FMO DATABASE

FMODB ID: 6YLVZ

Calculation Name: 2P58-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: A

ChEMBL ID:

UniProt ID: O68690

Base Structure: X-ray

Registration Date: 2023-09-20

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-262945.074762
FMO2-HF: Nuclear repulsion	240818.963709
FMO2-HF: Total energy	-22126.111054
FMO2-MP2: Total energy	-22188.341297

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:10:ASN)

Summations of interaction energy for fragment #1(A:10:ASN)

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.
-5.739	0.349	1.431	-2.875	-4.643	-0.004

Interaction energy analysis for fragmet #1(A:10:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.015

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	12	GLU	-1	-0.850	-0.931	2.678	-2.223	1.739	0.420	-1.849	-2.532	0.003
4	A	13	THR	0	-0.027	-0.013	2.188	-3.755	-1.900	1.010	-0.965	-1.900	-0.007
5	A	14	VAL	0	0.053	0.040	4.034	0.696	0.967	0.001	-0.061	-0.211	0.000
6	A	15	ARG	1	0.976	0.997	6.084	-1.168	-1.168	0.000	0.000	0.000	0.000
7	A	16	SER	0	-0.017	-0.013	6.687	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	17	ILE	0	0.024	-0.005	7.654	0.062	0.062	0.000	0.000	0.000	0.000
9	A	18	THR	0	0.003	-0.001	9.816	0.125	0.125	0.000	0.000	0.000	0.000
10	A	19	MET	0	-0.026	-0.017	11.336	0.156	0.156	0.000	0.000	0.000	0.000
11	A	20	GLN	0	-0.020	0.001	12.444	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.003	-0.007	13.169	0.030	0.030	0.000	0.000	0.000	0.000
13	A	22	GLU	-1	-0.858	-0.936	15.743	0.084	0.084	0.000	0.000	0.000	0.000
14	A	23	MET	0	-0.073	-0.030	15.025	0.040	0.040	0.000	0.000	0.000	0.000
15	A	24	ALA	0	-0.012	-0.002	18.440	0.008	0.008	0.000	0.000	0.000	0.000
16	A	25	LEU	0	0.031	0.022	20.115	0.010	0.010	0.000	0.000	0.000	0.000
17	A	26	THR	0	-0.021	-0.019	21.454	0.021	0.021	0.000	0.000	0.000	0.000
18	A	27	LYS	1	0.860	0.921	22.982	0.089	0.089	0.000	0.000	0.000	0.000
19	A	28	LEU	0	0.032	0.045	24.459	0.006	0.006	0.000	0.000	0.000	0.000
20	A	29	LYS	1	0.979	0.971	25.122	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	30	LYS	1	0.933	0.968	25.588	-0.068	-0.068	0.000	0.000	0.000	0.000
22	A	31	ASP	-1	-0.881	-0.937	28.365	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	32	MET	0	-0.035	-0.012	29.881	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	33	MET	0	-0.025	0.004	32.380	0.002	0.002	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.886	0.955	30.563	0.036	0.036	0.000	0.000	0.000	0.000
26	A	35	GLY	0	0.033	0.041	36.210	0.001	0.001	0.000	0.000	0.000	0.000
27	A	36	GLY	0	0.013	-0.009	37.281	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.859	-0.924	39.050	-0.066	-0.066	0.000	0.000	0.000	0.000
29	A	38	ALA	0	0.046	-0.007	38.457	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	39	LYS	1	0.963	0.979	37.496	0.083	0.083	0.000	0.000	0.000	0.000
31	A	40	GLN	0	0.016	0.026	32.640	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	41	TYR	0	-0.026	-0.039	33.502	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	42	GLN	0	-0.061	-0.017	33.096	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	43	VAL	0	-0.010	-0.002	29.999	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	44	TRP	0	0.066	0.008	29.043	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	45	GLN	0	0.014	0.012	28.248	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.926	0.956	27.830	0.133	0.133	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.920	-0.953	23.499	-0.204	-0.204	0.000	0.000	0.000	0.000
39	A	48	SER	0	0.040	0.005	23.538	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.911	0.964	23.616	0.107	0.107	0.000	0.000	0.000	0.000
41	A	50	ALA	0	0.001	0.008	21.503	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.007	0.002	18.732	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.920	-0.966	18.686	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	53	SER	0	-0.056	-0.040	19.520	0.014	0.014	0.000	0.000	0.000	0.000
45	A	54	ALA	0	-0.004	0.004	15.339	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	55	ILE	0	-0.008	-0.001	14.759	-0.050	-0.050	0.000	0.000	0.000	0.000
47	A	56	ALA	0	0.004	0.010	15.090	0.020	0.020	0.000	0.000	0.000	0.000
48	A	57	ILE	0	0.006	0.004	13.244	0.022	0.022	0.000	0.000	0.000	0.000
49	A	58	ILE	0	-0.007	-0.001	9.220	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	59	HIS	0	0.007	-0.001	11.469	0.073	0.073	0.000	0.000	0.000	0.000
51	A	60	TYR	0	-0.054	-0.046	13.794	0.066	0.066	0.000	0.000	0.000	0.000
52	A	61	VAL	0	-0.048	-0.012	10.335	0.036	0.036	0.000	0.000	0.000	0.000
53	A	62	ALA	0	-0.045	-0.015	7.388	0.043	0.043	0.000	0.000	0.000	0.000
54	A	63	GLY	0	-0.056	-0.012	9.319	0.194	0.194	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:10:ASN)