FMO DATABASE

FMODB ID: J2Z49

Calculation Name: 5F28-A-Xray540

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: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-388896.605929
FMO2-HF: Nuclear repulsion	359805.473433
FMO2-HF: Total energy	-29091.132497
FMO2-MP2: Total energy	-29173.74382

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.
-8.484	-5.894	0.118	-1.204	-1.501	0.003

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 : 0.154 / q_NPA : 0.050

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].
4	A	22	THR	0	-0.010	0.068	4.627	-1.083	-0.834	-0.001	-0.100	-0.147	0.000
5	A	23	LYS	0	0.116	-0.050	3.743	-1.710	-0.454	-0.001	-0.645	-0.609	0.002
6	A	23	LYS	1	0.935	1.070	4.772	-2.467	-2.387	-0.001	-0.012	-0.067	0.000
7	A	24	ARG	0	0.052	-0.091	3.683	-1.827	-1.509	0.008	-0.074	-0.251	0.000
8	A	24	ARG	1	0.913	1.082	2.922	-3.349	-2.977	0.115	-0.202	-0.285	0.001
9	A	25	LYS	0	0.152	-0.038	4.005	-0.364	-0.082	-0.001	-0.164	-0.117	0.000
10	A	25	LYS	1	0.739	1.008	4.709	2.011	2.044	-0.001	-0.007	-0.025	0.000
11	A	26	PHE	0	0.128	-0.076	5.873	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	26	PHE	0	-0.084	0.087	8.129	0.026	0.026	0.000	0.000	0.000	0.000
13	A	27	GLY	0	-0.020	-0.116	7.845	-0.093	-0.093	0.000	0.000	0.000	0.000
14	A	28	LEU	0	0.122	0.013	8.378	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	28	LEU	0	-0.083	0.108	8.667	0.003	0.003	0.000	0.000	0.000	0.000
16	A	29	MET	0	0.084	-0.081	9.967	-0.035	-0.035	0.000	0.000	0.000	0.000
17	A	29	MET	0	-0.109	0.073	9.982	-0.059	-0.059	0.000	0.000	0.000	0.000
18	A	30	LYS	0	0.158	-0.045	11.895	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	30	LYS	1	0.760	0.998	12.776	-0.472	-0.472	0.000	0.000	0.000	0.000
20	A	31	LYS	0	0.095	-0.107	12.986	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.765	1.023	13.359	-0.458	-0.458	0.000	0.000	0.000	0.000
22	A	32	ALA	0	0.124	-0.081	14.165	0.001	0.001	0.000	0.000	0.000	0.000
23	A	32	ALA	0	-0.071	0.099	14.522	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	33	TYR	0	0.122	-0.046	16.005	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	33	TYR	0	-0.139	0.058	16.840	0.009	0.009	0.000	0.000	0.000	0.000
26	A	34	GLU	0	0.099	-0.086	17.543	-0.031	-0.031	0.000	0.000	0.000	0.000
27	A	34	GLU	-1	-0.916	-0.819	17.142	0.457	0.457	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.093	-0.085	18.640	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.076	0.092	19.038	0.005	0.005	0.000	0.000	0.000	0.000
30	A	36	SER	0	0.017	-0.056	20.179	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	36	SER	0	-0.046	0.031	20.730	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.026	-0.106	22.075	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	37	VAL	0	-0.106	0.074	21.992	0.001	0.001	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.060	-0.090	23.284	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.091	0.070	21.914	0.008	0.008	0.000	0.000	0.000	0.000
36	A	39	CYS	0	0.014	-0.087	24.867	0.004	0.004	0.000	0.000	0.000	0.000
37	A	39	CYS	0	-0.120	0.044	24.550	0.008	0.008	0.000	0.000	0.000	0.000
38	A	40	ASP	0	0.124	-0.061	26.297	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.997	-0.844	29.104	0.034	0.034	0.000	0.000	0.000	0.000
40	A	41	CYS	0	0.140	-0.130	24.480	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.185	0.086	23.832	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	GLU	0	0.124	-0.073	23.655	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.864	-0.768	24.755	-0.055	-0.055	0.000	0.000	0.000	0.000
