FMO DATABASE

FMODB ID: 3JG5L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-572885.178669
FMO2-HF: Nuclear repulsion	539041.169797
FMO2-HF: Total energy	-33844.008872
FMO2-MP2: Total energy	-33942.11624

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.
-15.063	-11.743	7.521	-4.356	-6.484	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 : -0.021 / 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

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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	14	GLY	0	0.053	0.021	2.895	-4.414	-1.311	0.242	-1.667	-1.678	-0.007
4	A	15	ARG	1	0.753	0.876	5.312	0.376	0.420	-0.001	-0.001	-0.042	0.000
5	A	16	LEU	0	0.000	-0.009	7.241	-0.016	-0.016	0.000	0.000	0.000	0.000
6	A	17	ASP	-1	-0.836	-0.885	10.869	-0.033	-0.033	0.000	0.000	0.000	0.000
7	A	18	LEU	0	0.017	0.007	11.066	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	19	PRO	0	0.021	0.013	12.009	0.048	0.048	0.000	0.000	0.000	0.000
9	A	20	PRO	0	0.014	0.000	14.701	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	21	GLY	0	0.008	0.000	18.401	0.013	0.013	0.000	0.000	0.000	0.000
11	A	22	PHE	0	-0.035	-0.008	14.522	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	23	MET	0	-0.036	0.000	17.733	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	24	PHE	0	-0.026	-0.045	17.789	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	25	LYS	1	0.833	0.914	10.140	0.872	0.872	0.000	0.000	0.000	0.000
15	A	26	VAL	0	0.027	0.019	15.074	0.005	0.005	0.000	0.000	0.000	0.000
16	A	27	GLN	0	-0.049	-0.030	13.451	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	28	ALA	0	0.019	0.018	15.100	0.039	0.039	0.000	0.000	0.000	0.000
18	A	29	GLN	0	-0.040	-0.030	17.066	-0.062	-0.062	0.000	0.000	0.000	0.000
19	A	30	HIS	0	-0.067	-0.054	19.901	0.002	0.002	0.000	0.000	0.000	0.000
20	A	31	ASP	-1	-0.828	-0.890	18.575	-0.132	-0.132	0.000	0.000	0.000	0.000
21	A	32	TYR	0	-0.025	-0.024	18.783	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	33	THR	0	-0.052	-0.024	18.953	0.011	0.011	0.000	0.000	0.000	0.000
23	A	34	ALA	0	-0.022	-0.009	19.318	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	35	THR	0	-0.088	-0.061	21.284	0.004	0.004	0.000	0.000	0.000	0.000
25	A	36	ASP	-1	-0.841	-0.927	23.393	0.094	0.094	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.118	-0.070	21.546	0.009	0.009	0.000	0.000	0.000	0.000
27	A	38	ASP	-1	-0.889	-0.925	20.300	0.154	0.154	0.000	0.000	0.000	0.000
28	A	39	GLU	-1	-0.775	-0.856	20.447	0.031	0.031	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.064	-0.030	13.114	0.031	0.031	0.000	0.000	0.000	0.000
30	A	41	GLN	0	0.004	0.011	15.484	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	42	LEU	0	-0.029	-0.031	13.819	0.020	0.020	0.000	0.000	0.000	0.000
32	A	43	LYS	1	0.805	0.872	13.698	0.126	0.126	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.023	0.027	14.790	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	45	GLY	0	-0.004	-0.004	14.085	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	46	ASP	-1	-0.816	-0.893	10.697	-0.261	-0.261	0.000	0.000	0.000	0.000
36	A	47	VAL	0	-0.013	-0.001	9.673	0.032	0.032	0.000	0.000	0.000	0.000
37	A	48	VAL	0	-0.020	-0.016	10.347	0.057	0.057	0.000	0.000	0.000	0.000
38	A	49	LEU	0	-0.058	-0.031	9.445	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	50	VAL	0	0.043	0.024	13.365	0.058	0.058	0.000	0.000	0.000	0.000
