FMO DATABASE

FMODB ID: M38RZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1195156.670716
FMO2-HF: Nuclear repulsion	1134566.295208
FMO2-HF: Total energy	-60590.375508
FMO2-MP2: Total energy	-60763.677147

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.
-3.43	0.682	0.543	-1.481	-3.175	-0.001

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	0.008	0.002	3.587	-2.636	-0.621	0.004	-0.876	-1.143	0.001
4	A	201	GLU	-1	-0.858	-0.930	2.755	-2.564	-1.405	0.430	-0.388	-1.202	-0.002
5	A	202	CYS	0	-0.058	-0.036	2.872	0.191	1.001	0.110	-0.213	-0.707	0.000
6	A	203	GLN	0	-0.004	0.010	5.255	0.316	0.444	-0.001	-0.004	-0.123	0.000
7	A	204	ASN	0	0.053	0.018	7.651	0.240	0.240	0.000	0.000	0.000	0.000
8	A	205	LEU	0	-0.009	-0.002	6.932	0.179	0.179	0.000	0.000	0.000	0.000
9	A	206	GLU	-1	-0.880	-0.943	9.314	-0.146	-0.146	0.000	0.000	0.000	0.000
10	A	207	VAL	0	0.023	0.013	11.199	0.088	0.088	0.000	0.000	0.000	0.000
11	A	208	GLU	-1	-0.823	-0.899	12.585	-0.233	-0.233	0.000	0.000	0.000	0.000
12	A	209	ARG	1	0.903	0.943	12.570	0.306	0.306	0.000	0.000	0.000	0.000
13	A	210	GLN	0	0.008	0.004	14.799	0.049	0.049	0.000	0.000	0.000	0.000
14	A	211	ARG	1	0.922	0.975	17.001	0.237	0.237	0.000	0.000	0.000	0.000
15	A	212	ARG	1	0.809	0.883	16.544	0.278	0.278	0.000	0.000	0.000	0.000
16	A	213	LEU	0	0.019	0.012	18.039	0.014	0.014	0.000	0.000	0.000	0.000
17	A	214	GLU	-1	-0.891	-0.935	20.784	-0.064	-0.064	0.000	0.000	0.000	0.000
18	A	215	ARG	1	0.890	0.938	20.146	0.178	0.178	0.000	0.000	0.000	0.000
19	A	216	ILE	0	-0.013	-0.003	21.651	0.008	0.008	0.000	0.000	0.000	0.000
20	A	217	LYS	1	1.008	1.016	25.038	0.067	0.067	0.000	0.000	0.000	0.000
21	A	218	GLN	0	0.004	0.002	26.977	0.012	0.012	0.000	0.000	0.000	0.000
22	A	219	LYS	1	0.944	0.957	26.434	0.119	0.119	0.000	0.000	0.000	0.000
23	A	220	GLN	0	0.043	0.024	27.996	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	221	SER	0	0.021	0.023	30.980	0.006	0.006	0.000	0.000	0.000	0.000
25	A	222	GLN	0	-0.014	-0.012	32.000	0.000	0.000	0.000	0.000	0.000	0.000
26	A	223	LEU	0	-0.028	-0.003	33.306	0.003	0.003	0.000	0.000	0.000	0.000
27	A	224	GLN	0	0.038	-0.003	34.398	0.000	0.000	0.000	0.000	0.000	0.000
28	A	225	GLU	-1	-0.820	-0.888	37.160	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	226	LEU	0	-0.011	-0.018	36.685	0.002	0.002	0.000	0.000	0.000	0.000
30	A	227	ILE	0	-0.038	-0.018	37.617	0.002	0.002	0.000	0.000	0.000	0.000
31	A	228	LEU	0	0.012	0.007	41.042	0.002	0.002	0.000	0.000	0.000	0.000
32	A	229	GLN	0	0.036	0.025	42.684	0.003	0.003	0.000	0.000	0.000	0.000
33	A	230	GLN	0	-0.018	0.003	42.125	0.002	0.002	0.000	0.000	0.000	0.000
34	A	231	ILE	0	-0.002	0.004	44.020	0.002	0.002	0.000	0.000	0.000	0.000
35	A	232	ALA	0	0.028	0.016	47.091	0.002	0.002	0.000	0.000	0.000	0.000
36	A	233	PHE	0	0.014	-0.009	47.126	0.001	0.001	0.000	0.000	0.000	0.000
37	A	234	LYS	1	0.856	0.928	46.527	0.045	0.045	0.000	0.000	0.000	0.000
