FMO DATABASE

FMODB ID: QVGKY

Calculation Name: 2DLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-350250.374526
FMO2-HF: Nuclear repulsion	322755.679533
FMO2-HF: Total energy	-27494.694993
FMO2-MP2: Total energy	-27574.336918

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: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.
-2.993	0.862	1.007	-2.121	-2.741	-0.004

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 : 0.020 / q_NPA : 0.012

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	-0.008	-0.015	2.587	-2.470	1.385	1.007	-2.121	-2.741	-0.004
4	A	2005	LEU	0	0.003	0.005	6.061	0.159	0.159	0.000	0.000	0.000	0.000
5	A	2006	ASN	0	-0.026	-0.017	9.779	-0.072	-0.072	0.000	0.000	0.000	0.000
6	A	2007	ASN	0	0.008	-0.001	12.678	0.035	0.035	0.000	0.000	0.000	0.000
7	A	2008	ILE	0	0.017	0.000	15.578	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	2009	ALA	0	0.037	0.026	19.039	0.014	0.014	0.000	0.000	0.000	0.000
9	A	2010	LEU	0	-0.022	-0.013	21.845	0.008	0.008	0.000	0.000	0.000	0.000
10	A	2011	ASN	0	0.005	0.009	24.532	0.015	0.015	0.000	0.000	0.000	0.000
11	A	2012	LEU	0	-0.035	-0.024	27.396	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	2013	GLU	-1	-0.828	-0.869	30.400	-0.117	-0.117	0.000	0.000	0.000	0.000
13	A	2014	ILE	0	-0.033	-0.025	33.715	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	2015	VAL	0	0.002	0.001	36.265	0.007	0.007	0.000	0.000	0.000	0.000
15	A	2016	LEU	0	0.009	0.003	39.109	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	2017	LYS	1	0.953	0.974	42.208	0.086	0.086	0.000	0.000	0.000	0.000
17	A	2018	ASN	0	-0.027	0.008	45.999	0.002	0.002	0.000	0.000	0.000	0.000
18	A	2019	LYS	1	0.932	0.957	48.527	0.064	0.064	0.000	0.000	0.000	0.000
19	A	2020	ALA	0	0.018	0.015	51.514	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	2021	ASP	-1	-0.881	-0.927	53.569	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	2022	SER	0	-0.001	-0.005	54.216	0.001	0.001	0.000	0.000	0.000	0.000
22	A	2023	PRO	0	0.041	0.019	50.545	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	2024	GLU	-1	-0.788	-0.902	49.489	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	2025	VAL	0	-0.010	0.007	49.334	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	2026	SER	0	-0.043	-0.038	48.447	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	2027	GLU	-1	-0.790	-0.872	45.244	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	2028	THR	0	-0.055	-0.022	44.589	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	2029	LEU	0	-0.088	-0.048	45.144	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	2030	VAL	0	0.016	0.008	40.675	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	2031	THR	0	0.053	0.015	40.652	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	2032	ARG	1	0.923	0.967	40.228	0.073	0.073	0.000	0.000	0.000	0.000
32	A	2033	ILE	0	-0.049	-0.019	38.476	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	2034	CYS	0	-0.028	-0.015	36.393	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	2035	GLU	-1	-0.827	-0.897	35.489	-0.110	-0.110	0.000	0.000	0.000	0.000
35	A	2036	ASN	0	-0.124	-0.079	35.810	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	2037	LEU	0	-0.028	-0.006	32.628	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	2038	LEU	0	0.026	0.028	31.306	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	2039	LEU	0	-0.015	-0.005	29.802	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	2040	SER	0	0.019	0.019	28.634	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	2041	LYS	1	0.825	0.885	24.653	0.189	0.189	0.000	0.000	0.000	0.000
41	A	2042	GLU	-1	-0.921	-0.938	23.710	-0.293	-0.293	0.000	0.000	0.000	0.000
42	A	2043	VAL	0	0.018	0.021	24.097	0.024	0.024	0.000	0.000	0.000	0.000
43	A	2044	SER	0	-0.005	-0.005	24.850	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	2045	PHE	0	0.018	0.009	24.511	0.014	0.014	0.000	0.000	0.000	0.000
45	A	2046	LEU	0	-0.013	0.003	27.612	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	2047	LYS	1	0.843	0.921	23.193	0.304	0.304	0.000	0.000	0.000	0.000
47	A	2048	ALA	0	0.014	-0.004	28.927	0.012	0.012	0.000	0.000	0.000	0.000
48	A	2049	ASP	-1	-0.855	-0.896	26.918	-0.220	-0.220	0.000	0.000	0.000	0.000
49	A	2050	GLY	0	-0.008	0.001	30.190	0.007	0.007	0.000	0.000	0.000	0.000
50	A	2051	SER	0	-0.104	-0.076	26.581	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	2052	VAL	0	0.004	-0.015	27.631	0.003	0.003	0.000	0.000	0.000	0.000
52	A	2053	GLU	-1	-0.898	-0.925	20.144	-0.411	-0.411	0.000	0.000	0.000	0.000
53	A	2054	ASN	0	-0.029	-0.043	22.705	0.025	0.025	0.000	0.000	0.000	0.000
54	A	2055	PHE	0	-0.003	0.002	18.929	-0.044	-0.044	0.000	0.000	0.000	0.000
55	A	2056	LYS	1	0.954	0.974	17.312	0.419	0.419	0.000	0.000	0.000	0.000
56	A	2057	LEU	0	0.005	0.011	20.481	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	2058	SER	0	-0.087	-0.056	19.562	0.013	0.013	0.000	0.000	0.000	0.000
58	A	2059	ASH	0	-0.096	-0.098	21.957	0.019	0.019	0.000	0.000	0.000	0.000
59	A	2060	MET	0	-0.016	-0.001	24.936	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	2061	GLU	-1	-0.828	-0.858	28.024	-0.166	-0.166	0.000	0.000	0.000	0.000
61	A	2062	TYR	0	-0.075	-0.078	31.178	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	2063	GLU	-1	-0.931	-0.959	34.240	-0.102	-0.102	0.000	0.000	0.000	0.000
63	A	2064	ILE	0	-0.037	-0.029	37.537	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	2065	THR	0	-0.040	-0.029	37.676	0.005	0.005	0.000	0.000	0.000	0.000
65	A	2066	ASN	0	-0.074	-0.050	40.388	0.002	0.002	0.000	0.000	0.000	0.000
66	A	2067	THR	0	-0.037	-0.051	43.668	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	2068	GLU	-1	-0.940	-0.958	46.289	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	2069	GLU	-1	-0.957	-0.970	49.262	-0.056	-0.056	0.000	0.000	0.000	0.000
69	A	2070	LEU	0	-0.049	-0.036	48.867	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	2071	PRO	0	-0.017	-0.004	52.970	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)