FMO DATABASE

FMODB ID: 3JR7L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-713300.798709
FMO2-HF: Nuclear repulsion	675381.427904
FMO2-HF: Total energy	-37919.370805
FMO2-MP2: Total energy	-38030.42226

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.
0.731	2.791	0.075	-0.927	-1.207	0.003

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 : 0.044 / q_NPA : 0.021

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	0.916	0.972	3.127	1.274	3.048	0.076	-0.869	-0.981	0.003
4	A	904	PRO	0	0.018	0.015	6.786	0.101	0.101	0.000	0.000	0.000	0.000
5	A	905	LEU	0	0.041	0.030	10.417	0.134	0.134	0.000	0.000	0.000	0.000
6	A	906	HIS	0	-0.013	-0.006	4.170	-0.200	0.086	-0.001	-0.058	-0.226	0.000
7	A	907	LYS	1	0.898	0.945	9.864	0.900	0.900	0.000	0.000	0.000	0.000
8	A	908	VAL	0	-0.013	0.015	12.683	0.116	0.116	0.000	0.000	0.000	0.000
9	A	909	VAL	0	-0.008	0.007	14.811	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	910	VAL	0	0.030	0.010	17.432	0.047	0.047	0.000	0.000	0.000	0.000
11	A	911	CYS	0	-0.050	-0.018	19.777	0.023	0.023	0.000	0.000	0.000	0.000
12	A	912	VAL	0	0.007	0.023	22.531	0.008	0.008	0.000	0.000	0.000	0.000
13	A	913	SER	0	-0.011	-0.016	24.999	0.018	0.018	0.000	0.000	0.000	0.000
14	A	914	LYS	1	0.933	0.930	28.736	0.136	0.136	0.000	0.000	0.000	0.000
15	A	915	LYS	1	0.735	0.878	31.556	0.124	0.124	0.000	0.000	0.000	0.000
16	A	916	LEU	0	0.011	0.011	27.452	0.008	0.008	0.000	0.000	0.000	0.000
17	A	917	SER	0	0.007	-0.003	28.100	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	918	LYS	1	0.913	0.948	28.353	0.099	0.099	0.000	0.000	0.000	0.000
19	A	919	LYS	1	0.905	0.944	25.344	0.161	0.161	0.000	0.000	0.000	0.000
20	A	920	GLN	0	-0.065	-0.023	24.084	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	921	SER	0	0.036	-0.005	22.105	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	922	GLU	-1	-0.941	-0.952	20.544	-0.183	-0.183	0.000	0.000	0.000	0.000
23	A	923	LEU	0	0.026	0.002	19.612	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	924	ASN	0	0.014	0.002	18.527	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	925	GLY	0	0.021	0.023	16.172	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	926	ILE	0	0.002	0.010	14.776	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	927	ALA	0	0.016	0.001	14.265	-0.065	-0.065	0.000	0.000	0.000	0.000
28	A	928	ALA	0	0.013	0.009	12.393	-0.108	-0.108	0.000	0.000	0.000	0.000
29	A	929	SER	0	-0.077	-0.045	10.393	-0.122	-0.122	0.000	0.000	0.000	0.000
30	A	930	LEU	0	-0.011	-0.005	9.429	-0.136	-0.136	0.000	0.000	0.000	0.000
31	A	931	GLY	0	-0.037	-0.024	8.660	-0.224	-0.224	0.000	0.000	0.000	0.000
32	A	932	ALA	0	-0.028	-0.003	9.285	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	933	ASP	-1	-0.815	-0.892	12.943	-0.402	-0.402	0.000	0.000	0.000	0.000
34	A	934	TYR	0	-0.039	-0.023	14.619	0.048	0.048	0.000	0.000	0.000	0.000
35	A	935	ARG	1	0.814	0.900	17.257	0.350	0.350	0.000	0.000	0.000	0.000
36	A	936	TRP	0	0.030	0.007	21.293	0.000	0.000	0.000	0.000	0.000	0.000
37	A	937	SER	0	-0.050	-0.030	24.773	0.019	0.019	0.000	0.000	0.000	0.000
38	A	938	PHE	0	0.011	-0.012	25.702	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	939	ASP	-1	-0.766	-0.864	23.733	-0.212	-0.212	0.000	0.000	0.000	0.000
40	A	940	GLU	-1	-0.931	-0.974	25.343	-0.179	-0.179	0.000	0.000	0.000	0.000
41	A	941	THR	0	-0.073	-0.055	20.196	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	942	VAL	0	-0.052	-0.026	20.576	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	943	THR	0	0.013	-0.017	18.655	0.008	0.008	0.000	0.000	0.000	0.000
44	A	944	HIS	0	-0.026	-0.009	18.982	0.008	0.008	0.000	0.000	0.000	0.000
45	A	945	PHE	0	-0.002	0.001	22.024	0.003	0.003	0.000	0.000	0.000	0.000
46	A	946	ILE	0	0.034	0.025	21.271	0.006	0.006	0.000	0.000	0.000	0.000
