FMO DATABASE

FMODB ID: 945N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1280614.407966
FMO2-HF: Nuclear repulsion	1218891.734081
FMO2-HF: Total energy	-61722.673885
FMO2-MP2: Total energy	-61902.355308

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.
-6.254	1.06	4.069	-4.021	-7.362	-0.006

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 : 0.038 / q_NPA : 0.025

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	1.009	0.989	3.117	-1.757	1.483	0.112	-1.758	-1.594	0.006
4	C	610	GLU	-1	-0.879	-0.948	5.829	-0.322	-0.322	0.000	0.000	0.000	0.000
5	C	611	GLN	0	0.066	0.039	2.344	-1.883	0.061	1.477	-1.061	-2.360	-0.006
6	C	612	LEU	0	-0.013	-0.001	2.374	-1.648	-0.422	2.454	-0.927	-2.753	-0.004
7	C	613	TYR	0	-0.026	-0.005	4.007	0.105	0.239	0.004	-0.026	-0.111	0.000
8	C	614	GLN	0	0.012	-0.006	5.978	0.068	0.068	0.000	0.000	0.000	0.000
9	C	615	GLN	0	0.015	0.014	3.423	-1.058	-0.288	0.022	-0.249	-0.544	-0.002
10	C	616	ALA	0	0.019	0.011	6.263	0.104	0.104	0.000	0.000	0.000	0.000
11	C	617	MET	0	-0.022	-0.017	8.941	0.066	0.066	0.000	0.000	0.000	0.000
12	C	618	GLU	-1	-0.979	-0.981	9.300	0.146	0.146	0.000	0.000	0.000	0.000
13	C	619	GLU	-1	-0.966	-0.987	9.868	-0.091	-0.091	0.000	0.000	0.000	0.000
14	C	620	ALA	0	-0.043	-0.028	11.668	0.023	0.023	0.000	0.000	0.000	0.000
15	C	621	ALA	0	-0.012	-0.017	14.202	0.016	0.016	0.000	0.000	0.000	0.000
16	C	622	TRP	0	-0.038	-0.009	13.975	0.019	0.019	0.000	0.000	0.000	0.000
17	C	623	HIS	0	-0.020	-0.008	15.580	0.024	0.024	0.000	0.000	0.000	0.000
18	C	624	HIS	0	-0.095	-0.038	18.688	-0.006	-0.006	0.000	0.000	0.000	0.000
19	C	625	MET	0	0.001	0.009	17.833	0.002	0.002	0.000	0.000	0.000	0.000
20	C	626	PRO	0	-0.013	0.002	20.205	-0.002	-0.002	0.000	0.000	0.000	0.000
21	C	627	HIS	0	0.040	0.024	23.331	0.010	0.010	0.000	0.000	0.000	0.000
22	C	628	PRO	0	-0.005	-0.021	26.155	0.000	0.000	0.000	0.000	0.000	0.000
23	C	629	SER	0	-0.049	-0.035	28.036	0.001	0.001	0.000	0.000	0.000	0.000
24	C	630	ASP	-1	-0.872	-0.929	26.470	0.010	0.010	0.000	0.000	0.000	0.000
25	C	631	SER	0	-0.056	-0.018	27.093	0.001	0.001	0.000	0.000	0.000	0.000
26	C	632	GLU	-1	-0.869	-0.894	29.351	0.031	0.031	0.000	0.000	0.000	0.000
27	C	633	ARG	1	0.955	0.964	32.989	-0.018	-0.018	0.000	0.000	0.000	0.000
28	C	634	ILE	0	0.059	0.018	36.138	0.002	0.002	0.000	0.000	0.000	0.000
29	C	635	ARG	1	0.862	0.930	35.840	-0.025	-0.025	0.000	0.000	0.000	0.000
30	C	636	GLN	0	0.005	0.017	39.225	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	637	TYR	0	0.021	0.002	42.364	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	638	LEU	0	-0.014	-0.006	40.967	0.000	0.000	0.000	0.000	0.000	0.000
33	C	639	PRO	0	0.022	0.010	36.913	0.002	0.002	0.000	0.000	0.000	0.000
