FMO DATABASE

FMODB ID: 2NQNR

Calculation Name: 3HJ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HJ2

Chain ID: A

ChEMBL ID:

UniProt ID: P59665

Base Structure: X-ray

Registration Date: 2023-09-23

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	30
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-122477.99497
FMO2-HF: Nuclear repulsion	107984.236349
FMO2-HF: Total energy	-14493.758621
FMO2-MP2: Total energy	-14529.948203

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:1:CYS)

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

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.
-1.464	0.079	-0.021	-0.866	-0.656	0.004

Interaction energy analysis for fragmet #1(A:1:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.020

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	3	GLY	0	-0.005	-0.006	3.825	-0.535	1.008	-0.021	-0.866	-0.656	0.004
4	A	4	ALA	0	0.000	0.011	5.994	0.074	0.074	0.000	0.000	0.000	0.000
5	A	33	CYS	0	0.029	0.030	7.597	-0.044	-0.044	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.020	0.003	6.068	0.208	0.208	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.033	0.013	11.981	-0.100	-0.100	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.783	0.855	10.602	-0.983	-0.983	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.033	0.047	17.583	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.005	-0.015	21.208	0.014	0.014	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.006	-0.015	20.837	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.087	-0.034	13.852	-0.068	-0.068	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.053	0.029	13.535	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.032	0.007	15.948	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.015	0.009	14.160	0.054	0.054	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.791	-0.846	11.439	0.964	0.964	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.947	0.955	14.571	-0.335	-0.335	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.914	0.931	16.078	-0.259	-0.259	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.002	-0.003	15.043	-0.057	-0.057	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.031	0.023	18.581	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.031	-0.017	20.382	0.020	0.020	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.060	0.025	20.049	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.013	-0.002	19.047	0.013	0.013	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.024	0.006	21.694	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.038	0.029	24.227	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.912	0.963	24.201	-0.266	-0.266	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.018	0.009	23.812	0.017	0.017	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.037	-0.021	18.987	0.010	0.010	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.014	0.000	19.008	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.051	0.007	13.737	0.050	0.050	0.000	0.000	0.000	0.000

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