FMO DATABASE

FMODB ID: MN1VZ

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	OptAll
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	-220620.863768
FMO2-HF: Nuclear repulsion	201762.319183
FMO2-HF: Total energy	-18858.544585
FMO2-MP2: Total energy	-18913.699554

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.
-10.984	-6.188	4.328	-3.763	-5.363	-0.02

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 : 0.099 / q_NPA : 0.045

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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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	-0.008	-0.008	2.645	-2.565	-0.584	0.436	-1.051	-1.366	0.007
4	A	459	LEU	0	0.077	0.051	3.262	-0.567	0.178	0.052	-0.207	-0.591	0.000
5	A	460	LEU	0	0.022	0.019	4.270	0.856	1.124	-0.001	-0.103	-0.164	0.000
6	A	461	GLN	0	-0.033	-0.014	6.070	0.554	0.554	0.000	0.000	0.000	0.000
7	A	462	GLN	0	-0.006	-0.010	6.870	0.033	0.033	0.000	0.000	0.000	0.000
8	A	463	ILE	0	0.055	0.038	6.404	0.220	0.220	0.000	0.000	0.000	0.000
9	A	464	HIS	0	0.022	0.021	10.061	0.184	0.184	0.000	0.000	0.000	0.000
10	A	465	ASN	0	-0.035	-0.011	12.210	0.123	0.123	0.000	0.000	0.000	0.000
11	A	466	ILE	0	0.054	0.025	12.577	0.074	0.074	0.000	0.000	0.000	0.000
12	A	467	THR	0	-0.023	-0.025	13.360	0.072	0.072	0.000	0.000	0.000	0.000
13	A	468	SER	0	-0.071	-0.052	15.937	0.066	0.066	0.000	0.000	0.000	0.000
14	A	469	PHE	0	0.026	0.017	16.091	0.031	0.031	0.000	0.000	0.000	0.000
15	A	470	ILE	0	0.030	0.019	17.113	0.034	0.034	0.000	0.000	0.000	0.000
16	A	471	ARG	1	0.880	0.945	17.588	0.246	0.246	0.000	0.000	0.000	0.000
17	A	472	GLN	0	0.022	-0.001	22.150	0.009	0.009	0.000	0.000	0.000	0.000
18	A	473	ALA	0	-0.015	0.000	23.420	0.015	0.015	0.000	0.000	0.000	0.000
19	A	474	LYS	1	0.905	0.948	21.875	0.220	0.220	0.000	0.000	0.000	0.000
20	A	475	ALA	0	-0.031	-0.008	26.249	0.011	0.011	0.000	0.000	0.000	0.000
21	A	476	ALA	0	-0.005	0.007	28.267	0.010	0.010	0.000	0.000	0.000	0.000
22	A	477	GLY	0	0.015	0.011	29.780	0.004	0.004	0.000	0.000	0.000	0.000
23	A	478	ARG	1	0.806	0.875	24.648	0.142	0.142	0.000	0.000	0.000	0.000
24	A	479	MET	0	0.012	-0.004	27.046	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	480	ASP	-1	-0.873	-0.935	26.476	-0.163	-0.163	0.000	0.000	0.000	0.000
26	A	481	GLU	-1	-0.742	-0.831	22.770	-0.179	-0.179	0.000	0.000	0.000	0.000
27	A	482	VAL	0	-0.059	-0.029	22.353	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	483	ARG	1	0.854	0.910	21.775	0.153	0.153	0.000	0.000	0.000	0.000
29	A	484	THR	0	0.047	0.020	21.538	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	485	LEU	0	0.046	0.023	17.800	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	486	GLN	0	-0.022	-0.020	17.038	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	487	GLU	-1	-0.753	-0.819	17.019	-0.396	-0.396	0.000	0.000	0.000	0.000
33	A	488	ASN	0	-0.031	-0.020	15.063	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	489	LEU	0	-0.017	-0.009	11.805	-0.083	-0.083	0.000	0.000	0.000	0.000
35	A	490	ARG	1	0.831	0.882	11.998	0.299	0.299	0.000	0.000	0.000	0.000
36	A	491	GLN	0	-0.047	-0.037	12.565	-0.064	-0.064	0.000	0.000	0.000	0.000
37	A	492	LEU	0	0.019	0.005	8.503	-0.065	-0.065	0.000	0.000	0.000	0.000
38	A	493	GLN	0	-0.076	-0.046	7.576	-0.352	-0.352	0.000	0.000	0.000	0.000
39	A	494	ASP	-1	-0.879	-0.925	8.415	-0.669	-0.669	0.000	0.000	0.000	0.000
40	A	495	GLU	-1	-0.863	-0.931	6.381	-1.891	-1.891	0.000	0.000	0.000	0.000
41	A	496	TYR	0	-0.081	-0.048	2.787	-1.167	-0.472	0.913	-0.551	-1.057	-0.006
42	A	497	ASP	-1	-0.801	-0.908	4.970	-0.697	-0.614	-0.001	-0.004	-0.078	0.000
43	A	498	GLN	0	-0.087	-0.041	7.666	0.234	0.234	0.000	0.000	0.000	0.000
44	A	499	GLN	0	-0.092	-0.055	2.182	-6.177	-5.323	2.929	-1.804	-1.979	-0.021
45	A	500	GLN	0	-0.096	-0.033	4.092	0.393	0.563	0.000	-0.043	-0.128	0.000
46	A	501	THR	0	-0.071	-0.025	7.022	0.202	0.202	0.000	0.000	0.000	0.000

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