FMO DATABASE

FMODB ID: 46R9N

Calculation Name: 2M3D-A-Other547

Preferred Name: Nucleolar RNA helicase 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2M3D

Chain ID: A

ChEMBL ID: CHEMBL4296016

UniProt ID: Q9NR30

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-632917.584639
FMO2-HF: Nuclear repulsion	595055.914755
FMO2-HF: Total energy	-37861.669884
FMO2-MP2: Total energy	-37969.794931

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.
-44.861	-43.829	-0.014	-0.43	-0.588	-0.002

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 : 0.862 / 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	ILE	0	0.066	0.038	3.840	2.018	3.050	-0.014	-0.430	-0.588	-0.002
4	A	4	SER	0	-0.036	-0.019	7.169	2.112	2.112	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.031	0.016	10.572	0.180	0.180	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.035	0.026	13.708	0.798	0.798	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.014	-0.015	16.244	0.808	0.808	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.008	0.022	19.082	-0.477	-0.477	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.027	-0.031	21.922	-0.301	-0.301	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.829	-0.905	24.328	-10.274	-10.274	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.039	-0.010	26.559	-0.050	-0.050	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.853	0.921	29.076	10.525	10.525	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.013	-0.021	31.007	0.451	0.451	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.001	-0.009	30.058	-0.333	-0.333	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.018	0.008	28.258	-0.206	-0.206	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.005	0.003	26.754	0.254	0.254	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.071	0.037	23.388	0.215	0.215	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.066	-0.014	23.478	0.030	0.030	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.039	0.007	24.263	-0.319	-0.319	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.016	0.005	26.773	0.406	0.406	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.075	-0.034	27.222	0.154	0.154	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.047	0.040	20.851	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.009	-0.012	23.701	0.135	0.135	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.021	-0.007	19.262	-0.599	-0.599	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.011	-0.018	19.261	0.756	0.756	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.004	0.004	20.315	-0.451	-0.451	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.000	0.002	17.050	0.808	0.808	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.002	0.009	21.301	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.002	0.001	21.924	0.041	0.041	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.035	-0.028	24.357	0.334	0.334	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.808	-0.891	27.847	-9.327	-9.327	0.000	0.000	0.000	0.000
32	A	32	MET	0	-0.021	0.014	27.156	0.164	0.164	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.012	-0.003	31.523	0.111	0.111	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.006	-0.001	34.520	0.143	0.143	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.079	0.023	31.635	-0.210	-0.210	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.013	-0.021	31.897	-0.211	-0.211	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.052	-0.021	29.957	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.112	0.041	26.995	-0.141	-0.141	0.000	0.000	0.000	0.000
39	A	39	TRP	0	-0.006	-0.002	27.902	-0.244	-0.244	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.945	0.975	30.204	8.828	8.828	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.823	-0.918	24.666	-11.639	-11.639	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.017	-0.018	23.612	-0.289	-0.289	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.766	0.882	26.613	8.864	8.864	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.955	-0.966	27.275	-10.526	-10.526	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.041	-0.006	23.088	-0.392	-0.392	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.038	-0.026	23.310	-0.157	-0.157	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.011	0.026	26.843	0.230	0.230	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.866	-0.965	30.552	-8.799	-8.799	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.925	-0.940	33.428	-8.353	-8.353	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.033	-0.037	27.709	-0.179	-0.179	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.878	-0.940	31.638	-8.814	-8.814	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.020	-0.005	33.969	0.211	0.211	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.881	0.942	29.954	10.180	10.180	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.012	0.010	28.550	-0.345	-0.345	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.928	0.973	30.344	9.469	9.469	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.006	-0.011	32.185	0.028	0.028	0.000	0.000	0.000	0.000
57	A	57	MET	0	-0.008	0.014	28.059	-0.156	-0.156	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.005	-0.001	29.131	0.384	0.384	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.003	-0.017	28.721	-0.365	-0.365	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.003	0.029	22.523	0.026	0.026	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.978	0.967	25.990	11.820	11.820	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.009	-0.008	26.305	-0.350	-0.350	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.835	0.919	28.444	9.248	9.248	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.016	-0.008	24.735	0.208	0.208	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.079	0.020	24.263	-0.628	-0.628	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.061	-0.030	24.780	0.554	0.554	0.000	0.000	0.000	0.000
67	A	67	CYS	0	-0.014	0.001	24.223	-0.562	-0.562	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.069	0.020	24.444	0.596	0.596	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.842	-0.900	25.687	-11.369	-11.369	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.008	-0.008	24.236	0.425	0.425	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.039	0.024	26.333	-0.247	-0.247	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.056	0.002	22.799	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.001	0.007	23.456	-0.472	-0.472	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.023	-0.005	24.281	-0.207	-0.207	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.042	-0.008	19.926	-0.257	-0.257	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.026	-0.014	19.217	-0.915	-0.915	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.915	-0.950	20.247	-11.630	-11.630	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.001	-0.017	20.868	-0.196	-0.196	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.044	-0.037	15.505	-0.333	-0.333	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.936	-0.944	16.947	-16.422	-16.422	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.811	0.909	18.936	12.546	12.546	0.000	0.000	0.000	0.000
82	A	82	TRP	0	0.013	0.005	17.323	0.894	0.894	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.014	0.011	17.821	-1.093	-1.093	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.910	-0.927	14.640	-19.075	-19.075	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.052	0.026	17.117	0.790	0.790	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.922	0.947	19.472	12.717	12.717	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.812	0.888	21.265	11.975	11.975	0.000	0.000	0.000	0.000
88	A	88	TRP	0	0.007	0.018	21.535	0.043	0.043	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.042	-0.038	15.197	-1.229	-1.229	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.054	0.029	17.328	0.759	0.759	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.054	-0.029	15.563	-1.200	-1.200	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.003	0.009	15.482	1.040	1.040	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.011	0.001	17.055	-0.738	-0.738	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.056	-0.040	16.170	-0.384	-0.384	0.000	0.000	0.000	0.000
95	A	95	GLU	-2	-1.886	-1.929	18.169	-26.573	-26.573	0.000	0.000	0.000	0.000

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