FMO DATABASE

FMODB ID: R9N68

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:

Apendix: None

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-872532.796027
FMO2-HF: Nuclear repulsion	828077.680669
FMO2-HF: Total energy	-44455.115358
FMO2-MP2: Total energy	-44581.062177

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.
-7.224	-0.863	2.018	-3.712	-4.666	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 : -0.872 / q_NPA : -0.921

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	0.939	0.979	3.010	-62.842	-58.803	0.062	-1.907	-2.194	0.012
4	A	241	THR	0	-0.011	-0.010	2.408	-18.032	-16.098	1.923	-1.647	-2.210	0.025
5	A	242	PHE	0	0.003	0.002	5.107	-1.458	-1.470	-0.001	-0.010	0.024	0.000
6	A	243	LEU	0	-0.006	-0.011	8.100	-0.947	-0.947	0.000	0.000	0.000	0.000
7	A	244	SER	0	0.021	-0.017	10.310	-0.237	-0.237	0.000	0.000	0.000	0.000
8	A	245	GLU	-1	-0.860	-0.882	14.034	14.227	14.227	0.000	0.000	0.000	0.000
9	A	246	HIS	0	0.015	0.034	17.271	0.674	0.674	0.000	0.000	0.000	0.000
10	A	247	SER	0	0.049	0.006	20.517	-0.154	-0.154	0.000	0.000	0.000	0.000
11	A	248	LEU	0	-0.009	-0.016	23.697	0.245	0.245	0.000	0.000	0.000	0.000
12	A	249	ASP	-1	-0.841	-0.895	25.815	11.112	11.112	0.000	0.000	0.000	0.000
13	A	250	MET	0	-0.011	-0.016	18.848	0.006	0.006	0.000	0.000	0.000	0.000
14	A	251	LYS	1	0.872	0.939	22.101	-10.183	-10.183	0.000	0.000	0.000	0.000
15	A	252	PHE	0	-0.009	0.007	16.093	0.297	0.297	0.000	0.000	0.000	0.000
16	A	253	SER	0	-0.046	-0.065	20.104	-0.563	-0.563	0.000	0.000	0.000	0.000
17	A	254	TYR	0	0.004	-0.012	12.859	0.105	0.105	0.000	0.000	0.000	0.000
18	A	255	CYS	0	-0.037	-0.020	13.480	0.541	0.541	0.000	0.000	0.000	0.000
19	A	256	ASP	-1	-0.752	-0.843	8.148	29.063	29.063	0.000	0.000	0.000	0.000
20	A	257	GLU	-1	-0.860	-0.944	11.736	18.857	18.857	0.000	0.000	0.000	0.000
21	A	258	ARG	1	0.812	0.895	3.243	-40.537	-40.137	0.034	-0.148	-0.286	0.001
22	A	259	ILE	0	-0.032	-0.016	9.333	1.372	1.372	0.000	0.000	0.000	0.000
23	A	260	THR	0	0.010	-0.006	11.774	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	261	GLU	-1	-1.002	-0.993	8.858	31.255	31.255	0.000	0.000	0.000	0.000
25	A	262	LEU	0	-0.058	-0.019	7.103	0.194	0.194	0.000	0.000	0.000	0.000
26	A	263	MET	0	-0.056	-0.045	11.590	-1.452	-1.452	0.000	0.000	0.000	0.000
27	A	264	GLY	0	-0.015	0.003	15.031	-1.585	-1.585	0.000	0.000	0.000	0.000
28	A	265	TYR	0	-0.071	-0.062	16.841	-1.225	-1.225	0.000	0.000	0.000	0.000
29	A	266	GLU	-1	-0.840	-0.912	16.455	17.374	17.374	0.000	0.000	0.000	0.000
30	A	267	PRO	0	0.018	0.000	15.068	-0.655	-0.655	0.000	0.000	0.000	0.000
31	A	268	GLU	-1	-0.939	-0.977	17.754	12.393	12.393	0.000	0.000	0.000	0.000
32	A	269	GLU	-1	-0.863	-0.902	20.952	13.672	13.672	0.000	0.000	0.000	0.000
