FMO DATABASE

FMODB ID: 2J3LR

Calculation Name: 1YNZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YNZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q06449

Base Structure: X-ray

Registration Date: 2023-09-19

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-313979.699589
FMO2-HF: Nuclear repulsion	291322.860768
FMO2-HF: Total energy	-22656.838821
FMO2-MP2: Total energy	-22722.79881

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: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.
-12.988	-2.48	6.642	-5.067	-12.085	-0.008

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 : -0.049 / 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	A	3	TYR	0	0.021	0.012	3.388	0.015	2.731	-0.015	-1.390	-1.311	0.002
4	A	4	VAL	0	-0.025	-0.013	2.570	-2.486	-0.888	1.224	-0.663	-2.160	-0.005
5	A	5	GLU	-1	-0.836	-0.916	4.865	-0.250	-0.205	-0.001	-0.008	-0.036	0.000
6	A	6	ALA	0	0.025	0.026	7.797	0.053	0.053	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.020	-0.013	9.042	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.013	-0.008	10.752	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.025	-0.028	13.539	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.025	0.000	13.876	0.034	0.034	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.833	-0.909	15.882	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.062	-0.014	18.788	0.019	0.019	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.013	-0.019	19.830	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.067	-0.028	20.117	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.891	-0.938	21.417	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.004	-0.008	19.837	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.815	-0.903	17.110	0.138	0.138	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.105	-0.044	12.168	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.034	0.014	14.942	0.029	0.029	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.059	-0.031	10.837	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.910	0.941	15.021	0.111	0.111	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.012	-0.007	13.695	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.016	0.014	12.747	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.821	-0.903	12.664	-0.291	-0.291	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.794	0.873	8.846	0.471	0.471	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.022	-0.002	7.959	0.056	0.056	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.037	0.023	6.893	-0.376	-0.376	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.063	-0.043	3.055	0.145	0.998	0.926	-0.413	-1.366	-0.002
29	A	29	LEU	0	-0.043	-0.031	6.576	-0.507	-0.507	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.839	-0.911	7.817	-0.058	-0.058	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.916	0.971	2.717	-6.754	-5.402	1.666	-0.849	-2.169	0.007
32	A	32	LEU	0	0.015	0.017	7.430	-0.197	-0.197	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.002	-0.005	10.082	-0.099	-0.099	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.021	-0.024	8.904	0.336	0.336	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.915	-0.959	8.502	0.703	0.703	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.025	0.024	10.825	-0.106	-0.106	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.037	-0.027	3.174	-0.221	1.175	0.452	-0.500	-1.349	-0.003
38	A	38	LYS	1	0.918	0.954	8.953	-0.134	-0.134	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.037	0.005	9.541	-0.074	-0.074	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.008	-0.003	10.516	0.033	0.033	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.020	-0.013	11.517	-0.103	-0.103	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.004	-0.001	13.681	0.028	0.028	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.013	0.007	16.972	0.042	0.042	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.831	0.929	15.958	0.201	0.201	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.013	-0.008	14.537	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.012	0.017	14.549	0.017	0.017	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.038	-0.028	12.840	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.020	0.012	7.214	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.065	0.037	10.780	0.164	0.164	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.002	0.002	5.866	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.001	-0.015	6.192	-0.173	-0.173	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.012	0.003	8.359	-0.113	-0.113	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.036	-0.015	4.327	-0.173	-0.084	-0.001	-0.005	-0.083	0.000
54	A	54	LYS	1	0.897	0.962	4.459	0.340	0.459	-0.001	-0.012	-0.106	0.000
55	A	55	PRO	0	0.013	-0.011	2.293	-1.727	-0.876	1.958	-0.508	-2.301	0.001
56	A	56	ALA	0	-0.046	-0.009	3.420	0.536	0.661	0.034	0.097	-0.256	0.000
57	A	57	PHE	0	0.064	0.039	2.834	-2.239	-0.875	0.400	-0.816	-0.948	-0.008

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