FMO DATABASE

FMODB ID: 823KY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-684516.457243
FMO2-HF: Nuclear repulsion	641474.428526
FMO2-HF: Total energy	-43042.028717
FMO2-MP2: Total energy	-43164.383946

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.
-3.762	-1.412	0.066	-0.96	-1.456	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 : 0.002 / q_NPA : -0.022

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	0.033	0.022	3.091	-0.873	1.334	0.067	-0.944	-1.330	0.003
4	A	6	TYR	0	0.001	-0.008	4.935	-0.499	-0.356	-0.001	-0.016	-0.126	0.000
5	A	7	LEU	0	-0.005	-0.001	7.280	-0.116	-0.116	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.899	-0.940	5.871	-1.768	-1.768	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.009	-0.018	7.955	0.426	0.426	0.000	0.000	0.000	0.000
8	A	10	TYR	0	-0.042	-0.014	10.652	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.013	-0.008	11.665	0.009	0.009	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.814	-0.894	11.480	-0.338	-0.338	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.069	-0.012	14.029	0.019	0.019	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.056	0.012	17.422	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.909	-0.958	20.261	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.041	-0.045	16.743	0.007	0.007	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.010	0.013	18.973	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	18	PRO	0	-0.026	-0.012	20.287	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.005	-0.005	20.755	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.872	-0.941	15.318	-0.307	-0.307	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.012	-0.011	19.166	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	22	GLN	0	-0.018	-0.013	21.785	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.929	0.978	15.994	0.207	0.207	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.041	-0.006	17.209	0.005	0.005	0.000	0.000	0.000	0.000
23	A	25	PHE	0	-0.020	-0.008	20.631	0.006	0.006	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.027	-0.014	23.407	0.022	0.022	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.020	0.020	17.821	0.007	0.007	0.000	0.000	0.000	0.000
26	A	28	MET	0	0.009	0.016	22.165	0.003	0.003	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.909	0.952	24.308	0.120	0.120	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.906	-0.951	24.225	-0.117	-0.117	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.060	-0.040	21.236	0.008	0.008	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.887	-0.958	25.687	-0.143	-0.143	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.034	0.000	28.982	0.009	0.009	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.933	0.976	25.722	0.136	0.136	0.000	0.000	0.000	0.000
33	A	35	THR	0	-0.022	-0.035	28.424	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.886	-0.911	31.084	-0.106	-0.106	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.889	-0.943	33.094	-0.081	-0.081	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.068	-0.039	30.195	0.005	0.005	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.929	0.955	32.049	0.125	0.125	0.000	0.000	0.000	0.000
38	A	40	ALA	0	0.047	0.040	36.581	0.004	0.004	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.866	-0.917	37.395	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.014	-0.019	35.515	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.926	-0.952	39.676	-0.062	-0.062	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.847	0.912	40.541	0.067	0.067	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.009	0.002	40.053	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.040	-0.019	43.652	0.002	0.002	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.005	-0.013	45.259	0.003	0.003	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.932	-0.958	47.226	-0.049	-0.049	0.000	0.000	0.000	0.000
47	A	49	TYR	0	-0.049	-0.014	46.332	0.003	0.003	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.049	-0.028	48.030	0.002	0.002	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.070	-0.036	51.055	0.002	0.002	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.016	-0.025	53.375	0.003	0.003	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.037	0.025	54.890	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	54	ARG	1	0.862	0.930	57.260	0.035	0.035	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.021	-0.012	56.384	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.057	0.040	50.396	0.001	0.001	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.030	-0.008	54.054	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	SER	0	0.031	-0.013	50.872	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.913	-0.961	48.900	-0.051	-0.051	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.876	-0.934	48.636	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.947	0.974	47.684	0.055	0.055	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.030	-0.006	43.457	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.032	0.004	44.073	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.048	0.037	43.562	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.009	-0.008	42.551	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.908	0.980	36.063	0.076	0.076	0.000	0.000	0.000	0.000
65	A	67	GLN	0	0.015	-0.001	38.275	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	68	ILE	0	0.018	0.012	38.036	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	69	GLN	0	-0.026	-0.024	35.381	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	70	GLU	-1	-0.915	-0.968	33.530	-0.092	-0.092	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.017	0.019	32.934	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	72	TYR	0	0.020	-0.009	32.894	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.041	-0.014	30.796	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.941	0.971	28.452	0.088	0.088	0.000	0.000	0.000	0.000
73	A	75	CYS	0	-0.026	-0.011	28.063	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.815	0.885	24.438	0.202	0.202	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.915	-0.947	24.123	-0.178	-0.178	0.000	0.000	0.000	0.000
76	A	78	PHE	0	0.051	0.018	23.396	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.026	-0.009	24.254	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.822	-0.899	21.177	-0.250	-0.250	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.887	-0.954	19.772	-0.293	-0.293	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.809	0.897	20.288	0.140	0.140	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.008	0.003	21.002	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	84	GLN	0	0.007	0.003	15.601	-0.067	-0.067	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.012	0.022	17.561	-0.036	-0.036	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.002	-0.003	18.781	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	87	MET	0	-0.017	-0.013	17.624	0.008	0.008	0.000	0.000	0.000	0.000
86	A	88	GLN	0	0.007	0.003	13.756	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	THR	0	-0.018	-0.016	16.336	0.003	0.003	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.041	-0.013	19.193	0.034	0.034	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.881	-0.954	15.371	-0.417	-0.417	0.000	0.000	0.000	0.000
90	A	92	MET	0	-0.087	-0.022	15.326	0.034	0.034	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.020	-0.023	16.675	0.039	0.039	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.883	-0.942	18.922	-0.238	-0.238	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.837	0.918	12.873	0.406	0.406	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.027	-0.030	17.509	0.051	0.051	0.000	0.000	0.000	0.000
95	A	97	ILE	0	0.012	0.011	20.213	0.028	0.028	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.973	0.982	19.049	0.235	0.235	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.873	0.961	19.819	0.094	0.094	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.029	-0.032	21.677	0.020	0.020	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.887	-0.946	24.966	-0.112	-0.112	0.000	0.000	0.000	0.000
100	A	102	THR	0	-0.107	-0.056	22.426	0.006	0.006	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.940	-0.958	24.719	-0.041	-0.041	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.115	-0.038	27.005	0.011	0.011	0.000	0.000	0.000	0.000

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