FMO DATABASE

FMODB ID: R86G8

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-193041.113092
FMO2-HF: Nuclear repulsion	172734.360183
FMO2-HF: Total energy	-20306.752909
FMO2-MP2: Total energy	-20364.09612

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.
-59.438	-54.276	3.479	-2.883	-5.756	-0.018

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 : 0.956 / 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

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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	O	66	PRO	0	0.025	-0.008	2.434	-15.124	-10.884	2.456	-2.717	-3.978	-0.018
4	O	67	PRO	0	-0.029	-0.010	2.927	5.713	6.635	1.023	-0.166	-1.778	0.000
5	O	68	ASP	-1	-0.837	-0.915	5.769	-32.537	-32.537	0.000	0.000	0.000	0.000
6	O	69	ALA	0	-0.055	-0.043	9.163	0.317	0.317	0.000	0.000	0.000	0.000
7	O	70	ASP	-1	-0.923	-0.969	11.778	-19.673	-19.673	0.000	0.000	0.000	0.000
8	O	71	GLY	0	0.022	0.034	15.332	0.760	0.760	0.000	0.000	0.000	0.000
9	O	72	CYS	0	-0.072	-0.035	16.773	0.562	0.562	0.000	0.000	0.000	0.000
10	O	73	LEU	0	0.002	0.002	20.390	-0.212	-0.212	0.000	0.000	0.000	0.000
11	O	74	HIS	0	0.006	0.012	22.532	0.472	0.472	0.000	0.000	0.000	0.000
12	O	75	ALA	0	-0.011	-0.014	25.565	0.015	0.015	0.000	0.000	0.000	0.000
13	O	76	ASP	-1	-0.890	-0.940	28.806	-9.985	-9.985	0.000	0.000	0.000	0.000
14	O	77	PRO	0	-0.025	-0.032	27.659	-0.430	-0.430	0.000	0.000	0.000	0.000
15	O	78	ASP	-1	-0.909	-0.948	26.844	-10.818	-10.818	0.000	0.000	0.000	0.000
16	O	79	LEU	0	-0.098	-0.045	25.530	-0.354	-0.354	0.000	0.000	0.000	0.000
17	O	80	GLY	0	0.008	0.023	22.711	-0.596	-0.596	0.000	0.000	0.000	0.000
18	O	81	VAL	0	-0.026	-0.032	16.969	0.122	0.122	0.000	0.000	0.000	0.000
19	O	82	LEU	0	0.000	0.008	19.602	-0.145	-0.145	0.000	0.000	0.000	0.000
20	O	83	CYS	0	0.009	-0.009	15.207	-1.142	-1.142	0.000	0.000	0.000	0.000
21	O	84	PRO	0	0.003	0.006	14.865	1.019	1.019	0.000	0.000	0.000	0.000
22	O	85	THR	0	0.060	0.025	16.838	-0.480	-0.480	0.000	0.000	0.000	0.000
23	O	86	GLY	0	0.061	0.021	17.603	-0.537	-0.537	0.000	0.000	0.000	0.000
24	O	87	CYS	0	-0.006	-0.006	18.671	-0.110	-0.110	0.000	0.000	0.000	0.000
25	O	88	LYS	1	0.941	0.975	17.936	15.313	15.313	0.000	0.000	0.000	0.000
26	O	89	LEU	0	0.041	0.024	12.952	-0.250	-0.250	0.000	0.000	0.000	0.000
27	O	90	GLN	0	0.004	0.005	16.104	0.012	0.012	0.000	0.000	0.000	0.000
28	O	91	ASP	-1	-0.794	-0.869	18.428	-13.687	-13.687	0.000	0.000	0.000	0.000
29	O	92	THR	0	-0.048	-0.039	14.504	0.276	0.276	0.000	0.000	0.000	0.000
30	O	93	LEU	0	0.042	0.018	12.144	0.022	0.022	0.000	0.000	0.000	0.000
31	O	94	VAL	0	-0.016	-0.004	16.077	0.349	0.349	0.000	0.000	0.000	0.000
32	O	95	ARG	1	0.800	0.874	19.459	13.546	13.546	0.000	0.000	0.000	0.000
33	O	96	GLN	0	0.004	-0.006	13.017	-0.174	-0.174	0.000	0.000	0.000	0.000
34	O	97	GLU	-1	-0.826	-0.891	17.301	-15.387	-15.387	0.000	0.000	0.000	0.000
35	O	98	ARG	1	0.941	0.971	18.103	12.627	12.627	0.000	0.000	0.000	0.000
36	O	99	PRO	0	0.050	0.025	19.420	0.383	0.383	0.000	0.000	0.000	0.000
37	O	100	ILE	0	0.024	0.034	15.636	0.188	0.188	0.000	0.000	0.000	0.000
38	O	101	ARG	1	0.844	0.891	18.513	15.469	15.469	0.000	0.000	0.000	0.000
39	O	102	LYS	1	0.891	0.940	21.078	11.011	11.011	0.000	0.000	0.000	0.000
40	O	103	SER	0	0.006	-0.017	20.860	0.420	0.420	0.000	0.000	0.000	0.000
41	O	104	ILE	0	-0.037	-0.012	18.001	0.210	0.210	0.000	0.000	0.000	0.000
42	O	105	GLU	-1	-0.974	-0.990	22.500	-10.894	-10.894	0.000	0.000	0.000	0.000
43	O	106	ASP	-1	-0.827	-0.899	25.862	-10.410	-10.410	0.000	0.000	0.000	0.000
44	O	107	LEU	0	-0.010	-0.007	21.805	0.275	0.275	0.000	0.000	0.000	0.000
45	O	108	ARG	1	0.926	0.970	23.528	12.405	12.405	0.000	0.000	0.000	0.000
46	O	109	ASN	0	0.031	0.015	27.588	0.454	0.454	0.000	0.000	0.000	0.000
47	O	110	THR	0	-0.034	-0.019	28.376	0.301	0.301	0.000	0.000	0.000	0.000
48	O	111	VAL	0	-0.012	-0.014	26.574	0.192	0.192	0.000	0.000	0.000	0.000
49	O	112	ASP	-1	-0.912	-0.951	29.807	-9.621	-9.621	0.000	0.000	0.000	0.000
50	O	113	SER	0	-0.137	-0.048	33.018	0.308	0.308	0.000	0.000	0.000	0.000
51	O	114	VAL	0	-0.082	-0.033	30.868	0.387	0.387	0.000	0.000	0.000	0.000

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