FMO DATABASE

FMODB ID: 22R4R

Calculation Name: 2AZE-A-Xray372

Preferred Name: Transcription factor E2F1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1197500.494621
FMO2-HF: Nuclear repulsion	1136908.925276
FMO2-HF: Total energy	-60591.569345
FMO2-MP2: Total energy	-60764.77286

3D Structure Molmil

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.
-2.984	0.691	0.377	-1.307	-2.747	-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 : 0.065 / q_NPA : 0.013

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	-0.007	-0.013	3.869	-2.446	-0.735	-0.004	-0.727	-0.981	0.001
4	A	201	GLU	-1	-0.804	-0.891	2.788	-2.098	-1.189	0.148	-0.225	-0.833	-0.001
5	A	202	CYS	0	-0.074	-0.039	2.859	-0.114	0.941	0.233	-0.355	-0.933	-0.001
6	A	203	GLN	0	0.034	0.026	5.623	0.484	0.484	0.000	0.000	0.000	0.000
7	A	204	ASN	0	-0.025	-0.025	7.614	0.301	0.301	0.000	0.000	0.000	0.000
8	A	205	LEU	0	-0.008	-0.009	5.879	0.165	0.165	0.000	0.000	0.000	0.000
9	A	206	GLU	-1	-0.802	-0.883	9.382	-0.149	-0.149	0.000	0.000	0.000	0.000
10	A	207	VAL	0	-0.018	-0.011	11.469	0.084	0.084	0.000	0.000	0.000	0.000
11	A	208	GLU	-1	-0.725	-0.826	12.803	-0.169	-0.169	0.000	0.000	0.000	0.000
12	A	209	ARG	1	0.851	0.918	13.248	0.255	0.255	0.000	0.000	0.000	0.000
13	A	210	GLN	0	0.030	0.006	15.075	0.032	0.032	0.000	0.000	0.000	0.000
14	A	211	ARG	1	0.910	0.951	17.210	0.180	0.180	0.000	0.000	0.000	0.000
15	A	212	ARG	1	0.806	0.901	16.520	0.248	0.248	0.000	0.000	0.000	0.000
16	A	213	LEU	0	0.053	0.032	18.090	0.014	0.014	0.000	0.000	0.000	0.000
17	A	214	GLU	-1	-0.773	-0.868	21.139	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	215	ARG	1	0.783	0.863	18.412	0.169	0.169	0.000	0.000	0.000	0.000
19	A	216	ILE	0	-0.016	0.001	21.697	0.007	0.007	0.000	0.000	0.000	0.000
20	A	217	LYS	1	0.893	0.931	25.181	0.063	0.063	0.000	0.000	0.000	0.000
21	A	218	GLN	0	-0.008	-0.003	27.107	0.008	0.008	0.000	0.000	0.000	0.000
22	A	219	LYS	1	0.960	0.972	27.189	0.098	0.098	0.000	0.000	0.000	0.000
23	A	220	GLN	0	0.008	0.004	27.873	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	221	SER	0	0.021	0.008	31.047	0.005	0.005	0.000	0.000	0.000	0.000
25	A	222	GLN	0	-0.027	-0.019	31.025	0.000	0.000	0.000	0.000	0.000	0.000
26	A	223	LEU	0	-0.020	-0.001	33.323	0.002	0.002	0.000	0.000	0.000	0.000
27	A	224	GLN	0	0.030	0.000	34.724	0.000	0.000	0.000	0.000	0.000	0.000
28	A	225	GLU	-1	-0.808	-0.876	37.340	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	226	LEU	0	0.003	0.000	36.310	0.001	0.001	0.000	0.000	0.000	0.000
30	A	227	ILE	0	-0.042	-0.026	37.888	0.001	0.001	0.000	0.000	0.000	0.000
31	A	228	LEU	0	-0.006	0.010	41.275	0.002	0.002	0.000	0.000	0.000	0.000
32	A	229	GLN	0	0.028	0.008	41.612	0.000	0.000	0.000	0.000	0.000	0.000
33	A	230	GLN	0	-0.003	0.014	42.025	0.002	0.002	0.000	0.000	0.000	0.000
34	A	231	ILE	0	0.003	-0.001	44.306	0.001	0.001	0.000	0.000	0.000	0.000
35	A	232	ALA	0	0.036	0.025	47.293	0.002	0.002	0.000	0.000	0.000	0.000
