FMO DATABASE

FMODB ID: 17Y6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-563914.987178
FMO2-HF: Nuclear repulsion	522757.225949
FMO2-HF: Total energy	-41157.761229
FMO2-MP2: Total energy	-41273.848055

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.
-13.747	-13.295	13.271	-7.725	-5.997	-0.055

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 : 0.026 / q_NPA : 0.007

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	0.003	0.014	3.508	-1.309	1.326	-0.002	-1.453	-1.180	0.005
4	B	204	GLU	-1	-0.802	-0.894	1.863	-15.212	-17.553	13.274	-6.229	-4.704	-0.060
5	B	205	GLY	0	0.007	0.012	4.138	1.519	1.677	-0.001	-0.043	-0.113	0.000
6	B	206	LEU	0	0.045	0.007	5.766	0.914	0.914	0.000	0.000	0.000	0.000
7	B	207	THR	0	-0.048	-0.031	7.862	0.642	0.642	0.000	0.000	0.000	0.000
8	B	208	GLN	0	-0.062	-0.034	7.958	0.189	0.189	0.000	0.000	0.000	0.000
9	B	209	ASP	-1	-0.867	-0.933	9.759	-0.913	-0.913	0.000	0.000	0.000	0.000
10	B	210	LEU	0	-0.029	-0.026	11.911	0.204	0.204	0.000	0.000	0.000	0.000
11	B	211	ARG	1	0.861	0.927	12.901	0.893	0.893	0.000	0.000	0.000	0.000
12	B	212	GLN	0	-0.003	0.007	12.387	0.062	0.062	0.000	0.000	0.000	0.000
13	B	213	LEU	0	0.016	0.010	15.765	0.090	0.090	0.000	0.000	0.000	0.000
14	B	214	GLN	0	0.040	0.045	17.484	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	215	GLU	-1	-0.881	-0.935	18.775	-0.310	-0.310	0.000	0.000	0.000	0.000
16	B	216	SER	0	-0.032	-0.042	19.550	0.053	0.053	0.000	0.000	0.000	0.000
17	B	217	GLU	-1	-0.935	-0.959	21.876	-0.326	-0.326	0.000	0.000	0.000	0.000
18	B	218	GLN	0	0.010	0.017	22.543	0.010	0.010	0.000	0.000	0.000	0.000
19	B	219	GLN	0	-0.090	-0.057	23.264	0.041	0.041	0.000	0.000	0.000	0.000
20	B	220	LEU	0	-0.005	0.001	26.193	0.025	0.025	0.000	0.000	0.000	0.000
21	B	221	ASP	-1	-0.838	-0.930	27.743	-0.225	-0.225	0.000	0.000	0.000	0.000
22	B	222	HIS	0	-0.058	-0.020	29.328	0.018	0.018	0.000	0.000	0.000	0.000
23	B	223	LEU	0	-0.009	-0.010	29.833	0.018	0.018	0.000	0.000	0.000	0.000
24	B	224	MET	0	0.006	0.018	30.866	0.019	0.019	0.000	0.000	0.000	0.000
25	B	225	ASN	0	0.011	0.003	33.611	0.019	0.019	0.000	0.000	0.000	0.000
26	B	226	ILE	0	-0.007	0.004	34.514	0.012	0.012	0.000	0.000	0.000	0.000
27	B	227	CYS	0	-0.018	-0.019	36.596	0.011	0.011	0.000	0.000	0.000	0.000
28	B	228	THR	0	-0.024	-0.024	37.576	0.009	0.009	0.000	0.000	0.000	0.000
29	B	229	THR	0	-0.039	-0.022	39.341	0.008	0.008	0.000	0.000	0.000	0.000
30	B	230	GLN	0	-0.023	-0.009	41.318	0.010	0.010	0.000	0.000	0.000	0.000
31	B	231	LEU	0	-0.011	-0.004	41.206	0.005	0.005	0.000	0.000	0.000	0.000
32	B	232	ARG	1	0.942	0.981	40.627	0.120	0.120	0.000	0.000	0.000	0.000
33	B	233	LEU	0	0.036	0.022	45.156	0.004	0.004	0.000	0.000	0.000	0.000
34	B	234	LEU	0	-0.003	0.005	47.331	0.004	0.004	0.000	0.000	0.000	0.000
35	B	235	SER	0	-0.085	-0.041	48.509	0.003	0.003	0.000	0.000	0.000	0.000
36	B	236	GLU	-1	-0.959	-0.990	48.466	-0.087	-0.087	0.000	0.000	0.000	0.000
37	B	237	ASP	-1	-0.841	-0.888	51.860	-0.064	-0.064	0.000	0.000	0.000	0.000
38	B	238	THR	0	-0.014	-0.020	53.719	0.002	0.002	0.000	0.000	0.000	0.000
39	B	239	ASP	-1	-0.858	-0.917	57.243	-0.053	-0.053	0.000	0.000	0.000	0.000
40	B	240	SER	0	-0.005	-0.030	53.089	0.001	0.001	0.000	0.000	0.000	0.000
41	B	241	GLN	0	-0.062	-0.041	51.771	0.001	0.001	0.000	0.000	0.000	0.000
42	B	242	ARG	1	0.812	0.902	55.858	0.052	0.052	0.000	0.000	0.000	0.000
43	B	243	LEU	0	-0.057	-0.041	57.241	0.002	0.002	0.000	0.000	0.000	0.000
44	B	244	ALA	0	-0.023	0.017	53.798	0.000	0.000	0.000	0.000	0.000	0.000
45	B	245	TYR	0	-0.064	-0.025	55.637	0.000	0.000	0.000	0.000	0.000	0.000
46	B	246	VAL	0	-0.007	0.002	55.403	0.000	0.000	0.000	0.000	0.000	0.000
47	B	247	THR	0	-0.066	-0.067	58.399	0.002	0.002	0.000	0.000	0.000	0.000
48	B	248	CYS	0	0.021	-0.014	60.823	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	249	GLN	0	0.026	0.018	62.643	0.001	0.001	0.000	0.000	0.000	0.000
50	B	250	ASP	-1	-0.813	-0.874	57.446	-0.050	-0.050	0.000	0.000	0.000	0.000
