FMO DATABASE

FMODB ID: 9L5L2

Calculation Name: 2IPR-A-Xray547

Preferred Name: Large T antigen

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IPR

Chain ID: A

ChEMBL ID: CHEMBL1075257

UniProt ID: P03070

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1192408.423333
FMO2-HF: Nuclear repulsion	1140838.044302
FMO2-HF: Total energy	-51570.379031
FMO2-MP2: Total energy	-51720.867232

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:132:VAL)

Summations of interaction energy for fragment #1(A:132:VAL)

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.
53.988	56.785	0.615	-1.625	-1.787	-0.014

Interaction energy analysis for fragmet #1(A:132:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.911

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	A	134	ASP	-1	-0.811	-0.912	2.692	-48.262	-45.465	0.615	-1.625	-1.787	-0.014
4	A	135	PRO	0	-0.051	-0.026	4.948	1.464	1.464	0.000	0.000	0.000	0.000
5	A	136	LYS	1	0.886	0.926	7.057	34.249	34.249	0.000	0.000	0.000	0.000
6	A	137	ASP	-1	-0.819	-0.892	10.029	-16.145	-16.145	0.000	0.000	0.000	0.000
7	A	138	PHE	0	-0.024	-0.039	10.933	-1.667	-1.667	0.000	0.000	0.000	0.000
8	A	139	PRO	0	0.002	0.011	10.788	-0.158	-0.158	0.000	0.000	0.000	0.000
9	A	140	SER	0	0.011	-0.006	12.254	0.991	0.991	0.000	0.000	0.000	0.000
10	A	141	GLU	-1	-0.797	-0.871	13.541	-18.886	-18.886	0.000	0.000	0.000	0.000
11	A	142	LEU	0	-0.003	-0.015	15.171	0.998	0.998	0.000	0.000	0.000	0.000
12	A	143	LEU	0	0.011	0.010	14.772	0.954	0.954	0.000	0.000	0.000	0.000
13	A	144	SER	0	-0.027	-0.007	18.519	0.756	0.756	0.000	0.000	0.000	0.000
14	A	145	PHE	0	0.038	0.008	20.513	0.737	0.737	0.000	0.000	0.000	0.000
15	A	146	LEU	0	0.008	0.015	17.855	0.353	0.353	0.000	0.000	0.000	0.000
16	A	147	SER	0	-0.033	-0.019	22.234	0.528	0.528	0.000	0.000	0.000	0.000
17	A	148	HIS	0	0.059	0.026	18.902	-0.624	-0.624	0.000	0.000	0.000	0.000
18	A	149	ALA	0	0.007	0.016	21.970	-0.254	-0.254	0.000	0.000	0.000	0.000
19	A	150	VAL	0	0.018	-0.005	20.021	0.523	0.523	0.000	0.000	0.000	0.000
20	A	151	PHE	0	-0.004	-0.011	21.888	0.247	0.247	0.000	0.000	0.000	0.000
21	A	152	SER	0	-0.006	0.014	26.291	0.564	0.564	0.000	0.000	0.000	0.000
22	A	153	ASN	0	0.013	-0.016	29.027	-0.205	-0.205	0.000	0.000	0.000	0.000
23	A	154	ARG	1	0.883	0.943	28.220	10.482	10.482	0.000	0.000	0.000	0.000
24	A	155	THR	0	0.000	-0.001	30.402	-0.280	-0.280	0.000	0.000	0.000	0.000
25	A	156	LEU	0	-0.007	-0.005	26.923	0.220	0.220	0.000	0.000	0.000	0.000
