FMO DATABASE

FMODB ID: 3923L

Calculation Name: 4C0F-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0F

Chain ID: A

ChEMBL ID: CHEMBL4105920

UniProt ID: Q9NZN8

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-689345.838361
FMO2-HF: Nuclear repulsion	648247.990838
FMO2-HF: Total energy	-41097.847522
FMO2-MP2: Total energy	-41217.601285

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:433:ALA)

Summations of interaction energy for fragment #1(A:433: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.
0.635	1.697	-0.01	-0.542	-0.509	0.002

Interaction energy analysis for fragmet #1(A:433:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / 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

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	435	LYS	1	0.962	0.985	3.864	-0.155	0.907	-0.010	-0.542	-0.509	0.002
4	A	436	LEU	0	0.054	0.003	5.774	0.226	0.226	0.000	0.000	0.000	0.000
5	A	437	GLY	0	0.004	0.014	7.815	0.044	0.044	0.000	0.000	0.000	0.000
6	A	438	ARG	1	0.834	0.905	10.024	0.079	0.079	0.000	0.000	0.000	0.000
7	A	439	TYR	0	0.012	0.015	10.736	0.007	0.007	0.000	0.000	0.000	0.000
8	A	440	GLY	0	0.064	0.044	14.002	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	441	GLU	-1	-0.895	-0.961	15.120	0.092	0.092	0.000	0.000	0.000	0.000
10	A	442	ASP	-1	-0.862	-0.933	16.274	0.152	0.152	0.000	0.000	0.000	0.000
11	A	443	LEU	0	0.025	0.013	13.475	0.028	0.028	0.000	0.000	0.000	0.000
12	A	444	LEU	0	-0.038	-0.017	10.176	0.089	0.089	0.000	0.000	0.000	0.000
13	A	445	PHE	0	0.017	0.001	13.177	0.065	0.065	0.000	0.000	0.000	0.000
14	A	446	TYR	0	-0.026	-0.006	15.514	0.022	0.022	0.000	0.000	0.000	0.000
15	A	447	LEU	0	-0.025	-0.023	10.021	0.036	0.036	0.000	0.000	0.000	0.000
16	A	448	TYR	0	-0.049	-0.008	12.639	0.054	0.054	0.000	0.000	0.000	0.000
17	A	449	TYR	0	-0.020	-0.016	14.438	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	450	MET	0	-0.045	-0.019	17.501	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	451	ASN	0	-0.034	-0.021	14.719	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	452	GLY	0	0.047	0.037	16.875	0.007	0.007	0.000	0.000	0.000	0.000
21	A	453	GLY	0	0.008	-0.005	17.247	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	454	ASP	-1	-0.856	-0.935	18.042	0.241	0.241	0.000	0.000	0.000	0.000
23	A	455	VAL	0	0.011	0.006	21.485	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	456	LEU	0	-0.019	-0.011	17.564	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	457	GLN	0	-0.007	0.002	20.451	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	458	LEU	0	-0.001	0.002	21.914	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	459	LEU	0	-0.010	-0.010	23.937	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	460	ALA	0	0.000	0.000	22.076	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	461	ALA	0	0.002	0.007	24.220	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	462	VAL	0	-0.008	-0.011	26.819	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	463	GLU	-1	-0.785	-0.872	26.675	0.113	0.113	0.000	0.000	0.000	0.000
32	A	464	LEU	0	-0.049	-0.026	24.405	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	465	PHE	0	0.004	0.001	28.462	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	466	ASN	0	-0.025	-0.013	31.478	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	467	ARG	1	0.768	0.876	26.431	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	468	ASP	-1	-0.812	-0.902	32.062	0.078	0.078	0.000	0.000	0.000	0.000
37	A	469	TRP	0	-0.064	0.003	28.084	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	470	ARG	1	0.813	0.890	32.092	-0.086	-0.086	0.000	0.000	0.000	0.000
39	A	471	TYR	0	-0.020	-0.007	27.019	0.002	0.002	0.000	0.000	0.000	0.000
40	A	472	HIS	0	0.082	0.037	31.499	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	473	LYS	1	0.845	0.893	32.023	-0.099	-0.099	0.000	0.000	0.000	0.000
42	A	474	GLU	-1	-0.970	-0.974	32.518	0.067	0.067	0.000	0.000	0.000	0.000
43	A	475	GLU	-1	-0.823	-0.934	31.819	0.078	0.078	0.000	0.000	0.000	0.000
