FMO DATABASE

FMODB ID: 8Q53Y

Calculation Name: 1W1F-A-Other547

Preferred Name: Tyrosine-protein kinase Lyn

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1W1F

Chain ID: A

ChEMBL ID: CHEMBL3905

UniProt ID: P07948

Base Structure: SolutionNMR

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	60
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-342857.796427
FMO2-HF: Nuclear repulsion	319187.168292
FMO2-HF: Total energy	-23670.628135
FMO2-MP2: Total energy	-23740.933632

3D Structure Molmil

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(A:9:GLN)

Summations of interaction energy for fragment #1(A:9:GLN)

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.
-28.851	-26.613	-0.009	-0.896	-1.333	-0.003

Interaction energy analysis for fragmet #1(A:9:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.907

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

Sort

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	A	11	ASP	-1	-0.852	-0.909	3.770	-25.266	-23.028	-0.009	-0.896	-1.333	-0.003
4	A	12	ILE	0	-0.061	-0.041	5.994	1.237	1.237	0.000	0.000	0.000	0.000
5	A	13	VAL	0	0.038	0.015	8.577	1.069	1.069	0.000	0.000	0.000	0.000
6	A	14	VAL	0	-0.046	-0.019	12.200	0.360	0.360	0.000	0.000	0.000	0.000
7	A	15	ALA	0	0.025	0.020	15.613	0.001	0.001	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.019	-0.006	18.668	0.666	0.666	0.000	0.000	0.000	0.000
9	A	17	TYR	0	-0.025	-0.020	21.163	0.971	0.971	0.000	0.000	0.000	0.000
10	A	18	PRO	0	-0.096	-0.055	22.475	-0.454	-0.454	0.000	0.000	0.000	0.000
11	A	19	TYR	0	-0.025	-0.034	21.632	0.351	0.351	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.866	-0.942	23.718	-11.566	-11.566	0.000	0.000	0.000	0.000
13	A	21	GLY	0	-0.004	-0.001	23.781	-0.245	-0.245	0.000	0.000	0.000	0.000
14	A	22	ILE	0	-0.049	-0.025	24.783	0.378	0.378	0.000	0.000	0.000	0.000
15	A	23	HIS	0	0.030	0.021	22.097	0.670	0.670	0.000	0.000	0.000	0.000
16	A	24	PRO	0	-0.040	-0.012	23.393	-0.202	-0.202	0.000	0.000	0.000	0.000
17	A	25	ASP	-1	-0.841	-0.923	18.501	-16.042	-16.042	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.841	-0.881	18.615	-15.774	-15.774	0.000	0.000	0.000	0.000
19	A	27	LEU	0	-0.115	-0.043	16.458	0.511	0.511	0.000	0.000	0.000	0.000
20	A	28	SER	0	-0.008	0.000	19.056	0.200	0.200	0.000	0.000	0.000	0.000
21	A	29	PHE	0	0.007	-0.006	18.480	-0.447	-0.447	0.000	0.000	0.000	0.000
22	A	30	LYS	1	0.996	1.003	20.958	11.817	11.817	0.000	0.000	0.000	0.000
23	A	31	LYS	1	0.969	0.977	21.278	10.753	10.753	0.000	0.000	0.000	0.000
24	A	32	GLY	0	0.007	-0.003	20.790	0.527	0.527	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.889	-0.927	18.372	-14.717	-14.717	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.948	0.967	13.599	17.191	17.191	0.000	0.000	0.000	0.000
27	A	35	MET	0	0.015	0.019	13.018	0.447	0.447	0.000	0.000	0.000	0.000
28	A	36	LYS	1	0.895	0.963	5.213	33.148	33.148	0.000	0.000	0.000	0.000
29	A	37	VAL	0	0.030	0.021	7.377	1.651	1.651	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.102	-0.055	5.793	-6.790	-6.790	0.000	0.000	0.000	0.000
31	A	39	GLU	-1	-0.880	-0.930	5.200	-36.799	-36.799	0.000	0.000	0.000	0.000
32	A	40	GLU	-1	-0.943	-0.972	7.406	-27.368	-27.368	0.000	0.000	0.000	0.000
33	A	41	HIS	0	-0.063	-0.051	8.979	0.739	0.739	0.000	0.000	0.000	0.000
34	A	42	GLY	0	0.008	0.014	11.906	1.835	1.835	0.000	0.000	0.000	0.000
35	A	43	GLU	-1	-0.896	-0.964	13.343	-17.913	-17.913	0.000	0.000	0.000	0.000
36	A	44	TRP	0	-0.024	-0.006	14.698	0.678	0.678	0.000	0.000	0.000	0.000
37	A	45	TRP	0	-0.001	-0.003	10.050	-1.463	-1.463	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.879	0.953	10.652	21.290	21.290	0.000	0.000	0.000	0.000
39	A	47	ALA	0	0.020	0.003	9.993	-3.487	-3.487	0.000	0.000	0.000	0.000
40	A	48	LYS	1	0.899	0.950	11.870	23.407	23.407	0.000	0.000	0.000	0.000
41	A	49	SER	0	0.003	-0.005	13.423	-0.690	-0.690	0.000	0.000	0.000	0.000
42	A	50	LEU	0	-0.039	-0.041	11.967	-0.163	-0.163	0.000	0.000	0.000	0.000
43	A	51	LEU	0	-0.022	0.015	15.371	0.359	0.359	0.000	0.000	0.000	0.000
44	A	52	THR	0	0.022	-0.003	19.233	0.456	0.456	0.000	0.000	0.000	0.000
45	A	53	LYS	1	0.913	0.961	16.321	16.360	16.360	0.000	0.000	0.000	0.000
46	A	54	LYS	1	0.975	0.997	16.387	13.777	13.777	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.918	-0.982	11.819	-25.042	-25.042	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.017	-0.007	14.787	1.330	1.330	0.000	0.000	0.000	0.000
49	A	57	PHE	0	-0.021	-0.021	13.442	-1.514	-1.514	0.000	0.000	0.000	0.000
50	A	58	ILE	0	0.012	-0.002	12.861	1.052	1.052	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.048	0.039	15.362	-0.912	-0.912	0.000	0.000	0.000	0.000
52	A	60	SER	0	0.032	0.004	14.832	-0.403	-0.403	0.000	0.000	0.000	0.000
53	A	61	ASN	0	-0.066	-0.038	16.144	0.465	0.465	0.000	0.000	0.000	0.000
54	A	62	TYR	0	-0.006	0.003	18.856	0.679	0.679	0.000	0.000	0.000	0.000
55	A	63	VAL	0	-0.002	-0.002	14.417	0.378	0.378	0.000	0.000	0.000	0.000
56	A	64	ALA	0	0.041	0.027	14.608	-0.135	-0.135	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.932	0.975	9.154	25.801	25.801	0.000	0.000	0.000	0.000
58	A	66	LEU	0	-0.009	-0.015	13.285	0.717	0.717	0.000	0.000	0.000	0.000
59	A	67	ASN	0	-0.020	-0.020	15.543	0.341	0.341	0.000	0.000	0.000	0.000
60	A	68	THR	-1	-0.937	-0.943	19.329	-13.071	-13.071	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLN)