FMO DATABASE

FMODB ID: 53YRZ

Calculation Name: 2AV5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AV5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U151

Base Structure: X-ray

Registration Date: 2023-03-13

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-866273.574398
FMO2-HF: Nuclear repulsion	824569.019874
FMO2-HF: Total energy	-41704.554524
FMO2-MP2: Total energy	-41829.859476

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:15:LYS)

Summations of interaction energy for fragment #1(A:15:LYS)

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.
159.614	163.019	0.532	-1.291	-2.646	0

Interaction energy analysis for fragmet #1(A:15:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.006 / q_NPA : 0.991

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	17	ARG	1	0.947	0.985	3.805	29.713	31.704	-0.030	-0.966	-0.995	0.002
4	A	18	TYR	0	0.000	-0.002	7.003	-0.286	-0.286	0.000	0.000	0.000	0.000
5	A	19	ILE	0	0.027	0.010	10.471	0.447	0.447	0.000	0.000	0.000	0.000
6	A	20	ALA	0	0.006	0.003	13.619	0.215	0.215	0.000	0.000	0.000	0.000
7	A	21	PHE	0	0.011	0.012	17.099	-0.068	-0.068	0.000	0.000	0.000	0.000
8	A	22	LYS	1	0.987	1.001	20.073	10.313	10.313	0.000	0.000	0.000	0.000
9	A	23	VAL	0	0.000	0.000	23.800	-0.270	-0.270	0.000	0.000	0.000	0.000
10	A	24	ILE	0	-0.075	-0.037	26.222	0.216	0.216	0.000	0.000	0.000	0.000
11	A	25	SER	0	0.016	-0.022	29.585	0.010	0.010	0.000	0.000	0.000	0.000
12	A	26	GLU	-1	-0.897	-0.923	32.259	-7.830	-7.830	0.000	0.000	0.000	0.000
13	A	27	ASN	0	-0.022	-0.004	34.429	0.223	0.223	0.000	0.000	0.000	0.000
14	A	28	GLN	0	-0.035	-0.020	31.925	-0.283	-0.283	0.000	0.000	0.000	0.000
15	A	29	PHE	0	0.048	0.025	28.354	-0.076	-0.076	0.000	0.000	0.000	0.000
16	A	30	ASN	0	0.088	0.038	28.559	-0.063	-0.063	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.859	0.911	21.685	12.000	12.000	0.000	0.000	0.000	0.000
18	A	32	ASP	-1	-0.920	-0.974	24.143	-11.627	-11.627	0.000	0.000	0.000	0.000
19	A	33	GLU	-1	-0.764	-0.872	25.535	-10.003	-10.003	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.006	0.007	21.354	-0.395	-0.395	0.000	0.000	0.000	0.000
21	A	35	LYS	1	0.892	0.929	19.354	13.453	13.453	0.000	0.000	0.000	0.000
22	A	36	GLU	-1	-0.948	-0.958	21.259	-11.877	-11.877	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.068	0.042	23.054	-0.355	-0.355	0.000	0.000	0.000	0.000
24	A	38	ILE	0	-0.064	-0.045	17.513	-0.510	-0.510	0.000	0.000	0.000	0.000
25	A	39	TRP	0	-0.013	-0.004	16.289	-0.759	-0.759	0.000	0.000	0.000	0.000
26	A	40	ASN	0	0.050	0.011	20.031	-0.236	-0.236	0.000	0.000	0.000	0.000
27	A	41	ALA	0	-0.009	0.009	20.662	0.056	0.056	0.000	0.000	0.000	0.000
28	A	42	CYS	0	-0.059	-0.041	16.775	-0.533	-0.533	0.000	0.000	0.000	0.000
29	A	43	LEU	0	-0.010	0.009	18.763	-0.301	-0.301	0.000	0.000	0.000	0.000
30	A	44	ARG	1	0.953	0.979	20.863	11.969	11.969	0.000	0.000	0.000	0.000
