FMO DATABASE

FMODB ID: V5NK1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-563180.097094
FMO2-HF: Nuclear repulsion	522023.080037
FMO2-HF: Total energy	-41157.017056
FMO2-MP2: Total energy	-41273.13793

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.
-12.133	-7.204	3.344	-4.131	-4.143	-0.028

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 : 0.041 / q_NPA : 0.026

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

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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	-0.001	0.012	3.501	-1.365	1.306	-0.003	-1.470	-1.199	0.005
4	B	204	GLU	-1	-0.841	-0.931	2.255	-13.249	-11.143	3.348	-2.618	-2.836	-0.033
5	B	205	GLY	0	-0.006	0.005	4.204	1.656	1.808	-0.001	-0.043	-0.108	0.000
6	B	206	LEU	0	0.046	0.009	5.822	0.959	0.959	0.000	0.000	0.000	0.000
7	B	207	THR	0	-0.026	-0.006	7.958	0.678	0.678	0.000	0.000	0.000	0.000
8	B	208	GLN	0	-0.044	-0.024	7.609	0.008	0.008	0.000	0.000	0.000	0.000
9	B	209	ASP	-1	-0.880	-0.934	9.834	-1.182	-1.182	0.000	0.000	0.000	0.000
10	B	210	LEU	0	-0.033	-0.033	11.973	0.229	0.229	0.000	0.000	0.000	0.000
11	B	211	ARG	1	0.893	0.952	13.040	0.941	0.941	0.000	0.000	0.000	0.000
12	B	212	GLN	0	-0.021	-0.003	12.636	-0.020	-0.020	0.000	0.000	0.000	0.000
13	B	213	LEU	0	0.004	-0.009	16.009	0.095	0.095	0.000	0.000	0.000	0.000
14	B	214	GLN	0	0.057	0.046	17.564	0.012	0.012	0.000	0.000	0.000	0.000
15	B	215	GLU	-1	-0.905	-0.951	18.851	-0.333	-0.333	0.000	0.000	0.000	0.000
16	B	216	SER	0	-0.020	-0.024	20.082	0.055	0.055	0.000	0.000	0.000	0.000
17	B	217	GLU	-1	-0.934	-0.958	21.947	-0.347	-0.347	0.000	0.000	0.000	0.000
18	B	218	GLN	0	-0.008	-0.001	22.731	0.002	0.002	0.000	0.000	0.000	0.000
19	B	219	GLN	0	-0.062	-0.037	23.572	0.036	0.036	0.000	0.000	0.000	0.000
20	B	220	LEU	0	-0.010	-0.003	25.991	0.029	0.029	0.000	0.000	0.000	0.000
21	B	221	ASP	-1	-0.851	-0.932	27.815	-0.254	-0.254	0.000	0.000	0.000	0.000
22	B	222	HIS	0	-0.044	-0.016	29.400	0.020	0.020	0.000	0.000	0.000	0.000
23	B	223	LEU	0	-0.012	-0.012	30.254	0.020	0.020	0.000	0.000	0.000	0.000
24	B	224	MET	0	0.011	0.017	30.589	0.020	0.020	0.000	0.000	0.000	0.000
25	B	225	ASN	0	-0.029	-0.009	33.684	0.024	0.024	0.000	0.000	0.000	0.000
26	B	226	ILE	0	0.021	0.024	34.644	0.013	0.013	0.000	0.000	0.000	0.000
27	B	227	CYS	0	-0.040	-0.028	36.660	0.014	0.014	0.000	0.000	0.000	0.000
28	B	228	THR	0	-0.010	-0.017	37.282	0.010	0.010	0.000	0.000	0.000	0.000
29	B	229	THR	0	-0.034	-0.031	39.325	0.008	0.008	0.000	0.000	0.000	0.000
30	B	230	GLN	0	-0.030	-0.012	41.415	0.011	0.011	0.000	0.000	0.000	0.000
31	B	231	LEU	0	0.009	0.003	41.347	0.006	0.006	0.000	0.000	0.000	0.000
32	B	232	ARG	1	0.947	0.975	40.756	0.130	0.130	0.000	0.000	0.000	0.000
33	B	233	LEU	0	0.026	0.009	45.223	0.005	0.005	0.000	0.000	0.000	0.000
34	B	234	LEU	0	0.026	0.013	46.813	0.004	0.004	0.000	0.000	0.000	0.000
35	B	235	SER	0	-0.103	-0.044	48.557	0.004	0.004	0.000	0.000	0.000	0.000
36	B	236	GLU	-1	-0.962	-0.982	48.819	-0.093	-0.093	0.000	0.000	0.000	0.000
37	B	237	ASP	-1	-0.867	-0.891	51.935	-0.071	-0.071	0.000	0.000	0.000	0.000
38	B	238	THR	0	0.001	-0.014	53.788	0.002	0.002	0.000	0.000	0.000	0.000
39	B	239	ASP	-1	-0.904	-0.960	57.322	-0.059	-0.059	0.000	0.000	0.000	0.000
40	B	240	SER	0	-0.003	-0.036	53.140	0.001	0.001	0.000	0.000	0.000	0.000
41	B	241	GLN	0	-0.053	-0.030	51.738	0.002	0.002	0.000	0.000	0.000	0.000
42	B	242	ARG	1	0.838	0.933	55.921	0.058	0.058	0.000	0.000	0.000	0.000
43	B	243	LEU	0	-0.062	-0.042	57.399	0.003	0.003	0.000	0.000	0.000	0.000
44	B	244	ALA	0	-0.013	0.022	53.900	0.000	0.000	0.000	0.000	0.000	0.000
45	B	245	TYR	0	-0.075	-0.033	55.692	0.001	0.001	0.000	0.000	0.000	0.000
46	B	246	VAL	0	0.007	0.010	55.445	0.000	0.000	0.000	0.000	0.000	0.000
47	B	247	THR	0	-0.051	-0.035	58.444	0.002	0.002	0.000	0.000	0.000	0.000
48	B	248	CYS	0	0.016	-0.017	60.864	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	249	GLN	0	0.013	0.005	62.678	0.002	0.002	0.000	0.000	0.000	0.000
50	B	250	ASP	-1	-0.826	-0.903	57.509	-0.057	-0.057	0.000	0.000	0.000	0.000
