FMO DATABASE

FMODB ID: 728ZK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-88806.861303
FMO2-HF: Nuclear repulsion	77485.684653
FMO2-HF: Total energy	-11321.17665
FMO2-MP2: Total energy	-11354.905238

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.
0.522	3.855	3.495	-2.297	-4.531	0.006

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 : 0.024 / q_NPA : -0.010

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	0.979	0.986	2.228	-1.212	0.796	1.377	-1.063	-2.322	0.003
4	A	23	ARG	1	0.998	1.009	2.303	1.644	2.714	2.112	-1.165	-2.017	0.003
5	A	24	GLN	0	0.034	0.027	4.057	-0.384	-0.129	0.006	-0.069	-0.192	0.000
6	A	25	PHE	0	0.031	0.017	6.660	0.359	0.359	0.000	0.000	0.000	0.000
7	A	26	HIS	0	0.041	0.016	7.445	0.150	0.150	0.000	0.000	0.000	0.000
8	A	27	GLN	0	-0.052	-0.026	8.063	0.026	0.026	0.000	0.000	0.000	0.000
9	A	28	GLU	-1	-0.939	-0.983	9.824	-0.531	-0.531	0.000	0.000	0.000	0.000
10	A	29	LEU	0	-0.044	-0.008	11.735	0.073	0.073	0.000	0.000	0.000	0.000
11	A	30	GLN	0	-0.030	0.002	12.202	0.097	0.097	0.000	0.000	0.000	0.000
12	A	31	SER	0	-0.028	-0.035	15.590	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	32	SER	0	-0.038	-0.002	18.651	0.009	0.009	0.000	0.000	0.000	0.000
14	A	33	ASN	0	0.005	-0.005	21.547	0.022	0.022	0.000	0.000	0.000	0.000
15	A	34	LEU	0	0.141	0.080	22.608	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	35	ARG	1	0.947	0.956	24.172	0.087	0.087	0.000	0.000	0.000	0.000
17	A	36	ALA	0	-0.011	-0.006	22.852	0.001	0.001	0.000	0.000	0.000	0.000
18	A	37	ASP	-1	-0.818	-0.916	20.113	-0.248	-0.248	0.000	0.000	0.000	0.000
19	A	38	VAL	0	-0.019	-0.017	22.688	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	39	ARG	1	0.895	0.940	26.107	0.133	0.133	0.000	0.000	0.000	0.000
21	A	40	ARG	1	0.919	0.975	17.659	0.333	0.333	0.000	0.000	0.000	0.000
22	A	41	SER	0	-0.057	-0.010	24.516	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	42	SER	0	-0.001	0.001	25.913	0.007	0.007	0.000	0.000	0.000	0.000
24	A	43	VAL	0	0.001	-0.009	27.883	0.013	0.013	0.000	0.000	0.000	0.000
25	A	44	ILE	0	-0.007	0.007	26.858	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	45	VAL	0	-0.007	-0.002	27.676	0.010	0.010	0.000	0.000	0.000	0.000
27	A	46	ALA	0	0.001	0.004	28.515	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	47	ASN	0	0.017	0.010	30.971	0.002	0.002	0.000	0.000	0.000	0.000

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