FMO DATABASE

FMODB ID: G6RY1

Calculation Name: 2AZE-B-Xray372

Preferred Name: Transcription factor E2F1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2AZE

Chain ID: B

ChEMBL ID: CHEMBL4382

UniProt ID: Q01094

Base Structure: X-ray

Registration Date: 2023-06-22

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-564310.767348
FMO2-HF: Nuclear repulsion	523152.664345
FMO2-HF: Total energy	-41158.103003
FMO2-MP2: Total energy	-41274.17509

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(B:201:GLY)

Summations of interaction energy for fragment #1(B:201: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.
-12.386	-13	13.721	-7.282	-5.825	-0.048

Interaction energy analysis for fragmet #1(B:201:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.020

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	B	203	LEU	0	0.030	0.031	3.878	-1.128	1.154	-0.007	-1.272	-1.004	0.002
4	B	204	GLU	-1	-0.750	-0.861	1.809	-14.113	-17.398	13.730	-5.896	-4.549	-0.050
5	B	205	GLY	0	0.014	0.010	3.757	1.438	1.720	-0.001	-0.107	-0.174	0.000
6	B	206	LEU	0	0.045	0.015	5.377	0.819	0.926	-0.001	-0.007	-0.098	0.000
7	B	207	THR	0	-0.052	-0.036	7.613	0.624	0.624	0.000	0.000	0.000	0.000
8	B	208	GLN	0	-0.072	-0.035	7.563	0.321	0.321	0.000	0.000	0.000	0.000
9	B	209	ASP	-1	-0.844	-0.924	9.432	-0.796	-0.796	0.000	0.000	0.000	0.000
10	B	210	LEU	0	-0.019	-0.012	11.610	0.188	0.188	0.000	0.000	0.000	0.000
11	B	211	ARG	1	0.852	0.923	12.649	0.845	0.845	0.000	0.000	0.000	0.000
12	B	212	GLN	0	0.003	0.001	11.600	0.046	0.046	0.000	0.000	0.000	0.000
13	B	213	LEU	0	0.000	0.013	15.442	0.084	0.084	0.000	0.000	0.000	0.000
14	B	214	GLN	0	0.037	0.026	17.166	-0.010	-0.010	0.000	0.000	0.000	0.000
15	B	215	GLU	-1	-0.861	-0.920	18.379	-0.259	-0.259	0.000	0.000	0.000	0.000
16	B	216	SER	0	-0.024	-0.035	19.093	0.052	0.052	0.000	0.000	0.000	0.000
17	B	217	GLU	-1	-0.952	-0.971	21.455	-0.304	-0.304	0.000	0.000	0.000	0.000
18	B	218	GLN	0	-0.013	0.000	22.033	0.004	0.004	0.000	0.000	0.000	0.000
19	B	219	GLN	0	-0.079	-0.054	22.975	0.040	0.040	0.000	0.000	0.000	0.000
20	B	220	LEU	0	-0.005	0.003	25.732	0.023	0.023	0.000	0.000	0.000	0.000
21	B	221	ASP	-1	-0.833	-0.927	27.414	-0.197	-0.197	0.000	0.000	0.000	0.000
22	B	222	HIS	0	-0.072	-0.027	28.906	0.015	0.015	0.000	0.000	0.000	0.000
23	B	223	LEU	0	-0.011	-0.012	29.225	0.015	0.015	0.000	0.000	0.000	0.000
24	B	224	MET	0	0.014	0.021	30.587	0.017	0.017	0.000	0.000	0.000	0.000
25	B	225	ASN	0	0.017	0.015	33.292	0.015	0.015	0.000	0.000	0.000	0.000
26	B	226	ILE	0	-0.012	0.005	33.988	0.011	0.011	0.000	0.000	0.000	0.000
27	B	227	CYS	0	-0.005	-0.008	36.203	0.009	0.009	0.000	0.000	0.000	0.000
28	B	228	THR	0	-0.027	-0.035	37.001	0.007	0.007	0.000	0.000	0.000	0.000
29	B	229	THR	0	-0.006	-0.005	38.950	0.006	0.006	0.000	0.000	0.000	0.000
