FMO DATABASE

FMODB ID: 3Q84L

Calculation Name: 1TR8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TR8

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0K9

Base Structure: X-ray

Registration Date: 2023-06-19

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-542534.344331
FMO2-HF: Nuclear repulsion	504885.147299
FMO2-HF: Total energy	-37649.197032
FMO2-MP2: Total energy	-37755.124548

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:25:ASP)

Summations of interaction energy for fragment #1(A:25:ASP)

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.
-31.517	-27.785	2.031	-2.227	-3.536	0.016

Interaction energy analysis for fragmet #1(A:25:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.925 / q_NPA : -0.971

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	27	LYS	1	0.934	0.982	3.834	-28.432	-26.851	-0.015	-0.793	-0.773	0.003
4	A	28	ASP	-1	-0.854	-0.924	6.976	23.951	23.951	0.000	0.000	0.000	0.000
5	A	29	LEU	0	-0.026	-0.018	10.444	-0.364	-0.364	0.000	0.000	0.000	0.000
6	A	30	ARG	1	0.953	0.964	13.139	-15.163	-15.163	0.000	0.000	0.000	0.000
7	A	31	GLY	0	-0.006	-0.006	16.455	-0.190	-0.190	0.000	0.000	0.000	0.000
8	A	32	VAL	0	0.002	0.010	16.586	-0.291	-0.291	0.000	0.000	0.000	0.000
9	A	33	GLU	-1	-0.870	-0.934	19.776	11.367	11.367	0.000	0.000	0.000	0.000
10	A	34	GLU	-1	-0.934	-0.997	22.193	10.809	10.809	0.000	0.000	0.000	0.000
11	A	35	VAL	0	-0.035	-0.003	17.572	0.470	0.470	0.000	0.000	0.000	0.000
12	A	36	VAL	0	0.000	-0.004	20.942	-0.446	-0.446	0.000	0.000	0.000	0.000
13	A	37	ILE	0	-0.021	-0.011	19.110	0.376	0.376	0.000	0.000	0.000	0.000
14	A	38	LYS	1	0.896	0.936	22.643	-11.396	-11.396	0.000	0.000	0.000	0.000
15	A	39	LEU	0	-0.008	-0.001	24.452	0.304	0.304	0.000	0.000	0.000	0.000
16	A	40	LYS	1	0.990	0.987	27.325	-9.266	-9.266	0.000	0.000	0.000	0.000
17	A	41	ARG	1	0.879	0.906	30.850	-8.723	-8.723	0.000	0.000	0.000	0.000
18	A	42	LYS	1	0.854	0.915	27.528	-10.879	-10.879	0.000	0.000	0.000	0.000
19	A	43	GLU	-1	-0.784	-0.856	27.008	10.811	10.811	0.000	0.000	0.000	0.000
20	A	44	ILE	0	-0.016	-0.004	23.362	-0.222	-0.222	0.000	0.000	0.000	0.000
21	A	45	ILE	0	-0.008	-0.003	24.157	0.343	0.343	0.000	0.000	0.000	0.000
22	A	46	ILE	0	-0.040	-0.021	19.280	-0.210	-0.210	0.000	0.000	0.000	0.000
23	A	47	LYS	1	0.950	0.973	22.506	-10.189	-10.189	0.000	0.000	0.000	0.000
24	A	48	ASN	0	-0.035	-0.004	22.170	0.228	0.228	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.023	-0.001	17.646	0.096	0.096	0.000	0.000	0.000	0.000
26	A	50	LYS	1	0.875	0.926	11.923	-22.024	-22.024	0.000	0.000	0.000	0.000
27	A	51	VAL	0	-0.019	-0.026	12.569	0.277	0.277	0.000	0.000	0.000	0.000
28	A	52	ASN	0	-0.001	0.014	7.899	-1.623	-1.623	0.000	0.000	0.000	0.000
29	A	53	VAL	0	-0.027	-0.015	8.150	-1.338	-1.338	0.000	0.000	0.000	0.000
30	A	54	MET	0	0.064	0.032	2.278	-3.582	-1.862	2.048	-1.406	-2.362	0.013
31	A	55	GLU	-1	-0.907	-0.970	4.379	20.843	20.985	-0.001	-0.010	-0.131	0.000
32	A	56	PHE	0	0.030	0.012	4.507	5.704	5.993	-0.001	-0.018	-0.270	0.000
33	A	57	MET	0	-0.023	-0.016	6.723	-4.556	-4.556	0.000	0.000	0.000	0.000
34	A	58	GLY	0	0.023	0.022	9.861	-2.296	-2.296	0.000	0.000	0.000	0.000
35	A	59	GLN	0	-0.019	0.003	10.519	-2.832	-2.832	0.000	0.000	0.000	0.000
36	A	60	LYS	1	0.924	0.969	8.931	-20.732	-20.732	0.000	0.000	0.000	0.000
37	A	61	THR	0	-0.019	-0.006	7.281	-1.527	-1.527	0.000	0.000	0.000	0.000
38	A	62	TYR	0	0.009	-0.013	8.393	2.081	2.081	0.000	0.000	0.000	0.000
39	A	63	GLN	0	0.009	0.011	8.331	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	64	VAL	0	0.026	0.004	11.017	-0.075	-0.075	0.000	0.000	0.000	0.000
41	A	65	THR	0	-0.006	0.005	14.251	-0.412	-0.412	0.000	0.000	0.000	0.000
42	A	66	GLY	0	0.061	0.016	16.558	-0.163	-0.163	0.000	0.000	0.000	0.000
