FMO DATABASE

FMODB ID: MVK6Z

Calculation Name: 4C0D-C-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0D

Chain ID: C

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1284806.170545
FMO2-HF: Nuclear repulsion	1223083.123955
FMO2-HF: Total energy	-61723.04659
FMO2-MP2: Total energy	-61902.777934

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(C:607:LEU)

Summations of interaction energy for fragment #1(C:607:LEU)

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.
-4.654	1.19	4.563	-3.475	-6.931	-0.008

Interaction energy analysis for fragmet #1(C:607:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.024

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	C	609	LYS	1	0.989	0.980	3.223	-0.982	1.479	0.076	-1.329	-1.208	0.003
4	C	610	GLU	-1	-0.875	-0.945	5.895	-0.419	-0.419	0.000	0.000	0.000	0.000
5	C	611	GLN	0	0.064	0.042	2.308	-1.869	-0.182	2.327	-1.235	-2.778	-0.007
6	C	612	LEU	0	-0.004	0.006	2.392	-1.545	-0.249	2.159	-0.855	-2.600	-0.004
7	C	613	TYR	0	-0.021	0.000	4.196	0.169	0.295	0.002	-0.025	-0.103	0.000
8	C	614	GLN	0	0.004	-0.015	6.377	0.098	0.098	0.000	0.000	0.000	0.000
9	C	615	GLN	0	0.003	0.014	4.214	-0.304	-0.030	-0.001	-0.031	-0.242	0.000
10	C	616	ALA	0	0.023	0.010	6.503	0.116	0.116	0.000	0.000	0.000	0.000
11	C	617	MET	0	-0.037	-0.019	9.397	0.068	0.068	0.000	0.000	0.000	0.000
12	C	618	GLU	-1	-0.964	-0.974	9.392	0.122	0.122	0.000	0.000	0.000	0.000
13	C	619	GLU	-1	-0.950	-0.987	9.674	-0.133	-0.133	0.000	0.000	0.000	0.000
14	C	620	ALA	0	-0.045	-0.029	11.768	0.025	0.025	0.000	0.000	0.000	0.000
15	C	621	ALA	0	0.015	-0.005	14.341	0.021	0.021	0.000	0.000	0.000	0.000
16	C	622	TRP	0	-0.035	-0.011	14.055	0.021	0.021	0.000	0.000	0.000	0.000
17	C	623	HIS	0	-0.032	-0.019	15.469	0.027	0.027	0.000	0.000	0.000	0.000
18	C	624	HIS	0	-0.090	-0.039	18.919	-0.010	-0.010	0.000	0.000	0.000	0.000
19	C	625	MET	0	-0.008	0.010	17.885	0.003	0.003	0.000	0.000	0.000	0.000
20	C	626	PRO	0	-0.020	0.003	20.295	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	627	HIS	0	0.035	0.021	23.414	0.012	0.012	0.000	0.000	0.000	0.000
22	C	628	PRO	0	-0.026	-0.028	25.910	0.000	0.000	0.000	0.000	0.000	0.000
23	C	629	SER	0	-0.034	-0.020	28.246	0.001	0.001	0.000	0.000	0.000	0.000
24	C	630	ASP	-1	-0.861	-0.929	26.870	0.004	0.004	0.000	0.000	0.000	0.000
25	C	631	SER	0	-0.042	-0.019	27.257	0.001	0.001	0.000	0.000	0.000	0.000
26	C	632	GLU	-1	-0.847	-0.882	29.592	0.030	0.030	0.000	0.000	0.000	0.000
27	C	633	ARG	1	0.928	0.959	33.357	-0.015	-0.015	0.000	0.000	0.000	0.000
28	C	634	ILE	0	0.067	0.024	36.726	0.002	0.002	0.000	0.000	0.000	0.000
29	C	635	ARG	1	0.872	0.927	36.115	-0.022	-0.022	0.000	0.000	0.000	0.000
