FMO DATABASE

FMODB ID: J3G29

Calculation Name: 1YTF-C-Xray372

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: 2023-06-20

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	-211940.972667
FMO2-HF: Nuclear repulsion	192396.221132
FMO2-HF: Total energy	-19544.751535
FMO2-MP2: Total energy	-19600.191802

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:241:GLU)

Summations of interaction energy for fragment #1(C:241:GLU)

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.
-34.395	-28.443	1.62	-3.115	-4.457	0.03

Interaction energy analysis for fragmet #1(C:241:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.953 / q_NPA : -0.994

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	243	LEU	0	0.023	0.033	2.432	-12.066	-6.909	1.594	-2.760	-3.991	0.028
4	C	244	MET	0	-0.036	-0.026	4.338	-6.157	-5.951	0.001	-0.074	-0.133	0.000
5	C	245	LEU	0	0.001	0.014	7.182	-0.784	-0.784	0.000	0.000	0.000	0.000
6	C	246	CYS	0	-0.049	-0.028	9.793	-1.290	-1.290	0.000	0.000	0.000	0.000
7	C	247	LEU	0	0.042	0.044	13.508	-0.013	-0.013	0.000	0.000	0.000	0.000
8	C	248	TYR	0	-0.025	-0.023	16.615	0.197	0.197	0.000	0.000	0.000	0.000
9	C	249	ASP	-1	-0.855	-0.918	18.494	13.147	13.147	0.000	0.000	0.000	0.000
10	C	250	LYS	1	0.852	0.905	21.494	-12.957	-12.957	0.000	0.000	0.000	0.000
11	C	251	VAL	0	0.050	0.035	18.652	0.544	0.544	0.000	0.000	0.000	0.000
12	C	252	THR	0	-0.074	-0.031	21.569	-0.796	-0.796	0.000	0.000	0.000	0.000
13	C	253	ARG	1	0.986	0.971	22.877	-11.379	-11.379	0.000	0.000	0.000	0.000
14	C	254	THR	0	-0.036	-0.004	24.923	-0.587	-0.587	0.000	0.000	0.000	0.000
15	C	255	LYS	1	0.939	0.971	27.348	-9.640	-9.640	0.000	0.000	0.000	0.000
16	C	256	ALA	0	0.054	0.032	23.827	0.177	0.177	0.000	0.000	0.000	0.000
17	C	257	ARG	1	1.031	1.038	23.102	-11.370	-11.370	0.000	0.000	0.000	0.000
18	C	258	TRP	0	0.009	-0.014	19.636	-0.423	-0.423	0.000	0.000	0.000	0.000
19	C	259	LYS	1	0.933	0.966	21.026	-11.811	-11.811	0.000	0.000	0.000	0.000
20	C	260	CYS	0	-0.006	-0.004	17.508	-0.054	-0.054	0.000	0.000	0.000	0.000
21	C	261	SER	0	-0.012	0.000	19.410	-0.137	-0.137	0.000	0.000	0.000	0.000
22	C	262	LEU	0	0.024	0.004	13.963	-0.129	-0.129	0.000	0.000	0.000	0.000
23	C	263	LYN	0	0.055	0.014	17.599	-0.815	-0.815	0.000	0.000	0.000	0.000
24	C	264	ASP	-1	-0.882	-0.947	16.714	16.623	16.623	0.000	0.000	0.000	0.000
25	C	265	GLY	0	0.002	0.004	13.366	0.635	0.635	0.000	0.000	0.000	0.000
26	C	266	VAL	0	-0.026	-0.011	9.141	-1.480	-1.480	0.000	0.000	0.000	0.000
27	C	267	VAL	0	-0.020	-0.021	7.289	1.904	1.904	0.000	0.000	0.000	0.000
28	C	268	THR	0	0.026	0.030	3.763	-2.198	-1.531	0.026	-0.263	-0.430	0.002
29	C	269	ILE	0	-0.019	-0.012	4.953	4.795	4.717	-0.001	-0.018	0.097	0.000
30	C	270	ASN	0	-0.043	-0.030	5.397	-1.646	-1.646	0.000	0.000	0.000	0.000
31	C	271	ARG	1	0.899	0.934	4.860	-29.179	-29.179	0.000	0.000	0.000	0.000
32	C	272	ASN	0	0.017	0.035	6.418	-2.252	-2.252	0.000	0.000	0.000	0.000
33	C	273	ASP	-1	-0.817	-0.904	7.609	36.696	36.696	0.000	0.000	0.000	0.000
34	C	274	TYR	0	-0.067	-0.029	9.712	-3.011	-3.011	0.000	0.000	0.000	0.000
35	C	275	THR	0	0.037	0.015	11.392	1.441	1.441	0.000	0.000	0.000	0.000
36	C	276	PHE	0	-0.048	-0.033	11.879	-1.339	-1.339	0.000	0.000	0.000	0.000
37	C	277	GLN	0	0.050	0.030	16.435	-0.271	-0.271	0.000	0.000	0.000	0.000
38	C	278	LYS	1	0.891	0.927	19.386	-13.256	-13.256	0.000	0.000	0.000	0.000
39	C	279	ALA	0	0.022	0.025	15.917	0.302	0.302	0.000	0.000	0.000	0.000
40	C	280	GLN	0	-0.051	-0.018	17.860	-0.450	-0.450	0.000	0.000	0.000	0.000
41	C	281	VAL	0	-0.002	0.007	15.024	0.437	0.437	0.000	0.000	0.000	0.000
42	C	282	GLU	-1	-0.958	-0.983	17.952	12.480	12.480	0.000	0.000	0.000	0.000
43	C	283	ALA	0	0.003	0.001	17.011	0.328	0.328	0.000	0.000	0.000	0.000
44	C	284	GLU	-1	-0.951	-0.976	19.016	11.857	11.857	0.000	0.000	0.000	0.000
45	C	285	TRP	0	-0.042	-0.017	18.031	0.150	0.150	0.000	0.000	0.000	0.000
46	C	286	VAL	0	0.032	0.005	20.344	-0.618	-0.618	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:241:GLU)