FMO DATABASE

FMODB ID: Q1ZGY

Calculation Name: 3JRV-A-Xray372

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: 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:

IFIE MAP

IFIE Diagram

Modeling method

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1465677.525595
FMO2-HF: Nuclear repulsion	1405969.332696
FMO2-HF: Total energy	-59708.192898
FMO2-MP2: Total energy	-59881.591685

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: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.
140.856	147.166	6.073	-5.411	-6.97	0.053

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 : -0.923 / q_NPA : -0.975

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	-0.858	-0.928	1.975	16.694	19.617	5.669	-3.979	-4.612	0.051
4	A	9	ASP	-1	-0.944	-0.977	2.554	35.393	38.527	0.406	-1.419	-2.121	0.002
5	A	10	ALA	0	-0.090	-0.041	4.302	-6.385	-6.229	-0.001	-0.011	-0.144	0.000
6	A	11	VAL	0	-0.019	-0.006	6.312	-1.890	-1.890	0.000	0.000	0.000	0.000
7	A	12	PHE	0	-0.045	-0.031	9.359	-0.827	-0.827	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.018	-0.021	10.524	-0.872	-0.872	0.000	0.000	0.000	0.000
9	A	14	PHE	0	0.017	-0.001	15.259	-1.079	-1.079	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.041	-0.003	15.281	-0.817	-0.817	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.887	-0.951	17.993	15.381	15.381	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.902	-0.932	20.619	12.831	12.831	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.893	-0.977	22.887	11.228	11.228	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.796	0.875	25.695	-10.154	-10.154	0.000	0.000	0.000	0.000
15	A	20	ILE	0	0.052	0.019	22.870	0.367	0.367	0.000	0.000	0.000	0.000
16	A	21	CYS	0	-0.013	-0.003	26.373	-0.273	-0.273	0.000	0.000	0.000	0.000
17	A	22	SER	0	0.009	0.008	25.307	-0.241	-0.241	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.872	0.900	25.875	-9.482	-9.482	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.956	-0.980	24.860	10.797	10.797	0.000	0.000	0.000	0.000
20	A	25	SER	0	0.011	0.011	21.460	0.227	0.227	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.037	-0.003	21.139	0.503	0.503	0.000	0.000	0.000	0.000
22	A	27	ILE	0	0.007	-0.010	19.489	0.272	0.272	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.848	-0.918	16.875	15.516	15.516	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.021	0.002	16.843	0.808	0.808	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.063	-0.044	18.446	0.424	0.424	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.907	-0.956	14.246	19.525	19.525	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.727	-0.835	13.012	19.841	19.841	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.055	0.027	14.527	0.989	0.989	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.046	-0.029	16.768	0.225	0.225	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.001	0.010	10.361	0.791	0.791	0.000	0.000	0.000	0.000
31	A	36	TRP	0	0.017	0.007	12.896	0.628	0.628	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.724	0.804	14.004	-14.704	-14.704	0.000	0.000	0.000	0.000
33	A	38	ASN	0	-0.048	-0.007	11.463	1.949	1.949	0.000	0.000	0.000	0.000
34	A	39	HIS	0	0.002	0.003	6.859	-2.526	-2.526	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.014	-0.003	10.741	1.037	1.037	0.000	0.000	0.000	0.000
36	A	41	ILE	0	-0.029	-0.005	13.303	-0.622	-0.622	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.055	-0.027	8.352	-0.424	-0.424	0.000	0.000	0.000	0.000
38	A	43	PHE	0	-0.006	-0.003	4.951	0.899	0.996	-0.001	-0.002	-0.093	0.000
39	A	44	ASN	0	-0.109	-0.047	9.945	-1.620	-1.620	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.847	0.937	8.440	-32.715	-32.715	0.000	0.000	0.000	0.000
41	A	46	ASP	-1	-0.790	-0.860	13.905	14.289	14.289	0.000	0.000	0.000	0.000
42	A	47	ILE	0	0.018	0.002	17.597	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	48	THR	0	-0.095	-0.078	18.940	-0.790	-0.790	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.046	-0.041	18.386	-0.793	-0.793	0.000	0.000	0.000	0.000
