FMO DATABASE

FMODB ID: QNN6Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-138812.44997
FMO2-HF: Nuclear repulsion	123355.285588
FMO2-HF: Total energy	-15457.164382
FMO2-MP2: Total energy	-15498.133155

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.
-3.067	-1.236	-0.014	-0.618	-1.2	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 : 0.004 / q_NPA : -0.007

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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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	-0.039	-0.006	3.802	-2.923	-1.434	-0.012	-0.577	-0.901	0.002
4	C	47	ILE	0	-0.010	0.004	4.417	-0.232	0.004	-0.001	-0.026	-0.209	0.000
5	C	48	ASN	0	-0.050	-0.029	5.616	-0.090	-0.090	0.000	0.000	0.000	0.000
6	C	49	GLY	0	0.048	0.000	7.457	-0.106	-0.106	0.000	0.000	0.000	0.000
7	C	50	ALA	0	-0.053	-0.006	7.510	0.503	0.503	0.000	0.000	0.000	0.000
8	C	51	CYS	0	-0.008	-0.020	6.080	-0.369	-0.369	0.000	0.000	0.000	0.000
9	C	52	ALA	0	0.000	0.002	8.230	-0.232	-0.232	0.000	0.000	0.000	0.000
10	C	53	PHE	0	0.006	0.002	10.708	0.010	0.010	0.000	0.000	0.000	0.000
11	C	54	HIS	0	0.024	0.012	12.554	-0.115	-0.115	0.000	0.000	0.000	0.000
12	C	55	HIS	0	0.001	-0.021	16.064	0.068	0.068	0.000	0.000	0.000	0.000
13	C	56	GLU	-1	-0.852	-0.915	17.525	0.354	0.354	0.000	0.000	0.000	0.000
14	C	57	LEU	0	-0.083	-0.038	17.606	-0.033	-0.033	0.000	0.000	0.000	0.000
15	C	58	GLU	-1	-0.942	-0.961	16.017	0.442	0.442	0.000	0.000	0.000	0.000
16	C	59	LYS	1	0.878	0.938	13.464	-0.502	-0.502	0.000	0.000	0.000	0.000
17	C	60	ALA	0	-0.014	-0.004	8.629	0.036	0.036	0.000	0.000	0.000	0.000
18	C	61	ILE	0	0.005	0.002	10.767	-0.095	-0.095	0.000	0.000	0.000	0.000
19	C	63	ARG	1	0.967	0.983	10.517	-0.848	-0.848	0.000	0.000	0.000	0.000
20	C	64	CYS	0	-0.105	-0.016	8.170	0.027	0.027	0.000	0.000	0.000	0.000
21	C	65	PHE	0	0.027	0.009	9.097	0.001	0.001	0.000	0.000	0.000	0.000
22	C	66	THR	0	-0.018	-0.013	13.958	-0.020	-0.020	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.034	0.022	16.132	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	68	TYR	0	-0.022	-0.011	12.693	-0.025	-0.025	0.000	0.000	0.000	0.000
25	C	69	THR	0	-0.012	-0.029	14.497	0.076	0.076	0.000	0.000	0.000	0.000
26	C	70	GLY	0	0.039	0.025	13.880	-0.068	-0.068	0.000	0.000	0.000	0.000
27	C	71	GLU	-1	-0.882	-0.917	11.692	0.685	0.685	0.000	0.000	0.000	0.000
28	C	72	ARG	1	0.926	0.958	4.673	0.422	0.528	-0.001	-0.015	-0.090	0.000
29	C	74	GLU	-1	-0.752	-0.870	10.092	0.019	0.019	0.000	0.000	0.000	0.000
30	C	75	HIS	0	-0.049	-0.035	11.185	-0.099	-0.099	0.000	0.000	0.000	0.000
31	C	76	LEU	0	0.021	0.008	14.744	0.044	0.044	0.000	0.000	0.000	0.000
32	C	77	THR	0	-0.034	-0.010	16.883	0.013	0.013	0.000	0.000	0.000	0.000
33	C	78	LEU	0	-0.008	-0.003	19.388	-0.020	-0.020	0.000	0.000	0.000	0.000
34	C	79	THR	0	0.000	0.007	22.826	0.013	0.013	0.000	0.000	0.000	0.000

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