FMO DATABASE

FMODB ID: N9R5Q

Calculation Name: 1JPX-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JPX

Chain ID: D

ChEMBL ID:

UniProt ID: S4WCF9

Base Structure: X-ray

Registration Date: 2023-09-20

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	57
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-307290.92334
FMO2-HF: Nuclear repulsion	283332.273812
FMO2-HF: Total energy	-23958.649528
FMO2-MP2: Total energy	-24029.497912

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(D:6:GLY)

Summations of interaction energy for fragment #1(D:6: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.
-1.681	1.638	0.138	-1.35	-2.106	0.002

Interaction energy analysis for fragmet #1(D:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.017

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	D	8	VAL	0	0.074	0.029	3.311	-2.763	-0.768	0.048	-0.951	-1.091	0.004
4	D	9	GLN	0	0.024	0.025	3.004	-1.279	-0.209	0.091	-0.337	-0.824	-0.002
5	D	10	GLN	0	0.017	-0.013	4.432	0.724	0.978	-0.001	-0.062	-0.191	0.000
6	D	11	GLN	0	-0.059	-0.031	6.311	0.586	0.586	0.000	0.000	0.000	0.000
7	D	12	GLN	0	0.057	0.033	7.595	0.199	0.199	0.000	0.000	0.000	0.000
8	D	13	GLN	0	-0.041	-0.008	7.822	-0.126	-0.126	0.000	0.000	0.000	0.000
9	D	14	LEU	0	-0.017	-0.017	10.280	0.118	0.118	0.000	0.000	0.000	0.000
10	D	15	LEU	0	0.013	0.017	12.124	0.069	0.069	0.000	0.000	0.000	0.000
11	D	16	ASP	-1	-0.860	-0.935	13.579	-0.264	-0.264	0.000	0.000	0.000	0.000
12	D	17	VAL	0	-0.084	-0.037	14.211	0.040	0.040	0.000	0.000	0.000	0.000
13	D	18	VAL	0	0.040	0.009	16.669	0.034	0.034	0.000	0.000	0.000	0.000
14	D	19	LYS	1	0.931	0.977	17.474	0.136	0.136	0.000	0.000	0.000	0.000
15	D	20	ARG	1	0.920	0.960	17.632	0.228	0.228	0.000	0.000	0.000	0.000
16	D	21	GLN	0	-0.044	-0.022	20.625	0.018	0.018	0.000	0.000	0.000	0.000
17	D	22	GLN	0	0.056	0.043	22.518	0.010	0.010	0.000	0.000	0.000	0.000
18	D	23	GLU	-1	-0.923	-0.977	22.541	-0.122	-0.122	0.000	0.000	0.000	0.000
19	D	24	LEU	0	-0.008	-0.006	25.086	0.007	0.007	0.000	0.000	0.000	0.000
20	D	25	LEU	0	0.010	-0.001	26.190	0.007	0.007	0.000	0.000	0.000	0.000
21	D	26	ARG	1	0.979	0.992	25.893	0.070	0.070	0.000	0.000	0.000	0.000
22	D	27	LEU	0	-0.015	0.004	28.971	0.005	0.005	0.000	0.000	0.000	0.000
23	D	28	THR	0	-0.045	-0.012	30.357	0.005	0.005	0.000	0.000	0.000	0.000
24	D	29	VAL	0	0.025	0.033	32.230	0.005	0.005	0.000	0.000	0.000	0.000
25	D	30	TRP	0	-0.026	-0.009	34.279	0.004	0.004	0.000	0.000	0.000	0.000
26	D	31	GLY	0	-0.032	-0.021	35.786	0.002	0.002	0.000	0.000	0.000	0.000
27	D	32	THR	0	-0.098	-0.051	36.155	0.003	0.003	0.000	0.000	0.000	0.000
28	D	33	LYS	1	0.758	0.860	38.514	0.033	0.033	0.000	0.000	0.000	0.000
29	D	49	GLU	-1	-0.873	-0.940	41.690	-0.014	-0.014	0.000	0.000	0.000	0.000
30	D	50	TRP	0	0.049	0.017	36.510	0.001	0.001	0.000	0.000	0.000	0.000
31	D	51	DGL	-1	-0.687	-0.806	37.500	-0.031	-0.031	0.000	0.000	0.000	0.000
32	D	52	ARG	1	0.888	0.927	38.985	0.016	0.016	0.000	0.000	0.000	0.000
33	D	53	LYS	1	0.822	0.904	36.210	0.017	0.017	0.000	0.000	0.000	0.000
34	D	54	VAL	0	0.033	-0.002	33.516	0.000	0.000	0.000	0.000	0.000	0.000
35	D	55	ASP	-1	-0.859	-0.917	33.300	-0.030	-0.030	0.000	0.000	0.000	0.000
36	D	56	PHE	0	0.002	-0.011	33.128	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	57	LEU	0	-0.051	-0.023	29.243	0.001	0.001	0.000	0.000	0.000	0.000
38	D	58	GLU	-1	-0.916	-0.961	28.734	-0.050	-0.050	0.000	0.000	0.000	0.000
39	D	59	GLU	-1	-0.932	-0.947	28.591	-0.017	-0.017	0.000	0.000	0.000	0.000
40	D	60	ASN	0	-0.025	-0.014	26.431	0.007	0.007	0.000	0.000	0.000	0.000
41	D	61	ILE	0	0.011	0.004	23.280	0.003	0.003	0.000	0.000	0.000	0.000
42	D	62	THR	0	-0.043	-0.030	23.277	-0.011	-0.011	0.000	0.000	0.000	0.000
43	D	63	ALA	0	0.003	0.009	23.581	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	64	LEU	0	0.018	-0.005	21.551	0.002	0.002	0.000	0.000	0.000	0.000
45	D	65	LEU	0	-0.074	-0.033	18.746	-0.004	-0.004	0.000	0.000	0.000	0.000
46	D	66	GLU	-1	-0.931	-0.959	18.459	0.003	0.003	0.000	0.000	0.000	0.000
47	D	67	GLU	-1	-0.894	-0.947	18.869	0.043	0.043	0.000	0.000	0.000	0.000
48	D	68	ALA	0	-0.039	-0.021	15.787	0.026	0.026	0.000	0.000	0.000	0.000
49	D	69	GLN	0	-0.023	-0.012	13.625	-0.030	-0.030	0.000	0.000	0.000	0.000
50	D	70	ILE	0	0.031	-0.004	14.640	0.027	0.027	0.000	0.000	0.000	0.000
51	D	71	GLN	0	-0.038	-0.017	13.108	-0.021	-0.021	0.000	0.000	0.000	0.000
52	D	72	GLN	0	0.028	0.005	7.335	0.264	0.264	0.000	0.000	0.000	0.000
53	D	73	GLU	-1	-0.915	-0.938	10.448	0.117	0.117	0.000	0.000	0.000	0.000
54	D	74	LYS	1	0.856	0.931	12.515	-0.131	-0.131	0.000	0.000	0.000	0.000
55	D	75	ASN	0	-0.035	-0.033	8.305	0.125	0.125	0.000	0.000	0.000	0.000
56	D	76	MET	0	-0.064	-0.016	5.955	0.255	0.255	0.000	0.000	0.000	0.000
57	D	77	TYR	0	-0.084	-0.019	9.492	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:6:GLY)