FMO DATABASE

FMODB ID: LNMJ9

Calculation Name: 1YH2-A-Xray372

Preferred Name: Ubiquitin-conjugating enzyme E2 T

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1YH2

Chain ID: A

ChEMBL ID: CHEMBL4105763

UniProt ID: Q9NPD8

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1548266.141257
FMO2-HF: Nuclear repulsion	1485551.224015
FMO2-HF: Total energy	-62714.917243
FMO2-MP2: Total energy	-62896.868944

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(A:-1:GLY)

Summations of interaction energy for fragment #1(A:-1:GLY)

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.
-10.78	-22.769	30.598	-12.381	-6.231	-0.074

Interaction energy analysis for fragmet #1(A:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.019

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	A	1	MET	0	0.064	0.015	3.757	-0.830	0.193	-0.016	-0.603	-0.405	0.003
4	A	2	GLN	0	0.020	-0.005	6.937	0.070	0.070	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.813	0.907	2.348	0.554	1.335	1.100	-0.836	-1.045	0.003
6	A	4	ALA	0	0.039	0.016	5.310	0.234	0.234	0.000	0.000	0.000	0.000
7	A	5	SER	0	-0.052	-0.033	6.793	0.313	0.313	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.754	0.867	8.906	0.285	0.285	0.000	0.000	0.000	0.000
9	A	7	LEU	0	0.067	0.021	6.461	0.104	0.104	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.978	1.001	10.088	0.873	0.873	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.945	0.984	12.591	0.348	0.348	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.720	-0.833	12.508	-0.162	-0.162	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.041	0.014	12.494	0.033	0.033	0.000	0.000	0.000	0.000
14	A	12	HIS	0	0.010	0.012	15.583	0.019	0.019	0.000	0.000	0.000	0.000
15	A	13	MET	0	-0.010	-0.004	17.873	0.021	0.021	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.041	-0.019	15.842	0.021	0.021	0.000	0.000	0.000	0.000
17	A	15	ALA	0	-0.022	-0.011	19.624	0.017	0.017	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.097	-0.055	21.492	0.020	0.020	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.962	-0.975	23.021	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	18	PRO	0	-0.040	0.004	23.063	0.002	0.002	0.000	0.000	0.000	0.000
21	A	19	PRO	0	0.011	0.000	22.649	0.009	0.009	0.000	0.000	0.000	0.000
22	A	20	PRO	0	0.085	0.027	25.873	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.026	-0.004	28.582	0.004	0.004	0.000	0.000	0.000	0.000
24	A	22	ILE	0	-0.024	-0.009	22.633	0.001	0.001	0.000	0.000	0.000	0.000
25	A	23	THR	0	-0.001	0.009	23.260	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	24	CYS	0	-0.020	-0.026	17.266	0.001	0.001	0.000	0.000	0.000	0.000
27	A	25	TRP	0	-0.022	-0.003	18.190	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	26	GLN	0	0.007	-0.020	13.271	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	27	ASP	-1	-0.976	-0.978	15.422	-0.187	-0.187	0.000	0.000	0.000	0.000
30	A	28	LYS	1	1.000	0.978	15.344	0.262	0.262	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.910	-0.943	13.649	-0.414	-0.414	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.017	0.004	8.705	-0.266	-0.266	0.000	0.000	0.000	0.000
33	A	31	MET	0	-0.041	-0.030	8.188	0.112	0.112	0.000	0.000	0.000	0.000
34	A	32	ASP	-1	-0.849	-0.914	5.560	-1.488	-1.488	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.816	-0.872	8.924	-0.167	-0.167	0.000	0.000	0.000	0.000
36	A	34	LEU	0	0.003	-0.010	11.832	0.022	0.022	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.805	0.897	14.797	0.246	0.246	0.000	0.000	0.000	0.000
38	A	36	ALA	0	0.029	0.016	18.433	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	37	GLN	0	-0.032	-0.023	20.863	0.009	0.009	0.000	0.000	0.000	0.000
40	A	38	ILE	0	0.019	0.008	23.750	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	39	LEU	0	-0.065	-0.030	26.756	0.004	0.004	0.000	0.000	0.000	0.000
42	A	40	GLY	0	0.022	0.003	30.504	0.002	0.002	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.011	0.010	32.898	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	42	ALA	0	0.011	0.006	34.366	0.003	0.003	0.000	0.000	0.000	0.000
45	A	43	ASN	0	-0.040	-0.017	38.017	0.001	0.001	0.000	0.000	0.000	0.000
46	A	44	THR	0	0.023	-0.004	35.200	0.002	0.002	0.000	0.000	0.000	0.000
