FMO DATABASE

FMODB ID: LZ5M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1279799.112027
FMO2-HF: Nuclear repulsion	1218077.110102
FMO2-HF: Total energy	-61722.001925
FMO2-MP2: Total energy	-61901.651734

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.
-8.194	-1.563	4.642	-3.603	-7.67	-0.018

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 : 0.021 / q_NPA : 0.002

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	1.020	0.998	3.111	-1.303	0.672	0.122	-1.003	-1.093	0.001
4	C	610	GLU	-1	-0.889	-0.948	5.825	-0.581	-0.581	0.000	0.000	0.000	0.000
5	C	611	GLN	0	0.047	0.015	2.455	-2.055	0.220	2.392	-1.467	-3.199	-0.014
6	C	612	LEU	0	-0.006	0.002	2.469	-2.016	-0.670	2.079	-0.820	-2.606	-0.003
7	C	613	TYR	0	-0.011	0.000	4.021	0.100	0.237	0.004	-0.026	-0.115	0.000
8	C	614	GLN	0	0.000	-0.012	6.308	0.204	0.204	0.000	0.000	0.000	0.000
9	C	615	GLN	0	0.024	0.019	3.251	-1.930	-1.032	0.045	-0.287	-0.657	-0.002
10	C	616	ALA	0	0.012	0.007	6.228	0.223	0.223	0.000	0.000	0.000	0.000
11	C	617	MET	0	-0.033	-0.022	8.926	0.167	0.167	0.000	0.000	0.000	0.000
12	C	618	GLU	-1	-0.963	-0.971	9.219	-0.568	-0.568	0.000	0.000	0.000	0.000
13	C	619	GLU	-1	-0.970	-0.991	9.999	-0.715	-0.715	0.000	0.000	0.000	0.000
14	C	620	ALA	0	-0.044	-0.027	11.671	0.089	0.089	0.000	0.000	0.000	0.000
15	C	621	ALA	0	-0.021	-0.024	14.176	0.060	0.060	0.000	0.000	0.000	0.000
16	C	622	TRP	0	-0.044	-0.009	13.963	0.048	0.048	0.000	0.000	0.000	0.000
17	C	623	HIS	0	0.001	-0.004	15.898	0.053	0.053	0.000	0.000	0.000	0.000
18	C	624	HIS	0	-0.097	-0.037	18.694	0.022	0.022	0.000	0.000	0.000	0.000
19	C	625	MET	0	0.000	0.008	18.094	0.000	0.000	0.000	0.000	0.000	0.000
20	C	626	PRO	0	-0.008	0.007	20.271	0.014	0.014	0.000	0.000	0.000	0.000
21	C	627	HIS	0	0.047	0.046	23.402	0.008	0.008	0.000	0.000	0.000	0.000
22	C	628	PRO	0	-0.010	-0.023	26.593	0.007	0.007	0.000	0.000	0.000	0.000
23	C	629	SER	0	-0.108	-0.080	28.259	0.008	0.008	0.000	0.000	0.000	0.000
24	C	630	ASP	-1	-0.817	-0.905	26.585	-0.129	-0.129	0.000	0.000	0.000	0.000
25	C	631	SER	0	-0.067	-0.026	27.331	0.003	0.003	0.000	0.000	0.000	0.000
26	C	632	GLU	-1	-0.980	-0.979	29.589	-0.063	-0.063	0.000	0.000	0.000	0.000
27	C	633	ARG	1	0.951	0.960	33.223	0.052	0.052	0.000	0.000	0.000	0.000
28	C	634	ILE	0	0.092	0.038	36.377	0.000	0.000	0.000	0.000	0.000	0.000
29	C	635	ARG	1	0.907	0.959	36.571	0.064	0.064	0.000	0.000	0.000	0.000
30	C	636	GLN	0	0.018	0.022	39.458	-0.004	-0.004	0.000	0.000	0.000	0.000
31	C	637	TYR	0	0.001	-0.002	42.508	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	638	LEU	0	-0.016	-0.008	41.048	0.000	0.000	0.000	0.000	0.000	0.000
33	C	639	PRO	0	0.018	0.009	37.009	0.000	0.000	0.000	0.000	0.000	0.000