30	C	636	GLN	0	-0.025	-0.007	39.777	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	637	TYR	0	0.031	0.014	42.638	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	638	LEU	0	-0.012	-0.003	41.214	0.000	0.000	0.000	0.000	0.000	0.000
33	C	639	PRO	0	0.009	0.005	36.924	0.002	0.002	0.000	0.000	0.000	0.000
34	C	640	ARG	1	0.881	0.922	31.594	-0.032	-0.032	0.000	0.000	0.000	0.000
35	C	641	ASN	0	0.008	0.000	33.421	-0.003	-0.003	0.000	0.000	0.000	0.000
36	C	642	PRO	0	-0.008	-0.005	29.465	0.002	0.002	0.000	0.000	0.000	0.000
37	C	643	CYS	0	0.015	0.009	32.068	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	644	PRO	0	0.017	0.008	30.123	0.004	0.004	0.000	0.000	0.000	0.000
39	C	645	THR	0	0.011	0.011	31.896	-0.004	-0.004	0.000	0.000	0.000	0.000
40	C	646	PRO	0	0.007	0.004	33.365	0.004	0.004	0.000	0.000	0.000	0.000
41	C	647	PRO	0	0.031	0.012	32.295	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	648	TYR	0	-0.022	-0.008	34.236	0.002	0.002	0.000	0.000	0.000	0.000
43	C	649	HIS	0	-0.007	0.002	37.278	-0.001	-0.001	0.000	0.000	0.000	0.000
44	C	650	HIS	0	0.004	-0.014	36.531	0.003	0.003	0.000	0.000	0.000	0.000
45	C	651	GLN	0	-0.033	-0.015	32.162	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	652	MET	0	-0.016	0.000	32.006	0.002	0.002	0.000	0.000	0.000	0.000
47	C	653	PRO	0	0.006	0.010	35.563	-0.002	-0.002	0.000	0.000	0.000	0.000
48	C	654	PRO	0	0.030	0.008	38.551	0.003	0.003	0.000	0.000	0.000	0.000
49	C	655	PRO	0	0.059	0.042	39.838	0.000	0.000	0.000	0.000	0.000	0.000
50	C	656	HIS	0	-0.001	-0.013	40.856	-0.003	-0.003	0.000	0.000	0.000	0.000
51	C	657	SER	0	0.012	0.001	40.812	-0.003	-0.003	0.000	0.000	0.000	0.000
52	C	658	ASP	-1	-0.830	-0.891	38.517	0.042	0.042	0.000	0.000	0.000	0.000
53	C	659	THR	0	-0.038	-0.028	41.989	-0.002	-0.002	0.000	0.000	0.000	0.000
54	C	660	VAL	0	0.036	0.003	45.598	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	661	GLU	-1	-0.873	-0.957	49.005	0.029	0.029	0.000	0.000	0.000	0.000
56	C	662	PHE	0	-0.026	0.008	45.339	0.000	0.000	0.000	0.000	0.000	0.000
57	C	663	TYR	0	0.069	0.007	43.513	-0.002	-0.002	0.000	0.000	0.000	0.000
58	C	664	GLN	0	0.002	-0.002	49.544	-0.002	-0.002	0.000	0.000	0.000	0.000
59	C	665	ARG	1	0.887	0.959	50.149	-0.033	-0.033	0.000	0.000	0.000	0.000
60	C	666	LEU	0	-0.031	0.010	48.003	0.000	0.000	0.000	0.000	0.000	0.000
61	C	667	SER	0	0.044	0.034	52.412	-0.001	-0.001	0.000	0.000	0.000	0.000
62	C	668	THR	0	0.033	-0.001	54.207	0.000	0.000	0.000	0.000	0.000	0.000
63	C	669	GLU	-1	-0.845	-0.904	54.350	0.015	0.015	0.000	0.000	0.000	0.000
64	C	670	THR	0	0.003	-0.005	49.420	0.000	0.000	0.000	0.000	0.000	0.000
65	C	671	LEU	0	-0.027	-0.009	50.306	0.000	0.000	0.000	0.000	0.000	0.000
66	C	672	PHE	0	0.021	-0.006	51.241	0.000	0.000	0.000	0.000	0.000	0.000
67	C	673	PHE	0	0.025	0.007	46.048	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	674	ILE	0	-0.021	-0.011	45.779	0.000	0.000	0.000	0.000	0.000	0.000
