FMO DATABASE

FMODB ID: 49J1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1016255.792927
FMO2-HF: Nuclear repulsion	969555.328346
FMO2-HF: Total energy	-46700.464581
FMO2-MP2: Total energy	-46839.403968

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.
-7.178	-0.78	2.131	-2.644	-5.884	0.015

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 : 0.003 / 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

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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	B	26	GLN	0	-0.021	-0.011	2.830	-4.010	-0.791	0.285	-1.435	-2.069	0.007
4	B	27	LEU	0	0.033	0.026	3.777	-0.958	-0.665	0.000	-0.040	-0.252	0.000
5	B	28	GLU	-1	-0.757	-0.887	5.542	1.540	1.612	-0.001	-0.012	-0.058	0.000
6	B	29	ILE	0	0.001	-0.008	7.357	-0.196	-0.196	0.000	0.000	0.000	0.000
7	B	30	GLN	0	0.011	0.000	7.721	-0.137	-0.137	0.000	0.000	0.000	0.000
8	B	31	VAL	0	-0.020	0.018	9.998	-0.148	-0.148	0.000	0.000	0.000	0.000
9	B	32	ALA	0	0.013	0.004	11.938	-0.092	-0.092	0.000	0.000	0.000	0.000
10	B	33	LEU	0	-0.013	-0.008	12.192	-0.081	-0.081	0.000	0.000	0.000	0.000
11	B	34	ASN	0	0.010	-0.002	13.457	-0.068	-0.068	0.000	0.000	0.000	0.000
12	B	35	PHE	0	-0.015	0.008	15.948	-0.057	-0.057	0.000	0.000	0.000	0.000
13	B	36	ILE	0	0.029	0.033	17.351	-0.040	-0.040	0.000	0.000	0.000	0.000
14	B	37	ILE	0	0.026	0.000	17.775	-0.036	-0.036	0.000	0.000	0.000	0.000
15	B	38	SER	0	-0.115	-0.080	19.993	-0.033	-0.033	0.000	0.000	0.000	0.000
16	B	39	TYR	0	-0.023	-0.007	21.832	-0.029	-0.029	0.000	0.000	0.000	0.000
17	B	40	LEU	0	0.006	0.011	22.484	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	41	TYR	0	0.020	-0.023	20.168	-0.012	-0.012	0.000	0.000	0.000	0.000
19	B	42	ASN	0	-0.095	-0.058	25.583	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	43	LYS	1	0.941	1.006	28.489	-0.152	-0.152	0.000	0.000	0.000	0.000
21	B	44	LEU	0	0.055	0.039	26.728	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	45	PRO	0	-0.014	-0.019	28.401	0.011	0.011	0.000	0.000	0.000	0.000
23	B	46	ARG	1	0.934	0.968	24.032	-0.217	-0.217	0.000	0.000	0.000	0.000
24	B	47	ARG	1	0.982	0.977	24.410	-0.215	-0.215	0.000	0.000	0.000	0.000
25	B	48	ARG	1	0.937	0.979	23.984	-0.146	-0.146	0.000	0.000	0.000	0.000
26	B	49	VAL	0	0.063	0.049	21.626	0.014	0.014	0.000	0.000	0.000	0.000
27	B	50	ASN	0	0.021	0.017	20.007	0.035	0.035	0.000	0.000	0.000	0.000
28	B	51	ILE	0	-0.008	0.012	19.087	0.037	0.037	0.000	0.000	0.000	0.000
29	B	52	PHE	0	0.007	0.020	19.466	0.037	0.037	0.000	0.000	0.000	0.000
30	B	53	GLY	0	0.031	0.002	17.229	0.021	0.021	0.000	0.000	0.000	0.000
31	B	54	GLU	-1	-0.943	-0.982	14.981	0.630	0.630	0.000	0.000	0.000	0.000
32	B	55	GLU	-1	-0.792	-0.875	15.089	0.445	0.445	0.000	0.000	0.000	0.000
33	B	56	LEU	0	0.009	-0.008	15.099	0.008	0.008	0.000	0.000	0.000	0.000
34	B	57	GLU	-1	-0.814	-0.901	9.167	1.624	1.624	0.000	0.000	0.000	0.000
35	B	58	ARG	1	0.786	0.873	10.901	-0.282	-0.282	0.000	0.000	0.000	0.000
36	B	59	LEU	0	-0.037	-0.019	12.071	-0.024	-0.024	0.000	0.000	0.000	0.000
