FMO DATABASE

FMODB ID: JQG29

Calculation Name: 3JVE-A-Xray372

Preferred Name: Topoisomerase (DNA) II binding protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3JVE

Chain ID: A

ChEMBL ID: CHEMBL3175

UniProt ID: Q92547

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-712006.445725
FMO2-HF: Nuclear repulsion	674087.19854
FMO2-HF: Total energy	-37919.247185
FMO2-MP2: Total energy	-38030.316315

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:901:ALA)

Summations of interaction energy for fragment #1(A:901:ALA)

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.
0.843	2.792	-0.008	-0.827	-1.113	0.004

Interaction energy analysis for fragmet #1(A:901:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.011

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	903	LYS	1	0.930	0.975	3.505	1.278	2.927	-0.007	-0.764	-0.877	0.004
4	A	904	PRO	0	0.003	0.002	6.620	0.122	0.122	0.000	0.000	0.000	0.000
5	A	905	LEU	0	0.046	0.029	10.132	0.158	0.158	0.000	0.000	0.000	0.000
6	A	906	HIS	0	0.017	0.011	3.851	0.013	0.313	-0.001	-0.063	-0.236	0.000
7	A	907	LYS	1	0.883	0.930	9.598	0.958	0.958	0.000	0.000	0.000	0.000
8	A	908	VAL	0	0.011	0.034	12.473	0.129	0.129	0.000	0.000	0.000	0.000
9	A	909	VAL	0	-0.016	0.006	14.453	-0.043	-0.043	0.000	0.000	0.000	0.000
10	A	910	VAL	0	0.024	0.009	17.173	0.050	0.050	0.000	0.000	0.000	0.000
11	A	911	CYS	0	0.013	0.007	19.462	0.025	0.025	0.000	0.000	0.000	0.000
12	A	912	VAL	0	-0.011	0.010	22.649	0.007	0.007	0.000	0.000	0.000	0.000
13	A	913	SER	0	-0.045	-0.029	25.088	0.019	0.019	0.000	0.000	0.000	0.000
14	A	914	LYS	1	0.939	0.934	28.753	0.141	0.141	0.000	0.000	0.000	0.000
15	A	915	LYS	1	0.776	0.892	31.390	0.133	0.133	0.000	0.000	0.000	0.000
16	A	916	LEU	0	-0.019	-0.006	27.417	0.009	0.009	0.000	0.000	0.000	0.000
17	A	917	SER	0	0.048	0.017	28.309	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	918	LYS	1	0.902	0.945	28.744	0.105	0.105	0.000	0.000	0.000	0.000
19	A	919	LYS	1	0.892	0.933	25.822	0.170	0.170	0.000	0.000	0.000	0.000
20	A	920	GLN	0	-0.029	0.002	24.456	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	921	SER	0	0.040	0.001	22.437	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	922	GLU	-1	-0.943	-0.955	20.808	-0.199	-0.199	0.000	0.000	0.000	0.000
23	A	923	LEU	0	0.023	0.000	19.901	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	924	ASN	0	0.003	-0.001	18.766	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	925	GLY	0	0.007	0.012	16.365	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	926	ILE	0	0.011	0.012	15.046	-0.050	-0.050	0.000	0.000	0.000	0.000
27	A	927	ALA	0	0.020	0.001	14.481	-0.065	-0.065	0.000	0.000	0.000	0.000
28	A	928	ALA	0	0.000	0.002	12.633	-0.116	-0.116	0.000	0.000	0.000	0.000
29	A	929	SER	0	-0.067	-0.032	10.643	-0.125	-0.125	0.000	0.000	0.000	0.000
30	A	930	LEU	0	-0.021	-0.010	9.525	-0.128	-0.128	0.000	0.000	0.000	0.000
31	A	931	GLY	0	-0.043	-0.031	8.546	-0.252	-0.252	0.000	0.000	0.000	0.000
32	A	932	ALA	0	-0.028	0.006	9.181	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	933	ASP	-1	-0.821	-0.895	12.527	-0.526	-0.526	0.000	0.000	0.000	0.000
34	A	934	TYR	0	-0.043	-0.030	14.382	0.040	0.040	0.000	0.000	0.000	0.000
35	A	935	ARG	1	0.807	0.890	16.631	0.360	0.360	0.000	0.000	0.000	0.000
36	A	936	TRP	0	0.012	-0.008	21.443	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	937	SER	0	-0.034	-0.024	24.443	0.018	0.018	0.000	0.000	0.000	0.000
38	A	938	PHE	0	0.014	-0.012	25.402	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	939	ASP	-1	-0.781	-0.860	23.360	-0.219	-0.219	0.000	0.000	0.000	0.000
40	A	940	GLU	-1	-0.918	-0.972	24.791	-0.182	-0.182	0.000	0.000	0.000	0.000
41	A	941	THR	0	-0.083	-0.060	19.742	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	942	VAL	0	-0.057	-0.022	20.009	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	943	THR	0	0.004	-0.022	18.034	0.004	0.004	0.000	0.000	0.000	0.000
