FMO DATABASE

FMODB ID: 9GZY2

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	OptAll
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	-370415.622883
FMO2-HF: Nuclear repulsion	337376.393041
FMO2-HF: Total energy	-33039.229842
FMO2-MP2: Total energy	-33134.271614

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.
-7.076	-2.049	7.628	-2.902	-9.755	-0.016

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 : -0.020 / 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	5	LEU	0	0.062	0.023	2.636	-4.021	-1.568	0.768	-1.453	-1.768	-0.008
4	A	6	GLU	-1	-0.792	-0.882	4.966	0.243	0.451	-0.001	-0.006	-0.201	0.000
5	A	7	VAL	0	-0.029	-0.016	2.298	-1.272	-0.417	2.219	-0.568	-2.507	-0.002
6	A	8	PHE	0	0.004	-0.001	2.558	-0.666	1.197	3.181	-1.515	-3.530	-0.003
7	A	9	GLU	-1	-0.859	-0.931	3.852	0.300	-0.439	0.052	0.940	-0.253	-0.001
8	A	10	LYS	1	0.774	0.867	6.800	0.020	0.020	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.072	-0.029	2.764	-1.411	-1.024	1.409	-0.300	-1.496	-0.002
10	A	12	GLU	-1	-0.896	-0.954	6.787	0.105	0.105	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.027	0.010	8.712	-0.151	-0.151	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.928	0.961	9.608	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	15	VAL	0	-0.009	-0.002	8.413	-0.061	-0.061	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.009	0.011	11.261	-0.047	-0.047	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.039	0.027	14.339	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.032	-0.005	14.025	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.019	0.007	14.432	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	20	ASP	-1	-0.876	-0.934	17.410	0.033	0.033	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.048	-0.037	19.032	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.033	-0.019	18.701	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	23	THR	0	-0.041	-0.028	21.198	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.017	-0.004	23.461	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	LEU	0	0.003	0.002	22.912	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.023	-0.004	25.555	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.029	-0.010	27.377	0.000	0.000	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.875	-0.943	28.906	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.047	-0.029	29.043	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.839	-0.903	31.516	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.875	-0.938	33.428	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.041	-0.019	33.517	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.805	0.885	33.608	0.013	0.013	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.931	-0.952	37.320	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.869	0.923	39.361	0.007	0.007	0.000	0.000	0.000	0.000
34	A	36	ASN	0	-0.052	-0.027	40.249	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.007	-0.016	40.600	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.000	0.015	43.614	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	LEU	0	-0.008	-0.004	43.607	0.000	0.000	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.008	0.001	45.808	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	GLN	0	0.026	0.008	47.658	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.878	-0.949	48.146	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.012	-0.007	49.954	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.010	0.002	51.360	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	ASN	0	-0.001	-0.004	53.655	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.002	0.006	55.237	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.027	-0.026	54.961	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.002	0.007	57.852	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.014	-0.017	59.685	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.842	0.907	59.045	0.006	0.006	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.912	-0.948	61.939	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.855	-0.897	63.927	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.027	-0.019	64.256	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.886	-0.937	64.514	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.855	0.921	67.026	0.005	0.005	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.841	-0.908	70.084	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.069	-0.039	71.026	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.010	-0.016	71.724	0.000	0.000	0.000	0.000	0.000	0.000
57	A	59	HIS	0	0.005	0.002	74.661	0.000	0.000	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.002	-0.003	74.483	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.868	0.932	76.972	0.004	0.004	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.930	-0.962	78.700	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.005	-0.012	80.488	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	GLN	0	-0.019	-0.004	80.353	0.000	0.000	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.011	-0.004	81.963	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.067	0.044	84.767	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	TRP	0	-0.047	-0.039	84.812	0.000	0.000	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.059	-0.022	86.651	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.897	-0.946	88.565	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.912	0.963	90.653	0.003	0.003	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.033	-0.022	90.977	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	GLN	0	0.010	0.004	92.373	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ALA	0	0.030	0.014	94.862	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.085	-0.049	94.961	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.025	0.004	95.309	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.128	0.068	99.042	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.898	0.941	100.943	0.003	0.003	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.091	-0.044	101.854	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.970	-0.984	100.951	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-1.047	-1.007	104.967	-0.002	-0.002	0.000	0.000	0.000	0.000

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