FMO DATABASE

FMODB ID: Z62QN

Calculation Name: 2AZE-C-Xray372

Preferred Name: Transcription factor E2F1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2AZE

Chain ID: C

ChEMBL ID: CHEMBL4382

UniProt ID: Q01094

Base Structure: X-ray

Registration Date: 2023-06-21

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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-152252.362107
FMO2-HF: Nuclear repulsion	135022.170414
FMO2-HF: Total energy	-17230.191692
FMO2-MP2: Total energy	-17279.411314

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(C:829:SER)

Summations of interaction energy for fragment #1(C:829:SER)

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.
-1.384	-0.059	2.448	-1.658	-2.114	-0.003

Interaction energy analysis for fragmet #1(C:829:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.005

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	C	831	ILE	0	-0.005	0.007	3.820	0.255	1.972	-0.023	-0.821	-0.872	0.000
4	C	832	LEU	0	0.009	0.010	6.727	-0.444	-0.444	0.000	0.000	0.000	0.000
5	C	833	VAL	0	-0.027	-0.027	10.206	0.101	0.101	0.000	0.000	0.000	0.000
6	C	834	SER	0	0.051	0.027	13.522	-0.056	-0.056	0.000	0.000	0.000	0.000
7	C	835	ILE	0	-0.017	-0.005	16.690	0.016	0.016	0.000	0.000	0.000	0.000
8	C	836	GLY	0	0.017	-0.003	19.370	-0.016	-0.016	0.000	0.000	0.000	0.000
9	C	837	GLU	-1	-0.933	-0.945	18.583	0.134	0.134	0.000	0.000	0.000	0.000
10	C	838	SER	0	-0.015	0.000	20.463	0.009	0.009	0.000	0.000	0.000	0.000
11	C	839	PHE	0	0.037	0.025	21.066	0.001	0.001	0.000	0.000	0.000	0.000
12	C	840	GLY	0	0.044	0.028	17.105	0.007	0.007	0.000	0.000	0.000	0.000
13	C	841	THR	0	0.011	-0.017	15.567	0.049	0.049	0.000	0.000	0.000	0.000
14	C	842	SER	0	0.064	0.028	14.943	0.025	0.025	0.000	0.000	0.000	0.000
15	C	843	GLU	-1	-0.883	-0.938	15.395	0.244	0.244	0.000	0.000	0.000	0.000
16	C	844	LYS	1	0.918	0.944	11.251	-0.338	-0.338	0.000	0.000	0.000	0.000
17	C	845	PHE	0	0.007	0.004	10.552	0.073	0.073	0.000	0.000	0.000	0.000
18	C	846	GLN	0	0.029	0.018	11.660	0.012	0.012	0.000	0.000	0.000	0.000
19	C	847	LYS	1	0.939	0.964	8.745	-0.567	-0.567	0.000	0.000	0.000	0.000
20	C	848	ILE	0	-0.008	0.002	7.178	0.156	0.156	0.000	0.000	0.000	0.000
21	C	849	ASN	0	-0.011	-0.028	7.968	-0.024	-0.024	0.000	0.000	0.000	0.000
22	C	850	GLN	0	0.009	0.008	8.615	-0.011	-0.011	0.000	0.000	0.000	0.000
23	C	851	MET	0	-0.073	-0.040	2.905	-0.455	-0.847	2.471	-0.837	-1.242	-0.003
24	C	852	VAL	0	-0.057	-0.015	5.927	0.281	0.281	0.000	0.000	0.000	0.000
25	C	853	CYS	0	-0.046	0.001	7.805	-0.063	-0.063	0.000	0.000	0.000	0.000
26	C	854	ASN	0	0.025	0.009	9.649	-0.016	-0.016	0.000	0.000	0.000	0.000
27	C	855	SER	0	0.000	-0.013	9.476	0.193	0.193	0.000	0.000	0.000	0.000
28	C	856	ASP	-1	-0.867	-0.912	11.606	0.251	0.251	0.000	0.000	0.000	0.000
29	C	857	ARG	1	0.843	0.918	7.141	-1.132	-1.132	0.000	0.000	0.000	0.000
30	C	858	VAL	0	-0.021	-0.012	9.633	0.086	0.086	0.000	0.000	0.000	0.000
31	C	859	LEU	0	0.003	0.006	11.833	-0.054	-0.054	0.000	0.000	0.000	0.000
32	C	860	LYS	1	0.983	0.981	14.369	-0.141	-0.141	0.000	0.000	0.000	0.000
33	C	861	ARG	1	0.918	0.961	16.174	0.004	0.004	0.000	0.000	0.000	0.000
34	C	862	SER	0	0.020	0.014	18.626	0.004	0.004	0.000	0.000	0.000	0.000
35	C	863	ALA	0	0.006	0.002	22.073	-0.009	-0.009	0.000	0.000	0.000	0.000
36	C	864	GLU	-1	-0.859	-0.915	24.943	0.006	0.006	0.000	0.000	0.000	0.000
37	C	865	GLY	0	0.008	0.003	24.522	0.002	0.002	0.000	0.000	0.000	0.000
38	C	866	SER	0	-0.083	-0.055	21.950	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	867	ASN	0	0.008	0.000	23.910	0.008	0.008	0.000	0.000	0.000	0.000
40	C	868	PRO	0	-0.020	-0.001	24.909	-0.007	-0.007	0.000	0.000	0.000	0.000
41	C	869	PRO	0	0.016	0.007	23.759	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	870	LYS	1	0.957	0.971	26.283	0.042	0.042	0.000	0.000	0.000	0.000
43	C	871	PRO	0	0.029	0.010	29.464	-0.002	-0.002	0.000	0.000	0.000	0.000
44	C	872	LEU	0	-0.003	0.015	29.218	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:829:SER)