FMO DATABASE

FMODB ID: N3M3Q

Calculation Name: 2AZE-A-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1200175.397418
FMO2-HF: Nuclear repulsion	1139414.153671
FMO2-HF: Total energy	-60761.243747
FMO2-MP2: Total energy	-60935.089846

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:197:ACE )

Summations of interaction energy for fragment #1(A:197:ACE )

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.
1.677	2.649	-0.003	-0.449	-0.519	0

Interaction energy analysis for fragmet #1(A:197:ACE )

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 : -0.001

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].
3	A	199	ALA	0	0.017	0.006	3.796	1.032	2.004	-0.003	-0.449	-0.519
4	A	200	GLN	0	0.013	0.006	5.793	0.241	0.241	0.000	0.000	0.000
5	A	201	GLU	-1	-0.852	-0.927	7.658	-0.620	-0.620	0.000	0.000	0.000
6	A	202	CYS	0	-0.058	-0.036	6.271	0.301	0.301	0.000	0.000	0.000
7	A	203	GLN	0	-0.005	0.009	8.643	0.147	0.147	0.000	0.000	0.000
8	A	204	ASN	0	0.053	0.019	11.489	0.101	0.101	0.000	0.000	0.000
9	A	205	LEU	0	-0.008	-0.002	10.753	0.075	0.075	0.000	0.000	0.000
10	A	206	GLU	-1	-0.868	-0.932	12.708	-0.002	-0.002	0.000	0.000	0.000
11	A	207	VAL	0	0.022	0.012	14.344	0.038	0.038	0.000	0.000	0.000
12	A	208	GLU	-1	-0.822	-0.899	16.640	-0.127	-0.127	0.000	0.000	0.000
13	A	209	ARG	1	0.892	0.933	14.862	0.064	0.064	0.000	0.000	0.000
14	A	210	GLN	0	0.006	0.003	18.259	0.024	0.024	0.000	0.000	0.000
15	A	211	ARG	1	0.922	0.974	20.390	0.136	0.136	0.000	0.000	0.000
16	A	212	ARG	1	0.810	0.884	20.449	0.131	0.131	0.000	0.000	0.000
17	A	213	LEU	0	0.024	0.015	20.737	0.008	0.008	0.000	0.000	0.000
18	A	214	GLU	-1	-0.891	-0.936	23.952	-0.027	-0.027	0.000	0.000	0.000
19	A	215	ARG	1	0.890	0.937	24.424	0.090	0.090	0.000	0.000	0.000
20	A	216	ILE	0	-0.014	-0.002	24.839	0.003	0.003	0.000	0.000	0.000
21	A	217	LYS	1	1.004	1.015	28.233	0.020	0.020	0.000	0.000	0.000
22	A	218	GLN	0	0.005	0.003	30.048	0.007	0.007	0.000	0.000	0.000
23	A	219	LYS	1	0.945	0.957	30.395	0.055	0.055	0.000	0.000	0.000
24	A	220	GLN	0	0.040	0.022	30.728	0.001	0.001	0.000	0.000	0.000
25	A	221	SER	0	0.023	0.024	34.155	0.003	0.003	0.000	0.000	0.000
26	A	222	GLN	0	-0.014	-0.012	35.717	0.000	0.000	0.000	0.000	0.000
27	A	223	LEU	0	-0.028	-0.003	36.638	0.001	0.001	0.000	0.000	0.000
28	A	224	GLN	0	0.038	-0.003	37.181	0.001	0.001	0.000	0.000	0.000
29	A	225	GLU	-1	-0.820	-0.888	40.271	-0.013	-0.013	0.000	0.000	0.000
30	A	226	LEU	0	-0.012	-0.019	40.321	0.001	0.001	0.000	0.000	0.000
31	A	227	ILE	0	-0.037	-0.019	40.826	0.001	0.001	0.000	0.000	0.000
32	A	228	LEU	0	0.012	0.007	43.994	0.001	0.001	0.000	0.000	0.000
33	A	229	GLN	0	0.036	0.024	46.171	0.001	0.001	0.000	0.000	0.000