47	A	45	PRO	0	-0.069	-0.040	37.078	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	46	TYR	0	0.009	-0.025	33.594	0.000	0.000	0.000	0.000	0.000	0.000
49	A	47	GLU	-1	-0.862	-0.915	35.193	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	48	LYS	1	0.879	0.914	36.363	0.035	0.035	0.000	0.000	0.000	0.000
51	A	49	GLY	0	0.011	0.019	34.133	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	50	VAL	0	-0.065	-0.029	29.107	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	51	PHE	0	-0.008	-0.010	27.608	0.003	0.003	0.000	0.000	0.000	0.000
54	A	52	LYS	1	0.993	1.002	22.164	0.107	0.107	0.000	0.000	0.000	0.000
55	A	53	LEU	0	-0.006	-0.003	20.866	0.010	0.010	0.000	0.000	0.000	0.000
56	A	54	GLU	-1	-0.840	-0.914	16.121	-0.110	-0.110	0.000	0.000	0.000	0.000
57	A	55	VAL	0	-0.015	-0.022	13.721	0.025	0.025	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.046	0.044	10.351	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	57	ILE	0	-0.033	-0.020	7.230	0.087	0.087	0.000	0.000	0.000	0.000
60	A	58	PRO	0	0.084	0.059	7.493	-0.130	-0.130	0.000	0.000	0.000	0.000
61	A	59	GLU	-1	-0.789	-0.893	1.576	-10.829	-25.304	29.483	-10.727	-4.282	-0.079
62	A	60	ARG	1	0.919	0.959	3.561	-0.002	0.680	0.031	-0.215	-0.499	-0.001
63	A	61	TYR	0	-0.067	-0.008	6.177	-0.272	-0.272	0.000	0.000	0.000	0.000
64	A	62	PRO	0	-0.020	-0.034	6.102	0.046	0.046	0.000	0.000	0.000	0.000
65	A	63	PHE	0	-0.032	-0.053	8.630	-0.063	-0.063	0.000	0.000	0.000	0.000
66	A	64	GLU	-1	-0.909	-0.954	9.888	0.508	0.508	0.000	0.000	0.000	0.000
67	A	65	PRO	0	-0.007	-0.003	10.929	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	66	PRO	0	0.000	-0.002	12.008	0.015	0.015	0.000	0.000	0.000	0.000
69	A	67	GLN	0	-0.011	-0.004	11.593	0.002	0.002	0.000	0.000	0.000	0.000
70	A	68	ILE	0	-0.014	-0.007	14.712	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	69	ARG	1	0.850	0.928	17.845	0.069	0.069	0.000	0.000	0.000	0.000
72	A	70	PHE	0	0.014	-0.010	20.972	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	71	LEU	0	-0.044	-0.029	20.678	0.005	0.005	0.000	0.000	0.000	0.000
74	A	72	THR	0	-0.025	0.007	24.428	0.001	0.001	0.000	0.000	0.000	0.000
75	A	73	PRO	0	0.016	0.008	27.959	0.002	0.002	0.000	0.000	0.000	0.000
76	A	74	ILE	0	0.015	0.004	28.707	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	75	TYR	0	-0.088	-0.067	31.607	0.004	0.004	0.000	0.000	0.000	0.000
78	A	76	HIS	0	0.043	0.008	30.889	0.001	0.001	0.000	0.000	0.000	0.000
79	A	77	PRO	0	0.052	0.028	32.675	0.002	0.002	0.000	0.000	0.000	0.000
80	A	78	ASN	0	0.009	-0.001	28.626	0.001	0.001	0.000	0.000	0.000	0.000
81	A	79	ILE	0	0.006	0.012	26.629	0.001	0.001	0.000	0.000	0.000	0.000
82	A	80	ASP	-1	-0.762	-0.896	26.945	0.012	0.012	0.000	0.000	0.000	0.000
83	A	81	SER	0	-0.043	-0.024	28.719	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	82	ALA	0	-0.019	-0.012	25.237	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	83	GLY	0	-0.030	-0.003	24.516	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	84	ARG	1	0.907	0.955	22.440	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	85	ILE	0	0.051	0.020	21.635	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	86	CYS	0	-0.106	-0.035	23.064	0.010	0.010	0.000	0.000	0.000	0.000
89	A	87	LEU	0	0.061	0.016	22.299	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.788	-0.884	22.488	0.017	0.017	0.000	0.000	0.000	0.000
91	A	89	VAL	0	-0.022	-0.026	20.096	0.013	0.013	0.000	0.000	0.000	0.000
92	A	90	LEU	0	-0.010	-0.001	17.660	0.000	0.000	0.000	0.000	0.000	0.000
93	A	91	LYS	1	0.909	0.956	17.905	-0.087	-0.087	0.000	0.000	0.000	0.000
94	A	92	LEU	0	-0.024	-0.005	14.043	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	93	PRO	0	0.003	0.029	18.374	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	94	PRO	0	-0.017	-0.022	20.648	0.016	0.016	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.959	0.968	24.006	-0.060	-0.060	0.000	0.000	0.000	0.000
98	A	96	GLY	0	-0.015	-0.005	21.411	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	97	ALA	0	0.044	0.014	21.497	0.002	0.002	0.000	0.000	0.000	0.000
100	A	98	TRP	0	-0.045	-0.021	12.723	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	99	ARG	1	0.966	0.968	16.762	0.011	0.011	0.000	0.000	0.000	0.000
102	A	100	PRO	0	0.044	0.026	13.041	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	101	SER	0	-0.009	-0.008	14.640	-0.028	-0.028	0.000	0.000	0.000	0.000