31	A	45	THR	0	-0.034	-0.012	19.895	0.419	0.419	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.050	-0.023	14.876	-0.440	-0.440	0.000	0.000	0.000	0.000
33	A	47	GLY	0	0.071	0.052	18.291	-0.517	-0.517	0.000	0.000	0.000	0.000
34	A	48	GLU	-1	-0.887	-0.947	18.155	-15.325	-15.325	0.000	0.000	0.000	0.000
35	A	49	LEU	0	0.015	0.004	14.352	-1.384	-1.384	0.000	0.000	0.000	0.000
36	A	50	GLY	0	0.049	0.011	14.370	-1.856	-1.856	0.000	0.000	0.000	0.000
37	A	51	THR	0	0.002	-0.015	13.518	-1.810	-1.810	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.008	0.002	12.928	-1.660	-1.660	0.000	0.000	0.000	0.000
39	A	53	LYS	1	0.865	0.945	9.666	21.792	21.792	0.000	0.000	0.000	0.000
40	A	54	ALA	0	0.055	0.021	8.574	-4.089	-4.089	0.000	0.000	0.000	0.000
41	A	55	LYS	1	0.817	0.924	5.449	35.540	35.540	0.000	0.000	0.000	0.000
42	A	56	PRO	0	0.053	0.023	9.966	-1.220	-1.220	0.000	0.000	0.000	0.000
43	A	57	TRP	0	-0.017	-0.012	11.867	0.474	0.474	0.000	0.000	0.000	0.000
44	A	58	LEU	0	0.063	0.052	13.471	-0.416	-0.416	0.000	0.000	0.000	0.000
45	A	59	ILE	0	-0.072	-0.034	12.149	0.257	0.257	0.000	0.000	0.000	0.000
46	A	60	LYS	1	0.899	0.942	15.490	14.167	14.167	0.000	0.000	0.000	0.000
47	A	61	PHE	0	0.010	-0.006	18.650	-0.510	-0.510	0.000	0.000	0.000	0.000
48	A	62	ASP	-1	-0.854	-0.940	21.745	-10.390	-10.390	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.788	-0.913	24.548	-10.087	-10.087	0.000	0.000	0.000	0.000
50	A	64	THR	0	-0.038	0.025	27.683	0.298	0.298	0.000	0.000	0.000	0.000
51	A	65	THR	0	-0.054	-0.038	26.019	0.048	0.048	0.000	0.000	0.000	0.000
52	A	66	GLN	0	0.001	0.014	26.665	-0.211	-0.211	0.000	0.000	0.000	0.000
53	A	67	THR	0	-0.008	-0.006	21.505	-0.283	-0.283	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.012	-0.003	20.071	0.079	0.079	0.000	0.000	0.000	0.000
55	A	69	ILE	0	-0.119	-0.052	13.534	-0.376	-0.376	0.000	0.000	0.000	0.000
56	A	70	ILE	0	0.094	0.053	12.761	-0.080	-0.080	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.850	0.931	7.217	25.250	25.250	0.000	0.000	0.000	0.000
58	A	72	SER	0	0.059	0.025	8.429	1.438	1.438	0.000	0.000	0.000	0.000
59	A	73	ASP	-1	-0.930	-0.965	4.715	-60.539	-60.342	-0.001	-0.020	-0.176	0.000
60	A	74	ARG	1	0.889	0.917	2.671	48.538	49.534	0.564	-0.291	-1.269	-0.002
61	A	75	ASN	0	-0.048	-0.029	4.606	6.573	6.794	-0.001	-0.014	-0.206	0.000
62	A	76	HIS	0	0.057	0.039	7.365	-0.133	-0.133	0.000	0.000	0.000	0.000
63	A	77	VAL	0	-0.021	-0.003	8.057	2.004	2.004	0.000	0.000	0.000	0.000
64	A	78	TYR	0	0.022	-0.021	10.620	1.052	1.052	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.793	-0.873	13.086	-20.514	-20.514	0.000	0.000	0.000	0.000
66	A	80	VAL	0	-0.012	-0.014	12.031	0.971	0.971	0.000	0.000	0.000	0.000
67	A	81	ILE	0	-0.038	-0.023	14.565	1.054	1.054	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.004	0.010	16.754	0.806	0.806	0.000	0.000	0.000	0.000