34	C	640	ARG	1	0.939	0.975	31.245	0.078	0.078	0.000	0.000	0.000	0.000
35	C	641	ASN	0	0.014	0.001	33.498	-0.011	-0.011	0.000	0.000	0.000	0.000
36	C	642	PRO	0	-0.024	-0.012	29.521	0.004	0.004	0.000	0.000	0.000	0.000
37	C	643	CYS	0	0.007	0.004	31.897	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	644	PRO	0	0.022	0.000	29.758	0.003	0.003	0.000	0.000	0.000	0.000
39	C	645	THR	0	0.014	0.028	31.604	0.006	0.006	0.000	0.000	0.000	0.000
40	C	646	PRO	0	-0.013	-0.004	33.046	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	647	PRO	0	0.032	0.010	32.695	0.002	0.002	0.000	0.000	0.000	0.000
42	C	648	TYR	0	-0.013	-0.013	34.342	0.003	0.003	0.000	0.000	0.000	0.000
43	C	649	HIS	0	0.001	0.011	37.372	0.005	0.005	0.000	0.000	0.000	0.000
44	C	650	HIS	0	-0.001	-0.010	36.796	-0.003	-0.003	0.000	0.000	0.000	0.000
45	C	651	GLN	0	-0.005	-0.003	32.346	-0.005	-0.005	0.000	0.000	0.000	0.000
46	C	652	MET	0	-0.032	-0.011	31.832	-0.002	-0.002	0.000	0.000	0.000	0.000
47	C	653	PRO	0	-0.006	0.003	35.435	0.002	0.002	0.000	0.000	0.000	0.000
48	C	654	PRO	0	0.016	-0.001	38.295	0.001	0.001	0.000	0.000	0.000	0.000
49	C	655	PRO	0	0.050	0.030	39.710	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	656	HIS	0	0.001	-0.012	40.681	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	657	SER	0	0.012	0.013	40.521	0.000	0.000	0.000	0.000	0.000	0.000
52	C	658	ASP	-1	-0.910	-0.953	38.834	-0.031	-0.031	0.000	0.000	0.000	0.000
53	C	659	THR	0	-0.088	-0.045	42.213	0.001	0.001	0.000	0.000	0.000	0.000
54	C	660	VAL	0	0.038	0.000	45.567	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	661	GLU	-1	-0.878	-0.955	48.794	-0.014	-0.014	0.000	0.000	0.000	0.000
56	C	662	PHE	0	-0.030	0.000	45.229	0.000	0.000	0.000	0.000	0.000	0.000
57	C	663	TYR	0	0.034	-0.010	43.412	-0.002	-0.002	0.000	0.000	0.000	0.000
58	C	664	GLN	0	-0.030	-0.007	49.647	0.000	0.000	0.000	0.000	0.000	0.000
59	C	665	ARG	1	0.929	0.973	49.586	0.017	0.017	0.000	0.000	0.000	0.000
60	C	666	LEU	0	-0.029	0.016	47.942	0.000	0.000	0.000	0.000	0.000	0.000
61	C	667	SER	0	0.057	0.043	52.341	0.001	0.001	0.000	0.000	0.000	0.000
62	C	668	THR	0	0.052	0.003	54.034	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	669	GLU	-1	-0.852	-0.917	54.098	-0.030	-0.030	0.000	0.000	0.000	0.000
64	C	670	THR	0	0.009	0.001	49.291	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	671	LEU	0	-0.018	-0.007	50.361	-0.002	-0.002	0.000	0.000	0.000	0.000
66	C	672	PHE	0	0.008	-0.007	51.306	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	673	PHE	0	0.007	0.009	45.776	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	674	ILE	0	-0.012	-0.017	45.690	-0.002	-0.002	0.000	0.000	0.000	0.000
69	C	675	PHE	0	-0.056	-0.032	47.263	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	676	TYR	0	-0.034	-0.030	49.329	0.000	0.000	0.000	0.000	0.000	0.000
