Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: G5741

Calculation Name: 4XW3-A-Xray372

Preferred Name: ATP-dependent RNA helicase DDX1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4XW3

Chain ID: A

ChEMBL ID: CHEMBL2010634

UniProt ID: Q92499

Base Structure: X-ray

Registration Date: 2023-09-23

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2163423.673779
FMO2-HF: Nuclear repulsion 2087569.692779
FMO2-HF: Total energy -75853.981
FMO2-MP2: Total energy -76069.534399


3D Structure
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:86:SER)


Summations of interaction energy for fragment #1(A:86:SER)
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.
-1.5061.9350.339-1.442-2.336-0.001
Interaction energy analysis for fragmet #1(A:86:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.003
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].
3A88LEU00.010-0.0083.402-2.957-1.162-0.006-0.802-0.9860.002
4A89ASN0-0.017-0.0092.832-0.6400.5770.335-0.565-0.987-0.003
5A90LYS10.9811.0204.652-0.479-0.377-0.001-0.011-0.0890.000
6A91TRP00.0390.0257.0090.1120.1120.0000.0000.0000.000
7A92GLN0-0.042-0.0257.9170.2560.2560.0000.0000.0000.000
8A93MET00.0300.02411.282-0.093-0.0930.0000.0000.0000.000
9A94ASN00.026-0.0069.5110.3630.3630.0000.0000.0000.000
10A95PRO00.0160.0078.418-0.088-0.0880.0000.0000.0000.000
11A96TYR0-0.038-0.0285.8720.2620.2620.0000.0000.0000.000
12A97ASP-1-0.781-0.87811.5290.0460.0460.0000.0000.0000.000
13A98ARG10.8620.91213.001-0.603-0.6030.0000.0000.0000.000
14A99GLY00.0220.02117.084-0.009-0.0090.0000.0000.0000.000
15A100SER0-0.002-0.01519.1260.0330.0330.0000.0000.0000.000
16A101ALA00.0220.01720.3570.0260.0260.0000.0000.0000.000
17A102PHE0-0.028-0.00916.7830.0010.0010.0000.0000.0000.000
18A103ALA00.0100.00717.0110.0550.0550.0000.0000.0000.000
19A104ILE0-0.015-0.01512.386-0.038-0.0380.0000.0000.0000.000
20A105GLY00.0310.02014.0990.0660.0660.0000.0000.0000.000
21A106SER00.003-0.01611.5290.0620.0620.0000.0000.0000.000
22A107ASP-1-0.792-0.89910.7740.6420.6420.0000.0000.0000.000
23A108GLY0-0.039-0.01510.922-0.004-0.0040.0000.0000.0000.000
24A109LEU0-0.054-0.04311.750-0.101-0.1010.0000.0000.0000.000
25A110CYS0-0.036-0.00415.291-0.070-0.0700.0000.0000.0000.000
26A111CYS0-0.029-0.00317.0040.0740.0740.0000.0000.0000.000
27A112GLN00.0180.00218.745-0.039-0.0390.0000.0000.0000.000
28A113SER00.0120.01920.9450.0280.0280.0000.0000.0000.000
29A114ARG10.8850.94323.551-0.216-0.2160.0000.0000.0000.000
30A115GLU-1-0.844-0.90426.3080.1500.1500.0000.0000.0000.000
31A116VAL0-0.021-0.01528.176-0.006-0.0060.0000.0000.0000.000
32A117LYS10.8950.93131.668-0.100-0.1000.0000.0000.0000.000
33A118GLU-1-0.901-0.93328.3000.1070.1070.0000.0000.0000.000
34A119TRP0-0.045-0.02427.3990.0050.0050.0000.0000.0000.000
35A120HIS0-0.014-0.01322.3650.0150.0150.0000.0000.0000.000
36A121GLY00.0400.01521.519-0.001-0.0010.0000.0000.0000.000
37A122CYS0-0.087-0.02315.4220.0430.0430.0000.0000.0000.000
38A123ARG10.8380.88515.669-0.126-0.1260.0000.0000.0000.000
39A124ALA00.0280.00513.4270.0660.0660.0000.0000.0000.000
40A125THR0-0.075-0.0487.8680.0030.0030.0000.0000.0000.000
41A126LYS10.8590.9277.9690.6560.6560.0000.0000.0000.000
42A127GLY00.0250.01511.9570.0760.0760.0000.0000.0000.000
43A128LEU0-0.031-0.01415.552-0.048-0.0480.0000.0000.0000.000
44A129MET00.006-0.01118.4980.0260.0260.0000.0000.0000.000
45A130LYS10.8800.94020.5820.1210.1210.0000.0000.0000.000
46A131GLY00.0710.04321.866-0.011-0.0110.0000.0000.0000.000
47A132LYS10.8670.94324.2480.0610.0610.0000.0000.0000.000
48A133HIS0-0.026-0.01820.827-0.015-0.0150.0000.0000.0000.000
49A134TYR0-0.024-0.01722.0140.0090.0090.0000.0000.0000.000
50A135TYR0-0.050-0.02619.597-0.005-0.0050.0000.0000.0000.000
51A136GLU-1-0.740-0.85321.3440.0530.0530.0000.0000.0000.000
52A137VAL0-0.004-0.01121.1780.0150.0150.0000.0000.0000.000
53A138SER0-0.040-0.01023.366-0.015-0.0150.0000.0000.0000.000
54A139CYS00.0060.01224.7150.0190.0190.0000.0000.0000.000
55A140HIS0-0.021-0.02722.774-0.016-0.0160.0000.0000.0000.000
56A141ASP-1-0.773-0.89827.2610.1600.1600.0000.0000.0000.000
57A142GLN0-0.022-0.02229.951-0.011-0.0110.0000.0000.0000.000
58A143GLY00.0020.03130.051-0.007-0.0070.0000.0000.0000.000
59A144LEU0-0.035-0.01530.746-0.005-0.0050.0000.0000.0000.000
60A145CYS0-0.010-0.00226.3340.0110.0110.0000.0000.0000.000
61A146ARG10.8310.90426.698-0.092-0.0920.0000.0000.0000.000
62A147VAL00.0320.02123.9090.0140.0140.0000.0000.0000.000
63A148GLY00.0400.01123.337-0.011-0.0110.0000.0000.0000.000
64A149TRP00.0330.01719.4520.0030.0030.0000.0000.0000.000
65A150SER0-0.005-0.00320.5150.0070.0070.0000.0000.0000.000
66A151THR00.0840.04019.921-0.006-0.0060.0000.0000.0000.000
67A152MET0-0.0020.01114.6920.0140.0140.0000.0000.0000.000
68A153GLN0-0.045-0.01918.6220.0060.0060.0000.0000.0000.000
69A154ALA0-0.0570.00021.6190.0060.0060.0000.0000.0000.000
70A155SER00.0450.02621.7110.0160.0160.0000.0000.0000.000
71A156LEU0-0.022-0.00117.784-0.004-0.0040.0000.0000.0000.000
72A157ASP-1-0.848-0.91121.9930.0980.0980.0000.0000.0000.000
73A158LEU00.0110.01223.165-0.016-0.0160.0000.0000.0000.000
74A159GLY00.0350.02725.4970.0010.0010.0000.0000.0000.000
75A160THR0-0.099-0.06927.954-0.008-0.0080.0000.0000.0000.000
76A161ASP-1-0.730-0.86626.3290.0290.0290.0000.0000.0000.000
77A162LYS10.9590.97829.2840.0100.0100.0000.0000.0000.000
78A163PHE0-0.005-0.00124.312-0.009-0.0090.0000.0000.0000.000
79A164GLY00.0430.01824.334-0.003-0.0030.0000.0000.0000.000
80A165PHE0-0.0190.00325.521-0.003-0.0030.0000.0000.0000.000
81A166GLY00.0140.00226.0710.0050.0050.0000.0000.0000.000
82A167PHE0-0.004-0.00128.019-0.006-0.0060.0000.0000.0000.000
83A168GLY00.023-0.00228.9910.0100.0100.0000.0000.0000.000
84A169GLY00.0620.03131.237-0.006-0.0060.0000.0000.0000.000
85A170THR0-0.022-0.00632.826-0.002-0.0020.0000.0000.0000.000
86A171GLY00.0330.04035.026-0.004-0.0040.0000.0000.0000.000
87A172LYS10.8970.93734.841-0.044-0.0440.0000.0000.0000.000
88A173LYS10.8960.95732.583-0.008-0.0080.0000.0000.0000.000
89A174SER0-0.053-0.02630.3700.0020.0020.0000.0000.0000.000
90A175HIS0-0.010-0.03429.336-0.005-0.0050.0000.0000.0000.000
