FMO DATABASE

FMODB ID: QVM6Y

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	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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-596001.488271
FMO2-HF: Nuclear repulsion	553900.192905
FMO2-HF: Total energy	-42101.295366
FMO2-MP2: Total energy	-42213.533512

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.
132.044	120.875	40.388	-13.633	-15.583	-0.011

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 : -0.932 / q_NPA : -0.969

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	-0.013	-0.015	3.450	-5.599	-4.211	-0.014	-0.643	-0.731	0.006
4	R	4	GLU	-1	-0.966	-0.998	5.192	35.514	35.740	-0.001	-0.005	-0.219	0.000
5	R	5	PRO	0	0.015	0.009	2.102	-5.564	-6.682	4.741	-0.936	-2.687	0.004
6	R	6	CYS	0	-0.009	-0.007	4.107	0.789	1.262	0.025	-0.108	-0.390	0.000
7	R	7	ALA	0	-0.026	0.020	6.009	-3.611	-3.611	0.000	0.000	0.000	0.000
8	R	8	CYS	0	-0.052	-0.017	8.948	2.134	2.134	0.000	0.000	0.000	0.000
9	R	9	PRO	0	-0.011	-0.006	11.449	-1.000	-1.000	0.000	0.000	0.000	0.000
10	R	10	HIS	0	0.014	-0.005	13.774	0.284	0.284	0.000	0.000	0.000	0.000
11	R	11	ALA	0	-0.012	0.011	16.869	-0.857	-0.857	0.000	0.000	0.000	0.000
12	R	12	LEU	0	0.010	0.002	17.877	0.822	0.822	0.000	0.000	0.000	0.000
13	R	13	HIS	0	-0.031	-0.029	18.318	-0.348	-0.348	0.000	0.000	0.000	0.000
14	R	14	ARG	1	0.866	0.911	18.648	-11.572	-11.572	0.000	0.000	0.000	0.000
15	R	15	VAL	0	-0.046	-0.001	16.189	-0.326	-0.326	0.000	0.000	0.000	0.000
16	R	16	CYS	0	-0.014	0.007	18.754	0.412	0.412	0.000	0.000	0.000	0.000
17	R	17	GLY	0	0.047	0.011	16.295	0.229	0.229	0.000	0.000	0.000	0.000
18	R	18	SER	0	-0.014	-0.013	15.858	-0.414	-0.414	0.000	0.000	0.000	0.000
19	R	19	ASP	-1	-0.839	-0.919	14.282	18.914	18.914	0.000	0.000	0.000	0.000
20	R	20	GLY	0	-0.012	0.004	17.608	-0.488	-0.488	0.000	0.000	0.000	0.000
21	R	21	GLU	-1	-0.926	-0.949	16.109	16.474	16.474	0.000	0.000	0.000	0.000
22	R	22	THR	0	0.026	0.008	17.952	0.284	0.284	0.000	0.000	0.000	0.000
23	R	23	TYR	0	-0.046	-0.050	12.063	1.238	1.238	0.000	0.000	0.000	0.000
24	R	24	SER	0	0.031	-0.007	15.301	-0.736	-0.736	0.000	0.000	0.000	0.000
25	R	25	ASN	0	0.021	0.024	13.485	0.536	0.536	0.000	0.000	0.000	0.000
26	R	26	PRO	0	0.070	0.016	13.732	1.090	1.090	0.000	0.000	0.000	0.000
27	R	28	THR	0	-0.009	-0.005	9.007	2.288	2.288	0.000	0.000	0.000	0.000
28	R	29	LEU	0	0.010	0.015	9.925	1.167	1.167	0.000	0.000	0.000	0.000
29	R	30	ASN	0	-0.021	-0.027	7.852	1.409	1.409	0.000	0.000	0.000	0.000
