FMO DATABASE

FMODB ID: Z2M4N

Calculation Name: 1YTF-B-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTF

Chain ID: B

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	47
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-211897.118414
FMO2-HF: Nuclear repulsion	193459.744305
FMO2-HF: Total energy	-18437.374108
FMO2-MP2: Total energy	-18492.422953

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(B:2:SER )

Summations of interaction energy for fragment #1(B:2:SER )

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.
1.133	2.847	-0.02	-0.845	-0.849	0

Interaction energy analysis for fragmet #1(B:2:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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

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].
3	B	4	ALA	0	0.044	0.036	3.804	0.068	1.782	-0.020	-0.845	-0.849
4	B	5	GLU	-1	-0.908	-0.949	6.800	0.084	0.084	0.000	0.000	0.000
5	B	6	ALA	0	0.021	0.011	5.989	0.240	0.240	0.000	0.000	0.000
6	B	7	SER	0	-0.025	-0.013	7.274	0.117	0.117	0.000	0.000	0.000
7	B	8	ARG	1	0.948	0.980	8.893	0.085	0.085	0.000	0.000	0.000
8	B	9	VAL	0	0.029	0.010	11.373	0.049	0.049	0.000	0.000	0.000
9	B	10	TYR	0	-0.020	-0.030	9.352	0.021	0.021	0.000	0.000	0.000
10	B	11	GLU	-1	-0.894	-0.944	12.812	0.055	0.055	0.000	0.000	0.000
11	B	12	ILE	0	-0.035	-0.020	14.872	-0.017	-0.017	0.000	0.000	0.000
12	B	13	ILE	0	-0.021	-0.007	14.521	0.002	0.002	0.000	0.000	0.000
13	B	14	VAL	0	-0.034	-0.014	16.187	-0.004	-0.004	0.000	0.000	0.000
14	B	15	GLU	-1	-0.918	-0.972	18.671	0.144	0.144	0.000	0.000	0.000
15	B	16	SER	0	-0.060	-0.026	20.534	-0.018	-0.018	0.000	0.000	0.000
16	B	17	VAL	0	0.002	0.006	21.002	-0.003	-0.003	0.000	0.000	0.000
17	B	18	VAL	0	-0.008	-0.006	22.445	-0.008	-0.008	0.000	0.000	0.000
18	B	19	ASN	0	-0.032	-0.038	24.746	-0.001	-0.001	0.000	0.000	0.000
19	B	20	GLU	-1	-0.922	-0.947	25.275	0.098	0.098	0.000	0.000	0.000
20	B	21	VAL	0	-0.008	-0.010	26.023	-0.003	-0.003	0.000	0.000	0.000
21	B	22	ARG	1	0.845	0.929	27.766	-0.105	-0.105	0.000	0.000	0.000
22	B	23	GLU	-1	-0.908	-0.932	30.880	0.068	0.068	0.000	0.000	0.000
23	B	24	ASP	-1	-0.884	-0.946	32.161	0.102	0.102	0.000	0.000	0.000
24	B	25	PHE	0	-0.068	-0.051	29.121	0.004	0.004	0.000	0.000	0.000
25	B	26	GLU	-1	-0.946	-0.985	33.412	0.078	0.078	0.000	0.000	0.000
26	B	27	ASN	0	-0.035	-0.010	36.339	-0.008	-0.008	0.000	0.000	0.000
27	B	28	ALA	0	-0.116	-0.060	35.993	-0.003	-0.003	0.000	0.000	0.000
28	B	29	GLY	0	-0.017	-0.004	38.041	0.001	0.001	0.000	0.000	0.000
29	B	30	ILE	0	-0.050	-0.008	33.229	0.001	0.001	0.000	0.000	0.000
30	B	31	ASP	-1	-0.875	-0.965	34.002	0.113	0.113	0.000	0.000	0.000
31	B	32	GLU	-1	-0.788	-0.878	30.322	0.121	0.121	0.000	0.000	0.000
32	B	33	GLN	0	0.018	-0.015	30.540	0.016	0.016	0.000	0.000	0.000
33	B	34	THR	0	0.052	0.046	29.903	0.012	0.012	0.000	0.000	0.000
34	B	35	LEU	0	-0.052	-0.008	26.975	0.019	0.019	0.000	0.000	0.000
35	B	36	GLN	0	-0.062	-0.044	26.189	0.029	0.029	0.000	0.000	0.000
36	B	37	ASP	-1	-0.890	-0.941	25.084	0.203	0.203	0.000	0.000	0.000
37	B	38	LEU	0	-0.054	-0.024	23.854	0.033	0.033	0.000	0.000	0.000
38	B	39	LYS	1	0.910	0.959	20.429	-0.171	-0.171	0.000	0.000	0.000
39	B	40	ASN	0	0.046	0.014	20.344	0.046	0.046	0.000	0.000	0.000
40	B	41	ILE	0	-0.061	-0.044	20.238	0.051	0.051	0.000	0.000	0.000
41	B	42	TRP	0	-0.007	0.006	16.775	0.046	0.046	0.000	0.000	0.000
42	B	43	GLN	0	0.078	0.018	16.014	0.058	0.058	0.000	0.000	0.000
43	B	44	LYS	1	0.933	0.993	15.456	-0.332	-0.332	0.000	0.000	0.000
44	B	45	LYS	1	0.817	0.902	16.109	-0.353	-0.353	0.000	0.000	0.000
45	B	46	LEU	0	0.001	0.007	11.547	0.082	0.082	0.000	0.000	0.000
46	B	47	THR	0	-0.045	-0.002	11.110	0.177	0.177	0.000	0.000	0.000
47	B	1	NME	0	-0.027	-0.012	8.543	-0.064	-0.064	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER )