FMO DATABASE

FMODB ID: M314Z

Calculation Name: 4YII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YII

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UJX6

Base Structure: X-ray

Registration Date: 2023-06-19

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-485448.402181
FMO2-HF: Nuclear repulsion	455780.682771
FMO2-HF: Total energy	-29667.71941
FMO2-MP2: Total energy	-29754.067251

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:747:LYS)

Summations of interaction energy for fragment #1(A:747:LYS)

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.
-252.61	-250.87	45.433	-22.2	-24.972	-0.243

Interaction energy analysis for fragmet #1(A:747:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.887

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	749	GLU	-1	-0.878	-0.954	3.562	-30.263	-28.755	-0.002	-0.599	-0.907	0.001
4	A	750	GLU	-1	-0.866	-0.922	1.806	-124.452	-123.457	21.652	-10.962	-11.685	-0.108
5	A	751	LEU	0	0.013	0.013	2.573	4.494	6.244	0.999	-0.523	-2.225	0.000
6	A	752	LEU	0	0.023	0.031	4.818	6.384	6.516	-0.001	-0.011	-0.120	0.000
7	A	753	LEU	0	0.039	0.039	7.343	3.784	3.784	0.000	0.000	0.000	0.000
8	A	754	PHE	0	0.013	-0.016	2.634	6.498	7.224	0.350	-0.226	-0.849	0.000
9	A	755	TRP	0	-0.002	-0.008	8.354	3.232	3.232	0.000	0.000	0.000	0.000
10	A	756	THR	0	0.004	-0.005	10.598	3.069	3.069	0.000	0.000	0.000	0.000
11	A	757	TYR	0	-0.022	-0.031	11.090	2.410	2.410	0.000	0.000	0.000	0.000
12	A	758	ILE	0	-0.031	-0.009	9.908	1.725	1.725	0.000	0.000	0.000	0.000
13	A	759	GLN	0	0.009	0.004	13.782	1.174	1.174	0.000	0.000	0.000	0.000
14	A	760	ALA	0	0.017	0.028	16.314	1.411	1.411	0.000	0.000	0.000	0.000
15	A	761	MET	0	-0.014	-0.005	12.784	1.378	1.378	0.000	0.000	0.000	0.000
16	A	762	LEU	0	-0.009	-0.004	16.837	1.041	1.041	0.000	0.000	0.000	0.000
17	A	763	THR	0	-0.057	-0.045	19.681	1.033	1.033	0.000	0.000	0.000	0.000
18	A	764	ASN	0	-0.083	-0.048	21.232	1.293	1.293	0.000	0.000	0.000	0.000
19	A	765	LEU	0	-0.043	-0.018	19.525	0.442	0.442	0.000	0.000	0.000	0.000
20	A	766	GLU	-1	-0.791	-0.839	23.072	-12.475	-12.475	0.000	0.000	0.000	0.000
21	A	767	SER	0	-0.069	-0.073	21.106	-0.382	-0.382	0.000	0.000	0.000	0.000
22	A	768	LEU	0	-0.031	-0.017	16.671	0.141	0.141	0.000	0.000	0.000	0.000
23	A	769	SER	0	0.017	-0.024	18.558	-0.146	-0.146	0.000	0.000	0.000	0.000
24	A	770	LEU	0	0.013	0.003	11.897	-0.595	-0.595	0.000	0.000	0.000	0.000
25	A	771	ASP	-1	-0.794	-0.876	13.820	-18.864	-18.864	0.000	0.000	0.000	0.000
26	A	772	ARG	1	0.922	0.971	15.454	14.459	14.459	0.000	0.000	0.000	0.000
27	A	773	ILE	0	0.032	0.018	11.352	-0.363	-0.363	0.000	0.000	0.000	0.000
28	A	774	TYR	0	-0.010	-0.010	8.087	0.598	0.598	0.000	0.000	0.000	0.000
29	A	775	ASN	0	-0.040	-0.019	11.686	-0.761	-0.761	0.000	0.000	0.000	0.000
30	A	776	MET	0	0.037	0.014	14.115	-0.103	-0.103	0.000	0.000	0.000	0.000
31	A	777	LEU	0	0.006	0.003	7.807	-0.122	-0.122	0.000	0.000	0.000	0.000
32	A	778	ARG	1	0.837	0.916	8.008	31.016	31.016	0.000	0.000	0.000	0.000
