FMO DATABASE

FMODB ID: Z6RKN

Calculation Name: 4H6J-A-Xray372

Preferred Name: Aryl hydrocarbon receptor nuclear translocator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4H6J

Chain ID: A

ChEMBL ID: CHEMBL5618

UniProt ID: P27540

Base Structure: X-ray

Registration Date: 2023-06-21

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-871919.239853
FMO2-HF: Nuclear repulsion	827464.513762
FMO2-HF: Total energy	-44454.726091
FMO2-MP2: Total energy	-44580.637011

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(A:238:ASP)

Summations of interaction energy for fragment #1(A:238:ASP)

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.
-3.447	3.65	0.692	-3.507	-4.282	0.032

Interaction energy analysis for fragmet #1(A:238:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.861 / q_NPA : -0.907

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	A	240	LYS	1	0.932	0.976	2.945	-62.782	-58.220	0.063	-2.203	-2.423	0.015
4	A	241	THR	0	0.008	0.002	2.703	-15.243	-13.057	0.600	-1.161	-1.625	0.017
5	A	242	PHE	0	-0.014	-0.005	5.107	-1.457	-1.472	-0.001	-0.008	0.025	0.000
6	A	243	LEU	0	-0.007	-0.009	8.137	-0.775	-0.775	0.000	0.000	0.000	0.000
7	A	244	SER	0	0.026	-0.008	10.349	-0.219	-0.219	0.000	0.000	0.000	0.000
8	A	245	GLU	-1	-0.898	-0.925	14.072	14.410	14.410	0.000	0.000	0.000	0.000
9	A	246	HIS	0	0.019	0.037	17.306	0.617	0.617	0.000	0.000	0.000	0.000
10	A	247	SER	0	0.033	-0.012	20.558	-0.131	-0.131	0.000	0.000	0.000	0.000
11	A	248	LEU	0	-0.015	-0.022	23.697	0.249	0.249	0.000	0.000	0.000	0.000
12	A	249	ASP	-1	-0.875	-0.910	25.815	11.151	11.151	0.000	0.000	0.000	0.000
13	A	250	MET	0	-0.012	-0.023	18.817	0.038	0.038	0.000	0.000	0.000	0.000
14	A	251	LYS	1	0.918	0.968	22.101	-10.147	-10.147	0.000	0.000	0.000	0.000
15	A	252	PHE	0	-0.007	0.010	16.044	0.286	0.286	0.000	0.000	0.000	0.000
16	A	253	SER	0	-0.060	-0.064	20.126	-0.542	-0.542	0.000	0.000	0.000	0.000
17	A	254	TYR	0	0.008	-0.009	12.884	0.147	0.147	0.000	0.000	0.000	0.000
18	A	255	CYS	0	-0.037	-0.021	13.502	0.500	0.500	0.000	0.000	0.000	0.000
19	A	256	ASP	-1	-0.753	-0.852	8.245	27.965	27.965	0.000	0.000	0.000	0.000
20	A	257	GLU	-1	-0.850	-0.939	11.756	18.462	18.462	0.000	0.000	0.000	0.000
21	A	258	ARG	1	0.809	0.895	3.219	-39.664	-39.300	0.030	-0.135	-0.259	0.000
22	A	259	ILE	0	-0.032	-0.012	9.345	1.405	1.405	0.000	0.000	0.000	0.000
23	A	260	THR	0	0.012	-0.008	11.795	-0.252	-0.252	0.000	0.000	0.000	0.000
24	A	261	GLU	-1	-1.005	-0.996	8.773	31.681	31.681	0.000	0.000	0.000	0.000
25	A	262	LEU	0	-0.051	-0.016	7.211	0.211	0.211	0.000	0.000	0.000	0.000
26	A	263	MET	0	-0.055	-0.049	11.590	-1.465	-1.465	0.000	0.000	0.000	0.000
27	A	264	GLY	0	-0.027	-0.002	15.031	-1.558	-1.558	0.000	0.000	0.000	0.000
28	A	265	TYR	0	-0.090	-0.069	16.855	-1.179	-1.179	0.000	0.000	0.000	0.000
29	A	266	GLU	-1	-0.847	-0.908	16.472	17.237	17.237	0.000	0.000	0.000	0.000
