FMO DATABASE

FMODB ID: JL869

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

Total energy (hartree)

FMO2-HF: Electronic energy	-688594.382851
FMO2-HF: Nuclear repulsion	647496.665809
FMO2-HF: Total energy	-41097.717041
FMO2-MP2: Total energy	-41217.463249

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.
0.068	1.383	-0.02	-0.745	-0.551	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 : 0.034 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	435	LYS	1	0.953	0.972	3.800	-0.592	0.723	-0.020	-0.745	-0.551	0.002
4	A	436	LEU	0	0.066	0.016	6.082	0.149	0.149	0.000	0.000	0.000	0.000
5	A	437	GLY	0	-0.033	-0.011	8.109	-0.022	-0.022	0.000	0.000	0.000	0.000
6	A	438	ARG	1	0.890	0.943	10.291	0.016	0.016	0.000	0.000	0.000	0.000
7	A	439	TYR	0	0.010	0.010	10.885	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	440	GLY	0	0.060	0.045	13.832	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	441	GLU	-1	-0.885	-0.959	15.153	0.156	0.156	0.000	0.000	0.000	0.000
10	A	442	ASP	-1	-0.892	-0.951	16.401	0.214	0.214	0.000	0.000	0.000	0.000
11	A	443	LEU	0	0.015	0.005	13.185	0.023	0.023	0.000	0.000	0.000	0.000
12	A	444	LEU	0	-0.025	-0.011	10.534	0.098	0.098	0.000	0.000	0.000	0.000
13	A	445	PHE	0	0.026	0.005	13.471	0.064	0.064	0.000	0.000	0.000	0.000
14	A	446	TYR	0	-0.011	0.009	15.685	0.013	0.013	0.000	0.000	0.000	0.000
15	A	447	LEU	0	-0.015	-0.014	10.196	0.032	0.032	0.000	0.000	0.000	0.000
16	A	448	TYR	0	-0.064	-0.013	13.106	0.049	0.049	0.000	0.000	0.000	0.000
17	A	449	TYR	0	-0.022	-0.024	14.740	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	450	MET	0	-0.054	-0.019	17.668	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	451	ASN	0	-0.016	-0.012	14.476	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	452	GLY	0	0.041	0.031	16.424	0.000	0.000	0.000	0.000	0.000	0.000
21	A	453	GLY	0	0.008	-0.003	16.829	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	454	ASP	-1	-0.854	-0.936	17.567	0.235	0.235	0.000	0.000	0.000	0.000
23	A	455	VAL	0	0.005	0.002	20.932	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	456	LEU	0	-0.009	-0.014	17.284	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	457	GLN	0	-0.018	0.001	20.195	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	458	LEU	0	0.001	0.005	21.515	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	459	LEU	0	-0.004	-0.013	23.575	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	460	ALA	0	0.003	0.010	21.603	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	461	ALA	0	0.005	0.008	23.761	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	462	VAL	0	-0.009	-0.011	26.442	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	463	GLU	-1	-0.812	-0.883	26.082	0.103	0.103	0.000	0.000	0.000	0.000
32	A	464	LEU	0	-0.038	-0.025	23.948	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	465	PHE	0	0.022	0.004	28.041	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	466	ASN	0	-0.011	-0.003	31.099	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	467	ARG	1	0.783	0.889	26.027	-0.118	-0.118	0.000	0.000	0.000	0.000
36	A	468	ASP	-1	-0.836	-0.913	31.902	0.066	0.066	0.000	0.000	0.000	0.000
37	A	469	TRP	0	-0.071	-0.017	27.551	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	470	ARG	1	0.801	0.887	31.553	-0.075	-0.075	0.000	0.000	0.000	0.000
39	A	471	TYR	0	0.027	0.018	26.605	0.002	0.002	0.000	0.000	0.000	0.000
40	A	472	HIS	0	0.069	0.036	31.179	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	473	LYS	1	0.877	0.911	31.597	-0.091	-0.091	0.000	0.000	0.000	0.000
42	A	474	GLU	-1	-0.974	-0.980	31.977	0.060	0.060	0.000	0.000	0.000	0.000
43	A	475	GLU	-1	-0.882	-0.972	31.628	0.063	0.063	0.000	0.000	0.000	0.000
44	A	476	ARG	1	0.865	0.951	27.562	-0.081	-0.081	0.000	0.000	0.000	0.000
45	A	477	VAL	0	-0.026	-0.004	26.768	0.008	0.008	0.000	0.000	0.000	0.000
