FMO DATABASE

FMODB ID: K3JL3

Calculation Name: 3JRV-A-Xray372

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: A

ChEMBL ID: CHEMBL5553

UniProt ID: O00571

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1469062.860528
FMO2-HF: Nuclear repulsion	1409353.912246
FMO2-HF: Total energy	-59708.948283
FMO2-MP2: Total energy	-59882.167275

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.
134.37	138.799	11.606	-7.653	-8.383	0.058

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 : -1 / q_Mulliken : -0.914 / q_NPA : -0.968

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	-0.849	-0.922	1.814	14.960	15.029	10.288	-5.395	-4.962	0.060
4	A	9	ASP	-1	-0.938	-0.977	2.421	32.268	36.310	1.319	-2.249	-3.112	-0.002
5	A	10	ALA	0	-0.058	-0.027	3.930	-6.340	-6.153	0.000	-0.003	-0.185	0.000
6	A	11	VAL	0	-0.035	-0.013	6.182	-2.463	-2.463	0.000	0.000	0.000	0.000
7	A	12	PHE	0	-0.009	-0.009	9.007	-0.922	-0.922	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.020	-0.019	10.147	-1.095	-1.095	0.000	0.000	0.000	0.000
9	A	14	PHE	0	-0.005	-0.017	14.812	-1.145	-1.145	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.013	0.010	14.908	-0.783	-0.783	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.888	-0.957	17.554	15.521	15.521	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.845	-0.917	20.218	12.182	12.182	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.903	-0.971	22.279	11.126	11.126	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.794	0.883	25.469	-10.447	-10.447	0.000	0.000	0.000	0.000
15	A	20	ILE	0	0.070	0.032	23.152	0.372	0.372	0.000	0.000	0.000	0.000
16	A	21	CYS	0	-0.026	-0.006	26.566	-0.297	-0.297	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.015	-0.018	25.685	-0.187	-0.187	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.833	0.892	25.911	-9.442	-9.442	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.911	-0.959	25.246	10.805	10.805	0.000	0.000	0.000	0.000
20	A	25	SER	0	0.011	0.010	20.530	0.156	0.156	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.078	-0.035	21.189	0.495	0.495	0.000	0.000	0.000	0.000
22	A	27	ILE	0	-0.001	-0.006	19.634	0.229	0.229	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.828	-0.909	17.015	15.246	15.246	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.014	0.003	16.875	0.839	0.839	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.032	-0.020	18.506	0.424	0.424	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.900	-0.954	14.301	19.893	19.893	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.741	-0.831	12.905	20.271	20.271	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.026	0.007	14.485	1.078	1.078	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.038	-0.026	16.778	0.253	0.253	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.006	0.012	10.466	0.757	0.757	0.000	0.000	0.000	0.000
31	A	36	TRP	0	-0.007	-0.005	12.344	0.895	0.895	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.720	0.795	13.569	-14.740	-14.740	0.000	0.000	0.000	0.000
33	A	38	ASN	0	-0.040	-0.003	11.197	2.008	2.008	0.000	0.000	0.000	0.000
34	A	39	HIS	0	0.005	0.005	6.733	-3.269	-3.269	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.004	-0.004	10.245	0.853	0.853	0.000	0.000	0.000	0.000
36	A	41	ILE	0	-0.033	-0.005	12.981	-0.558	-0.558	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.049	-0.021	8.208	-0.517	-0.517	0.000	0.000	0.000	0.000
38	A	43	PHE	0	-0.018	-0.004	4.658	0.524	0.655	-0.001	-0.006	-0.124	0.000
39	A	44	ASN	0	-0.092	-0.042	9.462	-1.488	-1.488	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.803	0.900	8.385	-32.738	-32.738	0.000	0.000	0.000	0.000
41	A	46	ASP	-1	-0.800	-0.863	13.668	14.426	14.426	0.000	0.000	0.000	0.000
42	A	47	ILE	0	0.035	0.015	17.355	0.018	0.018	0.000	0.000	0.000	0.000
43	A	48	THR	0	-0.090	-0.071	18.544	-0.787	-0.787	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.040	-0.038	17.987	-0.830	-0.830	0.000	0.000	0.000	0.000