71	C	677	TYR	0	-0.016	-0.002	46.131	-0.002	-0.002	0.000	0.000	0.000	0.000
72	C	678	LEU	0	-0.054	-0.019	41.781	-0.003	-0.003	0.000	0.000	0.000	0.000
73	C	679	GLU	-1	-0.905	-0.947	44.547	-0.040	-0.040	0.000	0.000	0.000	0.000
74	C	680	GLY	0	0.003	0.006	43.465	-0.002	-0.002	0.000	0.000	0.000	0.000
75	C	681	THR	0	-0.043	-0.028	40.492	-0.001	-0.001	0.000	0.000	0.000	0.000
76	C	682	LYS	1	0.977	0.971	40.252	0.029	0.029	0.000	0.000	0.000	0.000
77	C	683	ALA	0	0.050	0.026	42.480	0.003	0.003	0.000	0.000	0.000	0.000
78	C	684	GLN	0	0.087	0.067	44.117	0.001	0.001	0.000	0.000	0.000	0.000
79	C	685	TYR	0	-0.012	-0.011	45.693	0.003	0.003	0.000	0.000	0.000	0.000
80	C	686	LEU	0	-0.015	-0.020	43.817	0.002	0.002	0.000	0.000	0.000	0.000
81	C	687	ALA	0	0.048	0.033	47.962	0.002	0.002	0.000	0.000	0.000	0.000
82	C	688	ALA	0	0.037	0.020	49.989	0.001	0.001	0.000	0.000	0.000	0.000
83	C	689	LYS	1	0.857	0.935	50.274	0.019	0.019	0.000	0.000	0.000	0.000
84	C	690	ALA	0	0.003	0.000	51.879	0.001	0.001	0.000	0.000	0.000	0.000
85	C	691	LEU	0	0.024	0.019	53.656	0.001	0.001	0.000	0.000	0.000	0.000
86	C	692	LYS	1	0.949	0.970	55.329	0.020	0.020	0.000	0.000	0.000	0.000
87	C	693	LYS	1	0.864	0.926	54.742	0.014	0.014	0.000	0.000	0.000	0.000
88	C	694	GLN	0	-0.008	0.023	57.874	0.000	0.000	0.000	0.000	0.000	0.000
89	C	695	SER	0	-0.061	-0.037	59.779	0.000	0.000	0.000	0.000	0.000	0.000
90	C	696	TRP	0	0.010	0.017	58.876	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	697	ARG	1	0.844	0.900	59.712	0.016	0.016	0.000	0.000	0.000	0.000
92	C	698	PHE	0	0.027	0.016	55.751	0.000	0.000	0.000	0.000	0.000	0.000
93	C	699	HIS	0	0.032	0.023	59.444	0.000	0.000	0.000	0.000	0.000	0.000
94	C	700	THR	0	0.009	0.000	58.616	-0.001	-0.001	0.000	0.000	0.000	0.000
95	C	701	LYS	1	0.913	0.965	59.530	0.020	0.020	0.000	0.000	0.000	0.000
96	C	702	TYR	0	-0.012	-0.029	61.469	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	703	MET	0	0.000	0.019	56.474	-0.001	-0.001	0.000	0.000	0.000	0.000
98	C	704	MET	0	0.023	0.017	57.430	-0.001	-0.001	0.000	0.000	0.000	0.000
99	C	705	TRP	0	-0.022	-0.006	53.944	0.002	0.002	0.000	0.000	0.000	0.000
100	C	706	PHE	0	-0.010	-0.022	59.911	0.000	0.000	0.000	0.000	0.000	0.000
101	C	707	GLN	0	0.042	0.022	63.242	0.000	0.000	0.000	0.000	0.000	0.000
102	C	708	ARG	1	0.866	0.908	65.173	0.013	0.013	0.000	0.000	0.000	0.000
103	C	709	HIS	0	-0.033	-0.009	68.812	0.000	0.000	0.000	0.000	0.000	0.000
104	C	710	GLU	-1	-0.870	-0.936	70.567	-0.012	-0.012	0.000	0.000	0.000	0.000
105	C	711	GLU	-1	-0.963	-0.964	73.457	-0.011	-0.011	0.000	0.000	0.000	0.000
106	C	712	PRO	0	-0.040	-0.012	72.999	0.000	0.000	0.000	0.000	0.000	0.000