46	A	478	TRP	0	0.010	0.007	25.112	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	479	ILE	0	-0.015	-0.016	28.483	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	480	THR	0	0.001	-0.011	30.926	0.000	0.000	0.000	0.000	0.000	0.000
49	A	481	ARG	1	0.896	0.934	33.172	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	482	ALA	0	0.006	0.013	34.993	0.002	0.002	0.000	0.000	0.000	0.000
51	A	483	PRO	0	0.007	-0.006	34.801	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	484	GLY	0	0.011	-0.003	37.783	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	485	MET	0	-0.060	-0.024	38.712	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	486	GLU	-1	-0.906	-0.948	41.315	0.041	0.041	0.000	0.000	0.000	0.000
55	A	487	PRO	0	-0.098	-0.043	43.376	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	488	THR	0	-0.002	-0.004	44.445	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	489	MET	0	-0.029	-0.006	46.256	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	490	LYS	1	0.909	0.941	45.051	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	491	THR	0	-0.006	0.005	47.976	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	492	ASN	0	0.015	-0.013	48.244	0.002	0.002	0.000	0.000	0.000	0.000
61	A	493	THR	0	0.014	0.005	47.015	0.001	0.001	0.000	0.000	0.000	0.000
62	A	494	TYR	0	0.008	0.007	44.211	0.002	0.002	0.000	0.000	0.000	0.000
63	A	495	GLU	-1	-0.748	-0.798	42.059	0.044	0.044	0.000	0.000	0.000	0.000
64	A	496	ARG	1	0.840	0.903	42.124	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	497	GLY	0	0.107	0.054	41.338	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	498	THR	0	-0.017	0.001	36.550	0.000	0.000	0.000	0.000	0.000	0.000
67	A	499	TYR	0	-0.046	-0.043	34.920	0.000	0.000	0.000	0.000	0.000	0.000
68	A	500	TYR	0	0.002	-0.020	30.047	0.000	0.000	0.000	0.000	0.000	0.000
69	A	501	PHE	0	0.053	0.016	29.008	0.002	0.002	0.000	0.000	0.000	0.000
70	A	502	PHE	0	-0.035	-0.013	19.971	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	503	ASP	-1	-0.764	-0.865	23.277	0.093	0.093	0.000	0.000	0.000	0.000
72	A	504	CYS	0	-0.004	-0.016	20.220	0.001	0.001	0.000	0.000	0.000	0.000
73	A	505	LEU	0	0.014	0.016	18.969	0.017	0.017	0.000	0.000	0.000	0.000
74	A	506	ASN	0	-0.090	-0.070	18.811	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	507	TRP	0	-0.046	-0.013	17.111	0.004	0.004	0.000	0.000	0.000	0.000
76	A	508	ARG	1	0.923	0.959	19.579	-0.067	-0.067	0.000	0.000	0.000	0.000
77	A	509	LYS	1	0.895	0.971	22.715	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	510	VAL	0	-0.016	-0.015	26.135	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	511	ALA	0	-0.001	0.006	28.758	0.002	0.002	0.000	0.000	0.000	0.000
80	A	512	LYS	1	0.886	0.961	31.999	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	513	GLU	-1	-0.833	-0.893	34.626	0.034	0.034	0.000	0.000	0.000	0.000
82	A	514	PHE	0	-0.026	-0.024	36.318	0.000	0.000	0.000	0.000	0.000	0.000
83	A	515	HIS	0	-0.011	-0.005	38.597	0.000	0.000	0.000	0.000	0.000	0.000
84	A	516	LEU	0	0.014	0.005	37.053	0.002	0.002	0.000	0.000	0.000	0.000
85	A	517	GLU	-1	-0.857	-0.939	40.198	0.044	0.044	0.000	0.000	0.000	0.000
86	A	518	TYR	0	-0.016	-0.040	40.270	0.002	0.002	0.000	0.000	0.000	0.000
87	A	519	ASP	-1	-0.831	-0.897	40.075	0.054	0.054	0.000	0.000	0.000	0.000
88	A	520	LYS	1	0.803	0.901	37.513	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	521	LEU	0	-0.091	-0.049	34.838	0.005	0.005	0.000	0.000	0.000	0.000
90	A	522	GLU	-1	-0.819	-0.892	31.809	0.098	0.098	0.000	0.000	0.000	0.000
91	A	523	GLU	-1	-0.928	-0.964	35.124	0.067	0.067	0.000	0.000	0.000	0.000
92	A	524	ARG	1	0.866	0.930	34.156	-0.078	-0.078	0.000	0.000	0.000	0.000
93	A	525	PRO	0	-0.001	-0.009	29.761	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	526	HIS	0	-0.028	-0.011	31.977	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	527	LEU	0	0.000	-0.005	30.486	0.007	0.007	0.000	0.000	0.000	0.000
96	A	528	PRO	0	0.028	0.029	28.590	-0.007	-0.007	0.000	0.000	0.000	0.000

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