FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: ZL64N

Calculation Name: 3FE2-A-Xray547

Preferred Name: Probable ATP-dependent RNA helicase DDX5

Target Type: SINGLE PROTEIN

Ligand Name: adenosine-5'-diphosphate | sulfate ion | chloride ion

Ligand 3-letter code: ADP | SO4 | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FE2

Chain ID: A

ChEMBL ID: CHEMBL4295722

UniProt ID: P17844

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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3014859.145059
FMO2-HF: Nuclear repulsion 2921408.005198
FMO2-HF: Total energy -93451.139862
FMO2-MP2: Total energy -93719.74456


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:71:GLN)


Summations of interaction energy for fragment #1(A:71:GLN)
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.
21.39126.4561.415-2.176-4.303-0.012
Interaction energy analysis for fragmet #1(A:71:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.913
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   
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].
3A73VAL00.0060.0062.3735.7508.1040.728-1.055-2.027-0.006
4A74GLU-1-0.893-0.9342.593-40.948-38.4980.685-1.059-2.076-0.006
5A75THR00.005-0.0083.9933.3773.6380.002-0.062-0.2000.000
6A76TYR00.0330.0146.2585.9435.9430.0000.0000.0000.000
7A77ARG10.8640.9095.53832.76132.7610.0000.0000.0000.000
8A78ARG10.8850.9356.20237.29437.2940.0000.0000.0000.000
9A79SER0-0.031-0.0029.5722.7182.7180.0000.0000.0000.000
10A80LYS10.8370.89811.62420.69220.6920.0000.0000.0000.000
11A81GLU-1-0.870-0.92813.227-15.393-15.3930.0000.0000.0000.000
12A82ILE0-0.054-0.02010.7920.7560.7560.0000.0000.0000.000
13A83THR00.0110.00310.508-2.258-2.2580.0000.0000.0000.000
14A84VAL0-0.012-0.0249.0710.8430.8430.0000.0000.0000.000
15A85ARG10.8980.95010.48317.80617.8060.0000.0000.0000.000
16A86GLY00.1040.06212.6140.4490.4490.0000.0000.0000.000
17A87HIS0-0.034-0.02011.161-2.346-2.3460.0000.0000.0000.000
18A88ASN0-0.037-0.0289.317-1.000-1.0000.0000.0000.0000.000
19A89CYS00.0380.0379.3760.7990.7990.0000.0000.0000.000
20A90PRO0-0.0140.0128.635-2.662-2.6620.0000.0000.0000.000
21A91LYS10.9580.9605.58931.16731.1670.0000.0000.0000.000
22A92PRO0-0.0120.0056.8021.7021.7020.0000.0000.0000.000
23A93VAL0-0.009-0.0029.531-1.458-1.4580.0000.0000.0000.000
24A94LEU0-0.044-0.0368.6650.0650.0650.0000.0000.0000.000
25A95ASN0-0.029-0.01912.6191.9941.9940.0000.0000.0000.000
26A96PHE00.0600.01016.420-0.190-0.1900.0000.0000.0000.000
27A97TYR0-0.004-0.00519.4410.3600.3600.0000.0000.0000.000
28A98GLU-1-0.858-0.92312.457-21.839-21.8390.0000.0000.0000.000
29A99ALA0-0.025-0.00616.624-0.383-0.3830.0000.0000.0000.000
30A100ASN0-0.052-0.01918.0340.6060.6060.0000.0000.0000.000
