FMO DATABASE

FMODB ID: 6NY5Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-445608.52159
FMO2-HF: Nuclear repulsion	416913.059242
FMO2-HF: Total energy	-28695.462348
FMO2-MP2: Total energy	-28777.664726

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.
-29.148	-27.286	-0.004	-0.758	-1.1	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 : 0.996 / q_NPA : 0.971

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	B	13	GLN	0	-0.012	-0.023	3.802	3.623	5.485	-0.004	-0.758	-1.100	0.002
4	B	14	PRO	0	0.053	0.001	6.367	1.704	1.704	0.000	0.000	0.000	0.000
5	B	15	ILE	0	-0.011	0.001	9.363	1.447	1.447	0.000	0.000	0.000	0.000
6	B	16	ASP	-1	-0.956	-0.971	8.424	-27.195	-27.195	0.000	0.000	0.000	0.000
7	B	17	TRP	0	-0.065	-0.009	5.373	2.161	2.161	0.000	0.000	0.000	0.000
8	B	18	THR	0	0.037	0.011	8.918	2.569	2.569	0.000	0.000	0.000	0.000
9	B	19	ILE	0	0.053	0.018	11.040	-0.280	-0.280	0.000	0.000	0.000	0.000
10	B	20	GLU	-1	-0.817	-0.914	11.561	-15.604	-15.604	0.000	0.000	0.000	0.000
11	B	21	GLU	-1	-0.870	-0.919	5.252	-29.753	-29.753	0.000	0.000	0.000	0.000
12	B	22	VAL	0	-0.013	0.005	8.941	-0.439	-0.439	0.000	0.000	0.000	0.000
13	B	23	ILE	0	-0.025	-0.013	11.564	0.489	0.489	0.000	0.000	0.000	0.000
14	B	24	GLN	0	0.053	0.039	8.719	1.441	1.441	0.000	0.000	0.000	0.000
15	B	25	TYR	0	-0.064	-0.041	9.508	0.020	0.020	0.000	0.000	0.000	0.000
16	B	26	ILE	0	-0.005	-0.012	10.922	0.722	0.722	0.000	0.000	0.000	0.000
17	B	27	GLU	-1	-0.897	-0.959	14.567	-13.907	-13.907	0.000	0.000	0.000	0.000
18	B	28	SER	0	-0.131	-0.058	11.492	0.225	0.225	0.000	0.000	0.000	0.000
19	B	29	ASN	0	-0.087	-0.052	11.595	0.181	0.181	0.000	0.000	0.000	0.000
20	B	30	ASP	-1	-0.847	-0.897	15.287	-11.980	-11.980	0.000	0.000	0.000	0.000
21	B	31	ASN	0	0.045	0.016	18.644	0.649	0.649	0.000	0.000	0.000	0.000
22	B	32	SER	0	-0.107	-0.077	19.920	0.475	0.475	0.000	0.000	0.000	0.000
23	B	33	LEU	0	-0.060	-0.042	19.148	0.573	0.573	0.000	0.000	0.000	0.000
24	B	34	ALA	0	0.091	0.041	19.336	-0.024	-0.024	0.000	0.000	0.000	0.000
25	B	35	VAL	0	-0.045	-0.006	20.242	0.089	0.089	0.000	0.000	0.000	0.000
26	B	36	HIS	0	-0.040	-0.032	21.706	0.356	0.356	0.000	0.000	0.000	0.000
27	B	37	GLY	0	0.094	0.050	18.845	-0.163	-0.163	0.000	0.000	0.000	0.000
28	B	38	ASP	-1	-0.846	-0.937	19.502	-11.929	-11.929	0.000	0.000	0.000	0.000
29	B	39	LEU	0	-0.090	-0.028	21.927	0.128	0.128	0.000	0.000	0.000	0.000
30	B	40	PHE	0	0.027	-0.012	16.783	0.096	0.096	0.000	0.000	0.000	0.000
31	B	41	ARG	1	0.858	0.936	16.303	13.746	13.746	0.000	0.000	0.000	0.000
32	B	42	LYS	1	0.896	0.956	19.731	10.019	10.019	0.000	0.000	0.000	0.000
33	B	43	HIS	0	-0.073	-0.047	22.104	0.162	0.162	0.000	0.000	0.000	0.000
