FMO DATABASE

FMODB ID: 4J6ZN

Calculation Name: 1TBR-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TBR

Chain ID: R

ChEMBL ID:

UniProt ID: Q06684

Base Structure: X-ray

Registration Date: 2023-09-23

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-596962.10576
FMO2-HF: Nuclear repulsion	554858.477072
FMO2-HF: Total energy	-42103.628688
FMO2-MP2: Total energy	-42215.747676

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(R:1:GLU)

Summations of interaction energy for fragment #1(R:1: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.
97.82	108.853	9.783	-8.5	-12.316	0.021

Interaction energy analysis for fragmet #1(R:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.873 / q_NPA : -0.931

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

Sort

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	R	3	GLY	0	-0.005	-0.019	2.641	-6.219	-3.488	0.827	-1.715	-1.843	-0.003
4	R	4	GLU	-1	-0.947	-0.973	5.148	35.685	35.685	0.000	0.000	0.000	0.000
5	R	5	PRO	0	-0.007	-0.006	2.522	-9.974	-7.908	2.452	-1.554	-2.964	0.018
6	R	6	CYS	0	-0.016	-0.005	4.513	0.584	0.957	0.005	-0.077	-0.301	0.000
7	R	7	ALA	0	-0.023	0.015	6.166	-3.603	-3.603	0.000	0.000	0.000	0.000
8	R	8	CYS	0	-0.067	-0.022	8.845	0.896	0.896	0.000	0.000	0.000	0.000
9	R	9	PRO	0	0.015	0.000	11.311	-1.027	-1.027	0.000	0.000	0.000	0.000
10	R	10	HIS	0	0.005	0.010	13.840	-0.015	-0.015	0.000	0.000	0.000	0.000
11	R	11	ALA	0	-0.018	-0.010	17.078	-0.964	-0.964	0.000	0.000	0.000	0.000
12	R	12	LEU	0	0.005	0.007	17.822	0.848	0.848	0.000	0.000	0.000	0.000
13	R	13	HIS	0	-0.022	-0.017	18.344	-0.541	-0.541	0.000	0.000	0.000	0.000
14	R	14	ARG	1	0.827	0.861	18.591	-11.403	-11.403	0.000	0.000	0.000	0.000
15	R	15	VAL	0	-0.043	-0.010	15.703	-0.268	-0.268	0.000	0.000	0.000	0.000
16	R	16	CYS	0	-0.018	0.022	18.215	0.351	0.351	0.000	0.000	0.000	0.000
17	R	17	GLY	0	0.044	0.007	16.188	0.398	0.398	0.000	0.000	0.000	0.000
18	R	18	SER	0	-0.015	-0.021	16.101	-0.554	-0.554	0.000	0.000	0.000	0.000
19	R	19	ASP	-1	-0.789	-0.873	14.731	18.025	18.025	0.000	0.000	0.000	0.000
20	R	20	GLY	0	-0.011	0.003	17.769	-0.539	-0.539	0.000	0.000	0.000	0.000
21	R	21	GLU	-1	-0.885	-0.930	15.934	16.513	16.513	0.000	0.000	0.000	0.000
22	R	22	THR	0	0.012	0.001	17.834	0.444	0.444	0.000	0.000	0.000	0.000
23	R	23	TYR	0	-0.048	-0.058	11.920	1.076	1.076	0.000	0.000	0.000	0.000
24	R	24	SER	0	0.021	-0.004	15.292	-0.708	-0.708	0.000	0.000	0.000	0.000
25	R	25	ASN	0	-0.001	0.010	13.416	0.535	0.535	0.000	0.000	0.000	0.000
26	R	26	PRO	0	0.051	0.013	13.587	1.034	1.034	0.000	0.000	0.000	0.000
