FMO DATABASE

FMODB ID: 98Z12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-303982.863687
FMO2-HF: Nuclear repulsion	279624.377338
FMO2-HF: Total energy	-24358.486349
FMO2-MP2: Total energy	-24426.960168

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.
-29.029	-19.951	11.743	-6.06	-14.758	-0.045

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 : -0.008 / 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	0.944	0.951	3.225	-1.323	0.760	0.102	-1.176	-1.009	0.000
4	A	4	GLN	0	0.029	0.027	5.478	0.763	0.763	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.763	-0.841	2.381	-4.678	-2.313	1.023	-1.490	-1.898	-0.012
6	A	6	LYS	1	0.984	0.988	2.569	-5.650	-4.535	4.806	-1.713	-4.207	0.009
7	A	7	THR	0	-0.062	-0.036	3.793	0.160	-1.734	0.042	2.236	-0.384	0.000
8	A	8	ALA	0	0.025	0.012	6.888	-0.263	-0.263	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.016	0.016	2.575	-0.814	-0.600	1.501	-0.239	-1.476	-0.001
10	A	10	ASN	0	-0.015	-0.018	6.440	-0.406	-0.406	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.005	0.011	8.276	-0.364	-0.364	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.055	0.030	9.289	-0.142	-0.142	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.882	0.932	5.650	-1.227	-1.227	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.026	-0.007	10.847	-0.074	-0.074	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.031	0.011	13.824	-0.063	-0.063	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.894	0.950	13.320	0.069	0.069	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.004	-0.005	15.172	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.041	-0.026	16.945	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.015	-0.009	18.166	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.009	0.034	19.491	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.011	-0.002	21.186	0.001	0.001	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.065	-0.031	23.110	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.056	0.025	24.194	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.928	-0.968	24.369	0.059	0.059	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.777	0.862	27.248	-0.067	-0.067	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.020	-0.010	27.690	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.041	0.011	28.284	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.904	-0.940	29.821	0.048	0.048	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.071	-0.025	32.951	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.003	0.002	34.935	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.927	-0.966	36.458	0.005	0.005	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.057	-0.022	38.358	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.042	-0.027	33.622	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.841	-0.904	33.739	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.903	-0.945	33.483	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.047	-0.057	31.226	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.003	0.009	29.490	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.879	-0.928	28.563	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.073	-0.038	27.606	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.061	-0.029	24.203	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.923	-0.953	23.935	-0.055	-0.055	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.009	0.004	23.335	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.020	-0.020	21.290	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.052	-0.034	17.903	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.855	-0.924	18.405	-0.147	-0.147	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.033	-0.009	18.055	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.003	0.000	15.940	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.778	-0.881	13.951	-0.294	-0.294	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.961	-0.964	13.381	-0.392	-0.392	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.014	0.005	12.043	-0.117	-0.117	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.018	-0.007	7.100	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.861	0.905	8.617	0.119	0.119	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.004	0.013	9.408	-0.345	-0.345	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.068	-0.043	6.500	-0.179	-0.179	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.045	-0.034	4.084	-1.124	-0.962	-0.001	-0.011	-0.149	0.000
56	A	56	ALA	0	-0.009	-0.004	5.385	-1.027	-1.027	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.920	0.975	7.151	0.952	0.952	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.025	-0.025	2.459	-1.083	0.335	1.176	-0.738	-1.855	-0.001
59	A	59	GLY	0	-0.013	0.006	2.477	-11.043	-7.428	3.094	-2.929	-3.780	-0.040

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