91A176ASN0-0.019-0.00130.8280.0000.0000.0000.0000.0000.000
92A177LYS10.9260.95232.122-0.048-0.0480.0000.0000.0000.000
93A178GLN0-0.0390.01033.9050.0020.0020.0000.0000.0000.000
94A179PHE0-0.013-0.02132.0670.0020.0020.0000.0000.0000.000
95A180ASP-1-0.889-0.93336.3860.0190.0190.0000.0000.0000.000
96A181ASN0-0.018-0.02337.3310.0060.0060.0000.0000.0000.000
97A182TYR0-0.034-0.05632.917-0.003-0.0030.0000.0000.0000.000
98A183GLY0-0.0060.01136.0780.0040.0040.0000.0000.0000.000
99A184GLU-1-0.874-0.93736.0630.0380.0380.0000.0000.0000.000
100A185GLU-1-0.901-0.95235.7700.0570.0570.0000.0000.0000.000
101A186PHE0-0.081-0.05229.156-0.001-0.0010.0000.0000.0000.000
102A187THR00.014-0.00132.3220.0070.0070.0000.0000.0000.000
103A188MET00.0070.00830.6630.0040.0040.0000.0000.0000.000
104A189HIS0-0.009-0.01030.225-0.005-0.0050.0000.0000.0000.000
105A190ASP-1-0.806-0.87131.2060.0640.0640.0000.0000.0000.000
106A191THR0-0.051-0.03626.1730.0130.0130.0000.0000.0000.000
107A192ILE0-0.028-0.01526.954-0.011-0.0110.0000.0000.0000.000
108A193GLY00.0410.02625.9280.0050.0050.0000.0000.0000.000
109A194CYS0-0.050-0.03223.593-0.002-0.0020.0000.0000.0000.000
110A195TYR00.012-0.00424.365-0.011-0.0110.0000.0000.0000.000
111A196LEU0-0.021-0.00922.1250.0040.0040.0000.0000.0000.000
112A197ASP-1-0.840-0.93025.212-0.067-0.0670.0000.0000.0000.000
113A198ILE0-0.0060.00123.0050.0070.0070.0000.0000.0000.000
114A199ASP-1-0.906-0.96226.418-0.098-0.0980.0000.0000.0000.000
115A200LYS10.9140.95528.9750.0460.0460.0000.0000.0000.000
116A201GLY0-0.047-0.00429.3560.0040.0040.0000.0000.0000.000
117A202HIS0-0.010-0.00329.8140.0060.0060.0000.0000.0000.000
118A203VAL00.0300.02027.116-0.004-0.0040.0000.0000.0000.000
119A204LYS10.9030.96228.9630.0130.0130.0000.0000.0000.000
120A205PHE00.0500.01826.590-0.001-0.0010.0000.0000.0000.000
121A206SER0-0.020-0.00629.853-0.002-0.0020.0000.0000.0000.000
122A207LYS10.8590.92330.601-0.046-0.0460.0000.0000.0000.000
123A208ASN0-0.021-0.02031.5800.0000.0000.0000.0000.0000.000
124A209GLY00.0330.02031.905-0.003-0.0030.0000.0000.0000.000
125A210LYS10.9200.97533.176-0.030-0.0300.0000.0000.0000.000
126A211ASP-1-0.868-0.94934.3520.0050.0050.0000.0000.0000.000
127A212LEU0-0.019-0.00233.1230.0010.0010.0000.0000.0000.000
128A213GLY00.0260.02835.5430.0000.0000.0000.0000.0000.000
129A214LEU0-0.050-0.01833.2780.0020.0020.0000.0000.0000.000
130A215ALA0-0.0070.01031.8360.0020.0020.0000.0000.0000.000
131A216PHE0-0.003-0.01730.3860.0020.0020.0000.0000.0000.000
132A217GLU-1-0.878-0.93332.196-0.024-0.0240.0000.0000.0000.000
133A218ILE0-0.054-0.03126.4180.0020.0020.0000.0000.0000.000
134A219PRO00.0420.02829.634-0.003-0.0030.0000.0000.0000.000
135A220PRO00.036-0.00930.863-0.005-0.0050.0000.0000.0000.000
136A221HIS0-0.048-0.03328.999-0.007-0.0070.0000.0000.0000.000
137A222MET00.0060.01225.2920.0010.0010.0000.0000.0000.000
138A223LYS10.9130.97826.1450.0460.0460.0000.0000.0000.000
139A224ASN0-0.041-0.02724.894-0.006-0.0060.0000.0000.0000.000
140A225GLN0-0.0030.00322.042-0.005-0.0050.0000.0000.0000.000
