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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

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FMODB ID: 89K6Y

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166531.667335
FMO2-HF: Nuclear repulsion 2090676.976613
FMO2-HF: Total energy -75854.690722
FMO2-MP2: Total energy -76070.374695


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.
-6.254-2.6340.372-1.607-2.385-0.001
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 : 0.024 / 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].
3A88LEU00.0310.0003.825-3.614-1.712-0.010-0.897-0.9940.003
4A89ASN0-0.0010.0032.834-0.5660.6840.375-0.596-1.029-0.004
5A90LYS10.8690.9454.646-0.0560.038-0.001-0.012-0.0820.000
6A91TRP00.0450.0317.0140.4570.4570.0000.0000.0000.000
7A92GLN0-0.013-0.0118.176-0.416-0.4160.0000.0000.0000.000
8A93MET00.0270.03011.2820.1540.1540.0000.0000.0000.000
9A94ASN00.022-0.0049.6760.3070.3070.0000.0000.0000.000
10A95PRO00.0070.0058.648-0.122-0.1220.0000.0000.0000.000
11A96TYR0-0.028-0.0365.6850.2110.2110.0000.0000.0000.000
12A97ASP-1-0.765-0.85311.3470.7300.7300.0000.0000.0000.000
13A98ARG10.8540.90613.437-0.642-0.6420.0000.0000.0000.000
14A99GLY00.0200.02216.9270.0010.0010.0000.0000.0000.000
15A100SER00.008-0.01119.0530.0170.0170.0000.0000.0000.000
16A101ALA00.0070.00820.534-0.006-0.0060.0000.0000.0000.000
17A102PHE0-0.017-0.00617.106-0.024-0.0240.0000.0000.0000.000
18A103ALA00.0060.01017.2680.0500.0500.0000.0000.0000.000
19A104ILE0-0.007-0.01912.796-0.005-0.0050.0000.0000.0000.000
20A105GLY00.0420.02614.322-0.013-0.0130.0000.0000.0000.000
21A106SER00.011-0.01011.5950.0610.0610.0000.0000.0000.000
22A107ASP-1-0.739-0.86210.871-0.193-0.1930.0000.0000.0000.000
23A108GLY0-0.038-0.00310.887-0.034-0.0340.0000.0000.0000.000
24A109LEU0-0.038-0.03211.8080.1100.1100.0000.0000.0000.000
25A110CYS00.0120.01715.1460.0250.0250.0000.0000.0000.000
26A111CYS0-0.061-0.01817.2410.0440.0440.0000.0000.0000.000
27A112GLN00.015-0.00919.000-0.022-0.0220.0000.0000.0000.000
28A113SER00.0090.01921.1440.0300.0300.0000.0000.0000.000
29A114ARG10.8520.91223.778-0.088-0.0880.0000.0000.0000.000
30A115GLU-1-0.855-0.91226.4890.1620.1620.0000.0000.0000.000
31A116VAL0-0.008-0.01028.4760.0030.0030.0000.0000.0000.000
32A117LYS10.8820.90831.930-0.121-0.1210.0000.0000.0000.000
33A118GLU-1-0.860-0.90528.2320.1470.1470.0000.0000.0000.000
34A119TRP0-0.017-0.00727.357-0.006-0.0060.0000.0000.0000.000
35A120HIS0-0.018-0.01322.2930.0430.0430.0000.0000.0000.000
36A121GLY00.0440.01821.503-0.022-0.0220.0000.0000.0000.000
37A122CYS0-0.094-0.02215.3640.0430.0430.0000.0000.0000.000
38A123ARG10.8420.88716.032-0.650-0.6500.0000.0000.0000.000
39A124ALA00.0430.00513.4480.0830.0830.0000.0000.0000.000
40A125THR0-0.072-0.0497.8920.0520.0520.0000.0000.0000.000
41A126LYS10.8550.9298.108-0.185-0.1850.0000.0000.0000.000
42A127GLY00.0210.01312.189-0.090-0.0900.0000.0000.0000.000
