FMO DATABASE

FMODB ID: Z6V9N

Calculation Name: 1PK1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PK1

Chain ID: B

ChEMBL ID:

UniProt ID: P39769

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	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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-445698.1022
FMO2-HF: Nuclear repulsion	417002.151005
FMO2-HF: Total energy	-28695.951195
FMO2-MP2: Total energy	-28778.114982

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(B:11:ARG)

Summations of interaction energy for fragment #1(B:11: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.
-29.051	-27.464	-0.003	-0.615	-0.968	0.002

Interaction energy analysis for fragmet #1(B:11:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.983 / q_NPA : 0.963

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	B	13	GLN	0	-0.020	-0.019	3.802	2.955	4.542	-0.003	-0.615	-0.968	0.002
4	B	14	PRO	0	0.052	0.012	6.367	1.744	1.744	0.000	0.000	0.000	0.000
5	B	15	ILE	0	-0.019	0.000	9.370	1.420	1.420	0.000	0.000	0.000	0.000
6	B	16	ASP	-1	-0.947	-0.969	8.337	-26.965	-26.965	0.000	0.000	0.000	0.000
7	B	17	TRP	0	-0.078	-0.027	4.961	1.987	1.987	0.000	0.000	0.000	0.000
8	B	18	THR	0	0.020	-0.021	8.946	2.446	2.446	0.000	0.000	0.000	0.000
9	B	19	ILE	0	0.034	0.003	11.053	-0.260	-0.260	0.000	0.000	0.000	0.000
10	B	20	GLU	-1	-0.789	-0.874	11.656	-15.278	-15.278	0.000	0.000	0.000	0.000
11	B	21	GLU	-1	-0.806	-0.861	5.415	-28.596	-28.596	0.000	0.000	0.000	0.000
12	B	22	VAL	0	-0.024	-0.001	8.946	-0.400	-0.400	0.000	0.000	0.000	0.000
13	B	23	ILE	0	-0.018	-0.010	11.568	0.462	0.462	0.000	0.000	0.000	0.000
14	B	24	GLN	0	0.042	0.033	8.845	1.139	1.139	0.000	0.000	0.000	0.000
15	B	25	TYR	0	-0.041	-0.013	9.430	0.071	0.071	0.000	0.000	0.000	0.000
16	B	26	ILE	0	-0.005	-0.016	10.919	0.726	0.726	0.000	0.000	0.000	0.000
17	B	27	GLU	-1	-0.900	-0.961	14.565	-13.656	-13.656	0.000	0.000	0.000	0.000
18	B	28	SER	0	-0.125	-0.080	11.418	0.155	0.155	0.000	0.000	0.000	0.000
19	B	29	ASN	0	-0.084	-0.042	11.634	0.134	0.134	0.000	0.000	0.000	0.000
20	B	30	ASP	-1	-0.789	-0.860	15.278	-11.653	-11.653	0.000	0.000	0.000	0.000
21	B	31	ASN	0	0.046	0.020	18.637	0.620	0.620	0.000	0.000	0.000	0.000
22	B	32	SER	0	-0.087	-0.060	19.913	0.448	0.448	0.000	0.000	0.000	0.000
23	B	33	LEU	0	-0.052	-0.038	19.162	0.539	0.539	0.000	0.000	0.000	0.000
24	B	34	ALA	0	0.090	0.045	19.329	-0.015	-0.015	0.000	0.000	0.000	0.000
25	B	35	VAL	0	-0.040	-0.004	20.239	0.089	0.089	0.000	0.000	0.000	0.000
26	B	36	HIS	0	-0.041	-0.029	21.682	0.389	0.389	0.000	0.000	0.000	0.000
27	B	37	GLY	0	0.090	0.047	18.845	-0.156	-0.156	0.000	0.000	0.000	0.000
28	B	38	ASP	-1	-0.818	-0.916	19.505	-11.978	-11.978	0.000	0.000	0.000	0.000
29	B	39	LEU	0	-0.094	-0.029	21.931	0.132	0.132	0.000	0.000	0.000	0.000
30	B	40	PHE	0	0.020	-0.012	16.736	0.092	0.092	0.000	0.000	0.000	0.000
