FMO DATABASE

FMODB ID: LZM59

Calculation Name: 5F28-A-Xray372

Preferred Name: Focal adhesion kinase 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5F28

Chain ID: A

ChEMBL ID: CHEMBL1075288

UniProt ID: P34152

Base Structure: X-ray

Registration Date: 2023-06-21

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-388911.34499
FMO2-HF: Nuclear repulsion	359805.473433
FMO2-HF: Total energy	-29105.871557
FMO2-MP2: Total energy	-29188.862632

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(A:21:PHE)

Summations of interaction energy for fragment #1(A:21:PHE)

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.
-20.179	-10.141	2.464	-3.837	-8.662	0.012

Interaction energy analysis for fragmet #1(A:21:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.027

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	A	23	LYS	1	1.019	1.005	3.743	-4.279	-2.406	0.008	-0.782	-1.098	0.004
4	A	24	ARG	1	0.977	0.995	2.922	-3.542	-2.661	0.104	-0.207	-0.777	0.000
5	A	25	LYS	1	0.870	0.964	2.767	-5.111	-2.104	1.004	-1.390	-2.621	0.016
6	A	26	PHE	0	0.049	0.019	5.618	-0.624	-0.459	-0.001	-0.010	-0.154	0.000
7	A	27	GLY	0	0.006	0.004	7.845	-0.256	-0.256	0.000	0.000	0.000	0.000
8	A	28	LEU	0	-0.002	0.001	7.002	-0.180	-0.180	0.000	0.000	0.000	0.000
9	A	29	MET	0	0.004	-0.001	6.641	0.000	0.000	0.000	0.000	0.000	0.000
10	A	30	LYS	1	0.881	0.939	11.008	-0.515	-0.515	0.000	0.000	0.000	0.000
11	A	31	LYS	1	0.877	0.925	12.986	-0.348	-0.348	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.041	0.020	12.893	-0.043	-0.043	0.000	0.000	0.000	0.000
13	A	33	TYR	0	0.016	0.017	14.767	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	34	GLU	-1	-0.832	-0.905	17.142	0.327	0.327	0.000	0.000	0.000	0.000
15	A	35	LEU	0	0.003	-0.007	17.698	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	36	SER	0	-0.041	-0.020	19.044	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	37	VAL	0	0.009	-0.012	20.682	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	38	LEU	0	-0.056	-0.028	21.914	0.001	0.001	0.000	0.000	0.000	0.000
19	A	39	CYS	0	-0.086	-0.051	23.399	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	40	ASP	-1	-0.906	-0.919	25.260	0.003	0.003	0.000	0.000	0.000	0.000
21	A	41	CYS	0	-0.016	-0.002	21.829	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	42	GLU	-1	-0.801	-0.862	21.376	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	43	ILE	0	-0.027	-0.019	15.439	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	44	ALA	0	0.033	0.020	14.951	0.013	0.013	0.000	0.000	0.000	0.000
25	A	45	LEU	0	-0.037	-0.016	8.692	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.044	0.014	9.170	0.005	0.005	0.000	0.000	0.000	0.000
27	A	47	ILE	0	-0.021	-0.020	3.283	-0.913	-0.301	0.050	-0.155	-0.507	-0.001
28	A	48	PHE	0	0.061	0.033	5.030	-0.223	-0.137	-0.001	-0.007	-0.077	0.000
29	A	49	ASN	0	-0.034	-0.025	2.696	-2.474	-1.069	0.670	-0.489	-1.586	0.002
30	A	50	SER	0	0.020	0.000	3.953	-0.102	0.146	0.012	-0.044	-0.215	0.000
31	A	51	THR	0	-0.011	0.000	6.766	0.054	0.054	0.000	0.000	0.000	0.000
32	A	52	ASN	0	0.017	0.012	7.998	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	53	LYS	1	0.964	0.984	5.558	0.493	0.493	0.000	0.000	0.000	0.000
34	A	54	LEU	0	0.022	0.017	5.051	-0.559	-0.488	-0.001	0.000	-0.070	0.000
35	A	55	PHE	0	-0.006	-0.025	2.603	-1.406	0.284	0.619	-0.753	-1.557	-0.009
36	A	56	GLN	0	0.021	0.004	6.400	-0.090	-0.090	0.000	0.000	0.000	0.000
37	A	57	TYR	0	-0.016	-0.024	9.132	0.120	0.120	0.000	0.000	0.000	0.000
38	A	58	ALA	0	0.039	0.015	11.856	-0.057	-0.057	0.000	0.000	0.000	0.000
39	A	59	SER	0	0.012	0.022	15.542	0.021	0.021	0.000	0.000	0.000	0.000
40	A	60	THR	0	-0.070	-0.054	18.485	0.015	0.015	0.000	0.000	0.000	0.000
41	A	61	ASP	-1	-0.802	-0.902	19.120	-0.085	-0.085	0.000	0.000	0.000	0.000
42	A	62	MET	0	-0.015	0.012	12.988	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.894	-0.936	17.602	-0.154	-0.154	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.858	0.897	20.664	0.059	0.059	0.000	0.000	0.000	0.000
45	A	65	VAL	0	0.000	0.006	18.673	0.000	0.000	0.000	0.000	0.000	0.000
46	A	66	LEU	0	-0.019	-0.018	16.368	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	67	LEU	0	-0.006	0.009	20.297	0.001	0.001	0.000	0.000	0.000	0.000
48	A	68	LYS	1	0.922	0.955	23.662	0.061	0.061	0.000	0.000	0.000	0.000
49	A	69	TYR	0	-0.062	-0.019	20.992	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.095	-0.065	22.878	0.002	0.002	0.000	0.000	0.000	0.000
51	A	71	GLU	-1	-0.909	-0.950	25.128	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	72	TYR	0	-0.047	-0.022	25.839	0.010	0.010	0.000	0.000	0.000	0.000
53	A	73	ASN	0	-0.095	-0.059	27.273	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.925	-0.944	29.081	-0.060	-0.060	0.000	0.000	0.000	0.000
55	A	75	PRO	0	0.003	-0.003	28.215	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	76	HIS	0	-0.024	-0.018	22.702	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	77	GLU	-1	-0.846	-0.892	22.020	-0.083	-0.083	0.000	0.000	0.000	0.000
58	A	78	SER	0	-0.005	-0.006	20.627	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	79	ARG	1	0.824	0.898	18.670	0.104	0.104	0.000	0.000	0.000	0.000
60	A	80	THR	0	-0.019	-0.017	16.547	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	81	ASN	0	0.002	-0.027	12.040	0.016	0.016	0.000	0.000	0.000	0.000
62	A	82	SER	0	0.021	0.003	15.958	0.022	0.022	0.000	0.000	0.000	0.000
63	A	83	ASP	-1	-0.755	-0.857	19.753	-0.147	-0.147	0.000	0.000	0.000	0.000
64	A	84	ILE	0	-0.040	-0.018	15.356	0.027	0.027	0.000	0.000	0.000	0.000
65	A	85	VAL	0	0.001	-0.001	17.289	0.029	0.029	0.000	0.000	0.000	0.000
66	A	86	GLU	-1	-0.918	-0.947	19.557	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	87	ALA	0	-0.015	-0.009	21.157	0.018	0.018	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.034	-0.024	16.530	0.020	0.020	0.000	0.000	0.000	0.000
69	A	89	ASN	0	-0.092	-0.030	21.245	0.025	0.025	0.000	0.000	0.000	0.000
70	A	90	LYS	1	0.868	0.938	24.257	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:PHE)