FMO DATABASE

FMODB ID: G6ML1

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	OptHSide
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	-749333.021036
FMO2-HF: Nuclear repulsion	710021.382525
FMO2-HF: Total energy	-39311.638511
FMO2-MP2: Total energy	-39428.419816

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.
-11.951	-4.973	0.744	-2.865	-4.857	0.002

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 : -0.014

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	-0.937	2.803	-3.058	0.542	0.212	-1.530	-2.281	-0.007
4	A	662	PHE	0	-0.037	-0.016	2.844	-4.184	-1.837	0.512	-1.066	-1.793	0.009
5	A	663	TYR	0	0.059	0.013	3.175	-1.593	-0.819	0.018	-0.202	-0.591	0.000
6	A	664	GLN	0	0.041	0.021	6.624	-0.259	-0.259	0.000	0.000	0.000	0.000
7	A	665	ARG	1	0.920	0.963	7.101	-0.704	-0.704	0.000	0.000	0.000	0.000
8	A	666	LEU	0	-0.039	0.002	7.861	-0.112	-0.112	0.000	0.000	0.000	0.000
9	A	667	SER	0	0.026	0.018	11.064	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	668	THR	0	0.067	0.006	13.810	0.005	0.005	0.000	0.000	0.000	0.000
11	A	669	GLU	-1	-0.873	-0.922	15.849	0.095	0.095	0.000	0.000	0.000	0.000
12	A	670	THR	0	0.037	0.027	12.113	0.000	0.000	0.000	0.000	0.000	0.000
13	A	671	LEU	0	-0.045	-0.013	9.681	0.009	0.009	0.000	0.000	0.000	0.000
14	A	672	PHE	0	0.008	-0.002	12.903	0.014	0.014	0.000	0.000	0.000	0.000
15	A	673	PHE	0	0.040	0.021	14.473	0.006	0.006	0.000	0.000	0.000	0.000
16	A	674	ILE	0	-0.014	-0.018	9.273	0.009	0.009	0.000	0.000	0.000	0.000
17	A	675	PHE	0	-0.043	-0.023	13.247	0.026	0.026	0.000	0.000	0.000	0.000
18	A	676	TYR	0	-0.033	-0.043	14.841	0.004	0.004	0.000	0.000	0.000	0.000
19	A	677	TYR	0	0.002	0.014	16.834	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	678	LEU	0	-0.056	-0.010	12.203	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	679	GLU	-1	-0.904	-0.939	14.180	0.210	0.210	0.000	0.000	0.000	0.000
22	A	680	GLY	0	0.009	0.010	16.119	0.000	0.000	0.000	0.000	0.000	0.000
23	A	681	THR	0	-0.018	-0.023	11.733	0.057	0.057	0.000	0.000	0.000	0.000
24	A	682	LYS	1	0.955	0.958	6.553	-1.426	-1.426	0.000	0.000	0.000	0.000
25	A	683	ALA	0	0.042	0.015	7.201	0.083	0.083	0.000	0.000	0.000	0.000
26	A	684	GLN	0	0.067	0.043	8.258	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	685	TYR	0	0.006	0.002	8.678	-0.066	-0.066	0.000	0.000	0.000	0.000
28	A	686	LEU	0	-0.061	-0.042	3.913	-0.151	0.106	0.002	-0.067	-0.192	0.000
29	A	687	ALA	0	0.041	0.028	7.951	-0.144	-0.144	0.000	0.000	0.000	0.000
30	A	688	ALA	0	0.041	0.024	10.062	-0.048	-0.048	0.000	0.000	0.000	0.000
31	A	689	LYS	1	0.896	0.941	9.311	-0.329	-0.329	0.000	0.000	0.000	0.000
32	A	690	ALA	0	-0.018	0.001	8.906	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	691	LEU	0	0.028	0.017	10.859	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	692	LYS	1	0.891	0.934	14.396	-0.171	-0.171	0.000	0.000	0.000	0.000
35	A	693	LYS	1	0.890	0.955	10.528	-0.142	-0.142	0.000	0.000	0.000	0.000
36	A	694	GLN	0	-0.018	-0.004	12.847	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	695	SER	0	-0.036	-0.019	16.463	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	696	TRP	0	0.020	0.021	17.362	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	697	ARG	1	0.835	0.894	18.418	-0.094	-0.094	0.000	0.000	0.000	0.000
40	A	698	PHE	0	0.021	0.011	19.633	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	699	HIS	0	0.048	0.037	21.650	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	700	THR	0	0.009	-0.009	23.665	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	701	LYS	1	0.955	0.991	25.597	-0.060	-0.060	0.000	0.000	0.000	0.000
