FMO DATABASE

FMODB ID: 4LLZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-207110.849479
FMO2-HF: Nuclear repulsion	187012.789536
FMO2-HF: Total energy	-20098.059943
FMO2-MP2: Total energy	-20149.640169

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.
2.455	4.199	-0.008	-0.622	-1.113	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 : 0.038 / q_NPA : 0.003

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	-0.005	0.005	3.720	1.495	2.728	-0.015	-0.543	-0.676	0.002
4	F	5	LYS	1	0.934	0.973	5.714	0.505	0.505	0.000	0.000	0.000	0.000
5	F	6	CYS	0	0.029	0.012	9.460	-0.145	-0.145	0.000	0.000	0.000	0.000
6	F	7	SER	0	0.070	0.039	11.830	0.094	0.094	0.000	0.000	0.000	0.000
7	F	8	SER	0	0.001	-0.011	14.681	0.016	0.016	0.000	0.000	0.000	0.000
8	F	9	ASP	-1	-0.914	-0.946	17.310	-0.294	-0.294	0.000	0.000	0.000	0.000
9	F	10	MET	0	-0.028	-0.012	15.278	0.031	0.031	0.000	0.000	0.000	0.000
10	F	11	ASN	0	-0.070	-0.045	18.069	0.012	0.012	0.000	0.000	0.000	0.000
11	F	12	GLY	0	0.056	0.022	20.619	0.015	0.015	0.000	0.000	0.000	0.000
12	F	13	TYR	0	-0.013	0.000	15.520	0.027	0.027	0.000	0.000	0.000	0.000
13	F	14	CYS	0	-0.053	-0.013	11.572	-0.040	-0.040	0.000	0.000	0.000	0.000
14	F	15	LEU	0	0.010	0.010	18.231	0.009	0.009	0.000	0.000	0.000	0.000
15	F	16	HIS	1	0.928	0.975	19.958	0.044	0.044	0.000	0.000	0.000	0.000
16	F	17	GLY	0	0.081	0.049	16.665	0.025	0.025	0.000	0.000	0.000	0.000
17	F	18	GLN	0	-0.060	-0.016	14.247	-0.037	-0.037	0.000	0.000	0.000	0.000
18	F	20	ILE	0	-0.063	-0.040	6.702	0.026	0.026	0.000	0.000	0.000	0.000
19	F	21	TYR	0	0.043	0.004	7.248	0.156	0.156	0.000	0.000	0.000	0.000
20	F	22	LEU	0	-0.014	-0.004	3.836	-1.182	-1.061	0.002	-0.040	-0.082	0.000
21	F	23	VAL	0	0.026	0.004	3.621	0.596	0.815	0.006	-0.033	-0.191	0.000
22	F	24	ASP	-1	-0.897	-0.937	4.465	0.702	0.873	-0.001	-0.006	-0.164	0.000
23	F	25	MET	0	-0.049	-0.029	5.762	0.263	0.263	0.000	0.000	0.000	0.000
24	F	26	SER	0	-0.014	0.003	7.832	0.086	0.086	0.000	0.000	0.000	0.000
25	F	27	GLN	0	-0.023	-0.017	9.211	0.241	0.241	0.000	0.000	0.000	0.000
26	F	28	ASN	0	-0.003	-0.006	9.645	-0.297	-0.297	0.000	0.000	0.000	0.000
27	F	29	TYR	0	0.016	0.007	9.283	0.169	0.169	0.000	0.000	0.000	0.000
28	F	31	ARG	1	0.962	0.994	10.585	-0.096	-0.096	0.000	0.000	0.000	0.000
29	F	32	CYS	0	-0.090	-0.036	12.444	-0.015	-0.015	0.000	0.000	0.000	0.000
30	F	33	GLU	-1	-0.937	-0.987	15.970	0.010	0.010	0.000	0.000	0.000	0.000
31	F	34	VAL	0	0.002	-0.014	18.692	0.004	0.004	0.000	0.000	0.000	0.000
32	F	35	GLY	0	0.033	0.013	19.644	-0.010	-0.010	0.000	0.000	0.000	0.000
33	F	36	TYR	0	-0.026	-0.006	20.055	-0.013	-0.013	0.000	0.000	0.000	0.000
34	F	37	THR	0	-0.025	-0.018	18.366	0.012	0.012	0.000	0.000	0.000	0.000
35	F	38	GLY	0	0.043	0.028	18.502	-0.014	-0.014	0.000	0.000	0.000	0.000
36	F	39	VAL	0	0.016	0.007	15.729	-0.007	-0.007	0.000	0.000	0.000	0.000
37	F	40	ARG	1	0.870	0.925	15.812	0.107	0.107	0.000	0.000	0.000	0.000
38	F	42	GLU	-1	-0.816	-0.924	18.834	-0.058	-0.058	0.000	0.000	0.000	0.000
39	F	43	HIS	0	-0.043	-0.021	22.131	0.009	0.009	0.000	0.000	0.000	0.000
40	F	44	PHE	0	0.018	0.022	22.746	0.005	0.005	0.000	0.000	0.000	0.000
41	F	45	PHE	0	-0.026	-0.020	21.872	0.001	0.001	0.000	0.000	0.000	0.000
42	F	46	LEU	0	0.017	0.016	24.632	0.003	0.003	0.000	0.000	0.000	0.000

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