31A101PHE00.0380.01020.7370.4520.4520.0000.0000.0000.000
32A102PRO00.0440.01023.7470.1530.1530.0000.0000.0000.000
33A103ALA00.0470.02327.3690.0170.0170.0000.0000.0000.000
34A104ASN00.019-0.00329.381-0.007-0.0070.0000.0000.0000.000
35A105VAL0-0.0060.00525.8630.1870.1870.0000.0000.0000.000
36A106MET0-0.019-0.00221.952-0.068-0.0680.0000.0000.0000.000
37A107ASP-1-0.873-0.93227.245-9.146-9.1460.0000.0000.0000.000
38A108VAL0-0.049-0.01130.2900.2110.2110.0000.0000.0000.000
39A109ILE00.0100.00323.5950.0510.0510.0000.0000.0000.000
40A110ALA0-0.003-0.00427.621-0.038-0.0380.0000.0000.0000.000
41A111ARG10.7830.87428.9999.0419.0410.0000.0000.0000.000
42A112GLN0-0.090-0.04328.3320.2830.2830.0000.0000.0000.000
43A113ASN0-0.067-0.02328.899-0.078-0.0780.0000.0000.0000.000
44A114PHE0-0.003-0.00123.923-0.171-0.1710.0000.0000.0000.000
45A115THR00.0350.00921.7280.0310.0310.0000.0000.0000.000
46A116GLU-1-0.885-0.93116.095-18.383-18.3830.0000.0000.0000.000
47A117PRO0-0.0270.00216.4580.5710.5710.0000.0000.0000.000
48A118THR00.006-0.01017.483-0.725-0.7250.0000.0000.0000.000
49A119ALA00.0330.01714.909-0.577-0.5770.0000.0000.0000.000
50A120ILE00.0150.00514.607-0.882-0.8820.0000.0000.0000.000
51A121GLN0-0.0270.01417.091-0.203-0.2030.0000.0000.0000.000
52A122ALA00.0330.01912.697-0.264-0.2640.0000.0000.0000.000
53A123GLN00.0250.0119.533-2.914-2.9140.0000.0000.0000.000
54A124GLY00.0500.01612.919-0.126-0.1260.0000.0000.0000.000
55A125TRP0-0.008-0.02016.3860.4350.4350.0000.0000.0000.000
56A126PRO00.0020.01412.4330.5950.5950.0000.0000.0000.000
57A127VAL0-0.0050.00913.6850.0510.0510.0000.0000.0000.000
58A128ALA00.0330.00915.9250.5690.5690.0000.0000.0000.000
59A129LEU0-0.015-0.01418.0260.6510.6510.0000.0000.0000.000
60A130SER0-0.062-0.03116.0110.0990.0990.0000.0000.0000.000
61A131GLY0-0.0120.00318.6070.1740.1740.0000.0000.0000.000
62A132LEU0-0.030-0.01414.6380.2460.2460.0000.0000.0000.000
63A133ASP-1-0.731-0.84519.103-11.624-11.6240.0000.0000.0000.000
64A134MET0-0.054-0.02818.216-0.907-0.9070.0000.0000.0000.000
65A135VAL0-0.0050.00419.0620.7290.7290.0000.0000.0000.000
66A136GLY00.0080.00518.720-0.822-0.8220.0000.0000.0000.000
67A137VAL0-0.033-0.01319.1990.7370.7370.0000.0000.0000.000
68A138ALA00.0580.02319.461-0.748-0.7480.0000.0000.0000.000
69A139GLN00.0890.05021.6240.4380.4380.0000.0000.0000.000
70A140THR00.013-0.00524.828-0.234-0.2340.0000.0000.0000.000
71A141GLY00.0150.01026.950-0.028-0.0280.0000.0000.0000.000
72A142SER0-0.003-0.00621.215-0.275-0.2750.0000.0000.0000.000
73A143GLY00.0300.02421.715-0.540-0.5400.0000.0000.0000.000
74A144LYS10.9290.95422.72811.48011.4800.0000.0000.0000.000
75A145THR00.0310.02023.754-0.215-0.2150.0000.0000.0000.000
76A146LEU00.0400.01723.6450.0630.0630.0000.0000.0000.000
