FMO DATABASE

FMODB ID: 59LJZ

Calculation Name: 3JRV-A-Xray312

Preferred Name: ATP-dependent RNA helicase DDX3X

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3JRV

Chain ID: A

ChEMBL ID: CHEMBL5553

UniProt ID: O00571

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1468602.795432
FMO2-HF: Nuclear repulsion	1408744.446911
FMO2-HF: Total energy	-59858.348521
FMO2-MP2: Total energy	-60032.175074

3D Structure

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:5:ACE )

Summations of interaction energy for fragment #1(A:5:ACE )

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.
0.062	0.993	-0.006	-0.447	-0.478	-0.002

Interaction energy analysis for fragmet #1(A:5:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.043

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	7	TYR	0	-0.032	-0.032	3.836	1.188	2.119	-0.006	-0.447	-0.478	-0.002
4	A	8	GLU	-1	-0.943	-0.975	6.586	-0.303	-0.303	0.000	0.000	0.000	0.000
5	A	9	ASP	-1	-0.944	-0.975	5.637	-0.955	-0.955	0.000	0.000	0.000	0.000
6	A	10	ALA	0	-0.090	-0.044	7.263	0.288	0.288	0.000	0.000	0.000	0.000
7	A	11	VAL	0	-0.028	-0.011	8.067	0.007	0.007	0.000	0.000	0.000	0.000
8	A	12	PHE	0	-0.033	-0.026	10.584	0.052	0.052	0.000	0.000	0.000	0.000
9	A	13	TYR	0	-0.029	-0.027	11.597	0.012	0.012	0.000	0.000	0.000	0.000
10	A	14	PHE	0	0.025	-0.002	16.150	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.057	-0.012	17.191	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.876	-0.946	19.500	-0.054	-0.054	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.913	-0.935	22.191	0.037	0.037	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.912	-0.979	24.083	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.800	0.873	26.769	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	20	ILE	0	0.049	0.019	23.588	0.002	0.002	0.000	0.000	0.000	0.000
17	A	21	CYS	0	-0.024	0.000	27.149	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.022	0.004	25.493	0.004	0.004	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.889	0.928	26.014	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	24	ASP	-1	-0.936	-0.966	24.002	0.098	0.098	0.000	0.000	0.000	0.000
21	A	25	SER	0	-0.005	0.000	21.399	0.010	0.010	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.034	-0.002	21.271	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	27	ILE	0	0.009	-0.012	18.813	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.852	-0.918	17.006	0.182	0.182	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.022	0.006	17.067	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	30	ILE	0	-0.065	-0.045	19.017	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.920	-0.959	14.225	0.125	0.125	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.715	-0.834	14.093	0.036	0.036	0.000	0.000	0.000	0.000
29	A	33	TYR	0	0.063	0.034	15.256	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	34	ILE	0	-0.044	-0.026	17.131	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	35	THR	0	0.006	0.010	11.133	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	36	TRP	0	0.015	0.005	14.466	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	37	ARG	1	0.750	0.855	15.875	0.043	0.043	0.000	0.000	0.000	0.000
34	A	38	ASN	0	-0.040	-0.004	14.129	-0.054	-0.054	0.000	0.000	0.000	0.000
35	A	39	HIS	0	-0.006	-0.003	10.314	0.038	0.038	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.014	-0.001	14.317	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.023	0.001	17.499	0.001	0.001	0.000	0.000	0.000	0.000
38	A	42	VAL	0	-0.064	-0.034	13.152	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	PHE	0	-0.006	-0.002	10.343	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.106	-0.041	15.809	0.028	0.028	0.000	0.000	0.000	0.000
41	A	45	LYS	1	0.954	0.993	14.653	0.315	0.315	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.828	-0.905	18.850	-0.087	-0.087	0.000	0.000	0.000	0.000
43	A	47	ILE	0	0.017	0.000	21.778	0.007	0.007	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.116	-0.085	23.008	0.016	0.016	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.065	-0.023	21.804	0.010	0.010	0.000	0.000	0.000	0.000
46	A	50	CYS	0	0.004	0.011	21.510	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.045	0.033	23.221	0.002	0.002	0.000	0.000	0.000	0.000
48	A	52	ARG	1	0.846	0.898	25.510	0.003	0.003	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.024	0.025	23.230	0.000	0.000	0.000	0.000	0.000	0.000
50	A	54	TYR	0	0.061	-0.003	17.469	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.947	0.970	24.052	0.034	0.034	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.922	-0.968	27.321	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.005	0.012	22.734	0.001	0.001	0.000	0.000	0.000	0.000
54	A	58	MET	0	-0.023	-0.004	24.500	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.855	0.937	26.648	0.013	0.013	0.000	0.000	0.000	0.000
56	A	60	PHE	0	-0.018	-0.027	26.932	0.002	0.002	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.788	-0.876	26.515	-0.044	-0.044	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.932	-0.971	29.263	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.108	-0.051	31.823	0.002	0.002	0.000	0.000	0.000	0.000
60	A	64	ALA	0	0.051	0.030	29.835	0.002	0.002	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.041	-0.028	31.963	0.000	0.000	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.888	0.941	34.304	0.014	0.014	0.000	0.000	0.000	0.000
63	A	67	TYR	0	-0.013	0.016	34.225	0.001	0.001	0.000	0.000	0.000	0.000
64	A	68	TYR	0	-0.008	-0.015	31.115	0.002	0.002	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.026	0.024	35.768	0.000	0.000	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.018	-0.032	32.463	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.882	-0.939	34.196	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.940	0.988	34.048	0.011	0.011	0.000	0.000	0.000	0.000
69	A	73	ILE	0	-0.026	-0.007	29.459	0.000	0.000	0.000	0.000	0.000	0.000