69	A	83	SER	0	0.017	-0.009	17.911	0.827	0.827	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.033	-0.018	16.992	0.581	0.581	0.000	0.000	0.000	0.000
71	A	85	THR	0	-0.033	-0.023	20.710	0.622	0.622	0.000	0.000	0.000	0.000
72	A	86	LEU	0	-0.034	-0.005	22.818	0.509	0.509	0.000	0.000	0.000	0.000
73	A	87	VAL	0	-0.073	-0.025	23.394	0.280	0.280	0.000	0.000	0.000	0.000
74	A	88	SER	0	-0.008	0.006	26.069	0.242	0.242	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.917	-0.973	29.821	-9.371	-9.371	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.046	-0.012	26.730	-0.478	-0.478	0.000	0.000	0.000	0.000
77	A	91	ASN	0	0.021	-0.001	29.500	0.271	0.271	0.000	0.000	0.000	0.000
78	A	92	GLY	0	0.019	0.026	31.887	0.283	0.283	0.000	0.000	0.000	0.000
79	A	93	ASN	0	-0.048	-0.018	33.469	0.410	0.410	0.000	0.000	0.000	0.000
80	A	94	LYS	1	0.967	0.972	32.648	8.159	8.159	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.001	-0.002	29.617	0.111	0.111	0.000	0.000	0.000	0.000
82	A	96	ILE	0	0.045	0.062	26.639	-0.207	-0.207	0.000	0.000	0.000	0.000
83	A	97	ILE	0	0.031	0.005	20.515	0.017	0.017	0.000	0.000	0.000	0.000
84	A	98	LYS	1	0.955	0.984	22.683	11.452	11.452	0.000	0.000	0.000	0.000
85	A	99	VAL	0	-0.006	-0.012	17.102	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	100	LEU	0	-0.059	-0.042	19.315	0.391	0.391	0.000	0.000	0.000	0.000
87	A	101	GLY	0	0.039	0.020	17.068	0.259	0.259	0.000	0.000	0.000	0.000
88	A	102	VAL	0	0.041	0.030	11.444	-0.438	-0.438	0.000	0.000	0.000	0.000
89	A	103	SER	0	-0.037	-0.039	11.173	0.792	0.792	0.000	0.000	0.000	0.000
90	A	104	GLY	0	-0.010	0.007	7.388	-1.259	-1.259	0.000	0.000	0.000	0.000
91	A	105	THR	0	0.068	0.026	7.380	-0.608	-0.608	0.000	0.000	0.000	0.000
92	A	106	ILE	0	0.121	0.053	9.440	0.955	0.955	0.000	0.000	0.000	0.000
93	A	107	LYS	1	0.927	0.971	12.165	14.240	14.240	0.000	0.000	0.000	0.000
94	A	108	ARG	1	0.980	0.984	12.436	16.254	16.254	0.000	0.000	0.000	0.000
95	A	109	LEU	0	0.017	0.008	12.741	0.584	0.584	0.000	0.000	0.000	0.000
96	A	110	LYS	1	0.925	0.953	14.724	15.028	15.028	0.000	0.000	0.000	0.000
97	A	111	ARG	1	0.887	0.963	17.062	12.576	12.576	0.000	0.000	0.000	0.000
98	A	112	LYS	1	0.942	0.963	16.352	14.207	14.207	0.000	0.000	0.000	0.000
99	A	113	PHE	0	0.043	0.033	16.025	-0.124	-0.124	0.000	0.000	0.000	0.000
100	A	114	LEU	0	0.049	0.033	18.458	0.271	0.271	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.105	-0.077	21.237	0.525	0.525	0.000	0.000	0.000	0.000
102	A	116	GLN	0	0.008	0.009	23.155	0.071	0.071	0.000	0.000	0.000	0.000
103	A	117	PHE	0	0.100	0.075	24.004	0.188	0.188	0.000	0.000	0.000	0.000
104	A	118	GLY	0	0.092	0.063	26.582	0.056	0.056	0.000	0.000	0.000	0.000
105	A	119	TRP	0	-0.039	-0.039	18.645	-0.750	-0.750	0.000	0.000	0.000	0.000
106	A	120	ARG	1	0.933	0.953	20.836	10.664	10.664	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:LYS)