FMO DATABASE

FMODB ID: 6YN6Z

Calculation Name: 2O8A-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8A

Chain ID: I

ChEMBL ID:

UniProt ID: Q9DCL8

Base Structure: X-ray

Registration Date: 2023-09-21

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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-248713.847858
FMO2-HF: Nuclear repulsion	223698.777946
FMO2-HF: Total energy	-25015.069913
FMO2-MP2: Total energy	-25087.768681

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(I:12:LYS)

Summations of interaction energy for fragment #1(I:12: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.
59.235	60.9	-0.012	-0.844	-0.809	0.002

Interaction energy analysis for fragmet #1(I:12:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.983 / q_NPA : 0.982

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	I	14	ILE	0	0.003	-0.008	3.822	-7.920	-6.255	-0.012	-0.844	-0.809	0.002
4	I	15	LEU	0	-0.011	0.007	5.879	2.621	2.621	0.000	0.000	0.000	0.000
5	I	16	LYS	1	0.948	0.969	9.093	25.213	25.213	0.000	0.000	0.000	0.000
6	I	17	ASN	0	0.051	0.038	10.657	-0.158	-0.158	0.000	0.000	0.000	0.000
7	I	44	LYS	1	0.998	0.999	8.718	29.796	29.796	0.000	0.000	0.000	0.000
8	I	45	SER	0	0.005	-0.022	15.529	0.544	0.544	0.000	0.000	0.000	0.000
9	I	46	GLN	0	-0.041	-0.008	16.669	-0.552	-0.552	0.000	0.000	0.000	0.000
10	I	47	LYS	1	0.949	0.970	17.269	18.082	18.082	0.000	0.000	0.000	0.000
11	I	48	TRP	0	0.034	0.020	18.921	-1.001	-1.001	0.000	0.000	0.000	0.000
12	I	49	ASP	-1	-0.892	-0.940	19.015	-15.546	-15.546	0.000	0.000	0.000	0.000
13	I	50	GLU	-1	-0.873	-0.963	20.965	-12.186	-12.186	0.000	0.000	0.000	0.000
14	I	51	MET	0	-0.001	0.002	23.701	0.674	0.674	0.000	0.000	0.000	0.000
15	I	52	ASN	0	-0.028	-0.011	21.161	0.417	0.417	0.000	0.000	0.000	0.000
16	I	53	ILE	0	0.002	-0.006	23.010	0.296	0.296	0.000	0.000	0.000	0.000
17	I	54	LEU	0	-0.032	-0.010	25.600	0.424	0.424	0.000	0.000	0.000	0.000
18	I	55	ALA	0	-0.026	0.003	25.470	0.342	0.342	0.000	0.000	0.000	0.000
19	I	56	THR	0	-0.095	-0.032	24.547	0.371	0.371	0.000	0.000	0.000	0.000
20	I	130	LEU	0	-0.011	-0.024	40.844	-0.046	-0.046	0.000	0.000	0.000	0.000
21	I	131	SER	0	0.015	0.026	44.097	0.231	0.231	0.000	0.000	0.000	0.000
22	I	132	PRO	0	0.028	0.010	46.119	-0.058	-0.058	0.000	0.000	0.000	0.000
23	I	133	GLU	-1	-0.855	-0.924	46.444	-6.541	-6.541	0.000	0.000	0.000	0.000
24	I	134	GLU	-1	-0.915	-0.991	41.015	-7.729	-7.729	0.000	0.000	0.000	0.000
25	I	135	ARG	1	0.907	0.964	41.944	7.236	7.236	0.000	0.000	0.000	0.000
