FMO DATABASE

FMODB ID: LN3Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-218522.459539
FMO2-HF: Nuclear repulsion	199664.17332
FMO2-HF: Total energy	-18858.28622
FMO2-MP2: Total energy	-18913.446607

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.
-7.64	-2.636	2.059	-3.041	-4.022	-0.005

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 : 0.080 / q_NPA : 0.033

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	458	PRO	0	0.020	0.004	3.236	-2.672	-0.544	0.106	-1.075	-1.158	0.007
4	A	459	LEU	0	0.068	0.040	3.084	-0.918	-0.143	0.052	-0.216	-0.612	-0.001
5	A	460	LEU	0	0.019	0.015	4.293	0.624	0.926	-0.001	-0.119	-0.182	0.000
6	A	461	GLN	0	-0.032	-0.005	5.942	0.582	0.582	0.000	0.000	0.000	0.000
7	A	462	GLN	0	-0.004	-0.009	7.769	0.057	0.057	0.000	0.000	0.000	0.000
8	A	463	ILE	0	0.053	0.037	6.545	0.186	0.186	0.000	0.000	0.000	0.000
9	A	464	HIS	0	0.004	0.008	9.949	0.147	0.147	0.000	0.000	0.000	0.000
10	A	465	ASN	0	-0.027	-0.018	11.989	0.105	0.105	0.000	0.000	0.000	0.000
11	A	466	ILE	0	0.041	0.023	12.751	0.062	0.062	0.000	0.000	0.000	0.000
12	A	467	THR	0	-0.025	-0.019	13.202	0.062	0.062	0.000	0.000	0.000	0.000
13	A	468	SER	0	-0.081	-0.050	15.863	0.056	0.056	0.000	0.000	0.000	0.000
14	A	469	PHE	0	0.041	0.019	16.847	0.029	0.029	0.000	0.000	0.000	0.000
15	A	470	ILE	0	0.015	0.018	17.245	0.029	0.029	0.000	0.000	0.000	0.000
16	A	471	ARG	1	0.908	0.959	17.905	0.225	0.225	0.000	0.000	0.000	0.000
17	A	472	GLN	0	0.007	-0.009	22.255	0.007	0.007	0.000	0.000	0.000	0.000
18	A	473	ALA	0	-0.034	0.008	23.560	0.015	0.015	0.000	0.000	0.000	0.000
19	A	474	LYS	1	0.949	0.962	22.455	0.195	0.195	0.000	0.000	0.000	0.000
20	A	475	ALA	0	-0.035	-0.003	26.443	0.009	0.009	0.000	0.000	0.000	0.000
21	A	476	ALA	0	-0.018	0.000	28.239	0.009	0.009	0.000	0.000	0.000	0.000
22	A	477	GLY	0	-0.005	0.006	29.745	0.005	0.005	0.000	0.000	0.000	0.000
23	A	478	ARG	1	0.871	0.924	24.866	0.123	0.123	0.000	0.000	0.000	0.000
24	A	479	MET	0	0.018	-0.007	27.347	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	480	ASP	-1	-0.892	-0.946	27.070	-0.133	-0.133	0.000	0.000	0.000	0.000
26	A	481	GLU	-1	-0.803	-0.906	23.685	-0.145	-0.145	0.000	0.000	0.000	0.000
27	A	482	VAL	0	-0.050	-0.027	23.045	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	483	ARG	1	0.873	0.928	22.179	0.136	0.136	0.000	0.000	0.000	0.000
29	A	484	THR	0	0.038	0.029	22.203	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	485	LEU	0	0.045	0.026	18.384	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	486	GLN	0	-0.024	-0.029	17.525	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	487	GLU	-1	-0.782	-0.858	17.537	-0.313	-0.313	0.000	0.000	0.000	0.000
33	A	488	ASN	0	-0.017	-0.015	15.333	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	489	LEU	0	-0.006	-0.007	12.005	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	490	ARG	1	0.817	0.895	12.497	0.233	0.233	0.000	0.000	0.000	0.000
36	A	491	GLN	0	-0.008	-0.011	13.269	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	492	LEU	0	0.031	0.016	8.820	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	493	GLN	0	-0.068	-0.034	8.193	-0.266	-0.266	0.000	0.000	0.000	0.000
39	A	494	ASP	-1	-0.909	-0.947	8.845	-0.635	-0.635	0.000	0.000	0.000	0.000
40	A	495	GLU	-1	-0.911	-0.955	6.301	-1.133	-1.133	0.000	0.000	0.000	0.000
41	A	496	TYR	0	-0.081	-0.048	2.382	-0.840	-0.443	1.704	-0.903	-1.197	-0.006
42	A	497	ASP	-1	-0.818	-0.924	5.260	-0.755	-0.755	0.000	0.000	0.000	0.000
43	A	498	GLN	0	-0.027	-0.001	7.868	0.167	0.167	0.000	0.000	0.000	0.000
44	A	499	GLN	0	-0.088	-0.041	3.124	-2.858	-1.881	0.098	-0.493	-0.583	-0.004
45	A	500	GLN	0	-0.079	-0.027	3.099	-0.021	0.404	0.100	-0.235	-0.290	-0.001
46	A	501	THR	0	-0.084	-0.040	6.805	0.234	0.234	0.000	0.000	0.000	0.000

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