FMO DATABASE

FMODB ID: LJK29

Calculation Name: 4DJG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DJG

Chain ID: A

ChEMBL ID:

UniProt ID: O48791

Base Structure: X-ray

Registration Date: 2023-06-20

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-219472.762474
FMO2-HF: Nuclear repulsion	200311.84465
FMO2-HF: Total energy	-19160.917824
FMO2-MP2: Total energy	-19217.216598

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(A:103:LEU)

Summations of interaction energy for fragment #1(A:103:LEU)

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.
-14.631	-6.162	13.887	-5.551	-16.809	-0.024

Interaction energy analysis for fragmet #1(A:103:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.007

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	A	105	LYS	1	0.948	0.978	3.369	-4.274	-2.446	0.007	-0.779	-1.058	0.001
4	A	106	HIS	0	0.006	0.005	2.300	-1.246	0.339	2.271	-1.145	-2.710	0.001
5	A	107	VAL	0	0.063	0.031	3.039	-2.046	-0.811	0.153	-0.607	-0.782	-0.006
6	A	108	LEU	0	0.022	0.011	5.212	0.043	0.144	-0.001	-0.004	-0.096	0.000
7	A	109	LEU	0	0.058	0.030	2.411	-1.249	-0.094	0.962	-0.354	-1.763	-0.001
8	A	110	LYS	1	0.859	0.914	2.329	-2.237	-0.405	3.521	-1.771	-3.582	-0.002
9	A	111	LYS	1	0.835	0.896	3.269	0.948	0.315	0.078	0.936	-0.382	0.000
10	A	112	LEU	0	0.030	0.035	6.036	0.117	0.117	0.000	0.000	0.000	0.000
11	A	113	ARG	1	0.990	0.996	2.423	-1.475	-0.343	1.941	-0.710	-2.363	-0.003
12	A	114	ASP	-1	-0.825	-0.910	5.864	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	115	ALA	0	-0.057	-0.029	7.699	0.026	0.026	0.000	0.000	0.000	0.000
14	A	116	LEU	0	0.004	-0.003	8.627	0.041	0.041	0.000	0.000	0.000	0.000
15	A	117	GLU	-1	-0.819	-0.919	8.828	-0.206	-0.206	0.000	0.000	0.000	0.000
16	A	118	SER	0	-0.029	-0.008	11.082	0.029	0.029	0.000	0.000	0.000	0.000
17	A	119	LEU	0	-0.052	-0.030	13.545	0.021	0.021	0.000	0.000	0.000	0.000
18	A	120	ARG	1	0.889	0.941	13.474	0.210	0.210	0.000	0.000	0.000	0.000
19	A	121	GLY	0	-0.055	-0.021	15.819	0.013	0.013	0.000	0.000	0.000	0.000
20	A	122	ARG	1	0.845	0.918	15.716	0.147	0.147	0.000	0.000	0.000	0.000
21	A	123	VAL	0	-0.018	0.020	18.373	0.008	0.008	0.000	0.000	0.000	0.000
22	A	124	ALA	0	0.011	-0.012	21.124	0.004	0.004	0.000	0.000	0.000	0.000
23	A	125	GLY	0	-0.004	-0.009	23.542	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	126	ARG	1	0.985	0.993	22.361	0.149	0.149	0.000	0.000	0.000	0.000
25	A	127	ASN	0	0.023	0.007	21.473	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	128	LYS	1	0.911	0.963	18.566	0.108	0.108	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.831	-0.915	17.730	-0.165	-0.165	0.000	0.000	0.000	0.000
28	A	130	ASP	-1	-0.879	-0.936	17.630	-0.214	-0.214	0.000	0.000	0.000	0.000
29	A	131	VAL	0	-0.074	-0.038	13.879	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	132	GLU	-1	-0.845	-0.931	13.278	-0.225	-0.225	0.000	0.000	0.000	0.000
31	A	133	GLU	-1	-0.902	-0.936	13.120	-0.350	-0.350	0.000	0.000	0.000	0.000
32	A	134	ALA	0	-0.025	-0.020	12.076	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	135	ILE	0	-0.048	-0.031	8.482	-0.108	-0.108	0.000	0.000	0.000	0.000
34	A	136	ALA	0	0.058	0.036	8.260	-0.147	-0.147	0.000	0.000	0.000	0.000
35	A	137	MET	0	-0.017	-0.009	9.625	-0.098	-0.098	0.000	0.000	0.000	0.000
36	A	138	VAL	0	-0.029	-0.022	4.719	-0.218	-0.146	-0.001	-0.003	-0.068	0.000
37	A	139	GLU	-1	-0.972	-0.985	5.035	-1.194	-1.194	0.000	0.000	0.000	0.000
38	A	140	ALA	0	0.014	0.012	6.072	-0.218	-0.218	0.000	0.000	0.000	0.000
39	A	141	LEU	0	-0.032	-0.027	6.832	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	142	ALA	0	-0.027	-0.027	2.101	-0.665	-1.206	3.182	-0.794	-1.848	-0.005
41	A	143	VAL	0	0.023	0.021	3.147	-0.070	0.159	0.010	0.246	-0.485	-0.003
42	A	144	GLN	0	-0.027	-0.012	5.650	0.388	0.388	0.000	0.000	0.000	0.000
43	A	145	LEU	0	-0.062	-0.019	3.477	-0.109	0.200	0.010	-0.064	-0.255	0.000
44	A	146	THR	0	-0.134	-0.087	2.287	-0.136	0.017	1.755	-0.499	-1.409	-0.006
45	A	147	GLN	0	-0.008	0.020	5.253	0.305	0.317	-0.001	-0.003	-0.008	0.000
46	A	148	ARG	1	0.901	0.958	8.856	-0.792	-0.792	0.000	0.000	0.000	0.000
47	A	149	GLU	-1	-0.925	-0.971	11.301	0.070	0.070	0.000	0.000	0.000	0.000
48	A	150	GLY	0	-0.024	-0.017	14.965	0.043	0.043	0.000	0.000	0.000	0.000
49	A	151	GLU	-1	-0.944	-0.958	10.301	0.270	0.270	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:103:LEU)