FMO DATABASE

FMODB ID: 6ZJKZ

Calculation Name: 2JW4-A-Other547

Preferred Name: Nck adaptor protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JW4

Chain ID: A

ChEMBL ID: CHEMBL4846

UniProt ID: P16333

Base Structure: SolutionNMR

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-432709.249026
FMO2-HF: Nuclear repulsion	403622.116676
FMO2-HF: Total energy	-29087.13235
FMO2-MP2: Total energy	-29171.835343

3D Structure Molmil

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:GLY)

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

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.
-27.761	-26.856	-0.012	-0.323	-0.569	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.895

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

Sort

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	A	3	THR	0	-0.020	-0.007	3.832	1.566	2.471	-0.012	-0.323	-0.569	-0.001
4	A	4	MET	0	0.018	0.002	6.320	4.562	4.562	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.005	0.007	8.580	-3.129	-3.129	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.930	-0.969	9.990	-21.769	-21.769	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.910	-0.956	6.779	-46.121	-46.121	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.024	-0.003	11.081	1.236	1.236	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.004	0.007	14.853	0.450	0.450	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.006	-0.003	17.567	0.360	0.360	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.070	-0.038	21.358	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.056	0.034	24.226	0.234	0.234	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.821	0.896	27.624	11.034	11.034	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.019	-0.025	30.594	0.378	0.378	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.885	-0.942	31.830	-9.287	-9.287	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.038	-0.044	31.378	0.261	0.261	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.004	0.001	33.308	-0.220	-0.220	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.003	-0.003	31.651	0.048	0.048	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.022	-0.010	33.477	0.426	0.426	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.001	0.002	33.592	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.901	-0.956	33.395	-9.268	-9.268	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.046	-0.016	28.532	-0.424	-0.424	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.817	-0.881	28.482	-10.299	-10.299	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.074	-0.036	24.626	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.859	-0.910	28.672	-10.649	-10.649	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.010	-0.001	28.068	-0.502	-0.502	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.835	0.906	29.352	9.841	9.841	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.969	0.978	29.737	8.680	8.680	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.070	-0.046	27.954	0.328	0.328	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.810	-0.873	25.446	-12.350	-12.350	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.894	0.936	19.311	15.080	15.080	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.052	0.035	21.810	-0.105	-0.105	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.020	-0.003	15.268	0.473	0.473	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.027	-0.023	17.262	0.906	0.906	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.041	-0.025	15.567	-1.086	-1.086	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.912	-0.967	16.399	-17.055	-17.055	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.934	-0.966	17.824	-16.530	-16.530	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.023	0.017	20.204	0.631	0.631	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.945	0.972	21.958	11.888	11.888	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.002	-0.013	25.495	-0.125	-0.125	0.000	0.000	0.000	0.000
41	A	41	TRP	0	-0.055	-0.004	27.514	0.086	0.086	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.035	0.017	22.750	-0.451	-0.451	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.943	0.987	19.688	15.808	15.808	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.021	0.002	20.512	-0.945	-0.945	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.925	0.962	16.486	18.129	18.129	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.030	0.003	21.382	-0.198	-0.198	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.002	-0.001	21.828	-0.612	-0.612	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.016	-0.017	22.806	-0.143	-0.143	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.027	-0.007	21.298	0.654	0.654	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.892	0.933	22.249	10.622	10.622	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.005	-0.020	21.080	-0.768	-0.768	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.035	0.032	23.724	0.470	0.470	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.045	-0.017	24.144	-0.573	-0.573	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.023	0.008	25.362	0.467	0.467	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.023	0.021	27.217	-0.292	-0.292	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.025	-0.005	26.761	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.016	-0.004	28.106	-0.154	-0.154	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.010	-0.003	30.286	0.240	0.240	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.002	-0.001	25.039	-0.107	-0.107	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.829	-0.898	25.016	-11.670	-11.670	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.979	1.002	16.799	17.106	17.106	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.956	0.968	18.985	14.695	14.695	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.006	-0.017	12.969	0.482	0.482	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.005	0.018	17.185	-0.227	-0.227	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.040	0.019	19.584	-0.328	-0.328	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.952	0.959	20.581	12.819	12.819	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.030	0.014	23.902	0.075	0.075	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.007	-0.002	26.865	0.166	0.166	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.002	0.009	24.511	0.220	0.220	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.024	-0.018	24.156	-0.433	-0.433	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.048	-0.026	21.631	-0.227	-0.227	0.000	0.000	0.000	0.000
72	A	72	SER	-1	-0.931	-0.949	23.116	-11.986	-11.986	0.000	0.000	0.000	0.000

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