FMO DATABASE

FMODB ID: 64VKZ

Calculation Name: 4D8D-B-Xray547

Preferred Name: Tyrosine-protein kinase FYN

Target Type: SINGLE PROTEIN

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4D8D

Chain ID: B

ChEMBL ID: CHEMBL1841

UniProt ID: P06241

Base Structure: X-ray

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-896705.274931
FMO2-HF: Nuclear repulsion	853330.382939
FMO2-HF: Total energy	-43374.891992
FMO2-MP2: Total energy	-43504.28892

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:69:PRO)

Summations of interaction energy for fragment #1(A:69:PRO)

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.
24.797	30.489	0.08	-2.43	-3.341	-0.015

Interaction energy analysis for fragmet #1(A:69:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.899

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	71	THR	0	0.054	0.051	3.788	3.858	7.706	-0.027	-1.767	-2.054	-0.009
45	A	113	TRP	0	-0.052	-0.014	3.248	-2.631	-2.094	0.017	-0.121	-0.432	-0.001
46	A	114	ILE	0	0.010	0.013	5.299	-0.756	-0.723	-0.001	-0.002	-0.030	0.000
48	A	116	HIS	0	-0.062	-0.045	3.458	-1.080	0.091	0.092	-0.515	-0.747	-0.005
49	A	117	THR	0	-0.072	-0.059	4.129	0.215	0.318	-0.001	-0.025	-0.078	0.000
4	A	72	PRO	0	0.009	0.003	5.213	-4.149	-4.149	0.000	0.000	0.000	0.000
5	A	73	GLN	0	0.045	0.025	6.933	-0.715	-0.715	0.000	0.000	0.000	0.000
6	A	74	VAL	0	-0.021	0.006	8.168	2.428	2.428	0.000	0.000	0.000	0.000
7	A	75	PRO	0	-0.012	-0.018	10.816	0.183	0.183	0.000	0.000	0.000	0.000
8	A	76	LEU	0	-0.007	0.004	13.951	-0.427	-0.427	0.000	0.000	0.000	0.000
9	A	77	ARG	1	0.855	0.918	13.268	20.123	20.123	0.000	0.000	0.000	0.000
10	A	78	PRO	0	0.030	0.021	16.783	-0.628	-0.628	0.000	0.000	0.000	0.000
11	A	79	MET	0	0.015	0.016	15.356	0.028	0.028	0.000	0.000	0.000	0.000
12	A	80	THR	0	-0.017	-0.018	18.971	0.718	0.718	0.000	0.000	0.000	0.000
13	A	81	TYR	0	0.020	-0.002	21.238	-0.506	-0.506	0.000	0.000	0.000	0.000
14	A	82	LYS	1	0.882	0.914	22.150	12.696	12.696	0.000	0.000	0.000	0.000
15	A	83	ALA	0	0.011	0.015	17.624	-0.220	-0.220	0.000	0.000	0.000	0.000
16	A	84	ALA	0	0.059	0.022	17.966	-0.756	-0.756	0.000	0.000	0.000	0.000
17	A	85	VAL	0	0.012	0.034	19.297	-0.312	-0.312	0.000	0.000	0.000	0.000
18	A	86	ASP	-1	-0.871	-0.916	18.801	-13.859	-13.859	0.000	0.000	0.000	0.000
19	A	87	LEU	0	-0.003	-0.002	12.217	-0.513	-0.513	0.000	0.000	0.000	0.000
20	A	88	SER	0	0.005	-0.015	15.877	-0.672	-0.672	0.000	0.000	0.000	0.000
21	A	89	HIS	0	0.021	0.004	18.359	-0.226	-0.226	0.000	0.000	0.000	0.000
22	A	90	PHE	0	-0.019	-0.001	10.962	-0.441	-0.441	0.000	0.000	0.000	0.000
23	A	91	LEU	0	-0.016	-0.023	11.260	-0.707	-0.707	0.000	0.000	0.000	0.000
24	A	92	LYS	1	0.918	0.977	15.096	13.001	13.001	0.000	0.000	0.000	0.000
25	A	93	GLU	-1	-0.961	-0.979	18.236	-13.586	-13.586	0.000	0.000	0.000	0.000
26	A	94	LYS	1	0.882	0.947	9.035	27.618	27.618	0.000	0.000	0.000	0.000
