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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

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FMODB ID: NN67Q

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 OptAll
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 -2169957.718053
FMO2-HF: Nuclear repulsion 2094102.858338
FMO2-HF: Total energy -75854.859714
FMO2-MP2: Total energy -76070.576648


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.
-6.081-2.4980.205-1.506-2.2830.002
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 : 0.032 / q_NPA : 0.011
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].
3A88LEU00.0390.0123.783-3.042-1.1640.001-0.897-0.9820.003
4A89ASN0-0.0070.0072.9160.1171.3410.193-0.493-0.925-0.001
5A90LYS10.8640.9314.609-0.217-0.077-0.001-0.033-0.1060.000
6A91TRP00.0420.0406.4910.5240.5240.0000.0000.0000.000
7A92GLN0-0.023-0.0177.782-0.360-0.3600.0000.0000.0000.000
8A93MET00.0260.03011.1110.1570.1570.0000.0000.0000.000
9A94ASN00.018-0.0049.7220.1930.1930.0000.0000.0000.000
10A95PRO00.0000.0008.209-0.112-0.1120.0000.0000.0000.000
11A96TYR0-0.029-0.0395.9820.1700.1700.0000.0000.0000.000
12A97ASP-1-0.766-0.86211.5660.6650.6650.0000.0000.0000.000
13A98ARG10.8670.91713.563-0.451-0.4510.0000.0000.0000.000
14A99GLY00.0290.02716.931-0.001-0.0010.0000.0000.0000.000
15A100SER0-0.001-0.01419.1830.0050.0050.0000.0000.0000.000
16A101ALA00.0170.01220.345-0.013-0.0130.0000.0000.0000.000
17A102PHE0-0.008-0.00416.807-0.018-0.0180.0000.0000.0000.000
18A103ALA0-0.009-0.00316.9050.0290.0290.0000.0000.0000.000
19A104ILE0-0.002-0.01712.6910.0110.0110.0000.0000.0000.000
20A105GLY00.0400.03114.280-0.028-0.0280.0000.0000.0000.000
21A106SER00.014-0.00811.2720.0620.0620.0000.0000.0000.000
22A107ASP-1-0.725-0.85410.345-0.161-0.1610.0000.0000.0000.000
23A108GLY0-0.0310.00010.625-0.011-0.0110.0000.0000.0000.000
24A109LEU0-0.044-0.02611.5130.1170.1170.0000.0000.0000.000
25A110CYS00.0380.02314.9600.0240.0240.0000.0000.0000.000
26A111CYS0-0.079-0.03316.7010.0350.0350.0000.0000.0000.000
27A112GLN0-0.006-0.01518.746-0.014-0.0140.0000.0000.0000.000
28A113SER0-0.0080.00820.7840.0230.0230.0000.0000.0000.000
29A114ARG10.8410.89123.500-0.057-0.0570.0000.0000.0000.000
30A115GLU-1-0.860-0.90826.2970.1120.1120.0000.0000.0000.000
31A116VAL0-0.005-0.01328.3440.0030.0030.0000.0000.0000.000
32A117LYS10.8730.90531.721-0.086-0.0860.0000.0000.0000.000
33A118GLU-1-0.792-0.85728.3450.1020.1020.0000.0000.0000.000
34A119TRP0-0.018-0.00427.394-0.008-0.0080.0000.0000.0000.000
35A120HIS0-0.023-0.01022.1140.0350.0350.0000.0000.0000.000
36A121GLY00.0700.02421.466-0.021-0.0210.0000.0000.0000.000
37A122CYS0-0.104-0.02915.2730.0320.0320.0000.0000.0000.000
38A123ARG10.8480.90315.756-0.573-0.5730.0000.0000.0000.000
39A124ALA00.0580.01513.4140.0550.0550.0000.0000.0000.000
40A125THR0-0.078-0.0597.7710.0290.0290.0000.0000.0000.000