33	A	270	LEU	0	-0.036	-0.015	17.054	-0.427	-0.427	0.000	0.000	0.000	0.000
34	A	271	LEU	0	-0.015	0.007	19.983	-0.284	-0.284	0.000	0.000	0.000	0.000
35	A	272	GLY	0	-0.025	-0.011	22.424	-0.498	-0.498	0.000	0.000	0.000	0.000
36	A	273	ARG	1	0.876	0.941	23.488	-12.298	-12.298	0.000	0.000	0.000	0.000
37	A	274	SER	0	0.009	0.000	23.207	0.657	0.657	0.000	0.000	0.000	0.000
38	A	275	ILE	0	0.038	0.018	16.849	0.016	0.016	0.000	0.000	0.000	0.000
39	A	276	TYR	0	-0.022	-0.045	21.333	0.167	0.167	0.000	0.000	0.000	0.000
40	A	277	GLU	-1	-0.931	-0.946	23.898	11.493	11.493	0.000	0.000	0.000	0.000
41	A	278	TYR	0	-0.011	-0.010	20.034	-0.143	-0.143	0.000	0.000	0.000	0.000
42	A	279	TYR	0	0.004	0.014	18.013	0.263	0.263	0.000	0.000	0.000	0.000
43	A	280	HIS	0	0.031	0.019	21.568	-0.709	-0.709	0.000	0.000	0.000	0.000
44	A	281	ALA	0	0.032	0.011	23.537	-0.071	-0.071	0.000	0.000	0.000	0.000
45	A	282	LEU	0	-0.062	-0.042	25.663	-0.232	-0.232	0.000	0.000	0.000	0.000
46	A	283	ASP	-1	-0.790	-0.898	21.548	14.595	14.595	0.000	0.000	0.000	0.000
47	A	284	SER	0	0.001	0.006	23.712	0.115	0.115	0.000	0.000	0.000	0.000
48	A	285	ASP	-1	-0.888	-0.928	25.417	10.487	10.487	0.000	0.000	0.000	0.000
49	A	286	HIS	0	-0.053	-0.040	20.455	-0.297	-0.297	0.000	0.000	0.000	0.000
50	A	287	LEU	0	0.024	0.023	19.124	0.205	0.205	0.000	0.000	0.000	0.000
51	A	288	THR	0	0.032	0.007	22.796	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	289	LYS	1	0.796	0.889	25.906	-10.758	-10.758	0.000	0.000	0.000	0.000
53	A	290	THR	0	-0.003	-0.014	19.960	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	291	HIS	0	0.071	0.032	19.215	-0.498	-0.498	0.000	0.000	0.000	0.000
55	A	292	HIS	0	-0.011	0.009	23.684	-0.127	-0.127	0.000	0.000	0.000	0.000
56	A	293	ASP	-1	-0.806	-0.885	24.829	11.040	11.040	0.000	0.000	0.000	0.000
57	A	294	MET	0	-0.008	0.004	20.866	0.235	0.235	0.000	0.000	0.000	0.000
58	A	295	PHE	0	-0.011	-0.004	23.465	0.058	0.058	0.000	0.000	0.000	0.000
59	A	296	THR	0	-0.070	-0.026	26.238	-0.406	-0.406	0.000	0.000	0.000	0.000
60	A	297	LYS	1	0.836	0.898	23.516	-12.226	-12.226	0.000	0.000	0.000	0.000
61	A	298	GLY	0	-0.005	0.024	23.070	0.100	0.100	0.000	0.000	0.000	0.000
62	A	299	GLN	0	-0.040	-0.045	15.655	0.223	0.223	0.000	0.000	0.000	0.000
63	A	300	VAL	0	-0.048	-0.012	18.300	-0.508	-0.508	0.000	0.000	0.000	0.000
64	A	301	THR	0	0.010	-0.004	14.018	0.674	0.674	0.000	0.000	0.000	0.000
65	A	302	THR	0	-0.026	-0.024	15.969	-0.485	-0.485	0.000	0.000	0.000	0.000
66	A	303	GLY	0	0.014	0.034	16.091	-0.865	-0.865	0.000	0.000	0.000	0.000
67	A	304	GLN	0	-0.015	-0.016	14.643	1.206	1.206	0.000	0.000	0.000	0.000
68	A	305	TYR	0	-0.028	-0.013	14.577	-1.476	-1.476	0.000	0.000	0.000	0.000
69	A	306	ARG	1	0.894	0.955	16.653	-13.045	-13.045	0.000	0.000	0.000	0.000
