FMO DATABASE

FMODB ID: JQR39

Calculation Name: 1KRL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KRL

Chain ID: A

ChEMBL ID:

UniProt ID: P02881

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-200193.512318
FMO2-HF: Nuclear repulsion	182219.496616
FMO2-HF: Total energy	-17974.015702
FMO2-MP2: Total energy	-18028.109393

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:101:ARG)

Summations of interaction energy for fragment #1(A:101:ARG)

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.
52.289	52.537	0	-0.042	-0.206	0

Interaction energy analysis for fragmet #1(A:101:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.048 / q_NPA : 1.011

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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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].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].
3	A	103	ILE	0	-0.022	-0.041	3.810	0.162	0.410	-0.042	-0.206
4	A	104	LYS	1	0.917	0.936	5.525	28.107	28.107	0.000	0.000
5	A	105	GLY	0	-0.016	-0.026	8.109	3.233	3.233	0.000	0.000
6	A	106	TYR	0	-0.023	0.005	9.224	-3.598	-3.598	0.000	0.000
7	A	107	GLU	-1	-0.864	-0.950	11.952	-18.524	-18.524	0.000	0.000
8	A	108	TYR	0	-0.096	-0.055	14.062	-0.729	-0.729	0.000	0.000
9	A	109	GLN	0	-0.023	-0.011	16.025	1.346	1.346	0.000	0.000
10	A	110	LEU	0	0.005	-0.009	18.597	0.054	0.054	0.000	0.000
11	A	111	TYR	0	0.061	0.026	21.865	0.017	0.017	0.000	0.000
12	A	112	VAL	0	-0.018	-0.021	25.120	0.010	0.010	0.000	0.000
13	A	113	TYR	0	0.055	0.023	27.805	0.081	0.081	0.000	0.000
14	A	114	ALA	0	0.020	0.010	31.543	-0.025	-0.025	0.000	0.000
15	A	115	SER	0	-0.001	-0.016	33.672	0.043	0.043	0.000	0.000
16	A	116	ASP	-1	-0.859	-0.915	36.540	-8.000	-8.000	0.000	0.000
17	A	117	LYS	1	0.848	0.928	34.820	8.386	8.386	0.000	0.000
18	A	118	LEU	0	-0.025	0.011	28.445	-0.232	-0.232	0.000	0.000
19	A	119	PHE	0	0.004	0.009	28.803	0.140	0.140	0.000	0.000
20	A	120	ARG	1	0.806	0.891	20.123	14.042	14.042	0.000	0.000
21	A	121	ALA	0	-0.013	-0.010	23.840	0.222	0.222	0.000	0.000
22	A	122	ASP	-1	-0.756	-0.840	19.011	-15.580	-15.580	0.000	0.000
23	A	123	ILE	0	-0.003	-0.013	19.091	0.626	0.626	0.000	0.000
24	A	124	SER	0	0.065	0.050	15.481	-0.718	-0.718	0.000	0.000
25	A	125	GLU	-1	-0.803	-0.881	14.784	-16.943	-16.943	0.000	0.000
26	A	126	ASP	-1	-0.826	-0.883	13.443	-21.908	-21.908	0.000	0.000
27	A	127	TYR	0	0.029	0.018	9.728	1.271	1.271	0.000	0.000
28	A	128	LYS	1	0.976	0.989	12.271	17.589	17.589	0.000	0.000
29	A	129	THR	0	-0.071	-0.077	14.638	1.080	1.080	0.000	0.000
30	A	130	ARG	1	0.927	0.981	16.402	19.067	19.067	0.000	0.000
31	A	131	GLY	0	0.022	0.020	17.809	0.793	0.793	0.000	0.000
32	A	132	ARG	1	0.842	0.893	17.922	14.552	14.552	0.000	0.000
33	A	133	LYS	1	0.926	0.964	19.656	14.204	14.204	0.000	0.000
34	A	134	LEU	0	0.003	0.017	20.589	-0.520	-0.520	0.000	0.000
35	A	135	LEU	0	-0.051	-0.030	16.866	0.417	0.417	0.000	0.000
36	A	136	ARG	1	0.890	0.933	21.136	14.031	14.031	0.000	0.000
37	A	137	PHE	0	0.029	0.009	23.875	-0.267	-0.267	0.000	0.000
38	A	138	ASN	0	-0.032	-0.013	26.262	-0.003	-0.003	0.000	0.000
39	A	139	GLY	0	0.056	0.039	28.466	-0.263	-0.263	0.000	0.000
40	A	140	PRO	0	-0.016	-0.019	31.034	0.173	0.173	0.000	0.000
41	A	141	VAL	0	-0.029	-0.009	27.331	-0.044	-0.044	0.000	0.000
42	A	142	PRO	0	0.009	0.004	29.572	0.172	0.172	0.000	0.000
43	A	143	PRO	0	0.015	-0.007	29.372	-0.335	-0.335	0.000	0.000
44	A	144	PRO	0	0.001	0.010	25.423	0.160	0.160	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:101:ARG)