45	A	50	CYS	0	0.010	0.016	18.736	0.505	0.505	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.061	0.052	20.882	-0.773	-0.773	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.831	0.894	23.678	-10.115	-10.115	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.013	0.007	22.038	-0.328	-0.328	0.000	0.000	0.000	0.000
49	A	54	TYR	0	0.061	-0.010	16.042	-0.108	-0.108	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.823	0.900	22.634	-13.060	-13.060	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.869	-0.932	25.403	9.861	9.861	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.004	0.013	21.697	-0.305	-0.305	0.000	0.000	0.000	0.000
53	A	58	MET	0	-0.013	-0.003	21.882	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	59	LYS	1	0.796	0.895	24.800	-10.491	-10.491	0.000	0.000	0.000	0.000
55	A	60	PHE	0	-0.022	-0.028	26.099	-0.499	-0.499	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.724	-0.812	24.603	13.022	13.022	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.852	-0.920	27.445	9.781	9.781	0.000	0.000	0.000	0.000
58	A	63	VAL	0	-0.085	-0.042	30.773	-0.379	-0.379	0.000	0.000	0.000	0.000
59	A	64	ALA	0	0.047	0.030	28.818	-0.282	-0.282	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.026	-0.023	29.480	-0.255	-0.255	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.798	0.892	32.515	-9.502	-9.502	0.000	0.000	0.000	0.000
62	A	67	TYR	0	-0.010	0.004	33.599	-0.314	-0.314	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.009	-0.013	30.511	-0.237	-0.237	0.000	0.000	0.000	0.000
64	A	69	GLY	0	0.025	0.024	34.690	-0.211	-0.211	0.000	0.000	0.000	0.000
65	A	70	ILE	0	-0.003	-0.023	29.757	0.227	0.227	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.893	-0.948	31.908	9.241	9.241	0.000	0.000	0.000	0.000
67	A	72	LYS	1	0.845	0.925	32.985	-9.049	-9.049	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.008	0.001	27.673	0.291	0.291	0.000	0.000	0.000	0.000
69	A	74	ASN	0	-0.013	-0.011	28.292	0.691	0.691	0.000	0.000	0.000	0.000
70	A	75	GLU	-1	-0.832	-0.887	28.573	9.636	9.636	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.020	-0.019	26.783	0.181	0.181	0.000	0.000	0.000	0.000
72	A	77	VAL	0	-0.010	-0.010	23.140	0.418	0.418	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.890	-0.933	24.448	12.675	12.675	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.004	0.009	26.068	0.212	0.212	0.000	0.000	0.000	0.000
75	A	80	MET	0	-0.042	0.008	20.661	0.051	0.051	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.035	-0.037	21.256	0.987	0.987	0.000	0.000	0.000	0.000
77	A	82	GLU	-1	-0.956	-0.976	22.300	12.045	12.045	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.070	-0.042	23.602	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.900	-0.972	24.392	10.863	10.863	0.000	0.000	0.000	0.000
80	A	85	HIS	1	0.777	0.905	22.303	-12.828	-12.828	0.000	0.000	0.000	0.000
81	A	86	TYR	0	0.053	0.015	27.085	-0.468	-0.468	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.013	0.005	27.518	-0.384	-0.384	0.000	0.000	0.000	0.000
83	A	88	ASN	0	0.009	0.020	28.103	0.402	0.402	0.000	0.000	0.000	0.000
84	A	89	PHE	0	0.084	0.020	22.583	-0.374	-0.374	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.009	-0.003	28.462	-0.311	-0.311	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.847	0.919	31.105	-9.227	-9.227	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.009	0.028	29.845	-0.241	-0.241	0.000	0.000	0.000	0.000
88	A	93	HIS	0	-0.024	-0.018	32.425	0.061	0.061	0.000	0.000	0.000	0.000
89	A	94	ASP	-1	-0.801	-0.889	34.499	8.480	8.480	0.000	0.000	0.000	0.000
90	A	95	GLN	0	0.015	-0.005	33.652	0.258	0.258	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.958	-0.964	33.042	8.822	8.822	0.000	0.000	0.000	0.000
92	A	97	SER	0	0.051	0.025	32.670	0.273	0.273	0.000	0.000	0.000	0.000
93	A	98	LEU	0	-0.034	0.000	27.788	0.420	0.420	0.000	0.000	0.000	0.000