41A126LYS10.8470.9278.079-0.456-0.4560.0000.0000.0000.000
42A127GLY00.0260.01012.294-0.112-0.1120.0000.0000.0000.000
43A128LEU0-0.045-0.01216.0820.0340.0340.0000.0000.0000.000
44A129MET00.008-0.00418.756-0.003-0.0030.0000.0000.0000.000
45A130LYS10.8390.91020.997-0.235-0.2350.0000.0000.0000.000
46A131GLY00.0650.03322.1570.0120.0120.0000.0000.0000.000
47A132LYS10.7860.89824.481-0.107-0.1070.0000.0000.0000.000
48A133HIS0-0.018-0.01620.4110.0000.0000.0000.0000.0000.000
49A134TYR0-0.017-0.02322.1440.0090.0090.0000.0000.0000.000
50A135TYR0-0.058-0.03819.4730.0060.0060.0000.0000.0000.000
51A136GLU-1-0.752-0.87121.1160.0300.0300.0000.0000.0000.000
52A137VAL00.000-0.01621.1080.0140.0140.0000.0000.0000.000
53A138SER0-0.0090.01722.938-0.014-0.0140.0000.0000.0000.000
54A139CYS0-0.0090.00524.2290.0090.0090.0000.0000.0000.000
55A140HIS0-0.036-0.04521.506-0.011-0.0110.0000.0000.0000.000
56A141ASP-1-0.761-0.87226.7480.0430.0430.0000.0000.0000.000
57A142GLN0-0.032-0.02929.5670.0050.0050.0000.0000.0000.000
58A143GLY00.0120.02329.8070.0020.0020.0000.0000.0000.000
59A144LEU0-0.021-0.00830.5870.0040.0040.0000.0000.0000.000
60A145CYS0-0.016-0.01126.5620.0090.0090.0000.0000.0000.000
61A146ARG10.7840.87026.780-0.177-0.1770.0000.0000.0000.000
62A147VAL00.0190.01423.7370.0190.0190.0000.0000.0000.000
63A148GLY00.0410.00723.176-0.017-0.0170.0000.0000.0000.000
64A149TRP00.0170.01619.4870.0320.0320.0000.0000.0000.000
65A150SER0-0.003-0.00420.896-0.017-0.0170.0000.0000.0000.000
66A151THR00.0700.04220.3170.0430.0430.0000.0000.0000.000
67A152MET0-0.0050.02315.3270.0360.0360.0000.0000.0000.000
68A153GLN0-0.027-0.01319.059-0.007-0.0070.0000.0000.0000.000
69A154ALA0-0.058-0.00122.194-0.025-0.0250.0000.0000.0000.000
70A155SER00.0300.01222.0250.0360.0360.0000.0000.0000.000
71A156LEU00.0020.00818.201-0.006-0.0060.0000.0000.0000.000
72A157ASP-1-0.814-0.89022.2680.1620.1620.0000.0000.0000.000
73A158LEU00.0130.01423.115-0.012-0.0120.0000.0000.0000.000
74A159GLY00.0240.03025.544-0.021-0.0210.0000.0000.0000.000
75A160THR0-0.097-0.07728.167-0.015-0.0150.0000.0000.0000.000
76A161ASP-1-0.747-0.87826.6060.2550.2550.0000.0000.0000.000
77A162LYS10.9680.98829.832-0.202-0.2020.0000.0000.0000.000
78A163PHE00.0230.00024.934-0.004-0.0040.0000.0000.0000.000
79A164GLY00.0350.00924.8130.0310.0310.0000.0000.0000.000
80A165PHE0-0.026-0.00325.812-0.020-0.0200.0000.0000.0000.000
81A166GLY00.0170.00126.0780.0170.0170.0000.0000.0000.000
82A167PHE00.0240.01228.026-0.011-0.0110.0000.0000.0000.000
83A168GLY00.0260.00128.8110.0090.0090.0000.0000.0000.000
84A169GLY00.0380.03431.013-0.006-0.0060.0000.0000.0000.000
85A170THR00.0150.01532.937-0.005-0.0050.0000.0000.0000.000
86A171GLY00.0310.02435.621-0.001-0.0010.0000.0000.0000.000
87A172LYS10.8590.93634.928-0.081-0.0810.0000.0000.0000.000
88A173LYS10.8740.96332.417-0.111-0.1110.0000.0000.0000.000
89A174SER0-0.028-0.02129.772-0.005-0.0050.0000.0000.0000.000
90A175HIS0-0.037-0.03429.7350.0080.0080.0000.0000.0000.000
