FMO DATABASE

FMODB ID: LJ479

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	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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-212607.312862
FMO2-HF: Nuclear repulsion	193062.084114
FMO2-HF: Total energy	-19545.228749
FMO2-MP2: Total energy	-19600.701208

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.
-38.321	-31.321	2.468	-3.894	-5.571	0.034

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 : -0.936 / q_NPA : -0.986

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	0.008	0.032	2.524	-18.021	-12.825	2.204	-3.077	-4.323	0.027
4	C	244	MET	0	-0.019	-0.019	4.231	-4.879	-4.654	0.002	-0.063	-0.163	0.000
5	C	245	LEU	0	-0.019	-0.002	6.765	-0.586	-0.586	0.000	0.000	0.000	0.000
6	C	246	CYS	0	-0.047	-0.023	9.531	-1.087	-1.087	0.000	0.000	0.000	0.000
7	C	247	LEU	0	0.037	0.037	13.302	-0.241	-0.241	0.000	0.000	0.000	0.000
8	C	248	TYR	0	-0.012	-0.027	16.713	0.505	0.505	0.000	0.000	0.000	0.000
9	C	249	ASP	-1	-0.818	-0.885	18.927	13.055	13.055	0.000	0.000	0.000	0.000
10	C	250	LYS	1	0.840	0.903	21.619	-13.141	-13.141	0.000	0.000	0.000	0.000
11	C	251	VAL	0	0.046	0.024	19.187	0.647	0.647	0.000	0.000	0.000	0.000
12	C	252	THR	0	-0.051	-0.017	22.139	-0.789	-0.789	0.000	0.000	0.000	0.000
13	C	253	ARG	1	0.917	0.949	23.329	-11.326	-11.326	0.000	0.000	0.000	0.000
14	C	254	THR	0	-0.031	-0.012	25.451	-0.614	-0.614	0.000	0.000	0.000	0.000
15	C	255	LYS	1	0.962	0.975	27.473	-9.167	-9.167	0.000	0.000	0.000	0.000
16	C	256	ALA	0	0.029	0.029	24.195	0.064	0.064	0.000	0.000	0.000	0.000
17	C	257	ARG	1	0.911	0.968	23.073	-11.223	-11.223	0.000	0.000	0.000	0.000
18	C	258	TRP	0	0.028	-0.007	19.898	-0.464	-0.464	0.000	0.000	0.000	0.000
19	C	259	LYS	1	0.813	0.893	21.425	-11.870	-11.870	0.000	0.000	0.000	0.000
20	C	260	CYS	0	-0.020	-0.005	18.142	-0.178	-0.178	0.000	0.000	0.000	0.000
21	C	261	SER	0	-0.018	-0.025	19.735	-0.125	-0.125	0.000	0.000	0.000	0.000
22	C	262	LEU	0	-0.004	-0.007	14.256	-0.104	-0.104	0.000	0.000	0.000	0.000
23	C	263	LYN	0	0.004	0.004	17.331	-0.786	-0.786	0.000	0.000	0.000	0.000
24	C	264	ASP	-1	-0.827	-0.909	16.524	16.624	16.624	0.000	0.000	0.000	0.000
25	C	265	GLY	0	0.017	0.011	13.323	0.475	0.475	0.000	0.000	0.000	0.000
26	C	266	VAL	0	-0.023	-0.007	8.807	-1.465	-1.465	0.000	0.000	0.000	0.000
27	C	267	VAL	0	-0.020	-0.025	6.968	1.386	1.386	0.000	0.000	0.000	0.000
28	C	268	THR	0	0.025	0.012	3.199	-4.371	-3.030	0.244	-0.608	-0.976	0.007
29	C	269	ILE	0	-0.023	-0.008	4.027	8.031	8.200	0.019	-0.142	-0.046	0.000
30	C	270	ASN	0	-0.008	-0.026	5.058	-1.348	-1.348	0.000	0.000	0.000	0.000
31	C	271	ARG	1	0.910	0.947	4.753	-30.824	-30.755	-0.001	-0.004	-0.063	0.000
32	C	272	ASN	0	-0.024	0.010	6.421	-4.122	-4.122	0.000	0.000	0.000	0.000
33	C	273	ASP	-1	-0.828	-0.895	7.062	41.139	41.139	0.000	0.000	0.000	0.000
34	C	274	TYR	0	-0.038	-0.016	9.240	-3.485	-3.485	0.000	0.000	0.000	0.000
35	C	275	THR	0	0.019	0.002	11.033	1.666	1.666	0.000	0.000	0.000	0.000
36	C	276	PHE	0	-0.046	-0.028	11.870	-1.418	-1.418	0.000	0.000	0.000	0.000
37	C	277	GLN	0	0.059	0.024	16.360	-0.311	-0.311	0.000	0.000	0.000	0.000
38	C	278	LYS	1	0.812	0.872	19.400	-13.399	-13.399	0.000	0.000	0.000	0.000
39	C	279	ALA	0	0.015	0.019	16.121	0.295	0.295	0.000	0.000	0.000	0.000
40	C	280	GLN	0	-0.004	0.015	18.027	-0.620	-0.620	0.000	0.000	0.000	0.000
41	C	281	VAL	0	0.030	0.022	15.105	0.486	0.486	0.000	0.000	0.000	0.000
42	C	282	GLU	-1	-0.761	-0.858	18.235	11.624	11.624	0.000	0.000	0.000	0.000
43	C	283	ALA	0	0.017	0.006	17.247	0.454	0.454	0.000	0.000	0.000	0.000
44	C	284	GLU	-1	-0.883	-0.947	19.248	11.778	11.778	0.000	0.000	0.000	0.000
45	C	285	TRP	0	0.007	0.010	18.319	0.395	0.395	0.000	0.000	0.000	0.000
46	C	286	VAL	0	-0.019	-0.013	20.717	-0.981	-0.981	0.000	0.000	0.000	0.000

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