34	A	230	GLN	0	-0.016	0.004	45.584	0.001	0.001	0.000	0.000	0.000
35	A	231	ILE	0	-0.002	0.004	47.067	0.001	0.001	0.000	0.000	0.000
36	A	232	ALA	0	0.029	0.016	50.313	0.001	0.001	0.000	0.000	0.000
37	A	233	PHE	0	0.008	-0.011	50.812	0.000	0.000	0.000	0.000	0.000
38	A	234	LYS	1	0.861	0.930	49.971	0.015	0.015	0.000	0.000	0.000
39	A	235	ASN	0	0.013	-0.005	54.426	0.001	0.001	0.000	0.000	0.000
40	A	236	LEU	0	0.008	0.009	56.259	0.001	0.001	0.000	0.000	0.000
41	A	237	VAL	0	-0.025	-0.021	57.857	0.000	0.000	0.000	0.000	0.000
42	A	238	GLN	0	-0.036	-0.028	57.287	0.000	0.000	0.000	0.000	0.000
43	A	239	ARG	1	0.928	0.972	60.498	0.007	0.007	0.000	0.000	0.000
44	A	240	ASN	0	0.030	0.002	62.371	0.001	0.001	0.000	0.000	0.000
45	A	241	ARG	1	0.987	1.001	60.629	0.010	0.010	0.000	0.000	0.000
46	A	242	HIS	0	-0.009	-0.009	64.834	0.000	0.000	0.000	0.000	0.000
47	A	243	ALA	0	-0.032	-0.033	66.541	0.000	0.000	0.000	0.000	0.000
48	A	244	GLU	-1	-0.918	-0.951	68.249	-0.008	-0.008	0.000	0.000	0.000
49	A	245	GLN	0	-0.046	-0.004	67.755	0.000	0.000	0.000	0.000	0.000
50	A	246	GLN	0	-0.097	-0.064	70.478	0.000	0.000	0.000	0.000	0.000
51	A	247	ALA	0	-0.019	0.001	73.104	0.000	0.000	0.000	0.000	0.000
52	A	248	SER	0	0.039	0.028	74.921	0.000	0.000	0.000	0.000	0.000
53	A	249	ARG	1	0.897	0.942	75.580	0.006	0.006	0.000	0.000	0.000
54	A	250	PRO	0	0.063	0.034	71.075	0.000	0.000	0.000	0.000	0.000
55	A	251	PRO	0	0.012	0.023	68.766	0.000	0.000	0.000	0.000	0.000
56	A	252	PRO	0	0.009	-0.003	71.983	0.000	0.000	0.000	0.000	0.000
57	A	253	PRO	0	0.037	0.011	70.550	0.000	0.000	0.000	0.000	0.000
58	A	254	ASN	0	0.013	0.006	69.752	0.000	0.000	0.000	0.000	0.000
59	A	255	SER	0	-0.118	-0.050	70.394	0.000	0.000	0.000	0.000	0.000
60	A	256	VAL	0	0.005	-0.008	65.546	0.000	0.000	0.000	0.000	0.000
61	A	257	ILE	0	0.013	0.017	61.828	0.000	0.000	0.000	0.000	0.000
62	A	258	HIS	0	-0.025	-0.009	61.289	0.000	0.000	0.000	0.000	0.000
63	A	259	LEU	0	-0.035	0.011	54.839	0.000	0.000	0.000	0.000	0.000
64	A	260	PRO	0	-0.004	-0.010	54.174	0.000	0.000	0.000	0.000	0.000
65	A	261	PHE	0	-0.047	-0.038	55.797	0.000	0.000	0.000	0.000	0.000
66	A	262	ILE	0	0.025	0.017	52.708	0.000	0.000	0.000	0.000	0.000
67	A	263	ILE	0	-0.044	-0.019	56.138	0.001	0.001	0.000	0.000	0.000
68	A	264	VAL	0	0.046	0.016	56.726	0.000	0.000	0.000	0.000	0.000
69	A	265	ASN	0	-0.067	-0.024	58.502	0.000	0.000	0.000	0.000	0.000
70	A	266	THR	0	0.057	0.006	59.719	0.000	0.000	0.000	0.000	0.000
71	A	267	SER	0	-0.038	-0.012	62.208	0.000	0.000	0.000	0.000	0.000
72	A	268	LYS	1	0.971	0.965	65.057	0.003	0.003	0.000	0.000	0.000
73	A	269	LYS	1	0.898	0.945	68.224	0.002	0.002	0.000	0.000	0.000
