FMO DATABASE

FMODB ID: 6NJRZ

Calculation Name: 5CUL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CUL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I337

Base Structure: X-ray

Registration Date: 2023-09-20

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	28
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-88693.339695
FMO2-HF: Nuclear repulsion	77371.788574
FMO2-HF: Total energy	-11321.551121
FMO2-MP2: Total energy	-11355.198325

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:20:SER)

Summations of interaction energy for fragment #1(A:20:SER)

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.
-5.314	-1.651	0.903	-1.774	-2.792	0.004

Interaction energy analysis for fragmet #1(A:20:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.016

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	22	ARG	1	0.989	0.993	3.013	-4.152	-2.094	0.038	-0.889	-1.207	0.001
4	A	23	ARG	1	0.938	0.983	2.623	-0.624	0.792	0.864	-0.845	-1.435	0.003
5	A	24	GLN	0	-0.040	-0.016	4.261	-0.461	-0.272	0.001	-0.040	-0.150	0.000
6	A	25	PHE	0	0.060	0.024	6.839	0.105	0.105	0.000	0.000	0.000	0.000
7	A	26	HIS	0	0.032	0.016	7.452	0.004	0.004	0.000	0.000	0.000	0.000
8	A	27	GLN	0	0.001	-0.004	7.856	-0.194	-0.194	0.000	0.000	0.000	0.000
9	A	28	GLU	-1	-0.877	-0.928	9.727	0.141	0.141	0.000	0.000	0.000	0.000
10	A	29	LEU	0	-0.003	0.006	12.010	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	30	GLN	0	-0.084	-0.035	12.213	-0.032	-0.032	0.000	0.000	0.000	0.000
12	A	31	SER	0	-0.011	-0.018	15.369	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	32	SER	0	-0.023	-0.009	18.343	0.009	0.009	0.000	0.000	0.000	0.000
14	A	33	ASN	0	0.022	-0.001	21.138	0.002	0.002	0.000	0.000	0.000	0.000
15	A	34	LEU	0	0.116	0.070	23.187	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	35	ARG	1	0.960	0.969	24.131	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	36	ALA	0	-0.027	-0.019	23.073	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	37	ASP	-1	-0.781	-0.883	20.089	0.061	0.061	0.000	0.000	0.000	0.000
19	A	38	VAL	0	-0.014	-0.002	22.870	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	39	ARG	1	0.907	0.949	26.331	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	40	ARG	1	0.852	0.929	16.984	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	41	SER	0	-0.051	-0.020	24.269	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	42	SER	0	-0.018	-0.015	25.663	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	43	VAL	0	-0.002	0.001	27.861	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	44	ILE	0	-0.009	-0.003	26.989	0.003	0.003	0.000	0.000	0.000	0.000
26	A	45	VAL	0	-0.001	0.006	27.402	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	46	ALA	0	0.007	0.001	28.531	0.005	0.005	0.000	0.000	0.000	0.000
28	A	47	ASN	0	0.006	0.010	30.969	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:20:SER)