FMO DATABASE

FMODB ID: 6YRLZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-892567.388271
FMO2-HF: Nuclear repulsion	843772.138698
FMO2-HF: Total energy	-48795.249574
FMO2-MP2: Total energy	-48931.991653

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.
-2.91	0.0049999999999997	0.042	-1.255	-1.701	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 : 0.004 / q_NPA : -0.008

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	0.037	0.033	3.073	-2.346	0.409	0.043	-1.241	-1.557	0.002
4	A	7	ARG	1	0.951	0.950	4.801	0.253	0.413	-0.001	-0.014	-0.144	0.000
5	A	8	GLU	-1	-0.909	-0.951	6.731	-0.508	-0.508	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.823	-0.934	6.565	0.623	0.623	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.027	-0.008	8.887	0.014	0.014	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.011	0.013	10.648	0.019	0.019	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.009	0.010	10.406	0.033	0.033	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.013	0.005	12.986	0.005	0.005	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.044	-0.029	14.637	0.006	0.006	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.868	-0.928	16.623	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.018	0.022	16.508	0.005	0.005	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.055	-0.036	17.896	0.004	0.004	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.077	-0.029	20.580	0.002	0.002	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.021	-0.023	19.818	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.838	-0.914	20.068	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.964	0.994	12.920	0.048	0.048	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.127	-0.098	17.704	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.041	0.017	18.714	0.003	0.003	0.000	0.000	0.000	0.000
21	A	24	TRP	0	-0.034	-0.034	10.060	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.040	0.022	14.158	0.013	0.013	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.025	0.013	14.900	0.017	0.017	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.130	0.050	14.358	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.044	0.041	18.192	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.049	-0.033	21.701	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	30	MET	0	0.000	0.013	14.581	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.990	1.009	20.048	-0.068	-0.068	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.916	0.950	21.872	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.021	-0.001	21.879	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.081	0.034	19.640	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	35	LEU	0	0.013	0.002	22.533	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.867	0.950	25.919	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.910	0.943	23.493	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	38	CYS	0	0.026	0.029	24.818	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.891	0.963	27.445	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.938	-0.987	29.275	0.001	0.001	0.000	0.000	0.000	0.000
38	A	41	PHE	0	-0.019	0.008	25.441	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.036	0.007	29.332	0.003	0.003	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.096	0.075	30.223	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-1.014	-1.003	31.537	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.867	0.932	32.577	0.012	0.012	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.032	-0.023	29.361	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.055	0.027	28.226	0.001	0.001	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.946	-0.994	23.907	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.732	-0.857	23.296	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-1.008	-0.983	19.691	-0.089	-0.089	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.891	0.945	19.722	0.020	0.020	0.000	0.000	0.000	0.000
49	A	52	MET	0	-0.034	-0.007	20.594	0.006	0.006	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.971	0.991	19.012	0.054	0.054	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.892	0.923	13.594	0.089	0.089	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.009	0.010	15.716	0.027	0.027	0.000	0.000	0.000	0.000
53	A	56	ASN	0	-0.027	-0.021	17.840	0.024	0.024	0.000	0.000	0.000	0.000
54	A	57	THR	0	-0.039	0.024	13.172	0.046	0.046	0.000	0.000	0.000	0.000
55	A	58	LEU	0	0.016	0.000	9.967	0.043	0.043	0.000	0.000	0.000	0.000
56	A	59	TYR	0	0.025	0.004	12.915	0.075	0.075	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.971	0.988	15.023	-0.080	-0.080	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.823	0.941	5.175	-1.609	-1.609	0.000	0.000	0.000	0.000
59	A	62	MET	0	-0.095	-0.067	9.040	0.205	0.205	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.861	-0.941	12.315	0.100	0.100	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.838	-0.940	12.650	0.277	0.277	0.000	0.000	0.000	0.000
62	A	65	GLY	0	-0.102	-0.045	12.487	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.068	-0.048	13.307	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.918	0.955	16.936	-0.166	-0.166	0.000	0.000	0.000	0.000
65	A	68	TYR	0	-0.041	-0.019	16.769	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.055	0.045	19.916	0.000	0.000	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.012	-0.017	16.045	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.075	0.036	20.903	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	72	PRO	0	-0.134	-0.072	20.599	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.893	-0.942	22.083	0.074	0.074	0.000	0.000	0.000	0.000
71	A	74	PHE	0	-0.044	-0.015	21.571	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.023	-0.013	20.729	0.009	0.009	0.000	0.000	0.000	0.000
73	A	76	GLY	0	-0.035	-0.018	21.675	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	77	PHE	0	0.062	0.027	22.628	0.009	0.009	0.000	0.000	0.000	0.000
75	A	78	TRP	0	-0.058	-0.012	21.483	0.000	0.000	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.933	-0.946	23.624	0.045	0.045	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.003	0.011	24.159	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	81	THR	0	-0.003	-0.043	25.380	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.951	-0.967	23.657	0.050	0.050	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.026	0.016	21.047	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	84	PRO	0	0.026	0.000	21.305	0.014	0.014	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.029	-0.030	17.984	0.000	0.000	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.051	-0.037	20.275	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	87	GLY	0	-0.010	-0.011	21.046	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.072	-0.046	21.965	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.863	-0.943	25.479	0.002	0.002	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.906	-0.945	27.572	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	91	TRP	0	0.076	0.018	25.041	0.005	0.005	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.874	-0.956	29.205	0.002	0.002	0.000	0.000	0.000	0.000
90	A	93	GLN	0	-0.015	0.004	31.511	0.000	0.000	0.000	0.000	0.000	0.000
91	A	94	TRP	0	-0.030	-0.017	23.856	0.004	0.004	0.000	0.000	0.000	0.000
92	A	95	TRP	0	0.015	-0.013	27.795	0.005	0.005	0.000	0.000	0.000	0.000
93	A	96	ASN	0	-0.078	-0.035	30.363	0.002	0.002	0.000	0.000	0.000	0.000
94	A	97	ALA	0	0.013	0.017	30.624	0.002	0.002	0.000	0.000	0.000	0.000
95	A	98	PHE	0	0.012	-0.008	26.658	0.004	0.004	0.000	0.000	0.000	0.000
96	A	99	ASN	0	-0.055	-0.039	30.390	0.004	0.004	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.940	-0.958	33.290	0.011	0.011	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.894	-0.956	31.893	0.028	0.028	0.000	0.000	0.000	0.000
99	A	102	ASN	0	-0.149	-0.059	29.900	0.000	0.000	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.046	-0.038	33.210	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	104	PHE	0	-0.024	0.010	36.333	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.041	-0.007	37.580	0.001	0.001	0.000	0.000	0.000	0.000
103	A	106	SER	0	-0.006	-0.009	35.897	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.974	-0.983	39.165	0.020	0.020	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.952	-0.984	41.934	0.014	0.014	0.000	0.000	0.000	0.000
106	A	109	MET	0	-0.055	-0.026	45.343	0.000	0.000	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.015	0.009	48.379	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	SER	0	-0.028	-0.018	50.137	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	112	SER	0	-0.064	-0.060	52.712	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	113	ASP	-1	-0.914	-0.944	56.056	0.009	0.009	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.967	-0.969	57.822	0.010	0.010	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.986	-1.009	59.683	0.010	0.010	0.000	0.000	0.000	0.000
113	A	116	ALA	0	-0.016	0.015	60.892	0.000	0.000	0.000	0.000	0.000	0.000
114	A	117	THR	0	-0.040	-0.017	62.576	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)