FMO DATABASE

FMODB ID: LNR29

Calculation Name: 1BB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BB9

Chain ID: A

ChEMBL ID:

UniProt ID: O08839

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-572950.661009
FMO2-HF: Nuclear repulsion	539106.378591
FMO2-HF: Total energy	-33844.282418
FMO2-MP2: Total energy	-33942.424187

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:12:THR)

Summations of interaction energy for fragment #1(A:12:THR)

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.
-16.162	-13.638	9.36	-4.689	-7.195	0.011

Interaction energy analysis for fragmet #1(A:12:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.017

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	A	14	GLY	0	0.039	0.015	2.736	-4.526	-1.652	0.466	-1.580	-1.760	-0.008
4	A	15	ARG	1	0.765	0.858	5.356	0.593	0.593	0.000	0.000	0.000	0.000
5	A	16	LEU	0	-0.004	-0.009	7.256	-0.029	-0.029	0.000	0.000	0.000	0.000
6	A	17	ASP	-1	-0.833	-0.877	10.895	-0.069	-0.069	0.000	0.000	0.000	0.000
7	A	18	LEU	0	0.020	0.010	10.785	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	19	PRO	0	0.017	0.014	12.038	0.043	0.043	0.000	0.000	0.000	0.000
9	A	20	PRO	0	-0.001	-0.013	14.810	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	21	GLY	0	0.012	0.009	18.519	0.015	0.015	0.000	0.000	0.000	0.000
11	A	22	PHE	0	-0.028	-0.009	14.060	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	23	MET	0	-0.012	0.009	17.760	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	24	PHE	0	-0.020	-0.035	17.540	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	25	LYS	1	0.825	0.917	10.141	0.770	0.770	0.000	0.000	0.000	0.000
15	A	26	VAL	0	0.027	0.008	14.729	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	27	GLN	0	-0.069	-0.045	12.743	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	28	ALA	0	0.044	0.025	14.551	0.017	0.017	0.000	0.000	0.000	0.000
18	A	29	GLN	0	-0.047	-0.035	16.465	-0.037	-0.037	0.000	0.000	0.000	0.000
19	A	30	HIS	0	-0.079	-0.056	19.260	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	31	ASP	-1	-0.825	-0.884	18.286	0.009	0.009	0.000	0.000	0.000	0.000
21	A	32	TYR	0	-0.030	-0.035	18.378	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	33	THR	0	-0.040	-0.019	18.682	0.023	0.023	0.000	0.000	0.000	0.000
23	A	34	ALA	0	-0.016	-0.004	18.886	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	35	THR	0	-0.092	-0.072	20.816	0.003	0.003	0.000	0.000	0.000	0.000
25	A	36	ASP	-1	-0.851	-0.919	23.283	0.137	0.137	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.112	-0.087	21.775	0.014	0.014	0.000	0.000	0.000	0.000
27	A	38	ASP	-1	-0.878	-0.907	20.315	0.216	0.216	0.000	0.000	0.000	0.000
28	A	39	GLU	-1	-0.782	-0.847	20.169	0.099	0.099	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.065	-0.037	12.646	0.045	0.045	0.000	0.000	0.000	0.000
30	A	41	GLN	0	-0.010	0.000	15.176	-0.059	-0.059	0.000	0.000	0.000	0.000
31	A	42	LEU	0	-0.037	-0.026	13.041	0.061	0.061	0.000	0.000	0.000	0.000
32	A	43	LYS	1	0.819	0.885	13.376	-0.034	-0.034	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.009	0.006	14.539	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	45	GLY	0	-0.003	0.001	13.494	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	46	ASP	-1	-0.793	-0.879	10.144	0.126	0.126	0.000	0.000	0.000	0.000
36	A	47	VAL	0	-0.020	0.004	9.203	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	48	VAL	0	-0.021	-0.010	9.640	0.082	0.082	0.000	0.000	0.000	0.000
38	A	49	LEU	0	-0.050	-0.026	9.414	-0.072	-0.072	0.000	0.000	0.000	0.000
