FMO DATABASE

FMODB ID: 7GNYK

Calculation Name: 2AZE-A-Xray372

Preferred Name: Transcription factor E2F1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2AZE

Chain ID: A

ChEMBL ID: CHEMBL4382

UniProt ID: Q01094

Base Structure: X-ray

Registration Date: 2023-03-13

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1195924.856129
FMO2-HF: Nuclear repulsion	1135333.583479
FMO2-HF: Total energy	-60591.27265
FMO2-MP2: Total energy	-60764.558586

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:198:PHE)

Summations of interaction energy for fragment #1(A:198:PHE)

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.
-3.272	0.972	0.71	-1.547	-3.408	-0.002

Interaction energy analysis for fragmet #1(A:198:PHE)

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 : 0.009

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	200	GLN	0	0.001	-0.001	3.598	-2.661	-0.619	0.005	-0.890	-1.157	0.001
4	A	201	GLU	-1	-0.815	-0.901	2.702	-2.118	-1.034	0.350	-0.348	-1.086	-0.002
5	A	202	CYS	0	-0.075	-0.043	2.622	-0.017	0.983	0.356	-0.304	-1.053	-0.001
6	A	203	GLN	0	0.011	0.018	5.360	0.324	0.442	-0.001	-0.005	-0.112	0.000
7	A	204	ASN	0	-0.007	-0.021	7.457	0.294	0.294	0.000	0.000	0.000	0.000
8	A	205	LEU	0	-0.003	-0.002	6.259	0.160	0.160	0.000	0.000	0.000	0.000
9	A	206	GLU	-1	-0.796	-0.881	9.412	-0.139	-0.139	0.000	0.000	0.000	0.000
10	A	207	VAL	0	-0.003	0.000	11.297	0.083	0.083	0.000	0.000	0.000	0.000
11	A	208	GLU	-1	-0.733	-0.841	12.712	-0.185	-0.185	0.000	0.000	0.000	0.000
12	A	209	ARG	1	0.829	0.904	12.949	0.253	0.253	0.000	0.000	0.000	0.000
13	A	210	GLN	0	0.038	0.001	14.886	0.036	0.036	0.000	0.000	0.000	0.000
14	A	211	ARG	1	0.881	0.943	17.096	0.200	0.200	0.000	0.000	0.000	0.000
15	A	212	ARG	1	0.794	0.874	16.718	0.254	0.254	0.000	0.000	0.000	0.000
16	A	213	LEU	0	0.034	0.020	17.767	0.012	0.012	0.000	0.000	0.000	0.000
17	A	214	GLU	-1	-0.790	-0.877	20.869	-0.051	-0.051	0.000	0.000	0.000	0.000
18	A	215	ARG	1	0.838	0.920	18.905	0.171	0.171	0.000	0.000	0.000	0.000
19	A	216	ILE	0	-0.007	-0.004	21.605	0.008	0.008	0.000	0.000	0.000	0.000
20	A	217	LYS	1	0.904	0.950	25.121	0.062	0.062	0.000	0.000	0.000	0.000
21	A	218	GLN	0	0.005	0.002	27.062	0.009	0.009	0.000	0.000	0.000	0.000
22	A	219	LYS	1	0.946	0.963	27.185	0.103	0.103	0.000	0.000	0.000	0.000
23	A	220	GLN	0	0.008	0.011	27.615	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	221	SER	0	0.028	0.019	31.057	0.005	0.005	0.000	0.000	0.000	0.000
25	A	222	GLN	0	-0.004	-0.007	31.525	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	223	LEU	0	-0.036	-0.005	33.112	0.002	0.002	0.000	0.000	0.000	0.000
27	A	224	GLN	0	0.033	-0.004	34.686	0.000	0.000	0.000	0.000	0.000	0.000
28	A	225	GLU	-1	-0.809	-0.873	37.236	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	226	LEU	0	0.007	-0.004	36.664	0.002	0.002	0.000	0.000	0.000	0.000
30	A	227	ILE	0	-0.046	-0.026	37.647	0.001	0.001	0.000	0.000	0.000	0.000
31	A	228	LEU	0	0.010	0.009	41.113	0.002	0.002	0.000	0.000	0.000	0.000
