FMO DATABASE

FMODB ID: MN63Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1550706.545474
FMO2-HF: Nuclear repulsion	1487990.262406
FMO2-HF: Total energy	-62716.283067
FMO2-MP2: Total energy	-62898.095892

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.
-5.628	-2.991	7.434	-4.641	-5.429	-0.039

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 : 0.060 / q_NPA : 0.036

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	0.058	0.011	3.852	-0.987	0.074	-0.006	-0.616	-0.438	0.003
4	A	2	GLN	0	0.009	0.000	6.862	0.049	0.049	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.772	0.874	2.472	-1.093	-0.292	1.507	-1.267	-1.041	-0.005
6	A	4	ALA	0	0.050	0.019	5.098	0.214	0.214	0.000	0.000	0.000	0.000
7	A	5	SER	0	-0.037	-0.025	6.341	0.233	0.233	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.733	0.827	9.103	0.156	0.156	0.000	0.000	0.000	0.000
9	A	7	LEU	0	0.039	0.019	5.913	0.065	0.065	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.977	0.991	9.657	0.701	0.701	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.923	0.978	11.964	0.263	0.263	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.699	-0.825	12.942	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.009	0.001	11.746	0.022	0.022	0.000	0.000	0.000	0.000
14	A	12	HIS	0	0.018	0.013	15.138	0.008	0.008	0.000	0.000	0.000	0.000
15	A	13	MET	0	-0.007	0.014	17.700	0.012	0.012	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.028	-0.027	15.620	0.016	0.016	0.000	0.000	0.000	0.000
17	A	15	ALA	0	-0.011	0.003	19.431	0.009	0.009	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.105	-0.069	21.090	0.011	0.011	0.000	0.000	0.000	0.000
19	A	17	GLU	-1	-0.958	-0.972	22.853	-0.079	-0.079	0.000	0.000	0.000	0.000
20	A	18	PRO	0	-0.040	-0.002	22.805	0.003	0.003	0.000	0.000	0.000	0.000
21	A	19	PRO	0	0.011	-0.004	22.734	0.006	0.006	0.000	0.000	0.000	0.000
22	A	20	PRO	0	0.044	0.026	25.913	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	21	GLY	0	0.014	0.007	29.336	0.004	0.004	0.000	0.000	0.000	0.000
24	A	22	ILE	0	-0.042	-0.014	22.992	0.001	0.001	0.000	0.000	0.000	0.000
25	A	23	THR	0	0.003	0.008	23.287	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	24	CYS	0	-0.057	-0.050	17.349	0.001	0.001	0.000	0.000	0.000	0.000
27	A	25	TRP	0	-0.007	0.001	17.695	0.002	0.002	0.000	0.000	0.000	0.000
28	A	26	GLN	0	0.027	0.000	12.552	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	27	ASP	-1	-0.769	-0.878	15.434	-0.155	-0.155	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.881	0.919	15.750	0.327	0.327	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.825	-0.891	14.080	-0.372	-0.372	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.018	-0.001	9.434	-0.194	-0.194	0.000	0.000	0.000	0.000
33	A	31	MET	0	-0.020	-0.013	7.279	0.095	0.095	0.000	0.000	0.000	0.000
34	A	32	ASP	-1	-0.814	-0.902	5.711	-0.996	-0.996	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.828	-0.878	8.945	-0.197	-0.197	0.000	0.000	0.000	0.000
36	A	34	LEU	0	-0.032	-0.007	11.825	0.025	0.025	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.720	0.831	14.359	0.238	0.238	0.000	0.000	0.000	0.000
38	A	36	ALA	0	0.027	0.020	18.053	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	37	GLN	0	-0.016	-0.009	20.737	0.004	0.004	0.000	0.000	0.000	0.000
40	A	38	ILE	0	0.018	0.015	23.851	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	39	LEU	0	-0.024	-0.011	26.896	0.002	0.002	0.000	0.000	0.000	0.000
42	A	40	GLY	0	0.005	0.002	30.615	0.002	0.002	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.032	0.014	32.979	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	42	ALA	0	0.017	0.001	34.880	0.002	0.002	0.000	0.000	0.000	0.000
45	A	43	ASN	0	-0.041	-0.025	38.581	0.002	0.002	0.000	0.000	0.000	0.000
46	A	44	THR	0	0.016	0.012	35.253	0.002	0.002	0.000	0.000	0.000	0.000
47	A	45	PRO	0	-0.076	-0.047	37.456	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	46	TYR	0	0.013	-0.035	33.802	0.000	0.000	0.000	0.000	0.000	0.000
49	A	47	GLU	-1	-0.800	-0.869	35.321	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	48	LYS	1	0.832	0.899	36.266	0.031	0.031	0.000	0.000	0.000	0.000