36	A	233	PHE	0	0.024	-0.002	46.272	0.001	0.001	0.000	0.000	0.000	0.000
37	A	234	LYS	1	0.794	0.889	46.198	0.041	0.041	0.000	0.000	0.000	0.000
38	A	235	ASN	0	0.020	0.011	51.385	0.002	0.002	0.000	0.000	0.000	0.000
39	A	236	LEU	0	0.027	0.014	53.258	0.001	0.001	0.000	0.000	0.000	0.000
40	A	237	VAL	0	-0.025	-0.011	54.133	0.001	0.001	0.000	0.000	0.000	0.000
41	A	238	GLN	0	-0.050	-0.048	54.513	0.000	0.000	0.000	0.000	0.000	0.000
42	A	239	ARG	1	0.919	0.961	57.412	0.020	0.020	0.000	0.000	0.000	0.000
43	A	240	ASN	0	0.047	0.018	59.178	0.001	0.001	0.000	0.000	0.000	0.000
44	A	241	ARG	1	0.998	1.005	56.871	0.027	0.027	0.000	0.000	0.000	0.000
45	A	242	HIS	0	0.015	0.012	61.696	0.000	0.000	0.000	0.000	0.000	0.000
46	A	243	ALA	0	-0.003	-0.012	63.434	0.001	0.001	0.000	0.000	0.000	0.000
47	A	244	GLU	-1	-0.948	-0.976	63.911	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	245	GLN	0	-0.062	-0.038	65.340	0.001	0.001	0.000	0.000	0.000	0.000
49	A	246	GLN	0	-0.089	-0.028	67.346	0.000	0.000	0.000	0.000	0.000	0.000
50	A	247	ALA	0	-0.018	-0.021	69.878	0.001	0.001	0.000	0.000	0.000	0.000
51	A	248	SER	0	-0.007	0.009	71.409	0.000	0.000	0.000	0.000	0.000	0.000
52	A	249	ARG	1	0.940	0.946	71.161	0.014	0.014	0.000	0.000	0.000	0.000
53	A	250	PRO	0	0.018	0.030	67.068	0.000	0.000	0.000	0.000	0.000	0.000
54	A	251	PRO	0	0.025	0.029	65.406	0.001	0.001	0.000	0.000	0.000	0.000
55	A	252	PRO	0	0.009	0.013	67.945	0.000	0.000	0.000	0.000	0.000	0.000
56	A	253	PRO	0	0.068	0.017	66.497	0.000	0.000	0.000	0.000	0.000	0.000
57	A	254	ASN	0	-0.038	-0.022	65.991	0.000	0.000	0.000	0.000	0.000	0.000
58	A	255	SER	0	-0.071	-0.036	66.750	0.000	0.000	0.000	0.000	0.000	0.000
59	A	256	VAL	0	-0.022	-0.009	61.723	0.000	0.000	0.000	0.000	0.000	0.000
60	A	257	ILE	0	-0.002	0.009	57.880	0.000	0.000	0.000	0.000	0.000	0.000
61	A	258	HIS	0	-0.014	-0.011	57.561	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	259	LEU	0	-0.009	0.019	51.613	0.000	0.000	0.000	0.000	0.000	0.000
63	A	260	PRO	0	-0.021	-0.012	50.000	0.000	0.000	0.000	0.000	0.000	0.000
64	A	261	PHE	0	-0.041	-0.046	52.001	0.001	0.001	0.000	0.000	0.000	0.000
65	A	262	ILE	0	0.004	0.001	48.957	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	263	ILE	0	-0.033	-0.007	52.790	0.001	0.001	0.000	0.000	0.000	0.000
67	A	264	VAL	0	0.043	0.013	53.624	0.000	0.000	0.000	0.000	0.000	0.000
68	A	265	ASN	0	-0.074	-0.044	55.863	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	266	THR	0	0.049	0.004	57.028	0.001	0.001	0.000	0.000	0.000	0.000
70	A	267	SER	0	0.006	0.013	59.546	0.000	0.000	0.000	0.000	0.000	0.000
71	A	268	LYS	1	0.945	0.959	62.753	0.006	0.006	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.913	0.942	65.701	0.002	0.002	0.000	0.000	0.000	0.000
73	A	270	THR	0	-0.037	-0.014	60.840	0.001	0.001	0.000	0.000	0.000	0.000
74	A	271	VAL	0	0.017	0.017	64.252	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	272	ILE	0	-0.014	-0.017	61.158	0.000	0.000	0.000	0.000	0.000	0.000
