FMO DATABASE

FMODB ID: 6YKVZ

Calculation Name: 1JY2-P-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: P

ChEMBL ID:

UniProt ID: P02672

Base Structure: X-ray

Registration Date: 2023-09-23

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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-163290.729396
FMO2-HF: Nuclear repulsion	144740.139505
FMO2-HF: Total energy	-18550.589891
FMO2-MP2: Total energy	-18601.570878

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(P:5:ARG)

Summations of interaction energy for fragment #1(P:5:ARG)

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.
-26.141	-22.158	0.467	-1.764	-2.686	-0.008

Interaction energy analysis for fragmet #1(P:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.969 / q_NPA : 0.976

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	P	7	ASN	0	-0.017	-0.020	2.591	5.367	8.720	0.350	-1.634	-2.069	-0.008
4	P	8	CYS	0	-0.023	-0.004	3.594	0.499	1.057	0.118	-0.127	-0.549	0.000
5	P	9	CYS	0	-0.009	0.007	5.311	1.938	2.010	-0.001	-0.003	-0.068	0.000
6	P	10	ILE	0	0.004	0.008	8.495	1.438	1.438	0.000	0.000	0.000	0.000
7	P	11	LEU	0	-0.020	0.002	11.225	1.069	1.069	0.000	0.000	0.000	0.000
8	P	12	ASP	-1	-0.792	-0.875	14.362	-13.826	-13.826	0.000	0.000	0.000	0.000
9	P	13	GLU	-1	-0.902	-0.955	14.639	-16.197	-16.197	0.000	0.000	0.000	0.000
10	P	14	ARG	1	0.773	0.865	15.717	13.747	13.747	0.000	0.000	0.000	0.000
11	P	15	PHE	0	-0.061	-0.034	16.331	0.591	0.591	0.000	0.000	0.000	0.000
12	P	16	GLY	0	0.026	0.035	12.284	-0.710	-0.710	0.000	0.000	0.000	0.000
13	P	17	SER	0	-0.033	-0.056	7.007	1.217	1.217	0.000	0.000	0.000	0.000
14	P	18	TYR	0	-0.003	0.000	9.853	0.719	0.719	0.000	0.000	0.000	0.000
15	P	19	CYS	0	-0.021	-0.026	7.099	-5.877	-5.877	0.000	0.000	0.000	0.000
16	P	20	PRO	0	-0.003	0.010	7.713	2.864	2.864	0.000	0.000	0.000	0.000
17	P	21	THR	0	0.046	0.015	10.773	-0.275	-0.275	0.000	0.000	0.000	0.000
18	P	22	THR	0	0.042	0.001	13.392	-0.579	-0.579	0.000	0.000	0.000	0.000
19	P	23	CYS	0	-0.008	0.007	14.920	0.227	0.227	0.000	0.000	0.000	0.000
20	P	24	GLY	0	0.089	0.056	14.099	0.208	0.208	0.000	0.000	0.000	0.000
21	P	25	ILE	0	-0.034	-0.021	8.924	-0.559	-0.559	0.000	0.000	0.000	0.000
22	P	26	ALA	0	0.009	0.005	12.827	0.155	0.155	0.000	0.000	0.000	0.000
23	P	27	ASP	-1	-0.894	-0.947	16.459	-15.378	-15.378	0.000	0.000	0.000	0.000
24	P	28	PHE	0	-0.050	-0.029	11.472	0.192	0.192	0.000	0.000	0.000	0.000
25	P	29	LEU	0	-0.003	-0.005	14.521	0.376	0.376	0.000	0.000	0.000	0.000
26	P	30	ASN	0	0.011	0.003	15.650	0.953	0.953	0.000	0.000	0.000	0.000
27	P	31	ASN	0	0.004	0.015	17.695	1.144	1.144	0.000	0.000	0.000	0.000
28	P	32	TYR	0	-0.021	-0.002	14.667	0.351	0.351	0.000	0.000	0.000	0.000
29	P	33	GLN	0	-0.001	-0.003	17.178	0.632	0.632	0.000	0.000	0.000	0.000
30	P	34	THR	0	-0.001	-0.025	19.335	0.657	0.657	0.000	0.000	0.000	0.000
31	P	35	SER	0	-0.036	-0.002	20.114	0.648	0.648	0.000	0.000	0.000	0.000
32	P	36	VAL	0	0.013	0.002	17.487	0.493	0.493	0.000	0.000	0.000	0.000
33	P	37	ASP	-1	-0.812	-0.874	20.900	-11.240	-11.240	0.000	0.000	0.000	0.000
34	P	38	LYS	1	0.876	0.933	23.902	12.206	12.206	0.000	0.000	0.000	0.000
35	P	39	ASP	-1	-0.851	-0.909	22.788	-12.274	-12.274	0.000	0.000	0.000	0.000
36	P	40	LEU	0	-0.011	-0.009	21.678	0.318	0.318	0.000	0.000	0.000	0.000
37	P	41	ARG	1	0.871	0.891	25.433	11.358	11.358	0.000	0.000	0.000	0.000
38	P	42	THR	0	-0.086	-0.043	28.183	0.519	0.519	0.000	0.000	0.000	0.000
39	P	43	LEU	0	-0.031	-0.017	25.348	0.324	0.324	0.000	0.000	0.000	0.000
40	P	44	GLU	-1	-0.850	-0.906	28.215	-10.583	-10.583	0.000	0.000	0.000	0.000
41	P	45	GLY	0	-0.028	-0.008	30.886	0.327	0.327	0.000	0.000	0.000	0.000
42	P	46	ILE	0	-0.078	-0.034	31.992	0.318	0.318	0.000	0.000	0.000	0.000
43	P	47	LEU	0	-0.054	-0.022	30.667	0.195	0.195	0.000	0.000	0.000	0.000
44	P	48	TYR	0	-0.120	-0.074	29.260	0.307	0.307	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(P:5:ARG)