FMO DATABASE

FMODB ID: 52J1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1016368.454908
FMO2-HF: Nuclear repulsion	969667.161171
FMO2-HF: Total energy	-46701.293737
FMO2-MP2: Total energy	-46840.19046

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.
-10.329	-3.136	4.033	-3.445	-7.778	0.024

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 : -0.004 / 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	B	26	GLN	0	-0.013	-0.005	2.777	-4.689	-1.358	0.304	-1.526	-2.109	0.008
4	B	27	LEU	0	0.037	0.023	3.738	-1.008	-0.703	0.000	-0.043	-0.261	0.000
5	B	28	GLU	-1	-0.749	-0.889	5.421	2.654	2.740	-0.001	-0.016	-0.068	0.000
6	B	29	ILE	0	-0.007	-0.016	7.178	-0.306	-0.306	0.000	0.000	0.000	0.000
7	B	30	GLN	0	-0.013	-0.019	8.368	-0.265	-0.265	0.000	0.000	0.000	0.000
8	B	31	VAL	0	-0.022	0.012	9.965	-0.199	-0.199	0.000	0.000	0.000	0.000
9	B	32	ALA	0	0.014	0.005	11.902	-0.131	-0.131	0.000	0.000	0.000	0.000
10	B	33	LEU	0	-0.010	-0.010	12.273	-0.113	-0.113	0.000	0.000	0.000	0.000
11	B	34	ASN	0	-0.009	-0.008	12.991	-0.112	-0.112	0.000	0.000	0.000	0.000
12	B	35	PHE	0	-0.005	0.010	15.913	-0.080	-0.080	0.000	0.000	0.000	0.000
13	B	36	ILE	0	0.027	0.018	17.056	-0.056	-0.056	0.000	0.000	0.000	0.000
14	B	37	ILE	0	0.021	0.003	17.507	-0.049	-0.049	0.000	0.000	0.000	0.000
15	B	38	SER	0	-0.104	-0.056	19.967	-0.049	-0.049	0.000	0.000	0.000	0.000
16	B	39	TYR	0	-0.028	-0.012	21.797	-0.043	-0.043	0.000	0.000	0.000	0.000
17	B	40	LEU	0	0.006	0.011	22.414	-0.021	-0.021	0.000	0.000	0.000	0.000
18	B	41	TYR	0	0.025	-0.019	20.299	-0.017	-0.017	0.000	0.000	0.000	0.000
19	B	42	ASN	0	-0.053	-0.036	25.547	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	43	LYS	1	0.959	1.015	28.460	-0.213	-0.213	0.000	0.000	0.000	0.000
21	B	44	LEU	0	0.041	0.036	26.903	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	45	PRO	0	-0.011	-0.018	28.363	0.009	0.009	0.000	0.000	0.000	0.000
23	B	46	ARG	1	0.918	0.955	23.911	-0.267	-0.267	0.000	0.000	0.000	0.000
24	B	47	ARG	1	0.963	0.973	24.374	-0.281	-0.281	0.000	0.000	0.000	0.000
25	B	48	ARG	1	0.922	0.958	23.947	-0.206	-0.206	0.000	0.000	0.000	0.000
26	B	49	VAL	0	0.058	0.044	21.647	0.024	0.024	0.000	0.000	0.000	0.000
27	B	50	ASN	0	0.010	0.009	19.970	0.038	0.038	0.000	0.000	0.000	0.000
28	B	51	ILE	0	0.015	0.020	19.049	0.044	0.044	0.000	0.000	0.000	0.000
29	B	52	PHE	0	-0.005	0.009	19.425	0.055	0.055	0.000	0.000	0.000	0.000
30	B	53	GLY	0	0.037	0.005	17.185	0.041	0.041	0.000	0.000	0.000	0.000
31	B	54	GLU	-1	-0.959	-0.990	14.948	0.738	0.738	0.000	0.000	0.000	0.000
32	B	55	GLU	-1	-0.783	-0.861	15.048	0.663	0.663	0.000	0.000	0.000	0.000
33	B	56	LEU	0	0.026	0.004	15.518	0.035	0.035	0.000	0.000	0.000	0.000
34	B	57	GLU	-1	-0.779	-0.862	9.433	1.947	1.947	0.000	0.000	0.000	0.000
35	B	58	ARG	1	0.774	0.853	11.088	-0.391	-0.391	0.000	0.000	0.000	0.000
36	B	59	LEU	0	-0.024	-0.014	12.237	0.028	0.028	0.000	0.000	0.000	0.000
37	B	60	LEU	0	0.001	0.000	11.216	-0.067	-0.067	0.000	0.000	0.000	0.000
