FMO DATABASE

FMODB ID: K2253

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

Total energy (hartree)

FMO2-HF: Electronic energy	-138605.464095
FMO2-HF: Nuclear repulsion	123148.239077
FMO2-HF: Total energy	-15457.225018
FMO2-MP2: Total energy	-15498.189215

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.
-1.918	0.0060000000000001	-0.013	-0.725	-1.187	0.001

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 : 0.013 / q_NPA : -0.001

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	-0.050	-0.005	3.849	-2.630	-1.151	-0.011	-0.634	-0.834	0.001
4	C	47	ILE	0	-0.010	-0.001	4.568	-0.175	0.063	-0.001	-0.020	-0.217	0.000
5	C	48	ASN	0	-0.025	-0.016	5.480	-0.010	-0.010	0.000	0.000	0.000	0.000
6	C	49	GLY	0	0.047	0.007	7.475	-0.111	-0.111	0.000	0.000	0.000	0.000
7	C	50	ALA	0	-0.030	0.004	7.551	0.486	0.486	0.000	0.000	0.000	0.000
8	C	51	CYS	0	-0.014	-0.020	6.321	0.110	0.110	0.000	0.000	0.000	0.000
9	C	52	ALA	0	-0.006	0.005	8.459	-0.217	-0.217	0.000	0.000	0.000	0.000
10	C	53	PHE	0	0.023	0.001	10.702	0.099	0.099	0.000	0.000	0.000	0.000
11	C	54	HIS	0	0.015	0.014	12.494	-0.099	-0.099	0.000	0.000	0.000	0.000
12	C	55	HIS	0	0.009	-0.019	16.075	0.044	0.044	0.000	0.000	0.000	0.000
13	C	56	GLU	-1	-0.846	-0.914	17.509	0.351	0.351	0.000	0.000	0.000	0.000
14	C	57	LEU	0	-0.075	-0.028	17.736	-0.043	-0.043	0.000	0.000	0.000	0.000
15	C	58	GLU	-1	-0.956	-0.974	16.339	0.405	0.405	0.000	0.000	0.000	0.000
16	C	59	LYS	1	0.864	0.933	13.287	-0.466	-0.466	0.000	0.000	0.000	0.000
17	C	60	ALA	0	0.003	0.005	8.599	0.050	0.050	0.000	0.000	0.000	0.000
18	C	61	ILE	0	0.003	-0.006	10.684	-0.215	-0.215	0.000	0.000	0.000	0.000
19	C	63	ARG	1	0.952	0.972	10.561	-0.846	-0.846	0.000	0.000	0.000	0.000
20	C	64	CYS	0	-0.120	-0.030	7.863	0.062	0.062	0.000	0.000	0.000	0.000
21	C	65	PHE	0	0.022	0.007	8.993	-0.009	-0.009	0.000	0.000	0.000	0.000
22	C	66	THR	0	-0.008	-0.030	13.793	-0.031	-0.031	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.029	0.039	15.933	-0.015	-0.015	0.000	0.000	0.000	0.000
24	C	68	TYR	0	-0.037	-0.010	12.005	-0.028	-0.028	0.000	0.000	0.000	0.000
25	C	69	THR	0	-0.006	-0.020	14.292	0.075	0.075	0.000	0.000	0.000	0.000
26	C	70	GLY	0	0.043	0.029	13.560	-0.066	-0.066	0.000	0.000	0.000	0.000
27	C	71	GLU	-1	-0.881	-0.919	11.106	0.564	0.564	0.000	0.000	0.000	0.000
28	C	72	ARG	1	0.922	0.952	4.165	0.890	1.097	-0.001	-0.071	-0.136	0.000
29	C	74	GLU	-1	-0.757	-0.873	9.877	-0.060	-0.060	0.000	0.000	0.000	0.000
30	C	75	HIS	0	-0.046	-0.024	10.906	-0.091	-0.091	0.000	0.000	0.000	0.000
31	C	76	LEU	0	0.031	0.010	14.352	0.046	0.046	0.000	0.000	0.000	0.000
32	C	77	THR	0	-0.043	-0.032	16.583	0.014	0.014	0.000	0.000	0.000	0.000
33	C	78	LEU	0	-0.007	-0.001	19.331	-0.013	-0.013	0.000	0.000	0.000	0.000
34	C	79	THR	0	-0.009	0.009	22.462	0.011	0.011	0.000	0.000	0.000	0.000

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