FMO DATABASE

FMODB ID: JL4R9

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	OptHSide
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	-497170.160674
FMO2-HF: Nuclear repulsion	463335.168803
FMO2-HF: Total energy	-33834.991871
FMO2-MP2: Total energy	-33934.494848

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.
-20.785	-18.911	-0.019	-0.915	-0.94	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 : -0.890 / q_NPA : -0.954

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	0.929	0.958	3.810	-45.230	-43.356	-0.019	-0.915	-0.940	0.005
4	D	6	ILE	0	0.023	0.019	6.487	-0.229	-0.229	0.000	0.000	0.000	0.000
5	D	7	ASP	-1	-0.779	-0.897	8.584	19.358	19.358	0.000	0.000	0.000	0.000
6	D	8	GLY	0	-0.006	-0.004	11.755	-0.501	-0.501	0.000	0.000	0.000	0.000
7	D	9	ARG	1	0.900	0.941	13.935	-17.133	-17.133	0.000	0.000	0.000	0.000
8	D	10	ARG	1	0.835	0.891	9.067	-22.536	-22.536	0.000	0.000	0.000	0.000
9	D	11	LYS	1	0.782	0.861	12.404	-18.027	-18.027	0.000	0.000	0.000	0.000
10	D	12	ALA	0	0.019	0.014	14.364	-0.707	-0.707	0.000	0.000	0.000	0.000
11	D	13	ALA	0	0.050	0.027	14.492	-0.657	-0.657	0.000	0.000	0.000	0.000
12	D	14	VAL	0	-0.014	-0.011	12.221	-0.606	-0.606	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.034	-0.015	15.449	-0.647	-0.647	0.000	0.000	0.000	0.000
14	D	16	LEU	0	-0.001	-0.010	18.798	-0.653	-0.653	0.000	0.000	0.000	0.000
15	D	17	VAL	0	-0.007	-0.001	17.132	-0.501	-0.501	0.000	0.000	0.000	0.000
16	D	18	ALA	0	-0.082	-0.038	18.949	-0.431	-0.431	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.044	-0.019	20.604	-0.550	-0.550	0.000	0.000	0.000	0.000
18	D	20	GLY	0	0.022	0.029	23.329	-0.478	-0.478	0.000	0.000	0.000	0.000
19	D	21	PRO	0	0.025	-0.011	25.236	-0.049	-0.049	0.000	0.000	0.000	0.000
20	D	22	GLU	-1	-0.843	-0.898	26.573	8.671	8.671	0.000	0.000	0.000	0.000
21	D	23	LYS	1	0.970	0.981	27.233	-9.422	-9.422	0.000	0.000	0.000	0.000
22	D	24	ALA	0	0.036	0.012	23.987	-0.045	-0.045	0.000	0.000	0.000	0.000
23	D	25	ALA	0	0.031	0.015	25.756	0.051	0.051	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.049	-0.039	28.522	-0.195	-0.195	0.000	0.000	0.000	0.000
25	D	27	VAL	0	-0.021	-0.005	24.827	-0.140	-0.140	0.000	0.000	0.000	0.000
26	D	28	MET	0	0.007	0.002	22.451	-0.011	-0.011	0.000	0.000	0.000	0.000
27	D	29	LYS	1	0.851	0.930	27.264	-8.671	-8.671	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.102	-0.044	29.515	-0.468	-0.468	0.000	0.000	0.000	0.000
29	D	31	LEU	0	-0.048	-0.012	23.933	0.154	0.154	0.000	0.000	0.000	0.000
30	D	32	ASP	-1	-0.833	-0.897	27.202	10.495	10.495	0.000	0.000	0.000	0.000
31	D	33	GLU	-1	-0.914	-0.974	27.323	9.776	9.776	0.000	0.000	0.000	0.000
32	D	34	GLU	-1	-0.957	-0.975	24.055	12.658	12.658	0.000	0.000	0.000	0.000
33	D	35	THR	0	0.031	-0.006	22.432	0.662	0.662	0.000	0.000	0.000	0.000
34	D	36	VAL	0	-0.043	-0.032	22.493	0.517	0.517	0.000	0.000	0.000	0.000
35	D	37	GLU	-1	-0.866	-0.915	22.978	13.400	13.400	0.000	0.000	0.000	0.000
36	D	38	GLN	0	0.026	0.002	19.408	1.340	1.340	0.000	0.000	0.000	0.000
37	D	39	LEU	0	-0.031	-0.026	18.093	0.896	0.896	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.016	0.002	18.879	0.364	0.364	0.000	0.000	0.000	0.000
39	D	41	VAL	0	-0.002	0.009	17.319	0.452	0.452	0.000	0.000	0.000	0.000
40	D	42	GLU	-1	-0.927	-0.962	11.877	21.235	21.235	0.000	0.000	0.000	0.000
41	D	43	ILE	0	-0.045	-0.033	14.609	0.622	0.622	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.031	-0.008	16.723	0.156	0.156	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.120	-0.058	12.685	0.719	0.719	0.000	0.000	0.000	0.000
