FMO DATABASE

FMODB ID: 2N5MR

Calculation Name: 1VKU-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: 1VKU

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9WY19

Base Structure: X-ray

Registration Date: 2023-09-23

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-630434.726689
FMO2-HF: Nuclear repulsion	595089.87898
FMO2-HF: Total energy	-35344.847709
FMO2-MP2: Total energy	-35447.991008

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:-2:HIS)

Summations of interaction energy for fragment #1(A:-2: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.
4.783	7.748	1.54	-1.429	-3.076	0.001

Interaction energy analysis for fragmet #1(A:-2:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.009

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

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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	0	HIS	0	0.033	0.000	2.789	-2.216	0.675	1.541	-1.421	-3.011	0.001
4	A	1	MET	0	-0.015	-0.015	4.706	-0.041	0.033	-0.001	-0.008	-0.065	0.000
5	A	2	GLU	-1	-0.839	-0.897	7.298	2.164	2.164	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.840	0.874	9.432	-1.094	-1.094	0.000	0.000	0.000	0.000
7	A	4	LYS	1	0.905	0.943	11.801	-0.555	-0.555	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.825	0.914	7.967	-0.500	-0.500	0.000	0.000	0.000	0.000
9	A	6	LEU	0	0.055	0.038	12.464	-0.056	-0.056	0.000	0.000	0.000	0.000
10	A	7	ILE	0	0.025	0.010	15.337	-0.049	-0.049	0.000	0.000	0.000	0.000
11	A	8	ALA	0	-0.028	-0.014	16.998	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.755	0.866	17.513	-0.357	-0.357	0.000	0.000	0.000	0.000
13	A	10	PHE	0	0.039	0.015	19.315	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.003	0.003	21.508	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.809	-0.885	21.564	0.262	0.262	0.000	0.000	0.000	0.000
16	A	13	ILE	0	0.003	-0.004	21.586	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	14	ALA	0	0.020	0.002	24.964	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.020	-0.006	27.027	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.934	-0.968	26.454	0.185	0.185	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.745	0.877	24.456	-0.257	-0.257	0.000	0.000	0.000	0.000
21	A	18	MET	0	-0.069	-0.021	28.669	0.002	0.002	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.026	0.010	31.488	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.771	0.881	30.404	-0.203	-0.203	0.000	0.000	0.000	0.000
24	A	21	ASP	-1	-0.834	-0.932	29.067	0.175	0.175	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.102	-0.060	25.620	0.002	0.002	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.927	-0.943	25.267	0.174	0.174	0.000	0.000	0.000	0.000
27	A	24	THR	0	-0.080	-0.050	22.775	0.015	0.015	0.000	0.000	0.000	0.000
28	A	25	VAL	0	-0.017	-0.001	21.781	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.886	-0.939	21.221	0.350	0.350	0.000	0.000	0.000	0.000
30	A	27	GLU	-1	-0.763	-0.867	15.689	0.716	0.716	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.875	-0.953	20.104	0.389	0.389	0.000	0.000	0.000	0.000
32	A	29	ASN	0	-0.032	-0.013	22.900	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	30	THR	0	-0.056	-0.080	25.078	0.017	0.017	0.000	0.000	0.000	0.000
34	A	31	PHE	0	0.073	0.022	23.044	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	32	LYS	1	0.964	0.985	28.251	-0.180	-0.180	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.881	-0.892	28.866	0.214	0.214	0.000	0.000	0.000	0.000
37	A	34	LEU	0	0.013	0.021	25.703	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.010	0.003	30.338	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	36	PHE	0	-0.034	-0.020	28.055	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.837	-0.914	31.766	0.177	0.177	0.000	0.000	0.000	0.000