51	B	251	LEU	0	-0.014	-0.020	56.800	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	252	ARG	1	0.892	0.941	58.835	0.038	0.038	0.000	0.000	0.000	0.000
53	B	253	SER	0	-0.095	-0.035	56.991	0.000	0.000	0.000	0.000	0.000	0.000
54	B	254	ILE	0	-0.053	-0.035	53.383	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	255	ALA	0	-0.023	-0.013	55.974	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	256	ASP	-1	-0.892	-0.934	58.853	-0.039	-0.039	0.000	0.000	0.000	0.000
57	B	257	PRO	0	-0.028	-0.006	62.523	0.001	0.001	0.000	0.000	0.000	0.000
58	B	258	ALA	0	-0.058	-0.029	65.267	0.001	0.001	0.000	0.000	0.000	0.000
59	B	259	GLU	-1	-0.915	-0.964	64.404	-0.030	-0.030	0.000	0.000	0.000	0.000
60	B	260	GLN	0	-0.079	-0.029	58.113	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	261	MET	0	0.018	0.026	62.226	0.000	0.000	0.000	0.000	0.000	0.000
62	B	262	VAL	0	0.015	0.002	59.266	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	263	MET	0	-0.041	-0.029	59.665	0.001	0.001	0.000	0.000	0.000	0.000
64	B	264	VAL	0	-0.012	0.003	58.332	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	265	ILE	0	-0.001	-0.004	56.044	0.001	0.001	0.000	0.000	0.000	0.000
66	B	266	LYS	1	0.871	0.915	56.707	0.051	0.051	0.000	0.000	0.000	0.000
67	B	267	ALA	0	0.021	0.006	54.598	0.002	0.002	0.000	0.000	0.000	0.000
68	B	268	PRO	0	0.019	0.019	54.831	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	269	PRO	0	0.048	0.008	49.978	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	270	GLU	-1	-0.935	-0.968	47.616	-0.089	-0.089	0.000	0.000	0.000	0.000
71	B	271	THR	0	-0.155	-0.050	50.155	0.001	0.001	0.000	0.000	0.000	0.000
72	B	272	GLN	0	-0.010	-0.010	48.029	0.000	0.000	0.000	0.000	0.000	0.000
73	B	273	LEU	0	0.038	0.021	50.340	0.004	0.004	0.000	0.000	0.000	0.000
74	B	274	GLN	0	-0.063	-0.035	50.065	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	275	ALA	0	0.031	0.020	50.443	0.003	0.003	0.000	0.000	0.000	0.000
76	B	276	VAL	0	-0.061	-0.045	51.080	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	277	ASP	-1	-0.872	-0.935	51.911	-0.047	-0.047	0.000	0.000	0.000	0.000
78	B	278	SER	0	-0.071	-0.028	53.741	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	279	SER	0	-0.021	-0.003	56.296	0.000	0.000	0.000	0.000	0.000	0.000
80	B	280	GLU	-1	-0.937	-0.988	57.844	-0.036	-0.036	0.000	0.000	0.000	0.000
81	B	281	ASN	0	-0.050	-0.027	59.242	0.001	0.001	0.000	0.000	0.000	0.000
82	B	282	PHE	0	0.040	0.035	55.301	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	283	GLN	0	-0.006	-0.003	56.337	0.003	0.003	0.000	0.000	0.000	0.000
84	B	284	ILE	0	0.047	0.022	54.563	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	285	SER	0	-0.061	-0.024	55.147	0.002	0.002	0.000	0.000	0.000	0.000
86	B	286	LEU	0	0.062	0.029	54.739	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	287	LYS	1	0.923	0.959	54.745	0.060	0.060	0.000	0.000	0.000	0.000
88	B	288	SER	0	0.039	0.008	54.577	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	289	LYS	1	0.920	0.945	53.095	0.070	0.070	0.000	0.000	0.000	0.000
90	B	290	GLN	0	-0.018	-0.008	55.318	0.002	0.002	0.000	0.000	0.000	0.000
91	B	291	GLY	0	0.079	0.051	57.435	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	292	PRO	0	-0.021	-0.006	59.841	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	293	ILE	0	-0.007	-0.009	57.889	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	294	ASP	-1	-0.868	-0.915	60.364	-0.047	-0.047	0.000	0.000	0.000	0.000
95	B	295	VAL	0	0.021	-0.008	60.680	-0.002	-0.002	0.000	0.000	0.000	0.000
96	B	296	PHE	0	-0.057	-0.012	61.788	0.002	0.002	0.000	0.000	0.000	0.000
97	B	297	LEU	0	0.056	0.019	63.352	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	298	CYS	0	-0.012	0.000	63.020	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	299	PRO	0	-0.041	-0.022	65.753	0.001	0.001	0.000	0.000	0.000	0.000
100	B	300	GLU	-1	-0.847	-0.929	66.483	-0.037	-0.037	0.000	0.000	0.000	0.000
101	B	301	GLU	-1	-0.972	-0.967	67.269	-0.034	-0.034	0.000	0.000	0.000	0.000

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