32	A	229	GLN	0	0.033	0.022	41.916	0.000	0.000	0.000	0.000	0.000	0.000
33	A	230	GLN	0	0.001	0.017	42.201	0.002	0.002	0.000	0.000	0.000	0.000
34	A	231	ILE	0	0.000	0.002	44.106	0.001	0.001	0.000	0.000	0.000	0.000
35	A	232	ALA	0	0.034	0.022	47.166	0.002	0.002	0.000	0.000	0.000	0.000
36	A	233	PHE	0	0.016	-0.010	46.591	0.001	0.001	0.000	0.000	0.000	0.000
37	A	234	LYS	1	0.791	0.884	46.349	0.041	0.041	0.000	0.000	0.000	0.000
38	A	235	ASN	0	0.022	0.008	51.239	0.001	0.001	0.000	0.000	0.000	0.000
39	A	236	LEU	0	0.021	0.015	53.078	0.001	0.001	0.000	0.000	0.000	0.000
40	A	237	VAL	0	-0.023	-0.019	54.321	0.001	0.001	0.000	0.000	0.000	0.000
41	A	238	GLN	0	-0.047	-0.042	54.351	0.000	0.000	0.000	0.000	0.000	0.000
42	A	239	ARG	1	0.917	0.962	57.331	0.020	0.020	0.000	0.000	0.000	0.000
43	A	240	ASN	0	0.039	0.010	59.174	0.001	0.001	0.000	0.000	0.000	0.000
44	A	241	ARG	1	1.002	1.007	57.062	0.027	0.027	0.000	0.000	0.000	0.000
45	A	242	HIS	0	0.012	0.011	61.622	0.000	0.000	0.000	0.000	0.000	0.000
46	A	243	ALA	0	-0.032	-0.031	63.375	0.001	0.001	0.000	0.000	0.000	0.000
47	A	244	GLU	-1	-0.923	-0.952	64.492	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	245	GLN	0	-0.121	-0.051	65.189	0.000	0.000	0.000	0.000	0.000	0.000
49	A	246	GLN	0	-0.071	-0.050	67.472	0.000	0.000	0.000	0.000	0.000	0.000
50	A	247	ALA	0	-0.020	-0.001	69.990	0.000	0.000	0.000	0.000	0.000	0.000
51	A	248	SER	0	0.042	0.031	71.586	0.000	0.000	0.000	0.000	0.000	0.000
52	A	249	ARG	1	0.905	0.948	72.187	0.014	0.014	0.000	0.000	0.000	0.000
53	A	250	PRO	0	0.054	0.026	67.452	0.000	0.000	0.000	0.000	0.000	0.000
54	A	251	PRO	0	0.021	0.026	65.443	0.001	0.001	0.000	0.000	0.000	0.000
55	A	252	PRO	0	0.016	0.006	68.488	0.000	0.000	0.000	0.000	0.000	0.000
56	A	253	PRO	0	0.045	0.015	66.974	0.000	0.000	0.000	0.000	0.000	0.000
57	A	254	ASN	0	-0.006	-0.001	66.229	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	255	SER	0	-0.106	-0.050	67.016	0.000	0.000	0.000	0.000	0.000	0.000
59	A	256	VAL	0	0.004	-0.008	62.083	0.000	0.000	0.000	0.000	0.000	0.000
60	A	257	ILE	0	0.001	0.013	58.392	0.000	0.000	0.000	0.000	0.000	0.000
61	A	258	HIS	0	-0.022	-0.008	57.730	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	259	LEU	0	-0.019	0.021	51.657	0.000	0.000	0.000	0.000	0.000	0.000
63	A	260	PRO	0	-0.018	-0.018	50.542	0.000	0.000	0.000	0.000	0.000	0.000
64	A	261	PHE	0	-0.046	-0.045	52.327	0.001	0.001	0.000	0.000	0.000	0.000
65	A	262	ILE	0	0.008	0.003	49.223	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	263	ILE	0	-0.031	-0.011	52.972	0.001	0.001	0.000	0.000	0.000	0.000
67	A	264	VAL	0	0.033	0.009	53.671	0.000	0.000	0.000	0.000	0.000	0.000
68	A	265	ASN	0	-0.076	-0.043	55.824	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	266	THR	0	0.047	0.000	57.010	0.001	0.001	0.000	0.000	0.000	0.000
70	A	267	SER	0	-0.014	0.000	59.551	0.000	0.000	0.000	0.000	0.000	0.000
71	A	268	LYS	1	0.956	0.963	62.544	0.005	0.005	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.904	0.945	65.726	0.001	0.001	0.000	0.000	0.000	0.000
