FMO DATABASE

FMODB ID: 76Y1K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-362427.157601
FMO2-HF: Nuclear repulsion	334484.810539
FMO2-HF: Total energy	-27942.347062
FMO2-MP2: Total energy	-28015.573172

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.
-135.926	-138.106	48.811	-18.82	-27.809	-0.162

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 : 0.878 / q_NPA : 0.950

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	-0.023	0.024	3.086	-9.634	-4.627	0.374	-2.108	-3.272	0.001
4	A	4	LEU	0	-0.031	0.011	5.572	3.075	3.075	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.022	-0.009	9.272	-0.549	-0.549	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.014	-0.014	11.749	0.816	0.816	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.003	0.032	14.911	0.318	0.318	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.011	-0.014	15.360	0.385	0.385	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.012	0.015	13.555	-0.175	-0.175	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.006	-0.020	12.753	0.211	0.211	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.005	-0.029	8.343	-1.171	-1.171	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.008	0.022	7.354	1.669	1.669	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.001	-0.011	4.490	-4.338	-4.234	-0.001	-0.028	-0.075	0.000
14	A	14	CYS	0	-0.036	0.008	2.295	-1.084	0.716	1.567	-1.071	-2.296	0.004
15	A	15	PRO	0	-0.008	-0.010	4.104	0.325	0.506	-0.001	-0.048	-0.132	0.000
16	A	16	ASN	0	0.020	0.012	4.972	-2.718	-2.652	-0.001	-0.001	-0.063	0.000
17	A	17	GLY	0	0.024	0.013	6.508	1.712	1.712	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.061	-0.024	5.031	0.203	0.203	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.850	-0.937	2.429	-50.958	-48.227	0.855	-1.458	-2.128	-0.010
20	A	20	ILE	0	-0.022	-0.013	1.885	-29.475	-34.466	14.675	-3.787	-5.897	-0.064
21	A	22	PHE	0	-0.041	-0.037	4.770	2.783	2.840	-0.001	-0.003	-0.053	0.000
22	A	23	LEU	0	0.050	0.022	8.487	0.411	0.411	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.868	0.944	11.839	18.325	18.325	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.027	0.015	14.795	0.517	0.517	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.050	0.006	18.367	-0.144	-0.144	0.000	0.000	0.000	0.000
26	A	27	CYS	0	-0.055	-0.009	20.940	0.059	0.059	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.771	-0.868	24.790	-10.997	-10.997	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.933	0.948	27.369	8.886	8.886	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.011	-0.018	29.835	0.342	0.342	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.037	-0.038	28.367	-0.098	-0.098	0.000	0.000	0.000	0.000
31	A	33	ILE	0	0.029	0.029	31.100	0.124	0.124	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.869	0.966	27.819	10.481	10.481	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.055	0.018	26.262	-0.127	-0.127	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.071	-0.040	21.555	0.104	0.104	0.000	0.000	0.000	0.000
35	A	37	VAL	0	0.014	-0.010	20.166	0.001	0.001	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.014	-0.007	15.884	-0.400	-0.400	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.916	-0.961	13.911	-17.623	-17.623	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.017	-0.010	10.850	0.202	0.202	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.069	0.039	8.565	1.360	1.360	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.044	-0.008	6.175	4.083	4.083	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.062	0.015	6.342	-3.564	-3.564	0.000	0.000	0.000	0.000
42	A	45	THR	0	-0.006	-0.004	8.604	0.618	0.618	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.022	-0.017	8.277	-0.976	-0.976	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.050	-0.025	10.731	1.597	1.597	0.000	0.000	0.000	0.000
45	A	48	GLN	0	0.062	0.019	13.891	0.711	0.711	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.007	-0.013	16.939	0.123	0.123	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.922	0.979	18.532	14.850	14.850	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.072	0.005	21.384	-0.189	-0.189	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.023	0.009	22.207	-0.201	-0.201	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.027	-0.010	17.304	-0.085	-0.085	0.000	0.000	0.000	0.000
51	A	54	ARG	1	0.959	0.986	21.055	12.392	12.392	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.011	-0.031	17.294	0.137	0.137	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.011	0.011	12.343	0.003	0.003	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.027	0.042	10.139	0.645	0.645	0.000	0.000	0.000	0.000
55	A	59	CYS	0	-0.032	0.013	5.047	5.443	5.443	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.062	-0.002	2.724	-3.767	-1.872	0.443	-0.744	-1.594	0.003
57	A	61	THR	0	-0.005	0.000	2.888	2.041	4.336	0.772	-0.627	-2.439	0.001
58	A	62	ASP	-1	-0.838	-0.891	1.704	-100.922	-112.535	30.112	-8.908	-9.591	-0.097
59	A	63	ASN	0	0.008	-0.042	3.674	3.637	3.925	0.017	-0.037	-0.269	0.000
60	A	65	ASN	0	-0.033	-0.012	6.726	1.908	1.908	0.000	0.000	0.000	0.000
61	A	66	HIS	0	-0.008	-0.002	8.658	2.772	2.772	0.000	0.000	0.000	0.000

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