FMO DATABASE

FMODB ID: 9GVZ2

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	OptHSide
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	-483057.782953
FMO2-HF: Nuclear repulsion	453390.234571
FMO2-HF: Total energy	-29667.548381
FMO2-MP2: Total energy	-29753.888889

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.
-238.107	-225.155	25.697	-17.575	-21.073	-0.195

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 : 0.877 / q_NPA : 0.926

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	-0.898	-0.962	3.462	-30.038	-28.262	-0.006	-0.710	-1.061	0.002
4	A	750	GLU	-1	-0.871	-0.938	2.033	-116.831	-111.785	13.505	-8.899	-9.652	-0.095
5	A	751	LEU	0	0.005	0.003	2.402	5.073	6.476	1.828	-0.655	-2.575	0.002
6	A	752	LEU	0	0.016	0.014	4.839	6.286	6.408	-0.001	-0.009	-0.112	0.000
7	A	753	LEU	0	0.036	0.035	7.281	3.838	3.838	0.000	0.000	0.000	0.000
8	A	754	PHE	0	0.011	-0.013	2.696	6.569	7.122	0.090	-0.144	-0.499	0.001
9	A	755	TRP	0	-0.008	-0.018	8.475	3.236	3.236	0.000	0.000	0.000	0.000
10	A	756	THR	0	0.027	0.019	11.058	2.861	2.861	0.000	0.000	0.000	0.000
11	A	757	TYR	0	-0.015	-0.015	11.405	2.154	2.154	0.000	0.000	0.000	0.000
12	A	758	ILE	0	-0.030	-0.009	9.829	1.599	1.599	0.000	0.000	0.000	0.000
13	A	759	GLN	0	0.009	-0.003	13.874	1.137	1.137	0.000	0.000	0.000	0.000
14	A	760	ALA	0	0.035	0.037	16.479	1.379	1.379	0.000	0.000	0.000	0.000
15	A	761	MET	0	-0.012	0.002	12.776	1.265	1.265	0.000	0.000	0.000	0.000
16	A	762	LEU	0	-0.027	-0.020	16.899	0.966	0.966	0.000	0.000	0.000	0.000
17	A	763	THR	0	-0.046	-0.024	19.866	0.987	0.987	0.000	0.000	0.000	0.000
18	A	764	ASN	0	-0.089	-0.055	21.234	1.248	1.248	0.000	0.000	0.000	0.000
19	A	765	LEU	0	-0.044	-0.022	19.929	0.526	0.526	0.000	0.000	0.000	0.000
20	A	766	GLU	-1	-0.792	-0.850	23.237	-12.210	-12.210	0.000	0.000	0.000	0.000
21	A	767	SER	0	-0.088	-0.075	21.670	-0.249	-0.249	0.000	0.000	0.000	0.000
22	A	768	LEU	0	-0.046	-0.017	17.499	0.110	0.110	0.000	0.000	0.000	0.000
23	A	769	SER	0	0.022	-0.011	18.932	-0.356	-0.356	0.000	0.000	0.000	0.000
24	A	770	LEU	0	0.046	0.009	12.165	-0.625	-0.625	0.000	0.000	0.000	0.000
25	A	771	ASP	-1	-0.833	-0.900	14.438	-18.786	-18.786	0.000	0.000	0.000	0.000
26	A	772	ARG	1	0.934	0.971	15.966	14.297	14.297	0.000	0.000	0.000	0.000
27	A	773	ILE	0	0.033	0.025	11.873	-0.419	-0.419	0.000	0.000	0.000	0.000
28	A	774	TYR	0	0.013	-0.003	8.471	0.145	0.145	0.000	0.000	0.000	0.000
29	A	775	ASN	0	-0.026	-0.018	11.860	-0.679	-0.679	0.000	0.000	0.000	0.000
30	A	776	MET	0	0.035	0.008	14.296	0.121	0.121	0.000	0.000	0.000	0.000
31	A	777	LEU	0	0.015	0.010	8.101	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	778	ARG	1	0.863	0.948	8.277	30.345	30.345	0.000	0.000	0.000	0.000
33	A	779	MET	0	-0.032	-0.004	11.185	0.523	0.523	0.000	0.000	0.000	0.000
34	A	780	PHE	0	-0.017	-0.016	13.251	1.015	1.015	0.000	0.000	0.000	0.000
