FMO DATABASE

FMODB ID: 6YZ1Z

Calculation Name: 1KBA-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: 1KBA

Chain ID: A

ChEMBL ID:
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UniProt ID: P01398

Base Structure: X-ray

Registration Date: 2023-09-22

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361562.76141
FMO2-HF: Nuclear repulsion	333618.335892
FMO2-HF: Total energy	-27944.425518
FMO2-MP2: Total energy	-28017.341993

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:ARG)

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

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.
-151.705	-141.961	43.851	-22.271	-31.323	-0.201

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.904

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	CYS	0	-0.007	0.012	2.689	-11.283	-8.129	5.262	-3.007	-5.408	-0.010
4	A	4	LEU	0	-0.009	0.011	4.719	3.334	3.383	-0.001	-0.011	-0.037	0.000
5	A	5	ILE	0	0.016	0.008	8.574	-0.803	-0.803	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.029	0.010	11.038	0.633	0.633	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.058	-0.031	14.247	0.435	0.435	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.012	-0.002	14.950	0.769	0.769	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.003	0.006	12.760	-0.168	-0.168	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.036	0.042	12.436	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.002	-0.015	8.010	-0.618	-0.618	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.011	0.008	6.903	1.861	1.861	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.022	-0.004	4.384	-3.426	-3.277	-0.001	-0.038	-0.110	0.000
14	A	14	CYS	0	-0.079	-0.012	2.116	-1.622	-0.420	3.803	-1.811	-3.194	0.010
15	A	15	PRO	0	0.043	0.023	3.514	-0.761	-0.199	0.008	-0.288	-0.282	-0.002
16	A	16	ASN	0	0.012	0.004	4.613	-2.959	-2.885	-0.001	-0.005	-0.068	0.000
17	A	17	GLY	0	0.006	-0.001	6.354	1.590	1.590	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.092	-0.055	5.110	2.451	2.451	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.850	-0.927	2.820	-60.722	-56.962	0.357	-1.844	-2.273	-0.011
20	A	20	ILE	0	-0.005	0.015	1.712	-41.924	-45.971	16.564	-6.976	-5.541	-0.089
21	A	22	PHE	0	-0.023	-0.022	4.516	2.745	2.836	-0.001	-0.014	-0.076	0.000
22	A	23	LEU	0	0.038	0.013	8.284	0.323	0.323	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.794	0.896	11.356	18.342	18.342	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.037	0.026	14.720	0.406	0.406	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.009	-0.003	18.257	0.746	0.746	0.000	0.000	0.000	0.000
26	A	27	CYS	0	-0.062	0.018	21.012	0.138	0.138	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.732	-0.863	24.797	-10.769	-10.769	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.928	0.951	27.498	8.868	8.868	0.000	0.000	0.000	0.000
29	A	30	PHE	0	0.025	0.015	29.993	0.326	0.326	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.013	-0.013	28.091	-0.269	-0.269	0.000	0.000	0.000	0.000
31	A	33	ILE	0	-0.013	-0.008	30.888	0.171	0.171	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.890	0.933	27.900	10.655	10.655	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.036	0.041	25.655	-0.230	-0.230	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.046	-0.051	21.359	0.156	0.156	0.000	0.000	0.000	0.000
35	A	37	VAL	0	0.007	0.001	19.832	-0.094	-0.094	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.012	0.007	15.514	-0.365	-0.365	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.850	-0.925	14.333	-17.669	-17.669	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.035	-0.033	10.321	0.757	0.757	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.067	0.035	8.439	1.671	1.671	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.057	-0.024	5.923	5.053	5.053	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.074	0.031	6.452	-4.124	-4.124	0.000	0.000	0.000	0.000
42	A	45	THR	0	-0.016	-0.006	8.840	1.052	1.052	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.005	-0.005	8.448	-0.284	-0.284	0.000	0.000	0.000	0.000
44	A	47	PRO	0	0.013	0.002	11.252	1.872	1.872	0.000	0.000	0.000	0.000
45	A	48	GLN	0	0.023	0.006	14.417	0.992	0.992	0.000	0.000	0.000	0.000
46	A	49	PHE	0	0.019	-0.005	17.457	0.202	0.202	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.895	0.949	19.372	14.741	14.741	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.034	0.008	22.179	-0.096	-0.096	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.016	0.006	22.962	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.035	-0.014	17.452	0.046	0.046	0.000	0.000	0.000	0.000
51	A	54	ARG	1	0.931	0.956	21.144	12.333	12.333	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.026	0.001	17.153	0.427	0.427	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.057	-0.035	12.687	0.055	0.055	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.014	0.034	9.592	0.595	0.595	0.000	0.000	0.000	0.000
55	A	59	CYS	0	0.014	0.023	4.889	6.150	6.150	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.071	0.046	2.793	-4.075	-2.444	0.574	-0.609	-1.597	0.004
57	A	61	THR	0	-0.039	-0.039	3.108	-1.375	1.054	1.237	-0.777	-2.889	0.000
58	A	62	ASP	-1	-0.745	-0.856	1.781	-103.322	-101.930	15.962	-7.879	-9.474	-0.102
59	A	63	ASN	0	-0.022	-0.025	2.967	10.979	10.277	0.088	0.988	-0.374	-0.001
60	A	65	ASN	0	-0.023	-0.004	6.410	0.979	0.979	0.000	0.000	0.000	0.000
61	A	66	HIS	0	-0.018	-0.012	8.089	3.410	3.410	0.000	0.000	0.000	0.000

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