141A226ALA00.0210.01117.7050.0070.0070.0000.0000.0000.000
142A227LEU0-0.020-0.00819.6660.0190.0190.0000.0000.0000.000
143A228PHE0-0.0040.00012.855-0.022-0.0220.0000.0000.0000.000
144A229PRO0-0.0080.01016.1640.0160.0160.0000.0000.0000.000
145A230ALA00.0020.00517.5550.0180.0180.0000.0000.0000.000
146A231CYS0-0.036-0.00319.934-0.001-0.0010.0000.0000.0000.000
147A232VAL0-0.0100.00021.7370.0130.0130.0000.0000.0000.000
148A233LEU0-0.002-0.00821.821-0.012-0.0120.0000.0000.0000.000
149A234LYS10.9500.98125.793-0.095-0.0950.0000.0000.0000.000
150A235ASN0-0.012-0.01527.6880.0020.0020.0000.0000.0000.000
151A236ALA00.0110.01426.487-0.010-0.0100.0000.0000.0000.000
152A237GLU-1-0.833-0.93022.3420.2630.2630.0000.0000.0000.000
153A238LEU0-0.014-0.01721.986-0.024-0.0240.0000.0000.0000.000
154A239LYS10.9490.99417.608-0.243-0.2430.0000.0000.0000.000
155A240PHE00.006-0.01417.083-0.033-0.0330.0000.0000.0000.000
156A241ASN00.0460.01417.8760.0180.0180.0000.0000.0000.000
157A242PHE0-0.006-0.02714.273-0.026-0.0260.0000.0000.0000.000
158A243GLY00.0440.01217.230-0.037-0.0370.0000.0000.0000.000
159A244GLU-1-0.946-0.94912.903-0.118-0.1180.0000.0000.0000.000
160A245GLU-1-0.950-0.95916.3040.1940.1940.0000.0000.0000.000
161A246GLU-1-0.938-0.96419.1850.0280.0280.0000.0000.0000.000
162A247PHE0-0.091-0.04920.8010.0060.0060.0000.0000.0000.000
163A248LYS10.9470.97324.456-0.114-0.1140.0000.0000.0000.000
164A249PHE0-0.019-0.02327.443-0.004-0.0040.0000.0000.0000.000
165A250PRO00.0050.00827.031-0.004-0.0040.0000.0000.0000.000
166A251PRO0-0.0340.00725.2120.0000.0000.0000.0000.0000.000
167A252LYS10.9230.95928.3020.0000.0000.0000.0000.0000.000
168A253ASP-1-0.889-0.96930.274-0.023-0.0230.0000.0000.0000.000
169A254GLY0-0.012-0.01729.725-0.004-0.0040.0000.0000.0000.000
170A255PHE0-0.061-0.01826.015-0.008-0.0080.0000.0000.0000.000
171A256VAL00.0260.01321.7450.0060.0060.0000.0000.0000.000
172A257ALA00.0640.02419.150-0.001-0.0010.0000.0000.0000.000
173A258LEU0-0.014-0.00216.389-0.019-0.0190.0000.0000.0000.000
174A259SER0-0.092-0.08014.165-0.029-0.0290.0000.0000.0000.000
175A260LYS10.9030.95914.8280.0710.0710.0000.0000.0000.000
176A261ALA0-0.0120.00516.7570.0010.0010.0000.0000.0000.000
177A262PRO00.0140.00016.102-0.036-0.0360.0000.0000.0000.000
178A263ASP-1-0.850-0.93113.118-0.529-0.5290.0000.0000.0000.000
179A264GLY0-0.045-0.01915.007-0.017-0.0170.0000.0000.0000.000
180A265TYR0-0.047-0.02317.6670.0230.0230.0000.0000.0000.000
181A266ILE0-0.033-0.00512.7280.0350.0350.0000.0000.0000.000
182A267VAL00.0080.01113.734-0.036-0.0360.0000.0000.0000.000
183A268LYS10.9080.9505.6571.5851.5850.0000.0000.0000.000
184A269SER00.0320.0169.9170.0680.0680.0000.0000.0000.000
185A270GLN0-0.009-0.03410.341-0.076-0.0760.0000.0000.0000.000
186A271HIS0-0.0320.00511.506-0.005-0.0050.0000.0000.0000.000
187A272SER0-0.012-0.0176.6130.0300.0300.0000.0000.0000.000
188A273GLY00.0410.0146.649-0.091-0.0910.0000.0000.0000.000
189A274ASN0-0.0030.0095.9400.1610.1610.0000.0000.0000.000
190A275ALA00.0070.0123.158-0.346-0.0190.011-0.064-0.2740.000