FMO DATABASE

FMODB ID: N9Z7Q

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	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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496438.836883
FMO2-HF: Nuclear repulsion	462604.402748
FMO2-HF: Total energy	-33834.434135
FMO2-MP2: Total energy	-33933.933814

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.
-14.632	-12.94	-0.021	-0.853	-0.818	0.005

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 : -0.910 / q_NPA : -0.966

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	0.958	0.967	3.810	-38.558	-36.866	-0.021	-0.853	-0.818	0.005
4	D	6	ILE	0	0.026	0.022	6.487	-0.150	-0.150	0.000	0.000	0.000	0.000
5	D	7	ASP	-1	-0.833	-0.917	8.674	20.611	20.611	0.000	0.000	0.000	0.000
6	D	8	GLY	0	-0.012	-0.022	11.856	-0.557	-0.557	0.000	0.000	0.000	0.000
7	D	9	ARG	1	0.948	0.978	14.041	-17.204	-17.204	0.000	0.000	0.000	0.000
8	D	10	ARG	1	0.857	0.919	9.282	-22.527	-22.527	0.000	0.000	0.000	0.000
9	D	11	LYS	1	0.835	0.912	12.506	-18.048	-18.048	0.000	0.000	0.000	0.000
10	D	12	ALA	0	0.024	0.019	14.453	-0.697	-0.697	0.000	0.000	0.000	0.000
11	D	13	ALA	0	0.050	0.028	14.566	-0.653	-0.653	0.000	0.000	0.000	0.000
12	D	14	VAL	0	-0.015	-0.013	12.283	-0.622	-0.622	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.023	-0.013	15.526	-0.649	-0.649	0.000	0.000	0.000	0.000
14	D	16	LEU	0	-0.006	-0.012	18.874	-0.653	-0.653	0.000	0.000	0.000	0.000
15	D	17	VAL	0	-0.002	0.002	17.123	-0.502	-0.502	0.000	0.000	0.000	0.000
16	D	18	ALA	0	-0.078	-0.037	19.053	-0.427	-0.427	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.049	-0.021	20.664	-0.549	-0.549	0.000	0.000	0.000	0.000
18	D	20	GLY	0	0.015	0.025	23.395	-0.475	-0.475	0.000	0.000	0.000	0.000
19	D	21	PRO	0	0.025	-0.010	25.301	-0.050	-0.050	0.000	0.000	0.000	0.000
20	D	22	GLU	-1	-0.858	-0.918	26.647	8.669	8.669	0.000	0.000	0.000	0.000
21	D	23	LYS	1	0.970	0.979	27.237	-9.357	-9.357	0.000	0.000	0.000	0.000
22	D	24	ALA	0	0.036	0.013	24.090	-0.044	-0.044	0.000	0.000	0.000	0.000
23	D	25	ALA	0	0.030	0.014	25.841	0.054	0.054	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.067	-0.046	28.611	-0.229	-0.229	0.000	0.000	0.000	0.000
25	D	27	VAL	0	-0.021	-0.006	24.961	-0.133	-0.133	0.000	0.000	0.000	0.000
26	D	28	MET	0	0.007	0.002	22.636	-0.013	-0.013	0.000	0.000	0.000	0.000
27	D	29	LYS	1	0.882	0.953	27.369	-8.630	-8.630	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.089	-0.033	29.622	-0.445	-0.445	0.000	0.000	0.000	0.000
29	D	31	LEU	0	-0.051	-0.016	23.994	0.162	0.162	0.000	0.000	0.000	0.000
30	D	32	ASP	-1	-0.822	-0.885	27.246	10.490	10.490	0.000	0.000	0.000	0.000
31	D	33	GLU	-1	-0.913	-0.971	27.434	9.789	9.789	0.000	0.000	0.000	0.000
32	D	34	GLU	-1	-0.952	-0.971	24.286	12.351	12.351	0.000	0.000	0.000	0.000
33	D	35	THR	0	0.009	-0.028	22.413	0.705	0.705	0.000	0.000	0.000	0.000
34	D	36	VAL	0	-0.040	-0.027	22.603	0.522	0.522	0.000	0.000	0.000	0.000
35	D	37	GLU	-1	-0.873	-0.906	23.217	13.295	13.295	0.000	0.000	0.000	0.000
36	D	38	GLN	0	-0.002	-0.033	19.468	1.418	1.418	0.000	0.000	0.000	0.000
37	D	39	LEU	0	-0.017	-0.020	18.282	0.901	0.901	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.021	0.001	18.980	0.362	0.362	0.000	0.000	0.000	0.000
39	D	41	VAL	0	0.005	0.005	17.043	0.418	0.418	0.000	0.000	0.000	0.000
40	D	42	GLU	-1	-0.937	-0.963	12.177	21.007	21.007	0.000	0.000	0.000	0.000
41	D	43	ILE	0	-0.047	-0.033	14.703	0.630	0.630	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.026	-0.006	16.803	0.149	0.149	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.111	-0.048	12.707	0.591	0.591	0.000	0.000	0.000	0.000
