FMO DATABASE

FMODB ID: RYY28

Calculation Name: 5WB8-C-Xray372

Preferred Name: Epidermal growth factor receptor erbB1

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 5WB8

Chain ID: C

ChEMBL ID: CHEMBL203

UniProt ID: P00533

Base Structure: X-ray

Registration Date: 2023-09-27

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	34
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-138921.132813
FMO2-HF: Nuclear repulsion	123464.133347
FMO2-HF: Total energy	-15456.999466
FMO2-MP2: Total energy	-15497.956198

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:44:SER)

Summations of interaction energy for fragment #1(C:44:SER)

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.
-2.836	-1.037	-0.011	-0.65	-1.138	0.002

Interaction energy analysis for fragmet #1(C:44:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.004

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	46	CYS	0	-0.049	-0.012	3.723	-1.763	-0.199	-0.010	-0.618	-0.936	0.002
4	C	47	ILE	0	-0.014	0.000	4.456	-1.545	-1.310	-0.001	-0.032	-0.202	0.000
5	C	48	ASN	0	-0.036	-0.015	5.631	0.010	0.010	0.000	0.000	0.000	0.000
6	C	49	GLY	0	0.047	0.004	7.332	0.424	0.424	0.000	0.000	0.000	0.000
7	C	50	ALA	0	-0.047	-0.003	6.696	-0.508	-0.508	0.000	0.000	0.000	0.000
8	C	51	CYS	0	-0.006	-0.023	5.372	0.202	0.202	0.000	0.000	0.000	0.000
9	C	52	ALA	0	-0.002	0.002	7.425	0.019	0.019	0.000	0.000	0.000	0.000
10	C	53	PHE	0	0.002	-0.001	10.745	0.070	0.070	0.000	0.000	0.000	0.000
11	C	54	HIS	0	0.017	0.003	12.328	-0.048	-0.048	0.000	0.000	0.000	0.000
12	C	55	HIS	0	-0.031	-0.031	15.859	0.058	0.058	0.000	0.000	0.000	0.000
13	C	56	GLU	-1	-0.834	-0.908	17.668	0.128	0.128	0.000	0.000	0.000	0.000
14	C	57	LEU	0	-0.095	-0.044	17.495	0.000	0.000	0.000	0.000	0.000	0.000
15	C	58	GLU	-1	-0.921	-0.950	16.373	0.316	0.316	0.000	0.000	0.000	0.000
16	C	59	LYS	1	0.916	0.959	13.761	-0.205	-0.205	0.000	0.000	0.000	0.000
17	C	60	ALA	0	-0.028	-0.008	8.517	-0.055	-0.055	0.000	0.000	0.000	0.000
18	C	61	ILE	0	0.010	0.001	10.666	-0.030	-0.030	0.000	0.000	0.000	0.000
19	C	63	ARG	1	0.970	0.984	9.796	0.400	0.400	0.000	0.000	0.000	0.000
20	C	64	CYS	0	-0.103	-0.013	8.190	-0.569	-0.569	0.000	0.000	0.000	0.000
21	C	65	PHE	0	0.034	0.009	9.270	0.092	0.092	0.000	0.000	0.000	0.000
22	C	66	THR	0	-0.031	-0.023	13.773	0.043	0.043	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.041	0.026	16.185	0.058	0.058	0.000	0.000	0.000	0.000
24	C	68	TYR	0	-0.020	-0.012	12.643	-0.020	-0.020	0.000	0.000	0.000	0.000
25	C	69	THR	0	-0.012	-0.030	14.515	0.044	0.044	0.000	0.000	0.000	0.000
26	C	70	GLY	0	0.037	0.024	13.900	-0.050	-0.050	0.000	0.000	0.000	0.000
27	C	71	GLU	-1	-0.931	-0.954	11.628	0.164	0.164	0.000	0.000	0.000	0.000
28	C	72	ARG	1	0.916	0.957	4.909	0.440	0.440	0.000	0.000	0.000	0.000
29	C	74	GLU	-1	-0.758	-0.890	10.102	-0.623	-0.623	0.000	0.000	0.000	0.000
30	C	75	HIS	0	-0.055	-0.032	11.191	0.101	0.101	0.000	0.000	0.000	0.000
31	C	76	LEU	0	0.022	0.007	14.804	-0.050	-0.050	0.000	0.000	0.000	0.000
32	C	77	THR	0	-0.038	-0.010	16.894	0.040	0.040	0.000	0.000	0.000	0.000
33	C	78	LEU	0	0.001	0.002	19.407	0.006	0.006	0.000	0.000	0.000	0.000
34	C	79	THR	0	-0.005	0.004	22.842	0.015	0.015	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:44:SER)