43A128LEU0-0.029-0.01315.8320.0060.0060.0000.0000.0000.000
44A129MET0-0.002-0.01118.5300.0070.0070.0000.0000.0000.000
45A130LYS10.8300.90220.762-0.194-0.1940.0000.0000.0000.000
46A131GLY00.0750.04321.8570.0050.0050.0000.0000.0000.000
47A132LYS10.8340.93124.240-0.065-0.0650.0000.0000.0000.000
48A133HIS0-0.018-0.01620.7050.0000.0000.0000.0000.0000.000
49A134TYR0-0.014-0.00821.9920.0150.0150.0000.0000.0000.000
50A135TYR0-0.052-0.03519.612-0.001-0.0010.0000.0000.0000.000
51A136GLU-1-0.747-0.85921.3270.0080.0080.0000.0000.0000.000
52A137VAL0-0.002-0.01221.3520.0100.0100.0000.0000.0000.000
53A138SER0-0.0120.01023.180-0.014-0.0140.0000.0000.0000.000
54A139CYS0-0.0080.00624.5700.0140.0140.0000.0000.0000.000
55A140HIS0-0.030-0.04522.274-0.016-0.0160.0000.0000.0000.000
56A141ASP-1-0.774-0.88427.3020.0630.0630.0000.0000.0000.000
57A142GLN0-0.019-0.02230.1580.0030.0030.0000.0000.0000.000
58A143GLY00.0070.03130.2890.0020.0020.0000.0000.0000.000
59A144LEU0-0.029-0.01230.9750.0010.0010.0000.0000.0000.000
60A145CYS0-0.014-0.01026.4010.0110.0110.0000.0000.0000.000
61A146ARG10.7970.87926.706-0.201-0.2010.0000.0000.0000.000
62A147VAL00.0340.02323.7160.0230.0230.0000.0000.0000.000
63A148GLY00.0480.01523.336-0.018-0.0180.0000.0000.0000.000
64A149TRP00.0220.01719.3770.0280.0280.0000.0000.0000.000
65A150SER00.000-0.00221.121-0.011-0.0110.0000.0000.0000.000
66A151THR00.0640.03320.5870.0390.0390.0000.0000.0000.000
67A152MET00.0140.01615.4770.0490.0490.0000.0000.0000.000
68A153GLN0-0.041-0.01719.375-0.001-0.0010.0000.0000.0000.000
69A154ALA0-0.0580.00022.301-0.026-0.0260.0000.0000.0000.000
70A155SER00.0440.01622.2980.0470.0470.0000.0000.0000.000
71A156LEU0-0.0210.00218.191-0.010-0.0100.0000.0000.0000.000
72A157ASP-1-0.849-0.90022.3120.1960.1960.0000.0000.0000.000
73A158LEU00.0270.01523.588-0.014-0.0140.0000.0000.0000.000
74A159GLY00.0140.01825.918-0.023-0.0230.0000.0000.0000.000
75A160THR0-0.100-0.06828.439-0.017-0.0170.0000.0000.0000.000
76A161ASP-1-0.728-0.86226.8710.2810.2810.0000.0000.0000.000
77A162LYS10.9670.97929.934-0.215-0.2150.0000.0000.0000.000
78A163PHE0-0.003-0.00425.016-0.008-0.0080.0000.0000.0000.000
79A164GLY00.0330.01425.0060.0290.0290.0000.0000.0000.000
80A165PHE0-0.026-0.00526.022-0.020-0.0200.0000.0000.0000.000
81A166GLY00.0070.00026.3750.0150.0150.0000.0000.0000.000
82A167PHE00.0130.00828.091-0.012-0.0120.0000.0000.0000.000
83A168GLY00.0260.00228.9910.0080.0080.0000.0000.0000.000
84A169GLY00.0650.03131.249-0.008-0.0080.0000.0000.0000.000
85A170THR00.0120.00732.826-0.004-0.0040.0000.0000.0000.000
86A171GLY0-0.0070.02235.024-0.005-0.0050.0000.0000.0000.000
87A172LYS10.8830.92334.830-0.090-0.0900.0000.0000.0000.000
88A173LYS10.9040.97232.720-0.107-0.1070.0000.0000.0000.000
89A174SER0-0.030-0.01730.241-0.003-0.0030.0000.0000.0000.000
90A175HIS0-0.016-0.03329.9300.0050.0050.0000.0000.0000.000
91A176ASN0-0.021-0.00331.419-0.002-0.0020.0000.0000.0000.000
92A177LYS10.9280.95932.346-0.189-0.1890.0000.0000.0000.000
