FMO DATABASE

FMODB ID: 2JK1R

Calculation Name: 2BO3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BO3

Chain ID: A

ChEMBL ID:

UniProt ID: O25025

Base Structure: X-ray

Registration Date: 2023-06-21

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
Remarks

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	-594697.867852
FMO2-HF: Nuclear repulsion	557005.752336
FMO2-HF: Total energy	-37692.115515
FMO2-MP2: Total energy	-37803.044889

3D Structure Molmil

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:1:MET)

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

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.
-7.826	-2.578	1.971	-2.935	-4.285	-0.012

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.004

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	3	ASP	-1	-0.895	-0.947	2.793	-7.038	-2.671	0.334	-2.447	-2.255	-0.008
4	A	4	TYR	0	-0.007	-0.019	2.384	-0.059	0.822	1.637	-0.488	-2.030	-0.004
5	A	5	SER	0	-0.029	-0.030	6.642	0.199	0.199	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.834	-0.915	8.498	-0.977	-0.977	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.084	-0.032	7.991	0.126	0.126	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.825	-0.881	10.287	-0.161	-0.161	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.028	-0.008	10.951	0.049	0.049	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.052	-0.031	12.316	0.035	0.035	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.920	-0.949	16.432	-0.073	-0.073	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.051	0.036	19.218	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.026	-0.037	20.463	0.029	0.029	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.010	-0.011	23.881	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.025	0.003	25.310	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.826	-0.896	24.480	-0.103	-0.103	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.844	0.900	18.537	0.129	0.129	0.000	0.000	0.000	0.000
18	A	18	TRP	0	-0.002	-0.016	24.137	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.029	0.012	27.268	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.878	-0.931	23.424	-0.190	-0.190	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.033	-0.024	22.036	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.031	-0.016	25.986	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.066	-0.038	29.057	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	HIS	0	-0.067	-0.028	24.000	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.010	0.022	26.883	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.004	-0.010	27.870	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.966	0.967	30.473	0.140	0.140	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.936	0.977	33.764	0.069	0.069	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.023	-0.015	29.515	0.007	0.007	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.072	0.042	31.560	0.009	0.009	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.810	0.891	33.265	0.057	0.057	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.974	0.986	35.537	0.035	0.035	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.743	-0.821	32.489	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.033	0.008	34.469	0.005	0.005	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.809	-0.883	37.474	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.848	0.916	34.458	0.017	0.017	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.045	-0.029	34.739	0.005	0.005	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.017	0.018	39.366	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.946	-0.971	42.532	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.026	-0.012	39.772	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.014	-0.003	42.593	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.073	0.038	44.262	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.044	-0.014	46.320	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.051	-0.034	42.812	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.941	-0.968	47.195	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.039	0.003	49.595	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.104	-0.048	49.818	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.010	-0.017	48.249	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.892	-0.928	52.509	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.788	0.897	55.149	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.967	-0.972	54.675	0.010	0.010	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.904	-0.939	56.742	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.115	-0.069	53.063	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.803	-0.915	53.850	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.886	-0.939	53.858	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.935	0.964	52.642	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.000	-0.009	45.794	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.881	-0.932	49.463	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.070	-0.045	50.722	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.032	-0.022	43.561	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.009	0.007	45.803	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.861	0.926	46.132	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.073	-0.022	47.872	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.023	0.013	40.573	0.003	0.003	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.903	0.948	42.670	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.039	-0.035	43.226	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.794	-0.865	42.534	0.031	0.031	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.931	-0.972	38.869	0.028	0.028	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.865	-0.927	38.080	0.047	0.047	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.034	-0.017	38.533	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.017	-0.018	37.451	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.049	0.023	30.716	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.854	0.930	34.072	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.003	-0.008	35.820	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.798	-0.888	31.274	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.040	-0.037	31.262	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.886	0.950	32.216	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.832	0.901	32.653	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.009	0.012	27.196	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.850	-0.915	29.182	0.045	0.045	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.038	-0.025	31.040	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.001	0.010	26.965	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.019	0.000	25.551	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.011	-0.007	27.863	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.043	-0.038	30.201	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.023	-0.018	23.957	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.029	0.020	26.834	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.045	-0.028	27.842	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.055	-0.030	27.302	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.015	-0.008	22.212	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.093	-0.019	26.390	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.076	-0.038	29.149	-0.008	-0.008	0.000	0.000	0.000	0.000

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