77A147SER0-0.028-0.00220.139-0.467-0.4670.0000.0000.0000.000
78A148TYR0-0.003-0.02421.397-0.181-0.1810.0000.0000.0000.000
79A149LEU00.006-0.00324.1190.1930.1930.0000.0000.0000.000
80A150LEU0-0.0180.00623.3800.2530.2530.0000.0000.0000.000
81A151PRO00.017-0.00120.9790.1510.1510.0000.0000.0000.000
82A152ALA00.0310.03223.5540.2040.2040.0000.0000.0000.000
83A153ILE00.000-0.00527.1050.3400.3400.0000.0000.0000.000
84A154VAL0-0.019-0.00423.3870.2710.2710.0000.0000.0000.000
85A155HIS00.0310.01926.076-0.077-0.0770.0000.0000.0000.000
86A156ILE0-0.023-0.01527.3770.3030.3030.0000.0000.0000.000
87A157ASN0-0.063-0.03329.1120.4990.4990.0000.0000.0000.000
88A158HIS0-0.064-0.02626.067-0.090-0.0900.0000.0000.0000.000
89A159GLN0-0.059-0.03128.9750.1270.1270.0000.0000.0000.000
90A160PRO0-0.017-0.00632.7670.1220.1220.0000.0000.0000.000
91A161PHE00.0510.02936.555-0.055-0.0550.0000.0000.0000.000
92A162LEU0-0.0260.00638.4960.0560.0560.0000.0000.0000.000
93A163GLU-1-0.886-0.94040.435-6.842-6.8420.0000.0000.0000.000
94A164ARG10.9270.94243.9306.1256.1250.0000.0000.0000.000
95A165GLY00.0090.00946.4610.0580.0580.0000.0000.0000.000
96A166ASP-1-0.845-0.90640.888-7.422-7.4220.0000.0000.0000.000
97A167GLY0-0.026-0.00640.5240.0540.0540.0000.0000.0000.000
98A168PRO0-0.042-0.01836.291-0.067-0.0670.0000.0000.0000.000
99A169ILE00.0290.02232.152-0.060-0.0600.0000.0000.0000.000
100A170CYS0-0.0080.00430.376-0.294-0.2940.0000.0000.0000.000
101A171LEU0-0.010-0.00631.9910.3230.3230.0000.0000.0000.000
102A172VAL00.0280.01230.353-0.248-0.2480.0000.0000.0000.000
103A173LEU0-0.010-0.00432.1780.3660.3660.0000.0000.0000.000
104A174ALA00.0480.01632.296-0.298-0.2980.0000.0000.0000.000
105A175PRO00.0240.01133.3070.3110.3110.0000.0000.0000.000
106A176THR00.0230.00136.3930.2510.2510.0000.0000.0000.000
107A177ARG10.9100.93838.4827.0097.0090.0000.0000.0000.000
108A178GLU-1-0.957-0.97238.698-7.619-7.6190.0000.0000.0000.000
109A179LEU00.0450.02633.376-0.062-0.0620.0000.0000.0000.000
110A180ALA00.0600.02435.093-0.169-0.1690.0000.0000.0000.000
111A181GLN00.026-0.00436.8100.0970.0970.0000.0000.0000.000
112A182GLN0-0.020-0.00234.011-0.213-0.2130.0000.0000.0000.000
113A183VAL00.0300.01531.233-0.117-0.1170.0000.0000.0000.000
114A184GLN00.0110.01233.359-0.257-0.2570.0000.0000.0000.000
115A185GLN0-0.043-0.02736.209-0.053-0.0530.0000.0000.0000.000
116A186VAL0-0.0080.00229.404-0.051-0.0510.0000.0000.0000.000
117A187ALA00.0250.00932.043-0.155-0.1550.0000.0000.0000.000
118A188ALA00.0130.01933.0280.0080.0080.0000.0000.0000.000
119A189GLU-1-0.822-0.90433.689-8.795-8.7950.0000.0000.0000.000
120A190TYR00.0620.02227.943-0.045-0.0450.0000.0000.0000.000
121A191CYS0-0.036-0.01132.569-0.006-0.0060.0000.0000.0000.000