94	A	99	PHE	0	-0.009	-0.034	28.526	0.422	0.422	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.026	0.024	28.513	0.412	0.412	0.000	0.000	0.000	0.000
96	A	101	THR	0	-0.023	-0.025	26.202	0.302	0.302	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.021	0.011	23.084	0.513	0.513	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.031	0.016	23.711	0.591	0.591	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.028	-0.016	24.667	0.366	0.366	0.000	0.000	0.000	0.000
100	A	105	CYS	0	-0.044	-0.021	20.913	0.383	0.383	0.000	0.000	0.000	0.000
101	A	106	ALA	0	0.033	0.020	19.976	0.808	0.808	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.802	0.884	20.170	-12.607	-12.607	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.001	0.006	19.506	0.242	0.242	0.000	0.000	0.000	0.000
104	A	109	THR	0	-0.042	-0.021	15.752	0.284	0.284	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.739	-0.841	16.185	15.950	15.950	0.000	0.000	0.000	0.000
106	A	111	HIS	0	-0.026	-0.015	17.856	0.310	0.310	0.000	0.000	0.000	0.000
107	A	112	TRP	0	-0.020	-0.038	15.440	0.444	0.444	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.086	0.044	13.978	0.702	0.702	0.000	0.000	0.000	0.000
109	A	114	TYR	0	-0.056	-0.032	14.913	0.101	0.101	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.844	0.942	17.650	-14.457	-14.457	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.906	0.953	13.749	-20.809	-20.809	0.000	0.000	0.000	0.000
112	A	117	ILE	0	-0.040	-0.003	13.625	0.890	0.890	0.000	0.000	0.000	0.000
113	A	118	SER	0	0.085	0.027	8.780	-0.593	-0.593	0.000	0.000	0.000	0.000
114	A	119	GLU	-1	-0.869	-0.939	5.279	50.304	50.304	0.000	0.000	0.000	0.000
115	A	120	SER	0	-0.082	-0.032	9.460	-1.641	-1.641	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.865	0.936	12.684	-18.942	-18.942	0.000	0.000	0.000	0.000
117	A	122	PHE	0	0.054	0.048	6.760	-2.231	-2.231	0.000	0.000	0.000	0.000
118	A	123	GLN	0	-0.039	-0.024	12.747	-1.222	-1.222	0.000	0.000	0.000	0.000
119	A	124	SER	0	-0.006	-0.020	15.566	-1.269	-1.269	0.000	0.000	0.000	0.000
120	A	125	LEU	0	0.040	0.015	18.105	-0.878	-0.878	0.000	0.000	0.000	0.000
121	A	126	GLY	0	-0.008	0.001	20.317	-0.825	-0.825	0.000	0.000	0.000	0.000
122	A	127	ASN	0	-0.069	-0.043	20.710	1.119	1.119	0.000	0.000	0.000	0.000
123	A	128	ILE	0	0.102	0.042	19.060	-0.653	-0.653	0.000	0.000	0.000	0.000
124	A	129	THR	0	0.018	0.000	21.901	-0.247	-0.247	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.926	-0.949	24.188	10.934	10.934	0.000	0.000	0.000	0.000
126	A	131	LEU	0	-0.018	0.005	24.221	-0.410	-0.410	0.000	0.000	0.000	0.000
127	A	132	MET	0	-0.046	-0.016	23.506	-0.434	-0.434	0.000	0.000	0.000	0.000
128	A	133	THR	0	0.056	0.025	26.420	-0.031	-0.031	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.800	-0.894	29.544	9.818	9.818	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.931	-0.969	31.076	8.542	8.542	0.000	0.000	0.000	0.000
131	A	136	ASN	0	0.000	-0.018	29.284	-0.238	-0.238	0.000	0.000	0.000	0.000
132	A	137	ILE	0	-0.002	0.002	26.139	0.145	0.145	0.000	0.000	0.000	0.000
133	A	138	ASN	0	0.008	0.006	28.779	0.201	0.201	0.000	0.000	0.000	0.000
134	A	139	ILE	0	-0.005	0.003	32.074	-0.081	-0.081	0.000	0.000	0.000	0.000
135	A	140	LEU	0	0.000	-0.004	25.135	-0.081	-0.081	0.000	0.000	0.000	0.000
136	A	141	ILE	0	0.001	0.010	27.697	0.029	0.029	0.000	0.000	0.000	0.000
137	A	142	LEU	0	0.032	0.025	29.770	-0.168	-0.168	0.000	0.000	0.000	0.000
138	A	143	PHE	0	-0.069	-0.037	30.887	-0.325	-0.325	0.000	0.000	0.000	0.000
139	A	144	LEU	0	0.029	0.005	26.189	-0.130	-0.130	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.843	-0.931	30.399	9.350	9.350	0.000	0.000	0.000	0.000
141	A	146	LYS	1	0.863	0.936	32.403	-8.681	-8.681	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.854	0.949	31.938	-9.337	-9.337	0.000	0.000	0.000	0.000
143	A	148	LEU	0	0.002	0.014	27.708	-0.091	-0.091	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.040	-0.001	32.054	0.075	0.075	0.000	0.000	0.000	0.000

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