39	A	50	VAL	0	0.039	0.023	13.035	0.065	0.065	0.000	0.000	0.000	0.000
40	A	51	ILE	0	-0.045	-0.030	15.572	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	52	PRO	0	0.008	-0.004	18.453	0.004	0.004	0.000	0.000	0.000	0.000
42	A	53	PHE	0	0.067	0.041	21.458	0.018	0.018	0.000	0.000	0.000	0.000
43	A	54	GLN	0	-0.078	-0.049	20.831	0.002	0.002	0.000	0.000	0.000	0.000
44	A	55	ASN	0	-0.029	-0.038	24.713	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	56	PRO	0	-0.017	-0.013	27.641	0.001	0.001	0.000	0.000	0.000	0.000
46	A	57	GLU	-1	-0.938	-0.964	29.694	0.038	0.038	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.852	-0.904	26.276	0.091	0.091	0.000	0.000	0.000	0.000
48	A	59	GLN	0	-0.116	-0.055	26.471	0.003	0.003	0.000	0.000	0.000	0.000
49	A	60	ASP	-1	-0.837	-0.907	27.996	0.026	0.026	0.000	0.000	0.000	0.000
50	A	61	GLU	-1	-1.011	-1.011	28.040	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	62	GLY	0	0.001	-0.001	27.720	0.001	0.001	0.000	0.000	0.000	0.000
52	A	63	TRP	0	-0.045	-0.018	22.972	0.002	0.002	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.058	-0.029	20.031	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	65	MET	0	0.051	0.046	18.782	0.031	0.031	0.000	0.000	0.000	0.000
55	A	66	GLY	0	0.009	-0.010	15.536	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	67	VAL	0	0.003	0.011	9.892	0.056	0.056	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.860	0.933	8.102	-0.555	-0.555	0.000	0.000	0.000	0.000
58	A	69	GLU	-1	-0.808	-0.911	6.280	-0.810	-0.810	0.000	0.000	0.000	0.000
59	A	70	SER	0	-0.034	-0.007	3.205	-0.674	-0.283	0.034	-0.113	-0.311	0.000
60	A	71	ASP	-1	-0.767	-0.894	3.659	1.937	2.388	0.012	-0.187	-0.276	-0.001
61	A	72	TRP	0	0.013	-0.006	6.423	0.182	0.182	0.000	0.000	0.000	0.000
62	A	73	ASN	0	-0.001	-0.011	2.446	-0.510	-0.425	1.236	-0.396	-0.925	-0.001
63	A	74	GLN	0	-0.070	-0.036	1.923	-10.207	-11.589	7.610	-2.382	-3.846	0.021
64	A	75	HIS	0	-0.045	-0.027	4.082	-0.108	-0.003	0.002	-0.031	-0.077	0.000
65	A	76	LYS	1	0.840	0.927	6.637	-2.650	-2.650	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.832	-0.905	9.652	0.301	0.301	0.000	0.000	0.000	0.000
67	A	78	LEU	0	0.033	0.015	13.254	0.015	0.015	0.000	0.000	0.000	0.000
68	A	79	GLU	-1	-0.846	-0.920	14.127	0.203	0.203	0.000	0.000	0.000	0.000
69	A	80	LYS	1	0.772	0.877	14.701	-0.424	-0.424	0.000	0.000	0.000	0.000
70	A	81	CYS	0	-0.031	-0.012	11.113	0.109	0.109	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.825	0.896	12.932	-0.204	-0.204	0.000	0.000	0.000	0.000
72	A	83	GLY	0	0.038	0.021	15.086	0.026	0.026	0.000	0.000	0.000	0.000
73	A	84	VAL	0	0.013	-0.006	17.659	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	85	PHE	0	-0.011	-0.010	16.852	0.014	0.014	0.000	0.000	0.000	0.000
75	A	86	PRO	0	0.073	0.046	20.295	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	87	GLU	-1	-0.923	-0.975	21.739	-0.056	-0.056	0.000	0.000	0.000	0.000
77	A	88	ASN	0	0.030	0.022	22.093	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	89	PHE	0	-0.060	-0.018	20.479	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	90	THR	0	-0.102	-0.061	17.539	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	91	GLU	-1	-0.837	-0.897	18.860	-0.184	-0.184	0.000	0.000	0.000	0.000
81	A	92	ARG	1	0.912	0.964	18.324	0.161	0.161	0.000	0.000	0.000	0.000
82	A	93	VAL	0	0.008	0.012	14.284	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	94	GLN	0	-0.026	-0.015	13.580	-0.051	-0.051	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:12:THR)