70	A	307	MET	0	0.016	0.005	16.170	-0.456	-0.456	0.000	0.000	0.000	0.000
71	A	308	LEU	0	-0.045	-0.018	18.140	0.483	0.483	0.000	0.000	0.000	0.000
72	A	309	ALA	0	0.036	0.033	17.253	0.255	0.255	0.000	0.000	0.000	0.000
73	A	310	LYS	1	0.835	0.911	18.805	-15.422	-15.422	0.000	0.000	0.000	0.000
74	A	311	ARG	1	0.911	0.928	20.230	-13.841	-13.841	0.000	0.000	0.000	0.000
75	A	312	GLY	0	0.012	0.009	20.058	0.717	0.717	0.000	0.000	0.000	0.000
76	A	313	GLY	0	-0.011	0.013	21.192	0.021	0.021	0.000	0.000	0.000	0.000
77	A	314	TYR	0	0.010	-0.015	19.333	0.048	0.048	0.000	0.000	0.000	0.000
78	A	315	VAL	0	0.011	0.016	12.659	0.231	0.231	0.000	0.000	0.000	0.000
79	A	316	TRP	0	-0.003	-0.013	14.487	-1.091	-1.091	0.000	0.000	0.000	0.000
80	A	317	VAL	0	-0.003	-0.003	11.375	2.413	2.413	0.000	0.000	0.000	0.000
81	A	318	GLU	-1	-0.857	-0.893	11.385	20.473	20.473	0.000	0.000	0.000	0.000
82	A	319	THR	0	0.015	-0.003	11.044	2.041	2.041	0.000	0.000	0.000	0.000
83	A	320	GLN	0	-0.026	0.004	11.889	-1.175	-1.175	0.000	0.000	0.000	0.000
84	A	321	ALA	0	0.019	0.006	13.533	0.475	0.475	0.000	0.000	0.000	0.000
85	A	322	THR	0	0.012	0.000	15.322	-0.572	-0.572	0.000	0.000	0.000	0.000
86	A	323	VAL	0	0.000	0.012	17.880	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	324	ILE	0	0.003	0.010	18.178	-0.069	-0.069	0.000	0.000	0.000	0.000
88	A	325	TYR	0	0.026	0.000	22.190	-0.301	-0.301	0.000	0.000	0.000	0.000
89	A	326	ASN	0	-0.041	-0.024	25.890	-0.060	-0.060	0.000	0.000	0.000	0.000
90	A	327	THR	0	0.033	0.005	27.833	-0.209	-0.209	0.000	0.000	0.000	0.000
91	A	328	LYS	1	0.899	0.960	30.072	-9.612	-9.612	0.000	0.000	0.000	0.000
92	A	329	ASN	0	0.064	0.023	32.421	0.045	0.045	0.000	0.000	0.000	0.000
93	A	330	SER	0	-0.017	-0.003	30.100	-0.103	-0.103	0.000	0.000	0.000	0.000
94	A	331	GLN	0	-0.006	0.003	30.385	-0.086	-0.086	0.000	0.000	0.000	0.000
95	A	332	PRO	0	0.009	0.004	26.129	0.194	0.194	0.000	0.000	0.000	0.000
96	A	333	GLN	0	-0.045	-0.025	24.880	-0.621	-0.621	0.000	0.000	0.000	0.000
97	A	334	CYS	0	-0.084	-0.052	20.930	-0.158	-0.158	0.000	0.000	0.000	0.000
98	A	335	ILE	0	0.001	0.001	18.323	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	336	VAL	0	0.043	0.022	14.052	0.251	0.251	0.000	0.000	0.000	0.000
100	A	337	CYS	0	-0.066	-0.027	13.827	-0.410	-0.410	0.000	0.000	0.000	0.000
101	A	338	VAL	0	0.030	0.014	7.725	1.210	1.210	0.000	0.000	0.000	0.000
102	A	339	ASN	0	-0.011	0.007	9.457	-1.947	-1.947	0.000	0.000	0.000	0.000
103	A	340	TYR	0	-0.029	-0.048	6.074	4.141	4.141	0.000	0.000	0.000	0.000
104	A	341	VAL	0	0.004	0.007	7.548	-3.677	-3.677	0.000	0.000	0.000	0.000
105	A	342	VAL	0	-0.022	-0.029	8.129	3.557	3.557	0.000	0.000	0.000	0.000
106	A	343	SER	0	-0.038	0.002	10.621	-1.387	-1.387	0.000	0.000	0.000	0.000

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