FMO DATABASE

FMODB ID: N9Z4Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-172716.013201
FMO2-HF: Nuclear repulsion	153664.46605
FMO2-HF: Total energy	-19051.547151
FMO2-MP2: Total energy	-19106.65362

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.
-4.473	-1.7	0.34	-1.155	-1.958	0

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 : 0.007 / q_NPA : -0.012

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	0.080	0.038	3.816	-3.020	-1.268	-0.013	-0.773	-0.966	0.001
4	A	5	LYS	1	0.921	0.957	2.697	-1.674	-1.089	0.338	-0.266	-0.657	-0.001
5	A	6	ILE	0	0.067	0.023	3.443	-0.499	-0.063	0.015	-0.116	-0.335	0.000
6	A	7	ASP	-1	-0.823	-0.895	6.234	0.767	0.767	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.030	-0.001	7.757	0.078	0.078	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.025	-0.018	7.364	-0.070	-0.070	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.004	0.000	10.053	0.014	0.014	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.022	-0.017	12.192	0.020	0.020	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.936	-0.960	13.193	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.035	0.004	14.049	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.011	0.021	16.184	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.041	-0.028	17.620	0.018	0.018	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.027	-0.020	17.368	0.003	0.003	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.023	-0.018	19.409	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.056	0.042	22.267	0.004	0.004	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.911	0.940	22.759	0.004	0.004	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.006	-0.008	24.035	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.893	-0.935	26.374	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.071	-0.052	27.979	0.003	0.003	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.011	0.017	27.588	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.014	0.008	30.626	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.027	-0.017	32.387	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.876	-0.937	33.274	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.055	-0.034	33.593	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.047	-0.023	36.249	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.027	0.009	38.371	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.050	0.031	39.073	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.890	0.947	38.663	0.046	0.046	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.012	-0.003	42.000	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.907	-0.942	43.917	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.050	-0.028	44.516	0.001	0.001	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.092	-0.059	46.273	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.051	0.026	48.160	0.000	0.000	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.001	0.004	49.416	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.898	0.952	49.137	0.028	0.028	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.830	-0.912	52.004	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.841	-0.892	54.013	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.002	-0.003	54.831	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.001	0.008	56.284	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.849	0.905	58.055	0.010	0.010	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.046	-0.028	59.689	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.012	-0.041	59.013	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.055	0.054	60.461	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.888	0.944	63.313	0.008	0.008	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.008	-0.003	63.529	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.879	-0.933	65.341	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.166	-0.088	67.793	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	MET	0	-0.086	-0.021	70.010	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)