FMO DATABASE

FMODB ID: R5268

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

Total energy (hartree)

FMO2-HF: Electronic energy	-71972.690109
FMO2-HF: Nuclear repulsion	61641.813048
FMO2-HF: Total energy	-10330.877061
FMO2-MP2: Total energy	-10360.718242

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.
13.068	17.003	-0.015	-1.939	-1.981	-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 : 0.987 / q_NPA : 0.964

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	0.049	0.031	3.429	-3.012	0.923	-0.015	-1.939	-1.981	-0.003
4	C	339	PRO	0	0.038	0.019	5.848	0.524	0.524	0.000	0.000	0.000	0.000
5	C	340	SER	0	-0.003	0.006	8.657	0.785	0.785	0.000	0.000	0.000	0.000
6	C	341	TYR	0	0.003	-0.002	10.490	0.886	0.886	0.000	0.000	0.000	0.000
7	C	342	LEU	0	0.036	0.012	13.737	-0.034	-0.034	0.000	0.000	0.000	0.000
8	C	343	ASN	0	0.008	0.003	15.368	0.917	0.917	0.000	0.000	0.000	0.000
9	C	344	GLY	0	-0.018	-0.005	14.147	0.466	0.466	0.000	0.000	0.000	0.000
10	C	345	VAL	0	-0.015	-0.009	15.178	-0.077	-0.077	0.000	0.000	0.000	0.000
11	C	346	MET	0	0.015	0.009	15.809	-1.045	-1.045	0.000	0.000	0.000	0.000
12	C	347	PRO	0	-0.030	-0.006	16.648	0.786	0.786	0.000	0.000	0.000	0.000
13	C	348	PRO	0	0.008	-0.003	19.520	-0.421	-0.421	0.000	0.000	0.000	0.000
14	C	349	THR	0	-0.007	-0.005	20.164	0.177	0.177	0.000	0.000	0.000	0.000
15	C	350	GLN	0	0.010	0.015	13.799	0.761	0.761	0.000	0.000	0.000	0.000
16	C	351	SER	0	-0.025	-0.003	17.900	0.523	0.523	0.000	0.000	0.000	0.000
17	C	352	PHE	0	0.032	-0.012	13.685	-0.937	-0.937	0.000	0.000	0.000	0.000
18	C	353	ALA	0	-0.008	0.027	18.941	0.089	0.089	0.000	0.000	0.000	0.000
19	C	354	PRO	0	-0.004	-0.029	21.115	-0.419	-0.419	0.000	0.000	0.000	0.000
20	C	355	ASP	-1	-0.838	-0.916	18.138	-16.050	-16.050	0.000	0.000	0.000	0.000
21	C	356	PRO	0	0.031	0.001	21.360	0.246	0.246	0.000	0.000	0.000	0.000
22	C	357	LYS	1	0.862	0.942	16.267	18.511	18.511	0.000	0.000	0.000	0.000
23	C	358	TYR	0	-0.017	-0.020	15.223	-0.247	-0.247	0.000	0.000	0.000	0.000
24	C	359	VAL	0	-0.022	0.015	21.816	0.373	0.373	0.000	0.000	0.000	0.000
25	C	360	SER	0	-0.007	0.000	24.976	0.179	0.179	0.000	0.000	0.000	0.000
26	C	361	SER	0	0.023	0.004	28.204	0.075	0.075	0.000	0.000	0.000	0.000
27	C	362	LYS	1	0.963	0.990	31.398	10.012	10.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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