FMO DATABASE

FMODB ID: N8NKQ

Calculation Name: 3JRV-B-Xray547

Preferred Name: ATP-dependent RNA helicase DDX3X

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JRV

Chain ID: B

ChEMBL ID: CHEMBL5553

UniProt ID: O00571

Base Structure: X-ray

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1464205.341612
FMO2-HF: Nuclear repulsion	1404496.696017
FMO2-HF: Total energy	-59708.645595
FMO2-MP2: Total energy	-59881.803918

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:6:ASP)

Summations of interaction energy for fragment #1(A:6:ASP)

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.
-60.13	-57.659	15.753	-10.867	-7.356	-0.104

Interaction energy analysis for fragmet #1(A:6:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.142 / q_NPA : -0.100

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	8	GLU	-1	-0.945	-0.973	3.049	-16.346	-13.326	0.068	-1.431	-1.657	0.005
4	A	9	ASP	-1	-0.898	-0.947	1.724	-66.106	-67.049	15.687	-9.403	-5.341	-0.109
5	A	10	ALA	0	-0.050	-0.018	4.089	5.068	5.315	-0.001	-0.028	-0.218	0.000
114	A	119	GLU	-1	-0.905	-0.951	4.753	8.601	8.748	-0.001	-0.005	-0.140	0.000
6	A	11	VAL	0	-0.030	-0.012	6.437	-0.448	-0.448	0.000	0.000	0.000	0.000
7	A	12	PHE	0	-0.041	-0.017	9.504	1.335	1.335	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.049	-0.044	10.834	-0.629	-0.629	0.000	0.000	0.000	0.000
9	A	14	PHE	0	0.051	0.018	15.808	-0.104	-0.104	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.044	-0.010	15.151	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.879	-0.949	18.025	-1.163	-1.163	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.876	-0.925	20.536	0.036	0.036	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.883	-0.961	23.176	-0.298	-0.298	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.819	0.894	26.300	0.037	0.037	0.000	0.000	0.000	0.000
15	A	20	ILE	0	0.050	0.036	23.112	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	21	CYS	0	-0.010	-0.005	26.878	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.028	-0.017	25.854	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.815	0.884	26.144	-0.749	-0.749	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.883	-0.942	24.482	0.857	0.857	0.000	0.000	0.000	0.000
20	A	25	SER	0	0.015	0.006	21.615	0.121	0.121	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.044	-0.018	21.207	0.012	0.012	0.000	0.000	0.000	0.000
22	A	27	ILE	0	-0.002	-0.005	18.454	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.862	-0.927	16.532	2.016	2.016	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.023	0.006	16.396	0.048	0.048	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.031	-0.025	18.138	-0.108	-0.108	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.891	-0.952	13.141	3.550	3.550	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.732	-0.824	13.030	0.774	0.774	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.045	0.021	13.982	-0.257	-0.257	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.039	-0.025	15.482	-0.215	-0.215	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.029	0.020	9.324	0.154	0.154	0.000	0.000	0.000	0.000
31	A	36	TRP	0	-0.001	-0.006	12.091	-0.227	-0.227	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.756	0.824	13.795	-0.523	-0.523	0.000	0.000	0.000	0.000
33	A	38	ASN	0	-0.017	0.013	10.988	0.035	0.035	0.000	0.000	0.000	0.000
34	A	39	HIS	0	0.012	0.010	7.025	-0.629	-0.629	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.021	-0.006	11.412	-0.914	-0.914	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.005	0.019	14.194	-0.321	-0.321	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.010	0.008	9.594	-0.216	-0.216	0.000	0.000	0.000	0.000
38	A	43	PHE	0	0.006	-0.009	6.135	-0.617	-0.617	0.000	0.000	0.000	0.000
39	A	44	ASN	0	-0.084	-0.029	10.824	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.901	0.963	8.963	5.784	5.784	0.000	0.000	0.000	0.000
41	A	46	ASP	-1	-0.812	-0.889	14.513	-1.008	-1.008	0.000	0.000	0.000	0.000