38	A	235	ASN	0	0.011	-0.005	51.169	0.001	0.001	0.000	0.000	0.000	0.000
39	A	236	LEU	0	0.010	0.011	53.004	0.002	0.002	0.000	0.000	0.000	0.000
40	A	237	VAL	0	-0.023	-0.021	54.457	0.001	0.001	0.000	0.000	0.000	0.000
41	A	238	GLN	0	-0.037	-0.028	54.220	0.001	0.001	0.000	0.000	0.000	0.000
42	A	239	ARG	1	0.927	0.972	57.261	0.023	0.023	0.000	0.000	0.000	0.000
43	A	240	ASN	0	0.032	0.002	59.005	0.002	0.002	0.000	0.000	0.000	0.000
44	A	241	ARG	1	0.989	1.002	57.101	0.030	0.030	0.000	0.000	0.000	0.000
45	A	242	HIS	0	-0.009	-0.009	61.555	0.000	0.000	0.000	0.000	0.000	0.000
46	A	243	ALA	0	-0.035	-0.034	63.304	0.001	0.001	0.000	0.000	0.000	0.000
47	A	244	GLU	-1	-0.915	-0.951	64.710	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	245	GLN	0	-0.045	-0.002	64.397	0.001	0.001	0.000	0.000	0.000	0.000
49	A	246	GLN	0	-0.095	-0.064	67.352	0.000	0.000	0.000	0.000	0.000	0.000
50	A	247	ALA	0	-0.019	0.002	69.920	0.000	0.000	0.000	0.000	0.000	0.000
51	A	248	SER	0	0.037	0.026	71.512	0.000	0.000	0.000	0.000	0.000	0.000
52	A	249	ARG	1	0.897	0.943	72.076	0.016	0.016	0.000	0.000	0.000	0.000
53	A	250	PRO	0	0.064	0.034	67.466	0.000	0.000	0.000	0.000	0.000	0.000
54	A	251	PRO	0	0.012	0.023	65.306	0.001	0.001	0.000	0.000	0.000	0.000
55	A	252	PRO	0	0.008	-0.004	68.407	0.000	0.000	0.000	0.000	0.000	0.000
56	A	253	PRO	0	0.037	0.011	66.900	0.000	0.000	0.000	0.000	0.000	0.000
57	A	254	ASN	0	0.013	0.006	66.143	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	255	SER	0	-0.118	-0.049	66.927	0.000	0.000	0.000	0.000	0.000	0.000
59	A	256	VAL	0	0.006	-0.008	62.001	0.000	0.000	0.000	0.000	0.000	0.000
60	A	257	ILE	0	0.013	0.017	58.289	0.000	0.000	0.000	0.000	0.000	0.000
61	A	258	HIS	0	-0.026	-0.008	57.553	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	259	LEU	0	-0.035	0.011	51.286	0.000	0.000	0.000	0.000	0.000	0.000
63	A	260	PRO	0	-0.001	-0.009	50.448	0.000	0.000	0.000	0.000	0.000	0.000
64	A	261	PHE	0	-0.048	-0.039	52.226	0.001	0.001	0.000	0.000	0.000	0.000
65	A	262	ILE	0	0.023	0.017	49.207	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	263	ILE	0	-0.040	-0.018	52.876	0.001	0.001	0.000	0.000	0.000	0.000
67	A	264	VAL	0	0.042	0.014	53.573	0.000	0.000	0.000	0.000	0.000	0.000
68	A	265	ASN	0	-0.064	-0.022	55.751	0.000	0.000	0.000	0.000	0.000	0.000
69	A	266	THR	0	0.054	0.007	56.909	0.001	0.001	0.000	0.000	0.000	0.000
70	A	267	SER	0	-0.034	-0.011	59.450	0.000	0.000	0.000	0.000	0.000	0.000
71	A	268	LYS	1	0.970	0.964	62.443	0.007	0.007	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.898	0.944	65.616	0.003	0.003	0.000	0.000	0.000	0.000
73	A	270	THR	0	-0.033	-0.009	60.566	0.001	0.001	0.000	0.000	0.000	0.000
74	A	271	VAL	0	0.023	0.022	63.955	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	272	ILE	0	-0.022	-0.017	61.319	0.000	0.000	0.000	0.000	0.000	0.000
