FMO DATABASE

FMODB ID: N93NQ

Calculation Name: 5KX4-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: 5KX4

Chain ID: A

ChEMBL ID:
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UniProt ID: Q5WPZ4

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	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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-719494.877848
FMO2-HF: Nuclear repulsion	678812.31481
FMO2-HF: Total energy	-40682.563038
FMO2-MP2: Total energy	-40794.949439

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:1:GLU)

Summations of interaction energy for fragment #1(A:1:GLU)

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.
186.903	191.019	2.35	-2.185	-4.279	-0.006

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.953 / q_NPA : -1.001

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	3	SER	0	-0.033	-0.041	1.975	-4.374	-1.703	2.335	-1.928	-3.079	-0.005
4	A	4	GLU	-1	-0.914	-0.934	3.063	24.921	25.738	0.019	-0.169	-0.667	-0.001
5	A	5	ASP	-1	-0.837	-0.924	4.897	19.879	20.049	-0.001	-0.009	-0.159	0.000
6	A	6	CYS	0	0.067	0.041	7.137	-2.939	-2.939	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.835	-0.921	4.512	40.624	40.737	-0.001	-0.009	-0.102	0.000
8	A	8	ASN	0	-0.031	-0.035	7.581	-2.169	-2.169	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.025	0.034	10.377	-1.626	-1.626	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.009	-0.020	11.863	-1.359	-1.359	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.104	-0.050	11.772	-1.217	-1.217	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.896	-0.957	13.576	16.140	16.140	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.028	-0.009	16.089	-1.369	-1.369	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.003	0.007	16.771	-0.754	-0.754	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.009	-0.014	17.827	-0.953	-0.953	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.005	-0.004	19.498	-0.608	-0.608	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.044	0.028	21.540	-0.565	-0.565	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.799	0.899	22.074	-12.289	-12.289	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.017	-0.009	23.256	-0.528	-0.528	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.854	-0.945	25.590	10.068	10.068	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.005	-0.005	26.785	-0.315	-0.315	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.843	-0.915	26.120	10.660	10.660	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.147	-0.060	29.706	-0.374	-0.374	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.021	-0.017	31.702	-0.292	-0.292	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.815	0.907	30.364	-9.335	-9.335	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.012	0.003	27.011	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.841	-0.934	30.514	8.922	8.922	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.022	-0.013	28.070	0.138	0.138	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.020	-0.015	28.846	0.245	0.245	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.955	-0.957	30.436	8.939	8.939	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.064	-0.037	24.835	0.142	0.142	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.816	-0.899	26.327	10.568	10.568	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-1.044	-1.024	27.078	10.228	10.228	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.030	0.022	22.395	0.279	0.279	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.037	-0.043	26.553	-0.082	-0.082	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.825	-0.916	25.911	11.523	11.523	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.938	-0.961	25.743	10.916	10.916	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.769	-0.850	24.150	11.549	11.549	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.014	-0.011	21.090	0.613	0.613	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.046	0.002	20.980	0.753	0.753	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.926	-0.969	21.491	12.139	12.139	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.062	-0.010	17.987	0.455	0.455	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.052	-0.053	16.997	1.061	1.061	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.010	0.000	17.655	0.492	0.492	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.892	-0.941	19.890	12.697	12.697	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.074	-0.039	15.971	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.010	-0.010	15.671	0.987	0.987	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.047	-0.004	14.128	0.934	0.934	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.019	-0.030	16.094	-0.793	-0.793	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.020	-0.021	18.209	-0.265	-0.265	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.868	-0.914	19.038	15.490	15.490	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.841	-0.926	15.651	19.481	19.481	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.024	0.034	18.158	0.276	0.276	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.886	-0.957	20.045	13.999	13.999	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.749	0.855	16.934	-17.066	-17.066	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.046	0.020	14.792	0.327	0.327	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.017	0.016	17.104	-0.231	-0.231	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.835	0.904	19.829	-14.863	-14.863	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.001	0.005	13.898	-0.363	-0.363	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.023	0.016	17.662	-0.220	-0.220	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.811	0.866	19.526	-12.248	-12.248	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.886	-0.903	19.931	14.801	14.801	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.144	-0.071	14.447	1.131	1.131	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.014	0.023	20.715	-0.260	-0.260	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.019	0.009	23.382	-0.381	-0.381	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.099	-0.059	20.571	0.070	0.070	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.026	0.016	21.814	-0.111	-0.111	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.013	-0.003	24.851	-0.190	-0.190	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.103	-0.071	25.727	-0.607	-0.607	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.013	-0.037	27.738	0.435	0.435	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.830	-0.875	28.126	10.372	10.372	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.103	-0.087	23.955	0.506	0.506	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.870	0.944	23.069	-10.608	-10.608	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.014	-0.012	21.409	0.482	0.482	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.023	0.000	18.497	0.455	0.455	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.845	-0.893	18.024	13.145	13.145	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.016	-0.008	18.905	0.679	0.679	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.014	0.017	10.169	0.603	0.603	0.000	0.000	0.000	0.000
79	A	80	ASP	-1	-0.866	-0.929	14.209	18.897	18.897	0.000	0.000	0.000	0.000
80	A	82	TYR	0	0.057	0.003	13.592	0.863	0.863	0.000	0.000	0.000	0.000
81	A	83	MET	0	0.020	0.022	9.689	2.515	2.515	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.888	0.962	10.377	-16.540	-16.540	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.750	0.842	12.240	-16.032	-16.032	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.833	0.923	4.563	-49.677	-49.557	-0.001	-0.008	-0.110	0.000
85	A	87	ILE	0	0.051	0.025	9.497	1.345	1.345	0.000	0.000	0.000	0.000
86	A	89	ASN	0	-0.099	-0.040	4.031	-1.763	-1.538	-0.001	-0.062	-0.162	0.000
87	A	90	TYR	0	-0.037	-0.022	7.775	-0.666	-0.666	0.000	0.000	0.000	0.000
88	A	91	TYR	0	-0.005	-0.012	9.704	-1.962	-1.962	0.000	0.000	0.000	0.000
89	A	92	PRO	0	-0.049	-0.013	9.406	2.589	2.589	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.929	-0.976	7.705	29.691	29.691	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.090	-0.031	8.675	-0.685	-0.685	0.000	0.000	0.000	0.000
92	A	95	MET	0	0.001	0.018	11.343	-0.395	-0.395	0.000	0.000	0.000	0.000

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Manual

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