44	A	476	ARG	1	0.864	0.946	27.878	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	477	VAL	0	-0.003	0.014	27.013	0.013	0.013	0.000	0.000	0.000	0.000
46	A	478	TRP	0	0.014	0.010	25.622	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	479	ILE	0	-0.006	-0.008	28.942	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	480	THR	0	0.005	-0.015	31.501	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	481	ARG	1	0.909	0.936	33.731	-0.061	-0.061	0.000	0.000	0.000	0.000
50	A	482	ALA	0	0.007	0.010	35.256	0.003	0.003	0.000	0.000	0.000	0.000
51	A	483	PRO	0	-0.006	-0.013	35.261	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	484	GLY	0	0.029	0.005	38.228	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	485	MET	0	-0.078	-0.025	38.854	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	486	GLU	-1	-0.897	-0.950	41.476	0.051	0.051	0.000	0.000	0.000	0.000
55	A	487	PRO	0	-0.114	-0.050	43.737	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	488	THR	0	0.014	-0.003	44.759	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	489	MET	0	-0.014	0.004	46.616	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	490	LYS	1	0.882	0.927	45.284	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	491	THR	0	-0.008	-0.003	48.319	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	492	ASN	0	0.014	-0.010	48.703	0.002	0.002	0.000	0.000	0.000	0.000
61	A	493	THR	0	-0.002	0.002	47.291	0.001	0.001	0.000	0.000	0.000	0.000
62	A	494	TYR	0	0.035	0.029	44.637	0.002	0.002	0.000	0.000	0.000	0.000
63	A	495	GLU	-1	-0.739	-0.795	42.520	0.052	0.052	0.000	0.000	0.000	0.000
64	A	496	ARG	1	0.860	0.900	42.860	-0.041	-0.041	0.000	0.000	0.000	0.000
65	A	497	GLY	0	0.068	0.043	41.800	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	498	THR	0	-0.015	-0.001	37.205	0.001	0.001	0.000	0.000	0.000	0.000
67	A	499	TYR	0	-0.036	-0.036	35.360	0.000	0.000	0.000	0.000	0.000	0.000
68	A	500	TYR	0	0.006	-0.009	30.535	0.000	0.000	0.000	0.000	0.000	0.000
69	A	501	PHE	0	0.058	0.021	29.316	0.001	0.001	0.000	0.000	0.000	0.000
70	A	502	PHE	0	-0.029	-0.014	20.216	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	503	ASP	-1	-0.776	-0.866	23.794	0.122	0.122	0.000	0.000	0.000	0.000
72	A	504	CYS	0	0.002	-0.016	20.260	0.003	0.003	0.000	0.000	0.000	0.000
73	A	505	LEU	0	0.019	0.018	19.345	0.021	0.021	0.000	0.000	0.000	0.000
74	A	506	ASN	0	-0.082	-0.069	19.517	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	507	TRP	0	-0.028	-0.007	17.283	0.004	0.004	0.000	0.000	0.000	0.000
76	A	508	ARG	1	0.879	0.947	19.728	-0.104	-0.104	0.000	0.000	0.000	0.000
77	A	509	LYS	1	0.903	0.971	22.776	-0.094	-0.094	0.000	0.000	0.000	0.000
78	A	510	VAL	0	-0.022	-0.010	26.194	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	511	ALA	0	-0.003	-0.004	28.911	0.002	0.002	0.000	0.000	0.000	0.000
80	A	512	LYS	1	0.827	0.920	32.733	-0.075	-0.075	0.000	0.000	0.000	0.000
81	A	513	GLU	-1	-0.818	-0.881	35.140	0.043	0.043	0.000	0.000	0.000	0.000
82	A	514	PHE	0	-0.028	-0.023	36.606	0.000	0.000	0.000	0.000	0.000	0.000
83	A	515	HIS	0	-0.009	-0.006	39.076	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	516	LEU	0	-0.006	-0.007	37.314	0.003	0.003	0.000	0.000	0.000	0.000
85	A	517	GLU	-1	-0.879	-0.953	40.618	0.050	0.050	0.000	0.000	0.000	0.000
86	A	518	TYR	0	-0.038	-0.052	40.660	0.002	0.002	0.000	0.000	0.000	0.000
87	A	519	ASP	-1	-0.813	-0.889	40.525	0.061	0.061	0.000	0.000	0.000	0.000
88	A	520	LYS	1	0.803	0.906	37.847	-0.055	-0.055	0.000	0.000	0.000	0.000
89	A	521	LEU	0	-0.080	-0.041	35.472	0.006	0.006	0.000	0.000	0.000	0.000
90	A	522	GLU	-1	-0.794	-0.878	32.259	0.104	0.104	0.000	0.000	0.000	0.000
91	A	523	GLU	-1	-0.915	-0.961	35.595	0.073	0.073	0.000	0.000	0.000	0.000
92	A	524	ARG	1	0.871	0.930	34.435	-0.086	-0.086	0.000	0.000	0.000	0.000
93	A	525	PRO	0	-0.012	-0.010	29.972	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	526	HIS	0	-0.028	-0.019	32.279	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	527	LEU	0	0.013	0.002	31.049	0.008	0.008	0.000	0.000	0.000	0.000
96	A	528	PRO	0	0.022	0.030	29.040	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:433:ALA)