FMO DATABASE

FMODB ID: MNVRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-159996.189932
FMO2-HF: Nuclear repulsion	144433.43655
FMO2-HF: Total energy	-15562.753382
FMO2-MP2: Total energy	-15607.581974

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.
-8.264	0.945	5.838	-4.063	-10.983	-0.009

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 : 0.021 / 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

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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	0.064	0.021	3.484	-1.685	0.645	0.028	-1.188	-1.170	0.005
4	B	53	ASP	-1	-0.864	-0.939	5.886	-0.789	-0.789	0.000	0.000	0.000	0.000
5	B	54	LEU	0	-0.026	-0.001	2.416	-1.014	0.095	1.573	-0.459	-2.223	-0.001
6	B	55	GLN	0	0.022	-0.003	3.016	-0.646	1.003	0.149	-0.559	-1.239	-0.004
7	B	56	HIS	0	0.012	0.002	4.619	0.286	0.406	-0.001	-0.016	-0.103	0.000
8	B	57	SER	0	-0.014	-0.006	7.095	0.220	0.220	0.000	0.000	0.000	0.000
9	B	58	ILE	0	0.026	0.009	2.600	-0.243	-0.006	0.997	-0.171	-1.063	-0.001
10	B	59	ASN	0	-0.032	-0.011	6.847	0.165	0.165	0.000	0.000	0.000	0.000
11	B	60	LYS	1	0.923	0.962	9.143	0.243	0.243	0.000	0.000	0.000	0.000
12	B	61	TRP	0	0.036	0.013	6.117	0.068	0.068	0.000	0.000	0.000	0.000
13	B	62	SER	0	-0.056	-0.031	11.723	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	63	VAL	0	0.039	0.007	14.123	0.001	0.001	0.000	0.000	0.000	0.000
15	B	64	ILE	0	-0.047	-0.013	12.734	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	65	TYR	0	-0.006	-0.009	11.767	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	66	ASN	0	-0.025	0.006	16.778	0.000	0.000	0.000	0.000	0.000	0.000
18	B	67	ILE	0	-0.002	0.015	12.774	0.015	0.015	0.000	0.000	0.000	0.000
19	B	68	ASN	0	0.069	0.029	15.693	0.009	0.009	0.000	0.000	0.000	0.000
20	B	69	SER	0	0.075	0.011	12.931	0.035	0.035	0.000	0.000	0.000	0.000
21	B	70	THR	0	-0.010	-0.001	12.240	0.060	0.060	0.000	0.000	0.000	0.000
22	B	71	ILE	0	0.030	0.029	12.872	0.055	0.055	0.000	0.000	0.000	0.000
23	B	72	VAL	0	0.039	0.025	8.367	0.067	0.067	0.000	0.000	0.000	0.000
24	B	73	ARG	1	0.946	0.972	8.295	-0.234	-0.234	0.000	0.000	0.000	0.000
25	B	74	SER	0	-0.014	0.001	8.166	0.136	0.136	0.000	0.000	0.000	0.000
26	B	75	MET	0	0.014	0.001	8.712	0.057	0.057	0.000	0.000	0.000	0.000
27	B	76	LYS	1	0.861	0.924	2.652	-3.172	-2.272	0.498	-0.292	-1.107	0.002
28	B	77	ASP	-1	-0.902	-0.964	4.269	1.403	1.556	-0.001	-0.032	-0.120	0.000
29	B	78	LEU	0	-0.021	-0.005	6.521	0.083	0.083	0.000	0.000	0.000	0.000
30	B	79	MET	0	-0.008	0.002	4.064	-0.362	-0.030	0.003	-0.060	-0.274	0.000
31	B	80	GLN	0	0.017	0.006	2.294	-1.273	0.498	2.199	-1.141	-2.829	-0.009
32	B	81	GLY	0	0.053	0.024	3.823	-0.109	0.005	0.003	-0.013	-0.103	0.000
33	B	82	ILE	0	-0.075	-0.047	7.195	-0.163	-0.163	0.000	0.000	0.000	0.000
34	B	83	LEU	0	0.014	0.001	2.706	-0.621	-0.127	0.390	-0.132	-0.752	-0.001
35	B	84	GLN	0	-0.035	-0.021	5.998	0.106	0.106	0.000	0.000	0.000	0.000
36	B	85	LYS	1	0.905	0.970	8.015	-0.851	-0.851	0.000	0.000	0.000	0.000
37	B	86	PHE	0	-0.054	-0.009	9.477	-0.123	-0.123	0.000	0.000	0.000	0.000
38	B	87	PRO	0	0.016	0.018	11.739	0.022	0.022	0.000	0.000	0.000	0.000

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