76	A	273	ASP	-1	-0.864	-0.910	63.136	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	274	CYS	0	-0.044	-0.014	61.992	0.000	0.000	0.000	0.000	0.000	0.000
78	A	275	SER	0	-0.032	-0.022	61.863	0.001	0.001	0.000	0.000	0.000	0.000
79	A	276	ILE	0	-0.018	-0.013	61.163	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	277	SER	0	0.003	-0.001	60.059	0.001	0.001	0.000	0.000	0.000	0.000
81	A	278	ASN	0	-0.028	-0.030	62.050	0.000	0.000	0.000	0.000	0.000	0.000
82	A	279	ASP	-1	-0.836	-0.899	60.206	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	280	LYS	1	0.883	0.945	61.183	0.009	0.009	0.000	0.000	0.000	0.000
84	A	281	PHE	0	-0.032	-0.019	56.183	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	282	GLU	-1	-0.954	-0.963	55.203	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	283	TYR	0	-0.027	-0.027	56.456	0.001	0.001	0.000	0.000	0.000	0.000
87	A	284	LEU	0	-0.009	0.008	56.253	0.000	0.000	0.000	0.000	0.000	0.000
88	A	285	PHE	0	0.010	-0.016	57.348	0.000	0.000	0.000	0.000	0.000	0.000
89	A	286	ASN	0	-0.044	-0.020	57.642	0.000	0.000	0.000	0.000	0.000	0.000
90	A	287	PHE	0	0.004	-0.019	56.671	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	288	ASP	-1	-0.852	-0.914	59.453	0.000	0.000	0.000	0.000	0.000	0.000
92	A	289	ASN	0	-0.054	-0.030	59.763	0.001	0.001	0.000	0.000	0.000	0.000
93	A	290	THR	0	0.027	0.010	54.302	0.000	0.000	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.042	0.002	52.547	0.000	0.000	0.000	0.000	0.000	0.000
95	A	292	GLU	-1	-0.836	-0.887	52.293	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	293	ILE	0	0.001	-0.018	49.900	0.000	0.000	0.000	0.000	0.000	0.000
97	A	294	HIS	0	-0.048	-0.014	49.711	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.815	-0.916	47.144	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	296	ASP	-1	-0.787	-0.895	49.261	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	297	ILE	0	0.007	0.006	44.391	0.000	0.000	0.000	0.000	0.000	0.000
101	A	298	GLU	-1	-0.842	-0.908	46.778	-0.021	-0.021	0.000	0.000	0.000	0.000
102	A	299	VAL	0	-0.025	-0.013	48.515	0.001	0.001	0.000	0.000	0.000	0.000
103	A	300	LEU	0	-0.006	-0.022	50.510	0.000	0.000	0.000	0.000	0.000	0.000
104	A	301	LYS	1	0.834	0.899	42.921	0.029	0.029	0.000	0.000	0.000	0.000
105	A	302	ARG	1	0.814	0.895	48.875	0.017	0.017	0.000	0.000	0.000	0.000
106	A	303	MET	0	-0.099	-0.039	52.363	0.001	0.001	0.000	0.000	0.000	0.000
107	A	304	GLY	0	0.042	0.027	52.253	0.000	0.000	0.000	0.000	0.000	0.000
108	A	305	MET	0	-0.080	-0.028	51.679	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	306	ALA	0	0.014	0.005	46.670	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	307	CYS	0	-0.043	-0.017	47.539	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	308	GLY	0	0.102	0.058	48.101	0.000	0.000	0.000	0.000	0.000	0.000
