FMO DATABASE

FMODB ID: YY1N2

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	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-865056.534587
FMO2-HF: Nuclear repulsion	823350.800769
FMO2-HF: Total energy	-41705.733817
FMO2-MP2: Total energy	-41830.883645

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.
145.236	148.722	0.542	-1.35	-2.677	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 : 1.009 / q_NPA : 0.990

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].
3	A	17	ARG	1	0.951	0.983	3.805	28.898	30.826	-0.028	-0.929	-0.970	0.002
4	A	18	TYR	0	0.015	0.003	7.003	-0.407	-0.407	0.000	0.000	0.000	0.000
5	A	19	ILE	0	0.024	0.006	10.438	0.552	0.552	0.000	0.000	0.000	0.000
6	A	20	ALA	0	0.001	0.009	13.619	0.206	0.206	0.000	0.000	0.000	0.000
7	A	21	PHE	0	0.019	0.013	17.099	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	22	LYS	1	0.939	0.978	20.073	10.411	10.411	0.000	0.000	0.000	0.000
9	A	23	VAL	0	0.001	-0.004	23.800	-0.237	-0.237	0.000	0.000	0.000	0.000
10	A	24	ILE	0	-0.073	-0.036	26.222	0.225	0.225	0.000	0.000	0.000	0.000
11	A	25	SER	0	0.011	-0.019	29.585	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	26	GLU	-1	-0.888	-0.917	32.259	-7.838	-7.838	0.000	0.000	0.000	0.000
13	A	27	ASN	0	-0.029	-0.013	33.508	0.253	0.253	0.000	0.000	0.000	0.000
14	A	28	GLN	0	-0.040	-0.026	31.519	-0.299	-0.299	0.000	0.000	0.000	0.000
15	A	29	PHE	0	0.075	0.040	28.331	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	30	ASN	0	0.058	0.009	28.519	-0.163	-0.163	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.724	0.827	22.943	11.104	11.104	0.000	0.000	0.000	0.000
18	A	32	ASP	-1	-0.853	-0.936	24.322	-12.143	-12.143	0.000	0.000	0.000	0.000
19	A	33	GLU	-1	-0.721	-0.835	25.592	-10.108	-10.108	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.004	-0.005	21.783	-0.387	-0.387	0.000	0.000	0.000	0.000
21	A	35	LYS	1	0.803	0.897	20.109	12.359	12.359	0.000	0.000	0.000	0.000
22	A	36	GLU	-1	-0.937	-0.957	21.233	-12.078	-12.078	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.053	0.033	23.033	-0.356	-0.356	0.000	0.000	0.000	0.000
24	A	38	ILE	0	-0.065	-0.042	17.602	-0.501	-0.501	0.000	0.000	0.000	0.000
25	A	39	TRP	0	0.003	0.003	16.340	-0.739	-0.739	0.000	0.000	0.000	0.000
26	A	40	ASN	0	0.059	0.015	20.011	-0.137	-0.137	0.000	0.000	0.000	0.000
27	A	41	ALA	0	-0.011	0.010	20.720	0.058	0.058	0.000	0.000	0.000	0.000
28	A	42	CYS	0	-0.056	-0.039	16.744	-0.486	-0.486	0.000	0.000	0.000	0.000
29	A	43	LEU	0	-0.002	0.011	18.760	-0.347	-0.347	0.000	0.000	0.000	0.000
30	A	44	ARG	1	0.949	0.977	20.855	12.049	12.049	0.000	0.000	0.000	0.000
31	A	45	THR	0	-0.049	-0.022	20.261	0.394	0.394	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.063	-0.030	14.860	-0.468	-0.468	0.000	0.000	0.000	0.000