73	A	270	THR	0	-0.037	-0.017	60.651	0.000	0.000	0.000	0.000	0.000	0.000
74	A	271	VAL	0	0.022	0.025	64.059	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	272	ILE	0	-0.024	-0.023	61.156	0.000	0.000	0.000	0.000	0.000	0.000
76	A	273	ASP	-1	-0.872	-0.926	62.611	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	274	CYS	0	-0.068	-0.031	61.914	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	275	SER	0	-0.019	-0.007	61.624	0.001	0.001	0.000	0.000	0.000	0.000
79	A	276	ILE	0	-0.015	-0.017	61.211	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	277	SER	0	0.007	0.012	60.255	0.001	0.001	0.000	0.000	0.000	0.000
81	A	278	ASN	0	-0.001	-0.017	62.294	0.000	0.000	0.000	0.000	0.000	0.000
82	A	279	ASP	-1	-0.855	-0.921	60.552	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	280	LYS	1	0.878	0.941	61.517	0.011	0.011	0.000	0.000	0.000	0.000
84	A	281	PHE	0	-0.036	-0.018	56.504	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	282	GLU	-1	-0.954	-0.965	55.339	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	283	TYR	0	-0.024	-0.025	56.667	0.001	0.001	0.000	0.000	0.000	0.000
87	A	284	LEU	0	-0.012	0.005	56.013	0.000	0.000	0.000	0.000	0.000	0.000
88	A	285	PHE	0	-0.001	-0.013	57.288	0.000	0.000	0.000	0.000	0.000	0.000
89	A	286	ASN	0	-0.038	-0.005	57.626	0.000	0.000	0.000	0.000	0.000	0.000
90	A	287	PHE	0	0.026	0.001	56.783	0.000	0.000	0.000	0.000	0.000	0.000
91	A	288	ASP	-1	-0.851	-0.914	59.413	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	289	ASN	0	-0.029	-0.030	59.389	0.001	0.001	0.000	0.000	0.000	0.000
93	A	290	THR	0	0.016	0.009	53.973	0.000	0.000	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.025	0.010	52.169	0.000	0.000	0.000	0.000	0.000	0.000
95	A	292	GLU	-1	-0.847	-0.897	52.423	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	293	ILE	0	-0.019	-0.015	49.895	0.000	0.000	0.000	0.000	0.000	0.000
97	A	294	HIS	0	-0.044	-0.017	49.680	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.830	-0.918	46.212	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	296	ASP	-1	-0.797	-0.909	49.327	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	297	ILE	0	0.018	0.010	44.485	0.000	0.000	0.000	0.000	0.000	0.000
101	A	298	GLU	-1	-0.830	-0.903	46.379	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	299	VAL	0	-0.003	-0.002	48.532	0.001	0.001	0.000	0.000	0.000	0.000
103	A	300	LEU	0	-0.011	-0.024	50.415	0.000	0.000	0.000	0.000	0.000	0.000
104	A	301	LYS	1	0.841	0.898	42.811	0.029	0.029	0.000	0.000	0.000	0.000
105	A	302	ARG	1	0.828	0.905	48.442	0.016	0.016	0.000	0.000	0.000	0.000
106	A	303	MET	0	-0.100	-0.042	52.035	0.001	0.001	0.000	0.000	0.000	0.000
107	A	304	GLY	0	0.042	0.032	51.807	0.000	0.000	0.000	0.000	0.000	0.000
108	A	305	MET	0	-0.084	-0.035	51.378	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	306	ALA	0	-0.007	-0.004	46.289	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	307	CYS	0	-0.028	-0.012	47.355	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	308	GLY	0	0.122	0.073	48.261	0.000	0.000	0.000	0.000	0.000	0.000
