FMO DATABASE

FMODB ID: YZV82

Calculation Name: 2D5R-B-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2D5R

Chain ID: B

ChEMBL ID: CHEMBL3616361

UniProt ID: Q9UIV1

Base Structure: X-ray

Registration Date: 2023-06-22

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1016643.894684
FMO2-HF: Nuclear repulsion	969942.325835
FMO2-HF: Total energy	-46701.568849
FMO2-MP2: Total energy	-46840.429103

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(B:24:HIS)

Summations of interaction energy for fragment #1(B:24:HIS)

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.
-11.352	-6.063	8.284	-4.164	-9.405	0.022

Interaction energy analysis for fragmet #1(B:24:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.016

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	B	26	GLN	0	-0.020	-0.003	2.964	-2.912	-0.014	0.106	-1.201	-1.802	0.002
4	B	27	LEU	0	0.037	0.030	4.243	-0.614	-0.363	-0.001	-0.029	-0.221	0.000
5	B	28	GLU	-1	-0.760	-0.900	5.444	3.573	3.656	-0.001	-0.015	-0.067	0.000
6	B	29	ILE	0	-0.007	-0.014	6.956	-0.323	-0.323	0.000	0.000	0.000	0.000
7	B	30	GLN	0	-0.005	-0.012	8.518	-0.371	-0.371	0.000	0.000	0.000	0.000
8	B	31	VAL	0	-0.013	0.009	10.205	-0.197	-0.197	0.000	0.000	0.000	0.000
9	B	32	ALA	0	0.015	0.010	12.240	-0.137	-0.137	0.000	0.000	0.000	0.000
10	B	33	LEU	0	-0.017	-0.010	12.272	-0.116	-0.116	0.000	0.000	0.000	0.000
11	B	34	ASN	0	-0.035	-0.029	13.026	-0.149	-0.149	0.000	0.000	0.000	0.000
12	B	35	PHE	0	0.011	0.019	16.203	-0.082	-0.082	0.000	0.000	0.000	0.000
13	B	36	ILE	0	0.021	0.016	17.275	-0.059	-0.059	0.000	0.000	0.000	0.000
14	B	37	ILE	0	0.018	-0.002	17.645	-0.050	-0.050	0.000	0.000	0.000	0.000
15	B	38	SER	0	-0.094	-0.054	20.336	-0.056	-0.056	0.000	0.000	0.000	0.000
16	B	39	TYR	0	-0.022	-0.010	22.183	-0.047	-0.047	0.000	0.000	0.000	0.000
17	B	40	LEU	0	0.029	0.023	22.433	-0.023	-0.023	0.000	0.000	0.000	0.000
18	B	41	TYR	0	0.015	-0.034	20.725	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	42	ASN	0	-0.048	-0.027	25.528	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	43	LYS	1	0.936	1.006	28.538	-0.239	-0.239	0.000	0.000	0.000	0.000
21	B	44	LEU	0	0.057	0.043	27.006	-0.010	-0.010	0.000	0.000	0.000	0.000
22	B	45	PRO	0	-0.007	-0.017	28.194	0.008	0.008	0.000	0.000	0.000	0.000
23	B	46	ARG	1	0.895	0.951	24.112	-0.279	-0.279	0.000	0.000	0.000	0.000
24	B	47	ARG	1	0.962	0.975	24.322	-0.314	-0.314	0.000	0.000	0.000	0.000
25	B	48	ARG	1	0.903	0.954	24.097	-0.243	-0.243	0.000	0.000	0.000	0.000
26	B	49	VAL	0	0.043	0.023	21.929	0.031	0.031	0.000	0.000	0.000	0.000
27	B	50	ASN	0	-0.014	0.002	19.946	0.024	0.024	0.000	0.000	0.000	0.000
28	B	51	ILE	0	0.046	0.031	19.009	0.050	0.050	0.000	0.000	0.000	0.000
29	B	52	PHE	0	0.001	0.003	19.468	0.059	0.059	0.000	0.000	0.000	0.000
30	B	53	GLY	0	0.047	0.023	16.981	0.045	0.045	0.000	0.000	0.000	0.000
31	B	54	GLU	-1	-0.938	-0.984	14.875	0.748	0.748	0.000	0.000	0.000	0.000
32	B	55	GLU	-1	-0.776	-0.851	14.921	0.801	0.801	0.000	0.000	0.000	0.000
33	B	56	LEU	0	0.019	0.004	15.179	0.060	0.060	0.000	0.000	0.000	0.000