35	A	781	VAL	0	-0.018	-0.012	8.065	0.414	0.414	0.000	0.000	0.000	0.000
36	A	782	VAL	0	-0.019	-0.003	6.763	0.072	0.072	0.000	0.000	0.000	0.000
37	A	783	THR	0	-0.054	-0.026	8.820	0.666	0.666	0.000	0.000	0.000	0.000
38	A	784	GLY	0	-0.022	0.008	11.646	2.245	2.245	0.000	0.000	0.000	0.000
39	A	785	PRO	0	-0.002	-0.030	12.542	-1.006	-1.006	0.000	0.000	0.000	0.000
40	A	786	ALA	0	-0.035	-0.012	8.897	0.364	0.364	0.000	0.000	0.000	0.000
41	A	787	LEU	0	-0.028	0.006	8.977	-1.376	-1.376	0.000	0.000	0.000	0.000
42	A	788	ALA	0	0.012	0.017	4.823	-2.488	-2.488	0.000	0.000	0.000	0.000
43	A	789	GLU	-1	-0.803	-0.914	4.082	-39.698	-39.484	-0.001	-0.050	-0.164	0.000
44	A	790	ILE	0	-0.061	-0.039	2.439	-30.279	-28.772	2.103	-1.569	-2.040	-0.022
45	A	791	ASP	-1	-0.849	-0.925	4.078	-28.776	-28.687	0.000	-0.018	-0.071	0.000
46	A	792	LEU	0	0.009	-0.005	6.789	-1.546	-1.546	0.000	0.000	0.000	0.000
47	A	793	GLN	0	-0.015	-0.009	9.482	0.771	0.771	0.000	0.000	0.000	0.000
48	A	794	GLU	-1	-0.784	-0.886	1.896	-121.548	-119.306	8.179	-5.521	-4.899	-0.083
49	A	795	LEU	0	0.014	0.012	6.609	1.406	1.406	0.000	0.000	0.000	0.000
50	A	796	GLN	0	-0.022	-0.017	7.757	3.894	3.894	0.000	0.000	0.000	0.000
51	A	797	GLY	0	0.009	0.000	9.932	2.009	2.009	0.000	0.000	0.000	0.000
52	A	798	TYR	0	-0.037	-0.034	7.137	3.343	3.343	0.000	0.000	0.000	0.000
53	A	799	LEU	0	0.011	0.000	9.279	2.425	2.425	0.000	0.000	0.000	0.000
54	A	800	GLN	0	0.023	0.005	12.323	1.860	1.860	0.000	0.000	0.000	0.000
55	A	801	LYS	1	0.815	0.885	11.311	21.979	21.979	0.000	0.000	0.000	0.000
56	A	802	LYS	1	0.922	0.970	10.811	25.661	25.661	0.000	0.000	0.000	0.000
57	A	803	VAL	0	-0.033	-0.014	14.538	1.235	1.235	0.000	0.000	0.000	0.000
58	A	804	ARG	1	0.871	0.944	13.948	20.498	20.498	0.000	0.000	0.000	0.000
59	A	805	ASP	-1	-0.860	-0.894	14.992	-18.233	-18.233	0.000	0.000	0.000	0.000
60	A	806	GLN	0	-0.057	-0.029	18.335	0.744	0.744	0.000	0.000	0.000	0.000
61	A	807	GLN	0	0.028	0.017	14.809	-0.945	-0.945	0.000	0.000	0.000	0.000
62	A	808	LEU	0	-0.035	-0.022	14.568	-0.252	-0.252	0.000	0.000	0.000	0.000
63	A	809	VAL	0	0.023	0.015	18.658	0.392	0.392	0.000	0.000	0.000	0.000
64	A	810	TYR	0	-0.014	-0.008	18.993	-0.267	-0.267	0.000	0.000	0.000	0.000
65	A	811	SER	0	-0.004	-0.012	21.158	0.466	0.466	0.000	0.000	0.000	0.000
66	A	812	ALA	0	0.010	-0.006	24.437	-0.124	-0.124	0.000	0.000	0.000	0.000
67	A	813	GLY	0	0.015	0.019	22.752	0.068	0.068	0.000	0.000	0.000	0.000
68	A	814	VAL	0	-0.061	-0.026	20.450	-0.730	-0.730	0.000	0.000	0.000	0.000
69	A	815	TYR	0	0.008	-0.008	15.515	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	816	ARG	1	0.920	0.952	19.376	13.030	13.030	0.000	0.000	0.000	0.000
71	A	817	LEU	0	0.001	0.015	18.589	-0.605	-0.605	0.000	0.000	0.000	0.000
72	A	818	PRO	0	-0.019	0.007	20.916	0.802	0.802	0.000	0.000	0.000	0.000

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