FMO DATABASE

FMODB ID: QY7ZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-874109.705345
FMO2-HF: Nuclear repulsion	829654.475415
FMO2-HF: Total energy	-44455.229931
FMO2-MP2: Total energy	-44581.202683

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.
-17.606	-20.791	16.601	-7.535	-5.882	0.038

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 : -0.852 / q_NPA : -0.882

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	0.955	0.982	3.324	-64.740	-61.492	0.084	-1.328	-2.004	0.013
4	A	241	THR	0	-0.014	-0.033	1.830	-23.728	-30.713	16.490	-5.953	-3.553	0.025
5	A	242	PHE	0	0.011	-0.004	4.541	-2.541	-2.478	0.001	-0.069	0.005	0.000
6	A	243	LEU	0	0.000	-0.006	7.817	-1.369	-1.369	0.000	0.000	0.000	0.000
7	A	244	SER	0	0.004	-0.021	10.170	-0.231	-0.231	0.000	0.000	0.000	0.000
8	A	245	GLU	-1	-0.868	-0.873	13.920	14.402	14.402	0.000	0.000	0.000	0.000
9	A	246	HIS	0	0.037	0.039	16.907	0.728	0.728	0.000	0.000	0.000	0.000
10	A	247	SER	0	0.035	0.004	20.421	-0.176	-0.176	0.000	0.000	0.000	0.000
11	A	248	LEU	0	-0.030	-0.034	23.397	0.286	0.286	0.000	0.000	0.000	0.000
12	A	249	ASP	-1	-0.817	-0.885	25.598	11.286	11.286	0.000	0.000	0.000	0.000
13	A	250	MET	0	0.015	-0.004	18.581	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	251	LYS	1	0.866	0.939	21.630	-10.373	-10.373	0.000	0.000	0.000	0.000
15	A	252	PHE	0	-0.002	0.011	15.746	0.217	0.217	0.000	0.000	0.000	0.000
16	A	253	SER	0	-0.039	-0.067	20.246	-0.517	-0.517	0.000	0.000	0.000	0.000
17	A	254	TYR	0	0.002	-0.012	12.876	0.128	0.128	0.000	0.000	0.000	0.000
18	A	255	CYS	0	-0.012	-0.012	13.497	0.484	0.484	0.000	0.000	0.000	0.000
19	A	256	ASP	-1	-0.785	-0.853	8.216	30.325	30.325	0.000	0.000	0.000	0.000
20	A	257	GLU	-1	-0.864	-0.942	11.739	19.549	19.549	0.000	0.000	0.000	0.000
21	A	258	ARG	1	0.834	0.902	3.368	-43.268	-42.779	0.026	-0.185	-0.330	0.000
22	A	259	ILE	0	-0.026	-0.019	9.430	1.011	1.011	0.000	0.000	0.000	0.000
23	A	260	THR	0	-0.012	-0.028	12.032	-0.586	-0.586	0.000	0.000	0.000	0.000
24	A	261	GLU	-1	-1.003	-0.991	8.787	31.538	31.538	0.000	0.000	0.000	0.000
25	A	262	LEU	0	-0.069	-0.031	7.001	-0.444	-0.444	0.000	0.000	0.000	0.000
26	A	263	MET	0	-0.065	-0.043	11.452	-1.456	-1.456	0.000	0.000	0.000	0.000
27	A	264	GLY	0	0.003	0.008	14.945	-1.603	-1.603	0.000	0.000	0.000	0.000
28	A	265	TYR	0	-0.055	-0.051	16.596	-1.285	-1.285	0.000	0.000	0.000	0.000
29	A	266	GLU	-1	-0.806	-0.894	16.517	17.128	17.128	0.000	0.000	0.000	0.000
30	A	267	PRO	0	0.006	-0.006	15.291	-0.599	-0.599	0.000	0.000	0.000	0.000
31	A	268	GLU	-1	-0.934	-0.971	17.974	12.727	12.727	0.000	0.000	0.000	0.000
32	A	269	GLU	-1	-0.855	-0.908	21.117	13.972	13.972	0.000	0.000	0.000	0.000
33	A	270	LEU	0	-0.039	-0.020	17.195	-0.350	-0.350	0.000	0.000	0.000	0.000
