FMO DATABASE

FMODB ID: 98NG2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1549220.848061
FMO2-HF: Nuclear repulsion	1486504.905776
FMO2-HF: Total energy	-62715.942286
FMO2-MP2: Total energy	-62897.819511

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.
-9.665	-9.959	14.518	-7.691	-6.532	-0.053

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 : 0.049 / q_NPA : 0.009

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	0.063	0.015	3.757	-0.979	0.082	-0.016	-0.635	-0.410	0.004
4	A	2	GLN	0	0.017	-0.002	6.937	0.006	0.006	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.809	0.909	2.090	1.465	1.899	2.359	-1.503	-1.290	0.006
6	A	4	ALA	0	0.043	0.014	5.303	0.271	0.271	0.000	0.000	0.000	0.000
7	A	5	SER	0	-0.035	-0.024	6.788	0.333	0.333	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.724	0.833	8.960	0.417	0.417	0.000	0.000	0.000	0.000
9	A	7	LEU	0	0.051	0.020	6.429	0.123	0.123	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.973	1.002	10.071	0.859	0.859	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.942	0.981	12.586	0.425	0.425	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.710	-0.835	12.606	-0.273	-0.273	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.029	0.008	12.461	0.040	0.040	0.000	0.000	0.000	0.000
14	A	12	HIS	0	0.016	0.012	15.580	0.026	0.026	0.000	0.000	0.000	0.000
15	A	13	MET	0	-0.012	0.007	17.873	0.023	0.023	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.045	-0.020	15.852	0.023	0.023	0.000	0.000	0.000	0.000
17	A	15	ALA	0	-0.030	-0.013	19.622	0.021	0.021	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.083	-0.060	21.489	0.022	0.022	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.965	-0.973	23.019	-0.128	-0.128	0.000	0.000	0.000	0.000
20	A	18	PRO	0	-0.030	0.003	23.065	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	19	PRO	0	0.003	-0.001	22.703	0.011	0.011	0.000	0.000	0.000	0.000
22	A	20	PRO	0	0.082	0.037	25.873	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.016	-0.005	28.582	0.003	0.003	0.000	0.000	0.000	0.000
24	A	22	ILE	0	-0.033	-0.015	22.687	0.001	0.001	0.000	0.000	0.000	0.000
25	A	23	THR	0	0.008	0.013	23.248	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	24	CYS	0	-0.046	-0.040	17.362	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	25	TRP	0	0.004	0.007	18.192	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	26	GLN	0	0.018	-0.008	12.925	-0.070	-0.070	0.000	0.000	0.000	0.000
29	A	27	ASP	-1	-0.883	-0.931	15.465	-0.182	-0.182	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.902	0.916	15.405	0.284	0.284	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.832	-0.889	13.580	-0.348	-0.348	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.037	-0.011	9.005	-0.203	-0.203	0.000	0.000	0.000	0.000
33	A	31	MET	0	-0.019	-0.014	7.871	0.107	0.107	0.000	0.000	0.000	0.000
34	A	32	ASP	-1	-0.831	-0.909	5.339	-2.029	-2.029	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.815	-0.866	8.941	-0.212	-0.212	0.000	0.000	0.000	0.000
36	A	34	LEU	0	0.003	-0.002	11.856	0.036	0.036	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.713	0.833	14.813	0.306	0.306	0.000	0.000	0.000	0.000
38	A	36	ALA	0	0.030	0.017	18.445	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	37	GLN	0	-0.036	-0.029	20.861	0.014	0.014	0.000	0.000	0.000	0.000
40	A	38	ILE	0	0.017	0.009	23.461	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	39	LEU	0	-0.047	-0.020	26.756	0.006	0.006	0.000	0.000	0.000	0.000
42	A	40	GLY	0	0.023	0.004	30.504	0.001	0.001	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.011	0.010	32.898	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	42	ALA	0	0.005	-0.004	34.367	0.003	0.003	0.000	0.000	0.000	0.000
45	A	43	ASN	0	-0.048	-0.028	38.017	0.002	0.002	0.000	0.000	0.000	0.000
46	A	44	THR	0	0.039	0.010	35.146	0.001	0.001	0.000	0.000	0.000	0.000
47	A	45	PRO	0	-0.066	-0.037	37.079	0.000	0.000	0.000	0.000	0.000	0.000
48	A	46	TYR	0	0.010	-0.029	33.591	0.001	0.001	0.000	0.000	0.000	0.000
49	A	47	GLU	-1	-0.798	-0.869	35.193	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	48	LYS	1	0.840	0.898	36.351	0.047	0.047	0.000	0.000	0.000	0.000