44	A	702	TYR	0	-0.034	-0.035	28.055	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	703	MET	0	0.036	0.039	22.850	0.001	0.001	0.000	0.000	0.000	0.000
46	A	704	MET	0	0.007	0.033	23.154	0.004	0.004	0.000	0.000	0.000	0.000
47	A	705	TRP	0	-0.016	-0.003	16.316	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	706	PHE	0	0.008	-0.015	21.724	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	707	GLN	0	0.003	-0.003	20.498	0.003	0.003	0.000	0.000	0.000	0.000
50	A	708	ARG	1	0.836	0.894	24.014	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	709	HIS	0	-0.037	-0.017	26.448	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	710	GLU	-1	-0.845	-0.915	28.776	0.041	0.041	0.000	0.000	0.000	0.000
53	A	711	GLU	-1	-0.962	-0.981	30.415	0.040	0.040	0.000	0.000	0.000	0.000
54	A	712	PRO	0	-0.048	-0.028	30.465	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	713	LYS	1	0.900	0.952	33.412	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	714	THR	0	-0.006	-0.015	36.760	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	715	ILE	0	-0.019	-0.020	31.642	0.003	0.003	0.000	0.000	0.000	0.000
58	A	716	THR	0	-0.022	-0.023	35.242	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	717	ASP	-1	-0.863	-0.932	33.825	0.038	0.038	0.000	0.000	0.000	0.000
60	A	718	GLU	-1	-0.910	-0.934	32.973	0.041	0.041	0.000	0.000	0.000	0.000
61	A	719	PHE	0	-0.059	-0.032	32.594	0.004	0.004	0.000	0.000	0.000	0.000
62	A	720	GLU	-1	-0.701	-0.750	29.042	0.056	0.056	0.000	0.000	0.000	0.000
63	A	721	GLN	0	0.015	-0.004	33.370	0.000	0.000	0.000	0.000	0.000	0.000
64	A	722	GLY	0	0.031	0.015	33.838	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	723	THR	0	-0.050	-0.029	32.025	0.000	0.000	0.000	0.000	0.000	0.000
66	A	724	TYR	0	-0.074	-0.056	27.447	0.002	0.002	0.000	0.000	0.000	0.000
67	A	725	ILE	0	-0.001	0.009	24.314	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	726	TYR	0	-0.016	-0.022	24.501	0.003	0.003	0.000	0.000	0.000	0.000
69	A	727	PHE	0	0.001	0.004	21.441	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	728	ASP	-1	-0.767	-0.885	23.649	0.069	0.069	0.000	0.000	0.000	0.000
71	A	729	TYR	0	0.021	0.004	22.658	0.000	0.000	0.000	0.000	0.000	0.000
72	A	730	GLU	-1	-0.903	-0.946	24.283	0.059	0.059	0.000	0.000	0.000	0.000
73	A	731	LYS	1	0.713	0.839	27.787	-0.063	-0.063	0.000	0.000	0.000	0.000
74	A	732	TRP	0	-0.065	-0.018	18.691	0.001	0.001	0.000	0.000	0.000	0.000
75	A	733	GLY	0	0.010	-0.001	24.949	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	734	GLN	0	-0.033	-0.011	22.508	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	735	ARG	1	0.893	0.949	25.482	-0.062	-0.062	0.000	0.000	0.000	0.000
78	A	736	LYS	1	0.889	0.929	28.121	-0.042	-0.042	0.000	0.000	0.000	0.000
79	A	737	LYS	1	0.915	0.969	30.739	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	738	GLU	-1	-0.758	-0.863	32.844	0.045	0.045	0.000	0.000	0.000	0.000
81	A	739	GLY	0	-0.021	-0.015	35.612	0.000	0.000	0.000	0.000	0.000	0.000
82	A	740	PHE	0	-0.070	-0.025	29.894	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	741	THR	0	0.049	0.008	34.361	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	742	PHE	0	-0.008	-0.002	25.456	0.002	0.002	0.000	0.000	0.000	0.000
85	A	743	GLU	-1	-0.789	-0.887	31.278	0.049	0.049	0.000	0.000	0.000	0.000
86	A	744	TYR	0	-0.022	-0.047	28.360	0.005	0.005	0.000	0.000	0.000	0.000
87	A	745	ARG	1	0.856	0.913	28.487	-0.049	-0.049	0.000	0.000	0.000	0.000
88	A	746	TYR	0	-0.090	-0.045	28.507	0.002	0.002	0.000	0.000	0.000	0.000
89	A	747	LEU	0	-0.007	0.006	23.257	0.007	0.007	0.000	0.000	0.000	0.000
90	A	748	GLU	-1	-0.904	-0.938	19.156	0.156	0.156	0.000	0.000	0.000	0.000

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