FMO DATABASE

FMODB ID: R9QM8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-140492.989491
FMO2-HF: Nuclear repulsion	123716.297751
FMO2-HF: Total energy	-16776.691739
FMO2-MP2: Total energy	-16826.830771

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.
-3.365	-1.78	-0.016	-0.722	-0.847	0.002

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 : 1.022 / q_NPA : 0.997

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	0.886	0.941	3.840	24.850	26.435	-0.016	-0.722	-0.847	0.002
4	C	225	PHE	0	0.045	0.007	6.134	0.555	0.555	0.000	0.000	0.000	0.000
5	C	226	LEU	0	0.061	0.049	9.324	1.246	1.246	0.000	0.000	0.000	0.000
6	C	227	PRO	0	0.058	0.025	10.088	-1.573	-1.573	0.000	0.000	0.000	0.000
7	C	228	GLN	0	-0.006	-0.017	8.681	-0.233	-0.233	0.000	0.000	0.000	0.000
8	C	229	SER	0	0.028	0.018	12.262	0.787	0.787	0.000	0.000	0.000	0.000
9	C	230	VAL	0	0.025	-0.006	15.743	-0.231	-0.231	0.000	0.000	0.000	0.000
10	C	231	LEU	0	0.015	-0.004	18.533	0.353	0.353	0.000	0.000	0.000	0.000
11	C	232	ILE	0	0.016	0.016	15.965	0.209	0.209	0.000	0.000	0.000	0.000
12	C	233	LYS	1	0.958	0.988	17.680	14.276	14.276	0.000	0.000	0.000	0.000
13	C	234	ARG	1	0.899	0.933	20.539	10.553	10.553	0.000	0.000	0.000	0.000
14	C	235	GLU	-1	-0.979	-0.976	21.067	-11.830	-11.830	0.000	0.000	0.000	0.000
15	C	236	ASP	-1	-0.906	-0.940	22.179	-11.812	-11.812	0.000	0.000	0.000	0.000
16	C	237	GLU	-1	-0.969	-0.973	23.881	-10.783	-10.783	0.000	0.000	0.000	0.000
17	C	238	ILE	0	-0.085	-0.054	26.786	0.400	0.400	0.000	0.000	0.000	0.000
18	C	239	ALA	0	0.043	0.039	28.614	-0.187	-0.187	0.000	0.000	0.000	0.000
19	C	240	PHE	0	-0.024	-0.035	26.693	0.250	0.250	0.000	0.000	0.000	0.000
20	C	241	ASP	-1	-0.913	-0.959	30.233	-8.912	-8.912	0.000	0.000	0.000	0.000
21	C	242	ASP	-1	-0.897	-0.946	32.979	-7.910	-7.910	0.000	0.000	0.000	0.000
22	C	243	PHE	0	-0.122	-0.062	35.696	0.295	0.295	0.000	0.000	0.000	0.000
23	C	244	HIS	0	0.010	0.027	33.372	-0.080	-0.080	0.000	0.000	0.000	0.000
24	C	245	LEU	0	-0.031	-0.018	38.089	0.216	0.216	0.000	0.000	0.000	0.000
25	C	246	ASP	-1	-0.801	-0.889	40.105	-6.732	-6.732	0.000	0.000	0.000	0.000
26	C	247	ALA	0	0.035	0.010	39.986	0.089	0.089	0.000	0.000	0.000	0.000
27	C	248	ARG	1	0.896	0.919	41.913	6.688	6.688	0.000	0.000	0.000	0.000
28	C	249	LYS	1	0.810	0.897	45.395	6.139	6.139	0.000	0.000	0.000	0.000
29	C	250	VAL	0	0.038	0.028	42.664	0.115	0.115	0.000	0.000	0.000	0.000
30	C	251	LEU	0	-0.026	-0.037	42.449	0.067	0.067	0.000	0.000	0.000	0.000
31	C	252	ASN	0	-0.035	0.003	46.222	0.124	0.124	0.000	0.000	0.000	0.000
32	C	253	ASP	-1	-0.813	-0.909	48.287	-5.921	-5.921	0.000	0.000	0.000	0.000
33	C	254	LEU	0	-0.053	-0.020	44.502	0.057	0.057	0.000	0.000	0.000	0.000
34	C	255	SER	0	-0.031	-0.006	49.203	0.045	0.045	0.000	0.000	0.000	0.000
35	C	256	ALA	0	-0.029	-0.008	52.286	0.123	0.123	0.000	0.000	0.000	0.000
36	C	257	THR	0	-0.017	-0.014	54.451	0.006	0.006	0.000	0.000	0.000	0.000
37	C	258	SER	0	0.009	0.004	57.839	0.028	0.028	0.000	0.000	0.000	0.000
38	C	259	GLU	-1	-0.973	-0.971	59.741	-4.861	-4.861	0.000	0.000	0.000	0.000
39	C	260	ASN	0	0.034	0.004	62.564	0.055	0.055	0.000	0.000	0.000	0.000
40	C	261	PRO	0	-0.011	-0.015	65.100	0.029	0.029	0.000	0.000	0.000	0.000
41	C	262	PHE	0	-0.047	-0.011	65.940	0.057	0.057	0.000	0.000	0.000	0.000
42	C	263	SER	0	-0.024	-0.002	65.374	0.088	0.088	0.000	0.000	0.000	0.000

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