69	C	675	PHE	0	-0.047	-0.028	47.248	0.000	0.000	0.000	0.000	0.000	0.000
70	C	676	TYR	0	-0.022	-0.024	49.509	0.000	0.000	0.000	0.000	0.000	0.000
71	C	677	TYR	0	-0.006	0.005	46.150	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	678	LEU	0	-0.031	-0.014	41.282	0.001	0.001	0.000	0.000	0.000	0.000
73	C	679	GLU	-1	-0.914	-0.934	44.191	0.011	0.011	0.000	0.000	0.000	0.000
74	C	680	GLY	0	0.004	0.012	43.158	0.000	0.000	0.000	0.000	0.000	0.000
75	C	681	THR	0	-0.074	-0.066	40.189	0.002	0.002	0.000	0.000	0.000	0.000
76	C	682	LYS	1	0.839	0.888	40.418	-0.039	-0.039	0.000	0.000	0.000	0.000
77	C	683	ALA	0	0.056	0.037	42.426	0.000	0.000	0.000	0.000	0.000	0.000
78	C	684	GLN	0	0.053	0.028	44.106	0.000	0.000	0.000	0.000	0.000	0.000
79	C	685	TYR	0	0.010	-0.003	45.537	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	686	LEU	0	-0.019	-0.018	43.827	0.000	0.000	0.000	0.000	0.000	0.000
81	C	687	ALA	0	0.034	0.021	47.777	0.000	0.000	0.000	0.000	0.000	0.000
82	C	688	ALA	0	0.025	0.016	50.061	-0.001	-0.001	0.000	0.000	0.000	0.000
83	C	689	LYS	1	0.858	0.938	49.776	-0.023	-0.023	0.000	0.000	0.000	0.000
84	C	690	ALA	0	0.004	0.003	51.765	0.000	0.000	0.000	0.000	0.000	0.000
85	C	691	LEU	0	0.008	0.009	53.510	0.000	0.000	0.000	0.000	0.000	0.000
86	C	692	LYS	1	0.922	0.950	55.581	-0.016	-0.016	0.000	0.000	0.000	0.000
87	C	693	LYS	1	0.848	0.929	53.355	-0.026	-0.026	0.000	0.000	0.000	0.000
88	C	694	GLN	0	0.001	0.018	57.702	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	695	SER	0	-0.042	-0.021	59.482	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	696	TRP	0	-0.033	-0.006	58.870	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	697	ARG	1	0.851	0.904	59.948	-0.011	-0.011	0.000	0.000	0.000	0.000
92	C	698	PHE	0	0.004	0.002	55.711	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	699	HIS	0	0.015	0.007	59.337	0.000	0.000	0.000	0.000	0.000	0.000
94	C	700	THR	0	0.010	-0.025	57.960	0.000	0.000	0.000	0.000	0.000	0.000
95	C	701	LYS	1	0.882	0.953	59.464	-0.005	-0.005	0.000	0.000	0.000	0.000
96	C	702	TYR	0	0.021	0.002	61.794	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	703	MET	0	0.037	0.037	56.200	0.000	0.000	0.000	0.000	0.000	0.000
98	C	704	MET	0	-0.005	0.027	57.042	0.000	0.000	0.000	0.000	0.000	0.000
99	C	705	TRP	0	-0.028	-0.009	53.914	0.000	0.000	0.000	0.000	0.000	0.000
100	C	706	PHE	0	0.008	-0.014	60.064	0.000	0.000	0.000	0.000	0.000	0.000
101	C	707	GLN	0	0.018	0.011	63.343	0.000	0.000	0.000	0.000	0.000	0.000
102	C	708	ARG	1	0.794	0.871	65.250	-0.012	-0.012	0.000	0.000	0.000	0.000
103	C	709	HIS	0	-0.027	-0.013	68.862	0.000	0.000	0.000	0.000	0.000	0.000
104	C	710	GLU	-1	-0.884	-0.964	70.755	0.010	0.010	0.000	0.000	0.000	0.000
105	C	711	GLU	-1	-0.811	-0.877	72.575	0.011	0.011	0.000	0.000	0.000	0.000
