FMO DATABASE

FMODB ID: KGJL3

Calculation Name: 1JY2-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: N

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	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	43
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-162214.325964
FMO2-HF: Nuclear repulsion	143782.893418
FMO2-HF: Total energy	-18431.432546
FMO2-MP2: Total energy	-18482.154982

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(N:35:GLY)

Summations of interaction energy for fragment #1(N:35:GLY)

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.
-0.959	0.171	-0.013	-0.531	-0.586	0.002

Interaction energy analysis for fragmet #1(N:35:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.014

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	N	37	PRO	0	-0.002	0.011	3.782	-0.811	0.319	-0.013	-0.531	-0.586	0.002
4	N	38	PHE	0	0.008	-0.011	6.621	0.445	0.445	0.000	0.000	0.000	0.000
5	N	39	CYS	0	-0.057	-0.025	8.627	-0.023	-0.023	0.000	0.000	0.000	0.000
6	N	40	SER	0	0.018	0.017	11.625	0.009	0.009	0.000	0.000	0.000	0.000
7	N	41	ASP	-1	-0.899	-0.973	14.974	0.018	0.018	0.000	0.000	0.000	0.000
8	N	42	GLU	-1	-0.979	-0.994	18.237	-0.087	-0.087	0.000	0.000	0.000	0.000
9	N	43	ASP	-1	-0.889	-0.931	13.549	-0.155	-0.155	0.000	0.000	0.000	0.000
10	N	44	TRP	0	-0.001	-0.005	16.603	0.047	0.047	0.000	0.000	0.000	0.000
11	N	45	ASN	0	-0.026	-0.029	18.481	-0.007	-0.007	0.000	0.000	0.000	0.000
12	N	46	THR	0	-0.013	0.018	17.590	-0.004	-0.004	0.000	0.000	0.000	0.000
13	N	47	LYS	1	0.901	0.951	11.586	0.187	0.187	0.000	0.000	0.000	0.000
14	N	48	CYS	0	-0.013	-0.010	15.805	-0.005	-0.005	0.000	0.000	0.000	0.000
15	N	49	PRO	0	0.039	0.020	14.635	0.058	0.058	0.000	0.000	0.000	0.000
16	N	50	SER	0	0.009	0.012	14.266	-0.059	-0.059	0.000	0.000	0.000	0.000
17	N	51	GLY	0	0.100	0.034	15.938	-0.017	-0.017	0.000	0.000	0.000	0.000
18	N	52	CYS	0	-0.007	-0.005	17.462	-0.023	-0.023	0.000	0.000	0.000	0.000
19	N	53	ARG	1	0.920	0.970	13.355	-0.597	-0.597	0.000	0.000	0.000	0.000
20	N	54	MET	0	0.051	0.019	17.985	-0.012	-0.012	0.000	0.000	0.000	0.000
21	N	55	LYS	1	0.872	0.939	20.799	-0.186	-0.186	0.000	0.000	0.000	0.000
22	N	56	GLY	0	0.029	0.019	21.437	-0.016	-0.016	0.000	0.000	0.000	0.000
23	N	57	LEU	0	0.009	-0.009	18.871	-0.008	-0.008	0.000	0.000	0.000	0.000
24	N	58	ILE	0	-0.034	-0.016	22.943	-0.019	-0.019	0.000	0.000	0.000	0.000
25	N	59	ASP	-1	-0.833	-0.910	25.735	0.161	0.161	0.000	0.000	0.000	0.000
26	N	60	GLU	-1	-0.979	-0.987	23.596	0.209	0.209	0.000	0.000	0.000	0.000
27	N	61	VAL	0	0.005	0.003	26.262	-0.013	-0.013	0.000	0.000	0.000	0.000
28	N	62	ASP	-1	-0.922	-0.962	28.650	0.096	0.096	0.000	0.000	0.000	0.000
29	N	63	GLN	0	-0.010	0.001	30.288	-0.007	-0.007	0.000	0.000	0.000	0.000
30	N	64	ASP	-1	-0.840	-0.921	30.184	0.104	0.104	0.000	0.000	0.000	0.000
31	N	65	PHE	0	-0.018	-0.032	31.644	-0.009	-0.009	0.000	0.000	0.000	0.000
32	N	66	THR	0	0.017	0.019	34.668	-0.010	-0.010	0.000	0.000	0.000	0.000
33	N	67	SER	0	-0.060	-0.030	35.189	-0.009	-0.009	0.000	0.000	0.000	0.000
34	N	68	ARG	1	0.863	0.922	33.031	-0.100	-0.100	0.000	0.000	0.000	0.000
35	N	69	ILE	0	0.006	0.006	37.984	-0.006	-0.006	0.000	0.000	0.000	0.000
36	N	70	ASN	0	-0.023	-0.018	39.770	-0.007	-0.007	0.000	0.000	0.000	0.000
37	N	71	LYS	1	0.972	0.992	37.161	-0.088	-0.088	0.000	0.000	0.000	0.000
38	N	72	LEU	0	-0.007	-0.001	41.088	-0.003	-0.003	0.000	0.000	0.000	0.000
39	N	73	ARG	1	0.932	0.966	43.746	-0.064	-0.064	0.000	0.000	0.000	0.000
40	N	74	ASP	-1	-0.891	-0.940	45.325	0.058	0.058	0.000	0.000	0.000	0.000
41	N	75	SER	0	-0.157	-0.064	46.286	-0.002	-0.002	0.000	0.000	0.000	0.000
42	N	76	LEU	0	-0.036	-0.023	47.640	-0.002	-0.002	0.000	0.000	0.000	0.000
43	N	77	PHE	0	-0.026	0.000	48.918	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(N:35:GLY)