FMO DATABASE

FMODB ID: R8KN8

Calculation Name: 1GH6-A-Xray372

Preferred Name: Large T antigen

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1GH6

Chain ID: A

ChEMBL ID: CHEMBL1075257

UniProt ID: P03070

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-892759.216242
FMO2-HF: Nuclear repulsion	843961.426129
FMO2-HF: Total energy	-48797.790113
FMO2-MP2: Total energy	-48934.284733

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:4:SER)

Summations of interaction energy for fragment #1(A:4:SER)

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.
-0.164	2.009	0.012	-0.951	-1.234	0.002

Interaction energy analysis for fragmet #1(A:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.026

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	6	MET	0	0.055	0.052	3.379	-0.705	1.323	0.013	-0.938	-1.104	0.002
4	A	7	ARG	1	0.929	0.947	5.044	1.102	1.247	-0.001	-0.013	-0.130	0.000
5	A	8	GLU	-1	-0.915	-0.952	6.515	-1.308	-1.308	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.776	-0.896	6.230	-0.050	-0.050	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.046	-0.016	8.979	0.200	0.200	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.005	-0.008	10.804	0.097	0.097	0.000	0.000	0.000	0.000
9	A	12	GLN	0	0.038	0.026	10.536	0.170	0.170	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.003	0.022	13.458	0.045	0.045	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.041	-0.029	14.941	0.043	0.043	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.880	-0.948	16.925	-0.227	-0.227	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.043	-0.012	17.255	0.029	0.029	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.048	-0.021	17.814	0.023	0.023	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.024	0.003	20.666	0.018	0.018	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.042	-0.026	19.893	0.015	0.015	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.800	-0.861	20.122	-0.150	-0.150	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.916	0.950	13.047	0.304	0.304	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.101	-0.087	18.084	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.037	0.012	19.784	0.004	0.004	0.000	0.000	0.000	0.000
21	A	24	TRP	0	-0.009	-0.021	9.862	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.060	0.031	14.585	0.003	0.003	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.002	0.007	15.479	0.030	0.030	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.103	0.043	14.213	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.051	0.034	18.229	0.000	0.000	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.040	-0.015	21.710	0.001	0.001	0.000	0.000	0.000	0.000
27	A	30	MET	0	-0.003	-0.012	14.374	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.950	0.974	20.033	0.022	0.022	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.939	0.975	21.961	0.049	0.049	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.018	-0.007	22.119	0.002	0.002	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.050	0.023	20.438	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	35	LEU	0	0.028	0.020	22.812	0.001	0.001	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.810	0.897	26.244	0.077	0.077	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.884	0.918	24.258	0.102	0.102	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.021	0.002	25.075	0.001	0.001	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.925	0.969	27.526	0.046	0.046	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.846	-0.901	29.119	-0.078	-0.078	0.000	0.000	0.000	0.000
38	A	41	PHE	0	-0.015	0.013	25.527	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	42	HIS	0	-0.006	-0.009	29.283	0.009	0.009	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.047	0.029	30.923	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.822	-0.903	32.094	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.708	0.836	33.408	0.052	0.052	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.020	0.027	29.510	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.015	0.006	28.334	0.005	0.005	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.871	-0.936	24.619	-0.114	-0.114	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.728	-0.835	23.814	-0.080	-0.080	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.907	-0.944	19.510	-0.156	-0.156	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.848	0.908	19.581	0.121	0.121	0.000	0.000	0.000	0.000
49	A	52	MET	0	0.004	0.003	19.806	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.825	0.907	18.768	0.079	0.079	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.814	0.913	13.897	0.339	0.339	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.003	0.004	15.551	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	56	ASN	0	-0.032	-0.016	17.169	0.011	0.011	0.000	0.000	0.000	0.000
