FMO DATABASE

FMODB ID: 762YK

Calculation Name: 2P58-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: B

ChEMBL ID:

UniProt ID: O68690

Base Structure: X-ray

Registration Date: 2023-09-21

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	38
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-160971.25788
FMO2-HF: Nuclear repulsion	145408.466958
FMO2-HF: Total energy	-15562.790922
FMO2-MP2: Total energy	-15607.629186

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:50:LEU)

Summations of interaction energy for fragment #1(B:50: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.
-9.25	0.449	6.057	-4.233	-11.524	-0.012

Interaction energy analysis for fragmet #1(B:50:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.011

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	B	52	ALA	0	0.043	0.017	3.381	-1.506	0.947	0.051	-1.272	-1.232	0.004
4	B	53	ASP	-1	-0.849	-0.932	5.847	-0.702	-0.702	0.000	0.000	0.000	0.000
5	B	54	LEU	0	-0.017	0.000	2.337	-1.109	0.004	1.646	-0.453	-2.306	-0.001
6	B	55	GLN	0	0.029	0.004	2.983	-0.824	0.887	0.154	-0.564	-1.301	-0.004
7	B	56	HIS	0	0.007	-0.009	4.522	0.163	0.283	0.000	-0.018	-0.102	0.000
8	B	57	SER	0	0.004	0.008	6.685	0.162	0.162	0.000	0.000	0.000	0.000
9	B	58	ILE	0	0.034	0.015	2.626	-0.254	-0.127	1.169	-0.184	-1.112	-0.001
10	B	59	ASN	0	-0.050	-0.022	6.812	0.106	0.106	0.000	0.000	0.000	0.000
11	B	60	LYS	1	0.921	0.959	9.156	0.162	0.162	0.000	0.000	0.000	0.000
12	B	61	TRP	0	0.037	0.013	5.720	0.060	0.060	0.000	0.000	0.000	0.000
13	B	62	SER	0	-0.046	-0.030	11.410	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	63	VAL	0	0.013	-0.003	13.777	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	64	ILE	0	-0.035	-0.014	12.288	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	65	TYR	0	0.002	-0.004	11.330	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	66	ASN	0	-0.034	0.002	16.565	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	67	ILE	0	-0.001	0.018	12.592	0.012	0.012	0.000	0.000	0.000	0.000
19	B	68	ASN	0	0.072	0.033	15.479	0.009	0.009	0.000	0.000	0.000	0.000
20	B	69	SER	0	0.081	0.020	12.526	0.036	0.036	0.000	0.000	0.000	0.000
21	B	70	THR	0	0.003	0.010	11.787	0.056	0.056	0.000	0.000	0.000	0.000
22	B	71	ILE	0	0.026	0.029	12.375	0.053	0.053	0.000	0.000	0.000	0.000
23	B	72	VAL	0	0.038	0.027	8.249	0.065	0.065	0.000	0.000	0.000	0.000
24	B	73	ARG	1	0.924	0.963	7.946	-0.233	-0.233	0.000	0.000	0.000	0.000
25	B	74	SER	0	-0.032	-0.020	7.693	0.132	0.132	0.000	0.000	0.000	0.000
26	B	75	MET	0	0.012	0.001	8.367	0.058	0.058	0.000	0.000	0.000	0.000
27	B	76	LYS	1	0.874	0.931	2.854	-2.558	-1.640	0.321	-0.248	-0.992	0.002
28	B	77	ASP	-1	-0.863	-0.941	3.901	1.100	1.412	0.002	-0.111	-0.203	-0.001
29	B	78	LEU	0	-0.014	-0.004	6.192	0.114	0.114	0.000	0.000	0.000	0.000
30	B	79	MET	0	-0.006	0.006	3.721	-0.431	-0.011	0.006	-0.086	-0.341	0.000
31	B	80	GLN	0	-0.016	-0.007	2.419	-1.820	0.204	1.963	-1.127	-2.860	-0.010
32	B	81	GLY	0	0.068	0.035	3.766	-0.185	-0.079	0.006	-0.015	-0.097	0.000
33	B	82	ILE	0	-0.065	-0.021	6.861	-0.237	-0.237	0.000	0.000	0.000	0.000
34	B	83	LEU	0	0.027	0.007	2.592	-0.576	-0.181	0.739	-0.155	-0.978	-0.001
35	B	84	GLN	0	-0.033	-0.029	6.221	0.012	0.012	0.000	0.000	0.000	0.000
36	B	85	LYS	1	0.857	0.925	8.245	-0.963	-0.963	0.000	0.000	0.000	0.000
37	B	86	PHE	0	-0.033	-0.004	9.476	-0.128	-0.128	0.000	0.000	0.000	0.000
38	B	87	PRO	0	-0.006	0.010	11.585	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:50:LEU)