51	A	49	GLY	0	0.006	0.017	34.134	0.000	0.000	0.000	0.000	0.000	0.000
52	A	50	VAL	0	-0.064	-0.028	29.184	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	51	PHE	0	0.003	-0.007	27.657	0.004	0.004	0.000	0.000	0.000	0.000
54	A	52	LYS	1	0.975	0.999	21.796	0.136	0.136	0.000	0.000	0.000	0.000
55	A	53	LEU	0	-0.005	-0.001	20.956	0.011	0.011	0.000	0.000	0.000	0.000
56	A	54	GLU	-1	-0.812	-0.866	16.230	-0.145	-0.145	0.000	0.000	0.000	0.000
57	A	55	VAL	0	-0.007	-0.024	13.925	0.021	0.021	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.036	0.033	10.352	-0.053	-0.053	0.000	0.000	0.000	0.000
59	A	57	ILE	0	-0.016	-0.010	7.237	0.084	0.084	0.000	0.000	0.000	0.000
60	A	58	PRO	0	0.077	0.051	7.494	-0.182	-0.182	0.000	0.000	0.000	0.000
61	A	59	GLU	-1	-0.805	-0.912	1.837	-10.255	-12.725	12.145	-5.342	-4.332	-0.062
62	A	60	ARG	1	0.818	0.885	3.570	0.012	0.693	0.030	-0.211	-0.500	-0.001
63	A	61	TYR	0	-0.059	0.000	6.193	-0.163	-0.163	0.000	0.000	0.000	0.000
64	A	62	PRO	0	-0.027	-0.035	6.108	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	63	PHE	0	-0.013	-0.045	8.499	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	64	GLU	-1	-0.819	-0.888	9.884	0.389	0.389	0.000	0.000	0.000	0.000
67	A	65	PRO	0	0.000	0.004	10.935	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	66	PRO	0	-0.001	-0.005	12.008	0.001	0.001	0.000	0.000	0.000	0.000
69	A	67	GLN	0	-0.019	-0.009	11.254	0.012	0.012	0.000	0.000	0.000	0.000
70	A	68	ILE	0	-0.012	-0.007	14.714	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	69	ARG	1	0.816	0.889	17.847	0.113	0.113	0.000	0.000	0.000	0.000
72	A	70	PHE	0	0.009	-0.012	20.944	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	71	LEU	0	-0.040	-0.025	20.677	0.006	0.006	0.000	0.000	0.000	0.000
74	A	72	THR	0	-0.020	0.007	24.422	0.003	0.003	0.000	0.000	0.000	0.000
75	A	73	PRO	0	0.004	-0.001	27.954	0.001	0.001	0.000	0.000	0.000	0.000
76	A	74	ILE	0	0.009	0.002	28.673	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	75	TYR	0	-0.073	-0.044	31.584	0.003	0.003	0.000	0.000	0.000	0.000
78	A	76	HIS	0	0.045	0.009	30.882	0.002	0.002	0.000	0.000	0.000	0.000
79	A	77	PRO	0	0.043	0.026	32.678	0.002	0.002	0.000	0.000	0.000	0.000
80	A	78	ASN	0	0.007	-0.009	28.667	0.001	0.001	0.000	0.000	0.000	0.000
81	A	79	ILE	0	0.004	0.010	26.455	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	80	ASP	-1	-0.744	-0.863	26.800	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	81	SER	0	-0.001	-0.006	28.686	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	82	ALA	0	-0.072	-0.034	25.238	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	83	GLY	0	-0.020	-0.001	24.490	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	84	ARG	1	0.881	0.925	22.404	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	85	ILE	0	0.048	0.017	21.560	0.002	0.002	0.000	0.000	0.000	0.000
88	A	86	CYS	0	-0.086	-0.029	23.068	0.005	0.005	0.000	0.000	0.000	0.000
89	A	87	LEU	0	0.064	0.013	22.619	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.798	-0.893	22.494	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	89	VAL	0	-0.014	-0.017	20.074	0.007	0.007	0.000	0.000	0.000	0.000
92	A	90	LEU	0	-0.012	-0.001	17.909	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	91	LYS	1	0.919	0.961	17.910	-0.036	-0.036	0.000	0.000	0.000	0.000
94	A	92	LEU	0	-0.012	0.002	14.152	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	93	PRO	0	-0.003	0.029	18.381	0.002	0.002	0.000	0.000	0.000	0.000
96	A	94	PRO	0	-0.021	-0.026	20.657	0.013	0.013	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.843	0.894	24.000	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	96	GLY	0	-0.019	-0.009	21.418	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	97	ALA	0	0.039	0.013	21.501	0.004	0.004	0.000	0.000	0.000	0.000
100	A	98	TRP	0	-0.041	-0.018	12.662	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	99	ARG	1	0.954	0.961	16.758	0.062	0.062	0.000	0.000	0.000	0.000
102	A	100	PRO	0	0.050	0.029	13.004	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	101	SER	0	-0.015	0.003	14.646	-0.030	-0.030	0.000	0.000	0.000	0.000