44	A	43	ILE	0	0.044	-0.095	19.950	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	43	ILE	0	-0.101	0.077	17.993	0.003	0.003	0.000	0.000	0.000	0.000
46	A	44	ALA	0	0.105	-0.109	18.481	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.028	0.122	19.176	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	45	LEU	0	0.068	-0.108	14.239	0.030	0.030	0.000	0.000	0.000	0.000
49	A	45	LEU	0	-0.129	0.082	11.110	0.002	0.002	0.000	0.000	0.000	0.000
50	A	46	ILE	0	0.059	-0.115	14.104	-0.041	-0.041	0.000	0.000	0.000	0.000
51	A	46	ILE	0	-0.031	0.136	14.704	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	47	ILE	0	0.097	-0.084	9.644	0.118	0.118	0.000	0.000	0.000	0.000
53	A	47	ILE	0	-0.116	0.058	7.465	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	48	PHE	0	0.089	-0.094	10.410	-0.169	-0.169	0.000	0.000	0.000	0.000
55	A	48	PHE	0	-0.025	0.133	11.886	0.023	0.023	0.000	0.000	0.000	0.000
56	A	49	ASN	0	0.091	-0.039	6.861	0.018	0.018	0.000	0.000	0.000	0.000
57	A	49	ASN	0	-0.120	0.017	5.911	0.314	0.314	0.000	0.000	0.000	0.000
58	A	50	SER	0	0.068	-0.054	7.022	0.421	0.421	0.000	0.000	0.000	0.000
59	A	50	SER	0	-0.026	0.058	7.436	-0.243	-0.243	0.000	0.000	0.000	0.000
60	A	51	THR	0	-0.057	-0.087	8.968	0.243	0.243	0.000	0.000	0.000	0.000
61	A	51	THR	0	-0.043	0.068	9.378	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	52	ASN	0	0.111	-0.060	11.158	0.057	0.057	0.000	0.000	0.000	0.000
63	A	52	ASN	0	-0.070	0.088	14.150	0.021	0.021	0.000	0.000	0.000	0.000
64	A	53	LYS	0	0.204	-0.058	10.683	0.213	0.213	0.000	0.000	0.000	0.000
65	A	53	LYS	1	0.827	1.047	9.597	1.255	1.255	0.000	0.000	0.000	0.000
66	A	54	LEU	0	0.102	-0.113	9.965	-0.336	-0.336	0.000	0.000	0.000	0.000
67	A	54	LEU	0	-0.078	0.128	13.222	0.019	0.019	0.000	0.000	0.000	0.000
68	A	55	PHE	0	-0.030	-0.097	10.081	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	55	PHE	0	-0.032	0.058	7.189	-0.207	-0.207	0.000	0.000	0.000	0.000
70	A	56	GLN	0	0.059	-0.086	11.459	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	56	GLN	0	-0.016	0.111	15.094	0.047	0.047	0.000	0.000	0.000	0.000
72	A	57	TYR	0	0.054	-0.099	13.878	-0.044	-0.044	0.000	0.000	0.000	0.000
73	A	57	TYR	0	-0.084	0.072	14.010	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	58	ALA	0	0.140	-0.097	15.535	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	58	ALA	0	-0.051	0.128	19.739	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	59	SER	0	-0.008	-0.115	19.076	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	59	SER	0	0.012	0.109	21.217	0.000	0.000	0.000	0.000	0.000	0.000
78	A	60	THR	0	-0.095	-0.077	21.187	0.015	0.015	0.000	0.000	0.000	0.000
79	A	60	THR	0	-0.063	0.014	24.805	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	61	ASP	0	0.108	-0.084	23.309	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	61	ASP	-1	-0.871	-0.803	25.147	-0.142	-0.142	0.000	0.000	0.000	0.000
82	A	62	MET	0	0.180	-0.051	21.316	0.022	0.022	0.000	0.000	0.000	0.000
83	A	62	MET	0	-0.143	0.086	17.742	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	63	ASP	0	0.075	-0.126	22.275	0.000	0.000	0.000	0.000	0.000	0.000
85	A	63	ASP	-1	-1.010	-0.842	24.842	-0.202	-0.202	0.000	0.000	0.000	0.000
86	A	64	LYS	0	0.089	-0.078	25.676	0.002	0.002	0.000	0.000	0.000	0.000
87	A	64	LYS	1	0.784	0.998	26.472	0.096	0.096	0.000	0.000	0.000	0.000
88	A	65	VAL	0	0.072	-0.079	23.711	0.012	0.012	0.000	0.000	0.000	0.000
89	A	65	VAL	0	-0.067	0.100	22.313	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	66	LEU	0	0.078	-0.092	24.472	0.013	0.013	0.000	0.000	0.000	0.000
91	A	66	LEU	0	-0.096	0.068	21.277	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	67	LEU	0	0.137	-0.086	25.023	0.002	0.002	0.000	0.000	0.000	0.000