51	A	49	GLY	0	0.010	0.026	34.126	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	50	VAL	0	-0.052	-0.029	29.279	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	51	PHE	0	-0.001	-0.018	27.667	0.000	0.000	0.000	0.000	0.000	0.000
54	A	52	LYS	1	0.872	0.951	21.186	0.127	0.127	0.000	0.000	0.000	0.000
55	A	53	LEU	0	-0.013	-0.013	21.180	0.008	0.008	0.000	0.000	0.000	0.000
56	A	54	GLU	-1	-0.794	-0.870	16.900	-0.111	-0.111	0.000	0.000	0.000	0.000
57	A	55	VAL	0	-0.015	-0.028	14.362	0.023	0.023	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.066	0.049	10.950	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	57	ILE	0	0.000	-0.003	8.000	0.063	0.063	0.000	0.000	0.000	0.000
60	A	58	PRO	0	0.058	0.044	7.943	-0.070	-0.070	0.000	0.000	0.000	0.000
61	A	59	GLU	-1	-0.808	-0.917	2.177	-3.591	-3.401	5.919	-2.520	-3.590	-0.035
62	A	60	ARG	1	0.827	0.888	3.557	-0.587	-0.002	0.014	-0.238	-0.360	-0.002
63	A	61	TYR	0	-0.052	-0.022	6.318	-0.127	-0.127	0.000	0.000	0.000	0.000
64	A	62	PRO	0	-0.038	-0.028	6.729	0.015	0.015	0.000	0.000	0.000	0.000
65	A	63	PHE	0	0.005	-0.023	8.480	-0.039	-0.039	0.000	0.000	0.000	0.000
66	A	64	GLU	-1	-0.839	-0.893	10.091	0.450	0.450	0.000	0.000	0.000	0.000
67	A	65	PRO	0	0.021	0.010	11.366	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	66	PRO	0	-0.015	-0.019	12.834	0.006	0.006	0.000	0.000	0.000	0.000
69	A	67	GLN	0	-0.008	-0.001	11.434	0.006	0.006	0.000	0.000	0.000	0.000
70	A	68	ILE	0	-0.027	-0.009	15.106	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	69	ARG	1	0.785	0.876	18.244	0.080	0.080	0.000	0.000	0.000	0.000
72	A	70	PHE	0	0.019	-0.010	21.364	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	71	LEU	0	-0.055	-0.023	20.949	0.001	0.001	0.000	0.000	0.000	0.000
74	A	72	THR	0	-0.014	0.016	25.043	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	PRO	0	-0.011	-0.007	28.435	0.003	0.003	0.000	0.000	0.000	0.000
76	A	74	ILE	0	0.000	0.003	29.085	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	75	TYR	0	-0.040	-0.034	31.967	0.003	0.003	0.000	0.000	0.000	0.000
78	A	76	HIS	0	0.043	0.009	31.283	0.001	0.001	0.000	0.000	0.000	0.000
79	A	77	PRO	0	0.018	0.016	33.209	0.001	0.001	0.000	0.000	0.000	0.000
80	A	78	ASN	0	0.013	-0.007	29.133	0.001	0.001	0.000	0.000	0.000	0.000
81	A	79	ILE	0	0.005	0.005	26.889	0.001	0.001	0.000	0.000	0.000	0.000
82	A	80	ASP	-1	-0.742	-0.858	27.174	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	81	SER	0	0.008	-0.009	28.986	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	82	ALA	0	-0.071	-0.027	25.425	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	83	GLY	0	-0.009	0.008	24.715	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	84	ARG	1	0.882	0.921	22.677	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	85	ILE	0	0.038	0.011	22.190	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	86	CYS	0	-0.093	-0.027	23.608	0.009	0.009	0.000	0.000	0.000	0.000
89	A	87	LEU	0	0.060	0.010	23.222	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.801	-0.898	22.942	0.027	0.027	0.000	0.000	0.000	0.000
91	A	89	VAL	0	-0.015	-0.018	20.544	0.011	0.011	0.000	0.000	0.000	0.000
92	A	90	LEU	0	-0.004	0.003	18.395	0.000	0.000	0.000	0.000	0.000	0.000
93	A	91	LYS	1	0.920	0.962	18.322	-0.082	-0.082	0.000	0.000	0.000	0.000
94	A	92	LEU	0	0.014	0.010	14.464	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	93	PRO	0	-0.006	0.024	18.663	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	94	PRO	0	-0.026	-0.022	21.108	0.013	0.013	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.805	0.870	24.240	-0.047	-0.047	0.000	0.000	0.000	0.000
98	A	96	GLY	0	0.002	0.008	21.981	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	97	ALA	0	0.018	0.005	21.826	0.005	0.005	0.000	0.000	0.000	0.000
100	A	98	TRP	0	-0.046	-0.022	13.156	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	99	ARG	1	0.963	0.960	16.979	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	100	PRO	0	0.024	0.013	13.453	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	101	SER	0	-0.006	0.009	15.072	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	102	LEU	0	-0.013	0.019	17.590	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	103	ASN	0	-0.003	0.001	15.556	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	104	ILE	0	0.082	0.043	12.178	0.014	0.014	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.072	0.042	16.540	0.007	0.007	0.000	0.000	0.000	0.000