26	I	136	GLU	-1	-0.738	-0.832	44.828	-6.636	-6.636	0.000	0.000	0.000	0.000
27	I	137	LYS	1	0.971	0.977	38.865	7.983	7.983	0.000	0.000	0.000	0.000
28	I	138	LYS	1	0.933	0.960	37.603	8.225	8.225	0.000	0.000	0.000	0.000
29	I	139	ARG	1	0.900	0.938	41.288	6.576	6.576	0.000	0.000	0.000	0.000
30	I	140	GLN	0	-0.049	-0.039	43.874	-0.048	-0.048	0.000	0.000	0.000	0.000
31	I	141	PHE	0	-0.025	-0.007	34.450	-0.042	-0.042	0.000	0.000	0.000	0.000
32	I	142	GLU	-1	-0.925	-0.978	39.110	-8.199	-8.199	0.000	0.000	0.000	0.000
33	I	143	MET	0	-0.026	-0.005	40.647	0.017	0.017	0.000	0.000	0.000	0.000
34	I	144	LYS	1	0.974	0.980	40.286	7.811	7.811	0.000	0.000	0.000	0.000
35	I	145	ARG	1	0.952	0.989	34.136	8.936	8.936	0.000	0.000	0.000	0.000
36	I	146	LYS	1	0.949	0.972	38.990	6.990	6.990	0.000	0.000	0.000	0.000
37	I	147	LEU	0	-0.038	-0.014	41.263	0.031	0.031	0.000	0.000	0.000	0.000
38	I	148	HIS	0	-0.030	-0.011	35.461	0.094	0.094	0.000	0.000	0.000	0.000
39	I	149	TYR	0	-0.057	-0.011	32.462	-0.104	-0.104	0.000	0.000	0.000	0.000
40	I	150	ASN	0	0.024	0.011	38.576	-0.056	-0.056	0.000	0.000	0.000	0.000
41	I	151	GLU	-1	-0.793	-0.910	35.590	-8.528	-8.528	0.000	0.000	0.000	0.000
42	I	152	GLY	0	-0.045	-0.028	39.177	0.054	0.054	0.000	0.000	0.000	0.000
43	I	153	LEU	0	-0.048	-0.018	40.586	0.141	0.141	0.000	0.000	0.000	0.000
44	I	154	ASN	0	0.009	-0.009	42.106	0.115	0.115	0.000	0.000	0.000	0.000
45	I	155	ILE	0	0.016	0.029	38.606	0.012	0.012	0.000	0.000	0.000	0.000
46	I	156	LYS	1	0.952	0.962	41.661	6.755	6.755	0.000	0.000	0.000	0.000
47	I	157	LEU	0	0.057	0.036	44.922	0.036	0.036	0.000	0.000	0.000	0.000
48	I	158	ALA	0	0.033	0.016	40.087	0.038	0.038	0.000	0.000	0.000	0.000
49	I	159	ARG	1	0.957	0.966	38.027	7.795	7.795	0.000	0.000	0.000	0.000
50	I	160	GLN	0	-0.021	-0.013	42.758	0.028	0.028	0.000	0.000	0.000	0.000
51	I	161	LEU	0	-0.001	-0.013	43.544	0.113	0.113	0.000	0.000	0.000	0.000
52	I	162	ILE	0	0.018	0.032	38.524	-0.026	-0.026	0.000	0.000	0.000	0.000
53	I	163	SER	0	-0.051	-0.044	42.343	-0.013	-0.013	0.000	0.000	0.000	0.000
54	I	164	LYS	1	0.912	0.951	45.210	6.126	6.126	0.000	0.000	0.000	0.000
55	I	165	ASP	-1	-0.865	-0.926	43.348	-6.729	-6.729	0.000	0.000	0.000	0.000
56	I	166	LEU	0	-0.042	-0.006	41.572	-0.050	-0.050	0.000	0.000	0.000	0.000
57	I	167	HIS	0	-0.085	-0.062	44.430	-0.015	-0.015	0.000	0.000	0.000	0.000
58	I	168	ASP	-1	-0.965	-0.968	47.197	-6.048	-6.048	0.000	0.000	0.000	0.000
59	I	169	ASP	-1	-1.023	-0.987	43.721	-6.657	-6.657	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:12:LYS)