33	A	47	GLY	0	0.072	0.053	17.845	-0.552	-0.552	0.000	0.000	0.000	0.000
34	A	48	GLU	-1	-0.890	-0.953	17.825	-15.605	-15.605	0.000	0.000	0.000	0.000
35	A	49	LEU	0	-0.004	-0.002	13.624	-1.440	-1.440	0.000	0.000	0.000	0.000
36	A	50	GLY	0	0.054	0.016	13.770	-1.941	-1.941	0.000	0.000	0.000	0.000
37	A	51	THR	0	0.005	-0.006	13.189	-1.962	-1.962	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.033	0.020	12.806	-1.814	-1.814	0.000	0.000	0.000	0.000
39	A	53	LYS	1	0.883	0.958	9.143	22.981	22.981	0.000	0.000	0.000	0.000
40	A	54	ALA	0	0.046	0.010	8.423	-4.523	-4.523	0.000	0.000	0.000	0.000
41	A	55	LYS	1	0.781	0.893	6.187	34.089	34.089	0.000	0.000	0.000	0.000
42	A	56	PRO	0	0.057	0.026	9.940	-1.214	-1.214	0.000	0.000	0.000	0.000
43	A	57	TRP	0	-0.025	-0.018	12.142	0.247	0.247	0.000	0.000	0.000	0.000
44	A	58	LEU	0	0.071	0.052	13.571	-0.346	-0.346	0.000	0.000	0.000	0.000
45	A	59	ILE	0	-0.066	-0.031	12.133	0.295	0.295	0.000	0.000	0.000	0.000
46	A	60	LYS	1	0.944	0.963	15.463	14.062	14.062	0.000	0.000	0.000	0.000
47	A	61	PHE	0	0.046	0.014	18.621	-0.475	-0.475	0.000	0.000	0.000	0.000
48	A	62	ASP	-1	-0.886	-0.943	21.714	-10.369	-10.369	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.730	-0.854	24.516	-10.524	-10.524	0.000	0.000	0.000	0.000
50	A	64	THR	0	0.012	0.028	27.652	0.320	0.320	0.000	0.000	0.000	0.000
51	A	65	THR	0	-0.007	-0.007	25.700	0.139	0.139	0.000	0.000	0.000	0.000
52	A	66	GLN	0	-0.016	0.002	26.613	-0.303	-0.303	0.000	0.000	0.000	0.000
53	A	67	THR	0	-0.030	-0.027	21.551	-0.161	-0.161	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.060	0.022	20.038	0.106	0.106	0.000	0.000	0.000	0.000
55	A	69	ILE	0	-0.123	-0.053	13.480	-0.341	-0.341	0.000	0.000	0.000	0.000
56	A	70	ILE	0	0.080	0.047	12.936	-0.081	-0.081	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.871	0.940	7.418	25.900	25.900	0.000	0.000	0.000	0.000
58	A	72	SER	0	0.072	0.037	8.414	1.487	1.487	0.000	0.000	0.000	0.000
59	A	73	ASP	-1	-0.885	-0.943	4.153	-68.038	-67.721	0.000	-0.085	-0.232	0.000
60	A	74	ARG	1	0.871	0.915	2.712	46.770	47.728	0.571	-0.313	-1.216	-0.002
61	A	75	ASN	0	-0.040	-0.028	3.873	7.576	7.859	-0.001	-0.023	-0.259	0.000
62	A	76	HIS	0	0.045	0.024	7.372	-0.297	-0.297	0.000	0.000	0.000	0.000
63	A	77	VAL	0	-0.030	-0.006	7.956	1.931	1.931	0.000	0.000	0.000	0.000
64	A	78	TYR	0	0.031	-0.015	10.606	0.951	0.951	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.772	-0.852	13.081	-21.173	-21.173	0.000	0.000	0.000	0.000
66	A	80	VAL	0	0.014	0.008	12.269	0.956	0.956	0.000	0.000	0.000	0.000
67	A	81	ILE	0	-0.041	-0.022	14.153	1.072	1.072	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.006	0.012	16.739	0.821	0.821	0.000	0.000	0.000	0.000
69	A	83	SER	0	0.027	-0.011	17.773	0.748	0.748	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.037	-0.020	17.053	0.585	0.585	0.000	0.000	0.000	0.000