47	A	947	TYR	0	-0.061	-0.070	25.321	0.021	0.021	0.000	0.000	0.000	0.000
48	A	948	GLN	0	0.094	0.050	29.035	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	949	GLY	0	-0.047	-0.040	31.635	0.007	0.007	0.000	0.000	0.000	0.000
50	A	950	ARG	1	0.887	0.970	35.257	0.090	0.090	0.000	0.000	0.000	0.000
51	A	951	PRO	0	0.097	0.030	37.793	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	952	ASN	0	0.009	0.004	39.610	0.002	0.002	0.000	0.000	0.000	0.000
53	A	953	ASP	-1	-0.755	-0.867	36.942	-0.103	-0.103	0.000	0.000	0.000	0.000
54	A	954	THR	0	0.000	-0.007	39.194	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	955	ASN	0	-0.012	0.006	35.398	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	956	ARG	1	1.026	0.999	37.013	0.082	0.082	0.000	0.000	0.000	0.000
57	A	957	GLU	-1	-0.779	-0.856	31.247	-0.145	-0.145	0.000	0.000	0.000	0.000
58	A	958	TYR	0	0.052	0.020	32.280	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	959	LYS	1	0.908	0.957	33.248	0.089	0.089	0.000	0.000	0.000	0.000
60	A	960	SER	0	0.023	0.001	33.514	0.000	0.000	0.000	0.000	0.000	0.000
61	A	961	VAL	0	0.011	0.009	28.049	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	962	LYS	1	0.865	0.930	30.472	0.115	0.115	0.000	0.000	0.000	0.000
63	A	963	GLU	-1	-0.928	-0.975	32.466	-0.108	-0.108	0.000	0.000	0.000	0.000
64	A	964	ARG	1	0.908	0.961	28.693	0.161	0.161	0.000	0.000	0.000	0.000
65	A	965	GLY	0	-0.016	0.006	29.731	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	966	VAL	0	-0.022	0.009	24.669	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	967	HIS	0	0.022	0.015	21.807	0.033	0.033	0.000	0.000	0.000	0.000
68	A	968	ILE	0	-0.069	-0.037	25.450	0.000	0.000	0.000	0.000	0.000	0.000
69	A	969	VAL	0	-0.019	-0.001	22.819	0.007	0.007	0.000	0.000	0.000	0.000
70	A	970	SER	0	0.017	0.019	26.318	0.003	0.003	0.000	0.000	0.000	0.000
71	A	971	GLU	-1	-0.795	-0.900	24.302	-0.187	-0.187	0.000	0.000	0.000	0.000
72	A	972	HIS	0	0.011	-0.007	23.089	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	973	TRP	0	0.014	0.019	17.622	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	974	LEU	0	0.003	0.003	16.750	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	975	LEU	0	-0.028	-0.013	18.328	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	976	ASP	-1	-0.769	-0.859	19.477	-0.223	-0.223	0.000	0.000	0.000	0.000
77	A	977	CYS	0	-0.049	-0.028	15.782	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	978	ALA	0	-0.037	-0.021	14.870	-0.057	-0.057	0.000	0.000	0.000	0.000
79	A	979	GLN	0	-0.082	-0.039	15.393	0.012	0.012	0.000	0.000	0.000	0.000
80	A	980	GLU	-1	-0.835	-0.898	16.550	-0.246	-0.246	0.000	0.000	0.000	0.000
81	A	981	CYS	0	-0.031	-0.001	10.227	-0.050	-0.050	0.000	0.000	0.000	0.000
82	A	982	LYS	1	0.779	0.859	11.939	0.251	0.251	0.000	0.000	0.000	0.000
83	A	983	HIS	0	0.005	-0.006	14.077	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	984	LEU	0	-0.007	-0.003	15.647	0.036	0.036	0.000	0.000	0.000	0.000
85	A	985	PRO	0	0.012	-0.004	19.388	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	986	GLU	-1	-0.739	-0.849	20.281	-0.332	-0.332	0.000	0.000	0.000	0.000
87	A	987	SER	0	-0.046	-0.025	23.711	0.013	0.013	0.000	0.000	0.000	0.000
88	A	988	LEU	0	-0.002	0.006	24.307	0.019	0.019	0.000	0.000	0.000	0.000
89	A	989	TYR	0	-0.090	-0.066	23.088	0.006	0.006	0.000	0.000	0.000	0.000
90	A	990	PRO	0	0.067	0.037	27.030	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	991	HIS	0	0.000	-0.014	29.745	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	992	THR	0	-0.036	-0.028	31.012	0.004	0.004	0.000	0.000	0.000	0.000
93	A	993	TYR	0	-0.024	0.008	26.739	0.010	0.010	0.000	0.000	0.000	0.000
94	A	994	ASN	0	0.022	0.009	31.417	-0.002	-0.002	0.000	0.000	0.000	0.000

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