FMO DATABASE

FMODB ID: QL86Y

Calculation Name: 1NE3-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NE3

Chain ID: A

ChEMBL ID:

UniProt ID: O26356

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-353267.328575
FMO2-HF: Nuclear repulsion	325310.300784
FMO2-HF: Total energy	-27957.027792
FMO2-MP2: Total energy	-28034.247542

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: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.
-61.435	-54.641	3.5	-5.398	-4.898	-0.068

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 : 1 / q_Mulliken : 0.763 / q_NPA : 0.867

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	A	3	ASP	-1	-0.929	-0.947	2.131	-98.690	-92.155	3.492	-5.343	-4.685	-0.067
4	A	4	ALA	0	-0.035	-0.031	3.747	9.006	9.265	0.008	-0.055	-0.213	-0.001
5	A	5	THR	0	-0.049	-0.041	7.178	-2.526	-2.526	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.025	0.013	8.664	2.003	2.003	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.007	-0.020	11.702	0.882	0.882	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.845	-0.913	15.204	-15.661	-15.661	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.101	-0.051	18.804	0.078	0.078	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.022	-0.016	21.270	0.449	0.449	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.798	-0.888	23.777	-10.939	-10.939	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.006	-0.006	24.810	-0.520	-0.520	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.050	-0.004	25.247	0.407	0.407	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.963	0.973	28.515	10.981	10.981	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.950	0.975	32.023	9.221	9.221	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.015	0.011	35.106	0.132	0.132	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.018	0.013	35.629	-0.203	-0.203	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.016	-0.020	34.467	-0.159	-0.159	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.030	-0.020	34.155	0.202	0.202	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.034	0.021	31.807	-0.072	-0.072	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.928	-0.938	28.349	-10.655	-10.655	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.052	-0.036	23.767	-0.201	-0.201	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.027	0.020	26.490	0.505	0.505	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.015	0.007	24.216	-0.282	-0.282	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.014	-0.015	21.251	0.505	0.505	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.846	0.910	21.671	11.514	11.514	0.000	0.000	0.000	0.000
27	A	27	CYS	0	0.000	0.026	17.130	-0.115	-0.115	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.959	0.972	18.357	14.433	14.433	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.021	-0.008	12.089	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.002	0.020	14.952	0.958	0.958	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.850	-0.936	11.201	-20.702	-20.702	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.010	0.001	9.762	-1.960	-1.960	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.916	0.954	5.096	43.462	43.462	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.888	-0.943	11.704	-21.640	-21.640	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.948	0.981	13.834	21.057	21.057	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.013	0.016	15.571	0.922	0.922	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.934	0.967	14.550	19.578	19.578	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.010	0.011	17.208	-0.473	-0.473	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.048	-0.022	14.744	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.007	0.003	18.640	0.301	0.301	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.928	0.960	14.520	18.928	18.928	0.000	0.000	0.000	0.000
42	A	42	ASN	0	0.028	0.014	20.343	0.378	0.378	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.012	0.001	19.962	-0.687	-0.687	0.000	0.000	0.000	0.000
44	A	44	MET	0	0.014	0.012	21.817	0.491	0.491	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.052	0.029	23.682	-0.348	-0.348	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.025	-0.018	26.319	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.019	0.021	20.732	0.102	0.102	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.813	0.866	24.950	12.737	12.737	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.913	-0.971	24.434	-11.562	-11.562	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.027	0.008	23.662	0.429	0.429	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.853	-0.914	20.994	-14.238	-14.238	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.025	0.017	15.410	-0.299	-0.299	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.061	-0.041	15.653	0.051	0.051	0.000	0.000	0.000	0.000
54	A	54	MET	0	0.006	0.007	9.546	-1.205	-1.205	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.067	-0.046	11.026	1.350	1.350	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.036	0.028	7.154	-2.634	-2.634	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.963	-0.974	8.255	-30.721	-30.721	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.025	-0.026	10.756	0.686	0.686	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.017	0.014	13.586	0.772	0.772	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.938	0.973	15.127	14.955	14.955	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.894	-0.944	18.969	-15.071	-15.071	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.028	-0.025	21.368	0.392	0.392	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.906	0.952	24.400	11.096	11.096	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.915	-0.949	27.663	-10.297	-10.297	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.031	-0.021	30.124	0.082	0.082	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.953	0.963	33.852	8.985	8.985	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.005	0.001	36.507	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	PRO	-1	-0.934	-0.954	40.184	-7.474	-7.474	0.000	0.000	0.000	0.000

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