FMO DATABASE

FMODB ID: ZVK5N

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	OptH
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	-192831.858899
FMO2-HF: Nuclear repulsion	172525.37422
FMO2-HF: Total energy	-20306.48468
FMO2-MP2: Total energy	-20363.840724

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.
-59.989	-56.84	7.252	-3.814	-6.587	-0.028

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 : 0.971 / q_NPA : 0.973

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	O	66	PRO	0	0.015	-0.013	2.092	-14.972	-12.984	6.103	-3.443	-4.648	-0.029
4	O	67	PRO	0	-0.054	-0.016	2.966	4.311	5.472	1.149	-0.371	-1.939	0.001
5	O	68	ASP	-1	-0.855	-0.912	5.635	-31.459	-31.459	0.000	0.000	0.000	0.000
6	O	69	ALA	0	-0.072	-0.057	9.271	0.379	0.379	0.000	0.000	0.000	0.000
7	O	70	ASP	-1	-0.941	-0.983	11.571	-19.977	-19.977	0.000	0.000	0.000	0.000
8	O	71	GLY	0	0.031	0.040	15.172	0.761	0.761	0.000	0.000	0.000	0.000
9	O	72	CYS	0	-0.071	-0.040	16.814	0.438	0.438	0.000	0.000	0.000	0.000
10	O	73	LEU	0	-0.007	0.000	20.245	-0.228	-0.228	0.000	0.000	0.000	0.000
11	O	74	HIS	0	0.003	0.023	22.327	0.462	0.462	0.000	0.000	0.000	0.000
12	O	75	ALA	0	-0.004	-0.012	25.639	0.021	0.021	0.000	0.000	0.000	0.000
13	O	76	ASP	-1	-0.894	-0.949	28.834	-10.090	-10.090	0.000	0.000	0.000	0.000
14	O	77	PRO	0	-0.026	-0.037	27.587	-0.428	-0.428	0.000	0.000	0.000	0.000
15	O	78	ASP	-1	-0.894	-0.941	27.060	-10.888	-10.888	0.000	0.000	0.000	0.000
16	O	79	LEU	0	-0.111	-0.050	25.526	-0.371	-0.371	0.000	0.000	0.000	0.000
17	O	80	GLY	0	0.003	0.020	22.791	-0.601	-0.601	0.000	0.000	0.000	0.000
18	O	81	VAL	0	-0.021	-0.029	17.023	0.148	0.148	0.000	0.000	0.000	0.000
19	O	82	LEU	0	-0.002	0.007	19.643	-0.124	-0.124	0.000	0.000	0.000	0.000
20	O	83	CYS	0	0.024	-0.001	15.186	-1.131	-1.131	0.000	0.000	0.000	0.000
21	O	84	PRO	0	-0.005	0.001	14.728	1.076	1.076	0.000	0.000	0.000	0.000
22	O	85	THR	0	0.067	0.031	16.740	-0.518	-0.518	0.000	0.000	0.000	0.000
23	O	86	GLY	0	0.058	0.016	17.425	-0.546	-0.546	0.000	0.000	0.000	0.000
24	O	87	CYS	0	-0.002	-0.002	18.492	0.060	0.060	0.000	0.000	0.000	0.000
25	O	88	LYS	1	0.997	1.009	17.606	15.241	15.241	0.000	0.000	0.000	0.000
26	O	89	LEU	0	0.034	0.016	12.824	-0.241	-0.241	0.000	0.000	0.000	0.000
27	O	90	GLN	0	0.003	0.002	15.866	0.008	0.008	0.000	0.000	0.000	0.000
28	O	91	ASP	-1	-0.883	-0.943	18.194	-13.597	-13.597	0.000	0.000	0.000	0.000
29	O	92	THR	0	-0.044	-0.026	14.050	0.200	0.200	0.000	0.000	0.000	0.000
30	O	93	LEU	0	0.026	0.005	12.051	0.007	0.007	0.000	0.000	0.000	0.000
31	O	94	VAL	0	-0.011	0.004	15.863	0.332	0.332	0.000	0.000	0.000	0.000
32	O	95	ARG	1	0.845	0.917	19.256	13.599	13.599	0.000	0.000	0.000	0.000
33	O	96	GLN	0	0.000	-0.006	12.778	-0.181	-0.181	0.000	0.000	0.000	0.000
34	O	97	GLU	-1	-0.856	-0.923	17.173	-15.208	-15.208	0.000	0.000	0.000	0.000
35	O	98	ARG	1	0.938	0.968	17.941	12.699	12.699	0.000	0.000	0.000	0.000
36	O	99	PRO	0	0.037	0.017	19.313	0.385	0.385	0.000	0.000	0.000	0.000
37	O	100	ILE	0	0.026	0.029	15.574	0.194	0.194	0.000	0.000	0.000	0.000
38	O	101	ARG	1	0.876	0.919	18.334	15.491	15.491	0.000	0.000	0.000	0.000
39	O	102	LYS	1	0.929	0.983	20.972	11.011	11.011	0.000	0.000	0.000	0.000
40	O	103	SER	0	0.014	-0.001	20.766	0.423	0.423	0.000	0.000	0.000	0.000
41	O	104	ILE	0	-0.038	-0.013	18.004	0.213	0.213	0.000	0.000	0.000	0.000
42	O	105	GLU	-1	-0.991	-0.997	22.444	-10.960	-10.960	0.000	0.000	0.000	0.000
43	O	106	ASP	-1	-0.838	-0.927	25.815	-10.599	-10.599	0.000	0.000	0.000	0.000
44	O	107	LEU	0	-0.022	-0.020	21.866	0.282	0.282	0.000	0.000	0.000	0.000
45	O	108	ARG	1	0.920	0.966	22.964	12.538	12.538	0.000	0.000	0.000	0.000
46	O	109	ASN	0	0.046	0.024	27.567	0.372	0.372	0.000	0.000	0.000	0.000
47	O	110	THR	0	-0.047	-0.022	28.524	0.322	0.322	0.000	0.000	0.000	0.000
48	O	111	VAL	0	-0.023	-0.022	26.861	0.181	0.181	0.000	0.000	0.000	0.000
49	O	112	ASP	-1	-0.901	-0.946	29.998	-9.621	-9.621	0.000	0.000	0.000	0.000
50	O	113	SER	0	-0.145	-0.049	33.143	0.327	0.327	0.000	0.000	0.000	0.000
51	O	114	VAL	0	-0.066	-0.025	30.742	0.270	0.270	0.000	0.000	0.000	0.000

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