34	C	640	ARG	1	0.877	0.922	31.188	-0.036	-0.036	0.000	0.000	0.000	0.000
35	C	641	ASN	0	0.018	0.003	33.398	-0.002	-0.002	0.000	0.000	0.000	0.000
36	C	642	PRO	0	-0.011	-0.004	29.349	0.001	0.001	0.000	0.000	0.000	0.000
37	C	643	CYS	0	0.018	0.005	31.823	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	644	PRO	0	0.007	-0.003	29.823	0.004	0.004	0.000	0.000	0.000	0.000
39	C	645	THR	0	0.009	0.025	31.708	-0.004	-0.004	0.000	0.000	0.000	0.000
40	C	646	PRO	0	0.010	0.006	33.113	0.004	0.004	0.000	0.000	0.000	0.000
41	C	647	PRO	0	0.025	0.007	32.625	0.000	0.000	0.000	0.000	0.000	0.000
42	C	648	TYR	0	-0.015	-0.011	34.382	0.001	0.001	0.000	0.000	0.000	0.000
43	C	649	HIS	0	-0.001	0.009	37.436	-0.001	-0.001	0.000	0.000	0.000	0.000
44	C	650	HIS	0	-0.002	-0.008	36.816	0.003	0.003	0.000	0.000	0.000	0.000
45	C	651	GLN	0	-0.017	-0.012	32.209	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	652	MET	0	-0.027	-0.010	31.601	0.001	0.001	0.000	0.000	0.000	0.000
47	C	653	PRO	0	-0.002	0.006	35.283	-0.002	-0.002	0.000	0.000	0.000	0.000
48	C	654	PRO	0	0.032	0.008	38.145	0.002	0.002	0.000	0.000	0.000	0.000
49	C	655	PRO	0	0.045	0.038	39.460	0.000	0.000	0.000	0.000	0.000	0.000
50	C	656	HIS	0	-0.001	-0.012	40.540	-0.002	-0.002	0.000	0.000	0.000	0.000
51	C	657	SER	0	0.019	-0.002	40.517	-0.003	-0.003	0.000	0.000	0.000	0.000
52	C	658	ASP	-1	-0.847	-0.910	38.634	0.043	0.043	0.000	0.000	0.000	0.000
53	C	659	THR	0	-0.072	-0.036	42.039	-0.002	-0.002	0.000	0.000	0.000	0.000
54	C	660	VAL	0	0.046	0.007	45.397	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	661	GLU	-1	-0.896	-0.965	48.617	0.030	0.030	0.000	0.000	0.000	0.000
56	C	662	PHE	0	-0.034	-0.003	44.908	-0.001	-0.001	0.000	0.000	0.000	0.000
57	C	663	TYR	0	0.039	-0.010	43.168	-0.001	-0.001	0.000	0.000	0.000	0.000
58	C	664	GLN	0	-0.002	0.008	49.467	-0.002	-0.002	0.000	0.000	0.000	0.000
59	C	665	ARG	1	0.922	0.971	49.865	-0.033	-0.033	0.000	0.000	0.000	0.000
60	C	666	LEU	0	-0.031	0.015	47.774	0.000	0.000	0.000	0.000	0.000	0.000
61	C	667	SER	0	0.053	0.041	52.162	-0.001	-0.001	0.000	0.000	0.000	0.000
62	C	668	THR	0	0.064	0.011	53.844	0.001	0.001	0.000	0.000	0.000	0.000
63	C	669	GLU	-1	-0.857	-0.913	54.318	0.016	0.016	0.000	0.000	0.000	0.000
64	C	670	THR	0	0.006	-0.003	49.164	0.000	0.000	0.000	0.000	0.000	0.000
65	C	671	LEU	0	-0.022	-0.004	50.161	0.000	0.000	0.000	0.000	0.000	0.000
66	C	672	PHE	0	0.013	-0.006	51.099	0.000	0.000	0.000	0.000	0.000	0.000
67	C	673	PHE	0	0.024	0.011	45.629	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	674	ILE	0	-0.023	-0.015	45.607	0.000	0.000	0.000	0.000	0.000	0.000
69	C	675	PHE	0	-0.039	-0.021	47.048	0.000	0.000	0.000	0.000	0.000	0.000
70	C	676	TYR	0	-0.013	-0.023	49.106	0.000	0.000	0.000	0.000	0.000	0.000
