FMO DATABASE

FMODB ID: JL689

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	OptH
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	-388130.331565
FMO2-HF: Nuclear repulsion	359024.850792
FMO2-HF: Total energy	-29105.480773
FMO2-MP2: Total energy	-29188.486832

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.
-20.729	-11.175	1.283	-3.66	-7.177	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 : 0.058 / q_NPA : 0.028

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	1.006	1.000	3.485	-6.751	-4.247	0.037	-0.978	-1.563	0.008
4	A	24	ARG	1	0.982	0.990	2.506	-3.853	-2.758	0.538	-0.431	-1.202	0.001
5	A	25	LYS	1	0.954	0.998	3.096	-3.901	-1.313	0.274	-1.028	-1.834	0.008
6	A	26	PHE	0	0.044	0.016	5.456	-0.747	-0.579	-0.001	-0.011	-0.155	0.000
7	A	27	GLY	0	0.003	0.002	7.621	-0.292	-0.292	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.004	0.006	7.135	-0.202	-0.202	0.000	0.000	0.000	0.000
9	A	29	MET	0	0.009	-0.001	6.904	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	30	LYS	1	0.888	0.953	11.089	-0.589	-0.589	0.000	0.000	0.000	0.000
11	A	31	LYS	1	0.863	0.926	12.865	-0.397	-0.397	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.033	0.019	13.037	-0.047	-0.047	0.000	0.000	0.000	0.000
13	A	33	TYR	0	0.023	0.007	14.811	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	34	GLU	-1	-0.846	-0.928	17.159	0.327	0.327	0.000	0.000	0.000	0.000
15	A	35	LEU	0	0.008	0.000	18.164	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	36	SER	0	-0.054	-0.016	19.131	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	37	VAL	0	0.025	-0.002	20.801	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	38	LEU	0	-0.055	-0.027	22.063	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	39	CYS	0	-0.066	-0.031	23.554	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	40	ASP	-1	-0.931	-0.931	25.209	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	41	CYS	0	-0.027	-0.015	21.682	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	42	GLU	-1	-0.875	-0.944	21.227	-0.054	-0.054	0.000	0.000	0.000	0.000
23	A	43	ILE	0	-0.023	-0.014	15.227	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	44	ALA	0	0.054	0.030	15.139	0.009	0.009	0.000	0.000	0.000	0.000
25	A	45	LEU	0	-0.041	-0.026	8.739	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.040	0.013	9.668	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	47	ILE	0	-0.027	-0.017	3.539	-0.694	-0.282	0.013	-0.089	-0.337	-0.001
28	A	48	PHE	0	0.085	0.038	6.026	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	49	ASN	0	-0.028	-0.009	2.719	-1.694	-0.479	0.348	-0.417	-1.145	0.002
30	A	50	SER	0	0.032	0.004	4.504	0.022	0.174	0.000	-0.027	-0.126	0.000
31	A	51	THR	0	-0.007	-0.003	7.119	0.053	0.053	0.000	0.000	0.000	0.000
32	A	52	ASN	0	-0.006	0.005	8.185	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	53	LYS	1	0.953	0.975	5.844	0.669	0.669	0.000	0.000	0.000	0.000
34	A	54	LEU	0	0.030	0.014	5.732	-0.392	-0.392	0.000	0.000	0.000	0.000
35	A	55	PHE	0	-0.106	-0.061	3.711	-1.662	-0.242	0.074	-0.679	-0.815	-0.006
36	A	56	GLN	0	0.021	0.008	6.548	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	57	TYR	0	0.003	-0.011	9.398	0.105	0.105	0.000	0.000	0.000	0.000
38	A	58	ALA	0	0.045	0.021	11.898	-0.047	-0.047	0.000	0.000	0.000	0.000
39	A	59	SER	0	-0.008	0.018	15.625	0.017	0.017	0.000	0.000	0.000	0.000
40	A	60	THR	0	-0.045	-0.018	18.192	0.015	0.015	0.000	0.000	0.000	0.000
41	A	61	ASP	-1	-0.861	-0.945	19.466	-0.094	-0.094	0.000	0.000	0.000	0.000
42	A	62	MET	0	-0.002	-0.006	13.386	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.885	-0.932	17.947	-0.166	-0.166	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.906	0.943	21.019	0.062	0.062	0.000	0.000	0.000	0.000
45	A	65	VAL	0	-0.003	0.006	18.961	0.000	0.000	0.000	0.000	0.000	0.000
46	A	66	LEU	0	-0.014	-0.013	16.728	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	67	LEU	0	0.010	0.023	20.708	0.001	0.001	0.000	0.000	0.000	0.000
48	A	68	LYS	1	0.965	0.999	24.024	0.069	0.069	0.000	0.000	0.000	0.000
49	A	69	TYR	0	-0.054	-0.027	21.203	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.119	-0.085	23.260	0.003	0.003	0.000	0.000	0.000	0.000
51	A	71	GLU	-1	-0.935	-0.960	25.393	-0.080	-0.080	0.000	0.000	0.000	0.000
52	A	72	TYR	0	-0.079	-0.023	26.033	0.012	0.012	0.000	0.000	0.000	0.000
53	A	73	ASN	0	-0.012	-0.018	27.508	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.966	-0.966	29.779	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	75	PRO	0	0.012	-0.003	28.596	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	76	HIS	0	-0.035	-0.029	23.349	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	77	GLU	-1	-0.947	-0.966	21.970	-0.095	-0.095	0.000	0.000	0.000	0.000
58	A	78	SER	0	-0.015	-0.007	21.014	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	79	ARG	1	0.950	0.980	18.807	0.112	0.112	0.000	0.000	0.000	0.000
60	A	80	THR	0	-0.020	-0.012	16.609	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	81	ASN	0	0.010	-0.024	12.325	0.012	0.012	0.000	0.000	0.000	0.000
62	A	82	SER	0	0.010	0.001	16.067	0.015	0.015	0.000	0.000	0.000	0.000
63	A	83	ASP	-1	-0.781	-0.882	19.614	-0.151	-0.151	0.000	0.000	0.000	0.000
64	A	84	ILE	0	-0.045	-0.019	15.388	0.025	0.025	0.000	0.000	0.000	0.000
65	A	85	VAL	0	-0.001	-0.010	17.075	0.028	0.028	0.000	0.000	0.000	0.000
66	A	86	GLU	-1	-0.925	-0.948	19.337	-0.072	-0.072	0.000	0.000	0.000	0.000
67	A	87	ALA	0	-0.007	-0.005	21.332	0.019	0.019	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.089	-0.049	16.359	0.021	0.021	0.000	0.000	0.000	0.000
69	A	89	ASN	0	-0.093	-0.029	21.103	0.026	0.026	0.000	0.000	0.000	0.000
70	A	90	LYS	1	0.951	0.984	24.144	0.037	0.037	0.000	0.000	0.000	0.000

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