41	A	38	SER	0	-0.095	-0.073	31.957	0.012	0.012	0.000	0.000	0.000	0.000
42	A	39	ILE	0	-0.002	-0.002	31.930	0.011	0.011	0.000	0.000	0.000	0.000
43	A	40	ASP	-1	-0.797	-0.888	30.793	0.199	0.199	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.028	-0.027	26.632	0.016	0.016	0.000	0.000	0.000	0.000
45	A	42	ILE	0	-0.017	-0.004	27.271	0.021	0.021	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.885	-0.946	28.297	0.221	0.221	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.042	-0.013	23.491	0.012	0.012	0.000	0.000	0.000	0.000
48	A	45	VAL	0	-0.019	-0.015	23.654	0.030	0.030	0.000	0.000	0.000	0.000
49	A	46	MET	0	-0.001	0.005	23.983	0.013	0.013	0.000	0.000	0.000	0.000
50	A	47	PHE	0	0.010	-0.005	24.822	0.002	0.002	0.000	0.000	0.000	0.000
51	A	48	PHE	0	-0.027	-0.023	17.558	0.018	0.018	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.819	-0.896	20.363	0.380	0.380	0.000	0.000	0.000	0.000
53	A	50	ASP	-1	-0.925	-0.958	22.199	0.294	0.294	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.848	-0.926	20.786	0.313	0.313	0.000	0.000	0.000	0.000
55	A	52	PHE	0	-0.086	-0.045	14.447	0.034	0.034	0.000	0.000	0.000	0.000
56	A	53	ALA	0	-0.052	-0.015	18.305	0.045	0.045	0.000	0.000	0.000	0.000
57	A	54	LEU	0	-0.047	-0.014	16.395	0.026	0.026	0.000	0.000	0.000	0.000
58	A	55	ARG	1	0.766	0.853	20.557	-0.362	-0.362	0.000	0.000	0.000	0.000
59	A	56	ILE	0	-0.016	-0.022	19.942	0.044	0.044	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.850	-0.926	23.365	0.337	0.337	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.826	-0.916	26.362	0.264	0.264	0.000	0.000	0.000	0.000
62	A	59	GLU	-1	-0.858	-0.926	28.333	0.243	0.243	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.778	-0.894	21.520	0.477	0.477	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.045	0.018	25.439	0.003	0.003	0.000	0.000	0.000	0.000
65	A	62	SER	0	-0.093	-0.047	26.823	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.764	0.879	26.546	-0.285	-0.285	0.000	0.000	0.000	0.000
67	A	64	ILE	0	0.010	0.040	23.509	0.002	0.002	0.000	0.000	0.000	0.000
68	A	65	ARG	1	0.746	0.854	25.616	-0.287	-0.287	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.810	0.898	23.353	-0.335	-0.335	0.000	0.000	0.000	0.000
70	A	67	VAL	0	0.032	0.026	19.907	0.022	0.022	0.000	0.000	0.000	0.000
71	A	68	LYS	1	0.801	0.892	16.254	-0.619	-0.619	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.755	-0.873	18.326	0.442	0.442	0.000	0.000	0.000	0.000
73	A	70	LEU	0	0.023	0.020	19.619	0.030	0.030	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.022	-0.006	14.355	0.045	0.045	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.761	-0.869	14.453	0.955	0.955	0.000	0.000	0.000	0.000
76	A	73	ILE	0	-0.039	-0.010	15.338	0.063	0.063	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.009	0.001	14.660	0.030	0.030	0.000	0.000	0.000	0.000
78	A	75	ILE	0	-0.029	-0.018	9.912	0.042	0.042	0.000	0.000	0.000	0.000
79	A	76	LYS	1	0.795	0.908	12.243	-0.543	-0.543	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.786	0.897	14.229	-0.482	-0.482	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.023	-0.007	11.512	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	79	GLU	-1	-0.950	-0.983	9.238	1.854	1.854	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.887	-0.947	11.585	0.615	0.615	0.000	0.000	0.000	0.000
84	A	81	ILE	0	-0.095	-0.034	14.254	-0.138	-0.138	0.000	0.000	0.000	0.000
85	A	82	ASP	-1	-1.002	-0.985	9.670	1.648	1.648	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:HIS)