALA	0	0.014	0.022	11.110	0.031	0.031	0.000	0.000	0.000	0.000
28	D	31	ASN	0	-0.022	-0.024	5.372	-0.344	-0.344	0.000	0.000	0.000	0.000
29	D	32	LEU	0	0.058	0.042	4.966	-0.149	-0.149	0.000	0.000	0.000	0.000
30	D	33	LEU	0	-0.059	-0.041	2.442	-1.318	-0.222	0.779	-0.594	-1.281	-0.002
31	D	34	THR	0	0.009	-0.007	5.515	0.198	0.198	0.000	0.000	0.000	0.000
32	D	35	TRP	0	-0.057	-0.019	6.292	0.139	0.139	0.000	0.000	0.000	0.000
33	D	36	GLN	0	-0.022	-0.029	10.980	0.008	0.008	0.000	0.000	0.000	0.000
34	D	37	GLY	0	0.012	0.003	14.824	0.038	0.038	0.000	0.000	0.000	0.000
35	D	38	LEU	0	-0.073	-0.028	17.613	-0.027	-0.027	0.000	0.000	0.000	0.000
36	D	39	ILE	0	0.021	0.014	20.281	0.023	0.023	0.000	0.000	0.000	0.000
37	D	40	VAL	0	-0.017	-0.027	22.587	-0.015	-0.015	0.000	0.000	0.000	0.000
38	D	41	PRO	0	0.003	0.002	26.169	0.011	0.011	0.000	0.000	0.000	0.000
39	D	42	ASP	-1	-0.795	-0.895	28.311	0.056	0.056	0.000	0.000	0.000	0.000
40	D	43	ASN	0	-0.038	-0.018	31.410	0.000	0.000	0.000	0.000	0.000	0.000
41	D	44	PRO	0	0.005	0.046	30.379	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	45	PRO	0	0.036	0.002	33.707	0.000	0.000	0.000	0.000	0.000	0.000
43	D	46	TYR	0	-0.063	-0.048	29.534	-0.004	-0.004	0.000	0.000	0.000	0.000
44	D	47	ASP	-1	-0.795	-0.890	30.775	0.026	0.026	0.000	0.000	0.000	0.000
45	D	48	LYS	1	0.730	0.845	31.218	-0.039	-0.039	0.000	0.000	0.000	0.000
46	D	49	GLY	0	0.056	0.039	30.826	-0.004	-0.004	0.000	0.000	0.000	0.000
47	D	50	ALA	0	-0.065	-0.021	25.594	0.001	0.001	0.000	0.000	0.000	0.000
48	D	51	PHE	0	0.014	-0.003	24.223	-0.013	-0.013	0.000	0.000	0.000	0.000
49	D	52	ARG	1	0.855	0.921	19.626	0.110	0.110	0.000	0.000	0.000	0.000
50	D	53	ILE	0	-0.022	-0.012	16.523	-0.014	-0.014	0.000	0.000	0.000	0.000
51	D	54	GLU	-1	-0.802	-0.891	13.594	-0.332	-0.332	0.000	0.000	0.000	0.000
52	D	55	ILE	0	-0.033	-0.015	9.847	0.009	0.009	0.000	0.000	0.000	0.000
53	D	56	ASN	0	-0.007	-0.008	9.358	-0.122	-0.122	0.000	0.000	0.000	0.000
54	D	57	PHE	0	0.020	0.002	4.787	0.383	0.444	-0.001	-0.003	-0.056	0.000
55	D	58	PRO	0	-0.004	0.021	5.880	-0.511	-0.511	0.000	0.000	0.000	0.000
56	D	59	ALA	0	0.047	0.011	3.423	-1.209	-0.839	0.009	-0.103	-0.276	0.000
57	D	60	GLU	-1	-0.829	-0.905	2.944	-9.787	-7.928	0.081	-1.063	-0.877	-0.010
58	D	61	TYR	0	-0.033	-0.007	2.984	-0.400	0.821	0.166	-0.549	-0.839	0.005
59	D	62	PRO	0	-0.051	-0.042	3.219	-1.256	-0.593	0.051	-0.346	-0.367	-0.003
60	D	63	PHE	0	-0.011	-0.016	6.520	0.126	0.126	0.000	0.000	0.000	0.000
61	D	64	LYS	1	0.859	0.928	7.887	1.127	1.127	0.000	0.000	0.000	0.000
62	D	65	PRO	0	0.018	0.019	8.057	0.049	0.049	0.000	0.000	0.000	0.000
63	D	66	PRO	0	0.002	-0.008	8.852	-0.209	-0.209	0.000	0.000	0.000	0.000
64	D	67	LYS	1	0.897	0.954	9.688	0.389	0.389	0.000	0.000	0.000	0.000
65	D	68	ILE	0	0.000	-0.012	12.320	0.002	0.002	0.000	0.000	0.000	0.000
66	D	69	THR	0	-0.007	0.000	15.040	-0.006	-0.006	0.000	0.000	0.000	0.000
67	D	70	PHE	0	0.000	-0.007	17.966	0.016	0.016	0.000	0.000	0.000	0.000
68	D	71	LYS	1	0.960	0.983	20.037	0.105	0.105	0.000	0.000	0.000	0.000
69	D	72	THR	0	-0.060	-0.021	21.912	-0.004	-0.004	0.000	0.000	0.000	0.000
70	D	73	LYS	1	0.942	0.972	25.164	0.083	0.083	0.000	0.000	0.000	0.000
71	D	74	ILE	0	0.032	0.023	25.583	0.009	0.009	0.000	0.000	0.000	0.000
72	D	75	TYR	0	-0.042	-0.029	28.505	-0.009	-0.009	0.000	0.000	0.000	0.000
73	D	76	HIS	1	0.863	0.922	26.434	0.024	0.024	0.000	0.000	0.000	0.000
74	D	77	PRO	0	0.058	0.036	29.050	-0.008	-0.008	0.000	0.000	0.000	0.000
75	D	78	ASN	0	-0.029	-0.024	25.237	-0.002	-0.002	0.000	0.000	0.000	0.000
76	D	79	ILE	0	-0.014	-0.009	23.219	-0.003	-0.003	0.000	0.000	0.000	0.000
77	D	80	ASP	-1	-0.777	-0.845	24.789	-0.115	-0.115	0.000	0.000	0.000	0.000
78	D	81	GLU	-1	-0.823	-0.908	25.993	-0.122	-0.122	0.000	0.000	0.000	0.000
79	D	82	LYS	1	0.749	0.844	23.420	0.142	0.142	0.000	0.000	0.000	0.000
80	D	83	GLY	0	0.017	0.014	22.275	-0.020	-0.020	0.000	0.000	0.000	0.000
81	D	84	GLN	0	-0.009	-0.006	17.483	-0.034	-0.034	0.000	0.000	0.000	0.000
82	D	85	VAL	0	0.032	0.014	18.883	0.021	0.021	0.000	0.000	0.000	0.000
83	D	86	CYS	0	0.015	0.011	19.547	-0.027	-0.027	0.000	0.000	0.000	0.000
84	D	87	LEU	0	0.025	0.016	16.750	0.012	0.012	0.000	0.000	0.000	0.000
85	D	88	PRO	0	0.062	0.017	18.770	-0.005	-0.005	0.000	0.000	0.000	0.000
86	D	89	VAL	0	-0.032	-0.010	16.188	-0.012	-0.012	0.000	0.000	0.000	0.000
87	D	90	ILE	0	-0.020	-0.015	12.995	0.044	0.044	0.000	0.000	0.000	0.000
88	D	91	SER	0	0.018	0.016	14.608	-0.065	-0.065	0.000	0.000	0.000	0.000
89	D	92	ALA	0	0.028	-0.001	16.607	0.026	0.026	0.000	0.000	0.000	0.000
90	D	93	GLU	-1	-0.873	-0.922	17.495	-0.064	-0.064	0.000	0.000	0.000	0.000
91	D	94	ASN	0	-0.064	-0.029	18.676	0.043	0.043	0.000	0.000	0.000	0.000
92	D	95	TRP	0	-0.003	0.010	9.106	0.055	0.055	0.000	0.000	0.000	0.000
93	D	96	LYS	1	0.874	0.918	14.182	-0.086	-0.086	0.000	0.000	0.000	0.000
94	D	97	PRO	0	0.039	0.032	10.419	0.072	0.072	0.000	0.000	0.000	0.000
95	D	98	ALA	0	0.006	-0.004	10.259	0.234	0.234	0.000	0.000	0.000	0.000
96	D	99	THR	0	0.006	0.012	12.740	0.018	0.018	0.000	0.000	0.000	0.000
97	D	100	LYS	1	0.891	0.950	10.737	-0.439	-0.439	0.000	0.000	0.000	0.000
98	D	101	THR	0	0.034	-0.013	9.120	-0.241	-0.241	0.000	0.000	0.000	0.000
99	D	102	ASP	-1	-0.889	-0.953	11.841	0.482	0.482	0.000	0.000	0.000	0.000
100	D	103	GLN	0	-0.011	-0.005	14.710	-0.008	-0.008	0.000	0.000	0.000	0.000
101	D	104	VAL	0	-0.015	0.024	11.984	-0.057	-0.057	0.000	0.000	0.000	0.000
102	D	105	ILE	0	0.049	0.010	13.732	-0.072	-0.072	0.000	0.000	0.000	0.000
103	D	106	GLN	0	-0.002	0.009	16.936	0.006	0.006	0.000	0.000	0.000	0.000
104	D	107	SER	0	-0.001	-0.020	18.622	-0.031	-0.031	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.010	0.004	18.038	-0.026	-0.026	0.000	0.000	0.000	0.000
106	D	109	ILE	0	-0.011	-0.003	20.463	-0.017	-0.017	0.000	0.000	0.000	0.000
