FMO DATABASE

FMODB ID: 72VMK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-313468.91835
FMO2-HF: Nuclear repulsion	290812.497748
FMO2-HF: Total energy	-22656.420602
FMO2-MP2: Total energy	-22722.352751

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.
-6.002	-0.32	9.685	-3.574	-11.794	-0.015

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 : -0.075 / q_NPA : -0.043

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	0.020	0.015	3.336	-0.477	1.778	-0.012	-1.082	-1.161	-0.001
4	A	4	VAL	0	-0.029	-0.012	2.230	-2.754	-1.522	2.220	-0.813	-2.639	-0.007
5	A	5	GLU	-1	-0.933	-0.990	4.764	-0.210	-0.141	-0.001	-0.014	-0.055	0.000
6	A	6	ALA	0	0.022	0.027	7.551	-0.006	-0.006	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.001	-0.002	8.371	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.024	-0.012	10.476	0.036	0.036	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.054	-0.058	13.482	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.030	-0.001	14.065	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.829	-0.906	16.040	-0.048	-0.048	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.055	-0.016	19.043	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.001	-0.007	20.133	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.051	-0.019	21.476	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.896	-0.940	21.474	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.011	-0.010	19.898	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.837	-0.911	17.095	0.055	0.055	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.119	-0.054	12.224	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.023	0.004	15.185	0.015	0.015	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.058	-0.041	10.905	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.943	0.977	14.925	0.115	0.115	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.004	-0.010	13.466	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.028	0.020	12.442	0.020	0.020	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.900	-0.954	12.566	-0.210	-0.210	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.896	0.945	9.090	0.322	0.322	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.029	-0.008	8.019	0.081	0.081	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.019	0.012	6.860	-0.283	-0.283	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.053	-0.038	2.851	-0.622	0.390	0.455	-0.314	-1.153	-0.001
29	A	29	LEU	0	-0.046	-0.040	6.658	-0.262	-0.262	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.911	-0.964	7.597	-0.072	-0.072	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.924	0.972	2.945	-0.325	0.640	0.109	-0.218	-0.856	0.001
32	A	32	LEU	0	0.013	0.016	7.439	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.006	-0.005	10.347	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.024	-0.022	9.136	0.214	0.214	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.916	-0.962	9.050	0.423	0.423	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.026	0.027	10.964	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.030	-0.015	3.761	-0.649	0.228	0.132	-0.259	-0.750	-0.001
38	A	38	LYS	1	0.993	1.015	9.084	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.034	-0.001	9.217	-0.106	-0.106	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.014	-0.014	10.592	0.063	0.063	0.000	0.000	0.000	0.000
41	A	41	CYS	0	0.011	0.004	11.510	-0.071	-0.071	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.006	-0.007	13.657	0.025	0.025	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.010	0.003	16.942	0.023	0.023	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.881	0.962	16.597	0.135	0.135	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.007	-0.013	14.609	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.011	0.016	14.622	0.013	0.013	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.037	-0.025	12.894	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.022	0.018	7.519	-0.037	-0.037	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.062	0.035	10.998	0.114	0.114	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.006	0.001	6.456	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.011	-0.019	6.578	-0.106	-0.106	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.016	0.017	8.705	-0.119	-0.119	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.038	-0.018	4.182	-0.182	-0.064	-0.001	-0.011	-0.107	0.000
54	A	54	LYS	1	0.926	0.988	4.047	0.465	0.627	0.000	-0.022	-0.140	0.000
55	A	55	PRO	0	0.001	-0.020	2.000	-0.591	-1.876	6.213	-1.324	-3.604	0.004
56	A	56	ALA	0	-0.028	0.002	2.983	1.779	0.726	0.130	1.290	-0.367	-0.001
57	A	57	PHE	0	0.045	0.028	2.817	-2.332	-1.002	0.440	-0.807	-0.962	-0.009

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