FMO DATABASE

FMODB ID: N9RVQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-688413.127233
FMO2-HF: Nuclear repulsion	647315.831264
FMO2-HF: Total energy	-41097.295968
FMO2-MP2: Total energy	-41216.9837

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.
-0.039	1.297	-0.021	-0.757	-0.558	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 : 0.038 / q_NPA : 0.008

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	435	LYS	1	0.952	0.975	3.809	-0.672	0.664	-0.021	-0.757	-0.558	0.002
4	A	436	LEU	0	0.062	0.011	6.041	0.136	0.136	0.000	0.000	0.000	0.000
5	A	437	GLY	0	-0.036	-0.014	8.127	-0.030	-0.030	0.000	0.000	0.000	0.000
6	A	438	ARG	1	0.894	0.945	10.304	0.000	0.000	0.000	0.000	0.000	0.000
7	A	439	TYR	0	0.016	0.013	11.208	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	440	GLY	0	0.059	0.043	13.851	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	441	GLU	-1	-0.873	-0.958	15.171	0.155	0.155	0.000	0.000	0.000	0.000
10	A	442	ASP	-1	-0.918	-0.961	16.418	0.222	0.222	0.000	0.000	0.000	0.000
11	A	443	LEU	0	0.013	0.011	12.925	0.021	0.021	0.000	0.000	0.000	0.000
12	A	444	LEU	0	-0.022	-0.010	10.646	0.097	0.097	0.000	0.000	0.000	0.000
13	A	445	PHE	0	0.032	0.005	13.488	0.062	0.062	0.000	0.000	0.000	0.000
14	A	446	TYR	0	-0.001	0.014	15.654	0.014	0.014	0.000	0.000	0.000	0.000
15	A	447	LEU	0	-0.023	-0.020	10.149	0.032	0.032	0.000	0.000	0.000	0.000
16	A	448	TYR	0	-0.064	-0.016	13.283	0.048	0.048	0.000	0.000	0.000	0.000
17	A	449	TYR	0	-0.024	-0.026	14.754	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	450	MET	0	-0.049	-0.014	17.693	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	451	ASN	0	-0.018	-0.007	14.496	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	452	GLY	0	0.036	0.027	16.444	0.000	0.000	0.000	0.000	0.000	0.000
21	A	453	GLY	0	0.018	0.000	16.855	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	454	ASP	-1	-0.841	-0.913	17.593	0.238	0.238	0.000	0.000	0.000	0.000
23	A	455	VAL	0	-0.004	-0.014	20.962	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	456	LEU	0	-0.012	-0.019	17.285	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	457	GLN	0	-0.017	0.003	20.333	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	458	LEU	0	-0.004	0.003	21.542	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	459	LEU	0	-0.005	-0.015	23.645	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	460	ALA	0	0.005	0.011	21.638	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	461	ALA	0	0.008	0.009	23.780	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	462	VAL	0	-0.012	-0.011	26.467	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	463	GLU	-1	-0.829	-0.901	26.109	0.103	0.103	0.000	0.000	0.000	0.000
32	A	464	LEU	0	-0.041	-0.027	24.028	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	465	PHE	0	0.000	0.001	28.061	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	466	ASN	0	-0.032	-0.031	31.127	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	467	ARG	1	0.788	0.907	25.774	-0.117	-0.117	0.000	0.000	0.000	0.000
36	A	468	ASP	-1	-0.913	-0.949	31.916	0.066	0.066	0.000	0.000	0.000	0.000
37	A	469	TRP	0	-0.073	-0.030	27.764	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	470	ARG	1	0.853	0.917	31.575	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	471	TYR	0	0.060	0.027	26.524	0.001	0.001	0.000	0.000	0.000	0.000
40	A	472	HIS	0	0.067	0.033	31.211	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	473	LYS	1	0.927	0.945	31.635	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	474	GLU	-1	-1.000	-0.999	32.018	0.060	0.060	0.000	0.000	0.000	0.000
43	A	475	GLU	-1	-0.929	-0.979	31.748	0.062	0.062	0.000	0.000	0.000	0.000
44	A	476	ARG	1	0.871	0.961	27.556	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	477	VAL	0	-0.021	-0.003	26.933	0.007	0.007	0.000	0.000	0.000	0.000
