FMO DATABASE

FMODB ID: 39K4L

Calculation Name: 5TDY-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TDY

Chain ID: D

ChEMBL ID:

UniProt ID: Q9WY63

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499777.480716
FMO2-HF: Nuclear repulsion	465942.396163
FMO2-HF: Total energy	-33835.084553
FMO2-MP2: Total energy	-33934.53787

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(D:3:GLU)

Summations of interaction energy for fragment #1(D:3:GLU)

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.
-23.599	-21.8	-0.001	-0.89	-0.907	0.004

Interaction energy analysis for fragmet #1(D:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.879 / q_NPA : -0.946

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	D	5	LYS	1	0.895	0.939	3.770	-47.868	-46.069	-0.001	-0.890	-0.907	0.004
4	D	6	ILE	0	0.023	0.010	6.520	-0.540	-0.540	0.000	0.000	0.000	0.000
5	D	7	ASP	-1	-0.775	-0.883	8.856	18.593	18.593	0.000	0.000	0.000	0.000
6	D	8	GLY	0	0.006	0.002	11.914	-0.449	-0.449	0.000	0.000	0.000	0.000
7	D	9	ARG	1	0.878	0.934	13.874	-17.046	-17.046	0.000	0.000	0.000	0.000
8	D	10	ARG	1	0.814	0.874	9.046	-22.248	-22.248	0.000	0.000	0.000	0.000
9	D	11	LYS	1	0.781	0.866	12.288	-18.306	-18.306	0.000	0.000	0.000	0.000
10	D	12	ALA	0	0.036	0.022	14.447	-0.672	-0.672	0.000	0.000	0.000	0.000
11	D	13	ALA	0	0.042	0.022	14.386	-0.670	-0.670	0.000	0.000	0.000	0.000
12	D	14	VAL	0	-0.025	-0.020	12.357	-0.599	-0.599	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.026	-0.008	15.538	-0.605	-0.605	0.000	0.000	0.000	0.000
14	D	16	LEU	0	0.004	-0.001	18.934	-0.632	-0.632	0.000	0.000	0.000	0.000
15	D	17	VAL	0	-0.019	-0.016	17.046	-0.497	-0.497	0.000	0.000	0.000	0.000
16	D	18	ALA	0	-0.084	-0.036	19.009	-0.351	-0.351	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.045	-0.020	20.678	-0.545	-0.545	0.000	0.000	0.000	0.000
18	D	20	GLY	0	0.037	0.035	23.210	-0.453	-0.453	0.000	0.000	0.000	0.000
19	D	21	PRO	0	0.000	-0.019	24.933	-0.138	-0.138	0.000	0.000	0.000	0.000
20	D	22	GLU	-1	-0.825	-0.895	26.551	8.695	8.695	0.000	0.000	0.000	0.000
21	D	23	LYS	1	0.953	0.976	27.234	-9.445	-9.445	0.000	0.000	0.000	0.000
22	D	24	ALA	0	0.036	0.010	23.838	0.003	0.003	0.000	0.000	0.000	0.000
23	D	25	ALA	0	0.040	0.018	25.582	0.036	0.036	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.065	-0.056	28.308	-0.152	-0.152	0.000	0.000	0.000	0.000
25	D	27	VAL	0	-0.012	0.007	24.597	-0.146	-0.146	0.000	0.000	0.000	0.000
26	D	28	MET	0	-0.003	0.001	22.127	-0.008	-0.008	0.000	0.000	0.000	0.000
27	D	29	LYS	1	0.853	0.935	27.172	-8.727	-8.727	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.099	-0.045	29.468	-0.496	-0.496	0.000	0.000	0.000	0.000
29	D	31	LEU	0	-0.044	-0.012	23.902	0.180	0.180	0.000	0.000	0.000	0.000
30	D	32	ASP	-1	-0.798	-0.871	27.022	10.569	10.569	0.000	0.000	0.000	0.000
31	D	33	GLU	-1	-0.924	-0.978	27.012	9.732	9.732	0.000	0.000	0.000	0.000
32	D	34	GLU	-1	-0.952	-0.960	23.249	12.750	12.750	0.000	0.000	0.000	0.000
33	D	35	THR	0	0.013	-0.034	22.256	0.682	0.682	0.000	0.000	0.000	0.000
34	D	36	VAL	0	-0.031	-0.030	22.131	0.487	0.487	0.000	0.000	0.000	0.000
35	D	37	GLU	-1	-0.871	-0.919	22.284	13.381	13.381	0.000	0.000	0.000	0.000
36	D	38	GLN	0	0.030	0.005	19.295	1.389	1.389	0.000	0.000	0.000	0.000
37	D	39	LEU	0	-0.032	-0.020	17.615	1.010	1.010	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.020	-0.006	18.359	0.424	0.424	0.000	0.000	0.000	0.000
39	D	41	VAL	0	0.003	0.005	17.068	0.396	0.396	0.000	0.000	0.000	0.000
40	D	42	GLU	-1	-0.923	-0.955	11.286	21.520	21.520	0.000	0.000	0.000	0.000
