FMO DATABASE

FMODB ID: 17Q2Z

Calculation Name: 4C0G-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0G

Chain ID: A

ChEMBL ID: CHEMBL4105769

UniProt ID: O75175

Base Structure: X-ray

Registration Date: 2023-09-20

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-748328.341464
FMO2-HF: Nuclear repulsion	709017.353343
FMO2-HF: Total energy	-39310.988121
FMO2-MP2: Total energy	-39427.712663

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:659:THR)

Summations of interaction energy for fragment #1(A:659:THR)

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.
-11.779	-4.318	0.813	-3.256	-5.02	0.015

Interaction energy analysis for fragmet #1(A:659:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.001

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

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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	661	GLU	-1	-0.855	-0.937	3.099	-4.232	-0.662	0.088	-1.627	-2.032	0.002
4	A	662	PHE	0	-0.057	-0.017	2.648	-5.116	-2.491	0.659	-1.265	-2.019	0.013
5	A	663	TYR	0	0.055	0.006	2.809	-1.514	-0.586	0.061	-0.263	-0.726	0.000
6	A	664	GLN	0	-0.001	-0.002	6.395	-0.160	-0.160	0.000	0.000	0.000	0.000
7	A	665	ARG	1	0.913	0.959	6.293	0.596	0.596	0.000	0.000	0.000	0.000
8	A	666	LEU	0	-0.042	0.002	8.026	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	667	SER	0	0.062	0.041	10.974	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	668	THR	0	0.062	0.003	13.886	0.014	0.014	0.000	0.000	0.000	0.000
11	A	669	GLU	-1	-0.888	-0.930	15.777	0.047	0.047	0.000	0.000	0.000	0.000
12	A	670	THR	0	0.026	0.015	11.768	0.016	0.016	0.000	0.000	0.000	0.000
13	A	671	LEU	0	-0.052	-0.020	9.850	0.025	0.025	0.000	0.000	0.000	0.000
14	A	672	PHE	0	0.006	-0.003	12.762	0.017	0.017	0.000	0.000	0.000	0.000
15	A	673	PHE	0	0.043	0.021	14.238	0.018	0.018	0.000	0.000	0.000	0.000
16	A	674	ILE	0	-0.034	-0.021	9.020	0.020	0.020	0.000	0.000	0.000	0.000
17	A	675	PHE	0	-0.069	-0.048	12.991	0.030	0.030	0.000	0.000	0.000	0.000
18	A	676	TYR	0	-0.026	-0.039	14.430	0.004	0.004	0.000	0.000	0.000	0.000
19	A	677	TYR	0	0.003	0.011	16.508	0.001	0.001	0.000	0.000	0.000	0.000
20	A	678	LEU	0	-0.057	-0.010	11.742	0.027	0.027	0.000	0.000	0.000	0.000
21	A	679	GLU	-1	-0.869	-0.899	13.684	0.228	0.228	0.000	0.000	0.000	0.000
22	A	680	GLY	0	-0.020	-0.007	15.450	0.025	0.025	0.000	0.000	0.000	0.000
23	A	681	THR	0	-0.015	-0.041	11.166	0.079	0.079	0.000	0.000	0.000	0.000
24	A	682	LYS	1	0.937	0.955	6.018	-1.654	-1.654	0.000	0.000	0.000	0.000
25	A	683	ALA	0	0.058	0.021	6.707	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	684	GLN	0	0.107	0.069	7.759	-0.175	-0.175	0.000	0.000	0.000	0.000
27	A	685	TYR	0	-0.033	-0.019	8.311	-0.094	-0.094	0.000	0.000	0.000	0.000
28	A	686	LEU	0	-0.063	-0.054	3.365	-0.190	0.148	0.005	-0.101	-0.243	0.000
29	A	687	ALA	0	0.044	0.036	7.345	-0.111	-0.111	0.000	0.000	0.000	0.000
30	A	688	ALA	0	0.053	0.029	9.658	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	689	LYS	1	0.896	0.941	9.251	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	690	ALA	0	0.000	0.009	8.724	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	691	LEU	0	0.033	0.019	10.623	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	692	LYS	1	0.975	0.987	14.111	0.044	0.044	0.000	0.000	0.000	0.000
35	A	693	LYS	1	0.925	0.975	10.431	0.403	0.403	0.000	0.000	0.000	0.000
36	A	694	GLN	0	-0.001	0.001	12.662	0.006	0.006	0.000	0.000	0.000	0.000
37	A	695	SER	0	-0.036	-0.018	16.354	0.015	0.015	0.000	0.000	0.000	0.000
38	A	696	TRP	0	0.020	0.024	17.226	0.021	0.021	0.000	0.000	0.000	0.000
39	A	697	ARG	1	0.829	0.891	18.508	0.069	0.069	0.000	0.000	0.000	0.000
40	A	698	PHE	0	0.034	0.017	19.152	0.001	0.001	0.000	0.000	0.000	0.000
41	A	699	HIS	0	0.039	0.029	21.154	0.005	0.005	0.000	0.000	0.000	0.000
