FMO DATABASE

FMODB ID: 3J4QL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-199485.683044
FMO2-HF: Nuclear repulsion	181510.377961
FMO2-HF: Total energy	-17975.305082
FMO2-MP2: Total energy	-18029.334892

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.
53.007	53.228	0	-0.041	-0.179	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 : 0.939 / q_NPA : 0.953

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	-0.019	3.976	-0.196	0.025	-0.041	-0.179
4	A	104	LYS	1	0.916	0.949	5.763	28.200	28.200	0.000	0.000
5	A	105	GLY	0	-0.013	-0.018	8.195	3.436	3.436	0.000	0.000
6	A	106	TYR	0	-0.023	0.003	9.248	-3.807	-3.807	0.000	0.000
7	A	107	GLU	-1	-0.865	-0.942	11.916	-18.311	-18.311	0.000	0.000
8	A	108	TYR	0	-0.089	-0.052	14.259	-0.730	-0.730	0.000	0.000
9	A	109	GLN	0	-0.023	-0.023	16.192	1.601	1.601	0.000	0.000
10	A	110	LEU	0	0.012	-0.001	18.642	0.026	0.026	0.000	0.000
11	A	111	TYR	0	0.030	0.020	21.962	0.066	0.066	0.000	0.000
12	A	112	VAL	0	-0.021	-0.018	25.153	-0.071	-0.071	0.000	0.000
13	A	113	TYR	0	0.052	0.022	28.015	0.106	0.106	0.000	0.000
14	A	114	ALA	0	0.007	0.000	31.817	-0.056	-0.056	0.000	0.000
15	A	115	SER	0	0.006	-0.009	34.071	0.066	0.066	0.000	0.000
16	A	116	ASP	-1	-0.879	-0.926	37.113	-7.968	-7.968	0.000	0.000
17	A	117	LYS	1	0.871	0.940	35.317	8.314	8.314	0.000	0.000
18	A	118	LEU	0	-0.013	0.013	28.783	-0.204	-0.204	0.000	0.000
19	A	119	PHE	0	-0.010	-0.007	29.095	0.168	0.168	0.000	0.000
20	A	120	ARG	1	0.815	0.876	20.227	14.007	14.007	0.000	0.000
21	A	121	ALA	0	-0.006	-0.002	24.139	0.262	0.262	0.000	0.000
22	A	122	ASP	-1	-0.758	-0.836	19.234	-15.412	-15.412	0.000	0.000
23	A	123	ILE	0	0.014	0.001	19.306	0.604	0.604	0.000	0.000
24	A	124	SER	0	0.061	0.043	15.397	-0.652	-0.652	0.000	0.000
25	A	125	GLU	-1	-0.802	-0.879	14.757	-17.012	-17.012	0.000	0.000
26	A	126	ASP	-1	-0.775	-0.853	13.343	-21.868	-21.868	0.000	0.000
27	A	127	TYR	0	0.014	0.012	9.320	1.418	1.418	0.000	0.000
28	A	128	LYS	1	0.956	0.988	12.363	17.549	17.549	0.000	0.000
29	A	129	THR	0	-0.070	-0.081	14.620	1.071	1.071	0.000	0.000
30	A	130	ARG	1	0.915	0.965	15.553	19.377	19.377	0.000	0.000
31	A	131	GLY	0	0.033	0.035	18.014	0.776	0.776	0.000	0.000
32	A	132	ARG	1	0.833	0.882	17.938	14.685	14.685	0.000	0.000
33	A	133	LYS	1	0.909	0.949	19.628	14.300	14.300	0.000	0.000
34	A	134	LEU	0	0.018	0.024	20.449	-0.596	-0.596	0.000	0.000
35	A	135	LEU	0	-0.055	-0.025	17.010	0.432	0.432	0.000	0.000
36	A	136	ARG	1	0.869	0.918	21.540	13.887	13.887	0.000	0.000
37	A	137	PHE	0	0.034	0.013	24.346	-0.247	-0.247	0.000	0.000
38	A	138	ASN	0	-0.027	-0.012	26.466	0.001	0.001	0.000	0.000
39	A	139	GLY	0	0.053	0.025	28.627	-0.255	-0.255	0.000	0.000
40	A	140	PRO	0	0.006	-0.007	31.251	0.165	0.165	0.000	0.000
41	A	141	VAL	0	-0.040	-0.004	27.855	-0.071	-0.071	0.000	0.000
42	A	142	PRO	0	0.018	0.015	29.520	0.184	0.184	0.000	0.000
43	A	143	PRO	0	0.023	-0.004	29.325	-0.363	-0.363	0.000	0.000
44	A	144	PRO	0	-0.011	0.007	25.336	0.125	0.125	0.000	0.000

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