34	A	271	LEU	0	-0.007	0.007	19.773	-0.193	-0.193	0.000	0.000	0.000	0.000
35	A	272	GLY	0	-0.026	-0.014	22.636	-0.530	-0.530	0.000	0.000	0.000	0.000
36	A	273	ARG	1	0.862	0.933	22.909	-12.662	-12.662	0.000	0.000	0.000	0.000
37	A	274	SER	0	-0.029	-0.012	22.714	0.602	0.602	0.000	0.000	0.000	0.000
38	A	275	ILE	0	0.015	0.009	16.224	-0.075	-0.075	0.000	0.000	0.000	0.000
39	A	276	TYR	0	-0.012	-0.040	20.714	0.201	0.201	0.000	0.000	0.000	0.000
40	A	277	GLU	-1	-0.906	-0.937	23.446	11.762	11.762	0.000	0.000	0.000	0.000
41	A	278	TYR	0	-0.003	0.001	19.786	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	279	TYR	0	0.025	0.022	17.656	0.335	0.335	0.000	0.000	0.000	0.000
43	A	280	HIS	0	0.021	0.017	21.212	-0.717	-0.717	0.000	0.000	0.000	0.000
44	A	281	ALA	0	0.032	0.017	23.180	-0.064	-0.064	0.000	0.000	0.000	0.000
45	A	282	LEU	0	-0.044	-0.036	25.528	-0.174	-0.174	0.000	0.000	0.000	0.000
46	A	283	ASP	-1	-0.783	-0.889	21.090	14.967	14.967	0.000	0.000	0.000	0.000
47	A	284	SER	0	0.007	0.002	23.055	0.200	0.200	0.000	0.000	0.000	0.000
48	A	285	ASP	-1	-0.896	-0.929	24.787	10.831	10.831	0.000	0.000	0.000	0.000
49	A	286	HIS	0	-0.039	-0.028	19.669	-0.302	-0.302	0.000	0.000	0.000	0.000
50	A	287	LEU	0	0.024	0.031	18.527	0.187	0.187	0.000	0.000	0.000	0.000
51	A	288	THR	0	0.031	0.003	22.177	-0.096	-0.096	0.000	0.000	0.000	0.000
52	A	289	LYS	1	0.787	0.876	25.512	-10.978	-10.978	0.000	0.000	0.000	0.000
53	A	290	THR	0	0.005	-0.012	19.322	0.014	0.014	0.000	0.000	0.000	0.000
54	A	291	HIS	0	0.075	0.035	18.844	-0.522	-0.522	0.000	0.000	0.000	0.000
55	A	292	HIS	0	0.009	0.020	23.325	-0.143	-0.143	0.000	0.000	0.000	0.000
56	A	293	ASP	-1	-0.809	-0.895	24.188	11.305	11.305	0.000	0.000	0.000	0.000
57	A	294	MET	0	-0.019	-0.002	20.277	0.201	0.201	0.000	0.000	0.000	0.000
58	A	295	PHE	0	-0.019	-0.015	22.845	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	296	THR	0	-0.088	-0.031	25.816	-0.445	-0.445	0.000	0.000	0.000	0.000
60	A	297	LYS	1	0.861	0.913	23.159	-12.414	-12.414	0.000	0.000	0.000	0.000
61	A	298	GLY	0	0.010	0.037	22.587	0.185	0.185	0.000	0.000	0.000	0.000
62	A	299	GLN	0	-0.059	-0.048	15.060	0.351	0.351	0.000	0.000	0.000	0.000
63	A	300	VAL	0	-0.041	-0.012	17.832	-0.657	-0.657	0.000	0.000	0.000	0.000
64	A	301	THR	0	0.024	0.000	13.499	0.545	0.545	0.000	0.000	0.000	0.000
65	A	302	THR	0	-0.042	-0.033	15.377	-0.447	-0.447	0.000	0.000	0.000	0.000
66	A	303	GLY	0	0.023	0.043	16.010	-0.920	-0.920	0.000	0.000	0.000	0.000
67	A	304	GLN	0	0.002	-0.004	14.042	1.308	1.308	0.000	0.000	0.000	0.000
68	A	305	TYR	0	-0.035	-0.016	14.122	-1.716	-1.716	0.000	0.000	0.000	0.000
69	A	306	ARG	1	0.820	0.911	16.129	-13.455	-13.455	0.000	0.000	0.000	0.000
70	A	307	MET	0	0.034	0.010	15.750	-0.522	-0.522	0.000	0.000	0.000	0.000
