FMO DATABASE

FMODB ID: R56G8

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	OptH
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	-1464195.46991
FMO2-HF: Nuclear repulsion	1404488.132366
FMO2-HF: Total energy	-59707.337544
FMO2-MP2: Total energy	-59880.748011

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.
168.822	179.193	4.471	-6.483	-8.36	0.045

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 : -0.972

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	-0.948	-0.978	2.132	27.970	33.666	3.412	-4.111	-4.996	0.053
4	A	9	ASP	-1	-0.946	-0.976	2.547	47.883	52.323	1.061	-2.361	-3.141	-0.008
5	A	10	ALA	0	-0.085	-0.041	4.215	-6.516	-6.371	-0.001	-0.009	-0.136	0.000
6	A	11	VAL	0	-0.027	-0.011	6.237	-1.781	-1.781	0.000	0.000	0.000	0.000
7	A	12	PHE	0	-0.033	-0.025	9.302	-0.932	-0.932	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.026	-0.026	11.490	-0.386	-0.386	0.000	0.000	0.000	0.000
9	A	14	PHE	0	0.022	-0.004	15.197	-1.118	-1.118	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.051	-0.010	15.153	-0.802	-0.802	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.882	-0.947	17.882	15.547	15.547	0.000	0.000	0.000	0.000
12	A	17	ASP	-1	-0.906	-0.931	20.479	13.285	13.285	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.915	-0.981	22.823	11.549	11.549	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.793	0.866	25.621	-10.302	-10.302	0.000	0.000	0.000	0.000
15	A	20	ILE	0	0.061	0.025	22.910	0.376	0.376	0.000	0.000	0.000	0.000
16	A	21	CYS	0	-0.031	-0.005	26.295	-0.225	-0.225	0.000	0.000	0.000	0.000
17	A	22	SER	0	0.027	0.008	25.205	-0.246	-0.246	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.891	0.929	25.794	-9.539	-9.539	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.936	-0.965	24.392	10.898	10.898	0.000	0.000	0.000	0.000
20	A	25	SER	0	-0.003	0.002	21.379	0.240	0.240	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.039	-0.005	21.051	0.490	0.490	0.000	0.000	0.000	0.000
22	A	27	ILE	0	0.013	-0.009	19.283	0.266	0.266	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.850	-0.916	16.876	15.821	15.821	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.026	0.003	16.747	0.772	0.772	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.069	-0.047	18.345	0.415	0.415	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.914	-0.957	14.592	19.491	19.491	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.715	-0.834	13.019	19.854	19.854	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.061	0.032	14.423	0.951	0.951	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.042	-0.025	16.640	0.200	0.200	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.005	0.010	10.233	0.734	0.734	0.000	0.000	0.000	0.000
31	A	36	TRP	0	0.016	0.005	13.042	0.589	0.589	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.755	0.854	14.161	-14.814	-14.814	0.000	0.000	0.000	0.000
33	A	38	ASN	0	-0.048	-0.006	11.448	1.990	1.990	0.000	0.000	0.000	0.000
34	A	39	HIS	0	-0.004	-0.002	6.676	-2.286	-2.286	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.011	-0.001	10.897	1.083	1.083	0.000	0.000	0.000	0.000
36	A	41	ILE	0	-0.025	0.000	13.464	-0.593	-0.593	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.063	-0.033	8.442	-0.457	-0.457	0.000	0.000	0.000	0.000
38	A	43	PHE	0	0.000	0.001	5.050	0.651	0.741	-0.001	-0.002	-0.087	0.000
39	A	44	ASN	0	-0.108	-0.042	10.082	-1.417	-1.417	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.956	0.994	9.868	-28.982	-28.982	0.000	0.000	0.000	0.000
41	A	46	ASP	-1	-0.829	-0.905	14.060	14.433	14.433	0.000	0.000	0.000	0.000
42	A	47	ILE	0	0.017	0.000	17.754	0.004	0.004	0.000	0.000	0.000	0.000
43	A	48	THR	0	-0.116	-0.085	19.103	-0.752	-0.752	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.065	-0.023	18.455	-0.667	-0.667	0.000	0.000	0.000	0.000