30	A	267	PRO	0	0.017	0.002	15.132	-0.609	-0.609	0.000	0.000	0.000	0.000
31	A	268	GLU	-1	-0.940	-0.981	17.775	12.084	12.084	0.000	0.000	0.000	0.000
32	A	269	GLU	-1	-0.921	-0.957	20.971	13.559	13.559	0.000	0.000	0.000	0.000
33	A	270	LEU	0	-0.035	-0.014	17.108	-0.414	-0.414	0.000	0.000	0.000	0.000
34	A	271	LEU	0	-0.010	0.012	20.379	-0.294	-0.294	0.000	0.000	0.000	0.000
35	A	272	GLY	0	-0.024	-0.009	22.454	-0.503	-0.503	0.000	0.000	0.000	0.000
36	A	273	ARG	1	0.916	0.961	23.594	-12.197	-12.197	0.000	0.000	0.000	0.000
37	A	274	SER	0	0.034	0.020	23.207	0.625	0.625	0.000	0.000	0.000	0.000
38	A	275	ILE	0	0.064	0.026	16.984	0.002	0.002	0.000	0.000	0.000	0.000
39	A	276	TYR	0	-0.046	-0.059	21.333	0.159	0.159	0.000	0.000	0.000	0.000
40	A	277	GLU	-1	-1.010	-0.996	23.898	11.228	11.228	0.000	0.000	0.000	0.000
41	A	278	TYR	0	-0.012	-0.009	20.063	-0.144	-0.144	0.000	0.000	0.000	0.000
42	A	279	TYR	0	0.003	0.017	18.195	0.273	0.273	0.000	0.000	0.000	0.000
43	A	280	HIS	0	0.035	0.023	21.543	-0.662	-0.662	0.000	0.000	0.000	0.000
44	A	281	ALA	0	0.040	0.012	23.475	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	282	LEU	0	-0.068	-0.044	25.547	-0.246	-0.246	0.000	0.000	0.000	0.000
46	A	283	ASP	-1	-0.792	-0.899	21.425	14.572	14.572	0.000	0.000	0.000	0.000
47	A	284	SER	0	-0.016	-0.006	23.712	0.069	0.069	0.000	0.000	0.000	0.000
48	A	285	ASP	-1	-0.874	-0.930	25.417	10.439	10.439	0.000	0.000	0.000	0.000
49	A	286	HIS	0	-0.067	-0.041	20.276	-0.337	-0.337	0.000	0.000	0.000	0.000
50	A	287	LEU	0	0.024	0.014	19.066	0.212	0.212	0.000	0.000	0.000	0.000
51	A	288	THR	0	0.045	0.024	22.796	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	289	LYS	1	0.800	0.911	25.906	-10.784	-10.784	0.000	0.000	0.000	0.000
53	A	290	THR	0	0.018	0.000	19.975	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	291	HIS	0	0.064	0.030	19.255	-0.461	-0.461	0.000	0.000	0.000	0.000
55	A	292	HIS	0	-0.048	-0.010	23.684	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	293	ASP	-1	-0.861	-0.946	24.751	11.090	11.090	0.000	0.000	0.000	0.000
57	A	294	MET	0	-0.013	0.004	20.981	0.254	0.254	0.000	0.000	0.000	0.000
58	A	295	PHE	0	-0.016	-0.006	23.507	0.073	0.073	0.000	0.000	0.000	0.000
59	A	296	THR	0	-0.057	-0.017	26.282	-0.403	-0.403	0.000	0.000	0.000	0.000
60	A	297	LYS	1	0.914	0.950	23.600	-12.444	-12.444	0.000	0.000	0.000	0.000
61	A	298	GLY	0	-0.005	0.025	23.112	0.107	0.107	0.000	0.000	0.000	0.000
62	A	299	GLN	0	-0.033	-0.035	16.102	0.378	0.378	0.000	0.000	0.000	0.000
63	A	300	VAL	0	-0.055	-0.013	18.342	-0.489	-0.489	0.000	0.000	0.000	0.000
64	A	301	THR	0	0.011	-0.002	14.249	1.141	1.141	0.000	0.000	0.000	0.000
65	A	302	THR	0	-0.033	-0.036	15.997	-0.438	-0.438	0.000	0.000	0.000	0.000
66	A	303	GLY	0	0.019	0.034	16.073	-0.859	-0.859	0.000	0.000	0.000	0.000
67	A	304	GLN	0	-0.016	-0.010	14.563	1.522	1.522	0.000	0.000	0.000	0.000
68	A	305	TYR	0	-0.036	-0.023	14.579	-1.418	-1.418	0.000	0.000	0.000	0.000