30	R	32	ALA	0	0.064	0.041	4.950	4.348	4.434	-0.001	-0.003	-0.081	0.000
31	R	33	LYS	1	0.903	0.977	6.783	-26.770	-26.770	0.000	0.000	0.000	0.000
32	R	34	PHE	0	-0.118	-0.068	2.412	-9.591	-6.540	2.403	-2.310	-3.143	0.028
33	R	35	ASN	0	-0.012	-0.020	1.686	13.441	-1.929	33.235	-9.584	-8.282	-0.049
34	R	36	GLY	0	0.027	0.022	4.319	-4.760	-4.665	0.000	-0.044	-0.050	0.000
35	R	37	LYS	1	0.893	0.963	7.665	-23.296	-23.296	0.000	0.000	0.000	0.000
36	R	38	PRO	0	0.025	-0.002	7.731	-0.294	-0.294	0.000	0.000	0.000	0.000
37	R	39	GLU	-1	-0.959	-0.978	9.722	17.452	17.452	0.000	0.000	0.000	0.000
38	R	40	LEU	0	-0.061	-0.007	10.463	-1.274	-1.274	0.000	0.000	0.000	0.000
39	R	41	VAL	0	-0.024	-0.031	12.503	1.435	1.435	0.000	0.000	0.000	0.000
40	R	42	LYS	1	0.933	0.971	14.744	-16.352	-16.352	0.000	0.000	0.000	0.000
41	R	43	VAL	0	-0.042	-0.003	17.005	-0.295	-0.295	0.000	0.000	0.000	0.000
42	R	44	HIS	0	-0.076	-0.064	20.575	-0.489	-0.489	0.000	0.000	0.000	0.000
43	R	45	ASP	-1	-0.886	-0.944	20.823	14.454	14.454	0.000	0.000	0.000	0.000
44	R	46	GLY	0	0.004	0.021	22.258	-0.448	-0.448	0.000	0.000	0.000	0.000
45	R	47	PRO	0	-0.012	-0.016	22.170	0.621	0.621	0.000	0.000	0.000	0.000
46	R	49	GLU	-1	-0.929	-0.962	23.744	11.980	11.980	0.000	0.000	0.000	0.000
47	R	50	PRO	0	-0.053	-0.042	26.649	0.189	0.189	0.000	0.000	0.000	0.000
48	R	51	ASP	-1	-0.796	-0.880	26.961	11.222	11.222	0.000	0.000	0.000	0.000
49	R	52	GLU	-1	-0.949	-0.975	29.638	9.236	9.236	0.000	0.000	0.000	0.000
50	R	53	ASP	-1	-0.973	-0.966	32.608	8.241	8.241	0.000	0.000	0.000	0.000
51	R	54	GLU	-1	-1.022	-1.033	31.779	9.079	9.079	0.000	0.000	0.000	0.000
52	R	55	ASP	-1	-0.899	-0.943	36.251	7.170	7.170	0.000	0.000	0.000	0.000
53	R	56	VAL	0	-0.022	-0.046	35.650	-0.030	-0.030	0.000	0.000	0.000	0.000
54	R	57	CYS	-1	-0.744	-0.840	38.807	7.357	7.357	0.000	0.000	0.000	0.000
55	R	58	GLN	0	-0.100	-0.040	40.537	-0.297	-0.297	0.000	0.000	0.000	0.000
56	R	59	GLU	-1	-1.016	-1.009	42.542	6.954	6.954	0.000	0.000	0.000	0.000
57	R	60	CYS	0	-0.009	0.018	45.441	0.004	0.004	0.000	0.000	0.000	0.000
58	R	61	ASP	-1	-0.907	-0.957	47.079	6.434	6.434	0.000	0.000	0.000	0.000
59	R	62	GLY	0	-0.109	-0.056	49.213	-0.067	-0.067	0.000	0.000	0.000	0.000
60	R	63	ASP	-1	-0.937	-0.961	51.445	5.900	5.900	0.000	0.000	0.000	0.000
61	R	64	GLU	-1	-1.036	-1.023	53.336	5.152	5.152	0.000	0.000	0.000	0.000
62	R	65	TYR	0	-0.040	-0.012	55.497	0.013	0.013	0.000	0.000	0.000	0.000
63	R	66	LYS	1	0.869	0.916	55.912	-5.539	-5.539	0.000	0.000	0.000	0.000
64	R	67	PRO	0	-0.003	-0.001	55.040	0.070	0.070	0.000	0.000	0.000	0.000