33	A	779	MET	0	-0.021	-0.004	10.929	0.249	0.249	0.000	0.000	0.000	0.000
34	A	780	PHE	0	0.010	-0.005	12.906	0.770	0.770	0.000	0.000	0.000	0.000
35	A	781	VAL	0	-0.031	-0.010	7.651	0.673	0.673	0.000	0.000	0.000	0.000
36	A	782	VAL	0	-0.029	0.009	6.533	-1.135	-1.135	0.000	0.000	0.000	0.000
37	A	783	THR	0	-0.034	-0.031	8.670	1.195	1.195	0.000	0.000	0.000	0.000
38	A	784	GLY	0	-0.007	0.017	11.616	2.290	2.290	0.000	0.000	0.000	0.000
39	A	785	PRO	0	-0.028	-0.049	11.914	-1.555	-1.555	0.000	0.000	0.000	0.000
40	A	786	ALA	0	-0.020	0.004	8.759	0.667	0.667	0.000	0.000	0.000	0.000
41	A	787	LEU	0	-0.028	-0.004	8.578	-1.776	-1.776	0.000	0.000	0.000	0.000
42	A	788	ALA	0	0.004	0.025	4.264	-2.437	-2.335	-0.001	-0.008	-0.093	0.000
43	A	789	GLU	-1	-0.767	-0.889	4.335	-41.347	-41.062	-0.001	-0.111	-0.173	0.000
44	A	790	ILE	0	-0.029	-0.018	2.021	-36.795	-37.574	6.168	-2.542	-2.847	-0.036
45	A	791	ASP	-1	-0.789	-0.891	3.874	-24.764	-24.648	0.002	-0.027	-0.091	0.000
46	A	792	LEU	0	0.006	-0.002	6.816	-0.959	-0.959	0.000	0.000	0.000	0.000
47	A	793	GLN	0	-0.055	-0.036	9.387	1.983	1.983	0.000	0.000	0.000	0.000
48	A	794	GLU	-1	-0.792	-0.894	1.739	-126.173	-129.268	16.267	-7.191	-5.982	-0.100
49	A	795	LEU	0	0.001	0.009	6.435	1.954	1.954	0.000	0.000	0.000	0.000
50	A	796	GLN	0	0.011	-0.001	7.684	3.942	3.942	0.000	0.000	0.000	0.000
51	A	797	GLY	0	0.003	0.001	9.842	2.241	2.241	0.000	0.000	0.000	0.000
52	A	798	TYR	0	-0.055	-0.044	6.970	3.422	3.422	0.000	0.000	0.000	0.000
53	A	799	LEU	0	0.026	0.006	9.075	2.563	2.563	0.000	0.000	0.000	0.000
54	A	800	GLN	0	0.025	0.006	12.198	2.056	2.056	0.000	0.000	0.000	0.000
55	A	801	LYS	1	0.806	0.887	10.974	22.140	22.140	0.000	0.000	0.000	0.000
56	A	802	LYS	1	0.911	0.963	10.942	25.683	25.683	0.000	0.000	0.000	0.000
57	A	803	VAL	0	-0.030	-0.008	14.275	1.205	1.205	0.000	0.000	0.000	0.000
58	A	804	ARG	1	0.869	0.935	13.760	20.201	20.201	0.000	0.000	0.000	0.000
59	A	805	ASP	-1	-0.864	-0.902	14.390	-18.639	-18.639	0.000	0.000	0.000	0.000
60	A	806	GLN	0	-0.054	-0.030	17.810	0.800	0.800	0.000	0.000	0.000	0.000
61	A	807	GLN	0	0.026	0.020	14.759	-0.896	-0.896	0.000	0.000	0.000	0.000
62	A	808	LEU	0	-0.048	-0.020	14.517	-0.372	-0.372	0.000	0.000	0.000	0.000
63	A	809	VAL	0	0.028	0.015	18.515	0.526	0.526	0.000	0.000	0.000	0.000
64	A	810	TYR	0	-0.026	-0.020	18.921	-0.456	-0.456	0.000	0.000	0.000	0.000
65	A	811	SER	0	0.002	-0.007	21.230	0.464	0.464	0.000	0.000	0.000	0.000
66	A	812	ALA	0	0.008	-0.006	24.445	-0.152	-0.152	0.000	0.000	0.000	0.000
67	A	813	GLY	0	0.032	0.030	23.040	0.106	0.106	0.000	0.000	0.000	0.000
68	A	814	VAL	0	-0.060	-0.021	20.302	-0.781	-0.781	0.000	0.000	0.000	0.000
69	A	815	TYR	0	0.027	0.001	15.437	0.104	0.104	0.000	0.000	0.000	0.000
70	A	816	ARG	1	0.870	0.922	18.992	13.124	13.124	0.000	0.000	0.000	0.000
71	A	817	LEU	0	0.035	0.022	18.722	-0.626	-0.626	0.000	0.000	0.000	0.000
72	A	818	PRO	0	-0.032	0.000	20.532	0.839	0.839	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:747:LYS)