27	R	28	THR	0	0.006	-0.012	8.905	2.128	2.128	0.000	0.000	0.000	0.000
28	R	29	LEU	0	0.014	0.025	9.663	1.242	1.242	0.000	0.000	0.000	0.000
29	R	30	ASN	0	-0.017	-0.022	6.360	-0.972	-0.972	0.000	0.000	0.000	0.000
30	R	32	ALA	0	0.069	0.028	5.112	3.361	3.424	-0.001	-0.001	-0.060	0.000
31	R	33	LYS	1	0.779	0.885	7.436	-26.035	-26.035	0.000	0.000	0.000	0.000
32	R	34	PHE	0	-0.061	-0.038	2.409	-10.353	-6.702	1.899	-2.429	-3.121	0.029
33	R	35	ASN	0	-0.055	-0.036	2.016	1.738	3.835	4.601	-2.712	-3.987	-0.023
34	R	36	GLY	0	-0.002	0.004	4.340	-3.485	-3.433	0.000	-0.012	-0.040	0.000
35	R	37	LYS	1	0.764	0.891	7.745	-22.227	-22.227	0.000	0.000	0.000	0.000
36	R	38	PRO	0	0.062	0.018	8.955	-0.220	-0.220	0.000	0.000	0.000	0.000
37	R	39	GLU	-1	-0.924	-0.953	10.433	18.072	18.072	0.000	0.000	0.000	0.000
38	R	40	LEU	0	-0.063	-0.003	10.301	-1.186	-1.186	0.000	0.000	0.000	0.000
39	R	41	VAL	0	-0.017	-0.015	12.166	1.751	1.751	0.000	0.000	0.000	0.000
40	R	42	LYS	1	0.826	0.895	14.618	-15.564	-15.564	0.000	0.000	0.000	0.000
41	R	43	VAL	0	-0.024	-0.003	16.974	-0.271	-0.271	0.000	0.000	0.000	0.000
42	R	44	HIS	0	-0.054	-0.045	20.518	-0.520	-0.520	0.000	0.000	0.000	0.000
43	R	45	ASP	-1	-0.802	-0.893	20.653	14.700	14.700	0.000	0.000	0.000	0.000
44	R	46	GLY	0	0.022	0.027	22.016	-0.549	-0.549	0.000	0.000	0.000	0.000
45	R	47	PRO	0	-0.024	-0.015	21.801	0.672	0.672	0.000	0.000	0.000	0.000
46	R	49	GLU	-1	-0.858	-0.928	23.614	12.031	12.031	0.000	0.000	0.000	0.000
47	R	50	PRO	0	-0.054	-0.040	26.555	0.134	0.134	0.000	0.000	0.000	0.000
48	R	51	ASP	-1	-0.764	-0.838	26.893	11.077	11.077	0.000	0.000	0.000	0.000
49	R	52	GLU	-1	-0.929	-0.964	29.444	9.000	9.000	0.000	0.000	0.000	0.000
50	R	53	ASP	-1	-0.967	-0.968	32.429	8.101	8.101	0.000	0.000	0.000	0.000
51	R	54	GLU	-1	-1.003	-1.008	32.300	8.743	8.743	0.000	0.000	0.000	0.000
52	R	55	ASP	-1	-0.831	-0.919	36.326	7.139	7.139	0.000	0.000	0.000	0.000
53	R	56	VAL	0	-0.020	-0.026	35.849	-0.076	-0.076	0.000	0.000	0.000	0.000
54	R	57	CYS	0	-0.038	0.002	38.992	0.197	0.197	0.000	0.000	0.000	0.000
55	R	58	GLN	0	-0.003	0.001	40.457	-0.276	-0.276	0.000	0.000	0.000	0.000
56	R	59	GLU	-1	-0.981	-0.986	43.149	6.912	6.912	0.000	0.000	0.000	0.000
57	R	60	CYS	0	0.003	0.027	45.807	0.046	0.046	0.000	0.000	0.000	0.000
58	R	61	ASP	-1	-0.854	-0.896	47.000	6.343	6.343	0.000	0.000	0.000	0.000
59	R	62	GLY	0	-0.035	-0.025	49.597	-0.049	-0.049	0.000	0.000	0.000	0.000
60	R	63	ASP	-1	-0.940	-0.958	51.760	5.734	5.734	0.000	0.000	0.000	0.000
61	R	64	GLU	-1	-0.925	-0.959	53.579	5.171	5.171	0.000	0.000	0.000	0.000
62	R	65	TYR	0	-0.039	-0.018	55.602	0.025	0.025	0.000	0.000	0.000	0.000
