FMO DATABASE

FMODB ID: J3JK9

Calculation Name: 4AFL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AFL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UNL4

Base Structure: X-ray

Registration Date: 2023-06-20

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-685303.036374
FMO2-HF: Nuclear repulsion	642260.313662
FMO2-HF: Total energy	-43042.722712
FMO2-MP2: Total energy	-43165.023208

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-4.545	-1.691	0.029	-1.379	-1.504	0.003

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / 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	5	MET	0	0.029	0.024	3.239	-1.804	0.898	0.030	-1.367	-1.365	0.003
4	A	6	TYR	0	-0.004	-0.010	4.968	-0.812	-0.660	-0.001	-0.012	-0.139	0.000
5	A	7	LEU	0	-0.018	0.001	7.455	-0.271	-0.271	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.931	-0.967	6.331	-1.176	-1.176	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.014	-0.040	8.508	0.177	0.177	0.000	0.000	0.000	0.000
8	A	10	TYR	0	-0.097	-0.041	10.818	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.012	-0.016	11.927	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.814	-0.882	11.428	-0.140	-0.140	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.060	-0.008	14.391	0.001	0.001	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.017	0.002	17.746	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.889	-0.966	20.671	0.040	0.040	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.001	-0.005	17.260	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.005	0.028	19.196	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	18	PRO	0	-0.006	-0.007	20.356	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.008	-0.004	20.965	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.771	-0.878	15.270	-0.077	-0.077	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.002	0.000	19.160	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	22	GLN	0	-0.048	-0.019	21.706	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.838	0.906	14.063	0.058	0.058	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.030	-0.013	16.735	0.008	0.008	0.000	0.000	0.000	0.000
23	A	25	PHE	0	0.008	-0.001	20.466	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.054	-0.030	23.196	0.010	0.010	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.014	0.002	17.665	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	MET	0	-0.003	0.007	21.917	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.887	0.951	24.003	0.052	0.052	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.870	-0.919	24.018	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.043	-0.029	20.978	0.001	0.001	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.877	-0.944	25.582	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.065	-0.031	28.909	0.004	0.004	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.935	0.985	25.213	0.074	0.074	0.000	0.000	0.000	0.000
33	A	35	THR	0	0.020	-0.016	28.065	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.821	-0.872	30.730	-0.069	-0.069	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.837	-0.907	32.495	-0.044	-0.044	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.047	-0.026	29.951	0.003	0.003	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.801	0.880	32.749	0.075	0.075	0.000	0.000	0.000	0.000
38	A	40	ALA	0	0.035	0.024	36.439	0.002	0.002	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.854	-0.910	37.452	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.026	-0.020	34.985	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.935	-0.958	39.321	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.837	0.911	40.557	0.039	0.039	0.000	0.000	0.000	0.000
43	A	45	LEU	0	0.025	0.012	39.775	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.020	-0.014	43.030	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.022	-0.025	44.762	0.002	0.002	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.935	-0.971	46.312	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	49	TYR	0	-0.039	-0.014	45.793	0.001	0.001	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.037	-0.019	47.510	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.061	-0.023	50.715	0.002	0.002	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.021	-0.028	52.997	0.002	0.002	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.022	0.018	54.674	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	54	ARG	1	0.887	0.943	57.053	0.024	0.024	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.025	-0.016	55.577	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.017	0.023	50.130	0.001	0.001	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.049	-0.065	53.443	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	SER	0	-0.028	-0.057	50.197	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.840	-0.900	48.611	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.824	-0.865	47.963	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.934	0.972	47.319	0.040	0.040	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.011	-0.001	42.811	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.023	0.003	43.424	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.002	0.026	43.042	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	65	LEU	0	0.001	-0.012	42.111	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.867	0.934	35.868	0.053	0.053	0.000	0.000	0.000	0.000
65	A	67	GLN	0	-0.041	-0.026	37.895	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	68	ILE	0	0.034	0.021	37.401	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	69	GLN	0	-0.015	-0.015	35.116	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	70	GLU	-1	-0.856	-0.910	32.781	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.011	0.014	32.410	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	72	TYR	0	0.030	-0.003	32.540	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.029	-0.009	30.266	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.926	0.954	27.978	0.058	0.058	0.000	0.000	0.000	0.000
73	A	75	CYS	0	-0.033	-0.016	27.689	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.798	0.884	24.219	0.157	0.157	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.918	-0.960	23.981	-0.122	-0.122	0.000	0.000	0.000	0.000
76	A	78	PHE	0	0.032	-0.003	23.050	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.010	0.013	24.239	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.843	-0.902	20.662	-0.190	-0.190	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.890	-0.942	19.170	-0.201	-0.201	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.819	0.898	19.599	0.087	0.087	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.020	-0.004	20.639	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	84	GLN	0	0.019	0.009	14.879	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.023	0.024	17.100	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.007	0.009	18.379	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	MET	0	-0.018	-0.012	17.274	0.006	0.006	0.000	0.000	0.000	0.000
86	A	88	GLN	0	-0.017	-0.013	13.359	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	THR	0	-0.026	-0.035	15.949	0.010	0.010	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.092	-0.050	18.901	0.031	0.031	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.893	-0.957	14.950	-0.343	-0.343	0.000	0.000	0.000	0.000
90	A	92	MET	0	-0.087	-0.030	15.996	0.022	0.022	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.009	0.000	17.015	0.036	0.036	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.839	-0.903	19.324	-0.181	-0.181	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.903	0.936	12.670	0.264	0.264	0.000	0.000	0.000	0.000
94	A	96	HIS	0	0.001	-0.008	17.605	0.026	0.026	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.029	-0.006	20.461	0.018	0.018	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.964	0.982	19.593	0.191	0.191	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.848	0.936	19.880	0.042	0.042	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.012	-0.015	21.897	0.015	0.015	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.899	-0.957	25.214	-0.091	-0.091	0.000	0.000	0.000	0.000
100	A	102	THR	0	-0.107	-0.062	23.255	0.003	0.003	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.893	-0.924	24.781	-0.021	-0.021	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.113	-0.043	27.274	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)