45	A	50	CYS	0	0.017	0.030	18.171	0.617	0.617	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.034	0.037	20.410	-0.792	-0.792	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.777	0.858	23.316	-10.196	-10.196	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.042	-0.014	21.595	-0.249	-0.249	0.000	0.000	0.000	0.000
49	A	54	TYR	0	0.055	-0.006	15.817	0.011	0.011	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.820	0.882	22.345	-13.330	-13.330	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.848	-0.918	24.984	9.840	9.840	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.026	0.021	22.037	-0.316	-0.316	0.000	0.000	0.000	0.000
53	A	58	MET	0	-0.023	0.003	21.753	0.089	0.089	0.000	0.000	0.000	0.000
54	A	59	LYS	1	0.789	0.890	24.562	-10.666	-10.666	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.002	-0.018	26.023	-0.480	-0.480	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.737	-0.817	24.374	13.145	13.145	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.830	-0.906	27.169	9.794	9.794	0.000	0.000	0.000	0.000
58	A	63	VAL	0	-0.062	-0.025	30.407	-0.359	-0.359	0.000	0.000	0.000	0.000
59	A	64	ALA	0	0.033	0.023	28.317	-0.270	-0.270	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.044	-0.026	29.434	-0.264	-0.264	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.787	0.875	32.343	-9.537	-9.537	0.000	0.000	0.000	0.000
62	A	67	TYR	0	0.029	0.025	33.520	-0.198	-0.198	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.018	-0.010	30.466	-0.220	-0.220	0.000	0.000	0.000	0.000
64	A	69	GLY	0	0.034	0.030	34.449	-0.211	-0.211	0.000	0.000	0.000	0.000
65	A	70	ILE	0	0.000	-0.017	29.614	0.218	0.218	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.896	-0.953	31.474	9.439	9.439	0.000	0.000	0.000	0.000
67	A	72	LYS	1	0.831	0.907	32.703	-9.100	-9.100	0.000	0.000	0.000	0.000
68	A	73	ILE	0	0.001	0.003	27.192	0.270	0.270	0.000	0.000	0.000	0.000
69	A	74	ASN	0	-0.018	-0.014	28.128	0.671	0.671	0.000	0.000	0.000	0.000
70	A	75	GLU	-1	-0.834	-0.882	28.412	9.687	9.687	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.010	-0.011	27.096	0.213	0.213	0.000	0.000	0.000	0.000
72	A	77	VAL	0	0.002	-0.001	22.936	0.409	0.409	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.793	-0.887	24.129	13.489	13.489	0.000	0.000	0.000	0.000
74	A	79	ALA	0	0.025	0.024	25.669	0.271	0.271	0.000	0.000	0.000	0.000
75	A	80	MET	0	-0.042	-0.006	20.510	0.023	0.023	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.065	-0.051	21.274	0.954	0.954	0.000	0.000	0.000	0.000
77	A	82	GLU	-1	-0.920	-0.955	22.206	12.604	12.604	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.042	-0.027	23.404	0.152	0.152	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.871	-0.937	24.455	10.784	10.784	0.000	0.000	0.000	0.000
80	A	85	HIS	1	0.755	0.860	22.437	-12.808	-12.808	0.000	0.000	0.000	0.000
81	A	86	TYR	0	0.004	-0.001	27.364	-0.400	-0.400	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.013	0.011	27.795	-0.372	-0.372	0.000	0.000	0.000	0.000
83	A	88	ASN	0	0.029	0.029	28.216	0.422	0.422	0.000	0.000	0.000	0.000
84	A	89	PHE	0	0.087	0.027	22.942	-0.435	-0.435	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.031	0.011	28.905	-0.398	-0.398	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.799	0.895	31.646	-9.455	-9.455	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.026	0.034	30.102	-0.250	-0.250	0.000	0.000	0.000	0.000
88	A	93	HIS	0	-0.031	-0.018	32.600	0.116	0.116	0.000	0.000	0.000	0.000
89	A	94	ASP	-1	-0.820	-0.904	34.684	8.516	8.516	0.000	0.000	0.000	0.000
90	A	95	GLN	0	0.013	-0.004	33.755	0.284	0.284	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.953	-0.967	33.042	8.945	8.945	0.000	0.000	0.000	0.000
92	A	97	SER	0	0.018	0.008	32.930	0.425	0.425	0.000	0.000	0.000	0.000
93	A	98	LEU	0	-0.014	0.007	27.991	0.407	0.407	0.000	0.000	0.000	0.000
94	A	99	PHE	0	-0.002	-0.017	28.586	0.411	0.411	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.034	0.023	28.286	0.417	0.417	0.000	0.000	0.000	0.000