107	C	713	LYS	1	0.903	0.943	75.745	0.012	0.012	0.000	0.000	0.000	0.000
108	C	714	THR	0	-0.031	-0.019	77.344	0.000	0.000	0.000	0.000	0.000	0.000
109	C	715	ILE	0	0.008	0.003	73.810	-0.001	-0.001	0.000	0.000	0.000	0.000
110	C	716	THR	0	-0.045	-0.020	75.289	0.000	0.000	0.000	0.000	0.000	0.000
111	C	717	ASP	-1	-0.845	-0.924	73.023	-0.010	-0.010	0.000	0.000	0.000	0.000
112	C	718	GLU	-1	-0.946	-0.965	71.990	-0.012	-0.012	0.000	0.000	0.000	0.000
113	C	719	PHE	0	-0.085	-0.059	71.595	-0.001	-0.001	0.000	0.000	0.000	0.000
114	C	720	GLU	-1	-0.697	-0.812	69.932	-0.013	-0.013	0.000	0.000	0.000	0.000
115	C	721	GLN	0	-0.045	-0.017	71.971	-0.001	-0.001	0.000	0.000	0.000	0.000
116	C	722	GLY	0	-0.014	-0.015	73.778	0.001	0.001	0.000	0.000	0.000	0.000
117	C	723	THR	0	-0.042	-0.052	72.905	0.000	0.000	0.000	0.000	0.000	0.000
118	C	724	TYR	0	-0.043	-0.018	67.981	0.000	0.000	0.000	0.000	0.000	0.000
119	C	725	ILE	0	-0.031	-0.013	65.211	0.000	0.000	0.000	0.000	0.000	0.000
120	C	726	TYR	0	0.038	0.001	62.994	0.001	0.001	0.000	0.000	0.000	0.000
121	C	727	PHE	0	0.013	0.000	55.956	0.000	0.000	0.000	0.000	0.000	0.000
122	C	728	ASP	-1	-0.902	-0.957	59.814	-0.027	-0.027	0.000	0.000	0.000	0.000
123	C	729	TYR	0	0.004	-0.001	55.691	-0.001	-0.001	0.000	0.000	0.000	0.000
124	C	730	GLU	-1	-0.933	-0.957	56.458	-0.031	-0.031	0.000	0.000	0.000	0.000
125	C	731	LYS	1	0.833	0.912	58.526	0.028	0.028	0.000	0.000	0.000	0.000
126	C	732	TRP	0	-0.010	0.011	52.450	0.000	0.000	0.000	0.000	0.000	0.000
127	C	733	GLY	0	0.037	0.008	58.193	0.000	0.000	0.000	0.000	0.000	0.000
128	C	734	GLN	0	-0.014	-0.007	60.864	0.000	0.000	0.000	0.000	0.000	0.000
129	C	735	ARG	1	0.886	0.957	63.288	0.025	0.025	0.000	0.000	0.000	0.000
130	C	736	LYS	1	0.919	0.950	66.422	0.016	0.016	0.000	0.000	0.000	0.000
131	C	737	LYS	1	0.895	0.951	68.212	0.020	0.020	0.000	0.000	0.000	0.000
132	C	738	GLU	-1	-0.765	-0.842	70.960	-0.015	-0.015	0.000	0.000	0.000	0.000
133	C	739	GLY	0	0.025	0.025	74.615	0.000	0.000	0.000	0.000	0.000	0.000
134	C	740	PHE	0	-0.024	-0.006	66.988	0.000	0.000	0.000	0.000	0.000	0.000
135	C	741	THR	0	0.055	0.010	72.362	0.001	0.001	0.000	0.000	0.000	0.000
136	C	742	PHE	0	-0.034	-0.025	63.701	-0.001	-0.001	0.000	0.000	0.000	0.000
137	C	743	GLU	-1	-0.821	-0.922	68.651	-0.016	-0.016	0.000	0.000	0.000	0.000
138	C	744	TYR	0	-0.018	-0.017	66.772	-0.001	-0.001	0.000	0.000	0.000	0.000
139	C	745	ARG	1	0.886	0.939	65.928	0.015	0.015	0.000	0.000	0.000	0.000
140	C	746	TYR	0	-0.064	-0.028	63.131	-0.001	-0.001	0.000	0.000	0.000	0.000
141	C	747	LEU	0	0.003	-0.001	60.851	-0.001	-0.001	0.000	0.000	0.000	0.000
142	C	748	GLU	-1	-0.950	-0.956	55.303	-0.019	-0.019	0.000	0.000	0.000	0.000

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