44	A	944	HIS	0	-0.027	-0.003	18.467	0.012	0.012	0.000	0.000	0.000	0.000
45	A	945	PHE	0	-0.003	-0.002	21.728	0.006	0.006	0.000	0.000	0.000	0.000
46	A	946	ILE	0	0.026	0.023	21.240	0.008	0.008	0.000	0.000	0.000	0.000
47	A	947	TYR	0	-0.050	-0.068	25.366	0.024	0.024	0.000	0.000	0.000	0.000
48	A	948	GLN	0	0.100	0.056	28.845	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	949	GLY	0	-0.055	-0.042	31.576	0.008	0.008	0.000	0.000	0.000	0.000
50	A	950	ARG	1	0.901	0.964	35.100	0.096	0.096	0.000	0.000	0.000	0.000
51	A	951	PRO	0	0.091	0.031	37.835	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	952	ASN	0	-0.012	-0.014	39.461	0.003	0.003	0.000	0.000	0.000	0.000
53	A	953	ASP	-1	-0.759	-0.859	36.980	-0.110	-0.110	0.000	0.000	0.000	0.000
54	A	954	THR	0	-0.004	0.003	39.063	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	955	ASN	0	-0.013	0.004	35.145	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	956	ARG	1	1.026	1.001	36.877	0.085	0.085	0.000	0.000	0.000	0.000
57	A	957	GLU	-1	-0.751	-0.856	30.825	-0.154	-0.154	0.000	0.000	0.000	0.000
58	A	958	TYR	0	0.037	0.010	31.983	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	959	LYS	1	0.915	0.954	33.056	0.092	0.092	0.000	0.000	0.000	0.000
60	A	960	SER	0	0.002	-0.001	33.159	0.002	0.002	0.000	0.000	0.000	0.000
61	A	961	VAL	0	0.022	0.014	27.835	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	962	LYS	1	0.925	0.959	30.192	0.122	0.122	0.000	0.000	0.000	0.000
63	A	963	GLU	-1	-0.987	-0.991	32.232	-0.113	-0.113	0.000	0.000	0.000	0.000
64	A	964	ARG	1	0.890	0.947	28.828	0.162	0.162	0.000	0.000	0.000	0.000
65	A	965	GLY	0	-0.010	0.008	29.004	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	966	VAL	0	-0.011	0.013	24.331	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	967	HIS	0	0.027	0.022	21.310	0.038	0.038	0.000	0.000	0.000	0.000
68	A	968	ILE	0	-0.063	-0.034	24.987	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	969	VAL	0	-0.001	0.004	22.503	0.006	0.006	0.000	0.000	0.000	0.000
70	A	970	SER	0	0.001	0.020	26.000	0.004	0.004	0.000	0.000	0.000	0.000
71	A	971	GLU	-1	-0.783	-0.902	24.097	-0.202	-0.202	0.000	0.000	0.000	0.000
72	A	972	HIS	0	0.002	-0.012	23.141	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	973	TRP	0	0.026	0.031	17.369	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	974	LEU	0	-0.002	0.006	16.748	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	975	LEU	0	-0.034	-0.022	18.499	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	976	ASP	-1	-0.762	-0.857	19.672	-0.244	-0.244	0.000	0.000	0.000	0.000
77	A	977	CYS	0	-0.050	-0.021	15.680	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	978	ALA	0	-0.024	-0.018	14.937	-0.053	-0.053	0.000	0.000	0.000	0.000
79	A	979	GLN	0	-0.078	-0.032	15.437	0.011	0.011	0.000	0.000	0.000	0.000
80	A	980	GLU	-1	-0.840	-0.903	16.436	-0.267	-0.267	0.000	0.000	0.000	0.000
81	A	981	CYS	0	-0.039	-0.009	10.100	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	982	LYS	1	0.768	0.859	11.808	0.283	0.283	0.000	0.000	0.000	0.000
83	A	983	HIS	0	-0.005	-0.009	13.692	-0.054	-0.054	0.000	0.000	0.000	0.000
84	A	984	LEU	0	-0.027	-0.017	15.321	0.040	0.040	0.000	0.000	0.000	0.000
85	A	985	PRO	0	0.032	0.007	18.929	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	986	GLU	-1	-0.740	-0.854	19.805	-0.372	-0.372	0.000	0.000	0.000	0.000
87	A	987	SER	0	-0.047	-0.024	23.314	0.015	0.015	0.000	0.000	0.000	0.000
88	A	988	LEU	0	-0.006	0.002	24.083	0.020	0.020	0.000	0.000	0.000	0.000
89	A	989	TYR	0	-0.092	-0.066	22.886	0.007	0.007	0.000	0.000	0.000	0.000
90	A	990	PRO	0	0.052	0.033	26.977	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	991	HIS	0	0.006	-0.011	29.725	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	992	THR	0	-0.036	-0.028	30.943	0.005	0.005	0.000	0.000	0.000	0.000
93	A	993	TYR	0	-0.028	0.003	26.952	0.011	0.011	0.000	0.000	0.000	0.000
94	A	994	ASN	0	0.027	0.012	31.582	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:901:ALA)