FMO DATABASE

FMODB ID: 63J1Z

Calculation Name: 1YTF-C-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTF

Chain ID: C

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	-214376.975352
FMO2-HF: Nuclear repulsion	194680.939805
FMO2-HF: Total energy	-19696.035547
FMO2-MP2: Total energy	-19751.906156

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(C:240:ACE )

Summations of interaction energy for fragment #1(C:240:ACE )

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.
2.358	3.832	0.075	-0.629	-0.919	-0.001

Interaction energy analysis for fragmet #1(C:240:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.003

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	C	242	ASN	0	0.003	-0.008	3.824	1.229	2.003	-0.006	-0.336	-0.432	-0.001
4	C	243	LEU	0	0.022	0.034	3.879	0.092	0.279	0.006	-0.055	-0.138	0.000
5	C	244	MET	0	-0.035	-0.026	5.621	0.268	0.268	0.000	0.000	0.000	0.000
6	C	245	LEU	0	-0.001	0.013	6.705	-0.046	-0.046	0.000	0.000	0.000	0.000
7	C	246	CYS	0	-0.047	-0.026	9.744	-0.019	-0.019	0.000	0.000	0.000	0.000
8	C	247	LEU	0	0.040	0.042	13.372	-0.008	-0.008	0.000	0.000	0.000	0.000
9	C	248	TYR	0	-0.023	-0.021	17.100	-0.016	-0.016	0.000	0.000	0.000	0.000
10	C	249	ASP	-1	-0.861	-0.921	19.504	0.077	0.077	0.000	0.000	0.000	0.000
11	C	250	LYS	1	0.850	0.904	22.668	-0.037	-0.037	0.000	0.000	0.000	0.000
12	C	251	VAL	0	0.051	0.035	21.017	-0.002	-0.002	0.000	0.000	0.000	0.000
13	C	252	THR	0	-0.079	-0.034	23.739	0.000	0.000	0.000	0.000	0.000	0.000
14	C	253	ARG	1	0.989	0.974	25.535	0.019	0.019	0.000	0.000	0.000	0.000
15	C	254	THR	0	-0.045	-0.011	27.847	0.005	0.005	0.000	0.000	0.000	0.000
16	C	255	LYS	1	0.931	0.967	30.406	0.026	0.026	0.000	0.000	0.000	0.000
17	C	256	ALA	0	0.096	0.056	27.657	0.003	0.003	0.000	0.000	0.000	0.000
18	C	257	ARG	1	1.020	1.033	26.328	0.028	0.028	0.000	0.000	0.000	0.000
19	C	258	TRP	0	0.007	-0.015	22.549	0.012	0.012	0.000	0.000	0.000	0.000
20	C	259	LYS	1	0.929	0.963	23.035	0.012	0.012	0.000	0.000	0.000	0.000
21	C	260	CYS	0	-0.005	-0.004	19.149	0.005	0.005	0.000	0.000	0.000	0.000
22	C	261	SER	0	-0.017	-0.003	20.531	-0.004	-0.004	0.000	0.000	0.000	0.000
23	C	262	LEU	0	0.026	0.005	14.674	0.006	0.006	0.000	0.000	0.000	0.000
24	C	263	LYN	0	0.052	0.013	17.579	-0.014	-0.014	0.000	0.000	0.000	0.000
25	C	264	ASP	-1	-0.884	-0.948	16.298	0.177	0.177	0.000	0.000	0.000	0.000
26	C	265	GLY	0	0.005	0.006	12.661	0.025	0.025	0.000	0.000	0.000	0.000
27	C	266	VAL	0	-0.029	-0.013	7.452	-0.037	-0.037	0.000	0.000	0.000	0.000
28	C	267	VAL	0	-0.019	-0.019	6.924	0.054	0.054	0.000	0.000	0.000	0.000
29	C	268	THR	0	0.018	0.024	3.167	-0.218	0.333	0.075	-0.235	-0.391	0.000
30	C	269	ILE	0	-0.018	-0.011	5.217	-0.442	-0.480	0.000	-0.003	0.042	0.000
31	C	270	ASN	0	-0.039	-0.028	7.928	0.038	0.038	0.000	0.000	0.000	0.000
32	C	271	ARG	1	0.902	0.938	6.637	0.594	0.594	0.000	0.000	0.000	0.000
33	C	272	ASN	0	0.015	0.034	7.595	0.229	0.229	0.000	0.000	0.000	0.000
34	C	273	ASP	-1	-0.817	-0.905	6.039	0.574	0.574	0.000	0.000	0.000	0.000
35	C	274	TYR	0	-0.067	-0.029	8.428	-0.064	-0.064	0.000	0.000	0.000	0.000
36	C	275	THR	0	0.036	0.015	10.111	0.082	0.082	0.000	0.000	0.000	0.000
37	C	276	PHE	0	-0.046	-0.032	11.632	-0.051	-0.051	0.000	0.000	0.000	0.000
38	C	277	GLN	0	0.046	0.028	15.524	0.004	0.004	0.000	0.000	0.000	0.000
39	C	278	LYS	1	0.890	0.927	18.717	-0.074	-0.074	0.000	0.000	0.000	0.000
40	C	279	ALA	0	0.022	0.024	16.023	-0.005	-0.005	0.000	0.000	0.000	0.000
41	C	280	GLN	0	-0.052	-0.018	18.059	0.000	0.000	0.000	0.000	0.000	0.000
42	C	281	VAL	0	-0.004	0.005	16.563	-0.012	-0.012	0.000	0.000	0.000	0.000
43	C	282	GLU	-1	-0.962	-0.985	19.345	-0.025	-0.025	0.000	0.000	0.000	0.000
44	C	283	ALA	0	-0.004	-0.004	19.565	-0.012	-0.012	0.000	0.000	0.000	0.000
45	C	284	GLU	-1	-0.962	-0.983	21.690	-0.046	-0.046	0.000	0.000	0.000	0.000
46	C	285	TRP	0	-0.085	-0.037	21.936	-0.008	-0.008	0.000	0.000	0.000	0.000
47	C	286	VAL	-1	-0.888	-0.955	24.491	-0.061	-0.061	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:240:ACE )