FMO DATABASE

FMODB ID: ZY8KN

Calculation Name: 2RF9-C-Xray372

Preferred Name: Epidermal growth factor receptor erbB1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2RF9

Chain ID: C

ChEMBL ID: CHEMBL203

UniProt ID: P00533

Base Structure: X-ray

Registration Date: 2023-06-20

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	27
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-72041.421506
FMO2-HF: Nuclear repulsion	61710.627271
FMO2-HF: Total energy	-10330.794234
FMO2-MP2: Total energy	-10360.643024

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(C:336:LYS)

Summations of interaction energy for fragment #1(C:336: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.
12.904	16.737	-0.009	-1.844	-1.98	-0.003

Interaction energy analysis for fragmet #1(C:336:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.989 / q_NPA : 0.966

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

Sort

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	C	338	LEU	0	0.040	0.025	3.367	-2.785	1.048	-0.009	-1.844	-1.980	-0.003
4	C	339	PRO	0	0.031	0.015	5.906	0.522	0.522	0.000	0.000	0.000	0.000
5	C	340	SER	0	0.008	0.013	8.736	0.776	0.776	0.000	0.000	0.000	0.000
6	C	341	TYR	0	0.000	0.001	10.526	0.979	0.979	0.000	0.000	0.000	0.000
7	C	342	LEU	0	0.034	0.011	13.778	-0.038	-0.038	0.000	0.000	0.000	0.000
8	C	343	ASN	0	0.002	-0.004	15.397	0.930	0.930	0.000	0.000	0.000	0.000
9	C	344	GLY	0	-0.015	-0.002	14.187	0.471	0.471	0.000	0.000	0.000	0.000
10	C	345	VAL	0	-0.022	-0.009	15.217	-0.082	-0.082	0.000	0.000	0.000	0.000
11	C	346	MET	0	0.017	0.005	15.644	-0.946	-0.946	0.000	0.000	0.000	0.000
12	C	347	PRO	0	-0.035	-0.007	16.667	0.791	0.791	0.000	0.000	0.000	0.000
13	C	348	PRO	0	0.009	-0.005	19.615	-0.420	-0.420	0.000	0.000	0.000	0.000
14	C	349	THR	0	-0.016	-0.014	20.206	-0.081	-0.081	0.000	0.000	0.000	0.000
15	C	350	GLN	0	0.030	0.030	14.156	0.558	0.558	0.000	0.000	0.000	0.000
16	C	351	SER	0	-0.015	-0.002	17.916	0.516	0.516	0.000	0.000	0.000	0.000
17	C	352	PHE	0	0.031	-0.010	13.611	-0.928	-0.928	0.000	0.000	0.000	0.000
18	C	353	ALA	0	-0.013	0.027	18.867	0.094	0.094	0.000	0.000	0.000	0.000
19	C	354	PRO	0	-0.012	-0.035	21.015	-0.435	-0.435	0.000	0.000	0.000	0.000
20	C	355	ASP	-1	-0.835	-0.904	18.527	-15.782	-15.782	0.000	0.000	0.000	0.000
21	C	356	PRO	0	0.037	-0.005	21.234	0.262	0.262	0.000	0.000	0.000	0.000
22	C	357	LYS	1	0.867	0.939	16.507	18.168	18.168	0.000	0.000	0.000	0.000
23	C	358	TYR	0	-0.017	-0.014	15.505	-0.314	-0.314	0.000	0.000	0.000	0.000
24	C	359	VAL	0	-0.028	0.014	21.745	0.394	0.394	0.000	0.000	0.000	0.000
25	C	360	SER	0	0.000	0.000	24.895	0.190	0.190	0.000	0.000	0.000	0.000
26	C	361	SER	0	0.017	0.001	28.128	0.082	0.082	0.000	0.000	0.000	0.000
27	C	362	LYS	1	0.959	0.989	31.307	9.982	9.982	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:336:LYS)