37	B	60	LEU	0	-0.007	-0.003	10.964	-0.100	-0.100	0.000	0.000	0.000	0.000
38	B	61	LYS	1	0.854	0.915	6.436	-2.690	-2.690	0.000	0.000	0.000	0.000
39	B	62	LYS	1	0.923	0.975	8.633	-0.340	-0.340	0.000	0.000	0.000	0.000
40	B	63	LYS	1	0.943	0.978	11.030	-0.190	-0.190	0.000	0.000	0.000	0.000
41	B	64	TYR	0	0.025	-0.028	7.781	-0.207	-0.207	0.000	0.000	0.000	0.000
42	B	65	GLU	-1	-0.934	-0.941	6.478	-0.721	-0.721	0.000	0.000	0.000	0.000
43	B	66	GLY	0	-0.010	-0.005	6.745	0.134	0.134	0.000	0.000	0.000	0.000
44	B	67	HIS	1	0.786	0.885	8.005	0.809	0.809	0.000	0.000	0.000	0.000
45	B	68	TRP	0	0.073	0.053	2.730	-2.127	-0.256	0.746	-0.689	-1.928	0.007
46	B	69	TYR	0	-0.037	-0.033	4.592	-1.785	-1.684	-0.001	-0.007	-0.093	0.000
47	B	70	PRO	0	0.050	0.013	2.184	-0.007	0.597	1.104	-0.447	-1.262	0.001
48	B	71	GLU	-1	-0.876	-0.916	4.826	-0.819	-0.745	-0.001	-0.007	-0.066	0.000
49	B	72	LYS	1	0.838	0.916	7.898	1.244	1.244	0.000	0.000	0.000	0.000
50	B	73	PRO	0	0.114	0.048	8.709	-0.103	-0.103	0.000	0.000	0.000	0.000
51	B	74	TYR	0	0.141	0.060	9.683	0.038	0.038	0.000	0.000	0.000	0.000
52	B	75	LYS	1	0.869	0.956	10.875	1.068	1.068	0.000	0.000	0.000	0.000
53	B	76	GLY	0	-0.019	-0.022	11.021	-0.104	-0.104	0.000	0.000	0.000	0.000
54	B	77	SER	0	0.084	0.034	12.883	0.083	0.083	0.000	0.000	0.000	0.000
55	B	78	GLY	0	-0.013	-0.003	14.425	0.065	0.065	0.000	0.000	0.000	0.000
56	B	79	PHE	0	-0.086	-0.044	12.298	0.027	0.027	0.000	0.000	0.000	0.000
57	B	80	ARG	1	0.731	0.825	9.527	0.397	0.397	0.000	0.000	0.000	0.000
58	B	81	CYS	0	-0.061	0.010	14.201	0.090	0.090	0.000	0.000	0.000	0.000
59	B	82	ILE	0	0.023	0.028	14.458	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	83	HIS	0	-0.033	-0.027	18.414	0.001	0.001	0.000	0.000	0.000	0.000
61	B	84	ILE	0	-0.018	-0.023	21.442	0.007	0.007	0.000	0.000	0.000	0.000
62	B	85	GLY	0	0.106	0.051	24.663	0.002	0.002	0.000	0.000	0.000	0.000
63	B	86	GLU	-1	-0.946	-0.953	28.257	0.049	0.049	0.000	0.000	0.000	0.000
64	B	87	LYS	1	0.930	0.975	24.326	-0.026	-0.026	0.000	0.000	0.000	0.000
65	B	88	VAL	0	0.001	-0.010	24.044	0.004	0.004	0.000	0.000	0.000	0.000
66	B	89	ASP	-1	-0.913	-0.957	19.350	0.061	0.061	0.000	0.000	0.000	0.000
67	B	90	PRO	0	0.061	0.020	20.839	0.019	0.019	0.000	0.000	0.000	0.000
68	B	91	VAL	0	-0.016	-0.004	16.139	0.010	0.010	0.000	0.000	0.000	0.000
69	B	92	ILE	0	0.027	0.020	18.937	0.039	0.039	0.000	0.000	0.000	0.000
70	B	93	GLU	-1	-0.875	-0.945	21.030	0.086	0.086	0.000	0.000	0.000	0.000
71	B	94	GLN	0	-0.040	-0.033	19.705	0.031	0.031	0.000	0.000	0.000	0.000
72	B	95	ALA	0	0.040	0.019	18.875	0.006	0.006	0.000	0.000	0.000	0.000
73	B	96	SER	0	-0.006	-0.014	20.865	0.008	0.008	0.000	0.000	0.000	0.000
74	B	97	LYS	1	0.936	0.985	24.237	-0.129	-0.129	0.000	0.000	0.000	0.000
75	B	98	GLU	-1	-0.971	-0.995	22.171	0.166	0.166	0.000	0.000	0.000	0.000
76	B	99	SER	0	-0.067	-0.025	23.056	0.014	0.014	0.000	0.000	0.000	0.000
77	B	100	GLY	0	-0.069	-0.044	25.055	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	101	LEU	0	-0.036	-0.027	24.687	-0.007	-0.007	0.000	0.000	0.000	0.000