70	A	74	ASN	0	-0.010	-0.012	30.137	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.874	-0.910	30.552	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.026	-0.024	27.753	0.000	0.000	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.017	-0.011	25.021	0.000	0.000	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.918	-0.937	26.038	-0.066	-0.066	0.000	0.000	0.000	0.000
75	A	79	ALA	0	0.011	0.012	27.624	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	80	MET	0	-0.066	-0.015	21.471	0.007	0.007	0.000	0.000	0.000	0.000
77	A	81	SER	0	-0.024	-0.011	22.794	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-1.031	-1.023	23.825	-0.041	-0.041	0.000	0.000	0.000	0.000
79	A	83	GLY	0	-0.031	-0.021	24.771	0.001	0.001	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.904	-0.976	26.255	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	85	HIS	1	0.815	0.924	22.372	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	86	TYR	0	0.032	-0.007	27.193	0.006	0.006	0.000	0.000	0.000	0.000
83	A	87	ILE	0	-0.028	-0.004	27.883	0.003	0.003	0.000	0.000	0.000	0.000
84	A	88	ASN	0	0.023	0.031	27.851	0.006	0.006	0.000	0.000	0.000	0.000
85	A	89	PHE	0	0.079	0.015	22.014	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	90	THR	0	-0.004	-0.011	27.795	0.000	0.000	0.000	0.000	0.000	0.000
87	A	91	LYS	1	0.831	0.908	30.192	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	92	VAL	0	0.008	0.031	29.499	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	93	HIS	0	-0.017	-0.011	31.911	0.004	0.004	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.809	-0.903	34.255	0.011	0.011	0.000	0.000	0.000	0.000
91	A	95	GLN	0	0.028	0.006	33.760	0.001	0.001	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.963	-0.971	33.276	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.039	0.022	33.395	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	98	LEU	0	0.002	0.010	27.617	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	99	PHE	0	-0.017	-0.034	28.677	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	100	ALA	0	0.026	0.019	29.031	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	101	THR	0	-0.025	-0.022	26.011	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	102	ILE	0	0.006	0.004	23.558	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.034	0.017	24.363	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	104	ILE	0	-0.033	-0.019	25.941	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	105	CYS	0	-0.035	-0.015	21.235	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	106	ALA	0	0.035	0.021	21.254	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.961	0.978	22.137	0.036	0.036	0.000	0.000	0.000	0.000
104	A	108	ILE	0	-0.004	0.009	20.712	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.048	-0.027	17.229	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.830	-0.906	18.771	-0.112	-0.112	0.000	0.000	0.000	0.000
107	A	111	HIS	0	-0.015	-0.010	20.997	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	112	TRP	0	-0.041	-0.051	17.460	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	113	GLY	0	0.085	0.043	17.891	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	114	TYR	0	-0.047	-0.026	18.781	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	115	LYS	1	0.835	0.933	21.562	0.103	0.103	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.908	0.954	18.353	0.223	0.223	0.000	0.000	0.000	0.000
113	A	117	ILE	0	-0.045	-0.004	16.941	-0.021	-0.021	0.000	0.000	0.000	0.000
114	A	118	SER	0	0.080	0.027	12.227	0.013	0.013	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.878	-0.942	7.518	-0.993	-0.993	0.000	0.000	0.000	0.000
116	A	120	SER	0	-0.090	-0.035	11.181	0.080	0.080	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.918	0.963	14.137	0.150	0.150	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.068	0.046	7.446	0.063	0.063	0.000	0.000	0.000	0.000
119	A	123	GLN	0	-0.043	-0.028	11.685	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	124	SER	0	-0.018	-0.021	14.770	0.004	0.004	0.000	0.000	0.000	0.000
121	A	125	LEU	0	0.027	0.007	18.023	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	126	GLY	0	-0.020	-0.002	19.758	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.050	-0.022	19.863	0.016	0.016	0.000	0.000	0.000	0.000
124	A	128	ILE	0	0.111	0.040	18.484	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	129	THR	0	0.014	-0.002	20.827	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	130	ASP	-1	-0.934	-0.961	23.138	0.061	0.061	0.000	0.000	0.000	0.000
127	A	131	LEU	0	-0.021	0.004	23.915	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	132	MET	0	-0.049	-0.015	23.258	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	133	THR	0	0.067	0.033	25.874	0.008	0.008	0.000	0.000	0.000	0.000
130	A	134	ASP	-1	-0.832	-0.933	28.819	0.070	0.070	0.000	0.000	0.000	0.000
131	A	135	ASP	-1	-0.956	-0.982	30.411	0.031	0.031	0.000	0.000	0.000	0.000
132	A	136	ASN	0	0.017	-0.012	29.022	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.015	-0.004	25.549	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	138	ASN	0	0.017	0.007	28.552	0.000	0.000	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.002	0.009	31.954	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.013	-0.010	25.557	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	141	ILE	0	0.004	0.007	27.977	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	142	LEU	0	0.030	0.029	30.094	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	143	PHE	0	-0.063	-0.040	31.337	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	144	LEU	0	0.027	0.000	26.887	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	145	GLU	-1	-0.846	-0.936	31.173	0.033	0.033	0.000	0.000	0.000	0.000
142	A	146	LYS	1	0.849	0.944	33.169	-0.015	-0.015	0.000	0.000	0.000	0.000
143	A	147	LYS	1	0.830	0.924	32.986	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	148	LEU	0	-0.034	-0.009	28.856	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	149	ASN	-1	-0.952	-0.948	33.240	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ACE )