43	A	67	LYS	1	0.925	0.965	20.258	-11.453	-11.453	0.000	0.000	0.000	0.000
44	A	68	ALA	0	0.035	0.021	22.777	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	69	ARG	1	0.924	0.956	24.543	-10.568	-10.568	0.000	0.000	0.000	0.000
46	A	70	GLU	-1	-0.805	-0.876	27.171	11.021	11.021	0.000	0.000	0.000	0.000
47	A	71	ARG	1	0.869	0.930	28.524	-10.408	-10.408	0.000	0.000	0.000	0.000
48	A	72	SER	0	-0.036	-0.040	31.329	0.319	0.319	0.000	0.000	0.000	0.000
49	A	73	LEU	0	-0.021	-0.016	31.589	0.020	0.020	0.000	0.000	0.000	0.000
50	A	74	GLU	-1	-0.852	-0.911	34.968	8.164	8.164	0.000	0.000	0.000	0.000
51	A	75	ALA	0	-0.039	-0.013	38.479	0.049	0.049	0.000	0.000	0.000	0.000
52	A	76	GLU	-1	-0.935	-0.957	40.428	7.080	7.080	0.000	0.000	0.000	0.000
53	A	77	MET	0	-0.034	-0.025	42.446	0.004	0.004	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-0.939	-0.958	45.839	6.108	6.108	0.000	0.000	0.000	0.000
55	A	79	ILE	0	-0.030	-0.018	47.229	0.018	0.018	0.000	0.000	0.000	0.000
56	A	80	PRO	0	0.002	0.007	51.051	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	81	GLU	-1	-0.754	-0.857	54.774	5.625	5.625	0.000	0.000	0.000	0.000
58	A	82	ASP	-1	-0.890	-0.943	56.850	5.267	5.267	0.000	0.000	0.000	0.000
59	A	83	ASP	-1	-0.884	-0.949	53.785	5.776	5.776	0.000	0.000	0.000	0.000
60	A	84	ILE	0	-0.048	-0.032	52.187	0.050	0.050	0.000	0.000	0.000	0.000
61	A	85	GLU	-1	-0.960	-0.993	54.510	5.218	5.218	0.000	0.000	0.000	0.000
62	A	86	LEU	0	-0.024	-0.004	56.954	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	87	VAL	0	0.034	0.005	51.542	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	88	MET	0	-0.055	0.014	54.744	0.027	0.027	0.000	0.000	0.000	0.000
65	A	89	ASN	0	-0.038	-0.021	56.150	-0.037	-0.037	0.000	0.000	0.000	0.000
66	A	90	GLN	0	-0.076	-0.026	57.143	-0.064	-0.064	0.000	0.000	0.000	0.000
67	A	91	THR	0	-0.067	-0.047	52.974	0.035	0.035	0.000	0.000	0.000	0.000
68	A	92	GLY	0	-0.020	0.001	55.475	0.024	0.024	0.000	0.000	0.000	0.000
69	A	93	ALA	0	-0.041	0.002	51.685	0.036	0.036	0.000	0.000	0.000	0.000
70	A	94	SER	0	-0.009	-0.035	50.698	-0.091	-0.091	0.000	0.000	0.000	0.000
71	A	95	ARG	1	0.937	0.908	52.362	-5.604	-5.604	0.000	0.000	0.000	0.000
72	A	96	GLU	-1	-0.878	-0.905	46.263	6.777	6.777	0.000	0.000	0.000	0.000
73	A	97	ASP	-1	-0.815	-0.882	47.366	6.681	6.681	0.000	0.000	0.000	0.000
74	A	98	ALA	0	0.012	0.016	48.023	0.100	0.100	0.000	0.000	0.000	0.000
75	A	99	THR	0	-0.006	-0.020	47.689	0.027	0.027	0.000	0.000	0.000	0.000
76	A	100	ARG	1	0.798	0.870	42.337	-6.880	-6.880	0.000	0.000	0.000	0.000
77	A	101	ALA	0	-0.046	-0.024	44.424	0.163	0.163	0.000	0.000	0.000	0.000
78	A	102	LEU	0	0.066	0.028	45.673	0.094	0.094	0.000	0.000	0.000	0.000
79	A	103	GLN	0	-0.032	-0.018	42.967	0.010	0.010	0.000	0.000	0.000	0.000
80	A	104	GLU	-1	-0.888	-0.913	39.518	8.175	8.175	0.000	0.000	0.000	0.000
81	A	105	THR	0	-0.054	-0.032	41.716	0.191	0.191	0.000	0.000	0.000	0.000
82	A	106	GLY	0	-0.038	-0.012	43.818	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	107	GLY	0	0.018	-0.001	44.798	-0.082	-0.082	0.000	0.000	0.000	0.000
84	A	108	ASP	-1	-0.891	-0.924	47.580	6.228	6.228	0.000	0.000	0.000	0.000
85	A	109	LEU	0	0.058	0.014	49.289	0.050	0.050	0.000	0.000	0.000	0.000
86	A	110	ALA	0	-0.004	-0.001	51.626	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	111	GLU	-1	-0.925	-0.979	45.346	7.003	7.003	0.000	0.000	0.000	0.000
88	A	112	ALA	0	-0.033	-0.015	48.002	0.077	0.077	0.000	0.000	0.000	0.000
89	A	113	ILE	0	-0.022	-0.021	49.009	0.005	0.005	0.000	0.000	0.000	0.000
90	A	114	MET	0	-0.063	-0.031	49.681	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	115	ARG	1	0.807	0.920	40.995	-7.253	-7.253	0.000	0.000	0.000	0.000
92	A	116	LEU	0	-0.047	-0.010	47.273	0.067	0.067	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:ASP)