71	C	677	TYR	0	-0.016	0.005	45.983	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	678	LEU	0	-0.045	-0.018	41.295	0.001	0.001	0.000	0.000	0.000	0.000
73	C	679	GLU	-1	-0.919	-0.949	44.326	0.013	0.013	0.000	0.000	0.000	0.000
74	C	680	GLY	0	0.015	0.009	43.236	0.000	0.000	0.000	0.000	0.000	0.000
75	C	681	THR	0	-0.061	-0.038	40.355	0.002	0.002	0.000	0.000	0.000	0.000
76	C	682	LYS	1	0.890	0.919	39.705	-0.040	-0.040	0.000	0.000	0.000	0.000
77	C	683	ALA	0	0.044	0.022	42.238	0.000	0.000	0.000	0.000	0.000	0.000
78	C	684	GLN	0	0.047	0.034	43.912	0.000	0.000	0.000	0.000	0.000	0.000
79	C	685	TYR	0	0.000	-0.007	45.510	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	686	LEU	0	-0.013	-0.015	43.691	-0.001	-0.001	0.000	0.000	0.000	0.000
81	C	687	ALA	0	0.038	0.021	47.764	0.000	0.000	0.000	0.000	0.000	0.000
82	C	688	ALA	0	0.035	0.019	49.788	-0.001	-0.001	0.000	0.000	0.000	0.000
83	C	689	LYS	1	0.865	0.940	49.979	-0.024	-0.024	0.000	0.000	0.000	0.000
84	C	690	ALA	0	-0.010	-0.006	51.663	0.000	0.000	0.000	0.000	0.000	0.000
85	C	691	LEU	0	0.022	0.019	53.463	-0.001	-0.001	0.000	0.000	0.000	0.000
86	C	692	LYS	1	0.946	0.968	55.623	-0.017	-0.017	0.000	0.000	0.000	0.000
87	C	693	LYS	1	0.866	0.929	54.092	-0.025	-0.025	0.000	0.000	0.000	0.000
88	C	694	GLN	0	-0.016	0.012	57.893	0.000	0.000	0.000	0.000	0.000	0.000
89	C	695	SER	0	-0.044	-0.025	59.588	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	696	TRP	0	0.009	0.017	58.682	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	697	ARG	1	0.852	0.909	59.503	-0.011	-0.011	0.000	0.000	0.000	0.000
92	C	698	PHE	0	0.006	0.003	55.440	0.000	0.000	0.000	0.000	0.000	0.000
93	C	699	HIS	0	0.032	0.017	59.224	0.000	0.000	0.000	0.000	0.000	0.000
94	C	700	THR	0	0.004	-0.010	58.185	0.000	0.000	0.000	0.000	0.000	0.000
95	C	701	LYS	1	0.901	0.956	59.294	-0.006	-0.006	0.000	0.000	0.000	0.000
96	C	702	TYR	0	0.021	-0.007	61.232	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	703	MET	0	0.021	0.030	56.221	0.000	0.000	0.000	0.000	0.000	0.000
98	C	704	MET	0	0.009	0.022	57.201	0.000	0.000	0.000	0.000	0.000	0.000
99	C	705	TRP	0	-0.025	-0.010	53.603	0.000	0.000	0.000	0.000	0.000	0.000
100	C	706	PHE	0	-0.007	-0.022	59.693	0.000	0.000	0.000	0.000	0.000	0.000
101	C	707	GLN	0	0.023	0.014	63.031	0.000	0.000	0.000	0.000	0.000	0.000
102	C	708	ARG	1	0.812	0.875	64.966	-0.012	-0.012	0.000	0.000	0.000	0.000
103	C	709	HIS	0	-0.030	-0.005	68.607	0.001	0.001	0.000	0.000	0.000	0.000
104	C	710	GLU	-1	-0.888	-0.944	70.364	0.011	0.011	0.000	0.000	0.000	0.000
105	C	711	GLU	-1	-0.853	-0.910	72.501	0.012	0.012	0.000	0.000	0.000	0.000
106	C	712	PRO	0	-0.032	-0.004	72.813	0.000	0.000	0.000	0.000	0.000	0.000