34	B	57	GLU	-1	-0.782	-0.864	9.376	2.048	2.048	0.000	0.000	0.000	0.000
35	B	58	ARG	1	0.777	0.849	10.641	-0.441	-0.441	0.000	0.000	0.000	0.000
36	B	59	LEU	0	-0.014	-0.006	12.117	0.068	0.068	0.000	0.000	0.000	0.000
37	B	60	LEU	0	0.000	0.000	10.902	-0.039	-0.039	0.000	0.000	0.000	0.000
38	B	61	LYS	1	0.821	0.881	6.423	-2.910	-2.910	0.000	0.000	0.000	0.000
39	B	62	LYS	1	0.800	0.893	8.674	-0.748	-0.748	0.000	0.000	0.000	0.000
40	B	63	LYS	1	0.872	0.962	11.541	-0.777	-0.777	0.000	0.000	0.000	0.000
41	B	64	TYR	0	0.019	-0.037	7.771	-0.219	-0.219	0.000	0.000	0.000	0.000
42	B	65	GLU	-1	-0.810	-0.874	7.644	0.792	0.792	0.000	0.000	0.000	0.000
43	B	66	GLY	0	-0.012	-0.007	7.955	-0.233	-0.233	0.000	0.000	0.000	0.000
44	B	67	HIS	1	0.803	0.900	9.129	-0.612	-0.612	0.000	0.000	0.000	0.000
45	B	68	TRP	0	0.048	0.038	2.177	-7.137	-6.936	7.182	-2.267	-5.116	0.021
46	B	69	TYR	0	-0.028	-0.029	5.104	-1.088	-0.964	-0.001	-0.002	-0.120	0.000
47	B	70	PRO	0	0.049	0.007	2.403	-0.537	0.620	0.997	-0.534	-1.619	-0.001
48	B	71	GLU	-1	-0.910	-0.937	4.358	-1.115	-1.001	0.000	-0.037	-0.076	0.000
49	B	72	LYS	1	0.882	0.939	7.777	1.204	1.204	0.000	0.000	0.000	0.000
50	B	73	PRO	0	0.089	0.052	7.480	0.089	0.089	0.000	0.000	0.000	0.000
51	B	74	TYR	0	0.087	0.040	8.597	0.164	0.164	0.000	0.000	0.000	0.000
52	B	75	LYS	1	0.880	0.955	10.249	0.525	0.525	0.000	0.000	0.000	0.000
53	B	76	GLY	0	0.002	-0.004	10.656	0.031	0.031	0.000	0.000	0.000	0.000
54	B	77	SER	0	0.032	-0.020	12.261	0.067	0.067	0.000	0.000	0.000	0.000
55	B	78	GLY	0	-0.018	-0.010	13.400	0.062	0.062	0.000	0.000	0.000	0.000
56	B	79	PHE	0	-0.056	-0.022	12.917	0.005	0.005	0.000	0.000	0.000	0.000
57	B	80	ARG	1	0.737	0.813	9.261	-0.616	-0.616	0.000	0.000	0.000	0.000
58	B	81	CYS	0	-0.078	0.007	13.698	0.098	0.098	0.000	0.000	0.000	0.000
59	B	82	ILE	0	0.007	0.010	14.375	0.008	0.008	0.000	0.000	0.000	0.000
60	B	83	HIS	0	-0.022	-0.023	18.375	-0.036	-0.036	0.000	0.000	0.000	0.000
61	B	84	ILE	0	-0.024	-0.030	20.831	0.013	0.013	0.000	0.000	0.000	0.000
62	B	85	GLY	0	0.116	0.064	24.666	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	86	GLU	-1	-0.934	-0.952	28.102	0.183	0.183	0.000	0.000	0.000	0.000
64	B	87	LYS	1	0.793	0.903	23.219	-0.296	-0.296	0.000	0.000	0.000	0.000
65	B	88	VAL	0	0.066	0.035	23.760	0.018	0.018	0.000	0.000	0.000	0.000
66	B	89	ASP	-1	-0.841	-0.930	19.270	0.423	0.423	0.000	0.000	0.000	0.000
67	B	90	PRO	0	0.040	0.019	21.002	0.027	0.027	0.000	0.000	0.000	0.000
68	B	91	VAL	0	-0.014	-0.007	15.964	0.005	0.005	0.000	0.000	0.000	0.000
69	B	92	ILE	0	0.018	0.011	18.874	0.033	0.033	0.000	0.000	0.000	0.000
70	B	93	GLU	-1	-0.870	-0.940	20.802	0.284	0.284	0.000	0.000	0.000	0.000
71	B	94	GLN	0	-0.034	-0.023	19.588	0.027	0.027	0.000	0.000	0.000	0.000
72	B	95	ALA	0	0.040	0.026	18.928	-0.016	-0.016	0.000	0.000	0.000	0.000
73	B	96	SER	0	-0.021	-0.012	20.982	-0.013	-0.013	0.000	0.000	0.000	0.000
74	B	97	LYS	1	0.822	0.900	24.492	-0.328	-0.328	0.000	0.000	0.000	0.000
75	B	98	GLU	-1	-0.835	-0.907	22.512	0.321	0.321	0.000	0.000	0.000	0.000