34	B	44	GLU	-1	-0.955	-0.972	19.089	-12.319	-12.319	0.000	0.000	0.000	0.000
35	B	45	ILE	0	-0.057	-0.036	16.303	-0.254	-0.254	0.000	0.000	0.000	0.000
36	B	46	ASP	-1	-0.812	-0.909	13.669	-17.440	-17.440	0.000	0.000	0.000	0.000
37	B	47	GLY	0	0.037	0.010	11.902	0.378	0.378	0.000	0.000	0.000	0.000
38	B	48	LYS	1	0.939	0.964	12.665	15.606	15.606	0.000	0.000	0.000	0.000
39	B	49	ALA	0	-0.053	-0.022	15.821	0.770	0.770	0.000	0.000	0.000	0.000
40	B	50	LEU	0	0.017	0.006	13.137	0.802	0.802	0.000	0.000	0.000	0.000
41	B	51	LEU	0	-0.005	-0.003	13.596	0.767	0.767	0.000	0.000	0.000	0.000
42	B	52	ARG	1	0.870	0.952	17.240	13.114	13.114	0.000	0.000	0.000	0.000
43	B	53	LEU	0	-0.025	-0.007	18.993	0.946	0.946	0.000	0.000	0.000	0.000
44	B	54	ASN	0	0.030	-0.007	21.707	0.287	0.287	0.000	0.000	0.000	0.000
45	B	55	SER	0	0.100	0.026	24.534	0.030	0.030	0.000	0.000	0.000	0.000
46	B	56	GLU	-1	-0.912	-0.947	26.847	-9.023	-9.023	0.000	0.000	0.000	0.000
47	B	57	ARG	1	0.917	0.973	25.612	11.003	11.003	0.000	0.000	0.000	0.000
48	B	58	MET	0	0.015	0.016	22.587	0.095	0.095	0.000	0.000	0.000	0.000
49	B	59	MET	0	-0.041	-0.012	26.142	0.227	0.227	0.000	0.000	0.000	0.000
50	B	60	LYS	1	0.902	0.956	29.667	8.501	8.501	0.000	0.000	0.000	0.000
51	B	61	TYR	0	-0.045	-0.044	27.643	0.176	0.176	0.000	0.000	0.000	0.000
52	B	62	MET	0	0.008	0.022	21.384	-0.028	-0.028	0.000	0.000	0.000	0.000
53	B	63	GLY	0	0.006	0.024	27.114	0.038	0.038	0.000	0.000	0.000	0.000
54	B	64	LEU	0	-0.014	0.003	23.302	0.170	0.170	0.000	0.000	0.000	0.000
55	B	65	LYS	1	0.968	0.971	27.947	8.765	8.765	0.000	0.000	0.000	0.000
56	B	66	LEU	0	0.098	0.027	28.392	-0.298	-0.298	0.000	0.000	0.000	0.000
57	B	67	GLY	0	0.005	0.016	28.229	-0.250	-0.250	0.000	0.000	0.000	0.000
58	B	68	PRO	0	0.014	-0.016	24.932	-0.274	-0.274	0.000	0.000	0.000	0.000
59	B	69	ALA	0	0.058	0.036	23.720	-0.449	-0.449	0.000	0.000	0.000	0.000
60	B	70	LEU	0	-0.002	-0.011	23.889	-0.415	-0.415	0.000	0.000	0.000	0.000
61	B	71	LYS	1	0.935	0.979	22.208	10.851	10.851	0.000	0.000	0.000	0.000
62	B	72	ILE	0	0.060	0.032	18.714	-0.553	-0.553	0.000	0.000	0.000	0.000
63	B	73	CYS	0	-0.044	-0.023	19.180	-0.606	-0.606	0.000	0.000	0.000	0.000
64	B	74	ASN	0	-0.048	-0.009	20.409	-0.746	-0.746	0.000	0.000	0.000	0.000
65	B	75	LEU	0	0.040	0.017	15.740	-0.497	-0.497	0.000	0.000	0.000	0.000
66	B	76	VAL	0	0.021	0.015	15.693	-1.102	-1.102	0.000	0.000	0.000	0.000
67	B	77	ASN	0	-0.013	-0.026	16.401	-0.866	-0.866	0.000	0.000	0.000	0.000
68	B	78	LYS	1	0.887	0.964	14.725	15.761	15.761	0.000	0.000	0.000	0.000
69	B	79	VAL	0	-0.028	0.004	10.957	-1.061	-1.061	0.000	0.000	0.000	0.000
70	B	80	ASN	0	-0.024	0.004	13.182	-0.855	-0.855	0.000	0.000	0.000	0.000

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