96	A	101	THR	0	-0.015	-0.023	26.373	0.299	0.299	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.011	0.010	23.137	0.505	0.505	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.032	0.014	23.630	0.588	0.588	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.021	-0.013	24.340	0.404	0.404	0.000	0.000	0.000	0.000
100	A	105	CYS	0	-0.064	-0.033	21.065	0.415	0.415	0.000	0.000	0.000	0.000
101	A	106	ALA	0	0.041	0.027	19.800	0.817	0.817	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.783	0.868	19.944	-12.935	-12.935	0.000	0.000	0.000	0.000
103	A	108	ILE	0	0.000	0.004	19.553	0.245	0.245	0.000	0.000	0.000	0.000
104	A	109	THR	0	-0.036	-0.018	15.571	0.211	0.211	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.732	-0.831	15.885	16.482	16.482	0.000	0.000	0.000	0.000
106	A	111	HIS	0	-0.051	-0.030	17.512	0.314	0.314	0.000	0.000	0.000	0.000
107	A	112	TRP	0	-0.040	-0.037	15.357	0.441	0.441	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.093	0.046	13.784	0.656	0.656	0.000	0.000	0.000	0.000
109	A	114	TYR	0	-0.052	-0.028	14.733	0.303	0.303	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.735	0.876	17.673	-14.081	-14.081	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.905	0.954	13.569	-21.415	-21.415	0.000	0.000	0.000	0.000
112	A	117	ILE	0	-0.031	0.000	13.264	1.169	1.169	0.000	0.000	0.000	0.000
113	A	118	SER	0	0.078	0.026	8.866	-0.539	-0.539	0.000	0.000	0.000	0.000
114	A	119	GLU	-1	-0.845	-0.917	5.778	49.785	49.785	0.000	0.000	0.000	0.000
115	A	120	SER	0	-0.079	-0.039	9.941	-1.744	-1.744	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.847	0.914	13.068	-19.451	-19.451	0.000	0.000	0.000	0.000
117	A	122	PHE	0	0.086	0.065	6.928	-2.346	-2.346	0.000	0.000	0.000	0.000
118	A	123	GLN	0	-0.027	-0.020	12.931	-1.255	-1.255	0.000	0.000	0.000	0.000
119	A	124	SER	0	-0.055	-0.029	15.719	-1.431	-1.431	0.000	0.000	0.000	0.000
120	A	125	LEU	0	0.034	0.020	18.034	-0.994	-0.994	0.000	0.000	0.000	0.000
121	A	126	GLY	0	0.011	-0.001	20.052	-0.879	-0.879	0.000	0.000	0.000	0.000
122	A	127	ASN	0	-0.074	-0.045	20.880	1.029	1.029	0.000	0.000	0.000	0.000
123	A	128	ILE	0	0.087	0.040	19.321	-0.665	-0.665	0.000	0.000	0.000	0.000
124	A	129	THR	0	0.004	-0.011	22.295	-0.205	-0.205	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.892	-0.934	24.749	11.021	11.021	0.000	0.000	0.000	0.000
126	A	131	LEU	0	-0.016	0.006	24.437	-0.407	-0.407	0.000	0.000	0.000	0.000
127	A	132	MET	0	-0.043	-0.011	23.617	-0.405	-0.405	0.000	0.000	0.000	0.000
128	A	133	THR	0	0.066	0.028	26.565	-0.049	-0.049	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.799	-0.895	29.722	9.882	9.882	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.885	-0.942	31.114	8.568	8.568	0.000	0.000	0.000	0.000
131	A	136	ASN	0	-0.023	-0.029	29.542	-0.289	-0.289	0.000	0.000	0.000	0.000
132	A	137	ILE	0	-0.004	0.001	26.022	0.162	0.162	0.000	0.000	0.000	0.000
133	A	138	ASN	0	-0.031	-0.014	28.965	0.195	0.195	0.000	0.000	0.000	0.000
134	A	139	ILE	0	-0.007	-0.007	32.307	-0.054	-0.054	0.000	0.000	0.000	0.000
135	A	140	LEU	0	0.010	0.007	25.179	-0.075	-0.075	0.000	0.000	0.000	0.000
136	A	141	ILE	0	0.016	0.017	27.763	0.057	0.057	0.000	0.000	0.000	0.000
137	A	142	LEU	0	0.041	0.028	29.793	-0.158	-0.158	0.000	0.000	0.000	0.000
138	A	143	PHE	0	-0.073	-0.027	30.671	-0.403	-0.403	0.000	0.000	0.000	0.000
139	A	144	LEU	0	0.035	0.012	25.931	-0.136	-0.136	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.822	-0.926	30.092	9.333	9.333	0.000	0.000	0.000	0.000
141	A	146	LYS	1	0.804	0.888	32.156	-8.802	-8.802	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.883	0.968	31.408	-9.562	-9.562	0.000	0.000	0.000	0.000
143	A	148	LEU	0	-0.004	0.018	27.265	-0.083	-0.083	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.057	-0.012	31.503	-0.016	-0.016	0.000	0.000	0.000	0.000

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