FMO DATABASE

FMODB ID: 3932L

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	OptHSide
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	-388043.496618
FMO2-HF: Nuclear repulsion	358937.739588
FMO2-HF: Total energy	-29105.75703
FMO2-MP2: Total energy	-29188.761442

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.
-20.302	-10.427	1.562	-3.843	-7.597	0.013

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 : 0.051 / q_NPA : 0.023

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	1.005	1.000	3.493	-5.931	-3.431	0.020	-1.056	-1.464	0.007
4	A	24	ARG	1	0.979	0.989	2.523	-3.867	-2.764	0.502	-0.435	-1.170	0.001
5	A	25	LYS	1	0.889	0.970	2.979	-4.038	-1.320	0.422	-1.099	-2.041	0.010
6	A	26	PHE	0	0.052	0.019	5.544	-0.719	-0.556	-0.001	-0.009	-0.152	0.000
7	A	27	GLY	0	0.005	0.003	7.609	-0.274	-0.274	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.000	0.006	6.946	-0.198	-0.198	0.000	0.000	0.000	0.000
9	A	29	MET	0	0.010	-0.002	6.937	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	30	LYS	1	0.872	0.935	11.154	-0.549	-0.549	0.000	0.000	0.000	0.000
11	A	31	LYS	1	0.863	0.914	12.862	-0.357	-0.357	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.029	0.014	12.966	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	33	TYR	0	0.022	0.006	14.824	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	34	GLU	-1	-0.831	-0.897	17.121	0.336	0.336	0.000	0.000	0.000	0.000
15	A	35	LEU	0	0.012	0.003	18.051	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	36	SER	0	-0.053	-0.027	19.103	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	37	VAL	0	0.028	0.003	20.833	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	38	LEU	0	-0.065	-0.028	22.124	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	39	CYS	0	-0.072	-0.042	23.500	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	40	ASP	-1	-0.930	-0.928	25.203	0.003	0.003	0.000	0.000	0.000	0.000
21	A	41	CYS	0	-0.019	-0.011	21.604	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	42	GLU	-1	-0.829	-0.886	21.192	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	43	ILE	0	-0.026	-0.021	15.248	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	44	ALA	0	0.054	0.032	15.096	0.011	0.011	0.000	0.000	0.000	0.000
25	A	45	LEU	0	-0.041	-0.024	8.793	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.038	0.012	9.552	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	47	ILE	0	-0.026	-0.018	3.360	-0.796	-0.314	0.024	-0.117	-0.389	-0.001
28	A	48	PHE	0	0.078	0.037	5.902	0.033	0.033	0.000	0.000	0.000	0.000
29	A	49	ASN	0	-0.031	-0.019	2.793	-2.056	-0.836	0.431	-0.435	-1.217	0.002
30	A	50	SER	0	0.035	0.012	4.249	-0.034	0.155	0.002	-0.040	-0.153	0.000
31	A	51	THR	0	-0.007	-0.006	6.983	0.020	0.020	0.000	0.000	0.000	0.000
32	A	52	ASN	0	-0.015	-0.001	7.984	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	53	LYS	1	0.959	0.980	5.817	0.517	0.517	0.000	0.000	0.000	0.000
34	A	54	LEU	0	0.024	0.018	5.682	-0.354	-0.354	0.000	0.000	0.000	0.000
35	A	55	PHE	0	-0.033	-0.036	3.165	-1.437	0.063	0.162	-0.652	-1.011	-0.006
36	A	56	GLN	0	0.027	0.011	6.641	-0.077	-0.077	0.000	0.000	0.000	0.000
37	A	57	TYR	0	0.007	-0.011	9.443	0.109	0.109	0.000	0.000	0.000	0.000
38	A	58	ALA	0	0.047	0.021	11.962	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	59	SER	0	0.006	0.030	15.666	0.017	0.017	0.000	0.000	0.000	0.000
40	A	60	THR	0	-0.059	-0.038	18.248	0.015	0.015	0.000	0.000	0.000	0.000
41	A	61	ASP	-1	-0.796	-0.906	19.525	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	62	MET	0	-0.017	0.000	13.263	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.894	-0.941	17.964	-0.145	-0.145	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.861	0.904	21.027	0.053	0.053	0.000	0.000	0.000	0.000
45	A	65	VAL	0	-0.005	0.005	18.911	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	66	LEU	0	-0.013	-0.011	16.648	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	67	LEU	0	0.005	0.019	20.619	0.000	0.000	0.000	0.000	0.000	0.000
48	A	68	LYS	1	0.923	0.953	23.914	0.060	0.060	0.000	0.000	0.000	0.000
49	A	69	TYR	0	-0.051	-0.023	21.187	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.094	-0.058	23.230	0.001	0.001	0.000	0.000	0.000	0.000
51	A	71	GLU	-1	-0.946	-0.966	25.244	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	72	TYR	0	-0.064	-0.027	25.969	0.011	0.011	0.000	0.000	0.000	0.000
53	A	73	ASN	0	-0.043	-0.034	27.452	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.948	-0.951	29.690	-0.063	-0.063	0.000	0.000	0.000	0.000
55	A	75	PRO	0	0.015	0.001	28.495	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	76	HIS	0	-0.041	-0.032	23.010	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	77	GLU	-1	-0.861	-0.905	22.197	-0.094	-0.094	0.000	0.000	0.000	0.000
58	A	78	SER	0	-0.014	-0.006	20.854	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	79	ARG	1	0.852	0.912	18.501	0.113	0.113	0.000	0.000	0.000	0.000
60	A	80	THR	0	-0.024	-0.027	16.396	-0.041	-0.041	0.000	0.000	0.000	0.000
61	A	81	ASN	0	0.009	-0.022	11.926	0.011	0.011	0.000	0.000	0.000	0.000
62	A	82	SER	0	0.017	0.007	15.796	0.015	0.015	0.000	0.000	0.000	0.000
63	A	83	ASP	-1	-0.776	-0.868	19.371	-0.165	-0.165	0.000	0.000	0.000	0.000
64	A	84	ILE	0	-0.045	-0.022	15.119	0.026	0.026	0.000	0.000	0.000	0.000
65	A	85	VAL	0	-0.003	-0.010	16.913	0.028	0.028	0.000	0.000	0.000	0.000
66	A	86	GLU	-1	-0.933	-0.948	19.187	-0.074	-0.074	0.000	0.000	0.000	0.000
67	A	87	ALA	0	-0.008	-0.008	21.068	0.020	0.020	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.078	-0.044	16.232	0.021	0.021	0.000	0.000	0.000	0.000
69	A	89	ASN	0	-0.093	-0.035	20.952	0.026	0.026	0.000	0.000	0.000	0.000
70	A	90	LYS	1	0.952	0.988	23.981	0.047	0.047	0.000	0.000	0.000	0.000

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