FMO DATABASE

FMODB ID: VRJ11

Calculation Name: 2I3S-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3S

Chain ID: B

ChEMBL ID:

UniProt ID: P41695

Base Structure: X-ray

Registration Date: 2023-06-19

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-145741.599538
FMO2-HF: Nuclear repulsion	130617.555293
FMO2-HF: Total energy	-15124.044245
FMO2-MP2: Total energy	-15168.416505

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:315:LYS)

Summations of interaction energy for fragment #1(B:315:LYS)

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.
-64.742	-61.679	0.299	-1.6	-1.763	-0.012

Interaction energy analysis for fragmet #1(B:315:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.955 / q_NPA : 0.960

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	317	GLU	-1	-0.917	-0.957	2.816	-50.096	-47.033	0.299	-1.600	-1.763	-0.012
4	B	318	ARG	1	0.933	0.967	5.508	27.503	27.503	0.000	0.000	0.000	0.000
5	B	319	ILE	0	0.073	0.042	8.958	-0.621	-0.621	0.000	0.000	0.000	0.000
6	B	320	VAL	0	-0.069	-0.050	11.969	0.752	0.752	0.000	0.000	0.000	0.000
7	B	321	PHE	0	0.054	0.014	14.462	0.897	0.897	0.000	0.000	0.000	0.000
8	B	322	ASN	0	-0.016	0.015	16.588	-0.956	-0.956	0.000	0.000	0.000	0.000
9	B	323	PHE	0	0.084	0.011	14.846	0.372	0.372	0.000	0.000	0.000	0.000
10	B	324	ASN	0	-0.027	-0.008	19.448	0.678	0.678	0.000	0.000	0.000	0.000
11	B	325	LEU	0	-0.061	-0.034	22.293	0.497	0.497	0.000	0.000	0.000	0.000
12	B	326	ILE	0	0.008	0.017	19.372	0.277	0.277	0.000	0.000	0.000	0.000
13	B	327	TYR	0	-0.029	-0.010	18.938	-0.031	-0.031	0.000	0.000	0.000	0.000
14	B	328	PRO	0	-0.004	0.004	23.788	-0.094	-0.094	0.000	0.000	0.000	0.000
15	B	329	GLU	-1	-0.992	-0.948	25.957	-9.514	-9.514	0.000	0.000	0.000	0.000
16	B	330	ASN	0	-0.097	-0.078	23.566	0.007	0.007	0.000	0.000	0.000	0.000
17	B	331	ASP	-1	-0.846	-0.913	26.707	-9.881	-9.881	0.000	0.000	0.000	0.000
18	B	332	GLU	-1	-1.002	-1.023	27.899	-9.519	-9.519	0.000	0.000	0.000	0.000
19	B	333	GLU	-1	-1.011	-1.008	22.948	-12.988	-12.988	0.000	0.000	0.000	0.000
20	B	334	PHE	0	0.025	0.025	25.289	0.248	0.248	0.000	0.000	0.000	0.000
21	B	335	ASN	0	0.014	-0.009	24.432	-0.415	-0.415	0.000	0.000	0.000	0.000
22	B	336	THR	0	-0.004	-0.025	23.144	0.072	0.072	0.000	0.000	0.000	0.000
23	B	337	GLU	-1	-0.897	-0.963	25.448	-11.679	-11.679	0.000	0.000	0.000	0.000
24	B	338	GLU	-1	-0.778	-0.851	28.987	-9.948	-9.948	0.000	0.000	0.000	0.000
25	B	339	ILE	0	0.027	0.020	24.505	0.257	0.257	0.000	0.000	0.000	0.000
26	B	340	LEU	0	-0.055	-0.028	28.628	0.306	0.306	0.000	0.000	0.000	0.000
27	B	341	ALA	0	-0.013	-0.016	30.303	0.336	0.336	0.000	0.000	0.000	0.000
28	B	342	MET	0	-0.010	-0.008	30.277	0.366	0.366	0.000	0.000	0.000	0.000
29	B	343	ILE	0	-0.061	-0.008	28.187	0.214	0.214	0.000	0.000	0.000	0.000
30	B	344	LYS	1	0.868	0.925	32.766	9.580	9.580	0.000	0.000	0.000	0.000
31	B	345	GLY	0	0.010	0.018	35.685	0.277	0.277	0.000	0.000	0.000	0.000
32	B	346	LEU	0	-0.088	-0.048	36.894	0.266	0.266	0.000	0.000	0.000	0.000
33	B	347	TYR	0	-0.034	-0.028	32.237	0.151	0.151	0.000	0.000	0.000	0.000
34	B	348	LYS	1	0.961	0.978	36.592	7.864	7.864	0.000	0.000	0.000	0.000
35	B	349	VAL	0	0.042	0.015	39.343	0.100	0.100	0.000	0.000	0.000	0.000
36	B	350	GLN	0	-0.034	-0.007	42.172	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:315:LYS)