FMO DATABASE

FMODB ID: 85N7Y

Calculation Name: 3S90-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3S90

Chain ID: C

ChEMBL ID:

UniProt ID: P26039

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	27
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-76448.481906
FMO2-HF: Nuclear repulsion	66481.519025
FMO2-HF: Total energy	-9966.962881
FMO2-MP2: Total energy	-9996.797518

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(C:1520:THR)

Summations of interaction energy for fragment #1(C:1520:THR)

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.
-13.882	-10.142	7.162	-4.101	-6.801	-0.001

Interaction energy analysis for fragmet #1(C:1520:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.006

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	C	1522	LYS	1	0.992	1.000	2.641	-8.492	-4.370	0.665	-2.054	-2.733	0.006
4	C	1523	ARG	1	0.974	0.968	1.716	-3.680	-4.787	6.477	-1.983	-3.387	-0.007
5	C	1524	GLN	0	0.046	0.028	3.522	-1.388	-0.818	0.021	-0.052	-0.540	0.000
6	C	1525	PHE	0	0.026	0.022	5.085	0.218	0.373	-0.001	-0.012	-0.141	0.000
7	C	1526	VAL	0	0.005	-0.008	6.522	-0.093	-0.093	0.000	0.000	0.000	0.000
8	C	1527	GLN	0	-0.017	-0.007	7.486	0.032	0.032	0.000	0.000	0.000	0.000
9	C	1528	SER	0	0.017	0.005	9.172	-0.041	-0.041	0.000	0.000	0.000	0.000
10	C	1529	ALA	0	-0.003	0.005	11.122	0.004	0.004	0.000	0.000	0.000	0.000
11	C	1530	LYS	1	0.939	0.960	11.866	-0.229	-0.229	0.000	0.000	0.000	0.000
12	C	1531	GLU	-1	-0.875	-0.934	13.233	-0.127	-0.127	0.000	0.000	0.000	0.000
13	C	1532	VAL	0	0.022	0.023	15.084	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	1533	ALA	0	-0.015	0.004	16.856	-0.004	-0.004	0.000	0.000	0.000	0.000
15	C	1534	ASN	0	-0.011	-0.012	16.400	0.014	0.014	0.000	0.000	0.000	0.000
16	C	1535	SER	0	-0.015	-0.007	19.168	-0.004	-0.004	0.000	0.000	0.000	0.000
17	C	1536	THR	0	0.019	0.000	21.139	-0.004	-0.004	0.000	0.000	0.000	0.000
18	C	1537	ALA	0	-0.016	-0.006	22.420	-0.002	-0.002	0.000	0.000	0.000	0.000
19	C	1538	ASN	0	-0.021	-0.017	23.680	-0.001	-0.001	0.000	0.000	0.000	0.000
20	C	1539	LEU	0	0.035	0.040	25.353	-0.004	-0.004	0.000	0.000	0.000	0.000
21	C	1540	VAL	0	0.015	-0.006	26.989	-0.001	-0.001	0.000	0.000	0.000	0.000
22	C	1541	LYS	1	0.904	0.952	27.721	-0.022	-0.022	0.000	0.000	0.000	0.000
23	C	1542	THR	0	-0.017	-0.028	29.039	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	1543	ILE	0	-0.031	-0.009	30.525	-0.001	-0.001	0.000	0.000	0.000	0.000
25	C	1544	LYS	1	0.901	0.947	30.394	-0.048	-0.048	0.000	0.000	0.000	0.000
26	C	1545	ALA	0	-0.016	0.004	34.234	0.001	0.001	0.000	0.000	0.000	0.000
27	C	1546	LEU	0	0.008	0.020	35.764	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:1520:THR)