FMO DATABASE

FMODB ID: 5NN6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-207368.612685
FMO2-HF: Nuclear repulsion	187270.421291
FMO2-HF: Total energy	-20098.191395
FMO2-MP2: Total energy	-20149.776596

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.
-1.081	1.569	0.024	-1.138	-1.536	-0.002

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 : 0.034 / q_NPA : 0.002

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	-0.016	0.001	3.805	1.576	2.777	-0.014	-0.527	-0.660	0.002
4	F	5	LYS	1	0.921	0.964	5.709	0.611	0.611	0.000	0.000	0.000	0.000
5	F	6	CYS	0	0.018	0.006	9.456	-0.183	-0.183	0.000	0.000	0.000	0.000
6	F	7	SER	0	0.066	0.038	11.824	0.122	0.122	0.000	0.000	0.000	0.000
7	F	8	SER	0	0.009	0.004	14.676	0.011	0.011	0.000	0.000	0.000	0.000
8	F	9	ASP	-1	-0.917	-0.956	17.304	-0.425	-0.425	0.000	0.000	0.000	0.000
9	F	10	MET	0	-0.029	-0.013	15.334	0.037	0.037	0.000	0.000	0.000	0.000
10	F	11	ASN	0	-0.066	-0.047	18.069	0.014	0.014	0.000	0.000	0.000	0.000
11	F	12	GLY	0	0.057	0.024	20.612	0.021	0.021	0.000	0.000	0.000	0.000
12	F	13	TYR	0	-0.008	0.001	15.421	0.043	0.043	0.000	0.000	0.000	0.000
13	F	14	CYS	0	-0.056	-0.011	11.885	-0.024	-0.024	0.000	0.000	0.000	0.000
14	F	15	LEU	0	0.007	0.007	18.424	0.016	0.016	0.000	0.000	0.000	0.000
15	F	16	HIS	1	0.886	0.954	20.063	0.100	0.100	0.000	0.000	0.000	0.000
16	F	17	GLY	0	0.085	0.052	16.612	0.027	0.027	0.000	0.000	0.000	0.000
17	F	18	GLN	0	-0.049	-0.018	14.237	-0.049	-0.049	0.000	0.000	0.000	0.000
18	F	20	ILE	0	-0.063	-0.031	7.215	0.056	0.056	0.000	0.000	0.000	0.000
19	F	21	TYR	0	0.046	0.004	7.428	0.011	0.011	0.000	0.000	0.000	0.000
20	F	22	LEU	0	-0.005	0.002	4.099	-1.170	-1.124	-0.001	-0.020	-0.025	0.000
21	F	23	VAL	0	0.032	0.010	3.583	0.792	1.010	0.006	-0.034	-0.190	0.000
22	F	24	ASP	-1	-0.912	-0.952	3.335	-3.407	-2.222	0.033	-0.557	-0.661	-0.004
23	F	25	MET	0	-0.028	-0.016	5.756	0.506	0.506	0.000	0.000	0.000	0.000
24	F	26	SER	0	-0.015	0.001	7.829	0.235	0.235	0.000	0.000	0.000	0.000
25	F	27	GLN	0	-0.014	0.006	9.216	0.285	0.285	0.000	0.000	0.000	0.000
26	F	28	ASN	0	-0.004	-0.005	9.649	-0.395	-0.395	0.000	0.000	0.000	0.000
27	F	29	TYR	0	-0.005	-0.020	9.399	0.208	0.208	0.000	0.000	0.000	0.000
28	F	31	ARG	1	0.964	0.993	10.413	-0.117	-0.117	0.000	0.000	0.000	0.000
29	F	32	CYS	0	-0.070	-0.027	12.382	-0.002	-0.002	0.000	0.000	0.000	0.000
30	F	33	GLU	-1	-0.912	-0.982	15.930	-0.020	-0.020	0.000	0.000	0.000	0.000
31	F	34	VAL	0	-0.003	-0.017	18.453	0.000	0.000	0.000	0.000	0.000	0.000
32	F	35	GLY	0	0.033	0.014	19.399	-0.009	-0.009	0.000	0.000	0.000	0.000
33	F	36	TYR	0	-0.014	-0.001	20.087	-0.013	-0.013	0.000	0.000	0.000	0.000
34	F	37	THR	0	-0.020	-0.017	18.681	0.008	0.008	0.000	0.000	0.000	0.000
35	F	38	GLY	0	0.034	0.024	18.809	-0.010	-0.010	0.000	0.000	0.000	0.000
36	F	39	VAL	0	0.011	0.008	15.718	-0.014	-0.014	0.000	0.000	0.000	0.000
37	F	40	ARG	1	0.861	0.915	16.154	0.191	0.191	0.000	0.000	0.000	0.000
38	F	42	GLU	-1	-0.802	-0.910	19.128	-0.139	-0.139	0.000	0.000	0.000	0.000
39	F	43	HIS	0	-0.034	-0.017	22.491	0.015	0.015	0.000	0.000	0.000	0.000
40	F	44	PHE	0	0.015	0.018	22.997	0.004	0.004	0.000	0.000	0.000	0.000
41	F	45	PHE	0	-0.037	-0.022	22.067	0.001	0.001	0.000	0.000	0.000	0.000
42	F	46	LEU	0	0.026	0.018	24.846	0.006	0.006	0.000	0.000	0.000	0.000

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