112	A	309	LEU	0	-0.033	-0.027	41.959	0.000	0.000	0.000	0.000	0.000	0.000
113	A	310	GLU	-1	-0.913	-0.979	42.751	-0.027	-0.027	0.000	0.000	0.000	0.000
114	A	311	SER	0	-0.050	-0.015	42.065	0.000	0.000	0.000	0.000	0.000	0.000
115	A	312	GLY	0	0.022	0.019	42.910	0.001	0.001	0.000	0.000	0.000	0.000
116	A	313	SER	0	-0.067	-0.026	43.616	0.001	0.001	0.000	0.000	0.000	0.000
117	A	314	CYS	0	-0.085	-0.040	46.582	0.000	0.000	0.000	0.000	0.000	0.000
118	A	315	SER	0	0.013	-0.011	48.570	0.000	0.000	0.000	0.000	0.000	0.000
119	A	316	ALA	0	0.013	-0.015	50.404	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	317	GLU	-1	-0.920	-0.972	51.272	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	318	ASP	-1	-0.805	-0.864	50.133	-0.024	-0.024	0.000	0.000	0.000	0.000
122	A	319	LEU	0	0.003	0.002	44.402	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	320	LYS	1	0.909	0.952	47.903	0.026	0.026	0.000	0.000	0.000	0.000
124	A	321	MET	0	0.007	0.019	50.155	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	322	ALA	0	0.050	0.016	46.006	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	323	ARG	1	0.874	0.924	42.594	0.039	0.039	0.000	0.000	0.000	0.000
127	A	324	SER	0	-0.103	-0.035	46.529	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	325	LEU	0	-0.024	-0.005	48.332	0.000	0.000	0.000	0.000	0.000	0.000
129	A	326	VAL	0	0.005	0.011	42.439	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	327	PRO	0	0.009	0.014	41.890	0.000	0.000	0.000	0.000	0.000	0.000
131	A	328	LYS	1	1.056	1.005	42.127	0.053	0.053	0.000	0.000	0.000	0.000
132	A	329	ALA	0	-0.036	-0.020	37.884	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	330	LEU	0	-0.017	-0.022	37.663	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	331	GLU	-1	-0.845	-0.916	39.272	-0.043	-0.043	0.000	0.000	0.000	0.000
135	A	332	PRO	0	-0.031	-0.017	35.995	0.002	0.002	0.000	0.000	0.000	0.000
136	A	333	TYR	0	0.037	0.004	32.013	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	334	VAL	0	0.051	0.025	36.683	0.002	0.002	0.000	0.000	0.000	0.000
138	A	335	THR	0	-0.039	-0.021	39.077	0.004	0.004	0.000	0.000	0.000	0.000
139	A	336	GLU	-1	-0.853	-0.907	33.583	-0.056	-0.056	0.000	0.000	0.000	0.000
140	A	337	MET	0	-0.081	-0.041	36.965	0.001	0.001	0.000	0.000	0.000	0.000
141	A	338	ALA	0	-0.017	-0.001	38.732	0.003	0.003	0.000	0.000	0.000	0.000
142	A	339	GLN	0	-0.053	-0.020	37.189	0.003	0.003	0.000	0.000	0.000	0.000
143	A	340	GLY	0	0.028	0.027	37.693	0.002	0.002	0.000	0.000	0.000	0.000
144	A	341	THR	0	-0.084	-0.046	33.863	0.001	0.001	0.000	0.000	0.000	0.000
145	A	342	VAL	0	0.007	0.001	32.821	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	343	GLY	0	0.004	0.006	29.635	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	344	GLY	0	-0.022	-0.014	26.793	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	345	VAL	0	-0.070	-0.040	23.214	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	346	PHE	0	0.029	0.031	22.979	-0.023	-0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:198:PHE)