41	D	43	ILE	0	-0.035	-0.031	14.328	0.591	0.591	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.048	-0.018	16.591	0.107	0.107	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.086	-0.048	12.165	0.770	0.770	0.000	0.000	0.000	0.000
44	D	46	ILE	0	-0.016	0.007	11.577	1.513	1.513	0.000	0.000	0.000	0.000
45	D	47	GLY	0	0.018	0.018	11.006	1.210	1.210	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.913	0.956	7.240	-25.787	-25.787	0.000	0.000	0.000	0.000
47	D	49	VAL	0	0.055	0.035	10.130	0.894	0.894	0.000	0.000	0.000	0.000
48	D	50	THR	0	-0.058	-0.052	11.441	-0.625	-0.625	0.000	0.000	0.000	0.000
49	D	51	PRO	0	0.016	-0.008	13.885	-0.104	-0.104	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.815	-0.892	13.544	16.126	16.126	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.784	-0.867	9.891	21.281	21.281	0.000	0.000	0.000	0.000
52	D	54	LYS	1	0.946	0.969	12.946	-14.858	-14.858	0.000	0.000	0.000	0.000
53	D	55	LYS	1	0.810	0.895	16.286	-13.661	-13.661	0.000	0.000	0.000	0.000
54	D	56	GLN	0	0.016	0.001	12.357	0.144	0.144	0.000	0.000	0.000	0.000
55	D	57	VAL	0	-0.002	0.007	13.956	-0.347	-0.347	0.000	0.000	0.000	0.000
56	D	58	LEU	0	-0.001	-0.002	16.580	-0.579	-0.579	0.000	0.000	0.000	0.000
57	D	59	GLU	-1	-0.790	-0.877	19.553	12.595	12.595	0.000	0.000	0.000	0.000
58	D	60	GLU	-1	-0.812	-0.871	16.073	15.839	15.839	0.000	0.000	0.000	0.000
59	D	61	PHE	0	-0.004	-0.009	19.758	-0.518	-0.518	0.000	0.000	0.000	0.000
60	D	62	LEU	0	0.014	-0.005	21.775	-0.483	-0.483	0.000	0.000	0.000	0.000
61	D	63	SER	0	-0.031	-0.017	22.693	-0.480	-0.480	0.000	0.000	0.000	0.000
62	D	64	LEU	0	-0.027	-0.014	20.592	-0.378	-0.378	0.000	0.000	0.000	0.000
63	D	65	ALA	0	-0.018	0.000	24.833	-0.385	-0.385	0.000	0.000	0.000	0.000
64	D	66	LYS	1	0.857	0.916	27.504	-8.932	-8.932	0.000	0.000	0.000	0.000
65	D	67	ALA	0	0.037	0.017	27.504	-0.318	-0.318	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.894	0.954	29.031	-9.105	-9.105	0.000	0.000	0.000	0.000
67	D	69	GLU	-1	-0.904	-0.941	30.787	8.514	8.514	0.000	0.000	0.000	0.000
68	D	70	MET	0	0.021	0.011	32.316	-0.194	-0.194	0.000	0.000	0.000	0.000
69	D	71	ILE	0	-0.027	-0.014	31.015	-0.246	-0.246	0.000	0.000	0.000	0.000
70	D	72	SER	0	-0.061	-0.040	34.853	-0.212	-0.212	0.000	0.000	0.000	0.000
71	D	73	GLU	-1	-0.846	-0.924	35.677	7.977	7.977	0.000	0.000	0.000	0.000
72	D	74	GLY	0	0.045	0.025	38.218	-0.211	-0.211	0.000	0.000	0.000	0.000
73	D	75	GLY	0	0.018	0.010	39.500	-0.174	-0.174	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.025	-0.025	40.429	-0.219	-0.219	0.000	0.000	0.000	0.000
75	D	77	GLU	-1	-0.816	-0.888	42.775	6.595	6.595	0.000	0.000	0.000	0.000
76	D	78	TYR	0	0.035	0.015	43.949	-0.176	-0.176	0.000	0.000	0.000	0.000
77	D	79	ALA	0	0.007	0.001	45.427	-0.161	-0.161	0.000	0.000	0.000	0.000
78	D	80	LYS	1	0.935	0.966	45.559	-6.650	-6.650	0.000	0.000	0.000	0.000
79	D	81	LYS	1	0.811	0.893	45.773	-6.745	-6.745	0.000	0.000	0.000	0.000
80	D	82	VAL	0	-0.025	-0.009	49.387	-0.123	-0.123	0.000	0.000	0.000	0.000
81	D	83	LEU	0	-0.029	-0.020	50.575	-0.109	-0.109	0.000	0.000	0.000	0.000
82	D	84	GLU	-1	-0.916	-0.953	53.084	5.359	5.359	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.754	0.839	53.889	-5.678	-5.678	0.000	0.000	0.000	0.000
84	D	86	ALA	0	-0.039	-0.002	56.073	-0.085	-0.085	0.000	0.000	0.000	0.000
85	D	87	PHE	0	-0.062	-0.035	55.542	-0.068	-0.068	0.000	0.000	0.000	0.000
86	D	88	GLY	0	0.054	0.045	58.983	-0.083	-0.083	0.000	0.000	0.000	0.000
87	D	89	PRO	0	-0.061	-0.032	60.507	-0.043	-0.043	0.000	0.000	0.000	0.000
88	D	90	GLU	-1	-0.842	-0.892	57.978	5.369	5.369	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:GLU)