93A178GLN0-0.0440.01034.411-0.015-0.0150.0000.0000.0000.000
94A179PHE0-0.009-0.02232.4590.0080.0080.0000.0000.0000.000
95A180ASP-1-0.864-0.92236.6810.1050.1050.0000.0000.0000.000
96A181ASN0-0.030-0.02637.4890.0050.0050.0000.0000.0000.000
97A182TYR0-0.022-0.04032.8400.0020.0020.0000.0000.0000.000
98A183GLY00.0030.01736.0770.0010.0010.0000.0000.0000.000
99A184GLU-1-0.840-0.90836.0620.0380.0380.0000.0000.0000.000
100A185GLU-1-0.887-0.94635.7700.0680.0680.0000.0000.0000.000
101A186PHE0-0.076-0.04728.982-0.005-0.0050.0000.0000.0000.000
102A187THR00.0200.00032.3060.0040.0040.0000.0000.0000.000
103A188MET00.0060.00830.633-0.002-0.0020.0000.0000.0000.000
104A189HIS0-0.016-0.01230.079-0.002-0.0020.0000.0000.0000.000
105A190ASP-1-0.781-0.85731.0250.0350.0350.0000.0000.0000.000
106A191THR0-0.056-0.04325.8960.0000.0000.0000.0000.0000.000
107A192ILE0-0.018-0.00426.990-0.002-0.0020.0000.0000.0000.000
108A193GLY00.0420.02725.9280.0020.0020.0000.0000.0000.000
109A194CYS0-0.046-0.02723.5780.0020.0020.0000.0000.0000.000
110A195TYR00.0230.00224.3630.0000.0000.0000.0000.0000.000
111A196LEU0-0.029-0.01522.1680.0090.0090.0000.0000.0000.000
112A197ASP-1-0.835-0.92825.2060.1060.1060.0000.0000.0000.000
113A198ILE00.000-0.00222.959-0.001-0.0010.0000.0000.0000.000
114A199ASP-1-0.856-0.92226.4070.1470.1470.0000.0000.0000.000
115A200LYS10.8350.91228.964-0.096-0.0960.0000.0000.0000.000
116A201GLY0-0.038-0.00229.502-0.002-0.0020.0000.0000.0000.000
117A202HIS00.0150.00929.797-0.010-0.0100.0000.0000.0000.000
118A203VAL00.0230.01327.0530.0070.0070.0000.0000.0000.000
119A204LYS10.8530.94528.968-0.083-0.0830.0000.0000.0000.000
120A205PHE00.0570.01826.4580.0090.0090.0000.0000.0000.000
121A206SER0-0.0060.00229.843-0.004-0.0040.0000.0000.0000.000
122A207LYS10.8310.90930.601-0.040-0.0400.0000.0000.0000.000
123A208ASN0-0.018-0.02731.442-0.004-0.0040.0000.0000.0000.000
124A209GLY00.0270.01731.788-0.005-0.0050.0000.0000.0000.000
125A210LYS10.8550.93433.086-0.042-0.0420.0000.0000.0000.000
126A211ASP-1-0.840-0.94934.3510.0690.0690.0000.0000.0000.000
127A212LEU0-0.039-0.00733.020-0.003-0.0030.0000.0000.0000.000
128A213GLY00.0210.02635.4990.0010.0010.0000.0000.0000.000
129A214LEU0-0.045-0.02033.2750.0060.0060.0000.0000.0000.000
130A215ALA0-0.0050.01431.876-0.003-0.0030.0000.0000.0000.000
131A216PHE0-0.015-0.03230.6340.0020.0020.0000.0000.0000.000
132A217GLU-1-0.807-0.88532.3490.1100.1100.0000.0000.0000.000
133A218ILE0-0.048-0.03626.7700.0070.0070.0000.0000.0000.000
134A219PRO00.0400.02230.366-0.010-0.0100.0000.0000.0000.000
135A220PRO00.043-0.00931.5740.0120.0120.0000.0000.0000.000
136A221HIS0-0.050-0.03229.857-0.003-0.0030.0000.0000.0000.000
137A222MET0-0.0090.02126.0260.0110.0110.0000.0000.0000.000
138A223LYS10.9000.97026.891-0.150-0.1500.0000.0000.0000.000
139A224ASN0-0.030-0.02225.4580.0020.0020.0000.0000.0000.000
140A225GLN0-0.015-0.00722.9030.0330.0330.0000.0000.0000.000
141A226ALA00.0200.01018.186-0.018-0.0180.0000.0000.0000.000