40	A	51	ILE	0	-0.047	-0.036	15.762	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	52	PRO	0	0.014	0.004	18.635	0.003	0.003	0.000	0.000	0.000	0.000
42	A	53	PHE	0	0.076	0.045	21.518	0.014	0.014	0.000	0.000	0.000	0.000
43	A	54	GLN	0	-0.054	-0.038	21.100	0.008	0.008	0.000	0.000	0.000	0.000
44	A	55	ASN	0	-0.025	-0.040	24.825	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	56	PRO	0	-0.005	-0.009	27.828	0.000	0.000	0.000	0.000	0.000	0.000
46	A	57	GLU	-1	-0.945	-0.961	29.783	0.015	0.015	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.895	-0.933	26.548	0.064	0.064	0.000	0.000	0.000	0.000
48	A	59	GLN	0	-0.120	-0.046	26.856	0.002	0.002	0.000	0.000	0.000	0.000
49	A	60	ASP	-1	-0.861	-0.927	27.716	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	61	GLU	-1	-0.985	-1.002	28.174	-0.041	-0.041	0.000	0.000	0.000	0.000
51	A	62	GLY	0	0.011	0.005	27.928	0.000	0.000	0.000	0.000	0.000	0.000
52	A	63	TRP	0	-0.025	0.000	23.191	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.069	-0.040	20.429	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	65	MET	0	0.049	0.048	18.847	0.023	0.023	0.000	0.000	0.000	0.000
55	A	66	GLY	0	-0.010	-0.021	15.780	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	67	VAL	0	0.016	0.018	10.315	0.060	0.060	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.878	0.931	8.802	-0.237	-0.237	0.000	0.000	0.000	0.000
58	A	69	GLU	-1	-0.821	-0.907	6.418	-0.949	-0.949	0.000	0.000	0.000	0.000
59	A	70	SER	0	-0.022	-0.011	3.762	0.072	0.221	0.001	-0.022	-0.128	0.000
60	A	71	ASP	-1	-0.777	-0.901	3.973	1.529	1.783	0.001	-0.087	-0.167	0.000
61	A	72	TRP	0	0.009	0.012	6.576	0.287	0.287	0.000	0.000	0.000	0.000
62	A	73	ASN	0	0.029	0.000	2.487	-0.173	0.094	0.852	-0.322	-0.797	-0.001
63	A	74	GLN	0	-0.074	-0.037	1.968	-9.651	-10.218	6.426	-2.240	-3.619	0.019
64	A	75	HIS	0	-0.053	-0.029	4.318	-0.172	-0.102	0.000	-0.017	-0.053	0.000
65	A	76	LYS	1	0.837	0.931	6.579	-2.302	-2.302	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.832	-0.912	9.862	0.319	0.319	0.000	0.000	0.000	0.000
67	A	78	LEU	0	0.017	0.001	13.181	0.003	0.003	0.000	0.000	0.000	0.000
68	A	79	GLU	-1	-0.865	-0.928	14.273	0.166	0.166	0.000	0.000	0.000	0.000
69	A	80	LYS	1	0.805	0.889	14.854	-0.420	-0.420	0.000	0.000	0.000	0.000
70	A	81	CYS	0	-0.032	-0.008	11.453	0.087	0.087	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.808	0.893	13.539	-0.176	-0.176	0.000	0.000	0.000	0.000
72	A	83	GLY	0	0.066	0.044	15.366	0.023	0.023	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.011	-0.019	17.983	-0.029	-0.029	0.000	0.000	0.000	0.000
74	A	85	PHE	0	-0.018	-0.013	17.421	0.005	0.005	0.000	0.000	0.000	0.000
75	A	86	PRO	0	0.080	0.053	20.647	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	87	GLU	-1	-0.922	-0.969	22.203	-0.116	-0.116	0.000	0.000	0.000	0.000
77	A	88	ASN	0	0.017	0.010	22.751	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	89	PHE	0	-0.049	-0.020	20.980	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	90	THR	0	-0.091	-0.045	17.932	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	91	GLU	-1	-0.844	-0.907	19.415	-0.240	-0.240	0.000	0.000	0.000	0.000
81	A	92	ARG	1	0.919	0.965	18.936	0.190	0.190	0.000	0.000	0.000	0.000
82	A	93	VAL	0	0.010	0.010	14.687	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	94	GLN	0	-0.048	-0.027	14.664	-0.005	-0.005	0.000	0.000	0.000	0.000

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