FMO DATABASE

FMODB ID: ZVGRN

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	OptHSide
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	-892577.847815
FMO2-HF: Nuclear repulsion	843781.173135
FMO2-HF: Total energy	-48796.67468
FMO2-MP2: Total energy	-48933.338881

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.
-0.794	2.197	0.044	-1.339	-1.696	0.004

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 : -0.012 / q_NPA : -0.018

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	0.047	0.041	2.972	-3.131	-0.303	0.045	-1.322	-1.551	0.004
4	A	7	ARG	1	0.942	0.948	4.691	0.886	1.049	-0.001	-0.017	-0.145	0.000
5	A	8	GLU	-1	-0.917	-0.954	6.678	1.029	1.029	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.781	-0.892	6.827	2.167	2.167	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.039	-0.016	8.785	-0.110	-0.110	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.021	0.012	10.546	0.001	0.001	0.000	0.000	0.000	0.000
9	A	12	GLN	0	0.054	0.042	10.930	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.010	0.001	13.070	0.007	0.007	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.029	-0.026	14.587	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.886	-0.934	16.517	0.197	0.197	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.043	0.004	17.189	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.058	-0.028	17.638	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.065	-0.028	20.469	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.040	-0.025	19.672	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.815	-0.879	19.970	0.017	0.017	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.949	0.985	12.982	0.105	0.105	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.140	-0.125	17.622	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.049	0.015	18.614	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	24	TRP	0	-0.018	-0.020	9.593	0.001	0.001	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.027	0.025	14.079	0.030	0.030	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.007	0.000	14.826	0.012	0.012	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.129	0.053	14.099	0.003	0.003	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.065	0.040	18.107	0.010	0.010	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.045	-0.020	21.603	0.004	0.004	0.000	0.000	0.000	0.000
27	A	30	MET	0	0.015	0.007	14.438	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.952	0.991	19.950	-0.130	-0.130	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.923	0.954	21.773	-0.084	-0.084	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.014	0.001	21.849	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.086	0.042	20.019	0.008	0.008	0.000	0.000	0.000	0.000
32	A	35	LEU	0	0.024	0.008	22.424	0.001	0.001	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.841	0.917	25.812	-0.103	-0.103	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.856	0.904	24.172	-0.149	-0.149	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.009	0.010	25.093	0.011	0.011	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.917	0.970	27.567	-0.093	-0.093	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.841	-0.909	29.243	0.104	0.104	0.000	0.000	0.000	0.000
38	A	41	PHE	0	-0.008	0.012	25.614	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.039	0.011	29.519	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.126	0.088	30.370	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.983	-0.975	31.752	0.093	0.093	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.742	0.843	33.317	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.016	0.013	29.619	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.051	0.025	28.501	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.882	-0.960	24.122	0.199	0.199	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.749	-0.853	23.529	0.248	0.248	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.914	-0.935	20.210	0.329	0.329	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.839	0.904	19.968	-0.179	-0.179	0.000	0.000	0.000	0.000
49	A	52	MET	0	-0.021	0.000	20.839	0.002	0.002	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.836	0.921	19.184	-0.245	-0.245	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.864	0.921	13.752	-0.423	-0.423	0.000	0.000	0.000	0.000
52	A	55	MET	0	-0.002	0.008	15.880	0.039	0.039	0.000	0.000	0.000	0.000
53	A	56	ASN	0	-0.032	-0.015	17.963	0.027	0.027	0.000	0.000	0.000	0.000
54	A	57	THR	0	-0.007	0.008	12.924	0.039	0.039	0.000	0.000	0.000	0.000
55	A	58	LEU	0	0.002	-0.005	10.167	0.055	0.055	0.000	0.000	0.000	0.000
