FMO DATABASE

FMODB ID: GNRR1

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	OptH
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-247056.889006
FMO2-HF: Nuclear repulsion	225307.449638
FMO2-HF: Total energy	-21749.439368
FMO2-MP2: Total energy	-21811.563194

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.
-13.004	-8.297	5.726	-3.648	-6.786	-0.01

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 : 0.007 / 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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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	0.952	3.623	-3.322	-1.774	0.010	-0.536	-1.022	0.002
4	B	22	LYS	1	0.959	0.976	2.174	1.133	1.013	5.489	-1.435	-3.935	0.003
5	B	23	ASP	-1	-0.883	-0.938	2.946	-12.085	-8.951	0.228	-1.662	-1.700	-0.015
6	B	24	ILE	0	-0.058	-0.022	4.622	1.003	1.148	-0.001	-0.015	-0.129	0.000
7	B	25	MET	0	-0.067	-0.018	6.689	0.625	0.625	0.000	0.000	0.000	0.000
8	B	26	GLY	0	0.005	0.011	8.721	-0.030	-0.030	0.000	0.000	0.000	0.000
9	B	27	ASP	-1	-0.856	-0.931	11.848	-0.831	-0.831	0.000	0.000	0.000	0.000
10	B	28	LYS	1	0.936	0.957	14.530	0.358	0.358	0.000	0.000	0.000	0.000
11	B	29	THR	0	-0.027	-0.009	17.355	-0.014	-0.014	0.000	0.000	0.000	0.000
12	B	30	VAL	0	0.051	0.014	19.912	0.027	0.027	0.000	0.000	0.000	0.000
13	B	31	ARG	1	0.928	0.963	22.150	0.159	0.159	0.000	0.000	0.000	0.000
14	B	32	VAL	0	0.041	0.031	22.587	0.016	0.016	0.000	0.000	0.000	0.000
15	B	33	ARG	1	0.891	0.924	25.704	0.106	0.106	0.000	0.000	0.000	0.000
16	B	34	ALA	0	0.068	0.025	27.998	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	35	ASP	-1	-0.792	-0.880	29.562	-0.122	-0.122	0.000	0.000	0.000	0.000
18	B	36	LEU	0	0.003	-0.009	25.981	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	37	HIS	0	0.000	0.003	24.260	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	38	HIS	0	-0.006	-0.012	26.048	-0.021	-0.021	0.000	0.000	0.000	0.000
21	B	39	ILE	0	0.016	0.006	26.082	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	40	ILE	0	0.042	0.035	21.069	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	41	LYS	1	0.921	0.981	23.762	0.219	0.219	0.000	0.000	0.000	0.000
24	B	42	ILE	0	-0.031	-0.022	25.516	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	43	GLU	-1	-0.858	-0.907	22.904	-0.179	-0.179	0.000	0.000	0.000	0.000
26	B	44	THR	0	-0.048	-0.039	20.015	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	45	ALA	0	-0.058	-0.015	22.555	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	46	LYS	1	0.867	0.939	25.432	0.146	0.146	0.000	0.000	0.000	0.000
29	B	47	ASN	0	-0.046	-0.043	23.279	0.007	0.007	0.000	0.000	0.000	0.000
30	B	48	GLY	0	0.005	0.017	20.701	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	49	GLY	0	0.066	0.040	17.004	0.010	0.010	0.000	0.000	0.000	0.000
32	B	50	ASN	0	-0.021	-0.030	15.278	0.040	0.040	0.000	0.000	0.000	0.000
33	B	51	VAL	0	0.052	0.003	17.838	0.003	0.003	0.000	0.000	0.000	0.000
34	B	52	LYS	1	0.869	0.946	11.340	0.975	0.975	0.000	0.000	0.000	0.000
35	B	53	GLU	-1	-0.882	-0.930	12.463	-0.687	-0.687	0.000	0.000	0.000	0.000
36	B	54	VAL	0	0.026	0.013	14.129	0.037	0.037	0.000	0.000	0.000	0.000
37	B	55	MET	0	-0.094	-0.049	16.343	0.054	0.054	0.000	0.000	0.000	0.000
38	B	56	ASP	-1	-0.861	-0.937	10.970	-0.750	-0.750	0.000	0.000	0.000	0.000
39	B	57	GLN	0	-0.010	0.000	12.546	0.009	0.009	0.000	0.000	0.000	0.000
40	B	58	ALA	0	-0.003	-0.007	13.526	0.069	0.069	0.000	0.000	0.000	0.000
41	B	59	LEU	0	-0.037	-0.024	14.226	0.051	0.051	0.000	0.000	0.000	0.000
42	B	60	GLU	-1	-0.902	-0.952	7.892	-0.012	-0.012	0.000	0.000	0.000	0.000
43	B	61	GLU	-1	-0.900	-0.957	12.125	0.004	0.004	0.000	0.000	0.000	0.000
44	B	62	TYR	0	-0.017	-0.009	14.723	0.040	0.040	0.000	0.000	0.000	0.000
45	B	63	ILE	0	0.004	-0.005	12.838	0.026	0.026	0.000	0.000	0.000	0.000
46	B	64	ARG	1	0.890	0.950	8.204	-0.190	-0.190	0.000	0.000	0.000	0.000
47	B	65	LYS	1	0.875	0.962	14.195	0.031	0.031	0.000	0.000	0.000	0.000
48	B	66	TYR	0	-0.023	-0.031	17.955	0.009	0.009	0.000	0.000	0.000	0.000
49	B	67	LEU	0	-0.071	-0.033	16.645	0.001	0.001	0.000	0.000	0.000	0.000
50	B	68	PRO	0	0.075	0.027	14.269	0.001	0.001	0.000	0.000	0.000	0.000
51	B	69	ASP	-1	-0.927	-0.957	13.514	0.207	0.207	0.000	0.000	0.000	0.000
52	B	70	LYS	1	0.849	0.929	13.771	-0.069	-0.069	0.000	0.000	0.000	0.000
53	B	71	LEU	0	-0.016	0.014	8.343	-0.004	-0.004	0.000	0.000	0.000	0.000

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