FMO DATABASE

FMODB ID: 72R3K

Calculation Name: 2QDO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QDO

Chain ID: A

ChEMBL ID:

UniProt ID: A7LBW5

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	OptAll
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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-243207.455608
FMO2-HF: Nuclear repulsion	220479.174475
FMO2-HF: Total energy	-22728.281133
FMO2-MP2: Total energy	-22791.00873

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:VAL)

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

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.
-2.971	0.639	-0.029	-1.892	-1.687	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.036

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	12	LEU	0	-0.011	0.001	3.862	-1.499	2.111	-0.029	-1.892	-1.687	-0.004
4	A	13	SER	0	-0.032	-0.032	5.544	0.213	0.213	0.000	0.000	0.000	0.000
5	A	14	PHE	0	0.031	0.013	7.239	-0.033	-0.033	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.838	-0.908	10.188	0.051	0.051	0.000	0.000	0.000	0.000
7	A	16	GLN	0	-0.003	-0.002	5.268	-0.289	-0.289	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.795	-0.891	10.234	-0.818	-0.818	0.000	0.000	0.000	0.000
9	A	18	PHE	0	-0.031	-0.008	12.051	0.055	0.055	0.000	0.000	0.000	0.000
10	A	19	GLN	0	-0.030	-0.029	11.475	0.025	0.025	0.000	0.000	0.000	0.000
11	A	20	MET	0	-0.034	-0.003	11.606	0.032	0.032	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.752	0.838	14.035	0.551	0.551	0.000	0.000	0.000	0.000
13	A	22	VAL	0	0.032	0.023	17.623	0.026	0.026	0.000	0.000	0.000	0.000
14	A	23	MET	0	-0.046	-0.018	15.129	0.030	0.030	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.815	-0.889	16.451	-0.426	-0.426	0.000	0.000	0.000	0.000
16	A	25	GLU	-1	-0.921	-0.959	19.817	-0.130	-0.130	0.000	0.000	0.000	0.000
17	A	26	GLN	0	-0.033	-0.002	20.337	0.013	0.013	0.000	0.000	0.000	0.000
18	A	27	VAL	0	0.006	-0.029	19.486	0.011	0.011	0.000	0.000	0.000	0.000
19	A	28	SER	0	-0.135	-0.068	22.641	0.008	0.008	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.008	-0.011	25.442	0.009	0.009	0.000	0.000	0.000	0.000
21	A	30	MET	0	-0.070	0.017	21.817	0.009	0.009	0.000	0.000	0.000	0.000
22	A	31	SER	0	-0.006	-0.004	26.770	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.015	-0.011	27.637	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	33	GLN	0	-0.007	-0.019	27.662	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	34	GLU	-1	-0.813	-0.901	25.302	-0.073	-0.073	0.000	0.000	0.000	0.000
26	A	35	ALA	0	0.055	0.020	23.376	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.898	0.951	22.761	0.084	0.084	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.857	-0.906	23.385	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	38	LEU	0	0.048	0.018	20.189	0.006	0.006	0.000	0.000	0.000	0.000
30	A	39	LEU	0	0.023	0.023	18.520	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	40	LEU	0	0.000	0.001	18.908	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	41	GLN	0	-0.082	-0.056	19.774	0.013	0.013	0.000	0.000	0.000	0.000
33	A	42	ALA	0	0.031	0.017	15.099	0.021	0.021	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.029	-0.024	14.937	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	44	ARG	1	0.949	0.973	16.157	0.010	0.010	0.000	0.000	0.000	0.000
36	A	45	LEU	0	0.023	-0.009	12.858	0.037	0.037	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.015	0.014	10.143	0.059	0.059	0.000	0.000	0.000	0.000
38	A	47	MET	0	0.016	0.006	11.983	0.045	0.045	0.000	0.000	0.000	0.000
39	A	48	MET	0	-0.051	-0.022	14.244	0.028	0.028	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.943	0.975	8.368	-0.225	-0.225	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.775	-0.858	9.762	0.044	0.044	0.000	0.000	0.000	0.000
42	A	51	ASN	0	0.003	-0.006	10.991	0.040	0.040	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.007	0.006	9.919	0.025	0.025	0.000	0.000	0.000	0.000
44	A	53	ILE	0	0.034	0.019	5.610	0.083	0.083	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.799	0.871	9.498	0.011	0.011	0.000	0.000	0.000	0.000
46	A	55	SER	0	-0.060	-0.020	12.891	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.009	-0.014	8.802	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	57	VAL	0	0.027	0.012	9.139	0.015	0.015	0.000	0.000	0.000	0.000
49	A	58	LYS	1	0.908	0.959	11.530	-0.204	-0.204	0.000	0.000	0.000	0.000
50	A	59	ARG	1	0.953	0.960	14.794	-0.459	-0.459	0.000	0.000	0.000	0.000
51	A	60	ALA	0	-0.004	0.021	11.926	0.001	0.001	0.000	0.000	0.000	0.000
52	A	61	ALA	0	0.019	0.016	14.063	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.899	0.964	16.909	-0.242	-0.242	0.000	0.000	0.000	0.000

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