31	B	41	ARG	1	0.824	0.883	15.908	13.707	13.707	0.000	0.000	0.000	0.000
32	B	42	LYS	1	0.892	0.955	19.738	10.050	10.050	0.000	0.000	0.000	0.000
33	B	43	HIS	0	-0.073	-0.050	22.207	0.180	0.180	0.000	0.000	0.000	0.000
34	B	44	GLU	-1	-0.962	-0.967	19.070	-12.246	-12.246	0.000	0.000	0.000	0.000
35	B	45	ILE	0	-0.056	-0.039	16.350	-0.240	-0.240	0.000	0.000	0.000	0.000
36	B	46	ASP	-1	-0.767	-0.887	13.864	-17.421	-17.421	0.000	0.000	0.000	0.000
37	B	47	GLY	0	0.044	0.014	11.914	0.395	0.395	0.000	0.000	0.000	0.000
38	B	48	LYS	1	0.918	0.954	12.675	15.497	15.497	0.000	0.000	0.000	0.000
39	B	49	ALA	0	-0.051	-0.025	15.832	0.750	0.750	0.000	0.000	0.000	0.000
40	B	50	LEU	0	0.007	0.000	13.038	0.778	0.778	0.000	0.000	0.000	0.000
41	B	51	LEU	0	-0.007	-0.003	13.541	0.766	0.766	0.000	0.000	0.000	0.000
42	B	52	ARG	1	0.877	0.956	17.246	12.863	12.863	0.000	0.000	0.000	0.000
43	B	53	LEU	0	-0.017	-0.002	19.001	0.926	0.926	0.000	0.000	0.000	0.000
44	B	54	ASN	0	0.018	-0.012	21.713	0.402	0.402	0.000	0.000	0.000	0.000
45	B	55	SER	0	0.065	0.002	24.538	-0.028	-0.028	0.000	0.000	0.000	0.000
46	B	56	GLU	-1	-0.851	-0.907	26.849	-9.228	-9.228	0.000	0.000	0.000	0.000
47	B	57	ARG	1	0.896	0.955	25.547	10.694	10.694	0.000	0.000	0.000	0.000
48	B	58	MET	0	0.020	0.009	22.476	0.071	0.071	0.000	0.000	0.000	0.000
49	B	59	MET	0	-0.054	-0.013	26.146	0.218	0.218	0.000	0.000	0.000	0.000
50	B	60	LYS	1	0.893	0.952	29.670	8.399	8.399	0.000	0.000	0.000	0.000
51	B	61	TYR	0	-0.030	-0.035	27.736	0.179	0.179	0.000	0.000	0.000	0.000
52	B	62	MET	0	0.012	0.028	21.363	-0.032	-0.032	0.000	0.000	0.000	0.000
53	B	63	GLY	0	0.025	0.034	27.119	0.043	0.043	0.000	0.000	0.000	0.000
54	B	64	LEU	0	-0.007	-0.001	23.346	0.207	0.207	0.000	0.000	0.000	0.000
55	B	65	LYS	1	0.919	0.950	27.949	9.010	9.010	0.000	0.000	0.000	0.000
56	B	66	LEU	0	0.107	0.032	28.392	-0.294	-0.294	0.000	0.000	0.000	0.000
57	B	67	GLY	0	0.009	0.020	28.228	-0.245	-0.245	0.000	0.000	0.000	0.000
58	B	68	PRO	0	0.031	-0.007	24.843	-0.265	-0.265	0.000	0.000	0.000	0.000
59	B	69	ALA	0	0.047	0.034	23.718	-0.456	-0.456	0.000	0.000	0.000	0.000
60	B	70	LEU	0	0.025	0.007	23.889	-0.430	-0.430	0.000	0.000	0.000	0.000
61	B	71	LYS	1	0.832	0.905	22.123	11.220	11.220	0.000	0.000	0.000	0.000
62	B	72	ILE	0	0.051	0.027	18.724	-0.552	-0.552	0.000	0.000	0.000	0.000
63	B	73	CYS	0	-0.056	-0.028	19.179	-0.563	-0.563	0.000	0.000	0.000	0.000
64	B	74	ASN	0	-0.035	-0.014	20.408	-0.865	-0.865	0.000	0.000	0.000	0.000
65	B	75	LEU	0	0.042	0.017	15.722	-0.430	-0.430	0.000	0.000	0.000	0.000
66	B	76	VAL	0	0.027	0.020	15.691	-1.067	-1.067	0.000	0.000	0.000	0.000
67	B	77	ASN	0	-0.016	-0.032	16.396	-0.764	-0.764	0.000	0.000	0.000	0.000
68	B	78	LYS	1	0.855	0.954	14.676	15.145	15.145	0.000	0.000	0.000	0.000
69	B	79	VAL	0	-0.027	0.002	10.915	-0.977	-0.977	0.000	0.000	0.000	0.000
70	B	80	ASN	0	-0.031	0.006	13.180	-1.039	-1.039	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:11:ARG)