104	A	102	LEU	0	-0.015	0.017	17.073	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	103	ASN	0	-0.020	-0.015	14.887	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	104	ILE	0	0.085	0.031	11.883	0.029	0.029	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.077	0.044	15.959	0.020	0.020	0.000	0.000	0.000	0.000
108	A	106	THR	0	-0.047	-0.014	18.888	0.022	0.022	0.000	0.000	0.000	0.000
109	A	107	VAL	0	0.020	0.005	16.907	0.014	0.014	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.018	0.013	18.657	0.012	0.012	0.000	0.000	0.000	0.000
111	A	109	THR	0	0.019	-0.012	21.417	0.011	0.011	0.000	0.000	0.000	0.000
112	A	110	SER	0	-0.030	-0.017	22.952	0.012	0.012	0.000	0.000	0.000	0.000
113	A	111	ILE	0	-0.009	0.002	20.648	0.008	0.008	0.000	0.000	0.000	0.000
114	A	112	GLN	0	-0.016	-0.025	24.874	0.006	0.006	0.000	0.000	0.000	0.000
115	A	113	LEU	0	-0.007	-0.001	27.417	0.005	0.005	0.000	0.000	0.000	0.000
116	A	114	LEU	0	0.020	0.016	26.541	0.005	0.005	0.000	0.000	0.000	0.000
117	A	115	MET	0	-0.081	-0.031	28.473	0.003	0.003	0.000	0.000	0.000	0.000
118	A	116	SER	0	-0.031	-0.021	30.873	0.003	0.003	0.000	0.000	0.000	0.000
119	A	117	GLU	-1	-1.005	-0.994	32.412	-0.036	-0.036	0.000	0.000	0.000	0.000
120	A	118	PRO	0	-0.058	-0.028	32.281	0.001	0.001	0.000	0.000	0.000	0.000
121	A	119	ASN	0	0.044	0.024	29.821	0.002	0.002	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.029	-0.006	33.184	0.002	0.002	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.893	-0.958	33.909	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	122	ASP	-1	-0.840	-0.897	29.517	0.006	0.006	0.000	0.000	0.000	0.000
125	A	123	PRO	0	-0.061	-0.019	30.738	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	124	LEU	0	-0.051	-0.029	26.544	0.004	0.004	0.000	0.000	0.000	0.000
127	A	125	MET	0	-0.021	0.003	30.832	0.003	0.003	0.000	0.000	0.000	0.000
128	A	126	ALA	0	0.040	0.016	34.010	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	127	ASP	-1	-0.857	-0.931	37.027	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	128	ILE	0	-0.004	0.000	34.774	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	129	SER	0	-0.006	-0.003	35.905	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	130	SER	0	-0.021	-0.019	37.727	0.000	0.000	0.000	0.000	0.000	0.000
133	A	131	GLU	-1	-0.798	-0.876	41.054	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	132	PHE	0	0.006	-0.019	37.809	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	133	LYS	1	0.882	0.942	39.734	0.007	0.007	0.000	0.000	0.000	0.000
136	A	134	TYR	0	-0.006	-0.002	42.317	0.000	0.000	0.000	0.000	0.000	0.000
137	A	135	ASN	0	-0.002	-0.001	44.720	0.000	0.000	0.000	0.000	0.000	0.000
138	A	136	LYS	1	0.994	1.019	40.105	0.023	0.023	0.000	0.000	0.000	0.000
139	A	137	PRO	0	0.014	0.003	43.996	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	138	ALA	0	0.006	0.007	45.642	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	139	PHE	0	0.071	0.053	36.191	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	140	LEU	0	-0.017	-0.017	40.468	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	141	LYS	1	0.875	0.956	41.722	0.018	0.018	0.000	0.000	0.000	0.000
144	A	142	ASN	0	-0.010	-0.021	40.796	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	143	ALA	0	0.031	0.018	37.350	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.955	0.976	37.894	0.027	0.027	0.000	0.000	0.000	0.000
147	A	145	GLN	0	-0.019	-0.005	39.949	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	146	TRP	0	0.010	0.002	33.674	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	147	THR	0	-0.004	-0.005	35.239	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	148	GLU	-1	-0.902	-0.947	36.480	-0.043	-0.043	0.000	0.000	0.000	0.000
151	A	149	LYS	1	0.918	0.965	37.488	0.028	0.028	0.000	0.000	0.000	0.000
152	A	150	HIS	0	-0.016	-0.017	32.737	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	151	ALA	0	0.009	0.023	32.457	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	152	ARG	1	0.822	0.900	33.416	0.042	0.042	0.000	0.000	0.000	0.000
155	A	153	GLN	0	0.024	0.018	31.677	0.005	0.005	0.000	0.000	0.000	0.000
156	A	154	LYS	1	0.971	1.001	35.891	0.060	0.060	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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