56	A	59	TYR	0	-0.002	-0.029	12.940	0.030	0.030	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.919	0.952	14.940	-0.340	-0.340	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.795	0.899	5.352	-2.531	-2.531	0.000	0.000	0.000	0.000
59	A	62	MET	0	-0.091	-0.055	9.121	0.171	0.171	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.839	-0.893	12.223	0.177	0.177	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.791	-0.910	12.675	0.453	0.453	0.000	0.000	0.000	0.000
62	A	65	GLY	0	-0.085	-0.035	12.430	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.077	-0.056	13.252	-0.064	-0.064	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.807	0.886	16.881	-0.340	-0.340	0.000	0.000	0.000	0.000
65	A	68	TYR	0	-0.030	-0.009	16.483	0.003	0.003	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.047	0.040	19.916	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.010	-0.015	16.083	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.055	0.027	20.892	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	72	PRO	0	-0.107	-0.051	20.387	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.890	-0.952	22.060	0.004	0.004	0.000	0.000	0.000	0.000
71	A	74	PHE	0	-0.056	-0.019	21.546	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.017	-0.010	20.705	0.006	0.006	0.000	0.000	0.000	0.000
73	A	76	GLY	0	-0.039	-0.020	21.652	0.003	0.003	0.000	0.000	0.000	0.000
74	A	77	PHE	0	0.058	0.027	22.589	0.007	0.007	0.000	0.000	0.000	0.000
75	A	78	TRP	0	-0.040	-0.017	20.867	0.002	0.002	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.931	-0.941	23.564	0.071	0.071	0.000	0.000	0.000	0.000
77	A	80	ALA	0	-0.005	0.000	24.040	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	81	THR	0	0.012	-0.025	25.299	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.911	-0.952	23.651	0.159	0.159	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.031	0.023	21.127	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	84	PRO	0	0.064	0.030	21.234	0.037	0.037	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.008	-0.018	17.581	0.011	0.011	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.065	-0.050	20.249	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.005	-0.005	21.119	0.021	0.021	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.029	-0.036	22.027	0.000	0.000	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.906	-0.944	25.561	0.181	0.181	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.884	-0.947	27.656	0.157	0.157	0.000	0.000	0.000	0.000
88	A	91	TRP	0	0.042	0.015	25.083	0.004	0.004	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.857	-0.953	29.317	0.124	0.124	0.000	0.000	0.000	0.000
90	A	93	GLN	0	-0.042	-0.006	30.727	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	94	TRP	0	-0.030	-0.015	23.607	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	95	TRP	0	0.010	-0.015	27.938	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	96	ASN	0	-0.066	-0.029	30.415	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	97	ALA	0	0.021	0.015	30.736	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	98	PHE	0	0.016	-0.008	27.017	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	99	ASN	0	-0.060	-0.049	30.364	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.943	-0.954	33.290	0.085	0.085	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.888	-0.951	31.979	0.095	0.095	0.000	0.000	0.000	0.000
99	A	102	ASN	0	-0.162	-0.063	30.557	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.036	-0.033	33.166	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	104	PHE	0	-0.007	0.014	36.335	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.065	-0.019	37.572	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	106	SER	0	-0.019	-0.008	36.028	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.943	-0.975	39.165	0.043	0.043	0.000	0.000	0.000	0.000
105	A	108	GLU	-1	-0.926	-0.973	41.934	0.045	0.045	0.000	0.000	0.000	0.000
106	A	109	MET	0	-0.070	-0.027	45.343	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.016	0.008	48.379	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	SER	0	-0.040	-0.025	50.098	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	SER	0	-0.054	-0.053	52.722	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	ASP	-1	-0.921	-0.958	56.019	0.018	0.018	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.940	-0.960	57.765	0.014	0.014	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-1.004	-0.999	59.627	0.011	0.011	0.000	0.000	0.000	0.000
113	A	116	ALA	0	-0.021	0.004	60.844	0.000	0.000	0.000	0.000	0.000	0.000
114	A	117	THR	0	-0.041	-0.015	62.527	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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