FMO DATABASE

FMODB ID: 946N2

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:

Apendix: None

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	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-243191.851831
FMO2-HF: Nuclear repulsion	220464.287028
FMO2-HF: Total energy	-22727.564803
FMO2-MP2: Total energy	-22790.417216

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.
-12.085	0.75	-0.088	-6.122	-6.625	-0.041

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 : -0.137 / q_NPA : -0.116

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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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	0.087	0.107	3.768	-12.349	0.486	-0.088	-6.122	-6.625	-0.041
4	A	13	SER	0	0.016	0.006	5.705	0.336	0.336	0.000	0.000	0.000	0.000
5	A	14	PHE	0	0.003	0.004	7.745	-0.224	-0.224	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.850	-0.949	10.946	0.472	0.472	0.000	0.000	0.000	0.000
7	A	16	GLN	0	-0.003	-0.009	5.748	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.785	-0.880	10.289	-0.262	-0.262	0.000	0.000	0.000	0.000
9	A	18	PHE	0	-0.017	-0.001	12.263	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	19	GLN	0	-0.026	-0.032	12.006	0.014	0.014	0.000	0.000	0.000	0.000
11	A	20	MET	0	-0.035	-0.005	11.575	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.787	0.883	14.056	0.083	0.083	0.000	0.000	0.000	0.000
13	A	22	VAL	0	0.016	0.022	17.449	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	23	MET	0	-0.035	-0.007	14.239	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.871	-0.948	17.191	-0.132	-0.132	0.000	0.000	0.000	0.000
16	A	25	GLU	-1	-0.950	-0.971	19.751	0.010	0.010	0.000	0.000	0.000	0.000
17	A	26	GLN	0	-0.038	-0.027	20.073	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	27	VAL	0	0.018	-0.014	19.184	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	28	SER	0	-0.100	-0.032	22.529	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.003	-0.001	25.362	0.004	0.004	0.000	0.000	0.000	0.000
21	A	30	MET	0	-0.040	0.024	22.269	0.004	0.004	0.000	0.000	0.000	0.000
22	A	31	SER	0	0.002	0.008	26.927	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.024	-0.012	27.848	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	33	GLN	0	-0.013	-0.013	27.600	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	34	GLU	-1	-0.888	-0.948	24.991	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	35	ALA	0	0.029	0.003	23.370	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.935	0.960	22.684	0.064	0.064	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.831	-0.903	23.392	-0.064	-0.064	0.000	0.000	0.000	0.000
29	A	38	LEU	0	0.064	0.034	20.201	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	39	LEU	0	0.022	0.018	17.919	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	40	LEU	0	-0.003	0.007	18.756	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	41	GLN	0	-0.100	-0.055	19.742	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	42	ALA	0	0.015	0.008	15.239	0.002	0.002	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.026	-0.046	15.105	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	44	ARG	1	0.932	0.975	16.182	0.062	0.062	0.000	0.000	0.000	0.000
36	A	45	LEU	0	0.014	-0.016	12.979	0.006	0.006	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.009	0.016	10.339	0.009	0.009	0.000	0.000	0.000	0.000
38	A	47	MET	0	0.034	0.020	11.781	0.004	0.004	0.000	0.000	0.000	0.000
39	A	48	MET	0	-0.046	-0.023	14.130	0.008	0.008	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.949	0.986	8.453	0.001	0.001	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.841	-0.915	9.820	-0.317	-0.317	0.000	0.000	0.000	0.000
42	A	51	ASN	0	-0.059	-0.036	10.937	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.003	0.011	9.970	0.014	0.014	0.000	0.000	0.000	0.000
44	A	53	ILE	0	0.056	0.021	5.723	0.032	0.032	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.881	0.929	9.522	0.223	0.223	0.000	0.000	0.000	0.000
46	A	55	SER	0	-0.072	-0.033	12.414	0.008	0.008	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.044	0.016	8.763	0.012	0.012	0.000	0.000	0.000	0.000
48	A	57	VAL	0	0.019	0.012	9.121	0.009	0.009	0.000	0.000	0.000	0.000
49	A	58	LYS	1	0.920	0.952	11.487	0.114	0.114	0.000	0.000	0.000	0.000
50	A	59	ARG	1	0.949	0.971	14.935	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	60	ALA	0	-0.006	0.030	12.313	0.013	0.013	0.000	0.000	0.000	0.000
52	A	61	ALA	0	-0.007	0.004	14.451	0.004	0.004	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.926	0.964	16.945	0.074	0.074	0.000	0.000	0.000	0.000

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