FMO DATABASE

FMODB ID: YNNG2

Calculation Name: 5WB7-F-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: 5WB7

Chain ID: F

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	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	42
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-207895.351928
FMO2-HF: Nuclear repulsion	187797.038389
FMO2-HF: Total energy	-20098.313539
FMO2-MP2: Total energy	-20149.922514

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(F:2:SER)

Summations of interaction energy for fragment #1(F:2: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.
-12.934	-6.974	3.682	-4.666	-4.978	-0.034

Interaction energy analysis for fragmet #1(F:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.022

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	F	4	THR	0	-0.003	0.014	3.874	-0.321	1.040	-0.004	-0.654	-0.704	0.003
4	F	5	LYS	1	0.886	0.951	5.686	0.454	0.454	0.000	0.000	0.000	0.000
5	F	6	CYS	0	0.008	0.002	9.508	-0.169	-0.169	0.000	0.000	0.000	0.000
6	F	7	SER	0	0.071	0.035	11.934	0.126	0.126	0.000	0.000	0.000	0.000
7	F	8	SER	0	0.009	0.015	14.739	0.037	0.037	0.000	0.000	0.000	0.000
8	F	9	ASP	-1	-0.909	-0.954	17.131	-0.432	-0.432	0.000	0.000	0.000	0.000
9	F	10	MET	0	0.008	0.010	14.745	0.057	0.057	0.000	0.000	0.000	0.000
10	F	11	ASN	0	-0.077	-0.059	17.815	0.056	0.056	0.000	0.000	0.000	0.000
11	F	12	GLY	0	0.045	0.031	20.316	0.038	0.038	0.000	0.000	0.000	0.000
12	F	13	TYR	0	-0.013	-0.004	14.438	0.022	0.022	0.000	0.000	0.000	0.000
13	F	14	CYS	0	-0.052	-0.014	11.362	-0.040	-0.040	0.000	0.000	0.000	0.000
14	F	15	LEU	0	0.003	0.000	18.315	-0.007	-0.007	0.000	0.000	0.000	0.000
15	F	16	HIS	1	0.870	0.943	19.997	-0.144	-0.144	0.000	0.000	0.000	0.000
16	F	17	GLY	0	0.074	0.048	17.022	0.061	0.061	0.000	0.000	0.000	0.000
17	F	18	GLN	0	-0.040	-0.016	15.168	-0.086	-0.086	0.000	0.000	0.000	0.000
18	F	20	ILE	0	-0.059	-0.035	7.421	0.125	0.125	0.000	0.000	0.000	0.000
19	F	21	TYR	0	0.013	-0.011	7.130	-0.113	-0.113	0.000	0.000	0.000	0.000
20	F	22	LEU	0	-0.004	-0.002	3.817	-0.776	-0.674	0.000	-0.047	-0.056	0.000
21	F	23	VAL	0	0.040	0.011	2.368	0.339	0.785	0.842	-0.532	-0.756	0.000
22	F	24	ASP	-1	-0.896	-0.954	2.448	-13.411	-9.360	2.844	-3.433	-3.462	-0.037
23	F	25	MET	0	-0.026	-0.011	4.851	0.937	0.937	0.000	0.000	0.000	0.000
24	F	26	SER	0	-0.027	0.003	7.306	0.402	0.402	0.000	0.000	0.000	0.000
25	F	27	GLN	0	0.011	0.021	8.417	0.419	0.419	0.000	0.000	0.000	0.000
26	F	28	ASN	0	-0.004	-0.010	9.153	-0.345	-0.345	0.000	0.000	0.000	0.000
27	F	29	TYR	0	0.010	-0.011	8.713	0.225	0.225	0.000	0.000	0.000	0.000
28	F	31	ARG	1	0.953	0.993	11.221	-0.763	-0.763	0.000	0.000	0.000	0.000
29	F	32	CYS	0	-0.065	-0.029	12.767	-0.056	-0.056	0.000	0.000	0.000	0.000
30	F	33	GLU	-1	-0.895	-0.965	16.315	0.313	0.313	0.000	0.000	0.000	0.000
31	F	34	VAL	0	-0.019	-0.021	19.412	0.008	0.008	0.000	0.000	0.000	0.000
32	F	35	GLY	0	0.047	0.024	20.612	-0.038	-0.038	0.000	0.000	0.000	0.000
33	F	36	TYR	0	-0.031	-0.010	20.372	-0.048	-0.048	0.000	0.000	0.000	0.000
34	F	37	THR	0	-0.005	-0.004	18.657	0.062	0.062	0.000	0.000	0.000	0.000
35	F	38	GLY	0	0.028	0.021	18.514	-0.038	-0.038	0.000	0.000	0.000	0.000
36	F	39	VAL	0	-0.024	-0.016	15.309	0.039	0.039	0.000	0.000	0.000	0.000
37	F	40	ARG	1	0.859	0.907	15.392	0.046	0.046	0.000	0.000	0.000	0.000
38	F	42	GLU	-1	-0.766	-0.877	19.010	0.067	0.067	0.000	0.000	0.000	0.000
39	F	43	HIS	0	-0.020	-0.012	22.260	0.002	0.002	0.000	0.000	0.000	0.000
40	F	44	PHE	0	0.019	0.008	22.994	0.027	0.027	0.000	0.000	0.000	0.000
41	F	45	PHE	0	-0.035	-0.023	22.253	-0.013	-0.013	0.000	0.000	0.000	0.000
42	F	46	LEU	0	0.003	0.008	25.069	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:SER)