FMO DATABASE

FMODB ID: 8518Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-750245.636373
FMO2-HF: Nuclear repulsion	710933.759833
FMO2-HF: Total energy	-39311.876539
FMO2-MP2: Total energy	-39428.682762

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.
-16.236	-8.593	2.863	-3.954	-6.551	-0.012

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 : 0.003 / q_NPA : -0.006

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	-0.863	-0.946	2.432	-8.754	-4.322	1.871	-2.533	-3.771	-0.022
4	A	662	PHE	0	-0.023	-0.007	2.730	-2.896	-0.582	0.981	-1.207	-2.088	0.010
5	A	663	TYR	0	0.060	0.012	3.718	-1.614	-0.963	0.008	-0.153	-0.505	0.000
6	A	664	GLN	0	0.024	0.011	6.593	-0.153	-0.153	0.000	0.000	0.000	0.000
7	A	665	ARG	1	0.933	0.968	6.900	-0.906	-0.906	0.000	0.000	0.000	0.000
8	A	666	LEU	0	-0.025	0.008	8.027	-0.081	-0.081	0.000	0.000	0.000	0.000
9	A	667	SER	0	0.004	0.000	10.884	-0.058	-0.058	0.000	0.000	0.000	0.000
10	A	668	THR	0	0.050	-0.005	14.426	0.007	0.007	0.000	0.000	0.000	0.000
11	A	669	GLU	-1	-0.837	-0.907	16.263	0.132	0.132	0.000	0.000	0.000	0.000
12	A	670	THR	0	0.038	0.033	13.026	0.004	0.004	0.000	0.000	0.000	0.000
13	A	671	LEU	0	-0.065	-0.024	10.056	0.009	0.009	0.000	0.000	0.000	0.000
14	A	672	PHE	0	0.011	-0.003	13.301	0.003	0.003	0.000	0.000	0.000	0.000
15	A	673	PHE	0	0.017	0.009	14.978	0.000	0.000	0.000	0.000	0.000	0.000
16	A	674	ILE	0	-0.015	-0.016	9.671	0.002	0.002	0.000	0.000	0.000	0.000
17	A	675	PHE	0	-0.046	-0.026	13.670	0.009	0.009	0.000	0.000	0.000	0.000
18	A	676	TYR	0	-0.037	-0.041	15.259	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	677	TYR	0	-0.006	0.011	17.188	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	678	LEU	0	-0.034	-0.005	12.346	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	679	GLU	-1	-0.900	-0.932	14.355	0.175	0.175	0.000	0.000	0.000	0.000
22	A	680	GLY	0	0.019	0.011	16.270	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	681	THR	0	-0.036	-0.031	11.588	0.051	0.051	0.000	0.000	0.000	0.000
24	A	682	LYS	1	0.947	0.951	6.466	-1.577	-1.577	0.000	0.000	0.000	0.000
25	A	683	ALA	0	0.052	0.024	7.655	0.165	0.165	0.000	0.000	0.000	0.000
26	A	684	GLN	0	0.057	0.040	8.684	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	685	TYR	0	0.010	0.001	8.846	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	686	LEU	0	-0.061	-0.037	3.771	-0.090	0.156	0.003	-0.061	-0.187	0.000
29	A	687	ALA	0	0.039	0.020	7.825	-0.172	-0.172	0.000	0.000	0.000	0.000
30	A	688	ALA	0	0.042	0.026	10.213	-0.050	-0.050	0.000	0.000	0.000	0.000
31	A	689	LYS	1	0.896	0.945	9.125	-0.358	-0.358	0.000	0.000	0.000	0.000
32	A	690	ALA	0	-0.009	0.005	8.882	-0.067	-0.067	0.000	0.000	0.000	0.000
33	A	691	LEU	0	0.020	0.016	10.687	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	692	LYS	1	0.841	0.904	14.216	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	693	LYS	1	0.897	0.952	10.185	0.146	0.146	0.000	0.000	0.000	0.000
36	A	694	GLN	0	-0.022	0.005	12.634	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	695	SER	0	-0.024	-0.020	15.722	0.001	0.001	0.000	0.000	0.000	0.000
38	A	696	TRP	0	0.024	0.028	17.691	0.000	0.000	0.000	0.000	0.000	0.000
39	A	697	ARG	1	0.841	0.899	17.984	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	698	PHE	0	0.026	0.019	19.699	0.000	0.000	0.000	0.000	0.000	0.000
41	A	699	HIS	0	0.030	0.019	21.666	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	700	THR	0	0.012	-0.015	23.913	0.000	0.000	0.000	0.000	0.000	0.000
43	A	701	LYS	1	0.929	0.982	25.877	-0.047	-0.047	0.000	0.000	0.000	0.000
