FMO DATABASE

FMODB ID: R9848

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

Total energy (hartree)

FMO2-HF: Electronic energy	-446702.838873
FMO2-HF: Nuclear repulsion	418006.75438
FMO2-HF: Total energy	-28696.084493
FMO2-MP2: Total energy	-28778.220445

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.
-29.421	-27.589	0.005	-0.811	-1.026	0.003

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 : 1.001 / q_NPA : 0.985

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	-0.030	-0.014	3.597	2.813	4.645	0.005	-0.811	-1.026	0.003
4	B	14	PRO	0	0.043	0.011	6.466	1.892	1.892	0.000	0.000	0.000	0.000
5	B	15	ILE	0	-0.035	-0.012	9.703	1.928	1.928	0.000	0.000	0.000	0.000
6	B	16	ASP	-1	-0.921	-0.971	8.003	-28.704	-28.704	0.000	0.000	0.000	0.000
7	B	17	TRP	0	-0.088	-0.023	5.028	2.615	2.615	0.000	0.000	0.000	0.000
8	B	18	THR	0	0.027	-0.029	8.851	2.760	2.760	0.000	0.000	0.000	0.000
9	B	19	ILE	0	0.026	0.008	11.111	-0.342	-0.342	0.000	0.000	0.000	0.000
10	B	20	GLU	-1	-0.779	-0.865	11.690	-15.277	-15.277	0.000	0.000	0.000	0.000
11	B	21	GLU	-1	-0.806	-0.838	5.749	-30.023	-30.023	0.000	0.000	0.000	0.000
12	B	22	VAL	0	-0.016	0.000	8.900	-0.170	-0.170	0.000	0.000	0.000	0.000
13	B	23	ILE	0	-0.017	-0.004	11.536	0.449	0.449	0.000	0.000	0.000	0.000
14	B	24	GLN	0	-0.006	0.005	8.976	0.693	0.693	0.000	0.000	0.000	0.000
15	B	25	TYR	0	-0.023	-0.015	9.367	0.110	0.110	0.000	0.000	0.000	0.000
16	B	26	ILE	0	-0.012	-0.018	10.889	0.847	0.847	0.000	0.000	0.000	0.000
17	B	27	GLU	-1	-0.893	-0.970	14.632	-13.498	-13.498	0.000	0.000	0.000	0.000
18	B	28	SER	0	-0.089	-0.060	11.692	0.304	0.304	0.000	0.000	0.000	0.000
19	B	29	ASN	0	-0.079	-0.036	12.014	0.282	0.282	0.000	0.000	0.000	0.000
20	B	30	ASP	-1	-0.790	-0.859	15.628	-11.460	-11.460	0.000	0.000	0.000	0.000
21	B	31	ASN	0	0.046	0.031	18.958	0.581	0.581	0.000	0.000	0.000	0.000
22	B	32	SER	0	-0.077	-0.061	19.912	0.430	0.430	0.000	0.000	0.000	0.000
23	B	33	LEU	0	-0.046	-0.034	19.118	0.494	0.494	0.000	0.000	0.000	0.000
24	B	34	ALA	0	0.079	0.041	19.497	0.018	0.018	0.000	0.000	0.000	0.000
25	B	35	VAL	0	-0.058	-0.014	20.520	0.121	0.121	0.000	0.000	0.000	0.000
26	B	36	HIS	0	-0.024	-0.019	21.866	0.413	0.413	0.000	0.000	0.000	0.000
27	B	37	GLY	0	0.093	0.054	18.843	-0.211	-0.211	0.000	0.000	0.000	0.000
28	B	38	ASP	-1	-0.828	-0.918	19.527	-12.078	-12.078	0.000	0.000	0.000	0.000
29	B	39	LEU	0	-0.082	-0.028	21.890	0.183	0.183	0.000	0.000	0.000	0.000
30	B	40	PHE	0	0.012	-0.021	16.795	0.073	0.073	0.000	0.000	0.000	0.000
31	B	41	ARG	1	0.817	0.876	15.980	13.743	13.743	0.000	0.000	0.000	0.000
32	B	42	LYS	1	0.876	0.941	19.903	10.545	10.545	0.000	0.000	0.000	0.000
33	B	43	HIS	0	-0.067	-0.033	22.362	0.310	0.310	0.000	0.000	0.000	0.000