112	A	309	LEU	0	-0.031	-0.027	42.005	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	310	GLU	-1	-0.880	-0.954	42.552	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	311	SER	0	-0.066	-0.032	42.207	0.000	0.000	0.000	0.000	0.000	0.000
115	A	312	GLY	0	0.022	0.024	43.120	0.001	0.001	0.000	0.000	0.000	0.000
116	A	313	SER	0	-0.064	-0.037	43.742	0.001	0.001	0.000	0.000	0.000	0.000
117	A	314	CYS	0	-0.116	-0.048	46.431	0.000	0.000	0.000	0.000	0.000	0.000
118	A	315	SER	0	0.038	-0.001	48.566	0.000	0.000	0.000	0.000	0.000	0.000
119	A	316	ALA	0	-0.002	-0.011	50.148	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	317	GLU	-1	-0.911	-0.974	51.150	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	318	ASP	-1	-0.781	-0.855	50.033	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	319	LEU	0	-0.007	0.002	44.390	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	320	LYS	1	0.906	0.947	47.938	0.027	0.027	0.000	0.000	0.000	0.000
124	A	321	MET	0	0.022	0.030	50.308	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	322	ALA	0	0.048	0.017	45.941	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	323	ARG	1	0.881	0.930	42.710	0.041	0.041	0.000	0.000	0.000	0.000
127	A	324	SER	0	-0.112	-0.055	46.611	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	325	LEU	0	-0.004	0.011	48.597	0.000	0.000	0.000	0.000	0.000	0.000
129	A	326	VAL	0	0.000	0.011	42.352	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	327	PRO	0	-0.005	0.007	41.745	0.000	0.000	0.000	0.000	0.000	0.000
131	A	328	LYS	1	1.021	0.984	42.090	0.052	0.052	0.000	0.000	0.000	0.000
132	A	329	ALA	0	-0.023	-0.013	37.694	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	330	LEU	0	0.007	-0.006	37.462	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	331	GLU	-1	-0.851	-0.919	39.058	-0.045	-0.045	0.000	0.000	0.000	0.000
135	A	332	PRO	0	-0.026	-0.007	35.814	0.002	0.002	0.000	0.000	0.000	0.000
136	A	333	TYR	0	0.023	0.003	32.040	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	334	VAL	0	0.057	0.021	36.823	0.002	0.002	0.000	0.000	0.000	0.000
138	A	335	THR	0	-0.035	-0.018	39.261	0.004	0.004	0.000	0.000	0.000	0.000
139	A	336	GLU	-1	-0.843	-0.890	33.625	-0.060	-0.060	0.000	0.000	0.000	0.000
140	A	337	MET	0	-0.071	-0.028	37.063	0.001	0.001	0.000	0.000	0.000	0.000
141	A	338	ALA	0	0.000	0.006	38.727	0.003	0.003	0.000	0.000	0.000	0.000
142	A	339	GLN	0	-0.071	-0.032	37.269	0.003	0.003	0.000	0.000	0.000	0.000
143	A	340	GLY	0	0.026	0.026	37.947	0.001	0.001	0.000	0.000	0.000	0.000
144	A	341	THR	0	-0.083	-0.082	34.099	0.001	0.001	0.000	0.000	0.000	0.000
145	A	342	VAL	0	-0.025	-0.006	32.596	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	343	GLY	0	0.017	0.022	30.132	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	344	GLY	0	-0.011	-0.017	26.567	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	345	VAL	0	-0.064	-0.023	23.458	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	346	PHE	0	0.001	0.008	23.368	-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)