107	C	713	LYS	1	0.875	0.924	75.534	-0.009	-0.009	0.000	0.000	0.000	0.000
108	C	714	THR	0	-0.012	0.005	77.209	0.000	0.000	0.000	0.000	0.000	0.000
109	C	715	ILE	0	-0.006	-0.015	73.060	0.000	0.000	0.000	0.000	0.000	0.000
110	C	716	THR	0	-0.038	-0.016	75.089	0.000	0.000	0.000	0.000	0.000	0.000
111	C	717	ASP	-1	-0.841	-0.925	72.806	0.010	0.010	0.000	0.000	0.000	0.000
112	C	718	GLU	-1	-0.948	-0.967	71.768	0.007	0.007	0.000	0.000	0.000	0.000
113	C	719	PHE	0	-0.079	-0.054	71.369	0.000	0.000	0.000	0.000	0.000	0.000
114	C	720	GLU	-1	-0.691	-0.798	69.422	0.011	0.011	0.000	0.000	0.000	0.000
115	C	721	GLN	0	-0.051	-0.014	71.751	0.000	0.000	0.000	0.000	0.000	0.000
116	C	722	GLY	0	0.008	-0.006	73.553	0.000	0.000	0.000	0.000	0.000	0.000
117	C	723	THR	0	-0.044	-0.036	72.834	0.000	0.000	0.000	0.000	0.000	0.000
118	C	724	TYR	0	-0.063	-0.041	67.737	0.001	0.001	0.000	0.000	0.000	0.000
119	C	725	ILE	0	-0.025	-0.011	65.029	-0.001	-0.001	0.000	0.000	0.000	0.000
120	C	726	TYR	0	0.043	0.006	62.672	0.000	0.000	0.000	0.000	0.000	0.000
121	C	727	PHE	0	0.024	0.005	56.208	0.000	0.000	0.000	0.000	0.000	0.000
122	C	728	ASP	-1	-0.886	-0.937	59.595	0.008	0.008	0.000	0.000	0.000	0.000
123	C	729	TYR	0	0.009	-0.013	55.480	0.000	0.000	0.000	0.000	0.000	0.000
124	C	730	GLU	-1	-0.866	-0.909	56.234	0.006	0.006	0.000	0.000	0.000	0.000
125	C	731	LYS	1	0.759	0.854	58.413	-0.007	-0.007	0.000	0.000	0.000	0.000
126	C	732	TRP	0	-0.046	-0.014	52.489	0.000	0.000	0.000	0.000	0.000	0.000
127	C	733	GLY	0	0.035	0.013	57.980	0.000	0.000	0.000	0.000	0.000	0.000
128	C	734	GLN	0	-0.014	-0.003	60.655	0.000	0.000	0.000	0.000	0.000	0.000
129	C	735	ARG	1	0.881	0.951	62.793	-0.010	-0.010	0.000	0.000	0.000	0.000
130	C	736	LYS	1	0.937	0.957	66.209	-0.009	-0.009	0.000	0.000	0.000	0.000
131	C	737	LYS	1	0.874	0.941	67.938	-0.008	-0.008	0.000	0.000	0.000	0.000
132	C	738	GLU	-1	-0.779	-0.864	70.741	0.009	0.009	0.000	0.000	0.000	0.000
133	C	739	GLY	0	0.021	0.019	74.396	0.000	0.000	0.000	0.000	0.000	0.000
134	C	740	PHE	0	-0.039	-0.013	66.739	0.000	0.000	0.000	0.000	0.000	0.000
135	C	741	THR	0	0.065	0.021	72.123	0.000	0.000	0.000	0.000	0.000	0.000
136	C	742	PHE	0	-0.036	-0.023	63.256	0.000	0.000	0.000	0.000	0.000	0.000
137	C	743	GLU	-1	-0.821	-0.921	68.342	0.007	0.007	0.000	0.000	0.000	0.000
138	C	744	TYR	0	-0.037	-0.032	66.516	0.000	0.000	0.000	0.000	0.000	0.000
139	C	745	ARG	1	0.879	0.939	65.702	-0.007	-0.007	0.000	0.000	0.000	0.000
140	C	746	TYR	0	-0.066	-0.029	62.900	0.000	0.000	0.000	0.000	0.000	0.000
141	C	747	LEU	0	0.011	0.003	60.787	0.000	0.000	0.000	0.000	0.000	0.000
142	C	748	GLU	-1	-0.939	-0.952	55.174	0.014	0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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