FMO DATABASE

FMODB ID: NNQ2Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-711751.574699
FMO2-HF: Nuclear repulsion	673832.612065
FMO2-HF: Total energy	-37918.962634
FMO2-MP2: Total energy	-38029.99112

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.
0.72	2.59	-0.013	-0.819	-1.038	0.005

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 : 0.024 / 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	0.929	0.970	3.764	1.263	2.837	-0.012	-0.752	-0.810	0.005
4	A	904	PRO	0	0.024	0.011	6.604	0.145	0.145	0.000	0.000	0.000	0.000
5	A	905	LEU	0	0.029	0.025	10.125	0.170	0.170	0.000	0.000	0.000	0.000
6	A	906	HIS	0	0.010	0.008	3.864	0.098	0.394	-0.001	-0.067	-0.228	0.000
7	A	907	LYS	1	0.887	0.931	9.581	0.970	0.970	0.000	0.000	0.000	0.000
8	A	908	VAL	0	0.004	0.031	12.456	0.133	0.133	0.000	0.000	0.000	0.000
9	A	909	VAL	0	-0.014	0.007	14.439	-0.043	-0.043	0.000	0.000	0.000	0.000
10	A	910	VAL	0	0.024	0.009	17.160	0.052	0.052	0.000	0.000	0.000	0.000
11	A	911	CYS	0	0.017	0.008	19.450	0.025	0.025	0.000	0.000	0.000	0.000
12	A	912	VAL	0	-0.012	0.008	22.631	0.007	0.007	0.000	0.000	0.000	0.000
13	A	913	SER	0	-0.040	-0.014	25.091	0.020	0.020	0.000	0.000	0.000	0.000
14	A	914	LYS	1	0.983	0.965	28.743	0.136	0.136	0.000	0.000	0.000	0.000
15	A	915	LYS	1	0.823	0.922	31.381	0.136	0.136	0.000	0.000	0.000	0.000
16	A	916	LEU	0	-0.029	-0.010	27.282	0.010	0.010	0.000	0.000	0.000	0.000
17	A	917	SER	0	0.041	0.017	28.306	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	918	LYS	1	0.914	0.950	28.750	0.111	0.111	0.000	0.000	0.000	0.000
19	A	919	LYS	1	0.919	0.955	25.833	0.171	0.171	0.000	0.000	0.000	0.000
20	A	920	GLN	0	-0.022	0.004	24.342	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	921	SER	0	0.036	-0.001	22.437	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	922	GLU	-1	-0.934	-0.950	20.814	-0.211	-0.211	0.000	0.000	0.000	0.000
23	A	923	LEU	0	0.019	-0.002	19.891	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	924	ASN	0	0.001	0.000	18.757	-0.051	-0.051	0.000	0.000	0.000	0.000
25	A	925	GLY	0	-0.004	0.004	16.372	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	926	ILE	0	0.013	0.005	15.039	-0.053	-0.053	0.000	0.000	0.000	0.000
27	A	927	ALA	0	0.017	0.003	14.457	-0.068	-0.068	0.000	0.000	0.000	0.000
28	A	928	ALA	0	0.006	0.005	12.638	-0.120	-0.120	0.000	0.000	0.000	0.000
29	A	929	SER	0	-0.058	-0.020	10.648	-0.135	-0.135	0.000	0.000	0.000	0.000
30	A	930	LEU	0	-0.019	-0.010	9.496	-0.142	-0.142	0.000	0.000	0.000	0.000
31	A	931	GLY	0	-0.051	-0.034	8.545	-0.258	-0.258	0.000	0.000	0.000	0.000
32	A	932	ALA	0	-0.017	0.011	9.183	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	933	ASP	-1	-0.882	-0.936	12.438	-0.632	-0.632	0.000	0.000	0.000	0.000
34	A	934	TYR	0	-0.036	-0.033	14.372	0.041	0.041	0.000	0.000	0.000	0.000
35	A	935	ARG	1	0.872	0.932	16.845	0.359	0.359	0.000	0.000	0.000	0.000
36	A	936	TRP	0	0.002	-0.008	21.435	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	937	SER	0	-0.025	-0.023	24.436	0.018	0.018	0.000	0.000	0.000	0.000
38	A	938	PHE	0	0.013	-0.010	25.392	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	939	ASP	-1	-0.796	-0.870	23.513	-0.220	-0.220	0.000	0.000	0.000	0.000
40	A	940	GLU	-1	-0.922	-0.978	24.985	-0.187	-0.187	0.000	0.000	0.000	0.000
41	A	941	THR	0	-0.082	-0.045	19.706	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	942	VAL	0	-0.050	-0.020	19.995	-0.037	-0.037	0.000	0.000	0.000	0.000
43	A	943	THR	0	0.001	-0.024	18.084	0.003	0.003	0.000	0.000	0.000	0.000
44	A	944	HIS	0	-0.029	-0.006	18.441	0.014	0.014	0.000	0.000	0.000	0.000
45	A	945	PHE	0	-0.016	-0.004	21.713	0.004	0.004	0.000	0.000	0.000	0.000
46	A	946	ILE	0	0.020	0.019	21.319	0.008	0.008	0.000	0.000	0.000	0.000