38	B	61	LYS	1	0.815	0.889	6.709	-2.794	-2.794	0.000	0.000	0.000	0.000
39	B	62	LYS	1	0.836	0.919	8.804	-0.499	-0.499	0.000	0.000	0.000	0.000
40	B	63	LYS	1	0.909	0.969	11.400	-0.519	-0.519	0.000	0.000	0.000	0.000
41	B	64	TYR	0	0.019	-0.040	8.354	-0.246	-0.246	0.000	0.000	0.000	0.000
42	B	65	GLU	-1	-0.858	-0.893	7.282	0.109	0.109	0.000	0.000	0.000	0.000
43	B	66	GLY	0	-0.009	-0.005	7.381	-0.085	-0.085	0.000	0.000	0.000	0.000
44	B	67	HIS	1	0.792	0.886	8.520	0.034	0.034	0.000	0.000	0.000	0.000
45	B	68	TRP	0	0.051	0.048	2.649	-4.497	-2.187	2.436	-1.302	-3.444	0.016
46	B	69	TYR	0	-0.033	-0.033	4.930	-1.346	-1.243	-0.001	-0.002	-0.100	0.000
47	B	70	PRO	0	0.053	0.015	2.221	-0.221	0.450	1.298	-0.499	-1.470	0.000
48	B	71	GLU	-1	-0.901	-0.928	4.504	-0.998	-0.901	-0.001	-0.027	-0.069	0.000
49	B	72	LYS	1	0.862	0.926	7.845	1.193	1.193	0.000	0.000	0.000	0.000
50	B	73	PRO	0	0.096	0.039	8.091	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	74	TYR	0	0.111	0.052	9.109	0.097	0.097	0.000	0.000	0.000	0.000
52	B	75	LYS	1	0.889	0.963	10.750	0.781	0.781	0.000	0.000	0.000	0.000
53	B	76	GLY	0	-0.019	-0.020	10.862	-0.033	-0.033	0.000	0.000	0.000	0.000
54	B	77	SER	0	0.044	-0.008	13.010	0.058	0.058	0.000	0.000	0.000	0.000
55	B	78	GLY	0	-0.017	-0.004	13.928	0.069	0.069	0.000	0.000	0.000	0.000
56	B	79	PHE	0	-0.067	-0.034	12.757	0.024	0.024	0.000	0.000	0.000	0.000
57	B	80	ARG	1	0.754	0.831	9.538	-0.093	-0.093	0.000	0.000	0.000	0.000
58	B	81	CYS	0	-0.063	0.013	14.233	0.096	0.096	0.000	0.000	0.000	0.000
59	B	82	ILE	0	0.015	0.017	14.546	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	83	HIS	0	-0.016	-0.018	18.664	-0.019	-0.019	0.000	0.000	0.000	0.000
61	B	84	ILE	0	-0.010	-0.020	21.434	0.011	0.011	0.000	0.000	0.000	0.000
62	B	85	GLY	0	0.117	0.058	24.911	-0.005	-0.005	0.000	0.000	0.000	0.000
63	B	86	GLU	-1	-0.941	-0.939	28.506	0.124	0.124	0.000	0.000	0.000	0.000
64	B	87	LYS	1	0.882	0.961	23.982	-0.179	-0.179	0.000	0.000	0.000	0.000
65	B	88	VAL	0	0.021	0.000	24.319	0.011	0.011	0.000	0.000	0.000	0.000
66	B	89	ASP	-1	-0.906	-0.962	19.614	0.268	0.268	0.000	0.000	0.000	0.000
67	B	90	PRO	0	0.062	0.024	21.144	0.018	0.018	0.000	0.000	0.000	0.000
68	B	91	VAL	0	-0.016	-0.007	16.515	0.008	0.008	0.000	0.000	0.000	0.000
69	B	92	ILE	0	0.027	0.021	19.132	0.037	0.037	0.000	0.000	0.000	0.000
70	B	93	GLU	-1	-0.859	-0.934	21.260	0.200	0.200	0.000	0.000	0.000	0.000
71	B	94	GLN	0	-0.041	-0.032	20.022	0.027	0.027	0.000	0.000	0.000	0.000
72	B	95	ALA	0	0.029	0.016	19.054	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	96	SER	0	0.010	0.010	21.064	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	97	LYS	1	0.806	0.904	24.442	-0.255	-0.255	0.000	0.000	0.000	0.000
75	B	98	GLU	-1	-0.848	-0.915	22.511	0.253	0.253	0.000	0.000	0.000	0.000
76	B	99	SER	0	-0.060	-0.047	23.011	0.008	0.008	0.000	0.000	0.000	0.000
77	B	100	GLY	0	-0.056	-0.033	25.085	-0.011	-0.011	0.000	0.000	0.000	0.000