44	A	702	TYR	0	-0.010	-0.021	28.103	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	703	MET	0	0.044	0.039	23.040	0.002	0.002	0.000	0.000	0.000	0.000
46	A	704	MET	0	0.016	0.039	23.496	0.006	0.006	0.000	0.000	0.000	0.000
47	A	705	TRP	0	-0.017	0.000	16.343	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	706	PHE	0	0.013	-0.012	22.049	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	707	GLN	0	-0.002	-0.007	20.138	0.003	0.003	0.000	0.000	0.000	0.000
50	A	708	ARG	1	0.850	0.902	24.046	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	709	HIS	0	-0.029	-0.019	26.226	0.000	0.000	0.000	0.000	0.000	0.000
52	A	710	GLU	-1	-0.850	-0.907	28.723	0.025	0.025	0.000	0.000	0.000	0.000
53	A	711	GLU	-1	-0.946	-0.974	30.204	0.014	0.014	0.000	0.000	0.000	0.000
54	A	712	PRO	0	-0.063	-0.038	30.359	0.000	0.000	0.000	0.000	0.000	0.000
55	A	713	LYS	1	0.937	0.969	33.422	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	714	THR	0	-0.046	-0.031	36.140	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	715	ILE	0	-0.023	-0.020	31.234	0.002	0.002	0.000	0.000	0.000	0.000
58	A	716	THR	0	-0.020	-0.024	34.637	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	717	ASP	-1	-0.867	-0.938	33.297	0.018	0.018	0.000	0.000	0.000	0.000
60	A	718	GLU	-1	-0.900	-0.922	32.728	0.025	0.025	0.000	0.000	0.000	0.000
61	A	719	PHE	0	-0.071	-0.033	32.438	0.004	0.004	0.000	0.000	0.000	0.000
62	A	720	GLU	-1	-0.701	-0.753	28.699	0.029	0.029	0.000	0.000	0.000	0.000
63	A	721	GLN	0	0.037	0.005	33.002	0.002	0.002	0.000	0.000	0.000	0.000
64	A	722	GLY	0	0.026	0.010	33.740	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	723	THR	0	-0.062	-0.036	32.283	0.002	0.002	0.000	0.000	0.000	0.000
66	A	724	TYR	0	-0.085	-0.063	27.565	0.000	0.000	0.000	0.000	0.000	0.000
67	A	725	ILE	0	-0.014	-0.003	24.544	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	726	TYR	0	-0.045	-0.034	24.920	0.000	0.000	0.000	0.000	0.000	0.000
69	A	727	PHE	0	0.003	0.000	21.790	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	728	ASP	-1	-0.748	-0.887	23.958	0.062	0.062	0.000	0.000	0.000	0.000
71	A	729	TYR	0	-0.016	-0.021	23.210	0.002	0.002	0.000	0.000	0.000	0.000
72	A	730	GLU	-1	-0.852	-0.911	24.724	0.058	0.058	0.000	0.000	0.000	0.000
73	A	731	LYS	1	0.730	0.854	27.927	-0.059	-0.059	0.000	0.000	0.000	0.000
74	A	732	TRP	0	-0.061	-0.030	19.167	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	733	GLY	0	0.020	0.012	24.602	0.000	0.000	0.000	0.000	0.000	0.000
76	A	734	GLN	0	-0.025	-0.001	22.989	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	735	ARG	1	0.867	0.946	25.709	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	736	LYS	1	0.882	0.932	28.386	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	737	LYS	1	0.887	0.947	31.072	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	738	GLU	-1	-0.748	-0.861	33.247	0.035	0.035	0.000	0.000	0.000	0.000
81	A	739	GLY	0	-0.004	0.002	35.976	0.000	0.000	0.000	0.000	0.000	0.000
82	A	740	PHE	0	-0.060	-0.023	29.806	0.000	0.000	0.000	0.000	0.000	0.000
83	A	741	THR	0	0.046	0.000	34.212	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	742	PHE	0	-0.027	-0.008	25.298	0.002	0.002	0.000	0.000	0.000	0.000
85	A	743	GLU	-1	-0.748	-0.851	31.020	0.035	0.035	0.000	0.000	0.000	0.000
86	A	744	TYR	0	-0.025	-0.047	28.082	0.004	0.004	0.000	0.000	0.000	0.000
87	A	745	ARG	1	0.843	0.905	28.485	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	746	TYR	0	-0.086	-0.060	28.448	0.003	0.003	0.000	0.000	0.000	0.000
89	A	747	LEU	0	-0.010	0.008	22.656	0.006	0.006	0.000	0.000	0.000	0.000
90	A	748	GLU	-1	-0.879	-0.920	18.727	0.121	0.121	0.000	0.000	0.000	0.000

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