FMO DATABASE

FMODB ID: 4J53N

Calculation Name: 4MBQ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MBQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HZA6

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	OptAll
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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-235258.030881
FMO2-HF: Nuclear repulsion	216098.689166
FMO2-HF: Total energy	-19159.341715
FMO2-MP2: Total energy	-19214.99928

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(B:869:GLY)

Summations of interaction energy for fragment #1(B:869: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.
-19.175	-18.619	10.706	-6.057	-5.209	-0.054

Interaction energy analysis for fragmet #1(B:869:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.005

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	B	871	ASP	-1	-0.921	-0.951	3.289	-2.812	-1.094	0.013	-0.785	-0.947	0.003
4	B	872	GLU	-1	-0.873	-0.932	1.858	-15.378	-17.410	10.652	-4.844	-3.776	-0.055
5	B	873	ALA	0	0.050	0.025	3.968	1.411	1.715	-0.001	-0.137	-0.167	0.000
6	B	874	ALA	0	-0.026	-0.022	5.875	0.770	0.770	0.000	0.000	0.000	0.000
7	B	875	THR	0	-0.022	-0.016	7.673	0.371	0.371	0.000	0.000	0.000	0.000
8	B	876	LYS	1	0.787	0.866	6.546	2.303	2.303	0.000	0.000	0.000	0.000
9	B	877	LEU	0	-0.004	0.009	9.897	0.226	0.226	0.000	0.000	0.000	0.000
10	B	878	ASP	-1	-0.844	-0.915	11.939	-0.255	-0.255	0.000	0.000	0.000	0.000
11	B	879	LEU	0	-0.053	-0.018	11.442	0.081	0.081	0.000	0.000	0.000	0.000
12	B	880	ALA	0	0.037	0.017	13.784	0.078	0.078	0.000	0.000	0.000	0.000
13	B	881	ARG	1	0.746	0.851	15.117	0.380	0.380	0.000	0.000	0.000	0.000
14	B	882	ALA	0	0.050	0.023	17.629	0.040	0.040	0.000	0.000	0.000	0.000
15	B	883	TYR	0	-0.046	-0.024	17.706	0.019	0.019	0.000	0.000	0.000	0.000
16	B	884	ILE	0	-0.015	-0.007	19.096	0.035	0.035	0.000	0.000	0.000	0.000
17	B	885	ASP	-1	-0.963	-0.974	21.786	-0.195	-0.195	0.000	0.000	0.000	0.000
18	B	886	MET	0	-0.140	-0.064	20.755	0.027	0.027	0.000	0.000	0.000	0.000
19	B	887	GLY	0	-0.037	-0.013	24.558	0.014	0.014	0.000	0.000	0.000	0.000
20	B	888	ASP	-1	-0.899	-0.944	22.128	-0.285	-0.285	0.000	0.000	0.000	0.000
21	B	889	SER	0	0.019	-0.038	21.350	-0.025	-0.025	0.000	0.000	0.000	0.000
22	B	890	GLU	-1	-0.863	-0.889	21.115	-0.240	-0.240	0.000	0.000	0.000	0.000
23	B	891	GLY	0	0.049	0.017	18.696	-0.026	-0.026	0.000	0.000	0.000	0.000
24	B	892	ALA	0	-0.017	-0.010	16.858	-0.061	-0.061	0.000	0.000	0.000	0.000
25	B	893	ARG	1	0.789	0.866	16.125	0.182	0.182	0.000	0.000	0.000	0.000
26	B	894	ASP	-1	-0.901	-0.945	15.924	-0.413	-0.413	0.000	0.000	0.000	0.000
27	B	895	ILE	0	-0.036	-0.016	11.543	-0.078	-0.078	0.000	0.000	0.000	0.000
28	B	896	LEU	0	-0.024	-0.023	11.264	-0.154	-0.154	0.000	0.000	0.000	0.000
29	B	897	ASP	-1	-0.931	-0.958	12.141	-0.467	-0.467	0.000	0.000	0.000	0.000
30	B	898	GLU	-1	-0.874	-0.931	8.291	-1.197	-1.197	0.000	0.000	0.000	0.000
31	B	899	VAL	0	-0.028	-0.016	7.631	-0.218	-0.218	0.000	0.000	0.000	0.000
32	B	900	LEU	0	-0.072	-0.034	8.416	0.036	0.036	0.000	0.000	0.000	0.000
33	B	901	ALA	0	-0.043	-0.008	8.647	0.152	0.152	0.000	0.000	0.000	0.000
34	B	902	GLU	-1	-0.888	-0.920	3.434	-2.670	-2.517	0.014	-0.049	-0.118	0.000
35	B	903	GLY	0	-0.015	-0.008	3.540	-1.099	-0.686	0.028	-0.242	-0.201	-0.002
36	B	904	ASN	0	-0.030	-0.022	5.996	0.302	0.302	0.000	0.000	0.000	0.000
37	B	905	ASP	-1	-0.863	-0.940	7.995	0.081	0.081	0.000	0.000	0.000	0.000
38	B	906	SER	0	-0.045	-0.031	11.680	-0.032	-0.032	0.000	0.000	0.000	0.000
39	B	907	GLN	0	-0.019	-0.011	6.643	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	908	GLN	0	0.056	0.030	9.782	0.019	0.019	0.000	0.000	0.000	0.000
41	B	909	ALA	0	-0.063	-0.031	11.868	0.014	0.014	0.000	0.000	0.000	0.000
42	B	910	GLU	-1	-0.810	-0.895	13.408	-0.243	-0.243	0.000	0.000	0.000	0.000
43	B	911	ALA	0	0.026	0.003	12.310	0.004	0.004	0.000	0.000	0.000	0.000
44	B	912	ARG	1	0.869	0.937	13.729	0.171	0.171	0.000	0.000	0.000	0.000
45	B	913	GLU	-1	-0.805	-0.888	17.382	-0.160	-0.160	0.000	0.000	0.000	0.000
46	B	914	LEU	0	-0.007	-0.001	15.476	0.014	0.014	0.000	0.000	0.000	0.000
47	B	915	LEU	0	-0.020	-0.010	15.969	0.013	0.013	0.000	0.000	0.000	0.000
48	B	916	GLU	-1	-0.986	-0.991	19.541	-0.111	-0.111	0.000	0.000	0.000	0.000
49	B	917	ARG	1	0.774	0.884	21.228	0.198	0.198	0.000	0.000	0.000	0.000
50	B	918	LEU	0	-0.100	-0.038	19.961	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:869:GLY)