FMO DATABASE

FMODB ID: JL419

Calculation Name: 1KFM-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: 1KFM

Chain ID: A

ChEMBL ID:
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UniProt ID: P69776

Base Structure: X-ray

Registration Date: 2023-06-22

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-172924.287114
FMO2-HF: Nuclear repulsion	153872.647536
FMO2-HF: Total energy	-19051.639579
FMO2-MP2: Total energy	-19106.71843

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-2.12	0.105	0.013	-0.814	-1.424	0.002

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.004

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	4	ALA	0	0.104	0.048	3.883	-2.858	-1.438	-0.007	-0.597	-0.816	0.002
4	A	5	LYS	1	0.902	0.961	3.565	-0.333	0.207	0.019	-0.168	-0.390	0.000
5	A	6	ILE	0	0.055	0.022	3.856	-0.147	0.118	0.001	-0.049	-0.218	0.000
6	A	7	ASP	-1	-0.793	-0.872	6.673	1.292	1.292	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.008	0.005	8.272	0.028	0.028	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.017	-0.017	7.768	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.008	-0.013	10.324	0.002	0.002	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.033	-0.024	12.589	0.035	0.035	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.943	-0.959	13.715	-0.103	-0.103	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.042	0.014	14.407	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.011	0.021	16.641	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.044	-0.032	18.084	0.016	0.016	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.045	-0.028	17.941	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.031	-0.028	19.655	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.070	0.043	22.702	0.004	0.004	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.904	0.954	23.151	0.011	0.011	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.001	0.003	24.387	0.000	0.000	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.889	-0.940	26.721	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.074	-0.048	28.419	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.027	0.014	27.990	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.029	-0.003	30.946	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.016	-0.012	32.692	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.886	-0.943	33.374	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.046	-0.031	34.223	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.042	-0.019	36.793	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.016	0.012	38.774	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.044	0.019	39.643	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.889	0.945	38.712	0.042	0.042	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.005	0.007	42.401	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.894	-0.945	44.615	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.036	-0.024	44.974	0.001	0.001	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.097	-0.059	46.774	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.039	0.013	48.553	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.002	-0.002	49.907	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.887	0.955	48.635	0.027	0.027	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.816	-0.901	52.492	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.835	-0.889	54.646	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.014	0.012	55.321	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.008	0.004	56.691	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.839	0.897	58.479	0.009	0.009	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.051	-0.032	60.159	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.030	-0.033	59.703	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.071	0.038	60.233	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.894	0.952	63.874	0.008	0.008	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.007	0.008	64.348	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.889	-0.931	65.315	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.139	-0.071	68.134	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	MET	0	-0.109	-0.052	70.493	0.001	0.001	0.000	0.000	0.000	0.000

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