65	R	68	VAL	0	0.005	0.017	51.374	-0.104	-0.104	0.000	0.000	0.000	0.000
66	R	69	CYS	0	-0.062	0.005	52.799	0.046	0.046	0.000	0.000	0.000	0.000
67	R	70	GLY	0	0.124	0.055	48.659	0.002	0.002	0.000	0.000	0.000	0.000
68	R	71	SER	0	-0.051	-0.036	45.761	-0.063	-0.063	0.000	0.000	0.000	0.000
69	R	72	ASP	-1	-0.716	-0.861	45.035	6.750	6.750	0.000	0.000	0.000	0.000
70	R	73	ASP	-1	-0.960	-0.987	46.983	6.059	6.059	0.000	0.000	0.000	0.000
71	R	74	ILE	0	0.000	0.016	46.179	-0.090	-0.090	0.000	0.000	0.000	0.000
72	R	75	THR	0	-0.071	-0.039	50.167	-0.085	-0.085	0.000	0.000	0.000	0.000
73	R	76	TYR	0	0.019	-0.003	45.706	0.058	0.058	0.000	0.000	0.000	0.000
74	R	77	ASP	-1	-0.864	-0.939	51.273	5.846	5.846	0.000	0.000	0.000	0.000
75	R	78	ASN	0	0.012	0.007	50.414	-0.014	-0.014	0.000	0.000	0.000	0.000
76	R	79	ASN	0	0.022	-0.013	49.034	-0.013	-0.013	0.000	0.000	0.000	0.000
77	R	81	ARG	1	0.970	0.981	45.647	-6.519	-6.519	0.000	0.000	0.000	0.000
78	R	82	LEU	0	-0.058	-0.003	45.496	0.082	0.082	0.000	0.000	0.000	0.000
79	R	83	GLU	-1	-0.960	-1.009	43.924	6.830	6.830	0.000	0.000	0.000	0.000
80	R	84	CYS	-1	-0.869	-0.908	41.575	7.639	7.639	0.000	0.000	0.000	0.000
81	R	85	ALA	0	0.109	0.063	40.702	0.181	0.181	0.000	0.000	0.000	0.000
82	R	86	SER	0	-0.157	-0.075	40.344	0.232	0.232	0.000	0.000	0.000	0.000
83	R	87	ILE	0	-0.007	-0.009	35.873	0.250	0.250	0.000	0.000	0.000	0.000
84	R	88	SER	0	-0.002	-0.027	35.896	0.181	0.181	0.000	0.000	0.000	0.000
85	R	89	SER	0	-0.020	-0.006	37.679	0.097	0.097	0.000	0.000	0.000	0.000
86	R	90	SER	0	-0.090	-0.042	40.235	0.035	0.035	0.000	0.000	0.000	0.000
87	R	91	PRO	0	-0.028	-0.026	35.981	-0.088	-0.088	0.000	0.000	0.000	0.000
88	R	92	GLY	0	-0.035	-0.025	38.186	-0.025	-0.025	0.000	0.000	0.000	0.000
89	R	93	VAL	0	-0.102	-0.016	39.928	-0.151	-0.151	0.000	0.000	0.000	0.000
90	R	94	GLU	-1	-0.908	-0.963	43.581	6.913	6.913	0.000	0.000	0.000	0.000
91	R	95	LEU	0	-0.025	-0.007	46.305	-0.101	-0.101	0.000	0.000	0.000	0.000
92	R	96	LYS	1	0.809	0.917	49.920	-6.154	-6.154	0.000	0.000	0.000	0.000
93	R	97	HIS	0	-0.145	-0.107	52.049	-0.076	-0.076	0.000	0.000	0.000	0.000
94	R	98	GLU	-1	-0.880	-0.932	55.037	5.454	5.454	0.000	0.000	0.000	0.000
95	R	99	GLY	0	-0.034	0.004	57.010	-0.076	-0.076	0.000	0.000	0.000	0.000
96	R	100	PRO	0	0.026	-0.015	56.581	0.078	0.078	0.000	0.000	0.000	0.000
97	R	102	ARG	1	0.902	0.946	55.990	-5.351	-5.351	0.000	0.000	0.000	0.000
98	R	103	THR	0	-0.018	0.002	54.200	-0.098	-0.098	0.000	0.000	0.000	0.000

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