FMO DATABASE

FMODB ID: 8QGQY

Calculation Name: 2FC8-A-Other547

Preferred Name: Nucleolin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FC8

Chain ID: A

ChEMBL ID: CHEMBL4295725

UniProt ID: P19338

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-620605.378723
FMO2-HF: Nuclear repulsion	583362.171462
FMO2-HF: Total energy	-37243.207262
FMO2-MP2: Total energy	-37352.226533

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.
-87.88	-86.826	-0.001	-0.531	-0.522	-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 : 0.880 / q_NPA : 0.924

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	SER	0	0.047	0.012	3.387	-6.036	-4.982	-0.001	-0.531	-0.522	-0.001
4	A	4	GLY	0	0.012	0.012	5.817	2.945	2.945	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.015	0.010	9.648	0.695	0.695	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.004	-0.004	12.974	0.888	0.888	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.047	0.027	16.710	0.352	0.352	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.037	0.002	18.727	-0.665	-0.665	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.046	-0.019	14.612	-1.453	-1.453	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.022	0.014	17.977	-0.141	-0.141	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.951	0.963	21.278	12.493	12.493	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.051	-0.010	24.301	0.409	0.409	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.009	0.017	24.950	-0.483	-0.483	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.007	0.008	23.543	0.083	0.083	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.011	-0.012	25.653	0.572	0.572	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.896	0.924	27.280	9.752	9.752	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.026	-0.009	29.590	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.033	-0.007	23.796	-0.182	-0.182	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.022	-0.026	27.298	0.467	0.467	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.040	0.020	26.639	-0.558	-0.558	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.912	0.950	25.541	12.688	12.688	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.011	-0.004	27.305	-0.502	-0.502	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.014	0.004	29.101	-0.181	-0.181	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.068	0.032	31.547	0.163	0.163	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.903	-0.944	34.544	-8.061	-8.061	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.942	-0.971	37.789	-7.857	-7.857	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.088	-0.053	32.735	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.027	0.001	35.830	0.028	0.028	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.843	-0.946	35.346	-8.451	-8.451	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.906	-0.960	35.006	-8.412	-8.412	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.000	0.009	32.699	-0.340	-0.340	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.008	0.012	29.775	-0.396	-0.396	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.845	0.909	30.274	9.111	9.111	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.885	-0.944	30.221	-9.902	-9.902	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.030	-0.019	26.865	-0.326	-0.326	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.042	-0.025	24.011	-0.661	-0.661	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.871	-0.928	25.256	-11.554	-11.554	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.004	-0.002	26.082	-0.400	-0.400	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.083	-0.037	28.615	0.365	0.365	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.053	-0.035	30.173	0.299	0.299	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.888	0.928	33.600	8.443	8.443	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.054	0.051	32.814	-0.328	-0.328	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.849	0.921	34.274	8.513	8.513	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.048	0.034	34.841	-0.311	-0.311	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.087	-0.024	36.172	0.264	0.264	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.035	0.013	38.632	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.814	-0.891	41.669	-7.309	-7.309	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.869	0.930	43.616	6.648	6.648	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.987	-0.978	46.719	-6.587	-6.587	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.010	-0.038	44.960	0.073	0.073	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.050	-0.014	46.517	0.053	0.053	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.020	-0.016	41.768	0.009	0.009	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.005	0.003	37.339	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.882	0.923	37.162	7.891	7.891	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.124	0.079	34.451	-0.100	-0.100	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.101	-0.069	32.018	-0.378	-0.378	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.035	0.014	31.858	0.404	0.404	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.070	-0.032	30.936	-0.318	-0.318	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.033	0.026	28.699	0.253	0.253	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.874	-0.918	29.938	-9.652	-9.652	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.039	0.007	26.516	0.009	0.009	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.070	-0.049	29.519	0.173	0.173	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.001	-0.018	29.057	0.282	0.282	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.856	-0.930	26.023	-11.331	-11.331	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.970	-0.970	23.566	-13.180	-13.180	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.818	-0.892	23.126	-12.377	-12.377	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.008	0.010	24.242	-0.319	-0.319	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.800	0.888	16.360	18.110	18.110	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.014	0.002	19.473	-0.713	-0.713	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.041	0.018	19.961	-0.486	-0.486	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.905	0.945	18.203	16.546	16.546	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.905	-0.943	15.522	-20.501	-20.501	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.004	0.009	17.016	-0.448	-0.448	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.003	0.011	18.992	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-1.024	-0.999	13.968	-21.917	-21.917	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-1.002	-1.003	16.321	-17.580	-17.580	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.026	0.019	18.400	0.424	0.424	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.971	-1.010	21.750	-12.401	-12.401	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.021	-0.005	25.138	0.122	0.122	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.830	-0.908	28.608	-9.445	-9.445	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.005	0.025	28.563	0.230	0.230	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.087	-0.047	28.558	0.252	0.252	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.989	0.993	22.447	13.334	13.334	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.008	0.006	23.721	0.315	0.315	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.120	-0.067	22.075	-0.482	-0.482	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.034	0.033	20.928	0.745	0.745	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.927	-0.970	22.017	-13.970	-13.970	0.000	0.000	0.000	0.000
88	A	88	TRP	0	-0.016	-0.016	21.238	0.448	0.448	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.028	0.020	25.785	0.215	0.215	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.947	0.972	27.715	11.318	11.318	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.001	0.008	30.492	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.927	0.957	28.905	10.486	10.486	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.014	0.009	32.997	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.957	-0.986	36.547	-7.912	-7.912	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.040	0.016	36.151	0.137	0.137	0.000	0.000	0.000	0.000
96	A	96	GLY	0	-0.040	-0.029	33.151	-0.364	-0.364	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.031	0.027	33.782	-0.126	-0.126	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.017	0.007	33.033	-0.098	-0.098	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.079	-0.028	27.909	-0.093	-0.093	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.008	-0.011	29.827	0.166	0.166	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.110	-0.053	28.614	-0.339	-0.339	0.000	0.000	0.000	0.000
102	A	102	GLY	-1	-0.866	-0.917	30.223	-9.224	-9.224	0.000	0.000	0.000	0.000

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