FMO DATABASE

FMODB ID: R8GQ8

Calculation Name: 2DLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DLB

Chain ID: A

ChEMBL ID:

UniProt ID: O34498

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	70
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-350247.065926
FMO2-HF: Nuclear repulsion	322752.525761
FMO2-HF: Total energy	-27494.540165
FMO2-MP2: Total energy	-27574.191779

3D Structure Molmil

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:2002:ALA)

Summations of interaction energy for fragment #1(A:2002:ALA)

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.
-3.877	0.786	1.042	-2.499	-3.207	-0.001

Interaction energy analysis for fragmet #1(A:2002:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.005

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	2004	TYR	0	-0.010	-0.017	2.718	-3.257	1.406	1.042	-2.499	-3.207	-0.001
4	A	2005	LEU	0	0.003	0.019	6.063	0.127	0.127	0.000	0.000	0.000	0.000
5	A	2006	ASN	0	-0.022	-0.025	9.617	-0.095	-0.095	0.000	0.000	0.000	0.000
6	A	2007	ASN	0	-0.003	-0.001	12.173	0.029	0.029	0.000	0.000	0.000	0.000
7	A	2008	ILE	0	-0.001	-0.010	14.860	0.000	0.000	0.000	0.000	0.000	0.000
8	A	2009	ALA	0	0.023	0.023	18.251	0.014	0.014	0.000	0.000	0.000	0.000
9	A	2010	LEU	0	-0.023	-0.015	21.411	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	2011	ASN	0	0.005	0.007	24.319	0.008	0.008	0.000	0.000	0.000	0.000
11	A	2012	LEU	0	-0.023	-0.019	26.934	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	2013	GLU	-1	-0.810	-0.867	30.207	-0.120	-0.120	0.000	0.000	0.000	0.000
13	A	2014	ILE	0	-0.041	-0.023	33.380	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	2015	VAL	0	0.016	0.004	35.930	0.007	0.007	0.000	0.000	0.000	0.000
15	A	2016	LEU	0	0.012	0.004	38.843	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	2017	LYS	1	0.947	0.977	41.760	0.089	0.089	0.000	0.000	0.000	0.000
17	A	2018	ASN	0	-0.035	0.007	45.543	0.002	0.002	0.000	0.000	0.000	0.000
18	A	2019	LYS	1	0.947	0.962	48.093	0.067	0.067	0.000	0.000	0.000	0.000
19	A	2020	ALA	0	0.019	0.005	51.167	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	2021	ASP	-1	-0.893	-0.941	53.207	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	2022	SER	0	0.003	0.007	54.091	0.001	0.001	0.000	0.000	0.000	0.000
22	A	2023	PRO	0	0.042	0.017	50.175	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	2024	GLU	-1	-0.785	-0.901	49.263	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	2025	VAL	0	-0.019	0.002	49.308	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	2026	SER	0	-0.048	-0.049	47.958	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	2027	GLU	-1	-0.773	-0.863	45.093	-0.082	-0.082	0.000	0.000	0.000	0.000
27	A	2028	THR	0	-0.053	-0.009	44.533	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	2029	LEU	0	-0.087	-0.048	45.045	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	2030	VAL	0	0.028	0.009	40.565	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	2031	THR	0	0.044	0.009	40.573	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	2032	ARG	1	0.926	0.976	40.113	0.077	0.077	0.000	0.000	0.000	0.000
32	A	2033	ILE	0	-0.030	-0.008	38.290	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	2034	CYS	0	-0.029	-0.015	36.239	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	2035	GLU	-1	-0.812	-0.884	35.396	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	2036	ASN	0	-0.154	-0.091	35.875	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	2037	LEU	0	-0.032	-0.022	32.487	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	2038	LEU	0	0.020	0.035	31.208	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	2039	LEU	0	-0.030	-0.011	29.210	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	2040	SER	0	0.006	0.005	28.763	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	2041	LYS	1	0.888	0.927	24.639	0.195	0.195	0.000	0.000	0.000	0.000
41	A	2042	GLU	-1	-0.906	-0.941	23.600	-0.315	-0.315	0.000	0.000	0.000	0.000
42	A	2043	VAL	0	-0.006	0.011	24.017	0.025	0.025	0.000	0.000	0.000	0.000
43	A	2044	SER	0	0.007	0.000	24.643	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	2045	PHE	0	0.009	0.007	24.167	0.016	0.016	0.000	0.000	0.000	0.000
45	A	2046	LEU	0	0.001	0.004	26.984	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	2047	LYS	1	0.843	0.911	22.179	0.331	0.331	0.000	0.000	0.000	0.000
47	A	2048	ALA	0	0.030	0.012	28.099	0.013	0.013	0.000	0.000	0.000	0.000
48	A	2049	ASP	-1	-0.877	-0.915	26.427	-0.220	-0.220	0.000	0.000	0.000	0.000
49	A	2050	GLY	0	-0.016	-0.007	30.045	0.008	0.008	0.000	0.000	0.000	0.000
50	A	2051	SER	0	-0.120	-0.076	25.965	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	2052	VAL	0	0.017	-0.006	26.884	0.001	0.001	0.000	0.000	0.000	0.000
52	A	2053	GLU	-1	-0.902	-0.930	19.185	-0.445	-0.445	0.000	0.000	0.000	0.000
53	A	2054	ASN	0	-0.025	-0.027	22.562	0.025	0.025	0.000	0.000	0.000	0.000
54	A	2055	PHE	0	-0.007	-0.004	18.327	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	2056	LYS	1	0.949	0.970	17.079	0.454	0.454	0.000	0.000	0.000	0.000
56	A	2057	LEU	0	-0.006	0.007	20.330	-0.027	-0.027	0.000	0.000	0.000	0.000
57	A	2058	SER	0	-0.086	-0.053	19.782	0.016	0.016	0.000	0.000	0.000	0.000
58	A	2059	ASH	0	-0.096	-0.104	21.922	0.022	0.022	0.000	0.000	0.000	0.000
59	A	2060	MET	0	-0.007	0.005	24.973	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	2061	GLU	-1	-0.838	-0.859	27.911	-0.173	-0.173	0.000	0.000	0.000	0.000
61	A	2062	TYR	0	-0.086	-0.095	30.954	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	2063	GLU	-1	-0.916	-0.954	33.908	-0.106	-0.106	0.000	0.000	0.000	0.000
63	A	2064	ILE	0	-0.045	-0.019	37.001	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	2065	THR	0	-0.021	-0.018	37.612	0.003	0.003	0.000	0.000	0.000	0.000
65	A	2066	ASN	0	-0.078	-0.055	40.227	0.003	0.003	0.000	0.000	0.000	0.000
66	A	2067	THR	0	-0.048	-0.056	43.519	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	2068	GLU	-1	-0.954	-0.973	45.842	-0.075	-0.075	0.000	0.000	0.000	0.000
68	A	2069	GLU	-1	-0.974	-0.976	48.961	-0.057	-0.057	0.000	0.000	0.000	0.000
69	A	2070	LEU	0	-0.048	-0.030	48.474	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	2071	PRO	0	0.003	0.003	52.525	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2002:ALA)