FMO DATABASE

FMODB ID: LJYL9

Calculation Name: 2JEE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JEE

Chain ID: A

ChEMBL ID:

UniProt ID: P0AF36

Base Structure: X-ray

Registration Date: 2023-06-19

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-369960.090378
FMO2-HF: Nuclear repulsion	336921.582889
FMO2-HF: Total energy	-33038.507489
FMO2-MP2: Total energy	-33133.595214

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:3:MET)

Summations of interaction energy for fragment #1(A:3:MET)

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.
-6.472	-1.704	7.705	-2.919	-9.553	-0.012

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.017

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	5	LEU	0	-0.002	-0.004	2.947	-3.585	-1.062	0.181	-1.336	-1.368	-0.005
4	A	6	GLU	-1	-0.807	-0.894	5.008	0.607	0.607	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.024	-0.021	2.232	-1.304	-0.659	2.845	-0.653	-2.837	0.000
6	A	8	PHE	0	0.023	-0.002	2.349	-0.792	1.136	4.188	-1.956	-4.159	-0.006
7	A	9	GLU	-1	-0.852	-0.920	3.676	0.669	-0.305	0.080	1.213	-0.319	-0.001
8	A	10	LYS	1	0.802	0.895	6.858	-0.274	-0.274	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.079	-0.046	3.305	-1.274	-0.628	0.411	-0.187	-0.870	0.000
10	A	12	GLU	-1	-0.905	-0.956	6.888	0.056	0.056	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.022	0.014	8.667	-0.170	-0.170	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.922	0.950	9.940	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	15	VAL	0	-0.010	-0.001	8.757	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.016	0.022	11.612	-0.063	-0.063	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.055	0.043	14.705	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.035	-0.004	14.146	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.051	0.002	14.798	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	20	ASP	-1	-0.941	-0.963	17.471	0.061	0.061	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.058	-0.049	19.532	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.002	-0.007	18.666	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	23	THR	0	-0.033	-0.021	21.454	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.041	0.040	23.721	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.025	-0.002	23.402	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.013	-0.002	25.673	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.064	-0.031	27.483	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.869	-0.946	29.011	0.007	0.007	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.059	-0.031	29.074	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.844	-0.908	31.584	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.879	-0.936	33.542	0.004	0.004	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.033	-0.019	34.239	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.795	0.870	33.543	0.009	0.009	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.926	-0.952	37.424	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.916	0.957	39.429	0.002	0.002	0.000	0.000	0.000	0.000
34	A	36	ASN	0	-0.048	-0.026	40.586	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	ASN	0	0.021	-0.002	40.821	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.005	0.010	43.712	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	LEU	0	-0.026	-0.019	44.183	0.000	0.000	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.020	-0.003	45.982	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	GLN	0	0.011	-0.001	47.799	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.933	-0.965	49.713	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.028	-0.026	50.271	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	GLN	0	0.017	0.021	51.795	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	ASN	0	0.003	-0.007	54.088	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.007	0.012	55.551	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.016	-0.016	55.018	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.002	0.008	58.061	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.011	0.005	59.926	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.918	0.938	58.788	0.004	0.004	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.933	-0.957	61.690	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.854	-0.912	64.108	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.044	-0.014	64.948	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.953	-0.979	65.697	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.851	0.921	66.847	0.004	0.004	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.826	-0.898	70.510	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.081	-0.053	71.328	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.002	-0.020	71.961	0.000	0.000	0.000	0.000	0.000	0.000
57	A	59	HIS	0	-0.015	-0.010	74.814	0.000	0.000	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.009	0.002	75.144	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.909	0.942	77.239	0.002	0.002	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.925	-0.946	79.101	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	63	GLN	0	0.028	0.011	80.722	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	GLN	0	-0.070	-0.028	80.620	0.000	0.000	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.003	-0.027	82.372	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.066	0.055	84.870	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	TRP	0	-0.030	-0.035	85.453	0.000	0.000	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.059	-0.017	86.799	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.891	-0.941	88.795	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.921	0.982	91.136	0.002	0.002	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.044	-0.030	90.930	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	GLN	0	0.027	0.004	92.971	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ALA	0	0.012	0.000	95.209	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.108	-0.069	95.033	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.001	0.011	95.832	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.104	0.062	99.382	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.915	0.946	101.399	0.002	0.002	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.092	-0.044	102.020	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.964	-0.975	101.466	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-1.044	-0.998	105.228	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)