FMO DATABASE

FMODB ID: Z67LN

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-140430.165226
FMO2-HF: Nuclear repulsion	123653.88848
FMO2-HF: Total energy	-16776.276746
FMO2-MP2: Total energy	-16826.418188

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.
-3.794	-2.235	-0.015	-0.708	-0.836	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 : 1.026 / q_NPA : 1.002

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	C	224	ARG	1	0.890	0.934	3.840	24.840	26.399	-0.015	-0.708	-0.836	0.002
4	C	225	PHE	0	0.013	0.001	6.163	0.540	0.540	0.000	0.000	0.000	0.000
5	C	226	LEU	0	0.060	0.044	9.360	1.288	1.288	0.000	0.000	0.000	0.000
6	C	227	PRO	0	0.051	0.028	10.108	-1.582	-1.582	0.000	0.000	0.000	0.000
7	C	228	GLN	0	0.000	-0.015	8.569	-0.711	-0.711	0.000	0.000	0.000	0.000
8	C	229	SER	0	-0.003	0.008	12.295	0.779	0.779	0.000	0.000	0.000	0.000
9	C	230	VAL	0	0.042	-0.002	15.778	-0.208	-0.208	0.000	0.000	0.000	0.000
10	C	231	LEU	0	0.025	-0.002	18.559	0.348	0.348	0.000	0.000	0.000	0.000
11	C	232	ILE	0	0.011	0.012	16.069	0.226	0.226	0.000	0.000	0.000	0.000
12	C	233	LYS	1	0.952	0.988	17.533	14.382	14.382	0.000	0.000	0.000	0.000
13	C	234	ARG	1	0.977	0.984	20.558	10.470	10.470	0.000	0.000	0.000	0.000
14	C	235	GLU	-1	-0.972	-0.974	20.771	-11.994	-11.994	0.000	0.000	0.000	0.000
15	C	236	ASP	-1	-0.917	-0.945	22.279	-11.729	-11.729	0.000	0.000	0.000	0.000
16	C	237	GLU	-1	-1.030	-1.011	24.385	-10.783	-10.783	0.000	0.000	0.000	0.000
17	C	238	ILE	0	-0.096	-0.056	26.801	0.400	0.400	0.000	0.000	0.000	0.000
18	C	239	ALA	0	0.059	0.040	28.637	-0.185	-0.185	0.000	0.000	0.000	0.000
19	C	240	PHE	0	-0.042	-0.042	27.220	0.230	0.230	0.000	0.000	0.000	0.000
20	C	241	ASP	-1	-0.898	-0.949	30.873	-8.863	-8.863	0.000	0.000	0.000	0.000
21	C	242	ASP	-1	-0.905	-0.941	33.007	-7.854	-7.854	0.000	0.000	0.000	0.000
22	C	243	PHE	0	-0.110	-0.056	35.970	0.286	0.286	0.000	0.000	0.000	0.000
23	C	244	HIS	0	0.001	0.004	33.648	-0.107	-0.107	0.000	0.000	0.000	0.000
24	C	245	LEU	0	-0.041	-0.019	38.123	0.216	0.216	0.000	0.000	0.000	0.000
25	C	246	ASP	-1	-0.866	-0.923	40.088	-6.698	-6.698	0.000	0.000	0.000	0.000
26	C	247	ALA	0	0.035	0.006	40.014	0.081	0.081	0.000	0.000	0.000	0.000
27	C	248	ARG	1	0.974	0.971	41.898	6.649	6.649	0.000	0.000	0.000	0.000
28	C	249	LYS	1	0.944	0.979	45.381	6.229	6.229	0.000	0.000	0.000	0.000
29	C	250	VAL	0	0.020	0.022	42.571	0.108	0.108	0.000	0.000	0.000	0.000
30	C	251	LEU	0	-0.028	-0.039	42.737	0.062	0.062	0.000	0.000	0.000	0.000
31	C	252	ASN	0	-0.051	-0.004	46.211	0.102	0.102	0.000	0.000	0.000	0.000
32	C	253	ASP	-1	-0.894	-0.971	48.287	-5.907	-5.907	0.000	0.000	0.000	0.000
33	C	254	LEU	0	-0.072	-0.029	44.584	0.054	0.054	0.000	0.000	0.000	0.000
34	C	255	SER	0	-0.019	-0.012	49.195	0.046	0.046	0.000	0.000	0.000	0.000
35	C	256	ALA	0	-0.044	-0.002	52.279	0.122	0.122	0.000	0.000	0.000	0.000
36	C	257	THR	0	-0.018	-0.017	54.443	0.008	0.008	0.000	0.000	0.000	0.000
37	C	258	SER	0	0.002	-0.001	57.830	0.031	0.031	0.000	0.000	0.000	0.000
38	C	259	GLU	-1	-0.987	-0.978	59.733	-4.860	-4.860	0.000	0.000	0.000	0.000
39	C	260	ASN	0	0.037	0.016	62.576	0.056	0.056	0.000	0.000	0.000	0.000
40	C	261	PRO	0	-0.002	-0.026	65.091	0.028	0.028	0.000	0.000	0.000	0.000
41	C	262	PHE	0	-0.042	-0.014	66.103	0.060	0.060	0.000	0.000	0.000	0.000
42	C	263	SER	0	-0.024	0.008	65.667	0.046	0.046	0.000	0.000	0.000	0.000

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