93	A	67	LEU	0	-0.117	0.100	29.304	0.000	0.000	0.000	0.000	0.000	0.000
94	A	68	LYS	0	0.176	-0.054	28.368	0.003	0.003	0.000	0.000	0.000	0.000
95	A	68	LYS	1	0.766	1.021	27.662	0.043	0.043	0.000	0.000	0.000	0.000
96	A	69	TYR	0	0.081	-0.079	25.959	0.015	0.015	0.000	0.000	0.000	0.000
97	A	69	TYR	0	-0.148	0.053	25.210	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	70	THR	0	-0.048	-0.088	27.422	0.007	0.007	0.000	0.000	0.000	0.000
99	A	70	THR	0	-0.091	0.002	27.760	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	71	GLU	0	0.086	-0.104	29.731	0.000	0.000	0.000	0.000	0.000	0.000
101	A	71	GLU	-1	-0.997	-0.837	31.584	-0.065	-0.065	0.000	0.000	0.000	0.000
102	A	72	TYR	0	0.085	-0.073	30.509	0.007	0.007	0.000	0.000	0.000	0.000
103	A	72	TYR	0	-0.154	0.067	29.632	0.003	0.003	0.000	0.000	0.000	0.000
104	A	73	ASN	0	0.055	-0.096	31.171	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	73	ASN	0	-0.174	0.022	34.680	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	74	GLU	0	0.069	-0.110	32.818	0.000	0.000	0.000	0.000	0.000	0.000
107	A	74	GLU	-1	-0.986	-0.837	33.474	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	75	PRO	0	0.006	-0.111	31.788	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	76	HIS	0	0.047	-0.001	28.484	0.005	0.005	0.000	0.000	0.000	0.000
110	A	76	HIS	0	-0.064	0.083	26.026	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	77	GLU	0	0.119	-0.091	26.462	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	77	GLU	-1	-0.927	-0.789	24.477	0.065	0.065	0.000	0.000	0.000	0.000
113	A	78	SER	0	0.033	-0.099	23.633	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	78	SER	0	-0.038	0.079	24.010	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	79	ARG	0	0.032	-0.077	21.834	0.005	0.005	0.000	0.000	0.000	0.000
116	A	79	ARG	1	0.755	0.965	21.054	-0.079	-0.079	0.000	0.000	0.000	0.000
117	A	80	THR	0	-0.002	-0.063	19.312	-0.020	-0.020	0.000	0.000	0.000	0.000
118	A	80	THR	0	-0.028	0.048	20.268	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	81	ASN	0	0.143	-0.058	17.200	0.032	0.032	0.000	0.000	0.000	0.000
120	A	81	ASN	0	-0.105	0.046	14.256	-0.016	-0.016	0.000	0.000	0.000	0.000
121	A	82	SER	0	-0.027	-0.084	17.900	0.039	0.039	0.000	0.000	0.000	0.000
122	A	82	SER	0	0.015	0.065	22.290	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	83	ASP	0	0.109	-0.098	21.489	0.020	0.020	0.000	0.000	0.000	0.000
124	A	83	ASP	-1	-0.828	-0.761	21.613	0.015	0.015	0.000	0.000	0.000	0.000
125	A	84	ILE	0	0.053	-0.079	18.026	0.011	0.011	0.000	0.000	0.000	0.000
126	A	84	ILE	0	-0.099	0.088	16.150	0.006	0.006	0.000	0.000	0.000	0.000
127	A	85	VAL	0	0.082	-0.093	19.497	0.040	0.040	0.000	0.000	0.000	0.000
128	A	85	VAL	0	-0.083	0.096	18.117	0.000	0.000	0.000	0.000	0.000	0.000
129	A	86	GLU	0	0.114	-0.117	20.205	0.023	0.023	0.000	0.000	0.000	0.000
130	A	86	GLU	-1	-0.978	-0.825	24.554	0.067	0.067	0.000	0.000	0.000	0.000
131	A	87	ALA	0	0.078	-0.114	22.787	0.000	0.000	0.000	0.000	0.000	0.000
132	A	87	ALA	0	-0.088	0.106	21.768	0.000	0.000	0.000	0.000	0.000	0.000
133	A	88	LEU	0	0.032	-0.112	19.996	0.002	0.002	0.000	0.000	0.000	0.000
134	A	88	LEU	0	-0.108	0.083	16.703	0.012	0.012	0.000	0.000	0.000	0.000
135	A	89	ASN	0	0.053	-0.048	21.351	0.022	0.022	0.000	0.000	0.000	0.000
136	A	89	ASN	0	-0.170	0.029	22.079	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	90	LYS	0	-0.071	-0.149	24.376	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	90	LYS	1	0.923	0.966	26.078	-0.128	-0.128	0.000	0.000	0.000	0.000

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