71	A	85	THR	0	-0.040	-0.030	20.640	0.639	0.639	0.000	0.000	0.000	0.000
72	A	86	LEU	0	-0.021	0.001	22.872	0.543	0.543	0.000	0.000	0.000	0.000
73	A	87	VAL	0	-0.077	-0.029	23.449	0.293	0.293	0.000	0.000	0.000	0.000
74	A	88	SER	0	-0.024	0.001	26.061	0.276	0.276	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.914	-0.971	29.813	-9.403	-9.403	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.038	-0.020	26.669	-0.487	-0.487	0.000	0.000	0.000	0.000
77	A	91	ASN	0	-0.019	-0.024	29.500	0.228	0.228	0.000	0.000	0.000	0.000
78	A	92	GLY	0	0.043	0.036	31.870	0.266	0.266	0.000	0.000	0.000	0.000
79	A	93	ASN	0	-0.042	-0.008	33.478	0.418	0.418	0.000	0.000	0.000	0.000
80	A	94	LYS	1	0.971	0.974	32.648	8.452	8.452	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.001	0.000	29.581	0.109	0.109	0.000	0.000	0.000	0.000
82	A	96	ILE	0	0.044	0.049	27.122	-0.207	-0.207	0.000	0.000	0.000	0.000
83	A	97	ILE	0	0.027	0.009	20.703	0.042	0.042	0.000	0.000	0.000	0.000
84	A	98	LYS	1	0.940	0.975	22.625	11.540	11.540	0.000	0.000	0.000	0.000
85	A	99	VAL	0	0.005	-0.012	17.105	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	100	LEU	0	-0.057	-0.038	19.307	0.432	0.432	0.000	0.000	0.000	0.000
87	A	101	GLY	0	0.040	0.019	17.027	0.280	0.280	0.000	0.000	0.000	0.000
88	A	102	VAL	0	0.038	0.026	11.473	-0.452	-0.452	0.000	0.000	0.000	0.000
89	A	103	SER	0	-0.031	-0.040	11.160	0.891	0.891	0.000	0.000	0.000	0.000
90	A	104	GLY	0	-0.010	0.009	7.387	-1.242	-1.242	0.000	0.000	0.000	0.000
91	A	105	THR	0	0.063	0.023	7.345	-0.636	-0.636	0.000	0.000	0.000	0.000
92	A	106	ILE	0	0.123	0.049	9.407	0.907	0.907	0.000	0.000	0.000	0.000
93	A	107	LYS	1	0.931	0.981	12.131	14.152	14.152	0.000	0.000	0.000	0.000
94	A	108	ARG	1	0.985	0.979	12.469	16.017	16.017	0.000	0.000	0.000	0.000
95	A	109	LEU	0	0.010	0.015	12.691	0.588	0.588	0.000	0.000	0.000	0.000
96	A	110	LYS	1	0.934	0.954	14.688	15.067	15.067	0.000	0.000	0.000	0.000
97	A	111	ARG	1	0.924	0.979	17.029	12.322	12.322	0.000	0.000	0.000	0.000
98	A	112	LYS	1	0.918	0.961	16.564	13.811	13.811	0.000	0.000	0.000	0.000
99	A	113	PHE	0	0.024	0.019	15.981	-0.095	-0.095	0.000	0.000	0.000	0.000
100	A	114	LEU	0	0.064	0.037	18.549	0.290	0.290	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.089	-0.064	21.201	0.518	0.518	0.000	0.000	0.000	0.000
102	A	116	GLN	0	-0.008	0.010	23.120	0.065	0.065	0.000	0.000	0.000	0.000
103	A	117	PHE	0	0.078	0.050	24.082	0.196	0.196	0.000	0.000	0.000	0.000
104	A	118	GLY	0	0.082	0.062	26.547	0.061	0.061	0.000	0.000	0.000	0.000
105	A	119	TRP	0	-0.071	-0.056	18.402	-0.737	-0.737	0.000	0.000	0.000	0.000
106	A	120	ARG	1	0.925	0.957	20.805	10.501	10.501	0.000	0.000	0.000	0.000

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