54	A	57	THR	0	0.011	0.010	13.039	0.029	0.029	0.000	0.000	0.000	0.000
55	A	58	LEU	0	-0.010	-0.004	10.400	0.031	0.031	0.000	0.000	0.000	0.000
56	A	59	TYR	0	-0.056	-0.064	13.064	0.031	0.031	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.888	0.940	15.147	0.005	0.005	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.810	0.893	5.642	-0.230	-0.230	0.000	0.000	0.000	0.000
59	A	62	MET	0	-0.051	-0.020	9.539	0.074	0.074	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.743	-0.846	12.487	0.011	0.011	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.826	-0.912	13.092	0.110	0.110	0.000	0.000	0.000	0.000
62	A	65	GLY	0	-0.043	-0.012	12.341	0.020	0.020	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.067	-0.047	12.978	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.723	0.852	16.734	-0.068	-0.068	0.000	0.000	0.000	0.000
65	A	68	TYR	0	-0.056	-0.034	16.076	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.023	0.029	19.879	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.017	-0.012	16.432	0.015	0.015	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.023	0.008	21.342	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	72	PRO	0	-0.086	-0.042	20.738	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.872	-0.941	22.278	0.016	0.016	0.000	0.000	0.000	0.000
71	A	74	PHE	0	-0.037	-0.021	21.453	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.002	-0.001	20.932	0.004	0.004	0.000	0.000	0.000	0.000
73	A	76	GLY	0	-0.038	-0.015	21.738	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	77	PHE	0	0.020	0.001	22.628	0.004	0.004	0.000	0.000	0.000	0.000
75	A	78	TRP	0	-0.005	-0.010	20.690	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.946	-0.966	23.533	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.012	0.023	24.677	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	81	THR	0	0.059	0.024	26.085	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.936	-0.953	23.833	0.008	0.008	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.019	-0.010	21.220	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	84	PRO	0	0.072	0.041	21.620	0.007	0.007	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.021	-0.021	17.924	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.072	-0.047	20.577	0.003	0.003	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.038	0.011	21.003	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.041	-0.047	22.357	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.887	-0.916	25.867	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.859	-0.921	27.812	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	91	TRP	0	-0.010	-0.011	25.216	0.000	0.000	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.849	-0.956	29.645	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	93	GLN	0	-0.084	-0.034	30.455	0.002	0.002	0.000	0.000	0.000	0.000
91	A	94	TRP	0	0.022	-0.004	23.671	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	95	TRP	0	0.005	-0.007	28.462	0.002	0.002	0.000	0.000	0.000	0.000
93	A	96	ASN	0	-0.046	-0.022	30.324	0.000	0.000	0.000	0.000	0.000	0.000
94	A	97	ALA	0	0.030	0.021	30.862	0.001	0.001	0.000	0.000	0.000	0.000
95	A	98	PHE	0	0.006	-0.001	26.962	0.001	0.001	0.000	0.000	0.000	0.000
96	A	99	ASN	0	-0.088	-0.068	30.353	0.001	0.001	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.921	-0.950	33.247	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.890	-0.952	31.857	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	102	ASN	0	-0.142	-0.065	31.135	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.041	-0.024	33.139	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	104	PHE	0	-0.019	0.005	36.261	0.001	0.001	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.076	-0.039	37.534	0.001	0.001	0.000	0.000	0.000	0.000
103	A	106	SER	0	-0.012	0.005	35.891	0.001	0.001	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.938	-0.965	38.905	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.907	-0.969	41.719	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	109	MET	0	-0.071	-0.023	45.170	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.020	-0.008	48.699	0.001	0.001	0.000	0.000	0.000	0.000
108	A	111	SER	0	-0.033	-0.015	50.266	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	SER	0	-0.044	-0.042	52.907	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	ASP	-1	-0.941	-0.963	56.013	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.973	-0.985	58.088	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.983	-0.992	59.317	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	116	ALA	0	0.014	0.016	60.297	0.000	0.000	0.000	0.000	0.000	0.000
114	A	117	THR	0	-0.059	-0.023	62.353	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:SER)