FMO DATABASE

FMODB ID: 8277Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-247209.69591
FMO2-HF: Nuclear repulsion	225459.792128
FMO2-HF: Total energy	-21749.903782
FMO2-MP2: Total energy	-21812.003378

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.
-11.75	-6.5	1.814	-2.385	-4.679	-0.005

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 : 0.010 / q_NPA : -0.014

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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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	0.950	0.954	3.571	-4.240	-2.726	0.010	-0.565	-0.959	0.002
4	B	22	LYS	1	0.955	0.972	2.412	1.326	2.737	1.738	-0.733	-2.416	0.000
5	B	23	ASP	-1	-0.876	-0.931	3.260	-8.962	-6.761	0.067	-1.077	-1.191	-0.007
6	B	24	ILE	0	-0.064	-0.025	4.791	0.826	0.950	-0.001	-0.010	-0.113	0.000
7	B	25	MET	0	-0.070	-0.017	7.043	0.550	0.550	0.000	0.000	0.000	0.000
8	B	26	GLY	0	0.012	0.013	8.760	-0.058	-0.058	0.000	0.000	0.000	0.000
9	B	27	ASP	-1	-0.828	-0.912	12.057	-0.850	-0.850	0.000	0.000	0.000	0.000
10	B	28	LYS	1	0.920	0.956	14.753	0.343	0.343	0.000	0.000	0.000	0.000
11	B	29	THR	0	-0.018	-0.006	17.539	-0.027	-0.027	0.000	0.000	0.000	0.000
12	B	30	VAL	0	0.039	0.010	20.049	0.029	0.029	0.000	0.000	0.000	0.000
13	B	31	ARG	1	0.934	0.966	22.344	0.179	0.179	0.000	0.000	0.000	0.000
14	B	32	VAL	0	0.040	0.028	22.763	0.015	0.015	0.000	0.000	0.000	0.000
15	B	33	ARG	1	0.858	0.885	25.913	0.171	0.171	0.000	0.000	0.000	0.000
16	B	34	ALA	0	0.051	0.023	28.232	-0.013	-0.013	0.000	0.000	0.000	0.000
17	B	35	ASP	-1	-0.747	-0.843	29.780	-0.183	-0.183	0.000	0.000	0.000	0.000
18	B	36	LEU	0	0.014	0.001	26.031	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	37	HIS	0	0.049	0.029	24.425	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	38	HIS	0	-0.019	-0.017	26.266	-0.024	-0.024	0.000	0.000	0.000	0.000
21	B	39	ILE	0	0.027	0.011	26.425	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	40	ILE	0	0.035	0.027	21.252	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	41	LYS	1	0.872	0.948	24.011	0.264	0.264	0.000	0.000	0.000	0.000
24	B	42	ILE	0	-0.002	-0.007	25.783	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	43	GLU	-1	-0.823	-0.885	23.394	-0.273	-0.273	0.000	0.000	0.000	0.000
26	B	44	THR	0	-0.055	-0.031	20.286	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	45	ALA	0	-0.041	-0.005	22.838	-0.007	-0.007	0.000	0.000	0.000	0.000
28	B	46	LYS	1	0.782	0.892	25.753	0.248	0.248	0.000	0.000	0.000	0.000
29	B	47	ASN	0	-0.047	-0.049	23.607	0.017	0.017	0.000	0.000	0.000	0.000
30	B	48	GLY	0	0.013	0.022	21.022	-0.017	-0.017	0.000	0.000	0.000	0.000
31	B	49	GLY	0	0.054	0.032	17.359	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	50	ASN	0	-0.030	-0.035	15.346	0.066	0.066	0.000	0.000	0.000	0.000
33	B	51	VAL	0	0.028	-0.005	18.112	-0.010	-0.010	0.000	0.000	0.000	0.000
34	B	52	LYS	1	0.819	0.903	11.671	1.001	1.001	0.000	0.000	0.000	0.000
35	B	53	GLU	-1	-0.850	-0.918	12.834	-0.844	-0.844	0.000	0.000	0.000	0.000
36	B	54	VAL	0	0.034	0.015	14.308	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	55	MET	0	-0.093	-0.050	16.476	0.044	0.044	0.000	0.000	0.000	0.000
38	B	56	ASP	-1	-0.826	-0.903	11.213	-0.993	-0.993	0.000	0.000	0.000	0.000
39	B	57	GLN	0	-0.030	-0.021	12.128	-0.025	-0.025	0.000	0.000	0.000	0.000
40	B	58	ALA	0	-0.003	-0.004	13.134	0.060	0.060	0.000	0.000	0.000	0.000
41	B	59	LEU	0	-0.029	-0.019	14.520	0.062	0.062	0.000	0.000	0.000	0.000
42	B	60	GLU	-1	-0.893	-0.936	7.760	-1.033	-1.033	0.000	0.000	0.000	0.000
43	B	61	GLU	-1	-0.876	-0.935	12.041	-0.361	-0.361	0.000	0.000	0.000	0.000
44	B	62	TYR	0	-0.027	-0.011	14.287	0.067	0.067	0.000	0.000	0.000	0.000
45	B	63	ILE	0	0.007	-0.006	13.031	0.050	0.050	0.000	0.000	0.000	0.000
46	B	64	ARG	1	0.878	0.928	7.445	0.559	0.559	0.000	0.000	0.000	0.000
47	B	65	LYS	1	0.875	0.959	13.932	0.202	0.202	0.000	0.000	0.000	0.000
48	B	66	TYR	0	-0.034	-0.032	17.609	0.025	0.025	0.000	0.000	0.000	0.000
49	B	67	LEU	0	-0.047	-0.021	16.758	0.024	0.024	0.000	0.000	0.000	0.000
50	B	68	PRO	0	0.077	0.031	14.195	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	69	ASP	-1	-0.855	-0.910	13.350	0.040	0.040	0.000	0.000	0.000	0.000
52	B	70	LYS	1	0.774	0.881	13.711	0.023	0.023	0.000	0.000	0.000	0.000
53	B	71	LEU	0	-0.022	0.007	8.548	0.022	0.022	0.000	0.000	0.000	0.000

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