46	A	478	TRP	0	0.009	0.010	25.161	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	479	ILE	0	0.004	-0.011	28.513	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	480	THR	0	0.018	0.007	30.926	0.000	0.000	0.000	0.000	0.000	0.000
49	A	481	ARG	1	0.888	0.937	33.194	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	482	ALA	0	0.011	0.018	35.006	0.002	0.002	0.000	0.000	0.000	0.000
51	A	483	PRO	0	0.007	-0.004	34.786	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	484	GLY	0	0.010	-0.004	37.795	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	485	MET	0	-0.062	-0.025	38.692	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	486	GLU	-1	-0.902	-0.947	41.334	0.040	0.040	0.000	0.000	0.000	0.000
55	A	487	PRO	0	-0.098	-0.042	43.439	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	488	THR	0	0.004	-0.002	44.469	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	489	MET	0	-0.033	-0.011	46.281	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	490	LYS	1	0.911	0.952	44.927	-0.038	-0.038	0.000	0.000	0.000	0.000
59	A	491	THR	0	-0.012	-0.003	48.004	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	492	ASN	0	0.007	-0.020	48.273	0.002	0.002	0.000	0.000	0.000	0.000
61	A	493	THR	0	0.028	0.015	47.064	0.001	0.001	0.000	0.000	0.000	0.000
62	A	494	TYR	0	0.009	-0.002	44.166	0.001	0.001	0.000	0.000	0.000	0.000
63	A	495	GLU	-1	-0.738	-0.793	41.839	0.044	0.044	0.000	0.000	0.000	0.000
64	A	496	ARG	1	0.929	0.971	42.034	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	497	GLY	0	0.093	0.044	41.344	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	498	THR	0	-0.016	0.006	36.448	0.000	0.000	0.000	0.000	0.000	0.000
67	A	499	TYR	0	-0.043	-0.048	34.949	0.000	0.000	0.000	0.000	0.000	0.000
68	A	500	TYR	0	-0.032	-0.034	30.061	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	501	PHE	0	0.052	0.016	29.050	0.003	0.003	0.000	0.000	0.000	0.000
70	A	502	PHE	0	-0.035	-0.012	19.837	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	503	ASP	-1	-0.793	-0.893	23.357	0.091	0.091	0.000	0.000	0.000	0.000
72	A	504	CYS	0	-0.005	-0.016	20.170	0.001	0.001	0.000	0.000	0.000	0.000
73	A	505	LEU	0	0.007	0.016	18.993	0.017	0.017	0.000	0.000	0.000	0.000
74	A	506	ASN	0	-0.105	-0.066	18.833	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	507	TRP	0	-0.033	-0.001	16.980	0.003	0.003	0.000	0.000	0.000	0.000
76	A	508	ARG	1	0.962	0.973	19.588	-0.062	-0.062	0.000	0.000	0.000	0.000
77	A	509	LYS	1	0.935	0.980	22.718	-0.075	-0.075	0.000	0.000	0.000	0.000
78	A	510	VAL	0	-0.003	-0.009	26.154	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	511	ALA	0	0.001	0.005	28.765	0.002	0.002	0.000	0.000	0.000	0.000
80	A	512	LYS	1	0.957	0.980	31.590	-0.059	-0.059	0.000	0.000	0.000	0.000
81	A	513	GLU	-1	-0.916	-0.945	34.638	0.033	0.033	0.000	0.000	0.000	0.000
82	A	514	PHE	0	-0.031	-0.033	36.473	0.000	0.000	0.000	0.000	0.000	0.000
83	A	515	HIS	0	-0.020	-0.007	38.615	0.000	0.000	0.000	0.000	0.000	0.000
84	A	516	LEU	0	0.028	0.013	37.105	0.002	0.002	0.000	0.000	0.000	0.000
85	A	517	GLU	-1	-0.891	-0.956	40.230	0.044	0.044	0.000	0.000	0.000	0.000
86	A	518	TYR	0	-0.058	-0.056	40.305	0.002	0.002	0.000	0.000	0.000	0.000
87	A	519	ASP	-1	-0.894	-0.938	40.109	0.054	0.054	0.000	0.000	0.000	0.000
88	A	520	LYS	1	0.935	0.975	37.447	-0.052	-0.052	0.000	0.000	0.000	0.000
89	A	521	LEU	0	-0.094	-0.055	34.815	0.005	0.005	0.000	0.000	0.000	0.000
90	A	522	GLU	-1	-0.896	-0.937	31.639	0.101	0.101	0.000	0.000	0.000	0.000
91	A	523	GLU	-1	-0.947	-0.971	35.157	0.067	0.067	0.000	0.000	0.000	0.000
92	A	524	ARG	1	0.896	0.947	34.195	-0.075	-0.075	0.000	0.000	0.000	0.000
93	A	525	PRO	0	0.012	0.000	29.833	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	526	HIS	0	-0.009	0.003	32.005	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	527	LEU	0	-0.009	-0.013	30.401	0.007	0.007	0.000	0.000	0.000	0.000
96	A	528	PRO	0	0.013	0.019	28.652	-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)