FMO DATABASE

FMODB ID: ZV57N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-350294.288762
FMO2-HF: Nuclear repulsion	322800.136597
FMO2-HF: Total energy	-27494.152165
FMO2-MP2: Total energy	-27573.796723

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.
-4.1	0.45	0.837	-2.431	-2.956	0.002

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 : 0.026 / q_NPA : 0.013

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

Sort

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	-0.009	-0.011	2.608	-3.402	1.148	0.837	-2.431	-2.956	0.002
4	A	2005	LEU	0	-0.003	0.014	5.972	0.163	0.163	0.000	0.000	0.000	0.000
5	A	2006	ASN	0	-0.013	-0.021	9.518	-0.152	-0.152	0.000	0.000	0.000	0.000
6	A	2007	ASN	0	-0.010	-0.006	12.087	0.037	0.037	0.000	0.000	0.000	0.000
7	A	2008	ILE	0	-0.005	-0.012	14.931	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	2009	ALA	0	0.025	0.024	18.174	0.017	0.017	0.000	0.000	0.000	0.000
9	A	2010	LEU	0	-0.021	-0.017	21.137	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	2011	ASN	0	0.005	0.010	24.244	0.013	0.013	0.000	0.000	0.000	0.000
11	A	2012	LEU	0	-0.022	-0.018	26.858	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	2013	GLU	-1	-0.807	-0.875	30.134	-0.130	-0.130	0.000	0.000	0.000	0.000
13	A	2014	ILE	0	-0.048	-0.025	33.345	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	2015	VAL	0	0.009	0.001	35.854	0.007	0.007	0.000	0.000	0.000	0.000
15	A	2016	LEU	0	0.032	0.008	39.376	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	2017	LYS	1	0.932	0.976	41.678	0.095	0.095	0.000	0.000	0.000	0.000
17	A	2018	ASN	0	-0.039	0.004	45.462	0.002	0.002	0.000	0.000	0.000	0.000
18	A	2019	LYS	1	0.947	0.960	48.008	0.070	0.070	0.000	0.000	0.000	0.000
19	A	2020	ALA	0	0.010	0.003	51.107	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	2021	ASP	-1	-0.906	-0.957	53.119	-0.057	-0.057	0.000	0.000	0.000	0.000
21	A	2022	SER	0	0.024	0.025	54.004	0.001	0.001	0.000	0.000	0.000	0.000
22	A	2023	PRO	0	0.053	0.023	50.118	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	2024	GLU	-1	-0.794	-0.903	49.177	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	2025	VAL	0	-0.030	-0.008	49.218	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	2026	SER	0	-0.058	-0.054	47.736	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	2027	GLU	-1	-0.768	-0.866	45.080	-0.088	-0.088	0.000	0.000	0.000	0.000
27	A	2028	THR	0	-0.040	-0.007	44.438	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	2029	LEU	0	-0.097	-0.059	44.944	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	2030	VAL	0	0.027	0.017	40.392	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	2031	THR	0	0.040	0.009	40.469	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	2032	ARG	1	0.914	0.968	40.011	0.080	0.080	0.000	0.000	0.000	0.000
32	A	2033	ILE	0	-0.056	-0.030	38.145	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	2034	CYS	0	-0.010	-0.008	36.203	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	2035	GLU	-1	-0.843	-0.918	35.291	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	2036	ASN	0	-0.084	-0.042	35.766	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	2037	LEU	0	-0.055	-0.032	32.292	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	2038	LEU	0	0.014	0.024	31.098	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	2039	LEU	0	-0.045	-0.021	29.091	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	2040	SER	0	-0.026	-0.009	28.645	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	2041	LYS	1	0.956	0.967	24.551	0.196	0.196	0.000	0.000	0.000	0.000
41	A	2042	GLU	-1	-0.968	-0.981	23.612	-0.325	-0.325	0.000	0.000	0.000	0.000
42	A	2043	VAL	0	-0.006	0.012	23.923	0.025	0.025	0.000	0.000	0.000	0.000
43	A	2044	SER	0	0.005	0.002	24.700	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	2045	PHE	0	0.019	0.009	24.411	0.015	0.015	0.000	0.000	0.000	0.000
45	A	2046	LEU	0	0.000	0.001	27.061	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	2047	LYS	1	0.846	0.922	22.116	0.349	0.349	0.000	0.000	0.000	0.000
47	A	2048	ALA	0	0.039	0.017	28.171	0.013	0.013	0.000	0.000	0.000	0.000
48	A	2049	ASP	-1	-0.895	-0.935	26.740	-0.226	-0.226	0.000	0.000	0.000	0.000
49	A	2050	GLY	0	-0.021	-0.009	30.119	0.008	0.008	0.000	0.000	0.000	0.000
50	A	2051	SER	0	-0.102	-0.053	26.016	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	2052	VAL	0	0.030	-0.002	26.737	0.000	0.000	0.000	0.000	0.000	0.000
52	A	2053	GLU	-1	-0.919	-0.955	19.039	-0.480	-0.480	0.000	0.000	0.000	0.000
53	A	2054	ASN	0	0.014	0.005	22.483	0.028	0.028	0.000	0.000	0.000	0.000
54	A	2055	PHE	0	0.007	0.005	18.297	-0.045	-0.045	0.000	0.000	0.000	0.000
55	A	2056	LYS	1	0.954	0.972	17.024	0.454	0.454	0.000	0.000	0.000	0.000
56	A	2057	LEU	0	-0.014	0.004	20.219	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	2058	SER	0	-0.084	-0.053	19.686	0.017	0.017	0.000	0.000	0.000	0.000
58	A	2059	ASH	0	-0.099	-0.121	21.815	0.023	0.023	0.000	0.000	0.000	0.000
59	A	2060	MET	0	-0.014	0.001	24.874	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	2061	GLU	-1	-0.840	-0.849	27.995	-0.181	-0.181	0.000	0.000	0.000	0.000
61	A	2062	TYR	0	-0.068	-0.055	30.865	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	2063	GLU	-1	-0.917	-0.959	33.820	-0.115	-0.115	0.000	0.000	0.000	0.000
63	A	2064	ILE	0	-0.045	-0.016	36.916	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	2065	THR	0	-0.013	-0.006	37.402	0.003	0.003	0.000	0.000	0.000	0.000
65	A	2066	ASN	0	-0.021	-0.022	40.152	0.007	0.007	0.000	0.000	0.000	0.000
66	A	2067	THR	0	-0.063	-0.060	43.441	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	2068	GLU	-1	-0.998	-1.000	45.895	-0.082	-0.082	0.000	0.000	0.000	0.000
68	A	2069	GLU	-1	-0.966	-0.970	48.886	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	2070	LEU	0	-0.056	-0.037	48.526	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	2071	PRO	0	0.006	0.005	52.451	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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