142A227LEU0-0.019-0.01020.2870.0180.0180.0000.0000.0000.000
143A228PHE0-0.0040.00013.508-0.005-0.0050.0000.0000.0000.000
144A229PRO0-0.0050.01216.320-0.029-0.0290.0000.0000.0000.000
145A230ALA0-0.0050.00417.7670.0700.0700.0000.0000.0000.000
146A231CYS0-0.047-0.00519.760-0.049-0.0490.0000.0000.0000.000
147A232VAL0-0.005-0.00421.8920.0340.0340.0000.0000.0000.000
148A233LEU0-0.0030.00022.070-0.025-0.0250.0000.0000.0000.000
149A234LYS10.8970.94925.812-0.123-0.1230.0000.0000.0000.000
150A235ASN0-0.016-0.01627.913-0.013-0.0130.0000.0000.0000.000
151A236ALA00.0250.02426.722-0.013-0.0130.0000.0000.0000.000
152A237GLU-1-0.792-0.88822.6270.0480.0480.0000.0000.0000.000
153A238LEU0-0.018-0.01322.094-0.007-0.0070.0000.0000.0000.000
154A239LYS10.8510.92516.9840.1160.1160.0000.0000.0000.000
155A240PHE0-0.013-0.01616.9510.0070.0070.0000.0000.0000.000
156A241ASN00.0560.00617.713-0.041-0.0410.0000.0000.0000.000
157A242PHE0-0.019-0.02714.0940.0310.0310.0000.0000.0000.000
158A243GLY00.0490.01717.2350.0170.0170.0000.0000.0000.000
159A244GLU-1-0.882-0.89312.822-0.228-0.2280.0000.0000.0000.000
160A245GLU-1-0.877-0.91916.243-0.189-0.1890.0000.0000.0000.000
161A246GLU-1-0.923-0.95319.096-0.068-0.0680.0000.0000.0000.000
162A247PHE0-0.084-0.04421.0280.0090.0090.0000.0000.0000.000
163A248LYS10.9140.94524.3620.0110.0110.0000.0000.0000.000
164A249PHE0-0.009-0.01527.345-0.001-0.0010.0000.0000.0000.000
165A250PRO00.0060.00826.9760.0110.0110.0000.0000.0000.000
166A251PRO0-0.0330.00625.1510.0050.0050.0000.0000.0000.000
167A252LYS10.8710.92228.306-0.055-0.0550.0000.0000.0000.000
168A253ASP-1-0.818-0.92630.2750.0580.0580.0000.0000.0000.000
169A254GLY00.0130.00129.7260.0080.0080.0000.0000.0000.000
170A255PHE0-0.068-0.01726.0570.0070.0070.0000.0000.0000.000
171A256VAL00.0300.01521.917-0.015-0.0150.0000.0000.0000.000
172A257ALA00.0730.02519.2080.0210.0210.0000.0000.0000.000
173A258LEU0-0.023-0.00416.4330.0030.0030.0000.0000.0000.000
174A259SER0-0.081-0.08614.1230.0410.0410.0000.0000.0000.000
175A260LYS10.8220.90014.8330.1370.1370.0000.0000.0000.000
176A261ALA0-0.0130.00616.635-0.004-0.0040.0000.0000.0000.000
177A262PRO00.0120.00016.1000.0000.0000.0000.0000.0000.000
178A263ASP-1-0.857-0.93512.5640.1640.1640.0000.0000.0000.000
179A264GLY0-0.045-0.01815.0000.0680.0680.0000.0000.0000.000
180A265TYR0-0.051-0.02717.6660.0090.0090.0000.0000.0000.000
181A266ILE0-0.019-0.00312.5890.0190.0190.0000.0000.0000.000
182A267VAL00.0100.01414.1570.0230.0230.0000.0000.0000.000
183A268LYS10.8960.9426.133-2.122-2.1220.0000.0000.0000.000
184A269SER00.0280.01110.655-0.108-0.1080.0000.0000.0000.000
185A270GLN0-0.016-0.03011.2160.1490.1490.0000.0000.0000.000
186A271HIS0-0.058-0.01912.141-0.034-0.0340.0000.0000.0000.000
187A272SER0-0.005-0.0137.2650.3110.3110.0000.0000.0000.000
188A273GLY00.0410.0156.825-0.611-0.6110.0000.0000.0000.000
189A274ASN0-0.0080.0075.6571.1721.1720.0000.0000.0000.000
190A275ALA00.0230.0283.699-0.828-0.4540.008-0.102-0.2800.000