45	A	50	CYS	0	0.008	0.014	18.774	0.559	0.559	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.043	0.033	20.830	-0.756	-0.756	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.837	0.893	23.566	-10.218	-10.218	0.000	0.000	0.000	0.000
48	A	53	LEU	0	0.013	0.019	22.036	-0.347	-0.347	0.000	0.000	0.000	0.000
49	A	54	TYR	0	0.077	0.004	16.142	-0.082	-0.082	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.944	0.970	22.545	-12.525	-12.525	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.931	-0.974	25.567	9.903	9.903	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.008	0.014	21.628	-0.312	-0.312	0.000	0.000	0.000	0.000
53	A	58	MET	0	-0.020	-0.003	22.062	-0.044	-0.044	0.000	0.000	0.000	0.000
54	A	59	LYS	1	0.857	0.937	24.961	-10.530	-10.530	0.000	0.000	0.000	0.000
55	A	60	PHE	0	-0.020	-0.027	26.185	-0.521	-0.521	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.790	-0.876	24.729	12.959	12.959	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.929	-0.970	27.595	10.000	10.000	0.000	0.000	0.000	0.000
58	A	63	VAL	0	-0.108	-0.051	30.909	-0.409	-0.409	0.000	0.000	0.000	0.000
59	A	64	ALA	0	0.049	0.030	28.915	-0.290	-0.290	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.034	-0.025	29.874	-0.233	-0.233	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.884	0.939	32.655	-9.394	-9.394	0.000	0.000	0.000	0.000
62	A	67	TYR	0	-0.012	0.016	33.632	-0.277	-0.277	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.006	-0.014	30.612	-0.280	-0.280	0.000	0.000	0.000	0.000
64	A	69	GLY	0	0.024	0.024	34.796	-0.212	-0.212	0.000	0.000	0.000	0.000
65	A	70	ILE	0	-0.017	-0.031	29.748	0.227	0.227	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.879	-0.937	32.028	9.181	9.181	0.000	0.000	0.000	0.000
67	A	72	LYS	1	0.938	0.987	33.021	-9.072	-9.072	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.026	-0.008	27.804	0.289	0.289	0.000	0.000	0.000	0.000
69	A	74	ASN	0	-0.008	-0.011	28.391	0.702	0.702	0.000	0.000	0.000	0.000
70	A	75	GLU	-1	-0.875	-0.910	28.673	9.601	9.601	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.035	-0.028	26.809	0.158	0.158	0.000	0.000	0.000	0.000
72	A	77	VAL	0	-0.009	-0.008	23.250	0.381	0.381	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.904	-0.932	24.497	12.414	12.414	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.011	0.003	26.118	0.210	0.210	0.000	0.000	0.000	0.000
75	A	80	MET	0	-0.039	-0.002	20.825	0.013	0.013	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.088	-0.046	21.382	0.918	0.918	0.000	0.000	0.000	0.000
77	A	82	GLU	-1	-0.984	-1.001	22.352	12.021	12.021	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.034	-0.007	23.603	-0.158	-0.158	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.897	-0.982	24.523	10.757	10.757	0.000	0.000	0.000	0.000
80	A	85	HIS	1	0.812	0.923	22.883	-12.519	-12.519	0.000	0.000	0.000	0.000
81	A	86	TYR	0	0.017	-0.016	27.164	-0.431	-0.431	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.023	-0.003	27.655	-0.396	-0.396	0.000	0.000	0.000	0.000
83	A	88	ASN	0	0.024	0.033	28.186	0.416	0.416	0.000	0.000	0.000	0.000
84	A	89	PHE	0	0.077	0.014	22.572	-0.359	-0.359	0.000	0.000	0.000	0.000
85	A	90	THR	0	-0.003	-0.011	28.405	-0.297	-0.297	0.000	0.000	0.000	0.000
86	A	91	LYS	1	0.832	0.908	31.030	-9.185	-9.185	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.008	0.031	29.738	-0.235	-0.235	0.000	0.000	0.000	0.000
88	A	93	HIS	0	-0.014	-0.010	32.314	0.087	0.087	0.000	0.000	0.000	0.000
89	A	94	ASP	-1	-0.809	-0.901	34.371	8.434	8.434	0.000	0.000	0.000	0.000
90	A	95	GLN	0	0.026	0.005	33.525	0.196	0.196	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.964	-0.972	32.931	8.804	8.804	0.000	0.000	0.000	0.000
92	A	97	SER	0	0.040	0.023	33.004	0.447	0.447	0.000	0.000	0.000	0.000
93	A	98	LEU	0	0.002	0.011	27.616	0.413	0.413	0.000	0.000	0.000	0.000
94	A	99	PHE	0	-0.020	-0.038	28.413	0.401	0.401	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.027	0.020	28.443	0.405	0.405	0.000	0.000	0.000	0.000
