FMO DATABASE

FMODB ID: MV76Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-243112.572898
FMO2-HF: Nuclear repulsion	220384.589483
FMO2-HF: Total energy	-22727.983416
FMO2-MP2: Total energy	-22790.778092

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.
-9.753	-0.319	-0.076	-4.957	-4.401	-0.015

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 : -0.088 / q_NPA : -0.059

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	0.058	0.076	3.773	-7.939	1.495	-0.076	-4.957	-4.401	-0.015
4	A	13	SER	0	-0.018	-0.036	5.684	-0.008	-0.008	0.000	0.000	0.000	0.000
5	A	14	PHE	0	0.011	0.008	7.709	-0.027	-0.027	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.836	-0.919	10.622	0.018	0.018	0.000	0.000	0.000	0.000
7	A	16	GLN	0	0.007	-0.002	5.300	-0.224	-0.224	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.771	-0.869	10.350	-0.756	-0.756	0.000	0.000	0.000	0.000
9	A	18	PHE	0	-0.020	0.000	12.249	0.051	0.051	0.000	0.000	0.000	0.000
10	A	19	GLN	0	-0.023	-0.029	11.580	0.030	0.030	0.000	0.000	0.000	0.000
11	A	20	MET	0	-0.047	-0.008	11.481	0.035	0.035	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.740	0.822	14.256	0.465	0.465	0.000	0.000	0.000	0.000
13	A	22	VAL	0	0.009	0.014	17.324	0.025	0.025	0.000	0.000	0.000	0.000
14	A	23	MET	0	-0.035	-0.002	14.581	0.024	0.024	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.821	-0.898	16.409	-0.354	-0.354	0.000	0.000	0.000	0.000
16	A	25	GLU	-1	-0.947	-0.960	19.678	-0.104	-0.104	0.000	0.000	0.000	0.000
17	A	26	GLN	0	-0.037	-0.029	20.011	0.007	0.007	0.000	0.000	0.000	0.000
18	A	27	VAL	0	0.032	-0.022	19.232	0.008	0.008	0.000	0.000	0.000	0.000
19	A	28	SER	0	-0.122	-0.042	22.475	0.004	0.004	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.002	-0.005	25.296	0.005	0.005	0.000	0.000	0.000	0.000
21	A	30	MET	0	-0.060	0.025	22.005	0.010	0.010	0.000	0.000	0.000	0.000
22	A	31	SER	0	0.007	0.010	26.882	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.030	-0.010	27.734	0.001	0.001	0.000	0.000	0.000	0.000
24	A	33	GLN	0	-0.018	-0.015	27.558	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	34	GLU	-1	-0.882	-0.948	24.974	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	35	ALA	0	0.033	0.006	23.330	0.001	0.001	0.000	0.000	0.000	0.000
27	A	36	ARG	1	0.943	0.968	22.639	0.059	0.059	0.000	0.000	0.000	0.000
28	A	37	GLU	-1	-0.846	-0.898	23.355	0.005	0.005	0.000	0.000	0.000	0.000
29	A	38	LEU	0	0.071	0.032	20.227	0.008	0.008	0.000	0.000	0.000	0.000
30	A	39	LEU	0	0.019	0.021	18.080	0.003	0.003	0.000	0.000	0.000	0.000
31	A	40	LEU	0	-0.008	-0.007	18.727	0.000	0.000	0.000	0.000	0.000	0.000
32	A	41	GLN	0	-0.088	-0.057	19.581	0.019	0.019	0.000	0.000	0.000	0.000
33	A	42	ALA	0	0.018	0.008	15.125	0.027	0.027	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.026	-0.034	15.071	0.003	0.003	0.000	0.000	0.000	0.000
35	A	44	ARG	1	0.937	0.974	16.189	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	45	LEU	0	0.024	-0.014	12.608	0.040	0.040	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.015	0.018	10.170	0.066	0.066	0.000	0.000	0.000	0.000
38	A	47	MET	0	0.015	0.013	11.803	0.055	0.055	0.000	0.000	0.000	0.000
39	A	48	MET	0	-0.047	-0.027	14.167	0.021	0.021	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.960	0.991	8.369	-0.350	-0.350	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.796	-0.881	9.840	0.155	0.155	0.000	0.000	0.000	0.000
42	A	51	ASN	0	-0.056	-0.029	11.007	0.046	0.046	0.000	0.000	0.000	0.000
43	A	52	VAL	0	0.005	0.012	9.950	0.016	0.016	0.000	0.000	0.000	0.000
44	A	53	ILE	0	0.058	0.020	5.840	0.065	0.065	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.817	0.889	9.584	-0.099	-0.099	0.000	0.000	0.000	0.000
46	A	55	SER	0	-0.061	-0.032	12.349	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	56	LEU	0	0.021	0.009	9.093	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	57	VAL	0	0.020	0.010	9.049	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	58	LYS	1	0.925	0.959	11.460	-0.259	-0.259	0.000	0.000	0.000	0.000
50	A	59	ARG	1	0.935	0.964	14.868	-0.496	-0.496	0.000	0.000	0.000	0.000
51	A	60	ALA	0	0.000	0.030	12.272	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	61	ALA	0	-0.016	-0.008	14.428	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.944	0.982	16.959	-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)