27	A	95	GLY	0	0.034	0.029	15.408	-0.301	-0.301	0.000	0.000	0.000	0.000
28	A	96	GLY	0	-0.017	-0.019	14.334	-1.313	-1.313	0.000	0.000	0.000	0.000
29	A	97	LEU	0	-0.030	-0.011	13.706	-0.515	-0.515	0.000	0.000	0.000	0.000
30	A	98	GLU	-1	-0.779	-0.901	15.811	-12.716	-12.716	0.000	0.000	0.000	0.000
31	A	99	GLY	0	-0.003	0.002	19.643	0.016	0.016	0.000	0.000	0.000	0.000
32	A	100	LEU	0	-0.046	0.009	13.307	-0.166	-0.166	0.000	0.000	0.000	0.000
33	A	101	ILE	0	0.048	0.011	17.913	0.083	0.083	0.000	0.000	0.000	0.000
34	A	102	HIS	1	0.886	0.937	16.863	14.559	14.559	0.000	0.000	0.000	0.000
35	A	103	SER	0	-0.015	-0.013	15.745	0.511	0.511	0.000	0.000	0.000	0.000
36	A	104	GLN	0	-0.002	-0.023	15.441	0.132	0.132	0.000	0.000	0.000	0.000
37	A	105	ARG	1	0.997	1.004	10.555	22.653	22.653	0.000	0.000	0.000	0.000
38	A	106	ARG	1	0.891	0.936	11.175	17.102	17.102	0.000	0.000	0.000	0.000
39	A	107	GLN	0	0.066	0.062	10.929	-0.824	-0.824	0.000	0.000	0.000	0.000
40	A	108	ASP	-1	-0.809	-0.895	11.272	-20.754	-20.754	0.000	0.000	0.000	0.000
41	A	109	ILE	0	-0.057	-0.033	5.701	-1.999	-1.999	0.000	0.000	0.000	0.000
42	A	110	LEU	0	-0.012	0.006	6.491	-3.931	-3.931	0.000	0.000	0.000	0.000
43	A	111	ASP	-1	-0.794	-0.899	8.593	-21.747	-21.747	0.000	0.000	0.000	0.000
44	A	112	LEU	0	0.008	-0.004	6.321	-0.486	-0.486	0.000	0.000	0.000	0.000
47	A	115	TYR	0	0.000	0.007	8.723	0.320	0.320	0.000	0.000	0.000	0.000
50	A	118	GLN	0	-0.050	-0.015	6.825	4.216	4.216	0.000	0.000	0.000	0.000
51	A	119	GLY	0	0.089	0.060	9.994	2.190	2.190	0.000	0.000	0.000	0.000
52	A	120	TYR	0	-0.033	-0.021	11.874	1.294	1.294	0.000	0.000	0.000	0.000
53	A	121	PHE	0	0.045	0.018	12.618	-1.720	-1.720	0.000	0.000	0.000	0.000
54	A	122	PRO	0	-0.030	-0.008	11.635	0.326	0.326	0.000	0.000	0.000	0.000
55	A	123	ASP	-1	-0.890	-0.955	13.712	-15.291	-15.291	0.000	0.000	0.000	0.000
56	A	124	TRP	0	0.052	0.026	12.624	1.140	1.140	0.000	0.000	0.000	0.000
57	A	125	GLN	0	-0.002	0.028	13.430	1.549	1.549	0.000	0.000	0.000	0.000
58	A	126	ASN	0	-0.006	-0.005	17.280	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	127	TYR	0	-0.050	-0.056	17.418	0.480	0.480	0.000	0.000	0.000	0.000
60	A	128	THR	0	0.026	0.030	22.738	0.009	0.009	0.000	0.000	0.000	0.000
61	A	129	PRO	0	0.003	-0.001	25.722	-0.341	-0.341	0.000	0.000	0.000	0.000
62	A	130	GLY	0	-0.044	0.002	27.871	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	131	PRO	0	-0.004	-0.012	29.100	0.152	0.152	0.000	0.000	0.000	0.000
64	A	132	GLY	0	0.043	0.019	30.425	0.109	0.109	0.000	0.000	0.000	0.000
65	A	133	VAL	0	-0.033	-0.024	26.940	-0.375	-0.375	0.000	0.000	0.000	0.000
66	A	134	ARG	1	0.821	0.909	23.983	11.416	11.416	0.000	0.000	0.000	0.000
67	A	135	TYR	0	0.052	0.003	24.606	-0.418	-0.418	0.000	0.000	0.000	0.000
68	A	136	PRO	0	-0.005	0.008	21.533	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	137	LEU	0	0.021	0.007	22.994	0.427	0.427	0.000	0.000	0.000	0.000