44	D	46	ILE	0	0.020	0.025	12.100	1.418	1.418	0.000	0.000	0.000	0.000
45	D	47	GLY	0	-0.007	0.009	10.548	1.440	1.440	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.932	0.958	6.966	-26.365	-26.365	0.000	0.000	0.000	0.000
47	D	49	VAL	0	0.041	0.023	9.912	0.852	0.852	0.000	0.000	0.000	0.000
48	D	50	THR	0	-0.062	-0.054	10.864	-0.617	-0.617	0.000	0.000	0.000	0.000
49	D	51	PRO	0	0.033	-0.002	13.368	-0.049	-0.049	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.817	-0.894	13.038	16.053	16.053	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.803	-0.877	9.625	21.839	21.839	0.000	0.000	0.000	0.000
52	D	54	LYS	1	0.952	0.969	12.400	-14.655	-14.655	0.000	0.000	0.000	0.000
53	D	55	LYS	1	0.814	0.899	15.715	-13.504	-13.504	0.000	0.000	0.000	0.000
54	D	56	GLN	0	0.017	0.006	11.462	0.230	0.230	0.000	0.000	0.000	0.000
55	D	57	VAL	0	0.003	0.013	13.456	-0.358	-0.358	0.000	0.000	0.000	0.000
56	D	58	LEU	0	-0.018	-0.012	16.044	-0.622	-0.622	0.000	0.000	0.000	0.000
57	D	59	GLU	-1	-0.798	-0.886	18.976	12.464	12.464	0.000	0.000	0.000	0.000
58	D	60	GLU	-1	-0.801	-0.869	15.852	15.774	15.774	0.000	0.000	0.000	0.000
59	D	61	PHE	0	-0.006	-0.013	19.321	-0.509	-0.509	0.000	0.000	0.000	0.000
60	D	62	LEU	0	0.009	-0.008	21.465	-0.480	-0.480	0.000	0.000	0.000	0.000
61	D	63	SER	0	-0.016	-0.005	22.333	-0.483	-0.483	0.000	0.000	0.000	0.000
62	D	64	LEU	0	-0.025	-0.010	20.410	-0.373	-0.373	0.000	0.000	0.000	0.000
63	D	65	ALA	0	-0.027	-0.009	24.609	-0.383	-0.383	0.000	0.000	0.000	0.000
64	D	66	LYS	1	0.887	0.945	27.126	-9.033	-9.033	0.000	0.000	0.000	0.000
65	D	67	ALA	0	0.034	0.013	27.290	-0.328	-0.328	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.943	0.972	28.789	-9.244	-9.244	0.000	0.000	0.000	0.000
67	D	69	GLU	-1	-0.885	-0.937	30.650	8.530	8.530	0.000	0.000	0.000	0.000
68	D	70	MET	0	0.008	0.004	32.074	-0.197	-0.197	0.000	0.000	0.000	0.000
69	D	71	ILE	0	-0.021	-0.001	31.057	-0.232	-0.232	0.000	0.000	0.000	0.000
70	D	72	SER	0	-0.069	-0.048	34.540	-0.238	-0.238	0.000	0.000	0.000	0.000
71	D	73	GLU	-1	-0.891	-0.948	35.724	7.901	7.901	0.000	0.000	0.000	0.000
72	D	74	GLY	0	0.037	0.026	37.835	-0.216	-0.216	0.000	0.000	0.000	0.000
73	D	75	GLY	0	0.004	0.001	39.353	-0.184	-0.184	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.030	-0.023	40.209	-0.223	-0.223	0.000	0.000	0.000	0.000
75	D	77	GLU	-1	-0.818	-0.888	42.513	6.577	6.577	0.000	0.000	0.000	0.000
76	D	78	TYR	0	0.036	0.015	43.753	-0.173	-0.173	0.000	0.000	0.000	0.000
77	D	79	ALA	0	0.006	-0.002	45.318	-0.164	-0.164	0.000	0.000	0.000	0.000
78	D	80	LYS	1	0.944	0.964	45.606	-6.617	-6.617	0.000	0.000	0.000	0.000
79	D	81	LYS	1	0.819	0.902	45.805	-6.725	-6.725	0.000	0.000	0.000	0.000
80	D	82	VAL	0	-0.027	-0.004	49.506	-0.129	-0.129	0.000	0.000	0.000	0.000
81	D	83	LEU	0	-0.020	-0.013	50.604	-0.116	-0.116	0.000	0.000	0.000	0.000
82	D	84	GLU	-1	-0.927	-0.956	52.935	5.352	5.352	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.782	0.867	53.975	-5.681	-5.681	0.000	0.000	0.000	0.000
84	D	86	ALA	0	-0.061	-0.020	55.841	-0.091	-0.091	0.000	0.000	0.000	0.000
85	D	87	PHE	0	-0.050	-0.033	55.379	-0.080	-0.080	0.000	0.000	0.000	0.000
86	D	88	GLY	0	0.021	0.026	58.738	-0.089	-0.089	0.000	0.000	0.000	0.000
87	D	89	PRO	0	-0.045	-0.029	60.344	-0.042	-0.042	0.000	0.000	0.000	0.000
88	D	90	GLU	-1	-0.857	-0.900	57.852	5.346	5.346	0.000	0.000	0.000	0.000

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