FMO DATABASE

FMODB ID: P7MMK

Calculation Name: 3JVE-A-Xray29

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: 2018-09-06

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	189
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-927468.743056
FMO2-HF: Nuclear repulsion	882307.907247
FMO2-HF: Total energy	-45160.835809
FMO2-MP2: Total energy	-45290.427228

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:900:ACE)

Summations of interaction energy for fragment #1(A:900:ACE)

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.
1.077	1.907	-0.012	-0.348	-0.47	0

Interaction energy analysis for fragmet #1(A:900:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.005

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].
3	A	902	PRO	0	0.036	0.031	3.847	1.000	1.810	-0.011	-0.345	-0.453
4	A	903	LYS	1	0.905	0.964	6.701	0.585	0.585	0.000	0.000	0.000
5	A	904	PRO	0	0.024	0.009	9.495	0.095	0.095	0.000	0.000	0.000
6	A	905	LEU	0	0.036	0.024	12.809	0.040	0.040	0.000	0.000	0.000
7	A	906	HIS	0	0.015	0.021	5.773	0.055	0.055	0.000	0.000	0.000
8	A	907	LYS	1	0.946	0.963	10.617	-0.353	-0.353	0.000	0.000	0.000
9	A	908	VAL	0	0.005	0.039	13.139	-0.003	-0.003	0.000	0.000	0.000
10	A	909	VAL	0	-0.008	0.009	15.648	0.018	0.018	0.000	0.000	0.000
11	A	910	VAL	0	0.019	0.006	18.264	-0.012	-0.012	0.000	0.000	0.000
12	A	911	CYS	0	-0.006	0.002	20.774	0.011	0.011	0.000	0.000	0.000
13	A	912	VAL	0	-0.001	0.010	24.050	-0.007	-0.007	0.000	0.000	0.000
14	A	913	SER	0	-0.024	-0.011	26.446	0.004	0.004	0.000	0.000	0.000
15	A	914	LYS	1	0.903	0.943	30.075	-0.032	-0.032	0.000	0.000	0.000
16	A	915	LYS	1	0.800	0.916	32.580	-0.001	-0.001	0.000	0.000	0.000
17	A	916	LEU	0	-0.060	-0.021	29.446	-0.002	-0.002	0.000	0.000	0.000
18	A	917	SER	0	0.058	0.039	30.162	-0.002	-0.002	0.000	0.000	0.000
19	A	918	LYS	1	0.936	0.961	30.400	0.001	0.001	0.000	0.000	0.000
20	A	919	LYS	1	0.884	0.947	28.227	0.019	0.019	0.000	0.000	0.000
21	A	920	GLN	0	-0.020	0.011	25.598	-0.004	-0.004	0.000	0.000	0.000
22	A	921	SER	0	0.051	0.012	23.954	0.004	0.004	0.000	0.000	0.000
23	A	922	GLU	-1	-0.770	-0.842	22.702	-0.034	-0.034	0.000	0.000	0.000
24	A	923	LEU	0	0.034	0.006	22.326	-0.007	-0.007	0.000	0.000	0.000
25	A	924	ASN	0	0.034	0.027	20.225	-0.005	-0.005	0.000	0.000	0.000
26	A	925	GLY	0	0.002	0.011	18.309	0.004	0.004	0.000	0.000	0.000
27	A	926	ILE	0	0.017	0.013	17.488	-0.014	-0.014	0.000	0.000	0.000
28	A	927	ALA	0	0.029	0.007	17.250	-0.022	-0.022	0.000	0.000	0.000
29	A	928	ALA	0	-0.011	0.003	14.230	-0.011	-0.011	0.000	0.000	0.000
30	A	929	SER	0	-0.014	0.011	12.711	-0.015	-0.015	0.000	0.000	0.000
31	A	930	LEU	0	0.012	0.010	12.723	-0.070	-0.070	0.000	0.000	0.000
