FMO DATABASE

FMODB ID: R56V8

Calculation Name: 3HLU-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3HLU

Chain ID: A

ChEMBL ID:
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UniProt ID: A5Z863

Base Structure: X-ray

Registration Date: 2023-06-19

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-447119.863339
FMO2-HF: Nuclear repulsion	416886.454425
FMO2-HF: Total energy	-30233.408914
FMO2-MP2: Total energy	-30316.894045

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:3:ASP)

Summations of interaction energy for fragment #1(A:3: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.
-201.641	-189.165	7.795	-8.844	-11.427	0.083

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.880 / q_NPA : -0.961

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	5	GLN	0	-0.043	-0.025	3.799	1.371	3.076	-0.013	-0.735	-0.957	0.004
4	A	6	THR	0	0.017	0.009	5.529	-3.890	-3.890	0.000	0.000	0.000	0.000
5	A	7	MET	0	0.027	0.021	7.801	0.653	0.653	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.022	-0.019	9.995	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	9	TYR	0	-0.001	0.003	12.740	-0.866	-0.866	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.008	0.003	14.628	0.554	0.554	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.000	0.003	17.834	-0.851	-0.851	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.000	-0.045	21.316	0.070	0.070	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.067	0.034	23.553	-0.220	-0.220	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.886	0.951	24.583	-11.645	-11.645	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.937	0.984	22.428	-11.996	-11.996	0.000	0.000	0.000	0.000
14	A	16	LYS	1	1.014	1.007	22.446	-10.668	-10.668	0.000	0.000	0.000	0.000
15	A	17	ILE	0	0.017	0.006	23.344	0.104	0.104	0.000	0.000	0.000	0.000
16	A	18	ILE	0	0.005	0.004	18.148	0.394	0.394	0.000	0.000	0.000	0.000
17	A	19	ALA	0	0.012	-0.010	18.932	0.847	0.847	0.000	0.000	0.000	0.000
18	A	20	ASP	-1	-0.918	-0.951	19.470	13.505	13.505	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.860	0.928	19.217	-15.197	-15.197	0.000	0.000	0.000	0.000
20	A	22	MET	0	-0.068	-0.031	13.340	0.738	0.738	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.008	0.017	15.408	1.025	1.025	0.000	0.000	0.000	0.000
22	A	24	GLN	0	-0.044	-0.032	17.927	0.118	0.118	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.864	-0.934	17.092	16.297	16.297	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.111	-0.056	11.796	1.818	1.818	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.912	-0.935	12.704	20.763	20.763	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.086	-0.042	9.888	1.122	1.122	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.026	0.015	13.839	-1.524	-1.524	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.048	-0.034	15.228	1.156	1.156	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.009	-0.009	17.563	-1.035	-1.035	0.000	0.000	0.000	0.000
30	A	32	MET	0	-0.012	0.009	20.213	0.700	0.700	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.005	0.007	20.780	-0.465	-0.465	0.000	0.000	0.000	0.000
32	A	34	GLN	0	0.027	0.012	23.155	0.119	0.119	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.017	-0.010	25.539	0.072	0.072	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.009	-0.001	26.465	-0.422	-0.422	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.017	0.013	29.216	0.146	0.146	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.013	-0.017	31.291	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	39	TYR	0	-0.010	-0.002	34.214	-0.237	-0.237	0.000	0.000	0.000	0.000
38	A	40	LYS	1	0.989	0.974	34.554	-8.002	-8.002	0.000	0.000	0.000	0.000
39	A	41	ASN	0	0.026	0.015	35.381	0.192	0.192	0.000	0.000	0.000	0.000
40	A	42	ASN	0	-0.070	-0.025	34.314	0.102	0.102	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.901	-0.942	31.566	9.776	9.776	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.050	-0.022	27.347	0.144	0.144	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.872	-0.956	25.442	11.986	11.986	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.029	-0.027	19.833	0.235	0.235	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.019	0.015	17.422	-0.143	-0.143	0.000	0.000	0.000	0.000
46	A	48	MET	0	0.009	0.007	16.617	0.708	0.708	0.000	0.000	0.000	0.000
47	A	49	CYS	0	-0.024	-0.014	12.905	0.314	0.314	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.028	0.021	10.732	1.081	1.081	0.000	0.000	0.000	0.000
49	A	51	MET	0	0.034	0.022	7.631	1.145	1.145	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.972	0.988	2.384	-48.920	-46.952	0.931	-1.063	-1.836	0.006
51	A	53	LYS	1	0.982	0.983	2.132	-75.251	-70.638	3.696	-3.676	-4.633	0.027
52	A	54	ALA	0	0.043	0.029	2.325	-23.235	-19.512	3.153	-3.097	-3.780	0.043
53	A	55	THR	0	-0.024	-0.019	3.842	-9.907	-9.440	0.028	-0.273	-0.221	0.003
54	A	56	LEU	0	0.062	0.031	6.260	-5.878	-5.878	0.000	0.000	0.000	0.000
55	A	57	VAL	0	-0.036	-0.011	7.027	-5.264	-5.264	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.950	0.977	7.063	-41.265	-41.265	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.076	0.039	10.374	-2.528	-2.528	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.976	0.984	11.841	-25.848	-25.848	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.025	-0.030	13.316	-2.022	-2.022	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.064	0.049	14.854	-1.155	-1.155	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.024	-0.016	16.023	-1.058	-1.058	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.886	0.943	15.563	-21.230	-21.230	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.924	-0.944	19.546	14.946	14.946	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.063	-0.030	21.029	-0.744	-0.744	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.811	-0.909	22.012	12.675	12.675	0.000	0.000	0.000	0.000
66	A	68	PRO	0	-0.023	-0.018	21.952	0.731	0.731	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.911	-0.945	22.827	12.550	12.550	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.076	-0.022	20.423	0.146	0.146	0.000	0.000	0.000	0.000
69	A	71	PHE	0	-0.042	-0.017	18.415	0.542	0.542	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.016	-0.015	12.201	0.291	0.291	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.023	-0.004	15.574	0.030	0.030	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.007	-0.010	9.128	0.706	0.706	0.000	0.000	0.000	0.000
73	A	75	SER	0	-0.003	0.010	11.523	0.126	0.126	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)