FMO DATABASE

FMODB ID: 3QR7L

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	OptHSide
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	-212455.971486
FMO2-HF: Nuclear repulsion	192910.897637
FMO2-HF: Total energy	-19545.073849
FMO2-MP2: Total energy	-19600.521618

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.
-33.324	-28.208	1.187	-2.467	-3.834	0.022

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 : -0.961 / q_NPA : -0.996

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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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	0.031	2.590	-12.183	-7.890	1.161	-2.117	-3.336	0.020
4	C	244	MET	0	-0.025	-0.015	4.497	-4.590	-4.432	0.000	-0.031	-0.126	0.000
5	C	245	LEU	0	-0.006	0.008	7.039	-1.151	-1.151	0.000	0.000	0.000	0.000
6	C	246	CYS	0	-0.038	-0.025	9.787	-1.129	-1.129	0.000	0.000	0.000	0.000
7	C	247	LEU	0	0.033	0.041	13.557	-0.133	-0.133	0.000	0.000	0.000	0.000
8	C	248	TYR	0	-0.025	-0.025	16.934	0.193	0.193	0.000	0.000	0.000	0.000
9	C	249	ASP	-1	-0.850	-0.915	18.831	13.146	13.146	0.000	0.000	0.000	0.000
10	C	250	LYS	1	0.869	0.914	21.911	-12.826	-12.826	0.000	0.000	0.000	0.000
11	C	251	VAL	0	0.044	0.025	19.206	0.521	0.521	0.000	0.000	0.000	0.000
12	C	252	THR	0	-0.062	-0.023	22.179	-0.740	-0.740	0.000	0.000	0.000	0.000
13	C	253	ARG	1	0.958	0.966	23.604	-11.276	-11.276	0.000	0.000	0.000	0.000
14	C	254	THR	0	-0.027	-0.004	25.662	-0.532	-0.532	0.000	0.000	0.000	0.000
15	C	255	LYS	1	0.951	0.975	27.750	-9.346	-9.346	0.000	0.000	0.000	0.000
16	C	256	ALA	0	0.020	0.016	24.221	0.171	0.171	0.000	0.000	0.000	0.000
17	C	257	ARG	1	0.940	0.983	23.418	-11.312	-11.312	0.000	0.000	0.000	0.000
18	C	258	TRP	0	0.004	-0.018	20.157	-0.394	-0.394	0.000	0.000	0.000	0.000
19	C	259	LYS	1	0.824	0.898	21.591	-11.809	-11.809	0.000	0.000	0.000	0.000
20	C	260	CYS	0	-0.018	-0.007	18.015	-0.054	-0.054	0.000	0.000	0.000	0.000
21	C	261	SER	0	-0.032	-0.015	19.845	-0.115	-0.115	0.000	0.000	0.000	0.000
22	C	262	LEU	0	0.031	0.005	14.217	-0.169	-0.169	0.000	0.000	0.000	0.000
23	C	263	LYN	0	0.041	0.027	17.743	-0.889	-0.889	0.000	0.000	0.000	0.000
24	C	264	ASP	-1	-0.843	-0.916	16.872	16.406	16.406	0.000	0.000	0.000	0.000
25	C	265	GLY	0	0.011	0.006	13.528	0.582	0.582	0.000	0.000	0.000	0.000
26	C	266	VAL	0	-0.028	-0.012	9.374	-1.414	-1.414	0.000	0.000	0.000	0.000
27	C	267	VAL	0	-0.039	-0.029	7.494	1.785	1.785	0.000	0.000	0.000	0.000
28	C	268	THR	0	0.037	0.019	3.783	-2.103	-1.366	0.027	-0.301	-0.464	0.002
29	C	269	ILE	0	-0.023	-0.015	4.953	4.940	4.868	-0.001	-0.018	0.092	0.000
30	C	270	ASN	0	-0.022	-0.024	5.401	-1.238	-1.238	0.000	0.000	0.000	0.000
31	C	271	ARG	1	0.913	0.943	4.839	-30.254	-30.254	0.000	0.000	0.000	0.000
32	C	272	ASN	0	-0.022	0.014	6.397	-3.153	-3.153	0.000	0.000	0.000	0.000
33	C	273	ASP	-1	-0.812	-0.883	7.425	38.673	38.673	0.000	0.000	0.000	0.000
34	C	274	TYR	0	-0.061	-0.026	9.712	-3.095	-3.095	0.000	0.000	0.000	0.000
35	C	275	THR	0	0.044	0.018	11.519	1.547	1.547	0.000	0.000	0.000	0.000
36	C	276	PHE	0	-0.049	-0.027	12.143	-1.332	-1.332	0.000	0.000	0.000	0.000
37	C	277	GLN	0	0.048	0.015	16.632	-0.415	-0.415	0.000	0.000	0.000	0.000
38	C	278	LYS	1	0.835	0.883	19.561	-13.179	-13.179	0.000	0.000	0.000	0.000
39	C	279	ALA	0	0.018	0.021	16.126	0.313	0.313	0.000	0.000	0.000	0.000
40	C	280	GLN	0	-0.030	-0.006	18.064	-0.402	-0.402	0.000	0.000	0.000	0.000
41	C	281	VAL	0	0.009	0.011	15.418	0.404	0.404	0.000	0.000	0.000	0.000
42	C	282	GLU	-1	-0.759	-0.856	18.356	11.674	11.674	0.000	0.000	0.000	0.000
43	C	283	ALA	0	0.003	0.003	17.299	0.321	0.321	0.000	0.000	0.000	0.000
44	C	284	GLU	-1	-0.897	-0.957	19.313	11.739	11.739	0.000	0.000	0.000	0.000
45	C	285	TRP	0	-0.033	-0.016	18.357	0.191	0.191	0.000	0.000	0.000	0.000
46	C	286	VAL	0	0.018	0.002	20.785	-0.697	-0.697	0.000	0.000	0.000	0.000

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