FMO DATABASE

FMODB ID: Q16ZY

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	OptAll
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	-72069.079288
FMO2-HF: Nuclear repulsion	61738.079903
FMO2-HF: Total energy	-10330.999385
FMO2-MP2: Total energy	-10360.823719

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.
15.557	17.407	-0.005	-0.638	-1.207	0.001

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 : 0.972 / 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

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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	0.030	0.028	3.391	-2.381	-0.531	-0.005	-0.638	-1.207	0.001
4	C	339	PRO	0	0.029	0.013	5.876	0.982	0.982	0.000	0.000	0.000	0.000
5	C	340	SER	0	0.006	0.012	8.914	0.957	0.957	0.000	0.000	0.000	0.000
6	C	341	TYR	0	0.000	-0.001	10.622	0.974	0.974	0.000	0.000	0.000	0.000
7	C	342	LEU	0	0.055	0.026	13.700	0.053	0.053	0.000	0.000	0.000	0.000
8	C	343	ASN	0	-0.009	-0.013	15.762	0.769	0.769	0.000	0.000	0.000	0.000
9	C	344	GLY	0	0.014	0.008	13.976	0.445	0.445	0.000	0.000	0.000	0.000
10	C	345	VAL	0	-0.038	-0.017	15.015	-0.128	-0.128	0.000	0.000	0.000	0.000
11	C	346	MET	0	-0.004	-0.002	15.757	-0.951	-0.951	0.000	0.000	0.000	0.000
12	C	347	PRO	0	-0.022	0.004	16.698	0.879	0.879	0.000	0.000	0.000	0.000
13	C	348	PRO	0	-0.004	-0.017	19.491	-0.440	-0.440	0.000	0.000	0.000	0.000
14	C	349	THR	0	-0.005	0.003	20.356	0.301	0.301	0.000	0.000	0.000	0.000
15	C	350	GLN	0	0.021	0.014	13.680	0.802	0.802	0.000	0.000	0.000	0.000
16	C	351	SER	0	-0.029	-0.007	18.003	0.628	0.628	0.000	0.000	0.000	0.000
17	C	352	PHE	0	0.023	-0.008	13.429	-0.937	-0.937	0.000	0.000	0.000	0.000
18	C	353	ALA	0	0.001	0.016	18.556	0.177	0.177	0.000	0.000	0.000	0.000
19	C	354	PRO	0	-0.011	-0.015	20.805	-0.455	-0.455	0.000	0.000	0.000	0.000
20	C	355	ASP	-1	-0.819	-0.916	18.170	-15.859	-15.859	0.000	0.000	0.000	0.000
21	C	356	PRO	0	0.028	0.007	21.229	0.105	0.105	0.000	0.000	0.000	0.000
22	C	357	LYS	1	0.866	0.947	15.860	18.855	18.855	0.000	0.000	0.000	0.000
23	C	358	TYR	0	-0.012	-0.015	15.235	-0.331	-0.331	0.000	0.000	0.000	0.000
24	C	359	VAL	0	-0.044	-0.010	21.969	0.431	0.431	0.000	0.000	0.000	0.000
25	C	360	SER	0	0.005	0.003	24.986	0.337	0.337	0.000	0.000	0.000	0.000
26	C	361	SER	0	0.050	0.026	28.068	0.053	0.053	0.000	0.000	0.000	0.000
27	C	362	LYS	1	0.919	0.966	30.963	10.291	10.291	0.000	0.000	0.000	0.000

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