FMO DATABASE

FMODB ID: QVZGY

Calculation Name: 1JY2-O-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: O

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:

Apendix: None

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	51
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-193159.399616
FMO2-HF: Nuclear repulsion	172852.548472
FMO2-HF: Total energy	-20306.851143
FMO2-MP2: Total energy	-20364.161068

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(O:64:ARG)

Summations of interaction energy for fragment #1(O:64: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.
-58.534	-53.324	1.939	-2.585	-4.563	-0.016

Interaction energy analysis for fragmet #1(O:64:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.963 / q_NPA : 0.965

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	O	66	PRO	0	0.025	-0.003	2.572	-14.404	-10.515	1.210	-2.185	-2.914	-0.017
4	O	67	PRO	0	-0.022	-0.002	3.000	4.392	5.713	0.729	-0.400	-1.649	0.001
5	O	68	ASP	-1	-0.820	-0.910	5.610	-31.525	-31.525	0.000	0.000	0.000	0.000
6	O	69	ALA	0	-0.007	-0.009	9.295	0.111	0.111	0.000	0.000	0.000	0.000
7	O	70	ASP	-1	-0.927	-0.971	12.230	-19.179	-19.179	0.000	0.000	0.000	0.000
8	O	71	GLY	0	0.004	0.013	15.288	0.945	0.945	0.000	0.000	0.000	0.000
9	O	72	CYS	0	-0.074	-0.043	16.949	0.414	0.414	0.000	0.000	0.000	0.000
10	O	73	LEU	0	-0.011	0.000	20.333	0.019	0.019	0.000	0.000	0.000	0.000
11	O	74	HIS	0	0.009	0.017	22.519	0.416	0.416	0.000	0.000	0.000	0.000
12	O	75	ALA	0	-0.020	-0.019	26.025	0.018	0.018	0.000	0.000	0.000	0.000
13	O	76	ASP	-1	-0.881	-0.947	29.376	-10.006	-10.006	0.000	0.000	0.000	0.000
14	O	77	PRO	0	-0.024	-0.024	27.636	-0.457	-0.457	0.000	0.000	0.000	0.000
15	O	78	ASP	-1	-0.900	-0.950	26.703	-10.853	-10.853	0.000	0.000	0.000	0.000
16	O	79	LEU	0	-0.088	-0.038	26.183	-0.318	-0.318	0.000	0.000	0.000	0.000
17	O	80	GLY	0	-0.001	0.017	23.084	-0.590	-0.590	0.000	0.000	0.000	0.000
18	O	81	VAL	0	-0.043	-0.032	17.645	0.085	0.085	0.000	0.000	0.000	0.000
19	O	82	LEU	0	0.034	0.032	19.674	-0.385	-0.385	0.000	0.000	0.000	0.000
20	O	83	CYS	0	0.010	-0.012	15.678	-1.296	-1.296	0.000	0.000	0.000	0.000
21	O	84	PRO	0	-0.008	0.002	15.162	0.984	0.984	0.000	0.000	0.000	0.000
22	O	85	THR	0	0.058	0.032	17.112	-0.477	-0.477	0.000	0.000	0.000	0.000
23	O	86	GLY	0	0.051	0.015	17.651	-0.450	-0.450	0.000	0.000	0.000	0.000
24	O	87	CYS	0	-0.004	-0.006	18.720	-0.215	-0.215	0.000	0.000	0.000	0.000
25	O	88	LYS	1	0.945	0.978	18.240	15.527	15.527	0.000	0.000	0.000	0.000
26	O	89	LEU	0	0.035	0.025	13.161	-0.335	-0.335	0.000	0.000	0.000	0.000
27	O	90	GLN	0	0.004	0.000	16.370	0.072	0.072	0.000	0.000	0.000	0.000
28	O	91	ASP	-1	-0.792	-0.873	18.647	-13.790	-13.790	0.000	0.000	0.000	0.000
29	O	92	THR	0	-0.047	-0.035	15.000	0.377	0.377	0.000	0.000	0.000	0.000
30	O	93	LEU	0	0.035	0.016	12.122	0.051	0.051	0.000	0.000	0.000	0.000
31	O	94	VAL	0	0.008	0.003	16.108	0.359	0.359	0.000	0.000	0.000	0.000
32	O	95	ARG	1	0.811	0.894	19.496	13.767	13.767	0.000	0.000	0.000	0.000
33	O	96	GLN	0	0.025	-0.003	13.144	-0.097	-0.097	0.000	0.000	0.000	0.000
34	O	97	GLU	-1	-0.826	-0.890	17.121	-15.536	-15.536	0.000	0.000	0.000	0.000
35	O	98	ARG	1	0.901	0.957	17.934	12.706	12.706	0.000	0.000	0.000	0.000
36	O	99	PRO	0	0.049	0.026	19.167	0.398	0.398	0.000	0.000	0.000	0.000
37	O	100	ILE	0	0.016	0.029	15.343	0.172	0.172	0.000	0.000	0.000	0.000
38	O	101	ARG	1	0.840	0.885	18.543	15.482	15.482	0.000	0.000	0.000	0.000
39	O	102	LYS	1	0.835	0.913	20.833	11.063	11.063	0.000	0.000	0.000	0.000
40	O	103	SER	0	0.017	-0.013	20.331	0.399	0.399	0.000	0.000	0.000	0.000
41	O	104	ILE	0	-0.037	-0.018	17.557	0.213	0.213	0.000	0.000	0.000	0.000
42	O	105	GLU	-1	-0.940	-0.962	22.038	-10.719	-10.719	0.000	0.000	0.000	0.000
43	O	106	ASP	-1	-0.795	-0.896	25.659	-10.475	-10.475	0.000	0.000	0.000	0.000
44	O	107	LEU	0	-0.008	0.010	21.292	0.243	0.243	0.000	0.000	0.000	0.000
45	O	108	ARG	1	0.925	0.976	23.408	12.376	12.376	0.000	0.000	0.000	0.000
46	O	109	ASN	0	0.021	0.007	27.394	0.403	0.403	0.000	0.000	0.000	0.000
47	O	110	THR	0	-0.030	-0.019	27.944	0.329	0.329	0.000	0.000	0.000	0.000
48	O	111	VAL	0	-0.013	-0.005	26.361	0.239	0.239	0.000	0.000	0.000	0.000
49	O	112	ASP	-1	-0.921	-0.957	29.561	-9.720	-9.720	0.000	0.000	0.000	0.000
50	O	113	SER	0	-0.126	-0.057	32.637	0.328	0.328	0.000	0.000	0.000	0.000
51	O	114	VAL	0	-0.091	-0.046	31.058	0.405	0.405	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(O:64:ARG)