78	B	101	LEU	0	-0.035	-0.013	24.618	-0.017	-0.017	0.000	0.000	0.000	0.000
79	B	102	ASP	-1	-0.815	-0.895	28.439	0.179	0.179	0.000	0.000	0.000	0.000
80	B	103	ILE	0	0.058	0.014	27.345	0.011	0.011	0.000	0.000	0.000	0.000
81	B	104	ASP	-1	-0.852	-0.916	29.153	0.163	0.163	0.000	0.000	0.000	0.000
82	B	105	ASP	-1	-0.932	-0.963	30.463	0.185	0.185	0.000	0.000	0.000	0.000
83	B	106	VAL	0	-0.079	-0.042	24.302	0.009	0.009	0.000	0.000	0.000	0.000
84	B	107	ARG	1	0.804	0.870	27.025	-0.158	-0.158	0.000	0.000	0.000	0.000
85	B	108	GLY	0	0.009	0.013	28.532	-0.005	-0.005	0.000	0.000	0.000	0.000
86	B	109	ASN	0	-0.104	-0.062	28.149	-0.014	-0.014	0.000	0.000	0.000	0.000
87	B	110	LEU	0	-0.044	-0.008	22.897	0.016	0.016	0.000	0.000	0.000	0.000
88	B	111	PRO	0	-0.044	-0.020	25.057	-0.018	-0.018	0.000	0.000	0.000	0.000
89	B	112	GLN	0	0.022	0.006	27.506	0.006	0.006	0.000	0.000	0.000	0.000
90	B	113	ASP	-1	-0.900	-0.967	27.735	0.135	0.135	0.000	0.000	0.000	0.000
91	B	114	LEU	0	-0.024	0.016	21.503	-0.003	-0.003	0.000	0.000	0.000	0.000
92	B	115	SER	0	0.003	0.004	21.259	0.008	0.008	0.000	0.000	0.000	0.000
93	B	116	VAL	0	-0.002	-0.014	15.856	0.000	0.000	0.000	0.000	0.000	0.000
94	B	117	TRP	0	-0.013	-0.006	14.526	0.011	0.011	0.000	0.000	0.000	0.000
95	B	118	ILE	0	0.003	-0.004	9.541	0.073	0.073	0.000	0.000	0.000	0.000
96	B	119	ASP	-1	-0.746	-0.834	9.015	0.275	0.275	0.000	0.000	0.000	0.000
97	B	120	PRO	0	-0.076	-0.034	4.169	0.130	0.214	-0.001	-0.010	-0.072	0.000
98	B	121	PHE	0	-0.012	-0.019	4.401	-0.779	-0.573	-0.001	-0.020	-0.185	0.000
99	B	122	GLU	-1	-0.943	-0.970	7.991	-0.020	-0.020	0.000	0.000	0.000	0.000
100	B	123	VAL	0	-0.029	0.005	10.948	0.060	0.060	0.000	0.000	0.000	0.000
101	B	124	SER	0	0.027	0.016	13.283	-0.065	-0.065	0.000	0.000	0.000	0.000
102	B	125	TYR	0	0.016	-0.006	16.824	0.016	0.016	0.000	0.000	0.000	0.000
103	B	126	GLN	0	-0.038	-0.026	19.955	-0.020	-0.020	0.000	0.000	0.000	0.000
104	B	127	ILE	0	-0.018	0.000	23.380	0.008	0.008	0.000	0.000	0.000	0.000
105	B	128	GLY	0	0.071	0.039	26.547	-0.016	-0.016	0.000	0.000	0.000	0.000
106	B	129	GLU	-1	-0.846	-0.920	27.462	0.073	0.073	0.000	0.000	0.000	0.000
107	B	130	LYS	1	0.846	0.902	28.345	-0.084	-0.084	0.000	0.000	0.000	0.000
108	B	131	GLY	0	-0.019	0.018	28.124	-0.007	-0.007	0.000	0.000	0.000	0.000
109	B	132	PRO	0	-0.008	-0.007	26.092	-0.004	-0.004	0.000	0.000	0.000	0.000
110	B	133	VAL	0	0.031	0.011	19.549	0.015	0.015	0.000	0.000	0.000	0.000
111	B	134	LYS	1	0.891	0.951	21.733	-0.196	-0.196	0.000	0.000	0.000	0.000
112	B	135	VAL	0	0.047	0.013	16.106	0.028	0.028	0.000	0.000	0.000	0.000
113	B	136	LEU	0	-0.087	-0.036	15.775	-0.013	-0.013	0.000	0.000	0.000	0.000
114	B	137	TYR	0	-0.081	-0.074	8.649	0.071	0.071	0.000	0.000	0.000	0.000
115	B	138	VAL	0	0.019	0.013	12.494	0.009	0.009	0.000	0.000	0.000	0.000
116	B	139	ASP	-1	-0.892	-0.908	10.099	0.315	0.315	0.000	0.000	0.000	0.000

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