FMO DATABASE

FMODB ID: 2J4LR

Calculation Name: 5GNJ-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5GNJ

Chain ID: G

ChEMBL ID:

UniProt ID: Q39204

Base Structure: X-ray

Registration Date: 2023-06-22

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-357443.651516
FMO2-HF: Nuclear repulsion	328483.121205
FMO2-HF: Total energy	-28960.530312
FMO2-MP2: Total energy	-29046.225412

3D Structure Molmil

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(G:452:ASN)

Summations of interaction energy for fragment #1(G:452:ASN)

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.
-17.952	-27.133	16.563	1.385	-8.768	0.023

Interaction energy analysis for fragmet #1(G:452:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.013

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	G	454	VAL	0	0.032	-0.011	2.709	8.208	3.114	0.331	6.392	-1.630	-0.002
4	G	455	GLU	-1	-0.823	-0.903	2.112	-7.696	-8.814	7.357	-2.610	-3.630	0.008
5	G	456	ALA	0	0.024	0.011	2.047	-8.413	-11.625	8.828	-2.401	-3.215	0.016
6	G	457	GLU	-1	-0.747	-0.833	3.416	-0.205	-0.066	0.048	0.008	-0.194	0.001
7	G	458	ARG	1	0.827	0.893	5.531	-2.572	-2.572	0.000	0.000	0.000	0.000
8	G	459	GLN	0	0.028	0.016	4.603	-0.535	-0.431	-0.001	-0.004	-0.099	0.000
9	G	460	ARG	1	0.875	0.921	7.516	-2.475	-2.475	0.000	0.000	0.000	0.000
10	G	461	ARG	1	0.844	0.896	9.573	-2.180	-2.180	0.000	0.000	0.000	0.000
11	G	462	GLU	-1	-0.826	-0.899	10.948	0.261	0.261	0.000	0.000	0.000	0.000
12	G	463	LYS	1	0.955	0.984	11.744	-0.721	-0.721	0.000	0.000	0.000	0.000
13	G	464	LEU	0	0.006	0.010	13.520	-0.112	-0.112	0.000	0.000	0.000	0.000
14	G	465	ASN	0	0.040	0.008	15.414	-0.107	-0.107	0.000	0.000	0.000	0.000
15	G	466	GLN	0	0.006	-0.003	14.576	-0.062	-0.062	0.000	0.000	0.000	0.000
16	G	467	ARG	1	0.856	0.915	16.418	-0.403	-0.403	0.000	0.000	0.000	0.000
17	G	468	PHE	0	0.049	0.012	19.250	-0.014	-0.014	0.000	0.000	0.000	0.000
18	G	469	TYR	0	-0.003	0.001	21.376	-0.026	-0.026	0.000	0.000	0.000	0.000
19	G	470	ALA	0	0.005	-0.007	22.690	-0.028	-0.028	0.000	0.000	0.000	0.000
20	G	471	LEU	0	0.011	0.008	24.471	-0.021	-0.021	0.000	0.000	0.000	0.000
21	G	472	ARG	1	0.843	0.896	25.953	-0.299	-0.299	0.000	0.000	0.000	0.000
22	G	473	ALA	0	-0.044	-0.005	27.864	-0.016	-0.016	0.000	0.000	0.000	0.000
23	G	474	VAL	0	-0.032	-0.007	28.723	-0.016	-0.016	0.000	0.000	0.000	0.000
24	G	475	VAL	0	0.002	0.005	30.717	-0.004	-0.004	0.000	0.000	0.000	0.000
25	G	476	PRO	0	0.028	0.013	33.126	0.002	0.002	0.000	0.000	0.000	0.000
26	G	477	ASN	0	0.023	0.004	35.675	0.006	0.006	0.000	0.000	0.000	0.000
27	G	478	VAL	0	0.032	0.039	30.598	0.005	0.005	0.000	0.000	0.000	0.000
28	G	479	SER	0	-0.018	-0.020	30.974	0.020	0.020	0.000	0.000	0.000	0.000
29	G	480	LYS	1	0.939	0.957	30.444	-0.158	-0.158	0.000	0.000	0.000	0.000
30	G	481	MET	0	0.022	0.045	31.157	0.005	0.005	0.000	0.000	0.000	0.000
31	G	482	ASP	-1	-0.735	-0.845	27.723	0.383	0.383	0.000	0.000	0.000	0.000
32	G	483	LYS	1	0.850	0.931	19.007	-0.635	-0.635	0.000	0.000	0.000	0.000