32	A	931	GLY	0	-0.026	-0.010	10.343	-0.037	-0.037	0.000	0.000	0.000
33	A	932	ALA	0	0.004	0.021	10.955	0.079	0.079	0.000	0.000	0.000
34	A	933	ASP	-1	-0.824	-0.893	13.029	0.263	0.263	0.000	0.000	0.000
35	A	934	TYR	0	-0.026	-0.023	15.281	-0.029	-0.029	0.000	0.000	0.000
36	A	935	ARG	1	0.815	0.910	17.195	-0.124	-0.124	0.000	0.000	0.000
37	A	936	TRP	0	-0.001	-0.015	22.142	-0.017	-0.017	0.000	0.000	0.000
38	A	937	SER	0	-0.039	-0.019	25.151	-0.008	-0.008	0.000	0.000	0.000
39	A	938	PHE	0	0.050	0.002	26.090	0.006	0.006	0.000	0.000	0.000
40	A	939	ASP	-1	-0.741	-0.832	24.013	0.095	0.095	0.000	0.000	0.000
41	A	940	GLU	-1	-0.863	-0.926	25.083	0.079	0.079	0.000	0.000	0.000
42	A	941	THR	0	-0.054	-0.018	20.062	0.006	0.006	0.000	0.000	0.000
43	A	942	VAL	0	-0.030	0.001	20.570	0.003	0.003	0.000	0.000	0.000
44	A	943	THR	0	0.013	-0.008	18.754	0.001	0.001	0.000	0.000	0.000
45	A	944	HIS	0	0.025	0.021	19.626	0.001	0.001	0.000	0.000	0.000
46	A	945	PHE	0	-0.011	0.000	23.084	0.002	0.002	0.000	0.000	0.000
47	A	946	ILE	0	0.014	0.016	23.057	-0.006	-0.006	0.000	0.000	0.000
48	A	947	TYR	0	-0.062	-0.068	27.046	0.005	0.005	0.000	0.000	0.000
49	A	948	GLN	0	0.074	0.039	30.828	-0.002	-0.002	0.000	0.000	0.000
50	A	949	GLY	0	-0.054	-0.044	33.693	0.003	0.003	0.000	0.000	0.000
51	A	950	ARG	1	0.914	0.982	37.103	-0.003	-0.003	0.000	0.000	0.000
52	A	951	PRO	0	0.109	0.042	39.575	0.002	0.002	0.000	0.000	0.000
53	A	952	ASN	0	0.027	0.032	40.878	-0.001	-0.001	0.000	0.000	0.000
54	A	953	ASP	-1	-0.715	-0.836	38.544	0.003	0.003	0.000	0.000	0.000
55	A	954	THR	0	0.033	0.007	40.507	0.001	0.001	0.000	0.000	0.000
56	A	955	ASN	0	-0.021	0.001	36.190	0.003	0.003	0.000	0.000	0.000
57	A	956	ARG	1	0.980	0.975	38.187	-0.019	-0.019	0.000	0.000	0.000
58	A	957	GLU	-1	-0.677	-0.819	31.088	0.026	0.026	0.000	0.000	0.000
59	A	958	TYR	0	0.010	0.017	33.445	0.002	0.002	0.000	0.000	0.000
60	A	959	LYS	1	0.865	0.925	34.284	-0.013	-0.013	0.000	0.000	0.000
61	A	960	SER	0	-0.007	0.000	34.434	0.001	0.001	0.000	0.000	0.000
62	A	961	VAL	0	0.056	0.037	28.915	0.002	0.002	0.000	0.000	0.000
63	A	962	LYS	1	0.914	0.964	31.107	-0.008	-0.008	0.000	0.000	0.000
64	A	963	GLU	-1	-0.889	-0.946	33.262	0.024	0.024	0.000	0.000	0.000
65	A	964	ARG	1	0.854	0.921	29.183	-0.049	-0.049	0.000	0.000	0.000
66	A	965	GLY	0	-0.011	0.008	29.516	0.003	0.003	0.000	0.000	0.000
67	A	966	VAL	0	-0.012	0.016	25.205	-0.001	-0.001	0.000	0.000	0.000
68	A	967	HIS	0	0.047	0.034	22.476	-0.008	-0.008	0.000	0.000	0.000
69	A	968	ILE	0	-0.047	-0.017	26.209	0.003	0.003	0.000	0.000	0.000
70	A	969	VAL	0	0.003	0.012	24.391	-0.003	-0.003	0.000	0.000	0.000
71	A	970	SER	0	0.023	0.030	27.825	0.003	0.003	0.000	0.000	0.000
