FMO DATABASE

FMODB ID: 17Y1Z

Calculation Name: 3LE5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LE5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R910

Base Structure: X-ray

Registration Date: 2023-06-22

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-514325.679966
FMO2-HF: Nuclear repulsion	480978.349881
FMO2-HF: Total energy	-33347.330085
FMO2-MP2: Total energy	-33444.062161

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-0.392	-3.199	10.027	-1.206	-6.014	-0.009

Interaction energy analysis for fragmet #1(A:1: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 : 0.003

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	3	GLU	-1	-0.912	-0.955	2.173	-1.366	-3.502	9.967	-2.078	-5.753	-0.009
4	A	4	VAL	0	-0.054	-0.035	3.139	0.618	-0.053	0.060	0.872	-0.261	0.000
5	A	5	THR	0	0.019	0.012	6.942	0.269	0.269	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.027	-0.005	9.757	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.912	-0.954	12.758	-0.146	-0.146	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.026	-0.015	15.136	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.984	0.983	18.267	0.207	0.207	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.028	-0.008	21.467	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	LYS	1	1.024	0.997	23.501	0.018	0.018	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.011	0.004	25.796	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.058	0.037	21.903	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.001	-0.003	16.735	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.048	-0.021	21.440	0.022	0.022	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.071	0.019	24.230	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.973	0.978	26.051	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.083	0.090	28.025	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.020	-0.012	28.106	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.001	-0.025	26.704	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.016	-0.014	28.276	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.027	0.023	31.266	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.024	0.025	28.586	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.037	-0.007	26.732	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.004	0.001	30.884	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.021	0.008	33.884	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.038	-0.046	30.909	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.847	0.950	33.034	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.022	0.031	34.960	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.028	-0.008	36.852	0.006	0.006	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.006	-0.012	39.159	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.068	-0.026	38.266	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.031	0.011	37.523	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.066	-0.037	37.715	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.017	-0.015	36.394	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.870	-0.958	38.150	0.050	0.050	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.915	0.962	37.748	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.944	-0.971	40.348	0.035	0.035	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.013	0.007	42.638	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.920	0.981	34.954	-0.053	-0.053	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.974	1.000	39.010	-0.059	-0.059	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.035	-0.007	33.702	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.058	0.037	32.901	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.048	0.013	33.110	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.906	0.944	32.087	-0.087	-0.087	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.037	-0.006	28.910	0.010	0.010	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.068	0.013	24.428	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.021	0.013	21.661	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.048	0.027	27.116	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.022	0.022	30.114	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.043	-0.031	23.807	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.074	-0.032	29.089	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.050	-0.027	30.633	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.011	-0.002	32.456	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.028	-0.015	33.533	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.029	-0.001	34.382	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.019	-0.013	36.407	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.026	0.012	38.736	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.041	-0.015	39.083	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.049	0.031	41.552	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.034	-0.023	38.871	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.907	0.955	42.271	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.011	0.000	39.083	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.031	-0.011	41.967	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.006	-0.020	41.754	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.927	-0.954	43.091	0.053	0.053	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.007	-0.030	43.681	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.912	-0.942	44.723	0.057	0.057	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.784	-0.868	41.736	0.062	0.062	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.927	-0.973	44.121	0.049	0.049	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.925	-0.964	45.183	0.038	0.038	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.923	-0.978	44.437	0.044	0.044	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.002	-0.010	40.522	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.014	-0.013	41.122	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.934	0.977	43.274	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.012	0.009	39.647	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.043	-0.014	36.497	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.020	0.003	39.629	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.783	-0.896	42.612	0.031	0.031	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.123	-0.065	34.743	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.064	-0.048	38.463	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.949	-0.971	39.766	0.024	0.024	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.067	-0.017	39.574	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.933	0.956	38.771	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.063	-0.037	34.360	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.047	-0.023	35.224	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.976	-0.963	34.999	0.010	0.010	0.000	0.000	0.000	0.000

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