96	A	101	THR	0	-0.026	-0.021	26.022	0.314	0.314	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.008	0.004	23.010	0.498	0.498	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.026	0.013	23.711	0.582	0.582	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.029	-0.017	24.805	0.349	0.349	0.000	0.000	0.000	0.000
100	A	105	CYS	0	-0.031	-0.013	20.870	0.393	0.393	0.000	0.000	0.000	0.000
101	A	106	ALA	0	0.030	0.019	20.095	0.803	0.803	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.961	0.978	20.307	-11.647	-11.647	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.001	0.010	19.478	0.233	0.233	0.000	0.000	0.000	0.000
104	A	109	THR	0	-0.052	-0.028	15.805	0.289	0.289	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.825	-0.905	16.309	16.056	16.056	0.000	0.000	0.000	0.000
106	A	111	HIS	0	-0.015	-0.010	17.982	0.165	0.165	0.000	0.000	0.000	0.000
107	A	112	TRP	0	-0.037	-0.048	15.731	0.351	0.351	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.084	0.043	14.088	0.675	0.675	0.000	0.000	0.000	0.000
109	A	114	TYR	0	-0.046	-0.027	15.028	0.057	0.057	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.839	0.935	17.749	-14.496	-14.496	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.907	0.955	13.822	-20.689	-20.689	0.000	0.000	0.000	0.000
112	A	117	ILE	0	-0.042	-0.002	13.677	0.874	0.874	0.000	0.000	0.000	0.000
113	A	118	SER	0	0.076	0.025	8.674	-0.614	-0.614	0.000	0.000	0.000	0.000
114	A	119	GLU	-1	-0.875	-0.941	5.474	47.734	47.734	0.000	0.000	0.000	0.000
115	A	120	SER	0	-0.090	-0.035	9.518	-1.911	-1.911	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.919	0.964	12.740	-19.212	-19.212	0.000	0.000	0.000	0.000
117	A	122	PHE	0	0.065	0.045	6.891	-1.929	-1.929	0.000	0.000	0.000	0.000
118	A	123	GLN	0	-0.042	-0.028	12.832	-1.118	-1.118	0.000	0.000	0.000	0.000
119	A	124	SER	0	-0.015	-0.021	15.601	-1.257	-1.257	0.000	0.000	0.000	0.000
120	A	125	LEU	0	0.025	0.006	18.272	-0.807	-0.807	0.000	0.000	0.000	0.000
121	A	126	GLY	0	-0.014	0.002	20.401	-0.816	-0.816	0.000	0.000	0.000	0.000
122	A	127	ASN	0	-0.050	-0.022	20.710	1.225	1.225	0.000	0.000	0.000	0.000
123	A	128	ILE	0	0.110	0.040	19.020	-0.628	-0.628	0.000	0.000	0.000	0.000
124	A	129	THR	0	0.013	-0.004	21.793	-0.259	-0.259	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.934	-0.960	24.086	10.747	10.747	0.000	0.000	0.000	0.000
126	A	131	LEU	0	-0.022	0.005	24.068	-0.398	-0.398	0.000	0.000	0.000	0.000
127	A	132	MET	0	-0.050	-0.017	23.477	-0.434	-0.434	0.000	0.000	0.000	0.000
128	A	133	THR	0	0.070	0.035	26.332	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.830	-0.932	29.443	9.787	9.787	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.956	-0.982	30.979	8.556	8.556	0.000	0.000	0.000	0.000
131	A	136	ASN	0	0.018	-0.012	29.184	-0.255	-0.255	0.000	0.000	0.000	0.000
132	A	137	ILE	0	-0.014	-0.003	26.052	0.146	0.146	0.000	0.000	0.000	0.000
133	A	138	ASN	0	0.017	0.006	28.679	0.215	0.215	0.000	0.000	0.000	0.000
134	A	139	ILE	0	0.000	0.010	31.976	-0.065	-0.065	0.000	0.000	0.000	0.000
135	A	140	LEU	0	-0.007	-0.007	25.094	-0.081	-0.081	0.000	0.000	0.000	0.000
136	A	141	ILE	0	0.001	0.006	27.667	0.039	0.039	0.000	0.000	0.000	0.000
137	A	142	LEU	0	0.033	0.030	29.676	-0.166	-0.166	0.000	0.000	0.000	0.000
138	A	143	PHE	0	-0.059	-0.037	30.534	-0.382	-0.382	0.000	0.000	0.000	0.000
139	A	144	LEU	0	0.034	0.006	26.150	-0.125	-0.125	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.841	-0.932	30.306	9.425	9.425	0.000	0.000	0.000	0.000
141	A	146	LYS	1	0.843	0.940	32.317	-8.750	-8.750	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.848	0.936	31.856	-9.186	-9.186	0.000	0.000	0.000	0.000
143	A	148	LEU	0	-0.002	0.012	27.655	-0.085	-0.085	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.056	-0.008	31.973	0.132	0.132	0.000	0.000	0.000	0.000

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