34	B	44	GLU	-1	-0.953	-0.970	19.337	-12.231	-12.231	0.000	0.000	0.000	0.000
35	B	45	ILE	0	-0.044	-0.032	16.409	-0.369	-0.369	0.000	0.000	0.000	0.000
36	B	46	ASP	-1	-0.753	-0.877	13.967	-17.674	-17.674	0.000	0.000	0.000	0.000
37	B	47	GLY	0	0.067	0.030	12.109	0.524	0.524	0.000	0.000	0.000	0.000
38	B	48	LYS	1	0.910	0.951	12.927	15.814	15.814	0.000	0.000	0.000	0.000
39	B	49	ALA	0	-0.048	-0.022	16.135	0.871	0.871	0.000	0.000	0.000	0.000
40	B	50	LEU	0	0.006	-0.004	13.006	0.807	0.807	0.000	0.000	0.000	0.000
41	B	51	LEU	0	-0.023	-0.011	13.489	0.766	0.766	0.000	0.000	0.000	0.000
42	B	52	ARG	1	0.883	0.952	17.374	12.817	12.817	0.000	0.000	0.000	0.000
43	B	53	LEU	0	-0.019	0.000	19.015	0.912	0.912	0.000	0.000	0.000	0.000
44	B	54	ASN	0	0.032	0.000	21.820	0.457	0.457	0.000	0.000	0.000	0.000
45	B	55	SER	0	0.044	-0.014	24.590	-0.022	-0.022	0.000	0.000	0.000	0.000
46	B	56	GLU	-1	-0.839	-0.890	27.152	-9.289	-9.289	0.000	0.000	0.000	0.000
47	B	57	ARG	1	0.886	0.937	25.486	10.631	10.631	0.000	0.000	0.000	0.000
48	B	58	MET	0	0.027	0.018	22.753	0.089	0.089	0.000	0.000	0.000	0.000
49	B	59	MET	0	-0.051	-0.022	26.356	0.224	0.224	0.000	0.000	0.000	0.000
50	B	60	LYS	1	0.902	0.963	30.006	8.433	8.433	0.000	0.000	0.000	0.000
51	B	61	TYR	0	-0.032	-0.027	28.117	0.227	0.227	0.000	0.000	0.000	0.000
52	B	62	MET	0	0.029	0.029	21.410	-0.038	-0.038	0.000	0.000	0.000	0.000
53	B	63	GLY	0	0.034	0.040	27.035	0.071	0.071	0.000	0.000	0.000	0.000
54	B	64	LEU	0	-0.008	-0.003	23.616	0.232	0.232	0.000	0.000	0.000	0.000
55	B	65	LYS	1	0.884	0.926	28.276	9.205	9.205	0.000	0.000	0.000	0.000
56	B	66	LEU	0	0.102	0.039	28.534	-0.305	-0.305	0.000	0.000	0.000	0.000
57	B	67	GLY	0	0.019	0.022	28.421	-0.235	-0.235	0.000	0.000	0.000	0.000
58	B	68	PRO	0	0.030	-0.002	25.063	-0.289	-0.289	0.000	0.000	0.000	0.000
59	B	69	ALA	0	0.036	0.028	23.902	-0.449	-0.449	0.000	0.000	0.000	0.000
60	B	70	LEU	0	0.024	0.009	24.174	-0.404	-0.404	0.000	0.000	0.000	0.000
61	B	71	LYS	1	0.822	0.899	22.289	11.031	11.031	0.000	0.000	0.000	0.000
62	B	72	ILE	0	0.060	0.027	18.985	-0.536	-0.536	0.000	0.000	0.000	0.000
63	B	73	CYS	0	-0.070	-0.033	19.501	-0.521	-0.521	0.000	0.000	0.000	0.000
64	B	74	ASN	0	-0.029	-0.016	20.560	-0.823	-0.823	0.000	0.000	0.000	0.000
65	B	75	LEU	0	0.019	0.016	15.939	-0.471	-0.471	0.000	0.000	0.000	0.000
66	B	76	VAL	0	0.037	0.022	15.700	-1.013	-1.013	0.000	0.000	0.000	0.000
67	B	77	ASN	0	-0.004	-0.020	16.416	-0.809	-0.809	0.000	0.000	0.000	0.000
68	B	78	LYS	1	0.848	0.953	14.513	15.196	15.196	0.000	0.000	0.000	0.000
69	B	79	VAL	0	-0.033	-0.004	11.185	-1.115	-1.115	0.000	0.000	0.000	0.000
70	B	80	ASN	0	-0.013	0.005	13.214	-0.976	-0.976	0.000	0.000	0.000	0.000

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