FMO DATABASE

FMODB ID: Q1K9Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-75121.961619
FMO2-HF: Nuclear repulsion	65228.2211
FMO2-HF: Total energy	-9893.740519
FMO2-MP2: Total energy	-9923.432171

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.
-18.657	-14.857	0.197	-1.596	-2.4	0

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 : -0.015 / q_NPA : -0.026

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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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	0.920	0.965	3.763	-3.746	-1.443	-0.017	-1.128	-1.158	-0.002
4	B	1947	LYS	1	0.950	0.977	2.728	-9.900	-8.750	0.215	-0.375	-0.989	0.002
5	B	1948	GLU	-1	-0.767	-0.883	4.342	-3.979	-3.632	-0.001	-0.093	-0.253	0.000
6	B	1949	LEU	0	0.046	0.055	6.313	0.033	0.033	0.000	0.000	0.000	0.000
7	B	1950	ILE	0	0.012	-0.010	8.433	0.019	0.019	0.000	0.000	0.000	0.000
8	B	1951	GLU	-1	-0.912	-0.937	6.073	-0.539	-0.539	0.000	0.000	0.000	0.000
9	B	1952	SER	0	-0.042	-0.043	9.351	-0.034	-0.034	0.000	0.000	0.000	0.000
10	B	1953	ALA	0	0.033	0.012	11.413	-0.036	-0.036	0.000	0.000	0.000	0.000
11	B	1954	ARG	1	0.942	0.992	11.355	-0.659	-0.659	0.000	0.000	0.000	0.000
12	B	1955	LYS	1	0.868	0.929	9.813	-0.002	-0.002	0.000	0.000	0.000	0.000
13	B	1956	VAL	0	-0.006	-0.001	15.303	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	1957	SER	0	-0.040	-0.030	17.201	0.005	0.005	0.000	0.000	0.000	0.000
15	B	1958	GLU	-1	-0.838	-0.928	15.851	0.251	0.251	0.000	0.000	0.000	0.000
16	B	1959	LYS	1	0.929	0.967	17.668	-0.030	-0.030	0.000	0.000	0.000	0.000
17	B	1960	VAL	0	0.003	0.008	21.508	-0.015	-0.015	0.000	0.000	0.000	0.000
18	B	1961	SER	0	-0.052	-0.037	22.510	0.005	0.005	0.000	0.000	0.000	0.000
19	B	1962	HIS	0	0.013	-0.006	21.605	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	1963	VAL	0	-0.010	-0.002	25.794	-0.009	-0.009	0.000	0.000	0.000	0.000
21	B	1964	LEU	0	-0.060	-0.018	26.679	-0.005	-0.005	0.000	0.000	0.000	0.000
22	B	1965	ALA	0	0.039	0.023	28.329	0.003	0.003	0.000	0.000	0.000	0.000
23	B	1966	ALA	0	-0.013	-0.005	30.128	0.000	0.000	0.000	0.000	0.000	0.000
24	B	1967	LEU	0	-0.047	-0.024	32.925	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	1968	GLN	0	-0.004	-0.001	32.101	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	1969	ALA	0	-0.018	0.007	36.252	-0.002	-0.002	0.000	0.000	0.000	0.000

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