122A192ARG10.9430.96635.0987.5017.5010.0000.0000.0000.000
123A193ALA0-0.0090.00433.5670.1660.1660.0000.0000.0000.000
124A194CYS0-0.081-0.04631.981-0.091-0.0910.0000.0000.0000.000
125A195ARG10.8870.95134.6698.2088.2080.0000.0000.0000.000
126A196LEU00.0160.02332.5150.0990.0990.0000.0000.0000.000
127A197LYS10.8330.90537.0527.3807.3800.0000.0000.0000.000
128A198SER00.029-0.00736.118-0.105-0.1050.0000.0000.0000.000
129A199THR0-0.051-0.05038.1400.1720.1720.0000.0000.0000.000
130A200CYS0-0.041-0.00338.412-0.154-0.1540.0000.0000.0000.000
131A201ILE0-0.005-0.00240.1950.2480.2480.0000.0000.0000.000
132A202TYR00.041-0.00241.253-0.047-0.0470.0000.0000.0000.000
133A203GLY00.0450.02643.4030.1680.1680.0000.0000.0000.000
134A204GLY00.0120.00746.225-0.047-0.0470.0000.0000.0000.000
135A205ALA00.0010.00847.4540.1380.1380.0000.0000.0000.000
136A206PRO00.0310.00349.4130.0000.0000.0000.0000.0000.000
137A207LYS10.9080.94049.8045.9545.9540.0000.0000.0000.000
138A208GLY0-0.0110.00850.211-0.057-0.0570.0000.0000.0000.000
139A209PRO0-0.025-0.03148.5560.0060.0060.0000.0000.0000.000
140A210GLN00.0580.04245.311-0.018-0.0180.0000.0000.0000.000
141A211ILE00.0260.01746.265-0.092-0.0920.0000.0000.0000.000
142A212ARG10.9360.97648.4775.8735.8730.0000.0000.0000.000
143A213ASP-1-0.846-0.89943.976-6.828-6.8280.0000.0000.0000.000
144A214LEU0-0.044-0.01542.206-0.101-0.1010.0000.0000.0000.000
145A215GLU-1-0.845-0.92945.116-6.027-6.0270.0000.0000.0000.000
146A216ARG10.8640.93646.7806.2856.2850.0000.0000.0000.000
147A217GLY00.0340.04343.492-0.042-0.0420.0000.0000.0000.000
148A218VAL0-0.030-0.02039.1520.0160.0160.0000.0000.0000.000
149A219GLU-1-0.757-0.88235.158-7.970-7.9700.0000.0000.0000.000
150A220ILE0-0.0030.00132.408-0.228-0.2280.0000.0000.0000.000
151A221CYS0-0.044-0.02235.4030.3100.3100.0000.0000.0000.000
152A222ILE00.0170.02733.786-0.220-0.2200.0000.0000.0000.000
153A223ALA00.017-0.00736.2410.2790.2790.0000.0000.0000.000
154A224THR0-0.0220.00437.074-0.080-0.0800.0000.0000.0000.000
155A225PRO00.0600.01637.3360.1870.1870.0000.0000.0000.000
156A226GLY00.0430.02039.9130.1040.1040.0000.0000.0000.000
157A227ARG10.8060.89043.6116.5966.5960.0000.0000.0000.000
158A228LEU00.0370.02038.5820.1040.1040.0000.0000.0000.000
159A229ILE00.0190.01541.3040.0680.0680.0000.0000.0000.000
160A230ASP-1-0.807-0.88444.078-6.084-6.0840.0000.0000.0000.000
161A231PHE00.002-0.02144.9370.1630.1630.0000.0000.0000.000
162A232LEU0-0.0300.00140.7360.0500.0500.0000.0000.0000.000
163A233GLU-1-0.865-0.93145.404-6.338-6.3380.0000.0000.0000.000
164A234CYS0-0.100-0.05148.4650.1690.1690.0000.0000.0000.000
165A235GLY00.0050.00848.3270.0890.0890.0000.0000.0000.000
166A236LYS10.7960.89348.1315.9365.9360.0000.0000.0000.000