44	D	46	ILE	0	0.015	0.021	12.183	1.462	1.462	0.000	0.000	0.000	0.000
45	D	47	GLY	0	-0.002	0.020	10.603	1.436	1.436	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.941	0.963	6.770	-26.690	-26.690	0.000	0.000	0.000	0.000
47	D	49	VAL	0	0.048	0.023	9.951	0.884	0.884	0.000	0.000	0.000	0.000
48	D	50	THR	0	-0.014	-0.007	11.011	-0.738	-0.738	0.000	0.000	0.000	0.000
49	D	51	PRO	0	0.021	-0.011	13.373	-0.033	-0.033	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.864	-0.936	13.139	15.626	15.626	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.820	-0.908	9.403	22.004	22.004	0.000	0.000	0.000	0.000
52	D	54	LYS	1	0.959	0.972	12.427	-14.355	-14.355	0.000	0.000	0.000	0.000
53	D	55	LYS	1	0.894	0.956	15.754	-13.330	-13.330	0.000	0.000	0.000	0.000
54	D	56	GLN	0	0.026	0.009	11.249	0.130	0.130	0.000	0.000	0.000	0.000
55	D	57	VAL	0	0.003	0.014	13.532	-0.368	-0.368	0.000	0.000	0.000	0.000
56	D	58	LEU	0	-0.032	-0.020	16.102	-0.620	-0.620	0.000	0.000	0.000	0.000
57	D	59	GLU	-1	-0.871	-0.936	19.021	12.483	12.483	0.000	0.000	0.000	0.000
58	D	60	GLU	-1	-0.846	-0.918	16.026	15.412	15.412	0.000	0.000	0.000	0.000
59	D	61	PHE	0	-0.014	-0.014	19.378	-0.490	-0.490	0.000	0.000	0.000	0.000
60	D	62	LEU	0	0.010	-0.012	21.532	-0.482	-0.482	0.000	0.000	0.000	0.000
61	D	63	SER	0	-0.025	-0.006	22.430	-0.501	-0.501	0.000	0.000	0.000	0.000
62	D	64	LEU	0	-0.018	-0.008	20.575	-0.382	-0.382	0.000	0.000	0.000	0.000
63	D	65	ALA	0	-0.024	-0.006	24.679	-0.373	-0.373	0.000	0.000	0.000	0.000
64	D	66	LYS	1	0.971	0.993	27.194	-9.489	-9.489	0.000	0.000	0.000	0.000
65	D	67	ALA	0	0.015	0.006	27.323	-0.322	-0.322	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.932	0.968	28.863	-9.252	-9.252	0.000	0.000	0.000	0.000
67	D	69	GLU	-1	-0.923	-0.974	30.726	8.581	8.581	0.000	0.000	0.000	0.000
68	D	70	MET	0	0.050	0.016	32.224	-0.174	-0.174	0.000	0.000	0.000	0.000
69	D	71	ILE	0	-0.026	0.000	31.185	-0.211	-0.211	0.000	0.000	0.000	0.000
70	D	72	SER	0	-0.064	-0.037	34.871	-0.256	-0.256	0.000	0.000	0.000	0.000
71	D	73	GLU	-1	-0.950	-0.972	36.493	7.776	7.776	0.000	0.000	0.000	0.000
72	D	74	GLY	0	0.042	0.028	37.903	-0.213	-0.213	0.000	0.000	0.000	0.000
73	D	75	GLY	0	-0.007	-0.004	39.427	-0.186	-0.186	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.022	-0.018	40.320	-0.224	-0.224	0.000	0.000	0.000	0.000
75	D	77	GLU	-1	-0.849	-0.907	42.582	6.598	6.598	0.000	0.000	0.000	0.000
76	D	78	TYR	0	0.016	0.007	43.823	-0.179	-0.179	0.000	0.000	0.000	0.000
77	D	79	ALA	0	0.008	-0.001	45.392	-0.165	-0.165	0.000	0.000	0.000	0.000
78	D	80	LYS	1	0.942	0.962	46.308	-6.549	-6.549	0.000	0.000	0.000	0.000
79	D	81	LYS	1	0.868	0.923	46.085	-6.681	-6.681	0.000	0.000	0.000	0.000
80	D	82	VAL	0	-0.042	-0.008	49.515	-0.131	-0.131	0.000	0.000	0.000	0.000
81	D	83	LEU	0	-0.015	-0.011	50.831	-0.116	-0.116	0.000	0.000	0.000	0.000
82	D	84	GLU	-1	-0.924	-0.955	53.005	5.342	5.342	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.884	0.941	53.991	-5.742	-5.742	0.000	0.000	0.000	0.000
84	D	86	ALA	0	-0.053	-0.017	55.914	-0.088	-0.088	0.000	0.000	0.000	0.000
85	D	87	PHE	0	-0.049	-0.032	55.641	-0.078	-0.078	0.000	0.000	0.000	0.000
86	D	88	GLY	0	0.014	0.021	58.803	-0.089	-0.089	0.000	0.000	0.000	0.000
87	D	89	PRO	0	-0.042	-0.028	60.412	-0.041	-0.041	0.000	0.000	0.000	0.000
88	D	90	GLU	-1	-0.967	-0.976	58.458	5.230	5.230	0.000	0.000	0.000	0.000

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