76	A	273	ASP	-1	-0.938	-0.959	62.569	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	274	CYS	0	-0.052	-0.028	62.149	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	275	SER	0	-0.012	-0.004	61.526	0.001	0.001	0.000	0.000	0.000	0.000
79	A	276	ILE	0	-0.023	-0.016	61.209	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	277	SER	0	-0.015	-0.003	60.181	0.001	0.001	0.000	0.000	0.000	0.000
81	A	278	ASN	0	0.033	-0.013	62.292	0.000	0.000	0.000	0.000	0.000	0.000
82	A	279	ASP	-1	-0.865	-0.920	60.059	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	280	LYS	1	0.884	0.944	61.515	0.013	0.013	0.000	0.000	0.000	0.000
84	A	281	PHE	0	-0.032	-0.009	56.329	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	282	GLU	-1	-0.958	-0.967	55.090	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	283	TYR	0	-0.032	-0.030	56.668	0.001	0.001	0.000	0.000	0.000	0.000
87	A	284	LEU	0	-0.004	0.006	56.111	0.000	0.000	0.000	0.000	0.000	0.000
88	A	285	PHE	0	-0.006	-0.015	57.371	0.000	0.000	0.000	0.000	0.000	0.000
89	A	286	ASN	0	-0.017	0.007	57.621	0.000	0.000	0.000	0.000	0.000	0.000
90	A	287	PHE	0	0.050	0.012	56.904	0.000	0.000	0.000	0.000	0.000	0.000
91	A	288	ASP	-1	-0.840	-0.907	59.306	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	289	ASN	0	-0.022	-0.024	59.267	0.001	0.001	0.000	0.000	0.000	0.000
93	A	290	THR	0	0.003	0.003	54.133	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.033	-0.002	51.813	0.000	0.000	0.000	0.000	0.000	0.000
95	A	292	GLU	-1	-0.897	-0.950	52.321	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	293	ILE	0	-0.010	-0.011	49.727	0.000	0.000	0.000	0.000	0.000	0.000
97	A	294	HIS	0	-0.057	-0.020	49.594	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.803	-0.912	46.053	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	296	ASP	-1	-0.784	-0.887	49.222	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	297	ILE	0	-0.018	-0.021	44.388	0.000	0.000	0.000	0.000	0.000	0.000
101	A	298	GLU	-1	-0.859	-0.922	45.868	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	299	VAL	0	0.001	0.002	48.443	0.001	0.001	0.000	0.000	0.000	0.000
103	A	300	LEU	0	-0.019	-0.033	50.309	0.001	0.001	0.000	0.000	0.000	0.000
104	A	301	LYS	1	0.852	0.919	42.756	0.034	0.034	0.000	0.000	0.000	0.000
105	A	302	ARG	1	0.875	0.944	47.992	0.020	0.020	0.000	0.000	0.000	0.000
106	A	303	MET	0	-0.094	-0.037	51.949	0.001	0.001	0.000	0.000	0.000	0.000
107	A	304	GLY	0	0.041	0.032	51.728	0.000	0.000	0.000	0.000	0.000	0.000
108	A	305	MET	0	-0.067	-0.027	51.337	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	306	ALA	0	0.000	0.002	46.200	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	307	CYS	0	-0.053	-0.020	47.282	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	308	GLY	0	0.122	0.068	48.187	0.000	0.000	0.000	0.000	0.000	0.000
112	A	309	LEU	0	-0.027	-0.026	42.205	0.000	0.000	0.000	0.000	0.000	0.000