33	G	484	ALA	0	0.004	-0.003	25.764	0.001	0.001	0.000	0.000	0.000	0.000
34	G	485	SER	0	0.004	-0.030	27.947	-0.019	-0.019	0.000	0.000	0.000	0.000
35	G	486	LEU	0	-0.062	-0.012	25.640	-0.010	-0.010	0.000	0.000	0.000	0.000
36	G	487	LEU	0	-0.004	-0.009	24.269	-0.008	-0.008	0.000	0.000	0.000	0.000
37	G	488	GLY	0	0.010	0.013	28.632	-0.012	-0.012	0.000	0.000	0.000	0.000
38	G	489	ASP	-1	-0.853	-0.945	32.184	0.208	0.208	0.000	0.000	0.000	0.000
39	G	490	ALA	0	-0.024	-0.006	30.004	-0.016	-0.016	0.000	0.000	0.000	0.000
40	G	491	ILE	0	-0.021	-0.010	29.984	-0.014	-0.014	0.000	0.000	0.000	0.000
41	G	492	ALA	0	-0.007	0.000	33.319	-0.014	-0.014	0.000	0.000	0.000	0.000
42	G	493	TYR	0	0.017	0.003	33.909	-0.016	-0.016	0.000	0.000	0.000	0.000
43	G	494	ILE	0	0.006	-0.003	31.111	-0.012	-0.012	0.000	0.000	0.000	0.000
44	G	495	ASN	0	-0.018	-0.022	35.731	-0.012	-0.012	0.000	0.000	0.000	0.000
45	G	496	GLU	-1	-0.864	-0.932	38.744	0.116	0.116	0.000	0.000	0.000	0.000
46	G	497	LEU	0	-0.021	-0.006	36.435	-0.009	-0.009	0.000	0.000	0.000	0.000
47	G	498	LYS	1	0.867	0.930	36.651	-0.187	-0.187	0.000	0.000	0.000	0.000
48	G	499	SER	0	-0.010	0.017	41.112	-0.009	-0.009	0.000	0.000	0.000	0.000
49	G	500	LYS	1	0.979	0.977	43.991	-0.092	-0.092	0.000	0.000	0.000	0.000
50	G	501	VAL	0	-0.010	0.018	41.650	-0.008	-0.008	0.000	0.000	0.000	0.000
51	G	502	VAL	0	0.018	0.005	44.532	-0.006	-0.006	0.000	0.000	0.000	0.000
52	G	503	LYS	1	0.838	0.912	46.942	-0.086	-0.086	0.000	0.000	0.000	0.000
53	G	504	THR	0	0.009	-0.020	47.697	-0.005	-0.005	0.000	0.000	0.000	0.000
54	G	505	GLU	-1	-0.797	-0.884	47.414	0.065	0.065	0.000	0.000	0.000	0.000
55	G	506	SER	0	0.014	0.014	50.228	-0.004	-0.004	0.000	0.000	0.000	0.000
56	G	507	GLU	-1	-0.869	-0.926	51.943	0.073	0.073	0.000	0.000	0.000	0.000
57	G	508	LYS	1	0.818	0.892	49.172	-0.067	-0.067	0.000	0.000	0.000	0.000
58	G	509	LEU	0	-0.015	-0.002	54.306	-0.004	-0.004	0.000	0.000	0.000	0.000
59	G	510	GLN	0	-0.038	-0.017	55.993	0.000	0.000	0.000	0.000	0.000	0.000
60	G	511	ILE	0	0.015	0.004	56.543	-0.003	-0.003	0.000	0.000	0.000	0.000
61	G	512	LYS	1	0.828	0.906	57.105	-0.046	-0.046	0.000	0.000	0.000	0.000
62	G	513	ASN	0	0.007	-0.013	59.177	-0.004	-0.004	0.000	0.000	0.000	0.000
63	G	514	GLN	0	0.024	0.014	62.011	0.000	0.000	0.000	0.000	0.000	0.000
64	G	515	LEU	0	-0.005	0.003	60.769	-0.002	-0.002	0.000	0.000	0.000	0.000
65	G	516	GLU	-1	-0.861	-0.915	62.737	0.034	0.034	0.000	0.000	0.000	0.000
66	G	517	GLU	-1	-0.869	-0.933	65.072	0.034	0.034	0.000	0.000	0.000	0.000
67	G	518	VAL	0	0.020	0.013	66.831	-0.002	-0.002	0.000	0.000	0.000	0.000
68	G	519	LYS	1	0.830	0.916	64.214	-0.032	-0.032	0.000	0.000	0.000	0.000
69	G	520	LEU	0	-0.039	-0.022	68.812	-0.002	-0.002	0.000	0.000	0.000	0.000
70	G	521	GLU	-1	-0.919	-0.960	71.289	0.029	0.029	0.000	0.000	0.000	0.000
71	G	522	LEU	0	-0.060	-0.026	70.424	-0.001	-0.001	0.000	0.000	0.000	0.000
72	G	523	ALA	0	-0.059	-0.020	72.390	-0.001	-0.001	0.000	0.000	0.000	0.000
73	G	524	GLY	0	-0.041	-0.011	74.372	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:452:ASN)