72	A	971	GLU	-1	-0.755	-0.904	26.514	-0.028	-0.028	0.000	0.000	0.000
73	A	972	HIS	0	0.012	0.007	25.899	-0.008	-0.008	0.000	0.000	0.000
74	A	973	TRP	0	0.008	0.016	19.207	-0.004	-0.004	0.000	0.000	0.000
75	A	974	LEU	0	-0.006	-0.002	19.301	-0.009	-0.009	0.000	0.000	0.000
76	A	975	LEU	0	-0.021	-0.007	21.580	-0.013	-0.013	0.000	0.000	0.000
77	A	976	ASP	-1	-0.667	-0.790	23.384	-0.080	-0.080	0.000	0.000	0.000
78	A	977	CYS	0	-0.041	-0.009	18.784	-0.013	-0.013	0.000	0.000	0.000
79	A	978	ALA	0	-0.033	-0.020	18.685	-0.027	-0.027	0.000	0.000	0.000
80	A	979	GLN	0	-0.008	0.014	19.724	-0.014	-0.014	0.000	0.000	0.000
81	A	980	GLU	-1	-0.807	-0.889	21.054	-0.149	-0.149	0.000	0.000	0.000
82	A	981	CYS	0	-0.039	0.000	14.805	-0.037	-0.037	0.000	0.000	0.000
83	A	982	LYS	1	0.826	0.897	16.207	0.149	0.149	0.000	0.000	0.000
84	A	983	HIS	0	0.023	0.001	16.026	0.008	0.008	0.000	0.000	0.000
85	A	984	LEU	0	-0.029	-0.009	17.904	0.003	0.003	0.000	0.000	0.000
86	A	985	PRO	0	0.064	0.032	21.702	0.010	0.010	0.000	0.000	0.000
87	A	986	GLU	-1	-0.735	-0.841	21.214	-0.029	-0.029	0.000	0.000	0.000
88	A	987	SER	0	-0.011	-0.003	25.257	0.002	0.002	0.000	0.000	0.000
89	A	988	LEU	0	0.053	0.037	26.934	0.003	0.003	0.000	0.000	0.000
90	A	989	TYR	0	-0.059	-0.034	25.826	-0.001	-0.001	0.000	0.000	0.000
91	A	990	PRO	0	0.038	0.034	29.285	0.005	0.005	0.000	0.000	0.000
92	A	991	HIS	0	0.004	-0.010	31.691	-0.002	-0.002	0.000	0.000	0.000
93	A	992	THR	0	-0.040	-0.022	32.934	-0.001	-0.001	0.000	0.000	0.000
94	A	993	TYR	0	-0.056	-0.034	31.040	0.001	0.001	0.000	0.000	0.000
95	A	994	ASN	0	-0.048	-0.027	34.271	0.000	0.000	0.000	0.000	0.000
96	A	995	NME	0	0.053	0.044	34.068	0.000	0.000	0.000	0.000	0.000
97	A	1	HOH	0	-0.010	-0.012	23.472	-0.003	-0.003	0.000	0.000	0.000
98	A	2	HOH	0	0.010	0.008	20.566	-0.003	-0.003	0.000	0.000	0.000
99	A	3	HOH	0	-0.003	-0.003	27.662	0.001	0.001	0.000	0.000	0.000
100	A	4	HOH	0	-0.010	-0.014	29.036	-0.001	-0.001	0.000	0.000	0.000
101	A	5	HOH	0	-0.015	-0.021	28.693	-0.001	-0.001	0.000	0.000	0.000
102	A	6	HOH	0	-0.036	-0.026	23.721	-0.001	-0.001	0.000	0.000	0.000
103	A	7	HOH	0	-0.021	-0.015	28.794	0.002	0.002	0.000	0.000	0.000
104	A	8	HOH	0	-0.028	-0.021	43.483	0.000	0.000	0.000	0.000	0.000
105	A	9	HOH	0	0.020	0.011	30.940	0.000	0.000	0.000	0.000	0.000
106	A	11	HOH	0	-0.027	-0.031	44.982	0.000	0.000	0.000	0.000	0.000
107	A	12	HOH	0	0.048	0.026	40.405	0.000	0.000	0.000	0.000	0.000
108	A	13	HOH	0	0.046	0.037	15.228	-0.007	-0.007	0.000	0.000	0.000
109	A	14	HOH	0	0.011	-0.008	33.486	-0.001	-0.001	0.000	0.000	0.000
110	A	15	HOH	0	-0.029	-0.021	30.737	0.002	0.002	0.000	0.000	0.000