51	B	251	LEU	0	-0.016	-0.027	56.796	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	252	ARG	1	0.945	1.002	58.870	0.044	0.044	0.000	0.000	0.000	0.000
53	B	253	SER	0	-0.082	-0.026	57.165	0.000	0.000	0.000	0.000	0.000	0.000
54	B	254	ILE	0	-0.058	-0.037	53.647	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	255	ALA	0	-0.019	-0.019	56.001	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	256	ASP	-1	-0.901	-0.942	58.880	-0.044	-0.044	0.000	0.000	0.000	0.000
57	B	257	PRO	0	-0.046	-0.015	62.551	0.001	0.001	0.000	0.000	0.000	0.000
58	B	258	ALA	0	-0.006	0.003	65.299	0.001	0.001	0.000	0.000	0.000	0.000
59	B	259	GLU	-1	-0.919	-0.968	64.569	-0.036	-0.036	0.000	0.000	0.000	0.000
60	B	260	GLN	0	-0.085	-0.030	58.565	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	261	MET	0	0.023	0.024	62.268	0.000	0.000	0.000	0.000	0.000	0.000
62	B	262	VAL	0	0.015	-0.002	59.246	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	263	MET	0	-0.045	-0.028	59.470	0.002	0.002	0.000	0.000	0.000	0.000
64	B	264	VAL	0	-0.007	0.004	58.294	-0.003	-0.003	0.000	0.000	0.000	0.000
65	B	265	ILE	0	0.006	-0.002	56.180	0.001	0.001	0.000	0.000	0.000	0.000
66	B	266	LYS	1	0.940	0.958	56.767	0.061	0.061	0.000	0.000	0.000	0.000
67	B	267	ALA	0	0.019	0.009	54.612	0.002	0.002	0.000	0.000	0.000	0.000
68	B	268	PRO	0	0.005	0.014	54.902	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	269	PRO	0	0.037	0.002	50.086	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	270	GLU	-1	-0.937	-0.974	48.061	-0.094	-0.094	0.000	0.000	0.000	0.000
71	B	271	THR	0	-0.152	-0.046	50.235	0.002	0.002	0.000	0.000	0.000	0.000
72	B	272	GLN	0	0.009	-0.008	47.668	0.000	0.000	0.000	0.000	0.000	0.000
73	B	273	LEU	0	0.042	0.023	50.339	0.004	0.004	0.000	0.000	0.000	0.000
74	B	274	GLN	0	-0.064	-0.035	50.065	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	275	ALA	0	0.029	0.017	50.467	0.003	0.003	0.000	0.000	0.000	0.000
76	B	276	VAL	0	-0.054	-0.036	51.080	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	277	ASP	-1	-0.892	-0.946	51.945	-0.053	-0.053	0.000	0.000	0.000	0.000
78	B	278	SER	0	-0.035	-0.018	53.741	0.000	0.000	0.000	0.000	0.000	0.000
79	B	279	SER	0	-0.030	-0.018	56.296	0.000	0.000	0.000	0.000	0.000	0.000
80	B	280	GLU	-1	-0.961	-0.987	57.844	-0.037	-0.037	0.000	0.000	0.000	0.000
81	B	281	ASN	0	-0.037	-0.018	59.214	0.001	0.001	0.000	0.000	0.000	0.000
82	B	282	PHE	0	0.059	0.050	54.735	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	283	GLN	0	-0.031	-0.017	56.340	0.002	0.002	0.000	0.000	0.000	0.000
84	B	284	ILE	0	0.055	0.026	54.632	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	285	SER	0	-0.076	-0.032	55.143	0.002	0.002	0.000	0.000	0.000	0.000
86	B	286	LEU	0	0.079	0.030	54.739	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	287	LYS	1	0.917	0.963	54.743	0.065	0.065	0.000	0.000	0.000	0.000
88	B	288	SER	0	0.034	0.012	54.577	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	289	LYS	1	0.924	0.945	53.644	0.072	0.072	0.000	0.000	0.000	0.000
90	B	290	GLN	0	-0.012	-0.006	55.477	0.002	0.002	0.000	0.000	0.000	0.000
91	B	291	GLY	0	0.066	0.048	57.518	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	292	PRO	0	-0.010	-0.002	59.919	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	293	ILE	0	-0.017	-0.015	58.159	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	294	ASP	-1	-0.930	-0.954	60.442	-0.050	-0.050	0.000	0.000	0.000	0.000
95	B	295	VAL	0	0.015	-0.010	60.784	-0.002	-0.002	0.000	0.000	0.000	0.000
96	B	296	PHE	0	-0.051	-0.009	62.112	0.002	0.002	0.000	0.000	0.000	0.000
97	B	297	LEU	0	0.045	0.016	63.403	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	298	CYS	0	-0.007	-0.004	63.037	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	299	PRO	0	-0.034	-0.018	65.796	0.001	0.001	0.000	0.000	0.000	0.000
100	B	300	GLU	-1	-0.951	-1.001	67.370	-0.042	-0.042	0.000	0.000	0.000	0.000
101	B	301	GLU	-1	-0.942	-0.943	67.523	-0.039	-0.039	0.000	0.000	0.000	0.000

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