FMO DATABASE

FMODB ID: N188Q

Calculation Name: 2BNW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BNW

Chain ID: B

ChEMBL ID:

UniProt ID: Q57468

Base Structure: X-ray

Registration Date: 2023-03-13

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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-247920.991388
FMO2-HF: Nuclear repulsion	226170.886575
FMO2-HF: Total energy	-21750.104813
FMO2-MP2: Total energy	-21812.208697

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(B:19:MET)

Summations of interaction energy for fragment #1(B:19: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.
-26.585	-18.653	6.425	-6.4	-7.958	-0.072

Interaction energy analysis for fragmet #1(B:19:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.015

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	B	21	LYS	1	0.948	0.963	3.827	-3.281	-1.692	0.000	-0.655	-0.934	0.001
4	B	22	LYS	1	0.909	0.951	2.366	2.068	3.426	1.211	-0.726	-1.843	0.000
5	B	23	ASP	-1	-0.835	-0.920	2.067	-25.913	-21.102	5.215	-5.003	-5.024	-0.073
6	B	24	ILE	0	-0.040	-0.014	4.839	1.185	1.359	-0.001	-0.016	-0.157	0.000
7	B	25	MET	0	-0.073	-0.016	6.944	0.716	0.716	0.000	0.000	0.000	0.000
8	B	26	GLY	0	0.012	0.015	8.703	0.007	0.007	0.000	0.000	0.000	0.000
9	B	27	ASP	-1	-0.812	-0.916	12.033	-1.041	-1.041	0.000	0.000	0.000	0.000
10	B	28	LYS	1	0.888	0.931	14.460	0.550	0.550	0.000	0.000	0.000	0.000
11	B	29	THR	0	0.001	0.017	17.398	-0.017	-0.017	0.000	0.000	0.000	0.000
12	B	30	VAL	0	0.038	0.012	19.715	0.034	0.034	0.000	0.000	0.000	0.000
13	B	31	ARG	1	0.911	0.953	22.173	0.247	0.247	0.000	0.000	0.000	0.000
14	B	32	VAL	0	0.052	0.032	22.019	0.026	0.026	0.000	0.000	0.000	0.000
15	B	33	ARG	1	0.860	0.886	25.139	0.220	0.220	0.000	0.000	0.000	0.000
16	B	34	ALA	0	0.043	0.014	27.789	-0.015	-0.015	0.000	0.000	0.000	0.000
17	B	35	ASP	-1	-0.743	-0.836	29.712	-0.238	-0.238	0.000	0.000	0.000	0.000
18	B	36	LEU	0	0.010	0.006	25.638	-0.007	-0.007	0.000	0.000	0.000	0.000
19	B	37	HIS	0	0.064	0.039	24.285	-0.013	-0.013	0.000	0.000	0.000	0.000
20	B	38	HIS	0	0.001	-0.004	25.992	-0.032	-0.032	0.000	0.000	0.000	0.000
21	B	39	ILE	0	0.024	0.013	26.191	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	40	ILE	0	0.035	0.021	21.091	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	41	LYS	1	0.854	0.936	23.797	0.344	0.344	0.000	0.000	0.000	0.000
24	B	42	ILE	0	0.013	-0.001	25.716	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	43	GLU	-1	-0.830	-0.886	23.556	-0.326	-0.326	0.000	0.000	0.000	0.000
26	B	44	THR	0	-0.025	-0.030	20.208	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	45	ALA	0	-0.043	-0.012	22.822	-0.009	-0.009	0.000	0.000	0.000	0.000
28	B	46	LYS	1	0.744	0.867	25.827	0.319	0.319	0.000	0.000	0.000	0.000
29	B	47	ASN	0	-0.038	-0.031	23.555	0.023	0.023	0.000	0.000	0.000	0.000
30	B	48	GLY	0	-0.004	0.018	20.884	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	49	GLY	0	0.050	0.022	17.130	0.004	0.004	0.000	0.000	0.000	0.000
32	B	50	ASN	0	-0.064	-0.059	15.580	0.120	0.120	0.000	0.000	0.000	0.000
33	B	51	VAL	0	0.021	-0.006	17.592	-0.025	-0.025	0.000	0.000	0.000	0.000
34	B	52	LYS	1	0.809	0.895	11.722	1.240	1.240	0.000	0.000	0.000	0.000
35	B	53	GLU	-1	-0.798	-0.883	12.665	-1.045	-1.045	0.000	0.000	0.000	0.000
36	B	54	VAL	0	0.030	0.016	13.905	0.000	0.000	0.000	0.000	0.000	0.000
37	B	55	MET	0	-0.081	-0.042	16.400	0.078	0.078	0.000	0.000	0.000	0.000
38	B	56	ASP	-1	-0.820	-0.894	10.945	-1.275	-1.275	0.000	0.000	0.000	0.000
39	B	57	GLN	0	-0.048	-0.030	11.724	-0.022	-0.022	0.000	0.000	0.000	0.000
40	B	58	ALA	0	0.020	0.011	12.727	0.079	0.079	0.000	0.000	0.000	0.000
41	B	59	LEU	0	-0.021	-0.010	13.797	0.083	0.083	0.000	0.000	0.000	0.000
42	B	60	GLU	-1	-0.847	-0.916	7.284	-1.272	-1.272	0.000	0.000	0.000	0.000
43	B	61	GLU	-1	-0.886	-0.943	11.623	-0.403	-0.403	0.000	0.000	0.000	0.000
44	B	62	TYR	0	-0.027	-0.014	13.928	0.084	0.084	0.000	0.000	0.000	0.000
45	B	63	ILE	0	0.005	-0.009	12.612	0.062	0.062	0.000	0.000	0.000	0.000
46	B	64	ARG	1	0.871	0.919	7.303	0.547	0.547	0.000	0.000	0.000	0.000
47	B	65	LYS	1	0.892	0.967	13.755	0.232	0.232	0.000	0.000	0.000	0.000
48	B	66	TYR	0	-0.033	-0.026	17.567	0.029	0.029	0.000	0.000	0.000	0.000
49	B	67	LEU	0	-0.036	-0.010	16.492	0.022	0.022	0.000	0.000	0.000	0.000
50	B	68	PRO	0	0.074	0.032	13.926	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	69	ASP	-1	-0.830	-0.896	12.811	0.052	0.052	0.000	0.000	0.000	0.000
52	B	70	LYS	1	0.764	0.868	13.650	0.023	0.023	0.000	0.000	0.000	0.000
53	B	71	LEU	0	-0.050	-0.006	8.300	-0.006	-0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:19:MET)