111	A	16	HOH	0	-0.022	-0.012	8.092	-0.126	-0.126	0.000	0.000	0.000
112	A	17	HOH	0	-0.052	-0.036	24.778	-0.002	-0.002	0.000	0.000	0.000
113	A	18	HOH	0	-0.010	-0.016	28.467	0.001	0.001	0.000	0.000	0.000
114	A	19	HOH	0	-0.016	-0.012	35.498	0.000	0.000	0.000	0.000	0.000
115	A	20	HOH	0	-0.040	-0.034	27.868	0.000	0.000	0.000	0.000	0.000
116	A	21	HOH	0	-0.009	-0.013	17.610	-0.001	-0.001	0.000	0.000	0.000
117	A	22	HOH	0	-0.052	-0.041	20.438	0.000	0.000	0.000	0.000	0.000
118	A	23	HOH	0	0.012	0.012	23.381	-0.003	-0.003	0.000	0.000	0.000
119	A	24	HOH	0	-0.013	-0.009	18.851	0.009	0.009	0.000	0.000	0.000
120	A	25	HOH	0	-0.001	0.011	29.156	0.003	0.003	0.000	0.000	0.000
121	A	26	HOH	0	0.049	0.034	24.981	-0.002	-0.002	0.000	0.000	0.000
122	A	28	HOH	0	0.009	0.008	29.091	0.000	0.000	0.000	0.000	0.000
123	A	29	HOH	0	0.003	0.004	33.782	0.000	0.000	0.000	0.000	0.000
124	A	30	HOH	0	0.006	0.005	36.122	0.000	0.000	0.000	0.000	0.000
125	A	31	HOH	0	-0.027	-0.023	23.297	-0.003	-0.003	0.000	0.000	0.000
126	A	32	HOH	0	-0.011	-0.001	20.456	-0.004	-0.004	0.000	0.000	0.000
127	A	33	HOH	0	-0.020	-0.016	21.388	0.003	0.003	0.000	0.000	0.000
128	A	34	HOH	0	-0.007	-0.016	28.418	0.002	0.002	0.000	0.000	0.000
129	A	36	HOH	0	-0.040	-0.028	21.450	0.003	0.003	0.000	0.000	0.000
130	A	37	HOH	0	-0.051	-0.034	16.275	0.013	0.013	0.000	0.000	0.000
131	A	39	HOH	0	-0.055	-0.043	37.112	-0.001	-0.001	0.000	0.000	0.000
132	A	40	HOH	0	0.002	-0.005	39.929	0.000	0.000	0.000	0.000	0.000
133	A	41	HOH	0	-0.020	-0.020	25.015	0.001	0.001	0.000	0.000	0.000
134	A	43	HOH	0	-0.052	-0.046	28.886	-0.001	-0.001	0.000	0.000	0.000
135	A	44	HOH	0	-0.047	-0.037	29.130	0.000	0.000	0.000	0.000	0.000
136	A	46	HOH	0	0.012	0.004	32.850	0.000	0.000	0.000	0.000	0.000
137	A	47	HOH	0	-0.021	-0.013	38.231	-0.001	-0.001	0.000	0.000	0.000
138	A	48	HOH	0	-0.026	-0.027	36.598	0.000	0.000	0.000	0.000	0.000
139	A	49	HOH	0	-0.017	-0.008	14.179	0.003	0.003	0.000	0.000	0.000
140	A	50	HOH	0	-0.037	-0.019	11.459	0.016	0.016	0.000	0.000	0.000
141	A	51	HOH	0	-0.012	-0.023	37.716	-0.001	-0.001	0.000	0.000	0.000
142	A	52	HOH	0	0.049	0.029	43.987	0.001	0.001	0.000	0.000	0.000
143	A	53	HOH	0	-0.021	-0.014	11.418	0.011	0.011	0.000	0.000	0.000
144	A	54	HOH	0	-0.037	-0.032	27.778	0.000	0.000	0.000	0.000	0.000
145	A	55	HOH	0	0.001	-0.001	14.524	-0.016	-0.016	0.000	0.000	0.000
146	A	56	HOH	0	-0.036	-0.022	15.164	0.010	0.010	0.000	0.000	0.000
147	A	57	HOH	0	-0.017	-0.018	26.834	-0.001	-0.001	0.000	0.000	0.000
148	A	58	HOH	0	-0.054	-0.040	25.238	0.003	0.003	0.000	0.000	0.000
149	A	60	HOH	0	0.050	0.025	32.884	0.000	0.000	0.000	0.000	0.000
150	A	61	HOH	0	-0.014	-0.012	30.089	-0.001	-0.001	0.000	0.000	0.000