167A237THR00.0200.00242.193-0.104-0.1040.0000.0000.0000.000
168A238ASN0-0.028-0.02442.071-0.007-0.0070.0000.0000.0000.000
169A239LEU00.0870.04036.969-0.072-0.0720.0000.0000.0000.000
170A240ARG10.9720.99437.1926.8066.8060.0000.0000.0000.000
171A241ARG10.7850.86636.3787.9257.9250.0000.0000.0000.000
172A242THR0-0.069-0.02632.818-0.138-0.1380.0000.0000.0000.000
173A243THR00.0120.00030.236-0.065-0.0650.0000.0000.0000.000
174A244TYR0-0.0030.00024.099-0.391-0.3910.0000.0000.0000.000
175A245LEU0-0.0020.00228.3240.3380.3380.0000.0000.0000.000
176A246VAL0-0.007-0.00926.752-0.406-0.4060.0000.0000.0000.000
177A247LEU00.0080.00627.7460.4520.4520.0000.0000.0000.000
178A248ASP-1-0.788-0.88627.695-10.971-10.9710.0000.0000.0000.000
179A249GLU-1-0.919-0.97228.606-9.366-9.3660.0000.0000.0000.000
180A250ALA00.0370.00327.5420.3210.3210.0000.0000.0000.000
181A251ASP-1-0.735-0.84828.331-10.147-10.1470.0000.0000.0000.000
182A252ARG10.9240.96130.1549.1299.1290.0000.0000.0000.000
183A253MET0-0.091-0.04732.5170.3000.3000.0000.0000.0000.000
184A254LEU0-0.0130.00031.0640.2350.2350.0000.0000.0000.000
185A255ASP-1-0.883-0.93134.000-8.499-8.4990.0000.0000.0000.000
186A256MET0-0.138-0.07436.2630.2010.2010.0000.0000.0000.000
187A257GLY00.0150.01837.8550.1860.1860.0000.0000.0000.000
188A258PHE0-0.049-0.03436.8700.1520.1520.0000.0000.0000.000
189A259GLU-1-0.790-0.87334.356-8.558-8.5580.0000.0000.0000.000
190A260PRO0-0.002-0.00536.805-0.033-0.0330.0000.0000.0000.000
191A261GLN0-0.008-0.01539.816-0.028-0.0280.0000.0000.0000.000
192A262ILE00.0240.00033.012-0.003-0.0030.0000.0000.0000.000
193A263ARG10.7680.85732.7328.5128.5120.0000.0000.0000.000
194A264LYS10.9020.96536.4716.7726.7720.0000.0000.0000.000
195A265ILE0-0.040-0.00836.1090.1360.1360.0000.0000.0000.000
196A266VAL00.009-0.00831.610-0.007-0.0070.0000.0000.0000.000
197A267ASP-1-0.908-0.94734.753-8.080-8.0800.0000.0000.0000.000
198A268GLN0-0.131-0.07436.8960.2340.2340.0000.0000.0000.000
199A269ILE0-0.092-0.03632.4910.0260.0260.0000.0000.0000.000
200A270ARG10.8250.90433.0658.5598.5590.0000.0000.0000.000
201A271PRO00.0560.02131.059-0.218-0.2180.0000.0000.0000.000
202A272ASP-1-0.868-0.92928.700-9.461-9.4610.0000.0000.0000.000
203A273ARG10.8440.93328.2399.4319.4310.0000.0000.0000.000
204A274GLN0-0.028-0.00921.3170.1540.1540.0000.0000.0000.000
205A275THR0-0.032-0.03524.3930.6080.6080.0000.0000.0000.000
206A276LEU0-0.0010.00221.787-0.490-0.4900.0000.0000.0000.000
207A277MET0-0.0300.00023.3510.5090.5090.0000.0000.0000.000
208A278TRP00.001-0.01019.826-0.833-0.8330.0000.0000.0000.000
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210A280ALA0-0.019-0.00524.211-0.468-0.4680.0000.0000.0000.000
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