42	A	700	THR	0	0.015	-0.005	23.075	0.004	0.004	0.000	0.000	0.000	0.000
43	A	701	LYS	1	0.971	0.997	25.011	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	702	TYR	0	-0.050	-0.041	27.520	0.003	0.003	0.000	0.000	0.000	0.000
45	A	703	MET	0	0.028	0.038	22.279	0.001	0.001	0.000	0.000	0.000	0.000
46	A	704	MET	0	0.025	0.044	22.814	0.002	0.002	0.000	0.000	0.000	0.000
47	A	705	TRP	0	-0.007	0.005	15.949	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	706	PHE	0	0.002	-0.017	21.359	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	707	GLN	0	-0.001	-0.009	20.139	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	708	ARG	1	0.844	0.912	23.771	0.056	0.056	0.000	0.000	0.000	0.000
51	A	709	HIS	0	-0.033	-0.015	26.221	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	710	GLU	-1	-0.902	-0.956	28.524	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	711	GLU	-1	-0.958	-0.976	30.355	-0.056	-0.056	0.000	0.000	0.000	0.000
54	A	712	PRO	0	-0.064	-0.038	30.549	0.003	0.003	0.000	0.000	0.000	0.000
55	A	713	LYS	1	0.889	0.952	33.473	0.020	0.020	0.000	0.000	0.000	0.000
56	A	714	THR	0	0.022	-0.002	36.647	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	715	ILE	0	-0.016	-0.015	32.340	0.000	0.000	0.000	0.000	0.000	0.000
58	A	716	THR	0	-0.025	-0.002	35.242	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	717	ASP	-1	-0.847	-0.927	33.803	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	718	GLU	-1	-0.933	-0.967	32.949	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	719	PHE	0	-0.058	-0.033	32.418	0.003	0.003	0.000	0.000	0.000	0.000
62	A	720	GLU	-1	-0.695	-0.737	29.189	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	721	GLN	0	0.015	-0.009	33.163	0.003	0.003	0.000	0.000	0.000	0.000
64	A	722	GLY	0	0.027	0.013	33.630	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	723	THR	0	-0.004	0.008	31.551	0.006	0.006	0.000	0.000	0.000	0.000
66	A	724	TYR	0	-0.087	-0.097	27.175	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	725	ILE	0	0.000	0.010	23.709	0.005	0.005	0.000	0.000	0.000	0.000
68	A	726	TYR	0	-0.009	-0.021	24.261	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	727	PHE	0	-0.011	-0.002	20.783	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	728	ASP	-1	-0.831	-0.918	23.431	0.032	0.032	0.000	0.000	0.000	0.000
71	A	729	TYR	0	0.002	-0.007	22.355	0.000	0.000	0.000	0.000	0.000	0.000
72	A	730	GLU	-1	-0.933	-0.968	24.015	0.048	0.048	0.000	0.000	0.000	0.000
73	A	731	LYS	1	0.842	0.920	27.520	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	732	TRP	0	-0.055	-0.008	18.699	0.001	0.001	0.000	0.000	0.000	0.000
75	A	733	GLY	0	0.006	-0.006	24.851	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	734	GLN	0	-0.029	-0.012	22.634	0.000	0.000	0.000	0.000	0.000	0.000
77	A	735	ARG	1	0.873	0.938	25.388	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	736	LYS	1	0.961	0.979	27.971	0.027	0.027	0.000	0.000	0.000	0.000
79	A	737	LYS	1	0.902	0.962	30.577	0.009	0.009	0.000	0.000	0.000	0.000
80	A	738	GLU	-1	-0.802	-0.905	32.608	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	739	GLY	0	-0.018	-0.009	35.380	0.003	0.003	0.000	0.000	0.000	0.000
82	A	740	PHE	0	-0.084	-0.036	29.500	0.004	0.004	0.000	0.000	0.000	0.000
83	A	741	THR	0	0.046	0.013	34.004	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	742	PHE	0	0.002	0.000	24.926	0.004	0.004	0.000	0.000	0.000	0.000
85	A	743	GLU	-1	-0.843	-0.929	30.857	0.007	0.007	0.000	0.000	0.000	0.000
86	A	744	TYR	0	-0.022	-0.029	28.402	0.004	0.004	0.000	0.000	0.000	0.000
87	A	745	ARG	1	0.881	0.941	28.332	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	746	TYR	0	-0.077	-0.040	27.943	0.007	0.007	0.000	0.000	0.000	0.000
89	A	747	LEU	0	-0.005	0.009	23.502	0.000	0.000	0.000	0.000	0.000	0.000
90	A	748	GLU	-1	-0.982	-0.989	19.048	0.058	0.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:659:THR)