42	A	47	ILE	0	0.020	0.008	18.028	0.073	0.073	0.000	0.000	0.000	0.000
43	A	48	THR	0	-0.100	-0.077	19.605	0.213	0.213	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.019	-0.002	18.198	0.099	0.099	0.000	0.000	0.000	0.000
45	A	50	CYS	0	0.009	0.023	18.534	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.060	0.034	20.745	0.014	0.014	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.774	0.866	23.633	0.166	0.166	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.016	-0.004	22.364	0.056	0.056	0.000	0.000	0.000	0.000
49	A	54	TYR	0	0.053	-0.004	16.273	0.055	0.055	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.800	0.884	22.624	0.603	0.603	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.923	-0.970	25.732	0.068	0.068	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.023	0.015	21.395	0.039	0.039	0.000	0.000	0.000	0.000
53	A	58	MET	0	-0.026	-0.008	22.537	0.020	0.020	0.000	0.000	0.000	0.000
54	A	59	LYS	1	0.847	0.937	24.767	0.031	0.031	0.000	0.000	0.000	0.000
55	A	60	PHE	0	-0.009	-0.022	25.019	0.003	0.003	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.773	-0.846	24.338	0.235	0.235	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.903	-0.954	27.022	0.051	0.051	0.000	0.000	0.000	0.000
58	A	63	VAL	0	-0.100	-0.048	29.924	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	64	ALA	0	0.042	0.026	27.771	0.017	0.017	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.047	-0.032	29.147	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.888	0.943	32.075	-0.162	-0.162	0.000	0.000	0.000	0.000
62	A	67	TYR	0	0.011	0.017	32.417	0.004	0.004	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.044	-0.028	29.137	0.013	0.013	0.000	0.000	0.000	0.000
64	A	69	GLY	0	0.034	0.033	33.551	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	70	ILE	0	-0.004	-0.020	30.043	0.029	0.029	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.883	-0.941	31.419	0.181	0.181	0.000	0.000	0.000	0.000
67	A	72	LYS	1	0.812	0.884	32.297	-0.344	-0.344	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.008	0.009	26.870	0.053	0.053	0.000	0.000	0.000	0.000
69	A	74	ASN	0	-0.020	-0.015	27.458	0.047	0.047	0.000	0.000	0.000	0.000
70	A	75	GLU	-1	-0.833	-0.890	28.040	0.433	0.433	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.013	-0.011	25.413	0.050	0.050	0.000	0.000	0.000	0.000
72	A	77	VAL	0	-0.011	-0.016	22.487	0.084	0.084	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.945	-0.966	23.470	0.500	0.500	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.042	-0.021	24.998	0.063	0.063	0.000	0.000	0.000	0.000
75	A	80	MET	0	-0.027	-0.005	20.497	0.071	0.071	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.020	-0.011	20.634	0.171	0.171	0.000	0.000	0.000	0.000
77	A	82	GLU	-1	-0.870	-0.945	19.521	0.986	0.986	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.033	-0.014	18.511	0.159	0.159	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.942	-0.958	19.468	1.330	1.330	0.000	0.000	0.000	0.000
80	A	85	HIS	0	-0.102	-0.057	22.343	-0.069	-0.069	0.000	0.000	0.000	0.000
81	A	86	TYR	0	0.000	0.003	18.420	0.050	0.050	0.000	0.000	0.000	0.000
82	A	87	ILE	0	0.014	-0.002	22.091	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.007	0.015	24.577	0.092	0.092	0.000	0.000	0.000	0.000
84	A	89	PHE	0	0.054	0.008	21.040	-0.146	-0.146	0.000	0.000	0.000	0.000
85	A	90	THR	0	-0.004	-0.014	26.855	-0.087	-0.087	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.904	0.955	30.016	-0.707	-0.707	0.000	0.000	0.000	0.000
87	A	92	VAL	0	-0.034	-0.001	28.034	-0.066	-0.066	0.000	0.000	0.000	0.000
88	A	93	HIS	1	0.853	0.931	31.298	-0.481	-0.481	0.000	0.000	0.000	0.000
89	A	94	ASP	-1	-0.851	-0.905	33.590	0.412	0.412	0.000	0.000	0.000	0.000
90	A	95	GLN	0	0.053	0.024	32.410	0.032	0.032	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.941	-0.960	31.753	0.316	0.316	0.000	0.000	0.000	0.000
92	A	97	SER	0	0.020	-0.022	31.623	0.034	0.034	0.000	0.000	0.000	0.000