113	A	310	GLU	-1	-0.921	-0.976	42.677	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	311	SER	0	-0.057	-0.013	41.985	0.000	0.000	0.000	0.000	0.000	0.000
115	A	312	GLY	0	0.033	0.024	42.839	0.001	0.001	0.000	0.000	0.000	0.000
116	A	313	SER	0	-0.076	-0.043	43.545	0.001	0.001	0.000	0.000	0.000	0.000
117	A	314	CYS	0	-0.076	-0.031	46.542	0.000	0.000	0.000	0.000	0.000	0.000
118	A	315	SER	0	0.048	0.031	48.503	0.000	0.000	0.000	0.000	0.000	0.000
119	A	316	ALA	0	0.017	-0.007	50.343	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	317	GLU	-1	-0.935	-0.986	51.215	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	318	ASP	-1	-0.814	-0.890	50.078	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	319	LEU	0	-0.002	-0.006	44.359	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	320	LYS	1	0.896	0.945	47.845	0.028	0.028	0.000	0.000	0.000	0.000
124	A	321	MET	0	0.003	0.009	50.099	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	322	ALA	0	0.064	0.016	45.917	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	323	ARG	1	0.863	0.899	42.654	0.041	0.041	0.000	0.000	0.000	0.000
127	A	324	SER	0	-0.076	-0.009	46.473	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	325	LEU	0	-0.040	-0.014	48.256	0.000	0.000	0.000	0.000	0.000	0.000
129	A	326	VAL	0	-0.027	-0.014	42.570	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	327	PRO	0	0.002	0.012	42.008	0.000	0.000	0.000	0.000	0.000	0.000
131	A	328	LYS	1	1.061	1.019	42.199	0.056	0.056	0.000	0.000	0.000	0.000
132	A	329	ALA	0	-0.051	-0.030	37.779	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	330	LEU	0	-0.017	-0.023	37.241	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	331	GLU	-1	-0.843	-0.922	39.218	-0.048	-0.048	0.000	0.000	0.000	0.000
135	A	332	PRO	0	-0.053	-0.029	36.021	0.002	0.002	0.000	0.000	0.000	0.000
136	A	333	TYR	0	0.089	0.035	31.841	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	334	VAL	0	0.033	0.017	36.625	0.002	0.002	0.000	0.000	0.000	0.000
138	A	335	THR	0	-0.035	-0.005	38.883	0.004	0.004	0.000	0.000	0.000	0.000
139	A	336	GLU	-1	-0.886	-0.943	33.538	-0.063	-0.063	0.000	0.000	0.000	0.000
140	A	337	MET	0	-0.082	-0.041	36.906	0.001	0.001	0.000	0.000	0.000	0.000
141	A	338	ALA	0	-0.017	-0.001	38.664	0.003	0.003	0.000	0.000	0.000	0.000
142	A	339	GLN	0	-0.046	-0.012	37.964	0.001	0.001	0.000	0.000	0.000	0.000
143	A	340	GLY	0	0.031	0.028	37.624	0.002	0.002	0.000	0.000	0.000	0.000
144	A	341	THR	0	-0.069	-0.029	33.634	0.001	0.001	0.000	0.000	0.000	0.000
145	A	342	VAL	0	0.025	0.004	32.978	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	343	GLY	0	-0.033	-0.005	29.561	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	344	GLY	0	-0.009	-0.008	26.726	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	345	VAL	0	-0.095	-0.056	22.992	-0.006	-0.006	0.000	0.000	0.000	0.000
149	A	346	PHE	0	0.045	0.039	22.922	-0.018	-0.018	0.000	0.000	0.000	0.000

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