FMO DATABASE

FMODB ID: Y95J2

Calculation Name: 1X0F-A-Other547

Preferred Name: Heterogeneous nuclear ribonucleoprotein D0

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X0F

Chain ID: A

ChEMBL ID: CHEMBL4296009

UniProt ID: Q14103

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-537979.913931
FMO2-HF: Nuclear repulsion	505573.558266
FMO2-HF: Total energy	-32406.355666
FMO2-MP2: Total energy	-32498.825574

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:181:VAL)

Summations of interaction energy for fragment #1(A:181:VAL)

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.
-58.943	-56.602	0.145	-0.656	-1.831	-0.003

Interaction energy analysis for fragmet #1(A:181:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.921

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	183	LYS	1	0.920	0.972	2.909	39.390	41.365	0.143	-0.604	-1.513	-0.003
4	A	184	ILE	0	-0.006	0.024	4.316	0.604	0.620	-0.001	-0.007	-0.009	0.000
49	A	229	THR	0	-0.019	-0.003	3.559	-4.123	-3.944	0.005	-0.034	-0.151	0.000
78	A	258	MET	0	-0.056	-0.031	5.018	-4.314	-4.274	-0.001	-0.002	-0.037	0.000
79	A	259	SER	-1	-0.913	-0.946	4.545	-32.223	-32.092	-0.001	-0.009	-0.121	0.000
5	A	185	PHE	0	-0.014	-0.009	7.890	1.087	1.087	0.000	0.000	0.000	0.000
6	A	186	VAL	0	0.031	-0.010	10.373	0.886	0.886	0.000	0.000	0.000	0.000
7	A	187	GLY	0	0.025	0.007	13.723	0.773	0.773	0.000	0.000	0.000	0.000
8	A	188	GLY	0	-0.008	-0.008	16.499	0.445	0.445	0.000	0.000	0.000	0.000
9	A	189	LEU	0	-0.047	-0.023	17.510	0.028	0.028	0.000	0.000	0.000	0.000
10	A	190	SER	0	-0.008	-0.017	20.774	0.392	0.392	0.000	0.000	0.000	0.000
11	A	191	PRO	0	-0.044	-0.024	23.285	-0.318	-0.318	0.000	0.000	0.000	0.000
12	A	192	ASP	-1	-0.889	-0.942	23.128	-11.054	-11.054	0.000	0.000	0.000	0.000
13	A	193	THR	0	-0.002	-0.024	19.454	0.286	0.286	0.000	0.000	0.000	0.000
14	A	194	PRO	0	0.024	0.021	20.531	-0.369	-0.369	0.000	0.000	0.000	0.000
15	A	195	GLU	-1	-0.813	-0.947	16.749	-14.977	-14.977	0.000	0.000	0.000	0.000
16	A	196	GLU	-1	-0.917	-0.953	17.869	-14.159	-14.159	0.000	0.000	0.000	0.000
17	A	197	LYS	1	0.982	0.991	20.218	11.384	11.384	0.000	0.000	0.000	0.000
18	A	198	ILE	0	-0.075	-0.018	14.881	-0.373	-0.373	0.000	0.000	0.000	0.000
19	A	199	ARG	1	0.990	0.970	14.443	16.124	16.124	0.000	0.000	0.000	0.000
20	A	200	GLU	-1	-0.911	-0.942	17.024	-12.941	-12.941	0.000	0.000	0.000	0.000
21	A	201	TYR	0	-0.084	-0.060	16.273	0.139	0.139	0.000	0.000	0.000	0.000
22	A	202	PHE	0	-0.018	-0.036	13.095	-0.373	-0.373	0.000	0.000	0.000	0.000
23	A	203	GLY	0	0.038	0.030	14.587	-1.170	-1.170	0.000	0.000	0.000	0.000
24	A	204	GLY	0	0.006	0.001	16.416	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	205	PHE	0	-0.086	-0.045	14.327	0.126	0.126	0.000	0.000	0.000	0.000
26	A	206	GLY	0	0.008	-0.002	14.146	-0.548	-0.548	0.000	0.000	0.000	0.000
27	A	207	GLU	-1	-0.804	-0.899	11.387	-20.971	-20.971	0.000	0.000	0.000	0.000
28	A	208	VAL	0	-0.031	-0.018	10.507	-2.710	-2.710	0.000	0.000	0.000	0.000
29	A	209	GLU	-1	-0.964	-0.982	6.621	-29.682	-29.682	0.000	0.000	0.000	0.000
30	A	210	SER	0	-0.081	-0.071	8.311	1.023	1.023	0.000	0.000	0.000	0.000
31	A	211	ILE	0	-0.006	-0.014	9.778	-0.828	-0.828	0.000	0.000	0.000	0.000
32	A	212	GLU	-1	-0.801	-0.868	9.033	-23.864	-23.864	0.000	0.000	0.000	0.000