26	A	157	ALA	0	0.080	0.032	30.458	0.033	0.033	0.000	0.000	0.000	0.000
27	A	158	CYS	0	0.006	0.035	26.133	-0.092	-0.092	0.000	0.000	0.000	0.000
28	A	159	PHE	0	-0.043	-0.021	23.020	-0.158	-0.158	0.000	0.000	0.000	0.000
29	A	160	ALA	0	0.055	0.034	18.596	0.029	0.029	0.000	0.000	0.000	0.000
30	A	161	ILE	0	-0.025	-0.027	16.062	0.063	0.063	0.000	0.000	0.000	0.000
31	A	162	TYR	0	-0.006	0.003	8.492	-0.227	-0.227	0.000	0.000	0.000	0.000
32	A	163	THR	0	0.009	-0.030	11.229	0.078	0.078	0.000	0.000	0.000	0.000
33	A	164	THR	0	0.061	0.023	9.150	-0.263	-0.263	0.000	0.000	0.000	0.000
34	A	165	LYS	1	0.903	0.930	11.118	24.987	24.987	0.000	0.000	0.000	0.000
35	A	166	GLU	-1	-0.788	-0.871	12.705	-21.595	-21.595	0.000	0.000	0.000	0.000
36	A	167	LYS	1	0.823	0.911	13.086	22.134	22.134	0.000	0.000	0.000	0.000
37	A	168	ALA	0	0.016	0.008	15.110	1.129	1.129	0.000	0.000	0.000	0.000
38	A	169	ALA	0	0.043	0.017	16.852	0.935	0.935	0.000	0.000	0.000	0.000
39	A	170	LEU	0	-0.005	0.003	18.940	0.868	0.868	0.000	0.000	0.000	0.000
40	A	171	LEU	0	-0.021	-0.023	17.396	0.803	0.803	0.000	0.000	0.000	0.000
41	A	172	TYR	0	0.040	0.025	20.853	0.498	0.498	0.000	0.000	0.000	0.000
42	A	173	LYS	1	0.920	0.949	22.553	11.050	11.050	0.000	0.000	0.000	0.000
43	A	174	LYS	1	0.873	0.921	23.712	11.381	11.381	0.000	0.000	0.000	0.000
44	A	175	ILE	0	0.001	0.002	22.141	0.403	0.403	0.000	0.000	0.000	0.000
45	A	176	MET	0	0.007	0.003	25.385	0.501	0.501	0.000	0.000	0.000	0.000
46	A	177	GLU	-1	-0.808	-0.885	27.987	-10.030	-10.030	0.000	0.000	0.000	0.000
47	A	178	LYS	1	0.868	0.961	27.843	10.247	10.247	0.000	0.000	0.000	0.000
48	A	179	TYR	0	-0.030	-0.037	25.922	0.065	0.065	0.000	0.000	0.000	0.000
49	A	180	SER	0	0.001	0.006	30.581	0.220	0.220	0.000	0.000	0.000	0.000
50	A	181	VAL	0	-0.042	-0.010	27.226	0.183	0.183	0.000	0.000	0.000	0.000
51	A	182	THR	0	0.022	0.006	30.637	0.059	0.059	0.000	0.000	0.000	0.000
52	A	183	PHE	0	0.029	0.015	25.585	0.070	0.070	0.000	0.000	0.000	0.000
53	A	184	ILE	0	-0.031	-0.010	23.173	-0.287	-0.287	0.000	0.000	0.000	0.000
54	A	185	SER	0	0.028	0.034	22.995	0.102	0.102	0.000	0.000	0.000	0.000
55	A	186	ARG	1	0.787	0.872	17.029	15.017	15.017	0.000	0.000	0.000	0.000
56	A	187	HIS	1	0.870	0.924	16.953	14.650	14.650	0.000	0.000	0.000	0.000
57	A	188	ASN	0	0.003	0.000	13.392	-1.619	-1.619	0.000	0.000	0.000	0.000
58	A	189	SER	0	0.035	0.001	11.297	0.673	0.673	0.000	0.000	0.000	0.000
59	A	190	TYR	0	0.016	-0.020	6.571	-2.444	-2.444	0.000	0.000	0.000	0.000
60	A	191	ASN	0	-0.036	-0.017	5.224	-0.454	-0.454	0.000	0.000	0.000	0.000