71	A	308	LEU	0	-0.046	-0.012	17.484	0.612	0.612	0.000	0.000	0.000	0.000
72	A	309	ALA	0	0.043	0.035	16.642	0.128	0.128	0.000	0.000	0.000	0.000
73	A	310	LYS	1	0.793	0.906	18.387	-15.988	-15.988	0.000	0.000	0.000	0.000
74	A	311	ARG	1	0.914	0.935	20.229	-14.071	-14.071	0.000	0.000	0.000	0.000
75	A	312	GLY	0	0.002	0.014	20.033	0.781	0.781	0.000	0.000	0.000	0.000
76	A	313	GLY	0	0.010	0.000	20.574	-0.483	-0.483	0.000	0.000	0.000	0.000
77	A	314	TYR	0	-0.008	-0.012	19.162	0.235	0.235	0.000	0.000	0.000	0.000
78	A	315	VAL	0	0.015	0.023	12.538	0.038	0.038	0.000	0.000	0.000	0.000
79	A	316	TRP	0	0.005	-0.012	14.508	-0.961	-0.961	0.000	0.000	0.000	0.000
80	A	317	VAL	0	-0.006	-0.011	10.824	2.510	2.510	0.000	0.000	0.000	0.000
81	A	318	GLU	-1	-0.860	-0.900	10.826	21.011	21.011	0.000	0.000	0.000	0.000
82	A	319	THR	0	0.021	-0.003	10.628	2.336	2.336	0.000	0.000	0.000	0.000
83	A	320	GLN	0	-0.022	0.012	11.384	-1.104	-1.104	0.000	0.000	0.000	0.000
84	A	321	ALA	0	0.011	-0.003	13.033	0.568	0.568	0.000	0.000	0.000	0.000
85	A	322	THR	0	0.001	-0.006	15.107	-0.588	-0.588	0.000	0.000	0.000	0.000
86	A	323	VAL	0	-0.006	0.004	17.640	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	324	ILE	0	0.000	0.010	17.972	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	325	TYR	0	0.043	0.000	21.918	-0.282	-0.282	0.000	0.000	0.000	0.000
89	A	326	ASN	0	0.000	0.004	25.659	-0.050	-0.050	0.000	0.000	0.000	0.000
90	A	327	THR	0	0.042	-0.008	27.339	-0.297	-0.297	0.000	0.000	0.000	0.000
91	A	328	LYS	1	0.834	0.927	29.763	-9.860	-9.860	0.000	0.000	0.000	0.000
92	A	329	ASN	0	0.031	-0.001	32.293	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	330	SER	0	-0.040	-0.010	29.780	-0.116	-0.116	0.000	0.000	0.000	0.000
94	A	331	GLN	0	0.044	0.040	29.734	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	332	PRO	0	0.005	-0.002	25.864	0.180	0.180	0.000	0.000	0.000	0.000
96	A	333	GLN	0	-0.055	-0.022	25.092	-0.718	-0.718	0.000	0.000	0.000	0.000
97	A	334	CYS	0	-0.073	-0.040	21.064	-0.182	-0.182	0.000	0.000	0.000	0.000
98	A	335	ILE	0	0.001	0.002	18.098	-0.112	-0.112	0.000	0.000	0.000	0.000
99	A	336	VAL	0	0.049	0.024	13.957	0.288	0.288	0.000	0.000	0.000	0.000
100	A	337	CYS	0	-0.074	-0.033	13.412	-0.528	-0.528	0.000	0.000	0.000	0.000
101	A	338	VAL	0	0.029	0.005	7.476	1.175	1.175	0.000	0.000	0.000	0.000
102	A	339	ASN	0	-0.009	0.016	9.274	-1.978	-1.978	0.000	0.000	0.000	0.000
103	A	340	TYR	0	-0.043	-0.053	5.667	4.755	4.755	0.000	0.000	0.000	0.000
104	A	341	VAL	0	0.005	0.012	7.271	-4.011	-4.011	0.000	0.000	0.000	0.000
105	A	342	VAL	0	-0.036	-0.031	7.866	3.943	3.943	0.000	0.000	0.000	0.000
106	A	343	SER	0	-0.038	-0.003	10.432	-0.905	-0.905	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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