69	A	306	ARG	1	0.898	0.952	16.577	-13.083	-13.083	0.000	0.000	0.000	0.000
70	A	307	MET	0	0.024	0.014	16.060	-0.441	-0.441	0.000	0.000	0.000	0.000
71	A	308	LEU	0	-0.043	-0.021	18.058	0.481	0.481	0.000	0.000	0.000	0.000
72	A	309	ALA	0	0.033	0.038	17.193	0.250	0.250	0.000	0.000	0.000	0.000
73	A	310	LYS	1	0.930	0.977	18.794	-14.833	-14.833	0.000	0.000	0.000	0.000
74	A	311	ARG	1	0.902	0.921	20.223	-13.823	-13.823	0.000	0.000	0.000	0.000
75	A	312	GLY	0	0.014	0.010	19.941	0.703	0.703	0.000	0.000	0.000	0.000
76	A	313	GLY	0	-0.010	0.013	21.030	0.021	0.021	0.000	0.000	0.000	0.000
77	A	314	TYR	0	0.002	-0.018	19.258	0.100	0.100	0.000	0.000	0.000	0.000
78	A	315	VAL	0	0.023	0.021	12.529	0.192	0.192	0.000	0.000	0.000	0.000
79	A	316	TRP	0	-0.014	-0.019	14.226	-1.056	-1.056	0.000	0.000	0.000	0.000
80	A	317	VAL	0	0.000	0.000	11.372	2.372	2.372	0.000	0.000	0.000	0.000
81	A	318	GLU	-1	-0.869	-0.896	11.323	20.641	20.641	0.000	0.000	0.000	0.000
82	A	319	THR	0	0.020	-0.006	11.044	2.040	2.040	0.000	0.000	0.000	0.000
83	A	320	GLN	0	-0.020	0.007	11.944	-1.562	-1.562	0.000	0.000	0.000	0.000
84	A	321	ALA	0	0.019	0.003	13.573	0.448	0.448	0.000	0.000	0.000	0.000
85	A	322	THR	0	0.013	-0.003	15.410	-0.622	-0.622	0.000	0.000	0.000	0.000
86	A	323	VAL	0	0.015	0.011	17.927	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	324	ILE	0	-0.009	0.009	18.448	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	325	TYR	0	0.039	0.004	22.239	-0.293	-0.293	0.000	0.000	0.000	0.000
89	A	326	ASN	0	0.008	0.001	25.939	0.033	0.033	0.000	0.000	0.000	0.000
90	A	327	THR	0	0.029	0.004	27.908	-0.203	-0.203	0.000	0.000	0.000	0.000
91	A	328	LYS	1	0.890	0.954	30.104	-9.521	-9.521	0.000	0.000	0.000	0.000
92	A	329	ASN	0	0.062	0.032	32.359	0.068	0.068	0.000	0.000	0.000	0.000
93	A	330	SER	0	-0.020	-0.011	30.155	-0.109	-0.109	0.000	0.000	0.000	0.000
94	A	331	GLN	0	-0.010	-0.005	30.433	-0.043	-0.043	0.000	0.000	0.000	0.000
95	A	332	PRO	0	-0.008	-0.004	26.209	0.209	0.209	0.000	0.000	0.000	0.000
96	A	333	GLN	0	-0.044	-0.020	24.862	-0.588	-0.588	0.000	0.000	0.000	0.000
97	A	334	CYS	0	-0.054	-0.026	20.963	-0.129	-0.129	0.000	0.000	0.000	0.000
98	A	335	ILE	0	0.005	0.008	18.261	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	336	VAL	0	0.036	0.018	14.091	0.228	0.228	0.000	0.000	0.000	0.000
100	A	337	CYS	0	-0.063	-0.027	13.802	-0.382	-0.382	0.000	0.000	0.000	0.000
101	A	338	VAL	0	0.026	0.015	7.742	1.152	1.152	0.000	0.000	0.000	0.000
102	A	339	ASN	0	-0.004	0.020	9.468	-1.805	-1.805	0.000	0.000	0.000	0.000
103	A	340	TYR	0	-0.026	-0.042	6.088	3.982	3.982	0.000	0.000	0.000	0.000
104	A	341	VAL	0	0.003	0.006	7.444	-3.588	-3.588	0.000	0.000	0.000	0.000
105	A	342	VAL	0	-0.007	-0.023	8.060	3.614	3.614	0.000	0.000	0.000	0.000
106	A	343	SER	0	-0.046	-0.002	10.557	-1.619	-1.619	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:238:ASP)