61	A	192	HIS	0	0.014	0.028	4.831	3.775	3.775	0.000	0.000	0.000	0.000
62	A	193	ASN	0	-0.017	-0.028	9.291	2.941	2.941	0.000	0.000	0.000	0.000
63	A	194	ILE	0	0.007	0.011	12.946	-0.436	-0.436	0.000	0.000	0.000	0.000
64	A	195	LEU	0	-0.046	-0.017	15.284	0.720	0.720	0.000	0.000	0.000	0.000
65	A	196	PHE	0	0.021	0.000	18.859	-0.347	-0.347	0.000	0.000	0.000	0.000
66	A	197	PHE	0	0.016	-0.007	21.272	0.266	0.266	0.000	0.000	0.000	0.000
67	A	198	LEU	0	0.049	0.032	25.169	-0.102	-0.102	0.000	0.000	0.000	0.000
68	A	199	THR	0	-0.024	-0.038	28.379	-0.086	-0.086	0.000	0.000	0.000	0.000
69	A	200	PRO	0	0.005	0.018	30.978	0.107	0.107	0.000	0.000	0.000	0.000
70	A	201	HIS	0	0.053	0.032	34.058	0.196	0.196	0.000	0.000	0.000	0.000
71	A	202	ARG	1	0.883	0.942	32.450	8.323	8.323	0.000	0.000	0.000	0.000
72	A	203	HIS	0	0.009	0.007	29.085	0.272	0.272	0.000	0.000	0.000	0.000
73	A	204	ARG	1	0.966	0.994	28.881	9.509	9.509	0.000	0.000	0.000	0.000
74	A	205	VAL	0	0.074	0.037	22.632	-0.104	-0.104	0.000	0.000	0.000	0.000
75	A	206	SER	0	0.014	0.011	24.034	-0.303	-0.303	0.000	0.000	0.000	0.000
76	A	207	ALA	0	-0.037	-0.021	25.221	-0.167	-0.167	0.000	0.000	0.000	0.000
77	A	208	ILE	0	0.021	0.023	22.593	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	209	ASN	0	0.041	0.019	19.215	-0.909	-0.909	0.000	0.000	0.000	0.000
79	A	210	ASN	0	0.002	-0.003	21.639	-0.461	-0.461	0.000	0.000	0.000	0.000
80	A	211	TYR	0	-0.042	-0.028	24.173	0.105	0.105	0.000	0.000	0.000	0.000
81	A	212	ALA	0	0.027	-0.001	19.539	-0.146	-0.146	0.000	0.000	0.000	0.000
82	A	213	GLN	0	-0.047	-0.045	16.003	-0.783	-0.783	0.000	0.000	0.000	0.000
83	A	214	LYS	1	0.872	0.942	19.579	11.677	11.677	0.000	0.000	0.000	0.000
84	A	215	LEU	0	-0.030	0.011	21.370	0.289	0.289	0.000	0.000	0.000	0.000
85	A	216	CYS	0	-0.050	-0.036	17.725	0.039	0.039	0.000	0.000	0.000	0.000
86	A	217	THR	0	0.028	0.016	17.674	-0.532	-0.532	0.000	0.000	0.000	0.000
87	A	218	PHE	0	0.033	0.029	13.024	-0.538	-0.538	0.000	0.000	0.000	0.000
88	A	219	SER	0	0.057	0.017	9.031	0.877	0.877	0.000	0.000	0.000	0.000
89	A	220	PHE	0	0.007	0.024	8.163	2.231	2.231	0.000	0.000	0.000	0.000
90	A	221	LEU	0	-0.018	0.005	10.794	0.879	0.879	0.000	0.000	0.000	0.000
91	A	222	ILE	0	-0.014	0.035	10.993	0.749	0.749	0.000	0.000	0.000	0.000
92	A	223	CYS	0	-0.043	-0.022	14.839	0.594	0.594	0.000	0.000	0.000	0.000
93	A	224	LYS	1	0.803	0.874	16.805	16.906	16.906	0.000	0.000	0.000	0.000
94	A	225	GLY	0	0.042	0.021	20.444	0.166	0.166	0.000	0.000	0.000	0.000
