FMO DATABASE

FMODB ID: QYKMY

Calculation Name: 5KTB-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KTB

Chain ID: C

ChEMBL ID:

UniProt ID: P25651

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:

Apendix: None

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	42
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140285.839721
FMO2-HF: Nuclear repulsion	123508.931351
FMO2-HF: Total energy	-16776.908369
FMO2-MP2: Total energy	-16827.012542

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:222:LYS)

Summations of interaction energy for fragment #1(C:222:LYS)

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.
-3.648	-2.121	-0.009	-0.691	-0.827	0.001

Interaction energy analysis for fragmet #1(C:222:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.020 / q_NPA : 0.996

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	224	ARG	1	0.910	0.950	3.883	25.682	27.209	-0.009	-0.691	-0.827	0.001
4	C	225	PHE	0	0.058	0.011	6.324	-0.520	-0.520	0.000	0.000	0.000	0.000
5	C	226	LEU	0	0.093	0.062	9.631	1.127	1.127	0.000	0.000	0.000	0.000
6	C	227	PRO	0	0.046	0.023	10.122	-1.827	-1.827	0.000	0.000	0.000	0.000
7	C	228	GLN	0	0.024	0.008	8.543	0.045	0.045	0.000	0.000	0.000	0.000
8	C	229	SER	0	0.015	0.008	12.021	0.902	0.902	0.000	0.000	0.000	0.000
9	C	230	VAL	0	0.015	-0.005	15.503	-0.169	-0.169	0.000	0.000	0.000	0.000
10	C	231	LEU	0	0.019	-0.002	18.226	0.288	0.288	0.000	0.000	0.000	0.000
11	C	232	ILE	0	0.017	0.012	15.853	0.242	0.242	0.000	0.000	0.000	0.000
12	C	233	LYS	1	0.964	0.993	17.808	14.190	14.190	0.000	0.000	0.000	0.000
13	C	234	ARG	1	0.886	0.916	20.626	10.574	10.574	0.000	0.000	0.000	0.000
14	C	235	GLU	-1	-0.961	-0.971	21.345	-11.716	-11.716	0.000	0.000	0.000	0.000
15	C	236	ASP	-1	-0.905	-0.935	21.689	-11.915	-11.915	0.000	0.000	0.000	0.000
16	C	237	GLU	-1	-0.977	-0.986	23.658	-10.806	-10.806	0.000	0.000	0.000	0.000
17	C	238	ILE	0	-0.081	-0.037	26.643	0.412	0.412	0.000	0.000	0.000	0.000
18	C	239	ALA	0	0.063	0.049	28.681	-0.186	-0.186	0.000	0.000	0.000	0.000
19	C	240	PHE	0	-0.040	-0.038	26.578	0.278	0.278	0.000	0.000	0.000	0.000
20	C	241	ASP	-1	-0.879	-0.930	30.170	-8.879	-8.879	0.000	0.000	0.000	0.000
21	C	242	ASP	-1	-0.914	-0.954	33.065	-7.936	-7.936	0.000	0.000	0.000	0.000
22	C	243	PHE	0	-0.127	-0.066	35.377	0.300	0.300	0.000	0.000	0.000	0.000
23	C	244	HIS	0	-0.009	0.001	33.352	-0.025	-0.025	0.000	0.000	0.000	0.000
24	C	245	LEU	0	-0.040	-0.024	38.126	0.224	0.224	0.000	0.000	0.000	0.000
25	C	246	ASP	-1	-0.791	-0.874	39.929	-6.781	-6.781	0.000	0.000	0.000	0.000
26	C	247	ALA	0	0.047	0.010	39.677	0.098	0.098	0.000	0.000	0.000	0.000
27	C	248	ARG	1	0.869	0.913	41.733	6.694	6.694	0.000	0.000	0.000	0.000
28	C	249	LYS	1	0.811	0.888	45.192	6.102	6.102	0.000	0.000	0.000	0.000
29	C	250	VAL	0	0.029	0.016	42.339	0.105	0.105	0.000	0.000	0.000	0.000
30	C	251	LEU	0	-0.018	-0.025	42.491	0.065	0.065	0.000	0.000	0.000	0.000
31	C	252	ASN	0	-0.040	-0.001	46.172	0.146	0.146	0.000	0.000	0.000	0.000
32	C	253	ASP	-1	-0.777	-0.877	48.244	-5.893	-5.893	0.000	0.000	0.000	0.000
33	C	254	LEU	0	-0.066	-0.034	44.299	0.074	0.074	0.000	0.000	0.000	0.000
34	C	255	SER	0	-0.033	-0.010	49.007	0.028	0.028	0.000	0.000	0.000	0.000
35	C	256	ALA	0	-0.058	-0.027	52.224	0.121	0.121	0.000	0.000	0.000	0.000
36	C	257	THR	0	-0.018	-0.008	54.606	0.003	0.003	0.000	0.000	0.000	0.000
37	C	258	SER	0	-0.005	-0.013	57.978	0.022	0.022	0.000	0.000	0.000	0.000
38	C	259	GLU	-1	-0.907	-0.933	59.622	-4.930	-4.930	0.000	0.000	0.000	0.000
39	C	260	ASN	0	0.010	-0.002	62.424	0.048	0.048	0.000	0.000	0.000	0.000
40	C	261	PRO	0	0.004	-0.008	64.909	0.033	0.033	0.000	0.000	0.000	0.000
41	C	262	PHE	0	-0.030	-0.004	66.227	0.071	0.071	0.000	0.000	0.000	0.000
42	C	263	SER	0	-0.059	-0.019	65.087	0.061	0.061	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:222:LYS)