79	B	102	ASP	-1	-0.820	-0.896	28.394	0.100	0.100	0.000	0.000	0.000	0.000
80	B	103	ILE	0	0.051	0.005	26.857	0.008	0.008	0.000	0.000	0.000	0.000
81	B	104	ASP	-1	-0.889	-0.940	28.928	0.086	0.086	0.000	0.000	0.000	0.000
82	B	105	ASP	-1	-0.929	-0.964	30.410	0.120	0.120	0.000	0.000	0.000	0.000
83	B	106	VAL	0	-0.085	-0.038	24.255	0.009	0.009	0.000	0.000	0.000	0.000
84	B	107	ARG	1	0.878	0.930	27.067	-0.072	-0.072	0.000	0.000	0.000	0.000
85	B	108	GLY	0	-0.002	0.007	28.460	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	109	ASN	0	-0.097	-0.068	28.064	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	110	LEU	0	-0.025	-0.001	23.118	0.014	0.014	0.000	0.000	0.000	0.000
88	B	111	PRO	0	-0.059	-0.020	25.116	-0.014	-0.014	0.000	0.000	0.000	0.000
89	B	112	GLN	0	0.027	0.000	27.545	-0.002	-0.002	0.000	0.000	0.000	0.000
90	B	113	ASP	-1	-0.890	-0.958	27.634	0.049	0.049	0.000	0.000	0.000	0.000
91	B	114	LEU	0	-0.017	0.014	21.543	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	115	SER	0	0.002	0.001	21.737	0.000	0.000	0.000	0.000	0.000	0.000
93	B	116	VAL	0	-0.010	-0.013	15.773	0.011	0.011	0.000	0.000	0.000	0.000
94	B	117	TRP	0	-0.016	-0.002	15.332	-0.008	-0.008	0.000	0.000	0.000	0.000
95	B	118	ILE	0	0.011	-0.001	9.757	0.084	0.084	0.000	0.000	0.000	0.000
96	B	119	ASP	-1	-0.788	-0.882	9.822	-0.136	-0.136	0.000	0.000	0.000	0.000
97	B	120	PRO	0	-0.106	-0.051	5.008	0.201	0.201	0.000	0.000	0.000	0.000
98	B	121	PHE	0	0.011	-0.011	4.598	-0.407	-0.243	-0.001	-0.007	-0.156	0.000
99	B	122	GLU	-1	-0.959	-0.981	8.649	-0.066	-0.066	0.000	0.000	0.000	0.000
100	B	123	VAL	0	-0.018	0.013	10.978	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	124	SER	0	0.030	0.012	13.594	-0.030	-0.030	0.000	0.000	0.000	0.000
102	B	125	TYR	0	-0.001	-0.011	17.368	0.000	0.000	0.000	0.000	0.000	0.000
103	B	126	GLN	0	-0.032	-0.020	20.277	-0.013	-0.013	0.000	0.000	0.000	0.000
104	B	127	ILE	0	-0.022	-0.002	23.944	0.003	0.003	0.000	0.000	0.000	0.000
105	B	128	GLY	0	0.056	0.032	26.673	-0.007	-0.007	0.000	0.000	0.000	0.000
106	B	129	GLU	-1	-0.881	-0.956	28.275	0.000	0.000	0.000	0.000	0.000	0.000
107	B	130	LYS	1	0.895	0.942	29.137	-0.028	-0.028	0.000	0.000	0.000	0.000
108	B	131	GLY	0	-0.025	0.017	28.901	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	132	PRO	0	-0.017	-0.012	26.931	-0.008	-0.008	0.000	0.000	0.000	0.000
110	B	133	VAL	0	0.046	0.018	20.313	0.012	0.012	0.000	0.000	0.000	0.000
111	B	134	LYS	1	0.894	0.953	22.393	-0.123	-0.123	0.000	0.000	0.000	0.000
112	B	135	VAL	0	0.049	0.014	16.673	0.010	0.010	0.000	0.000	0.000	0.000
113	B	136	LEU	0	-0.099	-0.043	15.829	-0.002	-0.002	0.000	0.000	0.000	0.000
114	B	137	TYR	0	-0.018	-0.020	9.050	0.054	0.054	0.000	0.000	0.000	0.000
115	B	138	VAL	0	0.027	0.017	13.134	-0.016	-0.016	0.000	0.000	0.000	0.000
116	B	139	ASP	-1	-0.963	-0.964	10.476	0.479	0.479	0.000	0.000	0.000	0.000

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