30	B	230	GLN	0	-0.038	-0.015	40.767	0.009	0.009	0.000	0.000	0.000	0.000
31	B	231	LEU	0	-0.002	-0.002	40.644	0.005	0.005	0.000	0.000	0.000	0.000
32	B	232	ARG	1	0.890	0.959	40.022	0.105	0.105	0.000	0.000	0.000	0.000
33	B	233	LEU	0	0.057	0.039	44.638	0.004	0.004	0.000	0.000	0.000	0.000
34	B	234	LEU	0	-0.032	-0.006	46.747	0.004	0.004	0.000	0.000	0.000	0.000
35	B	235	SER	0	-0.087	-0.050	47.974	0.003	0.003	0.000	0.000	0.000	0.000
36	B	236	GLU	-1	-0.922	-0.976	47.642	-0.078	-0.078	0.000	0.000	0.000	0.000
37	B	237	ASP	-1	-0.834	-0.884	51.182	-0.052	-0.052	0.000	0.000	0.000	0.000
38	B	238	THR	0	0.000	-0.013	53.236	0.001	0.001	0.000	0.000	0.000	0.000
39	B	239	ASP	-1	-0.872	-0.921	56.472	-0.043	-0.043	0.000	0.000	0.000	0.000
40	B	240	SER	0	-0.013	-0.045	52.282	0.001	0.001	0.000	0.000	0.000	0.000
41	B	241	GLN	0	-0.063	-0.039	51.388	0.001	0.001	0.000	0.000	0.000	0.000
42	B	242	ARG	1	0.799	0.890	55.306	0.043	0.043	0.000	0.000	0.000	0.000
43	B	243	LEU	0	-0.049	-0.033	56.433	0.002	0.002	0.000	0.000	0.000	0.000
44	B	244	ALA	0	-0.010	0.027	53.312	0.000	0.000	0.000	0.000	0.000	0.000
45	B	245	TYR	0	-0.090	-0.037	54.933	0.000	0.000	0.000	0.000	0.000	0.000
46	B	246	VAL	0	0.012	0.007	54.920	0.000	0.000	0.000	0.000	0.000	0.000
47	B	247	THR	0	-0.058	-0.064	58.003	0.001	0.001	0.000	0.000	0.000	0.000
48	B	248	CYS	0	0.028	-0.010	60.325	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	249	GLN	0	0.033	0.033	62.134	0.001	0.001	0.000	0.000	0.000	0.000
50	B	250	ASP	-1	-0.816	-0.876	56.749	-0.039	-0.039	0.000	0.000	0.000	0.000
51	B	251	LEU	0	-0.002	0.009	56.555	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	252	ARG	1	0.897	0.916	58.233	0.030	0.030	0.000	0.000	0.000	0.000
53	B	253	SER	0	-0.131	-0.061	56.083	0.000	0.000	0.000	0.000	0.000	0.000
54	B	254	ILE	0	-0.078	-0.046	52.630	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	255	ALA	0	0.009	0.004	55.517	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	256	ASP	-1	-0.837	-0.912	58.378	-0.030	-0.030	0.000	0.000	0.000	0.000
57	B	257	PRO	0	-0.018	-0.004	62.099	0.000	0.000	0.000	0.000	0.000	0.000
58	B	258	ALA	0	-0.088	-0.044	64.815	0.001	0.001	0.000	0.000	0.000	0.000
59	B	259	GLU	-1	-0.932	-0.964	63.550	-0.024	-0.024	0.000	0.000	0.000	0.000
60	B	260	GLN	0	-0.079	-0.041	57.382	0.000	0.000	0.000	0.000	0.000	0.000
61	B	261	MET	0	-0.015	0.014	62.000	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	262	VAL	0	0.004	0.000	59.093	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	263	MET	0	-0.038	-0.026	59.579	0.001	0.001	0.000	0.000	0.000	0.000
64	B	264	VAL	0	-0.019	0.001	58.092	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	265	ILE	0	0.006	-0.010	55.881	0.001	0.001	0.000	0.000	0.000	0.000
66	B	266	LYS	1	0.873	0.927	56.212	0.044	0.044	0.000	0.000	0.000	0.000