74	A	270	THR	0	-0.027	-0.006	63.296	0.000	0.000	0.000	0.000	0.000
75	A	271	VAL	0	0.018	0.019	66.642	0.000	0.000	0.000	0.000	0.000
76	A	272	ILE	0	-0.022	-0.016	64.335	0.000	0.000	0.000	0.000	0.000
77	A	273	ASP	-1	-0.937	-0.959	65.608	-0.007	-0.007	0.000	0.000	0.000
78	A	274	CYS	0	-0.053	-0.028	65.351	-0.001	-0.001	0.000	0.000	0.000
79	A	275	SER	0	-0.011	-0.003	65.088	0.000	0.000	0.000	0.000	0.000
80	A	276	ILE	0	-0.025	-0.017	64.846	0.000	0.000	0.000	0.000	0.000
81	A	277	SER	0	-0.013	-0.003	64.205	0.000	0.000	0.000	0.000	0.000
82	A	278	ASN	0	0.033	-0.013	66.303	0.000	0.000	0.000	0.000	0.000
83	A	279	ASP	-1	-0.866	-0.920	64.430	-0.015	-0.015	0.000	0.000	0.000
84	A	280	LYS	1	0.886	0.945	65.576	0.011	0.011	0.000	0.000	0.000
85	A	281	PHE	0	-0.033	-0.009	60.714	0.000	0.000	0.000	0.000	0.000
86	A	282	GLU	-1	-0.958	-0.967	59.053	-0.016	-0.016	0.000	0.000	0.000
87	A	283	TYR	0	-0.030	-0.029	60.466	0.001	0.001	0.000	0.000	0.000
88	A	284	LEU	0	-0.004	0.006	59.524	-0.001	-0.001	0.000	0.000	0.000
89	A	285	PHE	0	-0.006	-0.016	60.684	0.001	0.001	0.000	0.000	0.000
90	A	286	ASN	0	-0.015	0.007	60.736	-0.001	-0.001	0.000	0.000	0.000
91	A	287	PHE	0	0.050	0.012	59.996	0.000	0.000	0.000	0.000	0.000
92	A	288	ASP	-1	-0.844	-0.907	62.044	-0.005	-0.005	0.000	0.000	0.000
93	A	289	ASN	0	-0.023	-0.024	61.753	0.001	0.001	0.000	0.000	0.000
94	A	290	THR	0	0.004	0.003	56.654	-0.001	-0.001	0.000	0.000	0.000
95	A	291	PHE	0	-0.031	0.000	54.769	0.000	0.000	0.000	0.000	0.000
96	A	292	GLU	-1	-0.898	-0.951	55.029	-0.005	-0.005	0.000	0.000	0.000
97	A	293	ILE	0	-0.007	-0.010	52.801	0.000	0.000	0.000	0.000	0.000
98	A	294	HIS	0	-0.057	-0.021	52.597	0.000	0.000	0.000	0.000	0.000
99	A	295	ASP	-1	-0.801	-0.912	49.444	-0.015	-0.015	0.000	0.000	0.000
100	A	296	ASP	-1	-0.781	-0.885	52.507	-0.013	-0.013	0.000	0.000	0.000
101	A	297	ILE	0	-0.021	-0.022	47.798	0.001	0.001	0.000	0.000	0.000
102	A	298	GLU	-1	-0.858	-0.922	48.779	-0.007	-0.007	0.000	0.000	0.000
103	A	299	VAL	0	0.002	0.002	51.495	0.001	0.001	0.000	0.000	0.000
104	A	300	LEU	0	-0.018	-0.032	53.519	0.001	0.001	0.000	0.000	0.000
105	A	301	LYS	1	0.849	0.918	45.847	0.012	0.012	0.000	0.000	0.000
106	A	302	ARG	1	0.875	0.944	50.716	0.007	0.007	0.000	0.000	0.000
107	A	303	MET	0	-0.092	-0.036	54.707	0.001	0.001	0.000	0.000	0.000
108	A	304	GLY	0	0.042	0.033	54.441	0.000	0.000	0.000	0.000	0.000
109	A	305	MET	0	-0.069	-0.027	54.407	0.000	0.000	0.000	0.000	0.000
110	A	306	ALA	0	0.000	0.002	49.119	0.000	0.000	0.000	0.000	0.000
111	A	307	CYS	0	-0.050	-0.019	50.067	0.000	0.000	0.000	0.000	0.000
112	A	308	GLY	0	0.123	0.068	50.696	0.001	0.001	0.000	0.000	0.000
113	A	309	LEU	0	-0.029	-0.027	44.907	0.001	0.001	0.000	0.000	0.000
