FMO DATABASE

FMODB ID: QKZYY

Calculation Name: 1NER-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NER

Chain ID: A

ChEMBL ID:

UniProt ID: P06020

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-446748.990476
FMO2-HF: Nuclear repulsion	417826.579775
FMO2-HF: Total energy	-28922.410701
FMO2-MP2: Total energy	-29008.198669

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:CYS)

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

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.
77.982	79.304	-0.008	-0.357	-0.957	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.917

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	ASN	0	-0.010	0.007	3.876	3.916	5.109	-0.007	-0.344	-0.843	0.001
5	A	5	LYS	1	0.925	0.988	4.502	51.969	52.098	-0.001	-0.013	-0.114	0.000
4	A	4	GLU	-1	-0.809	-0.900	5.658	-24.017	-24.017	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.070	-0.055	7.657	-2.190	-2.190	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.843	0.898	8.488	27.791	27.791	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.784	-0.878	12.223	-20.769	-20.769	0.000	0.000	0.000	0.000
9	A	9	TRP	0	-0.055	-0.014	13.349	-0.835	-0.835	0.000	0.000	0.000	0.000
10	A	10	HIS	0	0.013	0.011	10.460	-2.079	-2.079	0.000	0.000	0.000	0.000
11	A	11	ARG	1	1.009	0.988	12.167	25.446	25.446	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.049	-0.017	14.494	1.239	1.239	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.778	-0.901	15.262	-19.414	-19.414	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.039	0.034	17.110	1.274	1.274	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.014	-0.010	19.006	1.180	1.180	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.016	-0.016	20.143	0.885	0.885	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.026	0.014	21.217	0.716	0.716	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.019	-0.006	22.823	0.753	0.753	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.911	0.946	24.170	13.486	13.486	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.918	0.968	25.585	11.927	11.927	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.938	0.982	27.291	11.472	11.472	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.975	0.974	30.430	9.087	9.087	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.033	0.041	27.492	0.177	0.177	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.005	-0.027	25.802	-0.325	-0.325	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.090	0.051	20.733	0.424	0.424	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.034	0.002	25.317	0.115	0.115	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.078	-0.018	27.598	0.407	0.407	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.055	0.007	26.060	0.258	0.258	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.047	-0.035	27.075	0.149	0.149	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.960	0.968	29.006	9.817	9.817	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.036	-0.020	32.360	0.173	0.173	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.021	0.014	31.732	0.211	0.211	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.002	0.020	33.144	0.184	0.184	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.005	0.005	28.654	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.069	0.050	27.861	-0.135	-0.135	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.033	0.000	25.055	-0.335	-0.335	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.009	-0.009	22.492	-0.501	-0.501	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.005	0.011	22.041	-0.631	-0.631	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.002	-0.001	22.902	-0.379	-0.379	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.024	-0.006	19.427	-0.498	-0.498	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.023	0.006	16.307	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.003	-0.009	18.772	-0.294	-0.294	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.032	0.000	16.153	0.202	0.202	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.918	-0.947	11.738	-23.645	-23.645	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.842	0.918	16.028	14.738	14.738	0.000	0.000	0.000	0.000
46	A	46	HIS	0	0.058	0.038	19.238	-0.363	-0.363	0.000	0.000	0.000	0.000
47	A	47	TRP	0	-0.023	-0.018	21.559	0.745	0.745	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.121	0.050	23.962	0.115	0.115	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.898	0.959	25.350	10.519	10.519	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.052	0.011	25.036	0.306	0.306	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.867	-0.935	20.776	-14.864	-14.864	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.001	-0.011	24.506	0.398	0.398	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.040	0.001	27.724	0.297	0.297	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.038	-0.029	22.293	0.198	0.198	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.003	0.004	25.861	0.101	0.101	0.000	0.000	0.000	0.000
56	A	56	ASN	0	0.018	0.010	27.201	0.334	0.334	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.010	-0.001	28.661	0.306	0.306	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.114	-0.062	25.146	0.099	0.099	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.950	-0.964	29.603	-9.090	-9.090	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.047	-0.017	26.779	0.139	0.139	0.000	0.000	0.000	0.000
61	A	61	LYS	1	1.006	1.001	27.343	10.514	10.514	0.000	0.000	0.000	0.000
62	A	62	PRO	0	-0.006	0.000	23.643	-0.319	-0.319	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.776	-0.903	22.372	-13.530	-13.530	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.064	-0.034	22.276	-0.396	-0.396	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.053	-0.026	19.237	-0.441	-0.441	0.000	0.000	0.000	0.000
66	A	66	TRP	0	0.023	-0.001	16.450	-0.651	-0.651	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.056	0.038	17.550	0.088	0.088	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.051	-0.031	14.900	-0.242	-0.242	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.811	0.904	12.211	20.946	20.946	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.027	0.030	18.121	0.528	0.528	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.034	-0.034	21.136	-0.113	-0.113	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.044	-0.026	23.631	0.376	0.376	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.013	0.009	26.082	0.365	0.365	0.000	0.000	0.000	0.000
74	A	74	GLU	-2	-1.924	-1.949	27.751	-20.254	-20.254	0.000	0.000	0.000	0.000

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