63	R	66	LYS	1	0.825	0.907	56.088	-5.469	-5.469	0.000	0.000	0.000	0.000
64	R	67	PRO	0	0.001	0.012	55.024	0.066	0.066	0.000	0.000	0.000	0.000
65	R	68	VAL	0	-0.001	-0.002	51.322	-0.095	-0.095	0.000	0.000	0.000	0.000
66	R	69	CYS	0	-0.111	-0.001	52.413	0.032	0.032	0.000	0.000	0.000	0.000
67	R	70	GLY	0	0.126	0.051	48.259	0.004	0.004	0.000	0.000	0.000	0.000
68	R	71	SER	0	-0.038	-0.034	45.377	-0.099	-0.099	0.000	0.000	0.000	0.000
69	R	72	ASP	-1	-0.707	-0.827	44.777	6.754	6.754	0.000	0.000	0.000	0.000
70	R	73	ASP	-1	-0.834	-0.900	46.730	5.922	5.922	0.000	0.000	0.000	0.000
71	R	74	ILE	0	-0.005	0.018	45.636	-0.126	-0.126	0.000	0.000	0.000	0.000
72	R	75	THR	0	-0.039	-0.032	49.675	-0.085	-0.085	0.000	0.000	0.000	0.000
73	R	76	TYR	0	-0.005	-0.024	45.392	0.068	0.068	0.000	0.000	0.000	0.000
74	R	77	ASP	-1	-0.872	-0.952	50.893	5.888	5.888	0.000	0.000	0.000	0.000
75	R	78	ASN	0	-0.006	-0.013	50.805	-0.008	-0.008	0.000	0.000	0.000	0.000
76	R	79	ASN	0	-0.023	-0.040	49.018	0.033	0.033	0.000	0.000	0.000	0.000
77	R	81	ARG	1	0.838	0.884	46.091	-6.338	-6.338	0.000	0.000	0.000	0.000
78	R	82	LEU	0	-0.018	0.008	45.462	0.124	0.124	0.000	0.000	0.000	0.000
79	R	83	GLU	-1	-0.870	-0.933	44.159	6.742	6.742	0.000	0.000	0.000	0.000
80	R	85	ALA	0	0.041	0.037	40.591	0.214	0.214	0.000	0.000	0.000	0.000
81	R	86	SER	0	-0.093	-0.044	40.346	0.228	0.228	0.000	0.000	0.000	0.000
82	R	87	ILE	0	-0.020	-0.014	36.334	0.226	0.226	0.000	0.000	0.000	0.000
83	R	88	SER	0	-0.001	-0.026	36.094	0.157	0.157	0.000	0.000	0.000	0.000
84	R	89	SER	0	-0.022	-0.010	37.567	0.101	0.101	0.000	0.000	0.000	0.000
85	R	90	SER	0	-0.093	-0.063	40.198	-0.001	-0.001	0.000	0.000	0.000	0.000
86	R	91	PRO	0	-0.012	-0.011	35.863	-0.072	-0.072	0.000	0.000	0.000	0.000
87	R	92	GLY	0	-0.027	-0.016	38.148	-0.010	-0.010	0.000	0.000	0.000	0.000
88	R	93	VAL	0	-0.083	-0.018	39.817	-0.144	-0.144	0.000	0.000	0.000	0.000
89	R	94	GLU	-1	-0.933	-0.972	43.536	6.895	6.895	0.000	0.000	0.000	0.000
90	R	95	LEU	0	-0.012	-0.016	46.356	-0.085	-0.085	0.000	0.000	0.000	0.000
91	R	96	LYS	1	0.776	0.895	50.048	-6.023	-6.023	0.000	0.000	0.000	0.000
92	R	97	HIS	0	-0.109	-0.077	51.869	-0.117	-0.117	0.000	0.000	0.000	0.000
93	R	98	GLU	-1	-0.874	-0.928	54.778	5.408	5.408	0.000	0.000	0.000	0.000
94	R	99	GLY	0	-0.025	-0.007	56.994	-0.076	-0.076	0.000	0.000	0.000	0.000
95	R	100	PRO	0	0.029	-0.008	56.287	0.079	0.079	0.000	0.000	0.000	0.000
96	R	102	ARG	1	0.872	0.950	55.729	-5.364	-5.364	0.000	0.000	0.000	0.000
97	R	103	THR	0	-0.081	-0.061	54.276	-0.117	-0.117	0.000	0.000	0.000	0.000

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