70	A	138	THR	0	-0.038	-0.028	20.333	0.487	0.487	0.000	0.000	0.000	0.000
71	A	139	PHE	0	0.027	0.013	22.940	-0.198	-0.198	0.000	0.000	0.000	0.000
72	A	140	GLY	0	0.027	-0.004	24.002	-0.248	-0.248	0.000	0.000	0.000	0.000
73	A	141	TRP	0	-0.011	-0.006	14.796	-0.617	-0.617	0.000	0.000	0.000	0.000
74	A	142	CYS	0	-0.086	-0.047	21.182	0.617	0.617	0.000	0.000	0.000	0.000
75	A	143	TYR	0	-0.011	-0.007	18.078	0.119	0.119	0.000	0.000	0.000	0.000
76	A	144	LYS	1	0.879	0.939	21.137	10.877	10.877	0.000	0.000	0.000	0.000
77	A	145	LEU	0	-0.035	-0.010	19.038	-0.408	-0.408	0.000	0.000	0.000	0.000
78	A	146	VAL	0	0.003	-0.009	22.885	0.590	0.590	0.000	0.000	0.000	0.000
79	A	147	PRO	0	-0.048	-0.033	25.263	-0.325	-0.325	0.000	0.000	0.000	0.000
80	A	148	VAL	-1	-0.907	-0.931	26.035	-11.291	-11.291	0.000	0.000	0.000	0.000
81	A	179	GLU	0	0.007	-0.003	26.727	0.256	0.256	0.000	0.000	0.000	0.000
82	A	180	VAL	0	0.061	0.033	23.768	-0.251	-0.251	0.000	0.000	0.000	0.000
83	A	181	LEU	0	0.036	0.023	21.992	0.303	0.303	0.000	0.000	0.000	0.000
84	A	182	GLU	-1	-0.798	-0.872	20.896	-13.460	-13.460	0.000	0.000	0.000	0.000
85	A	183	TRP	0	-0.031	-0.025	13.933	0.108	0.108	0.000	0.000	0.000	0.000
86	A	184	ARG	1	0.799	0.882	19.849	12.488	12.488	0.000	0.000	0.000	0.000
87	A	185	PHE	0	0.018	-0.005	21.197	0.180	0.180	0.000	0.000	0.000	0.000
88	A	186	ASP	-1	-0.798	-0.876	23.149	-9.840	-9.840	0.000	0.000	0.000	0.000
89	A	187	SER	0	0.045	0.019	26.044	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	188	ARG	1	0.872	0.906	26.981	9.777	9.777	0.000	0.000	0.000	0.000
91	A	189	LEU	0	0.016	0.017	24.631	0.269	0.269	0.000	0.000	0.000	0.000
92	A	190	ALA	0	0.005	0.009	25.928	-0.205	-0.205	0.000	0.000	0.000	0.000
93	A	191	PHE	0	-0.055	-0.022	27.505	0.164	0.164	0.000	0.000	0.000	0.000
94	A	192	HIS	0	0.005	0.000	30.867	0.125	0.125	0.000	0.000	0.000	0.000
95	A	193	HIS	0	-0.040	-0.018	26.906	-0.081	-0.081	0.000	0.000	0.000	0.000
96	A	194	VAL	0	0.030	0.005	29.285	0.038	0.038	0.000	0.000	0.000	0.000
97	A	195	ALA	0	0.020	0.010	26.950	0.203	0.203	0.000	0.000	0.000	0.000
98	A	196	ARG	1	0.905	0.966	29.069	9.457	9.457	0.000	0.000	0.000	0.000
99	A	197	GLU	-1	-0.921	-0.958	31.611	-8.272	-8.272	0.000	0.000	0.000	0.000
100	A	198	LEU	0	-0.045	-0.029	30.988	0.190	0.190	0.000	0.000	0.000	0.000
101	A	199	HIS	0	0.024	0.011	30.280	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	200	PRO	0	0.008	0.004	31.394	-0.254	-0.254	0.000	0.000	0.000	0.000
103	A	201	GLU	-1	-0.882	-0.957	32.176	-9.162	-9.162	0.000	0.000	0.000	0.000
104	A	202	TYR	0	-0.053	-0.034	27.618	-0.211	-0.211	0.000	0.000	0.000	0.000
105	A	203	PHE	0	-0.068	-0.039	27.253	-0.379	-0.379	0.000	0.000	0.000	0.000
106	A	204	LYS	0	0.012	0.034	30.987	-0.593	-0.593	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:69:PRO)