107	D	110	ALA	0	0.027	0.021	23.061	-0.013	-0.013	0.000	0.000	0.000	0.000
108	D	111	LEU	0	0.026	0.024	22.410	-0.011	-0.011	0.000	0.000	0.000	0.000
109	D	112	VAL	0	-0.042	-0.031	23.802	-0.015	-0.015	0.000	0.000	0.000	0.000
110	D	113	ASN	0	-0.053	-0.071	26.304	-0.010	-0.010	0.000	0.000	0.000	0.000
111	D	114	ASP	-1	-0.839	-0.896	28.364	0.015	0.015	0.000	0.000	0.000	0.000
112	D	115	PRO	0	-0.079	-0.022	28.464	0.000	0.000	0.000	0.000	0.000	0.000
113	D	116	GLN	0	0.055	0.026	25.599	-0.005	-0.005	0.000	0.000	0.000	0.000
114	D	117	PRO	0	-0.042	-0.031	29.535	-0.008	-0.008	0.000	0.000	0.000	0.000
115	D	118	GLU	-1	-0.894	-0.928	29.941	-0.003	-0.003	0.000	0.000	0.000	0.000
116	D	119	HIS	0	-0.010	-0.010	26.033	-0.007	-0.007	0.000	0.000	0.000	0.000
117	D	120	PRO	0	-0.074	-0.024	27.865	-0.004	-0.004	0.000	0.000	0.000	0.000
118	D	121	LEU	0	-0.006	-0.010	23.907	-0.005	-0.005	0.000	0.000	0.000	0.000
119	D	122	ARG	1	0.871	0.927	27.976	0.068	0.068	0.000	0.000	0.000	0.000
120	D	123	ALA	0	0.047	0.013	31.233	0.008	0.008	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.832	-0.915	34.270	-0.053	-0.053	0.000	0.000	0.000	0.000
122	D	125	LEU	0	-0.039	-0.025	31.635	0.006	0.006	0.000	0.000	0.000	0.000
123	D	126	ALA	0	-0.019	-0.006	32.948	0.006	0.006	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.773	-0.854	34.509	-0.021	-0.021	0.000	0.000	0.000	0.000
125	D	128	GLU	-1	-0.806	-0.869	37.658	-0.028	-0.028	0.000	0.000	0.000	0.000
126	D	129	TYR	0	-0.068	-0.058	33.651	0.003	0.003	0.000	0.000	0.000	0.000
127	D	130	SER	0	-0.062	-0.042	37.102	0.005	0.005	0.000	0.000	0.000	0.000
128	D	131	LYS	1	0.858	0.907	38.675	0.028	0.028	0.000	0.000	0.000	0.000
129	D	132	ASP	-1	-0.774	-0.887	41.187	-0.011	-0.011	0.000	0.000	0.000	0.000
130	D	133	ARG	1	0.905	0.967	36.496	-0.001	-0.001	0.000	0.000	0.000	0.000
131	D	134	LYS	1	0.923	0.952	40.622	0.003	0.003	0.000	0.000	0.000	0.000
132	D	135	LYS	1	0.765	0.864	41.166	0.030	0.030	0.000	0.000	0.000	0.000
133	D	136	PHE	0	0.057	0.023	32.896	-0.001	-0.001	0.000	0.000	0.000	0.000
134	D	137	CYS	0	-0.033	-0.020	37.362	-0.001	-0.001	0.000	0.000	0.000	0.000
135	D	138	LYS	1	1.036	1.018	38.054	0.011	0.011	0.000	0.000	0.000	0.000
136	D	139	ASN	0	-0.012	0.010	37.806	-0.001	-0.001	0.000	0.000	0.000	0.000
137	D	140	ALA	0	0.007	0.005	33.832	-0.004	-0.004	0.000	0.000	0.000	0.000
138	D	141	GLU	-1	-0.913	-0.938	34.540	-0.005	-0.005	0.000	0.000	0.000	0.000
139	D	142	GLU	-1	-0.768	-0.867	36.411	-0.026	-0.026	0.000	0.000	0.000	0.000
140	D	143	PHE	0	-0.048	-0.014	31.442	-0.005	-0.005	0.000	0.000	0.000	0.000
141	D	144	THR	0	0.047	0.004	31.163	-0.005	-0.005	0.000	0.000	0.000	0.000
142	D	145	LYS	1	0.854	0.926	32.974	0.019	0.019	0.000	0.000	0.000	0.000
143	D	146	LYS	1	0.777	0.876	35.060	0.036	0.036	0.000	0.000	0.000	0.000
144	D	147	TYR	0	-0.049	-0.025	29.619	-0.012	-0.012	0.000	0.000	0.000	0.000

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