67	B	267	ALA	0	0.031	0.008	54.510	0.002	0.002	0.000	0.000	0.000	0.000
68	B	268	PRO	0	0.020	0.023	54.353	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	269	PRO	0	0.055	0.016	49.385	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	270	GLU	-1	-0.942	-0.968	47.308	-0.083	-0.083	0.000	0.000	0.000	0.000
71	B	271	THR	0	-0.141	-0.052	49.922	0.001	0.001	0.000	0.000	0.000	0.000
72	B	272	GLN	0	-0.018	-0.011	47.995	0.000	0.000	0.000	0.000	0.000	0.000
73	B	273	LEU	0	0.025	0.012	50.196	0.003	0.003	0.000	0.000	0.000	0.000
74	B	274	GLN	0	-0.049	-0.030	49.931	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	275	ALA	0	0.034	0.022	50.262	0.003	0.003	0.000	0.000	0.000	0.000
76	B	276	VAL	0	-0.065	-0.039	50.972	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	277	ASP	-1	-0.879	-0.944	51.812	-0.043	-0.043	0.000	0.000	0.000	0.000
78	B	278	SER	0	-0.056	-0.023	53.514	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	279	SER	0	-0.051	-0.020	55.755	0.000	0.000	0.000	0.000	0.000	0.000
80	B	280	GLU	-1	-0.921	-0.977	57.752	-0.035	-0.035	0.000	0.000	0.000	0.000
81	B	281	ASN	0	-0.056	-0.034	58.909	0.001	0.001	0.000	0.000	0.000	0.000
82	B	282	PHE	0	0.051	0.046	54.819	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	283	GLN	0	-0.007	0.001	56.092	0.003	0.003	0.000	0.000	0.000	0.000
84	B	284	ILE	0	0.028	0.005	54.006	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	285	SER	0	-0.046	-0.004	55.070	0.002	0.002	0.000	0.000	0.000	0.000
86	B	286	LEU	0	0.053	0.014	54.648	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	287	LYS	1	0.918	0.956	54.602	0.059	0.059	0.000	0.000	0.000	0.000
88	B	288	SER	0	0.052	0.011	54.577	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	289	LYS	1	0.929	0.950	52.598	0.068	0.068	0.000	0.000	0.000	0.000
90	B	290	GLN	0	-0.031	-0.009	54.850	0.002	0.002	0.000	0.000	0.000	0.000
91	B	291	GLY	0	0.088	0.054	57.180	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	292	PRO	0	-0.032	-0.012	59.587	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	293	ILE	0	-0.011	-0.011	57.531	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	294	ASP	-1	-0.853	-0.917	60.021	-0.042	-0.042	0.000	0.000	0.000	0.000
95	B	295	VAL	0	0.018	-0.007	60.156	-0.002	-0.002	0.000	0.000	0.000	0.000
96	B	296	PHE	0	-0.068	-0.014	61.677	0.001	0.001	0.000	0.000	0.000	0.000
97	B	297	LEU	0	0.053	0.021	63.057	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	298	CYS	0	-0.023	-0.001	62.660	0.000	0.000	0.000	0.000	0.000	0.000
99	B	299	PRO	0	-0.048	-0.032	65.398	0.001	0.001	0.000	0.000	0.000	0.000
100	B	300	GLU	-1	-0.850	-0.918	66.105	-0.029	-0.029	0.000	0.000	0.000	0.000
101	B	301	GLU	-1	-0.945	-0.963	66.409	-0.029	-0.029	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:201:GLY)