106	C	712	PRO	0	-0.058	-0.019	72.820	0.000	0.000	0.000	0.000	0.000	0.000
107	C	713	LYS	1	0.873	0.921	75.391	-0.009	-0.009	0.000	0.000	0.000	0.000
108	C	714	THR	0	-0.026	0.002	77.369	0.000	0.000	0.000	0.000	0.000	0.000
109	C	715	ILE	0	-0.015	-0.015	72.718	0.000	0.000	0.000	0.000	0.000	0.000
110	C	716	THR	0	-0.018	-0.006	74.814	0.000	0.000	0.000	0.000	0.000	0.000
111	C	717	ASP	-1	-0.854	-0.933	72.590	0.009	0.009	0.000	0.000	0.000	0.000
112	C	718	GLU	-1	-0.902	-0.954	71.643	0.007	0.007	0.000	0.000	0.000	0.000
113	C	719	PHE	0	-0.091	-0.054	71.438	0.000	0.000	0.000	0.000	0.000	0.000
114	C	720	GLU	-1	-0.680	-0.779	69.246	0.011	0.011	0.000	0.000	0.000	0.000
115	C	721	GLN	0	-0.061	-0.023	71.894	0.000	0.000	0.000	0.000	0.000	0.000
116	C	722	GLY	0	0.021	0.001	73.955	0.000	0.000	0.000	0.000	0.000	0.000
117	C	723	THR	0	-0.044	-0.028	72.922	0.000	0.000	0.000	0.000	0.000	0.000
118	C	724	TYR	0	-0.033	-0.036	67.858	0.001	0.001	0.000	0.000	0.000	0.000
119	C	725	ILE	0	-0.011	-0.007	65.282	-0.001	-0.001	0.000	0.000	0.000	0.000
120	C	726	TYR	0	0.024	0.001	63.102	0.000	0.000	0.000	0.000	0.000	0.000
121	C	727	PHE	0	0.011	0.007	56.644	0.000	0.000	0.000	0.000	0.000	0.000
122	C	728	ASP	-1	-0.788	-0.882	60.134	0.007	0.007	0.000	0.000	0.000	0.000
123	C	729	TYR	0	-0.001	-0.018	55.691	0.000	0.000	0.000	0.000	0.000	0.000
124	C	730	GLU	-1	-0.856	-0.899	56.428	0.004	0.004	0.000	0.000	0.000	0.000
125	C	731	LYS	1	0.768	0.856	58.676	-0.005	-0.005	0.000	0.000	0.000	0.000
126	C	732	TRP	0	-0.057	-0.034	52.791	0.000	0.000	0.000	0.000	0.000	0.000
127	C	733	GLY	0	0.043	0.019	58.187	0.000	0.000	0.000	0.000	0.000	0.000
128	C	734	GLN	0	0.009	0.007	60.539	0.000	0.000	0.000	0.000	0.000	0.000
129	C	735	ARG	1	0.780	0.897	62.084	-0.009	-0.009	0.000	0.000	0.000	0.000
130	C	736	LYS	1	0.910	0.948	66.314	-0.008	-0.008	0.000	0.000	0.000	0.000
131	C	737	LYS	1	0.883	0.936	68.341	-0.007	-0.007	0.000	0.000	0.000	0.000
132	C	738	GLU	-1	-0.763	-0.855	71.181	0.008	0.008	0.000	0.000	0.000	0.000
133	C	739	GLY	0	0.016	0.011	74.692	0.000	0.000	0.000	0.000	0.000	0.000
134	C	740	PHE	0	-0.015	0.006	66.829	0.000	0.000	0.000	0.000	0.000	0.000
135	C	741	THR	0	0.044	0.014	71.811	0.000	0.000	0.000	0.000	0.000	0.000
136	C	742	PHE	0	-0.028	-0.012	63.343	0.000	0.000	0.000	0.000	0.000	0.000
137	C	743	GLU	-1	-0.780	-0.883	68.687	0.006	0.006	0.000	0.000	0.000	0.000
138	C	744	TYR	0	-0.022	-0.030	66.585	0.000	0.000	0.000	0.000	0.000	0.000
139	C	745	ARG	1	0.808	0.884	65.586	-0.006	-0.006	0.000	0.000	0.000	0.000
140	C	746	TYR	0	-0.049	-0.026	63.068	-0.001	-0.001	0.000	0.000	0.000	0.000
141	C	747	LEU	0	-0.004	0.020	60.756	0.000	0.000	0.000	0.000	0.000	0.000
142	C	748	GLU	-1	-0.913	-0.940	55.400	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:607:LEU)