FMO DATABASE

FMODB ID: 3JL1L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-303196.303481
FMO2-HF: Nuclear repulsion	278840.063241
FMO2-HF: Total energy	-24356.24024
FMO2-MP2: Total energy	-24424.83091

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.
-28.511	-14.88	10.552	-7.78	-16.403	-0.06

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 : 0.004 / q_NPA : 0.003

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	0.949	0.952	2.462	-2.622	-0.266	1.467	-1.619	-2.205	-0.006
4	A	4	GLN	0	0.040	0.009	5.020	0.438	0.672	-0.001	-0.011	-0.222	0.000
5	A	5	GLU	-1	-0.810	-0.895	2.564	-9.004	-4.900	1.833	-2.395	-3.543	-0.027
6	A	6	LYS	1	0.982	0.991	2.838	-3.207	-0.410	2.170	-1.850	-3.117	0.004
7	A	7	THR	0	-0.071	-0.035	3.777	0.076	-1.205	0.050	1.491	-0.260	0.001
8	A	8	ALA	0	0.036	0.021	6.777	-0.240	-0.240	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.036	0.032	2.278	-1.258	-0.990	1.801	-0.357	-1.711	-0.003
10	A	10	ASN	0	-0.057	-0.058	6.098	-0.725	-0.699	-0.001	-0.003	-0.021	0.000
11	A	11	MET	0	0.023	0.026	8.128	-0.384	-0.384	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.045	0.027	8.969	-0.179	-0.179	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.881	0.945	5.272	-0.864	-0.864	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.032	-0.023	10.627	-0.108	-0.108	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.048	0.022	13.577	-0.067	-0.067	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.922	0.958	12.590	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.038	-0.018	14.962	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.008	-0.015	16.805	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.003	-0.007	18.121	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.023	0.036	19.518	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.024	0.007	21.129	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.080	-0.038	23.059	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.053	0.024	24.076	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.933	-0.966	24.341	0.048	0.048	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.919	0.956	26.806	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.031	-0.025	27.852	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.047	0.013	28.323	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-1.019	-0.997	30.339	0.042	0.042	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.090	-0.047	33.221	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.005	0.006	35.118	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.890	-0.962	36.698	0.017	0.017	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.067	-0.020	38.293	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.056	-0.033	33.525	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.831	-0.900	33.708	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.945	-0.969	33.627	0.016	0.016	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.043	-0.040	31.292	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.005	-0.002	29.466	0.005	0.005	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.844	-0.908	28.726	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.087	-0.048	27.341	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.081	-0.039	24.244	0.007	0.007	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.913	-0.945	24.049	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.014	0.009	23.568	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.029	-0.016	21.132	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.051	-0.037	18.020	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.878	-0.929	18.511	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.020	-0.003	18.299	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.018	-0.016	15.876	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.826	-0.912	14.042	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.923	-0.940	13.468	-0.138	-0.138	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.006	-0.005	11.918	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.023	-0.023	7.078	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.867	0.920	8.594	0.060	0.060	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.006	0.012	9.610	-0.219	-0.219	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.041	-0.022	6.758	-0.102	-0.102	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.054	-0.029	4.184	-0.619	-0.440	-0.001	-0.010	-0.168	0.000
56	A	56	ALA	0	-0.032	-0.021	5.273	-0.776	-0.776	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.942	0.985	7.199	0.477	0.477	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.018	-0.031	2.573	-1.396	0.145	0.909	-0.651	-1.799	-0.001
59	A	59	GLY	0	-0.018	0.011	2.496	-7.354	-3.947	2.325	-2.375	-3.357	-0.028

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