FMO DATABASE

FMODB ID: M362Z

Calculation Name: 4YII-A-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	74
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-487435.687989
FMO2-HF: Nuclear repulsion	457597.693098
FMO2-HF: Total energy	-29837.994892
FMO2-MP2: Total energy	-29924.900726

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:746:ACE )

Summations of interaction energy for fragment #1(A:746:ACE )

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.
-2.241	-0.859	-0.003	-0.619	-0.759	-0.001

Interaction energy analysis for fragmet #1(A:746:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.012

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	A	748	GLU	-1	-0.943	-0.970	3.824	0.626	1.874	-0.006	-0.541	-0.702	-0.001
4	A	749	GLU	-1	-0.895	-0.954	4.445	0.264	0.369	0.000	-0.011	-0.093	0.000
5	A	750	GLU	-1	-0.820	-0.906	3.900	-3.110	-3.081	0.003	-0.067	0.036	0.000
6	A	751	LEU	0	0.009	0.001	6.576	0.293	0.293	0.000	0.000	0.000	0.000
7	A	752	LEU	0	0.016	0.000	9.092	0.137	0.137	0.000	0.000	0.000	0.000
8	A	753	LEU	0	0.020	0.029	9.386	0.073	0.073	0.000	0.000	0.000	0.000
9	A	754	PHE	0	0.025	-0.005	9.312	0.087	0.087	0.000	0.000	0.000	0.000
10	A	755	TRP	0	-0.052	-0.030	12.722	0.040	0.040	0.000	0.000	0.000	0.000
11	A	756	THR	0	0.048	0.037	14.072	0.040	0.040	0.000	0.000	0.000	0.000
12	A	757	TYR	0	-0.007	-0.014	13.616	0.022	0.022	0.000	0.000	0.000	0.000
13	A	758	ILE	0	-0.024	-0.009	16.073	0.014	0.014	0.000	0.000	0.000	0.000
14	A	759	GLN	0	0.007	-0.005	18.420	0.012	0.012	0.000	0.000	0.000	0.000
15	A	760	ALA	0	0.042	0.039	19.984	0.013	0.013	0.000	0.000	0.000	0.000
16	A	761	MET	0	-0.022	-0.003	18.377	0.007	0.007	0.000	0.000	0.000	0.000
17	A	762	LEU	0	-0.029	-0.026	22.772	0.007	0.007	0.000	0.000	0.000	0.000
18	A	763	THR	0	-0.044	-0.011	24.263	0.008	0.008	0.000	0.000	0.000	0.000
19	A	764	ASN	0	-0.083	-0.058	24.711	0.011	0.011	0.000	0.000	0.000	0.000
20	A	765	LEU	0	-0.047	-0.024	25.291	0.003	0.003	0.000	0.000	0.000	0.000
21	A	766	GLU	-1	-0.842	-0.899	28.288	-0.060	-0.060	0.000	0.000	0.000	0.000
22	A	767	SER	0	-0.067	-0.034	28.075	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	768	LEU	0	-0.033	-0.016	23.812	0.001	0.001	0.000	0.000	0.000	0.000
24	A	769	SER	0	0.075	0.037	26.340	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	770	LEU	0	0.048	0.006	20.797	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	771	ASP	-1	-0.888	-0.936	22.454	-0.146	-0.146	0.000	0.000	0.000	0.000
27	A	772	ARG	1	0.926	0.956	23.422	0.079	0.079	0.000	0.000	0.000	0.000
28	A	773	ILE	0	0.039	0.026	18.900	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	774	TYR	0	0.030	0.007	17.209	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	775	ASN	0	-0.033	-0.025	18.697	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	776	MET	0	0.032	0.006	20.261	0.004	0.004	0.000	0.000	0.000	0.000
32	A	777	LEU	0	0.010	0.012	14.594	0.006	0.006	0.000	0.000	0.000	0.000
33	A	778	ARG	1	0.955	0.985	15.347	0.223	0.223	0.000	0.000	0.000	0.000
34	A	779	MET	0	-0.040	-0.009	16.771	0.010	0.010	0.000	0.000	0.000	0.000
