FMO DATABASE

FMODB ID: 536YZ

Calculation Name: 2NN4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN4

Chain ID: A

ChEMBL ID:

UniProt ID: P54494

Base Structure: X-ray

Registration Date: 2023-06-20

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-393758.965692
FMO2-HF: Nuclear repulsion	367178.366646
FMO2-HF: Total energy	-26580.599046
FMO2-MP2: Total energy	-26657.526717

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:1:LEU)

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

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.
-4.148	3.769	1.483	-3.76	-5.639	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.007

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	A	3	THR	0	-0.027	-0.013	3.675	-4.697	-0.855	-0.037	-2.005	-1.800	-0.005
4	A	4	PHE	0	0.106	0.039	4.905	1.313	1.410	-0.001	-0.005	-0.091	0.000
5	A	5	TYR	0	0.007	0.005	7.358	-0.026	-0.026	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.798	-0.899	2.707	3.193	4.271	1.170	-0.764	-1.483	0.002
7	A	7	VAL	0	0.004	-0.002	3.467	-1.626	-1.227	0.009	-0.080	-0.328	0.000
8	A	8	GLN	0	0.025	0.008	5.041	-0.687	-0.657	-0.001	-0.003	-0.027	0.000
9	A	9	GLN	0	-0.044	-0.018	6.562	-0.512	-0.512	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.029	-0.005	4.558	-0.398	-0.306	-0.001	-0.002	-0.088	0.000
11	A	11	LEU	0	0.072	0.013	6.816	-0.120	-0.120	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.932	0.996	9.922	-0.287	-0.287	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.105	-0.043	9.842	-0.054	-0.054	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.047	-0.038	9.941	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.001	0.011	13.863	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.023	-0.007	13.517	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.070	-0.031	13.496	0.056	0.056	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.015	-0.008	14.621	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.029	-0.024	15.996	0.034	0.034	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.039	-0.029	18.133	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.028	0.001	20.019	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.866	-0.929	19.896	0.118	0.118	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.890	0.944	12.921	-0.395	-0.395	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.913	-0.958	15.452	0.104	0.104	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.049	0.019	16.804	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.871	-0.941	14.515	0.258	0.258	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.043	-0.031	11.430	0.022	0.022	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.932	-0.965	12.925	0.035	0.035	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.042	0.033	15.097	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.056	-0.037	8.911	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.030	-0.020	10.343	-0.062	-0.062	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.914	-0.942	12.310	-0.034	-0.034	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.878	-0.946	12.934	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.048	-0.027	7.470	-0.065	-0.065	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.929	0.966	11.336	0.019	0.019	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.852	-0.925	14.133	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.000	0.005	11.191	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.040	-0.027	12.503	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.077	-0.034	14.273	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.094	-0.053	17.378	0.014	0.014	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.036	-0.018	16.681	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.041	-0.014	14.573	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.041	-0.005	9.378	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.901	-0.947	10.175	-0.344	-0.344	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.949	0.968	10.585	0.199	0.199	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.913	-0.969	7.703	-0.355	-0.355	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.032	0.012	5.909	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	48	TRP	0	0.041	0.029	5.988	-0.240	-0.240	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.010	-0.004	8.026	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.820	0.896	2.888	0.154	1.966	0.298	-0.732	-1.378	0.002
51	A	51	ALA	0	0.016	0.009	3.710	-0.457	-0.356	0.000	-0.031	-0.070	0.000
52	A	52	ALA	0	0.065	0.025	4.671	0.365	0.384	-0.001	-0.002	-0.016	0.000
53	A	53	ALA	0	-0.027	-0.012	7.085	0.132	0.132	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.049	-0.020	2.883	-0.365	0.082	0.047	-0.136	-0.358	-0.001
55	A	55	LEU	0	0.025	0.008	6.075	0.279	0.279	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.935	0.970	8.537	0.084	0.084	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.923	0.974	9.181	-0.155	-0.155	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.906	-0.971	9.210	0.649	0.649	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.037	0.012	11.167	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.979	-0.972	13.929	0.029	0.029	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.091	-0.054	11.842	-0.050	-0.050	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.047	-0.002	14.623	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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