FMO DATABASE

FMODB ID: 98V42

Calculation Name: 1YZM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H1K0

Base Structure: X-ray

Registration Date: 2023-09-23

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-218665.345745
FMO2-HF: Nuclear repulsion	199806.842673
FMO2-HF: Total energy	-18858.503072
FMO2-MP2: Total energy	-18913.644018

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:456:GLY)

Summations of interaction energy for fragment #1(A:456:GLY)

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.
-8.179	-2.813	1.519	-2.92	-3.964	-0.009

Interaction energy analysis for fragmet #1(A:456:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.088 / q_NPA : 0.039

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	458	PRO	0	0.014	0.001	3.211	-2.480	-0.453	0.094	-1.012	-1.109	0.006
4	A	459	LEU	0	0.074	0.045	3.036	-0.823	-0.072	0.049	-0.207	-0.593	-0.001
5	A	460	LEU	0	0.012	0.012	4.294	0.683	0.985	-0.001	-0.119	-0.181	0.000
6	A	461	GLN	0	-0.037	-0.011	5.941	0.591	0.591	0.000	0.000	0.000	0.000
7	A	462	GLN	0	0.000	-0.005	7.669	0.073	0.073	0.000	0.000	0.000	0.000
8	A	463	ILE	0	0.054	0.036	6.460	0.206	0.206	0.000	0.000	0.000	0.000
9	A	464	HIS	0	0.005	0.008	9.878	0.174	0.174	0.000	0.000	0.000	0.000
10	A	465	ASN	0	-0.036	-0.020	11.988	0.114	0.114	0.000	0.000	0.000	0.000
11	A	466	ILE	0	0.044	0.022	12.926	0.067	0.067	0.000	0.000	0.000	0.000
12	A	467	THR	0	-0.020	-0.016	13.232	0.067	0.067	0.000	0.000	0.000	0.000
13	A	468	SER	0	-0.059	-0.045	15.862	0.061	0.061	0.000	0.000	0.000	0.000
14	A	469	PHE	0	0.035	0.018	16.693	0.030	0.030	0.000	0.000	0.000	0.000
15	A	470	ILE	0	0.021	0.019	17.261	0.031	0.031	0.000	0.000	0.000	0.000
16	A	471	ARG	1	0.883	0.948	17.601	0.246	0.246	0.000	0.000	0.000	0.000
17	A	472	GLN	0	0.018	-0.002	22.254	0.009	0.009	0.000	0.000	0.000	0.000
18	A	473	ALA	0	-0.005	0.008	23.561	0.016	0.016	0.000	0.000	0.000	0.000
19	A	474	LYS	1	0.922	0.958	22.123	0.212	0.212	0.000	0.000	0.000	0.000
20	A	475	ALA	0	-0.037	-0.006	26.443	0.010	0.010	0.000	0.000	0.000	0.000
21	A	476	ALA	0	-0.018	-0.001	28.239	0.009	0.009	0.000	0.000	0.000	0.000
22	A	477	GLY	0	0.001	0.010	29.733	0.005	0.005	0.000	0.000	0.000	0.000
23	A	478	ARG	1	0.815	0.876	25.124	0.131	0.131	0.000	0.000	0.000	0.000
24	A	479	MET	0	0.021	-0.004	27.347	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	480	ASP	-1	-0.886	-0.941	27.070	-0.143	-0.143	0.000	0.000	0.000	0.000
26	A	481	GLU	-1	-0.761	-0.856	23.569	-0.156	-0.156	0.000	0.000	0.000	0.000
27	A	482	VAL	0	-0.038	-0.021	23.038	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	483	ARG	1	0.878	0.930	22.178	0.144	0.144	0.000	0.000	0.000	0.000
29	A	484	THR	0	0.041	0.023	22.161	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	485	LEU	0	0.041	0.023	18.339	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	486	GLN	0	-0.033	-0.029	17.525	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	487	GLU	-1	-0.743	-0.815	17.537	-0.349	-0.349	0.000	0.000	0.000	0.000
33	A	488	ASN	0	-0.032	-0.023	15.395	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	489	LEU	0	0.005	-0.002	11.938	-0.063	-0.063	0.000	0.000	0.000	0.000
35	A	490	ARG	1	0.818	0.876	12.497	0.261	0.261	0.000	0.000	0.000	0.000
36	A	491	GLN	0	-0.054	-0.038	13.269	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	492	LEU	0	0.027	0.012	9.007	-0.052	-0.052	0.000	0.000	0.000	0.000
38	A	493	GLN	0	-0.083	-0.049	8.268	-0.322	-0.322	0.000	0.000	0.000	0.000
39	A	494	ASP	-1	-0.895	-0.945	8.845	-0.657	-0.657	0.000	0.000	0.000	0.000
40	A	495	GLU	-1	-0.870	-0.940	6.714	-1.347	-1.347	0.000	0.000	0.000	0.000
41	A	496	TYR	0	-0.059	-0.035	2.537	-1.219	-0.506	1.139	-0.771	-1.081	-0.006
42	A	497	ASP	-1	-0.812	-0.914	5.261	-0.821	-0.821	0.000	0.000	0.000	0.000
43	A	498	GLN	0	-0.053	-0.006	7.868	0.186	0.186	0.000	0.000	0.000	0.000
44	A	499	GLN	0	-0.116	-0.054	2.964	-3.535	-2.246	0.225	-0.697	-0.817	-0.007
45	A	500	GLN	0	-0.104	-0.037	3.850	0.378	0.662	0.013	-0.114	-0.183	-0.001
46	A	501	THR	0	-0.073	-0.036	6.805	0.257	0.257	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:456:GLY)