151	A	62	HOH	0	-0.017	-0.014	17.777	0.007	0.007	0.000	0.000	0.000
152	A	63	HOH	0	0.008	0.004	17.267	0.005	0.005	0.000	0.000	0.000
153	A	64	HOH	0	-0.023	-0.016	22.862	0.000	0.000	0.000	0.000	0.000
154	A	65	HOH	0	0.029	0.026	27.608	-0.002	-0.002	0.000	0.000	0.000
155	A	66	HOH	0	0.039	0.030	45.731	0.000	0.000	0.000	0.000	0.000
156	A	67	HOH	0	0.007	0.023	27.860	0.000	0.000	0.000	0.000	0.000
157	A	68	HOH	0	-0.043	-0.026	34.168	0.001	0.001	0.000	0.000	0.000
158	A	70	HOH	0	-0.026	-0.018	28.818	0.002	0.002	0.000	0.000	0.000
159	A	71	HOH	0	-0.034	-0.022	26.759	0.001	0.001	0.000	0.000	0.000
160	A	73	HOH	0	-0.005	-0.003	26.028	0.002	0.002	0.000	0.000	0.000
161	A	74	HOH	0	-0.038	-0.028	31.648	0.002	0.002	0.000	0.000	0.000
162	A	77	HOH	0	-0.064	-0.036	13.586	0.001	0.001	0.000	0.000	0.000
163	A	78	HOH	0	-0.017	-0.024	7.478	-0.071	-0.071	0.000	0.000	0.000
164	A	85	HOH	0	0.008	0.003	34.570	-0.001	-0.001	0.000	0.000	0.000
165	A	88	HOH	0	-0.037	-0.024	24.195	-0.003	-0.003	0.000	0.000	0.000
166	A	93	HOH	0	-0.038	-0.028	26.869	0.000	0.000	0.000	0.000	0.000
167	A	95	HOH	0	-0.027	-0.024	31.823	0.001	0.001	0.000	0.000	0.000
168	A	101	HOH	0	-0.016	-0.010	39.831	-0.001	-0.001	0.000	0.000	0.000
169	A	103	HOH	0	-0.029	-0.025	16.439	0.001	0.001	0.000	0.000	0.000
170	A	104	HOH	0	0.054	0.025	31.746	-0.002	-0.002	0.000	0.000	0.000
171	A	106	HOH	0	-0.021	-0.022	4.604	0.002	0.022	-0.001	-0.003	-0.017
172	A	109	HOH	0	-0.039	-0.042	24.004	0.004	0.004	0.000	0.000	0.000
173	A	117	HOH	0	-0.025	-0.024	34.162	-0.001	-0.001	0.000	0.000	0.000
174	A	119	HOH	0	-0.009	-0.009	26.707	0.001	0.001	0.000	0.000	0.000
175	A	121	HOH	0	-0.011	-0.008	36.184	0.000	0.000	0.000	0.000	0.000
176	A	123	HOH	0	-0.102	-0.083	28.880	0.001	0.001	0.000	0.000	0.000
177	A	129	HOH	0	0.057	0.037	28.277	-0.002	-0.002	0.000	0.000	0.000
178	A	130	HOH	0	-0.002	-0.011	41.703	0.000	0.000	0.000	0.000	0.000
179	A	131	HOH	0	-0.049	-0.056	15.200	-0.016	-0.016	0.000	0.000	0.000
180	A	134	HOH	0	0.031	0.020	7.658	-0.031	-0.031	0.000	0.000	0.000
181	A	135	HOH	0	0.011	-0.003	31.164	-0.001	-0.001	0.000	0.000	0.000
182	A	137	HOH	0	-0.018	-0.003	39.500	-0.001	-0.001	0.000	0.000	0.000
183	A	138	HOH	0	-0.020	-0.020	39.573	-0.001	-0.001	0.000	0.000	0.000
184	A	139	HOH	0	0.002	0.007	35.671	-0.001	-0.001	0.000	0.000	0.000
185	A	141	HOH	0	-0.026	-0.015	32.420	0.001	0.001	0.000	0.000	0.000
186	A	143	HOH	0	0.025	0.001	36.341	0.000	0.000	0.000	0.000	0.000
187	A	144	HOH	0	-0.037	-0.022	36.800	0.000	0.000	0.000	0.000	0.000
188	A	150	HOH	0	-0.044	-0.032	12.044	-0.021	-0.021	0.000	0.000	0.000
189	A	152	HOH	0	-0.054	-0.030	38.279	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:900:ACE)