47	A	947	TYR	0	-0.043	-0.059	25.354	0.024	0.024	0.000	0.000	0.000	0.000
48	A	948	GLN	0	0.085	0.050	28.517	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	949	GLY	0	-0.064	-0.053	31.552	0.008	0.008	0.000	0.000	0.000	0.000
50	A	950	ARG	1	0.935	0.990	35.076	0.097	0.097	0.000	0.000	0.000	0.000
51	A	951	PRO	0	0.089	0.028	37.810	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	952	ASN	0	-0.020	-0.019	39.427	0.004	0.004	0.000	0.000	0.000	0.000
53	A	953	ASP	-1	-0.795	-0.887	36.833	-0.115	-0.115	0.000	0.000	0.000	0.000
54	A	954	THR	0	0.005	-0.005	39.049	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	955	ASN	0	-0.019	0.000	34.846	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	956	ARG	1	1.003	0.989	36.864	0.088	0.088	0.000	0.000	0.000	0.000
57	A	957	GLU	-1	-0.778	-0.897	30.019	-0.163	-0.163	0.000	0.000	0.000	0.000
58	A	958	TYR	0	0.046	0.020	31.927	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	959	LYS	1	0.910	0.951	33.042	0.095	0.095	0.000	0.000	0.000	0.000
60	A	960	SER	0	0.003	0.006	33.419	0.003	0.003	0.000	0.000	0.000	0.000
61	A	961	VAL	0	0.036	0.024	27.854	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	962	LYS	1	0.914	0.955	30.176	0.125	0.125	0.000	0.000	0.000	0.000
63	A	963	GLU	-1	-0.983	-0.991	32.217	-0.115	-0.115	0.000	0.000	0.000	0.000
64	A	964	ARG	1	0.888	0.946	28.955	0.162	0.162	0.000	0.000	0.000	0.000
65	A	965	GLY	0	-0.009	0.009	28.987	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	966	VAL	0	-0.008	0.014	24.294	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	967	HIS	0	0.023	0.018	21.386	0.034	0.034	0.000	0.000	0.000	0.000
68	A	968	ILE	0	-0.058	-0.032	24.971	0.000	0.000	0.000	0.000	0.000	0.000
69	A	969	VAL	0	0.002	0.009	22.488	0.007	0.007	0.000	0.000	0.000	0.000
70	A	970	SER	0	0.002	0.016	25.973	0.003	0.003	0.000	0.000	0.000	0.000
71	A	971	GLU	-1	-0.788	-0.928	24.066	-0.216	-0.216	0.000	0.000	0.000	0.000
72	A	972	HIS	0	0.010	-0.008	23.103	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	973	TRP	0	0.019	0.024	17.442	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	974	LEU	0	-0.005	-0.001	16.770	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	975	LEU	0	-0.034	-0.022	18.453	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	976	ASP	-1	-0.768	-0.858	19.636	-0.253	-0.253	0.000	0.000	0.000	0.000
77	A	977	CYS	0	-0.053	-0.018	15.546	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	978	ALA	0	-0.026	-0.017	14.903	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	979	GLN	0	-0.051	-0.016	15.400	0.010	0.010	0.000	0.000	0.000	0.000
80	A	980	GLU	-1	-0.866	-0.933	16.372	-0.278	-0.278	0.000	0.000	0.000	0.000
81	A	981	CYS	0	-0.062	-0.015	9.745	-0.087	-0.087	0.000	0.000	0.000	0.000
82	A	982	LYS	1	0.787	0.876	11.731	0.304	0.304	0.000	0.000	0.000	0.000
83	A	983	HIS	0	-0.013	-0.022	13.682	-0.050	-0.050	0.000	0.000	0.000	0.000
84	A	984	LEU	0	-0.038	-0.017	15.262	0.041	0.041	0.000	0.000	0.000	0.000
85	A	985	PRO	0	0.041	0.013	18.852	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	986	GLU	-1	-0.731	-0.842	19.650	-0.388	-0.388	0.000	0.000	0.000	0.000
87	A	987	SER	0	-0.053	-0.027	23.314	0.016	0.016	0.000	0.000	0.000	0.000
88	A	988	LEU	0	0.002	0.004	23.991	0.021	0.021	0.000	0.000	0.000	0.000
89	A	989	TYR	0	-0.097	-0.063	22.754	0.007	0.007	0.000	0.000	0.000	0.000
90	A	990	PRO	0	0.052	0.034	26.919	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	991	HIS	0	0.000	-0.014	29.725	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	992	THR	0	-0.058	-0.037	30.913	0.003	0.003	0.000	0.000	0.000	0.000
93	A	993	TYR	0	-0.012	0.010	27.430	0.009	0.009	0.000	0.000	0.000	0.000
94	A	994	ASN	0	0.021	0.013	31.536	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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