95	A	226	VAL	0	-0.036	-0.022	22.159	-0.377	-0.377	0.000	0.000	0.000	0.000
96	A	227	ASN	0	-0.015	-0.006	24.480	0.703	0.703	0.000	0.000	0.000	0.000
97	A	228	LYS	1	0.949	0.987	25.649	11.328	11.328	0.000	0.000	0.000	0.000
98	A	229	GLU	-1	-0.853	-0.930	25.636	-10.535	-10.535	0.000	0.000	0.000	0.000
99	A	230	TYR	0	0.078	0.047	25.628	-0.484	-0.484	0.000	0.000	0.000	0.000
100	A	231	LEU	0	-0.015	-0.004	25.093	-0.222	-0.222	0.000	0.000	0.000	0.000
101	A	232	MET	0	-0.011	0.002	17.691	-0.437	-0.437	0.000	0.000	0.000	0.000
102	A	233	TYR	0	-0.046	-0.052	21.115	-0.543	-0.543	0.000	0.000	0.000	0.000
103	A	234	SER	0	0.018	0.005	22.661	-0.288	-0.288	0.000	0.000	0.000	0.000
104	A	235	ALA	0	0.003	0.007	19.637	-0.095	-0.095	0.000	0.000	0.000	0.000
105	A	236	LEU	0	-0.005	-0.009	16.537	-0.514	-0.514	0.000	0.000	0.000	0.000
106	A	237	THR	0	-0.082	-0.036	19.290	-0.118	-0.118	0.000	0.000	0.000	0.000
107	A	238	ARG	1	0.863	0.932	20.194	11.778	11.778	0.000	0.000	0.000	0.000
108	A	239	ASP	-1	-0.863	-0.911	16.957	-16.315	-16.315	0.000	0.000	0.000	0.000
109	A	240	PRO	0	0.010	0.015	12.884	0.407	0.407	0.000	0.000	0.000	0.000
110	A	241	PHE	0	-0.098	-0.059	12.629	-1.108	-1.108	0.000	0.000	0.000	0.000
111	A	242	SER	0	0.049	0.023	16.080	0.564	0.564	0.000	0.000	0.000	0.000
112	A	243	VAL	0	-0.011	-0.006	18.148	-0.633	-0.633	0.000	0.000	0.000	0.000
113	A	244	ILE	0	-0.077	-0.024	16.006	-0.110	-0.110	0.000	0.000	0.000	0.000
114	A	245	GLU	-1	-0.810	-0.894	20.588	-12.733	-12.733	0.000	0.000	0.000	0.000
115	A	246	GLU	-1	-0.826	-0.918	23.146	-11.933	-11.933	0.000	0.000	0.000	0.000
116	A	247	SER	0	-0.015	-0.002	25.847	0.195	0.195	0.000	0.000	0.000	0.000
117	A	248	LEU	0	0.013	0.015	29.140	0.349	0.349	0.000	0.000	0.000	0.000
118	A	249	PRO	0	0.011	0.009	29.958	-0.298	-0.298	0.000	0.000	0.000	0.000
119	A	250	GLY	0	0.020	0.003	30.119	0.265	0.265	0.000	0.000	0.000	0.000
120	A	251	GLY	0	-0.013	0.003	28.243	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	252	LEU	0	-0.028	-0.002	27.078	0.257	0.257	0.000	0.000	0.000	0.000
122	A	253	LYS	1	0.831	0.892	29.797	9.412	9.412	0.000	0.000	0.000	0.000
123	A	254	GLU	-1	-0.904	-0.963	31.844	-9.066	-9.066	0.000	0.000	0.000	0.000
124	A	255	HIS	0	-0.032	-0.029	32.721	0.084	0.084	0.000	0.000	0.000	0.000
125	A	256	ASP	-1	-0.826	-0.894	33.051	-8.751	-8.751	0.000	0.000	0.000	0.000
126	A	257	PHE	0	-0.093	-0.062	29.482	-0.119	-0.119	0.000	0.000	0.000	0.000
127	A	258	ASN	-1	-0.954	-0.955	34.835	-7.925	-7.925	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:132:VAL)