FMO DATABASE

FMODB ID: 76ZKK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-629499.496608
FMO2-HF: Nuclear repulsion	594154.86565
FMO2-HF: Total energy	-35344.630958
FMO2-MP2: Total energy	-35447.711641

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.
5.87	8.897	0.73	-1.097	-2.661	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 : -0.007 / q_NPA : -0.013

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	0.031	0.004	3.016	-1.721	1.247	0.731	-1.091	-2.609	0.001
4	A	1	MET	0	-0.026	-0.029	4.678	-0.021	0.038	-0.001	-0.006	-0.052	0.000
5	A	2	GLU	-1	-0.861	-0.919	7.305	2.042	2.042	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.834	0.871	9.187	-0.921	-0.921	0.000	0.000	0.000	0.000
7	A	4	LYS	1	0.929	0.955	11.607	-0.378	-0.378	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.846	0.922	7.986	-0.331	-0.331	0.000	0.000	0.000	0.000
9	A	6	LEU	0	0.052	0.039	12.642	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	7	ILE	0	0.012	0.009	15.428	-0.043	-0.043	0.000	0.000	0.000	0.000
11	A	8	ALA	0	-0.031	-0.013	16.674	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.781	0.893	17.576	-0.327	-0.327	0.000	0.000	0.000	0.000
13	A	10	PHE	0	0.028	0.006	19.329	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	11	VAL	0	-0.006	-0.006	21.230	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.813	-0.893	21.692	0.238	0.238	0.000	0.000	0.000	0.000
16	A	13	ILE	0	0.023	0.006	21.706	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	14	ALA	0	0.020	0.001	25.190	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.018	-0.003	26.878	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.945	-0.972	26.521	0.168	0.168	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.763	0.886	24.913	-0.229	-0.229	0.000	0.000	0.000	0.000
21	A	18	MET	0	-0.055	-0.017	28.775	0.001	0.001	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.025	0.012	31.536	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.793	0.898	30.100	-0.173	-0.173	0.000	0.000	0.000	0.000
24	A	21	ASP	-1	-0.920	-0.964	29.501	0.135	0.135	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.050	-0.032	25.303	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.937	-0.966	25.562	0.119	0.119	0.000	0.000	0.000	0.000
27	A	24	THR	0	-0.065	-0.034	23.161	0.008	0.008	0.000	0.000	0.000	0.000
28	A	25	VAL	0	-0.005	0.002	21.352	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.869	-0.924	21.136	0.272	0.272	0.000	0.000	0.000	0.000
30	A	27	GLU	-1	-0.744	-0.872	15.624	0.599	0.599	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.890	-0.940	20.360	0.326	0.326	0.000	0.000	0.000	0.000
32	A	29	ASN	0	-0.055	-0.023	23.113	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	30	THR	0	-0.057	-0.072	25.231	0.019	0.019	0.000	0.000	0.000	0.000
34	A	31	PHE	0	0.081	0.025	23.101	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	32	LYS	1	0.967	0.993	28.438	-0.159	-0.159	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.879	-0.901	29.232	0.174	0.174	0.000	0.000	0.000	0.000
37	A	34	LEU	0	0.009	0.021	25.541	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.029	-0.014	30.207	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	36	PHE	0	-0.024	-0.015	27.913	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.834	-0.943	31.801	0.165	0.165	0.000	0.000	0.000	0.000
41	A	38	SER	0	-0.101	-0.053	32.193	0.010	0.010	0.000	0.000	0.000	0.000
42	A	39	ILE	0	0.005	-0.011	32.130	0.011	0.011	0.000	0.000	0.000	0.000
43	A	40	ASP	-1	-0.778	-0.874	30.946	0.180	0.180	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.055	-0.032	26.736	0.015	0.015	0.000	0.000	0.000	0.000
45	A	42	ILE	0	-0.009	-0.007	27.502	0.020	0.020	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.889	-0.939	28.637	0.207	0.207	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.048	-0.021	23.799	0.013	0.013	0.000	0.000	0.000	0.000
48	A	45	VAL	0	-0.014	-0.014	23.819	0.026	0.026	0.000	0.000	0.000	0.000
49	A	46	MET	0	0.008	0.009	24.045	0.016	0.016	0.000	0.000	0.000	0.000
50	A	47	PHE	0	0.002	-0.006	25.069	0.003	0.003	0.000	0.000	0.000	0.000
51	A	48	PHE	0	-0.016	-0.020	17.651	0.016	0.016	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.804	-0.900	20.610	0.373	0.373	0.000	0.000	0.000	0.000
53	A	50	ASP	-1	-0.948	-0.963	22.165	0.297	0.297	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.904	-0.955	20.166	0.309	0.309	0.000	0.000	0.000	0.000
55	A	52	PHE	0	-0.083	-0.051	14.475	0.028	0.028	0.000	0.000	0.000	0.000
56	A	53	ALA	0	-0.044	-0.004	17.999	0.050	0.050	0.000	0.000	0.000	0.000
57	A	54	LEU	0	-0.048	-0.019	16.206	0.040	0.040	0.000	0.000	0.000	0.000
58	A	55	ARG	1	0.786	0.877	20.333	-0.362	-0.362	0.000	0.000	0.000	0.000
59	A	56	ILE	0	-0.043	-0.035	20.054	0.041	0.041	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.863	-0.937	23.445	0.337	0.337	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.825	-0.921	26.392	0.254	0.254	0.000	0.000	0.000	0.000
62	A	59	GLU	-1	-0.906	-0.939	28.193	0.230	0.230	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.801	-0.900	21.895	0.451	0.451	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.058	0.034	25.590	0.002	0.002	0.000	0.000	0.000	0.000
65	A	62	SER	0	-0.083	-0.037	26.903	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.801	0.878	26.445	-0.273	-0.273	0.000	0.000	0.000	0.000
67	A	64	ILE	0	-0.003	0.030	23.449	0.003	0.003	0.000	0.000	0.000	0.000
68	A	65	ARG	1	0.772	0.871	25.496	-0.261	-0.261	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.809	0.897	23.448	-0.287	-0.287	0.000	0.000	0.000	0.000
70	A	67	VAL	0	0.050	0.025	20.059	0.024	0.024	0.000	0.000	0.000	0.000
71	A	68	LYS	1	0.830	0.898	16.589	-0.544	-0.544	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.787	-0.889	18.439	0.409	0.409	0.000	0.000	0.000	0.000
73	A	70	LEU	0	0.007	0.008	19.875	0.027	0.027	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.036	-0.018	14.453	0.043	0.043	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.772	-0.861	14.952	0.824	0.824	0.000	0.000	0.000	0.000
76	A	73	ILE	0	-0.034	-0.005	15.421	0.072	0.072	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.019	0.007	14.653	0.041	0.041	0.000	0.000	0.000	0.000
78	A	75	ILE	0	0.000	-0.006	9.882	0.027	0.027	0.000	0.000	0.000	0.000
79	A	76	LYS	1	0.841	0.931	11.990	-0.538	-0.538	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.768	0.881	14.203	-0.478	-0.478	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.035	-0.024	11.529	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	79	GLU	-1	-0.975	-0.985	8.962	1.952	1.952	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.890	-0.940	11.241	0.672	0.672	0.000	0.000	0.000	0.000
84	A	81	ILE	0	-0.072	-0.013	14.679	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	82	ASP	-1	-1.002	-1.001	10.452	1.956	1.956	0.000	0.000	0.000	0.000

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