FMO DATABASE

FMODB ID: K3K13

Calculation Name: 1RKC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RKC

Chain ID: B

ChEMBL ID:

UniProt ID: P54939

Base Structure: X-ray

Registration Date: 2023-03-13

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	26
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-75411.746032
FMO2-HF: Nuclear repulsion	65517.74306
FMO2-HF: Total energy	-9894.002972
FMO2-MP2: Total energy	-9923.675732

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(B:1944:TYR)

Summations of interaction energy for fragment #1(B:1944:TYR)

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.
-30.365	-24.72	2.526	-3.267	-4.904	0.021

Interaction energy analysis for fragmet #1(B:1944:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : -0.008

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	B	1946	LYS	1	0.894	0.946	3.551	-1.096	0.555	-0.003	-0.709	-0.939	-0.001
4	B	1947	LYS	1	0.930	0.968	2.574	-22.918	-20.092	2.496	-2.091	-3.230	0.025
5	B	1948	GLU	-1	-0.781	-0.868	3.528	-5.391	-4.223	0.033	-0.467	-0.735	-0.003
6	B	1949	LEU	0	0.053	0.050	5.877	0.206	0.206	0.000	0.000	0.000	0.000
7	B	1950	ILE	0	0.006	0.002	8.415	0.023	0.023	0.000	0.000	0.000	0.000
8	B	1951	GLU	-1	-0.904	-0.937	5.668	0.038	0.038	0.000	0.000	0.000	0.000
9	B	1952	SER	0	-0.006	-0.020	8.949	-0.085	-0.085	0.000	0.000	0.000	0.000
10	B	1953	ALA	0	0.035	0.012	11.044	-0.017	-0.017	0.000	0.000	0.000	0.000
11	B	1954	ARG	1	0.942	0.985	11.369	-0.962	-0.962	0.000	0.000	0.000	0.000
12	B	1955	LYS	1	0.876	0.932	9.455	-0.319	-0.319	0.000	0.000	0.000	0.000
13	B	1956	VAL	0	-0.018	-0.002	14.774	-0.037	-0.037	0.000	0.000	0.000	0.000
14	B	1957	SER	0	-0.045	-0.034	16.785	0.000	0.000	0.000	0.000	0.000	0.000
15	B	1958	GLU	-1	-0.862	-0.946	15.175	0.439	0.439	0.000	0.000	0.000	0.000
16	B	1959	LYS	1	0.934	0.973	17.816	-0.146	-0.146	0.000	0.000	0.000	0.000
17	B	1960	VAL	0	0.028	0.017	20.950	-0.018	-0.018	0.000	0.000	0.000	0.000
18	B	1961	SER	0	-0.057	-0.040	21.945	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	1962	HIS	0	0.014	-0.009	21.033	-0.022	-0.022	0.000	0.000	0.000	0.000
20	B	1963	VAL	0	-0.039	-0.011	25.182	-0.014	-0.014	0.000	0.000	0.000	0.000
21	B	1964	LEU	0	-0.013	-0.015	26.033	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	1965	ALA	0	0.001	0.008	27.629	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	1966	ALA	0	-0.016	-0.005	29.503	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	1967	LEU	0	-0.044	-0.015	31.948	-0.009	-0.009	0.000	0.000	0.000	0.000
25	B	1968	GLN	0	0.014	0.013	32.402	-0.007	-0.007	0.000	0.000	0.000	0.000
26	B	1969	ALA	0	-0.057	-0.016	35.827	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1944:TYR)