35	A	780	PHE	0	-0.013	-0.006	17.267	0.017	0.017	0.000	0.000	0.000	0.000
36	A	781	VAL	0	-0.023	-0.011	11.013	0.020	0.020	0.000	0.000	0.000	0.000
37	A	782	VAL	0	-0.014	0.003	11.906	0.011	0.011	0.000	0.000	0.000	0.000
38	A	783	THR	0	-0.115	-0.064	12.931	0.023	0.023	0.000	0.000	0.000	0.000
39	A	784	GLY	0	0.017	0.024	14.398	0.032	0.032	0.000	0.000	0.000	0.000
40	A	785	PRO	0	-0.006	-0.032	13.521	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	786	ALA	0	-0.029	-0.009	9.132	0.045	0.045	0.000	0.000	0.000	0.000
42	A	787	LEU	0	-0.042	0.001	8.573	0.010	0.010	0.000	0.000	0.000	0.000
43	A	788	ALA	0	-0.007	0.008	7.477	-0.073	-0.073	0.000	0.000	0.000	0.000
44	A	789	GLU	-1	-0.875	-0.941	7.897	-0.346	-0.346	0.000	0.000	0.000	0.000
45	A	790	ILE	0	-0.085	-0.048	9.500	-0.157	-0.157	0.000	0.000	0.000	0.000
46	A	791	ASP	-1	-0.832	-0.920	12.264	-0.339	-0.339	0.000	0.000	0.000	0.000
47	A	792	LEU	0	0.002	-0.012	15.563	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	793	GLN	0	-0.007	-0.009	18.077	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	794	GLU	-1	-0.843	-0.919	10.923	-0.832	-0.832	0.000	0.000	0.000	0.000
50	A	795	LEU	0	-0.001	0.010	15.591	0.015	0.015	0.000	0.000	0.000	0.000
51	A	796	GLN	0	-0.036	-0.027	16.616	0.047	0.047	0.000	0.000	0.000	0.000
52	A	797	GLY	0	0.030	0.015	18.406	0.022	0.022	0.000	0.000	0.000	0.000
53	A	798	TYR	0	0.021	-0.006	13.655	0.034	0.034	0.000	0.000	0.000	0.000
54	A	799	LEU	0	0.001	-0.008	16.974	0.033	0.033	0.000	0.000	0.000	0.000
55	A	800	GLN	0	0.000	-0.005	20.004	0.015	0.015	0.000	0.000	0.000	0.000
56	A	801	LYS	1	0.811	0.893	16.890	0.203	0.203	0.000	0.000	0.000	0.000
57	A	802	LYS	1	0.933	0.982	16.039	0.228	0.228	0.000	0.000	0.000	0.000
58	A	803	VAL	0	-0.019	-0.006	21.043	0.017	0.017	0.000	0.000	0.000	0.000
59	A	804	ARG	1	0.889	0.952	21.064	0.181	0.181	0.000	0.000	0.000	0.000
60	A	805	ASP	-1	-0.843	-0.898	20.881	-0.131	-0.131	0.000	0.000	0.000	0.000
61	A	806	GLN	0	-0.059	-0.028	24.102	0.011	0.011	0.000	0.000	0.000	0.000
62	A	807	GLN	0	-0.016	-0.006	19.816	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	808	LEU	0	-0.048	-0.028	20.802	0.000	0.000	0.000	0.000	0.000	0.000
64	A	809	VAL	0	0.045	0.026	24.735	0.002	0.002	0.000	0.000	0.000	0.000
65	A	810	TYR	0	-0.009	-0.003	26.962	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	811	SER	0	0.000	-0.015	28.787	0.004	0.004	0.000	0.000	0.000	0.000
67	A	812	ALA	0	0.018	-0.001	32.216	0.000	0.000	0.000	0.000	0.000	0.000
68	A	813	GLY	0	0.007	0.016	31.272	0.001	0.001	0.000	0.000	0.000	0.000
69	A	814	VAL	0	-0.063	-0.025	28.387	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	815	TYR	0	-0.002	-0.013	24.050	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	816	ARG	1	0.936	0.958	26.642	0.073	0.073	0.000	0.000	0.000	0.000
72	A	817	LEU	0	-0.015	0.004	23.085	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	818	PRO	0	-0.025	0.002	26.094	0.004	0.004	0.000	0.000	0.000	0.000
74	A	819	NME	0	0.015	0.010	28.382	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:746:ACE )