104	A	102	LEU	0	-0.017	0.019	17.041	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	103	ASN	0	-0.044	-0.032	14.894	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	104	ILE	0	0.091	0.032	11.932	0.021	0.021	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.066	0.039	15.957	0.014	0.014	0.000	0.000	0.000	0.000
108	A	106	THR	0	-0.043	-0.011	19.065	0.019	0.019	0.000	0.000	0.000	0.000
109	A	107	VAL	0	0.033	0.005	16.961	0.010	0.010	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.021	0.012	18.696	0.008	0.008	0.000	0.000	0.000	0.000
111	A	109	THR	0	0.020	-0.008	21.415	0.006	0.006	0.000	0.000	0.000	0.000
112	A	110	SER	0	-0.031	-0.009	22.863	0.009	0.009	0.000	0.000	0.000	0.000
113	A	111	ILE	0	-0.012	0.002	20.631	0.006	0.006	0.000	0.000	0.000	0.000
114	A	112	GLN	0	-0.011	-0.021	24.871	0.004	0.004	0.000	0.000	0.000	0.000
115	A	113	LEU	0	-0.005	0.001	27.415	0.002	0.002	0.000	0.000	0.000	0.000
116	A	114	LEU	0	0.025	0.019	26.403	0.004	0.004	0.000	0.000	0.000	0.000
117	A	115	MET	0	-0.081	-0.031	28.564	0.001	0.001	0.000	0.000	0.000	0.000
118	A	116	SER	0	-0.020	-0.016	30.871	0.001	0.001	0.000	0.000	0.000	0.000
119	A	117	GLU	-1	-1.025	-1.005	32.411	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	118	PRO	0	-0.061	-0.031	32.293	0.002	0.002	0.000	0.000	0.000	0.000
121	A	119	ASN	0	0.055	0.028	29.503	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.052	-0.023	33.179	0.003	0.003	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.903	-0.966	33.689	0.013	0.013	0.000	0.000	0.000	0.000
124	A	122	ASP	-1	-0.896	-0.940	30.338	0.031	0.031	0.000	0.000	0.000	0.000
125	A	123	PRO	0	-0.088	-0.033	30.733	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	124	LEU	0	-0.056	-0.034	26.348	0.005	0.005	0.000	0.000	0.000	0.000
127	A	125	MET	0	-0.042	-0.005	30.828	0.002	0.002	0.000	0.000	0.000	0.000
128	A	126	ALA	0	0.036	0.016	34.006	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	127	ASP	-1	-0.844	-0.929	37.022	0.009	0.009	0.000	0.000	0.000	0.000
130	A	128	ILE	0	-0.025	-0.006	34.741	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	129	SER	0	-0.007	-0.004	35.811	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	130	SER	0	0.012	-0.001	37.723	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	131	GLU	-1	-0.820	-0.878	41.038	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	132	PHE	0	-0.013	-0.023	38.084	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	133	LYS	1	0.897	0.955	39.809	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	134	TYR	0	-0.024	-0.011	42.313	0.000	0.000	0.000	0.000	0.000	0.000
137	A	135	ASN	0	-0.001	-0.004	44.717	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	136	LYS	1	1.028	1.027	40.397	0.008	0.008	0.000	0.000	0.000	0.000
139	A	137	PRO	0	0.005	0.001	43.993	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	138	ALA	0	0.009	0.006	45.625	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	139	PHE	0	0.065	0.052	36.128	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	140	LEU	0	-0.040	-0.031	40.422	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	141	LYS	1	0.930	0.974	41.720	0.008	0.008	0.000	0.000	0.000	0.000
144	A	142	ASN	0	-0.006	-0.011	40.691	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	143	ALA	0	0.019	0.015	37.317	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.950	0.978	37.893	0.015	0.015	0.000	0.000	0.000	0.000
147	A	145	GLN	0	-0.022	-0.009	39.949	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	146	TRP	0	0.013	0.007	33.514	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	147	THR	0	-0.008	-0.007	35.339	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	148	GLU	-1	-1.004	-1.005	36.485	-0.030	-0.030	0.000	0.000	0.000	0.000
151	A	149	LYS	1	0.926	0.967	37.378	0.016	0.016	0.000	0.000	0.000	0.000
152	A	150	HIS	0	-0.010	-0.018	32.694	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	151	ALA	0	0.011	0.028	32.450	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	152	ARG	1	0.935	0.977	33.417	0.031	0.031	0.000	0.000	0.000	0.000
155	A	153	GLN	0	0.042	0.025	32.119	0.005	0.005	0.000	0.000	0.000	0.000
156	A	154	LYS	1	0.965	0.998	35.875	0.049	0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:GLY)