FMO DATABASE

FMODB ID: 6Y2YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-122477.719587
FMO2-HF: Nuclear repulsion	107983.933814
FMO2-HF: Total energy	-14493.785773
FMO2-MP2: Total energy	-14529.967047

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.
-2.765	0.168	-0.019	-1.794	-1.119	0.009

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 : 0.041 / q_NPA : 0.024

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	-0.009	-0.009	3.730	-3.510	-0.577	-0.019	-1.794	-1.119	0.009
4	A	4	ALA	0	-0.003	0.008	5.535	0.522	0.522	0.000	0.000	0.000	0.000
5	A	33	CYS	0	0.026	0.027	7.185	0.065	0.065	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.020	0.009	6.305	0.355	0.355	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.051	0.003	11.981	-0.115	-0.115	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.799	0.869	10.680	-0.255	-0.255	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.026	0.042	17.589	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.005	-0.014	21.219	0.026	0.026	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.009	-0.016	20.847	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.097	-0.038	13.940	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.053	0.024	13.681	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.026	0.009	15.547	-0.066	-0.066	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.024	0.011	13.571	0.038	0.038	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.791	-0.841	11.558	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.944	0.952	13.988	0.296	0.296	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.911	0.928	16.087	0.051	0.051	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.001	-0.003	14.925	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.038	0.025	18.568	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.033	-0.016	20.383	0.019	0.019	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.063	0.025	20.042	0.014	0.014	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.025	0.005	19.017	0.000	0.000	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.040	0.020	21.685	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.034	0.028	24.217	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.898	0.953	24.156	-0.119	-0.119	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.016	0.007	23.798	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.040	-0.030	19.031	0.021	0.021	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.009	0.006	19.052	-0.032	-0.032	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.059	0.010	13.479	0.038	0.038	0.000	0.000	0.000	0.000

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