76	B	99	SER	0	-0.066	-0.045	23.047	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	100	GLY	0	-0.029	-0.019	24.958	-0.020	-0.020	0.000	0.000	0.000	0.000
78	B	101	LEU	0	-0.047	-0.024	24.630	-0.024	-0.024	0.000	0.000	0.000	0.000
79	B	102	ASP	-1	-0.813	-0.889	28.198	0.234	0.234	0.000	0.000	0.000	0.000
80	B	103	ILE	0	0.027	0.005	26.834	0.017	0.017	0.000	0.000	0.000	0.000
81	B	104	ASP	-1	-0.841	-0.900	28.649	0.214	0.214	0.000	0.000	0.000	0.000
82	B	105	ASP	-1	-0.923	-0.958	30.251	0.224	0.224	0.000	0.000	0.000	0.000
83	B	106	VAL	0	-0.057	-0.034	24.176	0.007	0.007	0.000	0.000	0.000	0.000
84	B	107	ARG	1	0.781	0.852	27.279	-0.220	-0.220	0.000	0.000	0.000	0.000
85	B	108	GLY	0	0.007	0.016	28.455	-0.007	-0.007	0.000	0.000	0.000	0.000
86	B	109	ASN	0	-0.095	-0.060	28.537	-0.020	-0.020	0.000	0.000	0.000	0.000
87	B	110	LEU	0	-0.048	-0.010	23.048	0.010	0.010	0.000	0.000	0.000	0.000
88	B	111	PRO	0	-0.033	-0.010	25.355	-0.021	-0.021	0.000	0.000	0.000	0.000
89	B	112	GLN	0	0.020	-0.006	27.491	0.011	0.011	0.000	0.000	0.000	0.000
90	B	113	ASP	-1	-0.860	-0.950	27.539	0.189	0.189	0.000	0.000	0.000	0.000
91	B	114	LEU	0	-0.043	0.006	21.647	0.002	0.002	0.000	0.000	0.000	0.000
92	B	115	SER	0	-0.012	0.005	21.417	0.011	0.011	0.000	0.000	0.000	0.000
93	B	116	VAL	0	0.000	-0.010	15.630	-0.015	-0.015	0.000	0.000	0.000	0.000
94	B	117	TRP	0	-0.015	-0.008	14.073	0.009	0.009	0.000	0.000	0.000	0.000
95	B	118	ILE	0	0.013	0.006	9.083	0.048	0.048	0.000	0.000	0.000	0.000
96	B	119	ASP	-1	-0.734	-0.821	8.417	0.672	0.672	0.000	0.000	0.000	0.000
97	B	120	PRO	0	-0.084	-0.038	3.497	0.035	0.232	0.003	-0.037	-0.163	0.000
98	B	121	PHE	0	0.012	-0.001	4.317	-1.244	-0.980	-0.001	-0.042	-0.221	0.000
99	B	122	GLU	-1	-0.927	-0.963	7.400	-0.026	-0.026	0.000	0.000	0.000	0.000
100	B	123	VAL	0	-0.039	-0.004	10.429	0.204	0.204	0.000	0.000	0.000	0.000
101	B	124	SER	0	0.038	0.018	12.880	-0.097	-0.097	0.000	0.000	0.000	0.000
102	B	125	TYR	0	0.019	-0.002	16.288	0.031	0.031	0.000	0.000	0.000	0.000
103	B	126	GLN	0	-0.026	-0.016	19.540	-0.026	-0.026	0.000	0.000	0.000	0.000
104	B	127	ILE	0	0.006	-0.001	23.064	0.022	0.022	0.000	0.000	0.000	0.000
105	B	128	GLY	0	0.063	0.035	26.324	-0.021	-0.021	0.000	0.000	0.000	0.000
106	B	129	GLU	-1	-0.818	-0.900	27.425	0.123	0.123	0.000	0.000	0.000	0.000
107	B	130	LYS	1	0.837	0.900	28.023	-0.122	-0.122	0.000	0.000	0.000	0.000
108	B	131	GLY	0	-0.011	0.020	27.696	-0.011	-0.011	0.000	0.000	0.000	0.000
109	B	132	PRO	0	-0.026	-0.014	26.019	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	133	VAL	0	0.020	0.004	19.457	0.018	0.018	0.000	0.000	0.000	0.000
111	B	134	LYS	1	0.873	0.941	21.142	-0.244	-0.244	0.000	0.000	0.000	0.000
112	B	135	VAL	0	0.042	0.016	15.529	0.037	0.037	0.000	0.000	0.000	0.000
113	B	136	LEU	0	-0.089	-0.041	15.774	-0.022	-0.022	0.000	0.000	0.000	0.000
114	B	137	TYR	0	-0.077	-0.079	8.296	0.082	0.082	0.000	0.000	0.000	0.000
115	B	138	VAL	0	0.027	0.015	11.961	0.049	0.049	0.000	0.000	0.000	0.000
116	B	139	ASP	-1	-0.902	-0.898	9.798	0.073	0.073	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:24:HIS)