FMO DATABASE

FMODB ID: R5Q38

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

Total energy (hartree)

FMO2-HF: Electronic energy	-75323.185376
FMO2-HF: Nuclear repulsion	65429.834442
FMO2-HF: Total energy	-9893.350934
FMO2-MP2: Total energy	-9923.0757

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.
-19.281	-15.675	0.003	-1.431	-2.178	-0.001

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 : -0.029 / q_NPA : -0.036

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	0.878	0.944	3.704	-3.668	-1.416	-0.018	-1.092	-1.142	-0.002
4	B	1947	LYS	1	0.951	0.971	3.324	-9.643	-8.717	0.022	-0.229	-0.719	0.001
5	B	1948	GLU	-1	-0.777	-0.894	4.091	-4.608	-4.239	0.000	-0.110	-0.259	0.000
6	B	1949	LEU	0	0.022	0.015	6.287	0.114	0.114	0.000	0.000	0.000	0.000
7	B	1950	ILE	0	-0.013	-0.009	8.219	0.064	0.064	0.000	0.000	0.000	0.000
8	B	1951	GLU	-1	-0.954	-0.975	5.138	-1.208	-1.149	-0.001	0.000	-0.058	0.000
9	B	1952	SER	0	-0.059	-0.028	9.329	-0.006	-0.006	0.000	0.000	0.000	0.000
10	B	1953	ALA	0	0.052	0.014	11.389	-0.015	-0.015	0.000	0.000	0.000	0.000
11	B	1954	ARG	1	0.932	0.990	11.138	-0.608	-0.608	0.000	0.000	0.000	0.000
12	B	1955	LYS	1	0.951	0.991	10.664	0.047	0.047	0.000	0.000	0.000	0.000
13	B	1956	VAL	0	-0.018	-0.003	15.283	0.007	0.007	0.000	0.000	0.000	0.000
14	B	1957	SER	0	-0.026	-0.018	17.261	0.014	0.014	0.000	0.000	0.000	0.000
15	B	1958	GLU	-1	-0.824	-0.938	15.640	0.192	0.192	0.000	0.000	0.000	0.000
16	B	1959	LYS	1	0.941	0.973	17.580	0.052	0.052	0.000	0.000	0.000	0.000
17	B	1960	VAL	0	0.002	0.010	21.489	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	1961	SER	0	-0.045	-0.028	22.414	0.008	0.008	0.000	0.000	0.000	0.000
19	B	1962	HIS	0	0.015	-0.004	22.124	0.000	0.000	0.000	0.000	0.000	0.000
20	B	1963	VAL	0	0.003	-0.002	25.776	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	1964	LEU	0	-0.072	-0.025	26.400	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	1965	ALA	0	0.032	0.026	28.368	0.005	0.005	0.000	0.000	0.000	0.000
23	B	1966	ALA	0	-0.003	-0.004	30.110	0.002	0.002	0.000	0.000	0.000	0.000
24	B	1967	LEU	0	-0.051	-0.026	32.754	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	1968	GLN	0	-0.010	0.002	31.798	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	1969	ALA	0	-0.022	0.004	36.236	-0.001	-0.001	0.000	0.000	0.000	0.000

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