93	A	98	LEU	0	0.004	0.022	26.633	0.048	0.048	0.000	0.000	0.000	0.000
94	A	99	PHE	0	0.014	-0.009	27.267	0.041	0.041	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.023	0.017	27.118	0.008	0.008	0.000	0.000	0.000	0.000
96	A	101	THR	0	-0.009	-0.025	25.018	0.006	0.006	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.028	0.020	21.910	0.080	0.080	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.011	0.009	22.513	0.025	0.025	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.016	-0.014	23.551	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	105	CYS	0	-0.058	-0.028	19.398	0.067	0.067	0.000	0.000	0.000	0.000
101	A	106	ALA	0	0.033	0.021	19.064	0.085	0.085	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.875	0.935	19.603	-0.198	-0.198	0.000	0.000	0.000	0.000
103	A	108	ILE	0	0.012	0.007	18.383	-0.087	-0.087	0.000	0.000	0.000	0.000
104	A	109	THR	0	-0.025	-0.024	14.789	-0.082	-0.082	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.780	-0.862	15.818	-0.132	-0.132	0.000	0.000	0.000	0.000
106	A	111	HIS	0	-0.018	0.008	18.351	-0.136	-0.136	0.000	0.000	0.000	0.000
107	A	112	TRP	0	-0.031	-0.038	14.851	-0.050	-0.050	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.077	0.035	14.434	-0.119	-0.119	0.000	0.000	0.000	0.000
109	A	114	TYR	0	-0.060	-0.042	15.478	-0.395	-0.395	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.847	0.938	17.823	-0.607	-0.607	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.796	0.893	13.394	1.945	1.945	0.000	0.000	0.000	0.000
112	A	117	ILE	0	-0.016	0.006	12.430	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	118	SER	0	0.066	0.027	7.759	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	120	SER	0	-0.066	-0.038	8.524	-0.176	-0.176	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.830	0.919	11.689	-2.057	-2.057	0.000	0.000	0.000	0.000
117	A	122	PHE	0	0.037	0.042	5.343	-0.562	-0.562	0.000	0.000	0.000	0.000
118	A	123	GLN	0	-0.042	-0.030	11.354	-0.599	-0.599	0.000	0.000	0.000	0.000
119	A	124	SER	0	0.016	0.000	13.827	-0.374	-0.374	0.000	0.000	0.000	0.000
120	A	125	LEU	0	0.040	0.013	16.629	-0.306	-0.306	0.000	0.000	0.000	0.000
121	A	126	GLY	0	0.044	0.034	18.754	-0.258	-0.258	0.000	0.000	0.000	0.000
122	A	127	ASN	0	-0.089	-0.058	18.965	0.367	0.367	0.000	0.000	0.000	0.000
123	A	128	ILE	0	0.079	0.032	17.480	-0.219	-0.219	0.000	0.000	0.000	0.000
124	A	129	THR	0	0.002	-0.005	20.212	-0.097	-0.097	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.880	-0.926	23.046	1.290	1.290	0.000	0.000	0.000	0.000
126	A	131	LEU	0	-0.060	-0.017	21.881	-0.130	-0.130	0.000	0.000	0.000	0.000
127	A	132	MET	0	-0.044	-0.017	22.314	-0.168	-0.168	0.000	0.000	0.000	0.000
128	A	133	THR	0	0.077	0.037	24.903	0.035	0.035	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.790	-0.892	27.954	0.866	0.866	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.929	-0.959	29.989	0.590	0.590	0.000	0.000	0.000	0.000
131	A	136	ASN	0	-0.025	-0.028	28.020	-0.115	-0.115	0.000	0.000	0.000	0.000
132	A	137	ILE	0	0.010	0.005	25.083	-0.040	-0.040	0.000	0.000	0.000	0.000
133	A	138	ASN	0	0.018	0.005	27.942	-0.045	-0.045	0.000	0.000	0.000	0.000
134	A	139	ILE	0	-0.025	-0.016	31.419	-0.059	-0.059	0.000	0.000	0.000	0.000
135	A	140	LEU	0	0.007	0.006	24.400	-0.057	-0.057	0.000	0.000	0.000	0.000
136	A	141	ILE	0	0.001	0.011	27.624	-0.053	-0.053	0.000	0.000	0.000	0.000
137	A	142	LEU	0	0.012	0.012	29.547	-0.065	-0.065	0.000	0.000	0.000	0.000
138	A	143	PHE	0	-0.063	-0.031	30.139	-0.064	-0.064	0.000	0.000	0.000	0.000
139	A	144	LEU	0	0.031	0.003	25.662	-0.056	-0.056	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.841	-0.933	30.051	0.281	0.281	0.000	0.000	0.000	0.000
141	A	146	LYS	1	0.843	0.921	32.492	-0.247	-0.247	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.880	0.951	31.654	-0.142	-0.142	0.000	0.000	0.000	0.000
143	A	148	LEU	0	-0.037	0.001	27.726	-0.045	-0.045	0.000	0.000	0.000	0.000
144	A	149	ASN	-1	-0.893	-0.936	31.981	-0.045	-0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ASP)