108	A	106	THR	0	-0.029	-0.015	19.495	0.012	0.012	0.000	0.000	0.000	0.000
109	A	107	VAL	0	0.022	0.017	17.471	0.006	0.006	0.000	0.000	0.000	0.000
110	A	108	LEU	0	0.021	0.012	18.860	0.004	0.004	0.000	0.000	0.000	0.000
111	A	109	THR	0	0.011	-0.019	21.902	0.003	0.003	0.000	0.000	0.000	0.000
112	A	110	SER	0	-0.034	-0.027	23.446	0.006	0.006	0.000	0.000	0.000	0.000
113	A	111	ILE	0	-0.008	0.005	21.302	0.004	0.004	0.000	0.000	0.000	0.000
114	A	112	GLN	0	-0.007	-0.021	25.454	0.003	0.003	0.000	0.000	0.000	0.000
115	A	113	LEU	0	0.004	0.012	28.001	0.002	0.002	0.000	0.000	0.000	0.000
116	A	114	LEU	0	0.015	0.017	26.985	0.002	0.002	0.000	0.000	0.000	0.000
117	A	115	MET	0	-0.067	-0.024	28.822	0.000	0.000	0.000	0.000	0.000	0.000
118	A	116	SER	0	-0.062	-0.033	31.301	0.000	0.000	0.000	0.000	0.000	0.000
119	A	117	GLU	-1	-0.983	-0.991	32.957	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	118	PRO	0	-0.056	-0.032	32.675	0.002	0.002	0.000	0.000	0.000	0.000
121	A	119	ASN	0	0.030	0.023	31.048	0.002	0.002	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.032	-0.007	33.447	0.002	0.002	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.887	-0.944	34.536	0.014	0.014	0.000	0.000	0.000	0.000
124	A	122	ASP	-1	-0.787	-0.868	29.197	0.035	0.035	0.000	0.000	0.000	0.000
125	A	123	PRO	0	-0.048	-0.019	30.899	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	124	LEU	0	-0.067	-0.035	27.016	0.004	0.004	0.000	0.000	0.000	0.000
127	A	125	MET	0	-0.029	-0.004	31.032	0.000	0.000	0.000	0.000	0.000	0.000
128	A	126	ALA	0	0.055	0.024	34.296	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	127	ASP	-1	-0.863	-0.920	37.331	0.004	0.004	0.000	0.000	0.000	0.000
130	A	128	ILE	0	0.009	0.006	35.132	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	129	SER	0	-0.031	-0.025	36.399	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	130	SER	0	-0.008	-0.019	38.193	0.000	0.000	0.000	0.000	0.000	0.000
133	A	131	GLU	-1	-0.805	-0.882	41.395	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	132	PHE	0	0.040	-0.001	38.105	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	133	LYS	1	0.906	0.960	40.005	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	134	TYR	0	0.015	0.008	42.906	0.000	0.000	0.000	0.000	0.000	0.000
137	A	135	ASN	0	-0.003	-0.005	45.237	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	136	LYS	1	0.895	0.968	40.563	0.004	0.004	0.000	0.000	0.000	0.000
139	A	137	PRO	0	0.032	0.004	44.523	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	138	ALA	0	-0.002	0.017	46.116	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	139	PHE	0	0.065	0.045	36.750	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	140	LEU	0	0.028	0.009	40.992	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	141	LYS	1	0.899	0.975	42.274	0.010	0.010	0.000	0.000	0.000	0.000
144	A	142	ASN	0	-0.024	-0.031	41.101	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	143	ALA	0	0.052	0.027	37.489	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.893	0.952	37.947	0.014	0.014	0.000	0.000	0.000	0.000
147	A	145	GLN	0	-0.024	-0.017	40.038	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	146	TRP	0	-0.003	-0.009	34.030	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	147	THR	0	-0.002	-0.015	35.324	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	148	GLU	-1	-0.882	-0.938	36.661	-0.032	-0.032	0.000	0.000	0.000	0.000
151	A	149	LYS	1	0.909	0.963	38.169	0.021	0.021	0.000	0.000	0.000	0.000
152	A	150	HIS	0	-0.016	-0.012	33.325	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	151	ALA	0	-0.005	0.010	32.588	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	152	ARG	1	0.853	0.910	33.575	0.030	0.030	0.000	0.000	0.000	0.000
155	A	153	GLN	0	0.013	0.025	31.146	0.005	0.005	0.000	0.000	0.000	0.000
156	A	154	LYS	1	0.964	0.979	36.087	0.048	0.048	0.000	0.000	0.000	0.000

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