FMO DATABASE

FMODB ID: 857YY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-513322.561254
FMO2-HF: Nuclear repulsion	479973.665754
FMO2-HF: Total energy	-33348.8955
FMO2-MP2: Total energy	-33445.52286

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.
-9.799	-5.378	1.616	-2.438	-3.599	-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 : 0.045 / q_NPA : 0.027

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	-0.880	-0.936	2.776	-10.976	-6.619	1.617	-2.428	-3.546	-0.009
4	A	4	VAL	0	-0.027	-0.032	4.785	0.473	0.537	-0.001	-0.010	-0.053	0.000
5	A	5	THR	0	0.039	0.040	8.219	0.136	0.136	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.021	-0.016	10.194	0.096	0.096	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.793	-0.878	13.332	-0.440	-0.440	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.019	-0.011	14.728	0.026	0.026	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.860	0.910	18.411	0.499	0.499	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.027	-0.010	21.309	0.004	0.004	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.995	0.984	23.819	0.164	0.164	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.008	0.006	25.693	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.040	0.021	21.467	0.009	0.009	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.025	0.014	16.484	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.000	0.010	21.061	0.036	0.036	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.006	-0.002	23.551	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.970	0.983	25.353	0.100	0.100	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.046	0.035	27.148	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.048	0.016	28.213	0.011	0.011	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.018	-0.009	25.671	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.003	-0.002	27.567	0.012	0.012	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.042	0.031	30.516	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.028	0.020	28.469	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.045	-0.021	25.782	0.008	0.008	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.037	-0.014	30.447	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.060	0.022	33.940	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.065	-0.066	31.124	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.842	0.943	33.246	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.012	0.028	35.140	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.053	-0.053	37.514	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.012	-0.028	39.597	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.018	-0.002	38.906	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.031	0.007	37.710	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.052	-0.041	37.800	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.005	0.006	36.568	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.818	-0.901	38.768	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.858	0.927	37.037	0.055	0.055	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.881	-0.940	40.690	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.012	-0.010	42.609	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.870	0.945	35.068	0.043	0.043	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.907	0.978	39.256	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.032	-0.018	34.254	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.028	0.007	33.536	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.032	0.004	33.536	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.856	0.928	32.198	-0.051	-0.051	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.015	0.001	29.119	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.031	0.008	24.523	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.042	0.010	21.885	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.035	0.027	27.397	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.036	0.022	30.501	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.022	-0.017	23.947	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.048	-0.020	29.576	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.006	0.011	31.313	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.029	0.022	32.672	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.042	-0.026	33.676	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.024	-0.001	34.526	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.040	0.002	36.526	0.007	0.007	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.036	0.020	38.644	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.052	-0.021	38.740	0.002	0.002	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.077	0.043	41.356	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.030	-0.023	39.157	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.830	0.907	42.510	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.019	-0.008	39.401	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.014	-0.012	42.059	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.019	-0.023	41.979	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.899	-0.943	43.354	0.026	0.026	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.012	-0.021	43.768	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.888	-0.943	45.184	0.040	0.040	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.747	-0.811	41.857	0.038	0.038	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.872	-0.933	44.023	0.017	0.017	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.920	-0.957	44.928	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.914	-0.966	43.653	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.024	-0.007	40.487	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.027	-0.023	40.892	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.842	0.905	42.897	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.006	0.008	39.249	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.056	-0.043	36.298	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.010	0.009	39.383	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.780	-0.868	41.466	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.058	-0.017	34.063	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.042	-0.021	37.861	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.927	-0.965	39.265	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.095	-0.046	38.487	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.835	0.885	37.653	0.072	0.072	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.049	-0.041	33.136	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.019	-0.002	33.864	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.923	-0.927	34.665	-0.091	-0.091	0.000	0.000	0.000	0.000

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