FMO DATABASE

FMODB ID: LNYK9

Calculation Name: 1NKD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NKD

Chain ID: A

ChEMBL ID:

UniProt ID: P03051

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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-303204.22027
FMO2-HF: Nuclear repulsion	278845.98506
FMO2-HF: Total energy	-24358.23521
FMO2-MP2: Total energy	-24426.761669

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:1:MET)

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

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.
-25.565	-14.559	8.645	-5.773	-13.876	-0.04

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.009

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].	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	A	3	LYS	1	0.941	0.949	2.751	-1.711	0.806	0.472	-1.465	-1.523	-0.004
4	A	4	GLN	0	0.035	0.009	4.968	0.655	0.847	-0.001	-0.009	-0.181	0.000
5	A	5	GLU	-1	-0.757	-0.840	2.497	-4.842	-2.567	0.701	-1.220	-1.756	-0.009
6	A	6	LYS	1	0.979	0.991	2.499	-4.389	-2.226	3.067	-1.773	-3.457	0.008
7	A	7	THR	0	-0.070	-0.040	3.743	0.235	-1.343	0.034	1.875	-0.330	0.000
8	A	8	ALA	0	0.035	0.026	7.127	-0.264	-0.264	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.030	0.027	2.398	-1.059	-0.857	1.695	-0.305	-1.592	-0.002
10	A	10	ASN	0	-0.040	-0.040	6.272	-0.475	-0.475	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.005	0.014	8.025	-0.422	-0.422	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.052	0.031	8.971	-0.192	-0.192	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.878	0.935	5.345	-1.403	-1.403	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.031	-0.021	10.629	-0.115	-0.115	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.039	0.022	13.613	-0.079	-0.079	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.904	0.952	13.065	-0.066	-0.066	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.008	-0.012	14.954	-0.038	-0.038	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.031	-0.013	16.790	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.012	-0.011	18.030	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.011	0.030	19.496	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.020	0.007	21.108	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.057	-0.029	23.055	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.056	0.024	23.972	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.927	-0.963	24.451	0.079	0.079	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.759	0.862	27.292	-0.091	-0.091	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.026	-0.021	27.719	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.054	0.015	28.057	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.893	-0.926	30.098	0.066	0.066	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.087	-0.038	33.156	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.000	0.005	35.078	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.918	-0.971	36.664	0.022	0.022	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.047	-0.019	38.381	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.037	-0.020	33.524	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.847	-0.905	33.685	0.017	0.017	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.910	-0.958	33.589	0.019	0.019	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.058	-0.043	31.219	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.001	-0.005	29.442	0.005	0.005	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.863	-0.917	28.685	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.079	-0.044	27.415	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.073	-0.034	24.184	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.922	-0.955	24.013	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.012	0.015	23.509	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.029	-0.020	21.184	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.058	-0.045	17.723	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.859	-0.919	18.456	-0.054	-0.054	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.042	-0.018	18.228	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.012	-0.007	15.879	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.795	-0.892	14.001	-0.124	-0.124	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.936	-0.944	13.385	-0.246	-0.246	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.009	0.002	12.010	-0.079	-0.079	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.004	-0.009	7.002	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.865	0.908	8.517	0.047	0.047	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.004	0.006	9.493	-0.289	-0.289	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.062	-0.033	6.678	-0.144	-0.144	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.056	-0.038	3.848	-0.970	-0.769	0.000	-0.021	-0.181	0.000
56	A	56	ALA	0	-0.033	-0.018	5.262	-0.867	-0.867	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.954	0.993	7.102	0.669	0.669	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.023	-0.027	2.706	-1.252	0.224	0.583	-0.554	-1.504	-0.002
59	A	59	GLY	0	-0.024	0.001	2.473	-8.037	-4.479	2.094	-2.301	-3.352	-0.031

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