33	A	213	LEU	0	0.009	0.004	13.127	-0.577	-0.577	0.000	0.000	0.000	0.000
34	A	214	PRO	0	-0.054	-0.020	14.293	0.815	0.815	0.000	0.000	0.000	0.000
35	A	215	MET	0	0.032	0.019	17.028	0.535	0.535	0.000	0.000	0.000	0.000
36	A	216	ASP	-1	-0.860	-0.947	20.856	-12.295	-12.295	0.000	0.000	0.000	0.000
37	A	217	ASN	0	0.046	0.010	23.029	0.050	0.050	0.000	0.000	0.000	0.000
38	A	218	LYS	1	0.949	0.988	26.031	10.030	10.030	0.000	0.000	0.000	0.000
39	A	219	THR	0	-0.036	-0.027	25.116	0.303	0.303	0.000	0.000	0.000	0.000
40	A	220	ASN	0	-0.007	0.012	25.177	0.230	0.230	0.000	0.000	0.000	0.000
41	A	221	LYS	1	0.995	0.997	21.054	12.932	12.932	0.000	0.000	0.000	0.000
42	A	222	ARG	1	0.967	0.975	22.621	11.541	11.541	0.000	0.000	0.000	0.000
43	A	223	ARG	1	0.838	0.930	17.611	14.051	14.051	0.000	0.000	0.000	0.000
44	A	224	GLY	0	0.043	0.018	18.743	-0.408	-0.408	0.000	0.000	0.000	0.000
45	A	225	PHE	0	-0.020	-0.002	12.994	0.165	0.165	0.000	0.000	0.000	0.000
46	A	226	CYS	0	0.005	0.015	14.192	0.277	0.277	0.000	0.000	0.000	0.000
47	A	227	PHE	0	0.039	0.013	8.088	-0.564	-0.564	0.000	0.000	0.000	0.000
48	A	228	ILE	0	0.004	0.009	8.876	1.174	1.174	0.000	0.000	0.000	0.000
50	A	230	PHE	0	0.001	-0.012	5.594	4.414	4.414	0.000	0.000	0.000	0.000
51	A	231	LYS	1	0.881	0.960	5.757	16.918	16.918	0.000	0.000	0.000	0.000
52	A	232	GLU	-1	-0.898	-0.944	6.642	-30.862	-30.862	0.000	0.000	0.000	0.000
53	A	233	GLU	-1	-0.946	-0.998	6.353	-39.267	-39.267	0.000	0.000	0.000	0.000
54	A	234	GLU	-1	-0.810	-0.893	7.945	-26.004	-26.004	0.000	0.000	0.000	0.000
55	A	235	PRO	0	-0.015	-0.006	10.502	1.303	1.303	0.000	0.000	0.000	0.000
56	A	236	VAL	0	0.006	0.003	5.981	0.671	0.671	0.000	0.000	0.000	0.000
57	A	237	LYS	1	0.895	0.942	9.132	24.981	24.981	0.000	0.000	0.000	0.000
58	A	238	LYS	1	0.966	0.985	11.559	19.858	19.858	0.000	0.000	0.000	0.000
59	A	239	ILE	0	-0.085	-0.046	10.798	1.738	1.738	0.000	0.000	0.000	0.000
60	A	240	MET	0	-0.028	-0.002	9.529	0.086	0.086	0.000	0.000	0.000	0.000
61	A	241	GLU	-1	-0.881	-0.925	12.785	-17.794	-17.794	0.000	0.000	0.000	0.000
62	A	242	LYS	1	0.849	0.929	15.888	17.559	17.559	0.000	0.000	0.000	0.000
63	A	243	LYS	1	0.871	0.936	17.075	14.129	14.129	0.000	0.000	0.000	0.000
64	A	244	TYR	0	0.006	-0.021	18.853	0.090	0.090	0.000	0.000	0.000	0.000
65	A	245	HIS	0	0.012	0.038	14.981	0.496	0.496	0.000	0.000	0.000	0.000
66	A	246	ASN	0	-0.022	-0.023	18.901	0.972	0.972	0.000	0.000	0.000	0.000
67	A	247	VAL	0	0.055	0.042	17.321	0.099	0.099	0.000	0.000	0.000	0.000
68	A	248	GLY	0	0.058	0.037	20.458	0.215	0.215	0.000	0.000	0.000	0.000
69	A	249	LEU	0	-0.065	-0.039	23.630	0.518	0.518	0.000	0.000	0.000	0.000
70	A	250	SER	0	0.001	0.035	20.940	0.188	0.188	0.000	0.000	0.000	0.000
71	A	251	LYS	1	0.870	0.908	21.142	11.328	11.328	0.000	0.000	0.000	0.000
72	A	252	CYS	0	0.021	0.044	17.035	0.377	0.377	0.000	0.000	0.000	0.000
73	A	253	GLU	-1	-0.834	-0.901	17.309	-15.574	-15.574	0.000	0.000	0.000	0.000
74	A	254	ILE	0	-0.043	-0.020	11.528	-0.412	-0.412	0.000	0.000	0.000	0.000
75	A	255	LYS	1	0.892	0.959	12.086	17.388	17.388	0.000	0.000	0.000	0.000
76	A	256	VAL	0	0.050	0.018	5.917	-0.362	-0.362	0.000	0.000	0.000	0.000
77	A	257	ALA	0	-0.061	-0.035	6.014	2.058	2.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:181:VAL)