FMO DATABASE

FMODB ID: 85J9Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-720440.898958
FMO2-HF: Nuclear repulsion	679759.918657
FMO2-HF: Total energy	-40680.980301
FMO2-MP2: Total energy	-40793.145936

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.
178.537	183.141	1.031	-1.983	-3.65	-0.007

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 : -0.966 / q_NPA : -1.013

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	3	SER	0	-0.007	-0.006	2.219	-4.026	-0.677	1.016	-1.719	-2.647	-0.006
4	A	4	GLU	-1	-0.927	-0.944	3.089	24.699	25.533	0.019	-0.231	-0.622	-0.001
5	A	5	ASP	-1	-0.878	-0.943	4.937	19.382	19.535	-0.001	-0.008	-0.143	0.000
6	A	6	CYS	0	0.110	0.058	7.451	-2.469	-2.469	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.920	-0.987	4.488	36.640	36.744	-0.001	-0.012	-0.090	0.000
8	A	8	ASN	0	-0.024	-0.026	7.929	-2.398	-2.398	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.029	0.045	10.417	-1.502	-1.502	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.023	-0.028	11.784	-1.243	-1.243	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.084	-0.033	11.744	-1.193	-1.193	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.915	-0.968	13.624	15.907	15.907	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.028	-0.017	16.144	-1.341	-1.341	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.000	0.009	16.862	-0.726	-0.726	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.021	-0.020	17.895	-0.832	-0.832	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.004	-0.006	19.587	-0.567	-0.567	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.049	0.035	21.715	-0.554	-0.554	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.873	0.956	21.856	-12.554	-12.554	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.005	-0.007	23.385	-0.490	-0.490	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.881	-0.948	25.692	10.153	10.153	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.013	-0.014	26.750	-0.305	-0.305	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.870	-0.959	26.377	10.638	10.638	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.175	-0.075	29.805	-0.384	-0.384	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.012	-0.006	31.793	-0.285	-0.285	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.815	0.894	30.470	-9.316	-9.316	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.011	0.006	27.150	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.851	-0.938	30.518	8.875	8.875	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.029	-0.015	28.138	0.149	0.149	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.012	-0.016	28.808	0.241	0.241	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.939	-0.947	30.377	8.854	8.854	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.072	-0.035	24.577	0.125	0.125	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.850	-0.937	26.242	10.488	10.488	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-1.043	-1.021	27.257	10.163	10.163	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.038	0.016	22.799	0.265	0.265	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.057	-0.025	26.798	-0.121	-0.121	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.922	-1.001	26.168	11.275	11.275	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.937	-0.967	25.964	11.032	11.032	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.782	-0.889	24.367	11.484	11.484	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.036	-0.021	21.253	0.582	0.582	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.044	-0.006	21.210	0.777	0.777	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.926	-0.970	21.708	11.878	11.878	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.075	-0.014	18.236	0.470	0.470	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.059	-0.062	17.205	1.000	1.000	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.012	-0.006	17.841	0.452	0.452	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.889	-0.933	20.043	12.437	12.437	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.064	-0.036	16.320	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.017	-0.014	15.801	0.914	0.914	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.040	-0.005	14.235	0.878	0.878	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.009	-0.001	16.188	-0.805	-0.805	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.026	0.005	18.215	-0.172	-0.172	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.937	-0.972	19.108	15.050	15.050	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.854	-0.974	15.635	19.035	19.035	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.032	0.046	18.330	0.257	0.257	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.885	-0.954	20.133	13.615	13.615	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.752	0.883	17.221	-16.686	-16.686	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.051	0.027	14.930	0.344	0.344	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.009	0.010	17.263	-0.209	-0.209	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.905	0.946	20.217	-14.547	-14.547	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.002	0.011	14.265	-0.246	-0.246	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.022	0.012	18.055	-0.167	-0.167	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.933	0.978	19.764	-12.290	-12.290	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.980	-0.979	20.283	14.667	14.667	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.136	-0.071	14.581	1.198	1.198	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.007	0.021	20.934	-0.252	-0.252	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.019	0.009	23.438	-0.373	-0.373	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.141	-0.086	20.690	-0.236	-0.236	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.031	0.013	21.840	-0.081	-0.081	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.021	-0.013	24.952	-0.165	-0.165	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.057	-0.043	25.967	-0.588	-0.588	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.032	-0.039	27.729	0.416	0.416	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.828	-0.867	27.922	10.349	10.349	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.131	-0.091	24.038	0.515	0.515	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.953	0.992	23.123	-10.573	-10.573	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.023	-0.020	21.456	0.464	0.464	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.024	-0.001	18.551	0.437	0.437	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.856	-0.902	18.071	13.110	13.110	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.001	-0.001	18.763	0.672	0.672	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.023	0.019	10.370	0.485	0.485	0.000	0.000	0.000	0.000
79	A	80	ASP	-1	-0.864	-0.922	14.184	18.899	18.899	0.000	0.000	0.000	0.000
80	A	82	TYR	0	0.033	-0.005	13.531	0.947	0.947	0.000	0.000	0.000	0.000
81	A	83	MET	0	0.026	0.022	9.612	2.258	2.258	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.900	0.975	10.610	-16.348	-16.348	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.822	0.898	12.545	-16.837	-16.837	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.886	0.944	4.456	-53.338	-53.256	-0.001	-0.011	-0.069	0.000
85	A	87	ILE	0	0.063	0.027	9.760	1.271	1.271	0.000	0.000	0.000	0.000
86	A	89	ASN	0	-0.101	-0.047	4.839	1.248	1.330	-0.001	-0.002	-0.079	0.000
87	A	90	TYR	0	-0.031	-0.018	7.880	-0.584	-0.584	0.000	0.000	0.000	0.000
88	A	91	TYR	0	0.015	0.018	9.798	-1.719	-1.719	0.000	0.000	0.000	0.000
89	A	92	PRO	0	-0.048	-0.014	9.468	2.321	2.321	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.926	-0.968	7.712	28.064	28.064	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.056	-0.014	8.767	0.117	0.117	0.000	0.000	0.000	0.000
92	A	95	MET	0	-0.007	0.008	11.553	-0.369	-0.369	0.000	0.000	0.000	0.000

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