114	A	310	GLU	-1	-0.921	-0.975	45.240	-0.006	-0.006	0.000	0.000	0.000
115	A	311	SER	0	-0.058	-0.013	44.511	0.000	0.000	0.000	0.000	0.000
116	A	312	GLY	0	0.034	0.024	44.969	0.001	0.001	0.000	0.000	0.000
117	A	313	SER	0	-0.073	-0.041	45.747	0.001	0.001	0.000	0.000	0.000
118	A	314	CYS	0	-0.080	-0.034	48.932	-0.001	-0.001	0.000	0.000	0.000
119	A	315	SER	0	0.027	0.021	50.740	0.001	0.001	0.000	0.000	0.000
120	A	316	ALA	0	0.018	-0.007	52.581	-0.001	-0.001	0.000	0.000	0.000
121	A	317	GLU	-1	-0.925	-0.980	53.513	-0.001	-0.001	0.000	0.000	0.000
122	A	318	ASP	-1	-0.806	-0.890	52.558	-0.003	-0.003	0.000	0.000	0.000
123	A	319	LEU	0	-0.005	-0.004	46.781	-0.001	-0.001	0.000	0.000	0.000
124	A	320	LYS	1	0.902	0.947	50.432	0.002	0.002	0.000	0.000	0.000
125	A	321	MET	0	0.003	0.009	52.808	-0.001	-0.001	0.000	0.000	0.000
126	A	322	ALA	0	0.059	0.014	48.718	-0.001	-0.001	0.000	0.000	0.000
127	A	323	ARG	1	0.865	0.901	44.967	0.003	0.003	0.000	0.000	0.000
128	A	324	SER	0	-0.072	-0.007	49.276	-0.001	-0.001	0.000	0.000	0.000
129	A	325	LEU	0	-0.039	-0.013	51.268	-0.001	-0.001	0.000	0.000	0.000
130	A	326	VAL	0	-0.028	-0.015	45.612	-0.002	-0.002	0.000	0.000	0.000
131	A	327	PRO	0	0.002	0.011	45.423	0.000	0.000	0.000	0.000	0.000
132	A	328	LYS	1	1.062	1.019	45.103	0.012	0.012	0.000	0.000	0.000
133	A	329	ALA	0	-0.051	-0.029	41.066	0.001	0.001	0.000	0.000	0.000
134	A	330	LEU	0	-0.017	-0.024	40.539	-0.001	-0.001	0.000	0.000	0.000
135	A	331	GLU	-1	-0.844	-0.922	42.336	-0.009	-0.009	0.000	0.000	0.000
136	A	332	PRO	0	-0.051	-0.029	38.736	0.001	0.001	0.000	0.000	0.000
137	A	333	TYR	0	0.092	0.036	34.784	0.001	0.001	0.000	0.000	0.000
138	A	334	VAL	0	0.030	0.016	39.417	0.001	0.001	0.000	0.000	0.000
139	A	335	THR	0	-0.036	-0.005	41.060	0.002	0.002	0.000	0.000	0.000
140	A	336	GLU	-1	-0.884	-0.942	35.987	-0.003	-0.003	0.000	0.000	0.000
141	A	337	MET	0	-0.088	-0.042	39.266	0.001	0.001	0.000	0.000	0.000
142	A	338	ALA	0	-0.013	0.000	41.158	0.001	0.001	0.000	0.000	0.000
143	A	339	GLN	0	-0.046	-0.012	39.754	0.000	0.000	0.000	0.000	0.000
144	A	340	GLY	0	0.031	0.027	39.669	0.002	0.002	0.000	0.000	0.000
145	A	341	THR	0	-0.068	-0.028	35.465	0.001	0.001	0.000	0.000	0.000
146	A	342	VAL	0	0.025	0.003	35.338	-0.001	-0.001	0.000	0.000	0.000
147	A	343	GLY	0	-0.036	-0.007	31.933	-0.003	-0.003	0.000	0.000	0.000
148	A	344	GLY	0	-0.007	-0.007	28.558	0.000	0.000	0.000	0.000	0.000
149	A	345	VAL	0	-0.098	-0.061	25.753	0.000	0.000	0.000	0.000	0.000
150	A	346	PHE	0	0.067	0.047	25.907	-0.001	-0.001	0.000	0.000	0.000
151	A	347	NME	0	-0.024	-0.007	25.697	-0.005	-0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:197:ACE )