FMO DATABASE

FMODB ID: JV4V9

Calculation Name: 2FC9-A-Other547

Preferred Name: Nucleolin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FC9

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	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-650401.123289
FMO2-HF: Nuclear repulsion	612728.191013
FMO2-HF: Total energy	-37672.932276
FMO2-MP2: Total energy	-37783.713969

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.
17.027	17.987	-0.015	-0.414	-0.531	-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 : 0.851 / q_NPA : 0.913

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	0.041	0.033	3.848	0.408	1.368	-0.015	-0.414	-0.531	-0.001
4	A	4	GLY	0	0.040	0.011	5.633	5.539	5.539	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.080	-0.033	5.274	-6.692	-6.692	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.004	0.009	5.703	4.477	4.477	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.070	0.020	7.082	4.202	4.202	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.010	0.004	7.726	-5.734	-5.734	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.005	0.007	6.798	0.310	0.310	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.014	-0.017	8.820	0.360	0.360	0.000	0.000	0.000	0.000
11	A	11	TRP	0	-0.073	-0.027	7.947	-2.506	-2.506	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.023	0.002	9.260	2.388	2.388	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.007	0.003	11.779	0.365	0.365	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.942	-0.950	13.576	-16.158	-16.158	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.045	-0.050	15.189	0.703	0.703	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.978	1.008	16.880	14.493	14.493	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.010	-0.001	17.944	0.604	0.604	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.025	-0.003	15.105	-1.512	-1.512	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.020	-0.015	13.590	1.264	1.264	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.030	0.025	14.606	-1.169	-1.169	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.017	-0.029	13.700	0.841	0.841	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.003	-0.002	15.703	0.181	0.181	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.019	0.015	17.486	0.476	0.476	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.005	0.000	20.870	0.127	0.127	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.014	-0.037	24.113	0.340	0.340	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.029	0.023	27.170	0.185	0.185	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.011	0.020	25.470	0.221	0.221	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.024	-0.034	26.997	-0.383	-0.383	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.770	-0.906	27.720	-11.209	-11.209	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.868	-0.909	28.784	-9.483	-9.483	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.021	-0.001	26.946	-0.076	-0.076	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.042	-0.023	22.848	-0.392	-0.392	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.022	0.001	26.054	-0.586	-0.586	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.913	-0.937	28.675	-9.863	-9.863	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.133	-0.065	22.374	-0.191	-0.191	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.055	-0.047	19.777	-0.726	-0.726	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.849	-0.920	25.068	-10.376	-10.376	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.801	0.889	24.575	12.277	12.277	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.050	-0.019	24.339	-0.195	-0.195	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.046	-0.050	25.647	0.326	0.326	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.014	-0.011	26.034	0.467	0.467	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.014	0.011	24.166	-0.731	-0.731	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.836	0.920	24.103	11.454	11.454	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.023	0.001	23.710	-0.760	-0.760	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.053	-0.002	22.421	0.545	0.545	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.045	0.010	25.165	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.087	-0.059	25.997	-0.045	-0.045	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.015	-0.008	29.398	0.148	0.148	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.007	0.002	31.238	0.043	0.043	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.082	0.061	32.125	0.221	0.221	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.880	0.960	27.767	10.331	10.331	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.072	0.037	24.289	-0.085	-0.085	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.887	0.930	22.527	12.261	12.261	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.034	0.037	20.179	-0.398	-0.398	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.061	-0.036	17.612	-0.705	-0.705	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.004	-0.008	18.954	0.953	0.953	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.046	-0.012	17.340	-1.052	-1.052	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.015	0.019	19.527	0.760	0.760	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.912	-0.928	20.158	-13.087	-13.087	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.043	0.023	20.034	0.210	0.210	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.064	0.028	23.639	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.008	-0.002	23.002	0.105	0.105	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.037	-0.030	14.536	-0.811	-0.811	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.830	-0.916	18.707	-14.607	-14.607	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.804	-0.907	20.510	-12.874	-12.874	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.008	0.013	18.062	-0.255	-0.255	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.906	0.954	11.575	23.033	23.033	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.891	-0.936	17.093	-13.632	-13.632	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.024	0.011	19.649	-0.159	-0.159	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.035	-0.021	12.011	-0.460	-0.460	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.047	-0.049	14.669	-2.472	-2.472	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.027	0.002	16.165	-0.279	-0.279	0.000	0.000	0.000	0.000
73	A	73	CYS	0	-0.018	-0.008	18.688	0.131	0.131	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.005	-0.011	10.907	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.890	0.932	10.325	24.677	24.677	0.000	0.000	0.000	0.000
76	A	76	ARG	1	1.022	1.035	15.886	13.814	13.814	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.945	-0.974	19.620	-14.026	-14.026	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.014	-0.013	21.834	0.577	0.577	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.890	-0.953	23.953	-10.741	-10.741	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.005	0.007	25.196	0.038	0.038	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.826	0.902	19.159	14.191	14.191	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.051	0.037	17.090	0.059	0.059	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.023	0.007	17.066	-0.781	-0.781	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.763	0.862	8.164	30.225	30.225	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.017	0.011	13.017	0.896	0.896	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.843	-0.908	8.143	-37.118	-37.118	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.009	0.007	10.503	2.123	2.123	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.002	0.002	11.538	-2.086	-2.086	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.037	0.020	13.533	0.904	0.904	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.014	0.020	12.702	-0.817	-0.817	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.960	0.972	5.510	39.276	39.276	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.028	0.020	8.919	0.142	0.142	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.049	-0.040	6.606	-6.415	-6.415	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.007	0.003	5.259	2.540	2.540	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.030	0.012	8.063	1.811	1.811	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.018	-0.018	11.360	-1.522	-1.522	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.037	0.015	12.409	1.352	1.352	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.055	-0.016	14.741	-0.400	-0.400	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.013	-0.006	16.711	0.578	0.578	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.048	-0.015	19.586	-0.360	-0.360	0.000	0.000	0.000	0.000
101	A	101	GLY	-1	-0.926	-0.950	20.516	-12.900	-12.900	0.000	0.000	0.000	0.000

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