91A176ASN0-0.017-0.00131.248-0.003-0.0030.0000.0000.0000.000
92A177LYS10.9130.95731.781-0.168-0.1680.0000.0000.0000.000
93A178GLN0-0.0350.01134.320-0.015-0.0150.0000.0000.0000.000
94A179PHE00.005-0.02632.2560.0100.0100.0000.0000.0000.000
95A180ASP-1-0.848-0.92136.6480.1020.1020.0000.0000.0000.000
96A181ASN0-0.007-0.01237.2170.0040.0040.0000.0000.0000.000
97A182TYR0-0.039-0.05732.4940.0030.0030.0000.0000.0000.000
98A183GLY00.0150.01435.7310.0010.0010.0000.0000.0000.000
99A184GLU-1-0.842-0.90535.9000.0420.0420.0000.0000.0000.000
100A185GLU-1-0.882-0.95135.5000.0650.0650.0000.0000.0000.000
101A186PHE0-0.076-0.03228.853-0.004-0.0040.0000.0000.0000.000
102A187THR00.0290.00531.9700.0030.0030.0000.0000.0000.000
103A188MET0-0.0010.00130.353-0.001-0.0010.0000.0000.0000.000
104A189HIS00.002-0.00529.662-0.003-0.0030.0000.0000.0000.000
105A190ASP-1-0.802-0.87730.2270.0400.0400.0000.0000.0000.000
106A191THR0-0.060-0.04225.760-0.001-0.0010.0000.0000.0000.000
107A192ILE0-0.017-0.00126.787-0.002-0.0020.0000.0000.0000.000
108A193GLY00.0470.02925.7090.0010.0010.0000.0000.0000.000
109A194CYS0-0.042-0.02623.298-0.002-0.0020.0000.0000.0000.000
110A195TYR00.0320.00524.1700.0060.0060.0000.0000.0000.000
111A196LEU0-0.025-0.00622.0380.0060.0060.0000.0000.0000.000
112A197ASP-1-0.829-0.93225.2930.1410.1410.0000.0000.0000.000
113A198ILE0-0.0040.00022.834-0.004-0.0040.0000.0000.0000.000
114A199ASP-1-0.846-0.90526.4800.1910.1910.0000.0000.0000.000
115A200LYS10.8240.90029.079-0.120-0.1200.0000.0000.0000.000
116A201GLY0-0.028-0.00429.686-0.004-0.0040.0000.0000.0000.000
117A202HIS00.0050.00830.048-0.009-0.0090.0000.0000.0000.000
118A203VAL00.0340.01126.8490.0120.0120.0000.0000.0000.000
119A204LYS10.8150.92028.831-0.107-0.1070.0000.0000.0000.000
120A205PHE00.0540.02226.1940.0110.0110.0000.0000.0000.000
121A206SER0-0.009-0.00329.551-0.004-0.0040.0000.0000.0000.000
122A207LYS10.8150.90230.233-0.043-0.0430.0000.0000.0000.000
123A208ASN0-0.014-0.02631.118-0.003-0.0030.0000.0000.0000.000
124A209GLY00.0330.02431.710-0.005-0.0050.0000.0000.0000.000
125A210LYS10.8380.92733.128-0.047-0.0470.0000.0000.0000.000
126A211ASP-1-0.807-0.92433.8670.0850.0850.0000.0000.0000.000
127A212LEU0-0.032-0.00432.563-0.005-0.0050.0000.0000.0000.000
128A213GLY00.0190.02435.3100.0010.0010.0000.0000.0000.000
129A214LEU0-0.045-0.02233.3020.0060.0060.0000.0000.0000.000
130A215ALA00.0050.02131.352-0.003-0.0030.0000.0000.0000.000
131A216PHE0-0.018-0.03730.457-0.001-0.0010.0000.0000.0000.000
132A217GLU-1-0.805-0.87732.1710.1300.1300.0000.0000.0000.000
133A218ILE0-0.027-0.01827.0130.0040.0040.0000.0000.0000.000
134A219PRO00.0350.01330.419-0.008-0.0080.0000.0000.0000.000
135A220PRO00.046-0.00631.4970.0130.0130.0000.0000.0000.000
136A221HIS0-0.062-0.04129.783-0.001-0.0010.0000.0000.0000.000
137A222MET0-0.0170.02226.0430.0090.0090.0000.0000.0000.000
138A223LYS10.8980.96926.807-0.164-0.1640.0000.0000.0000.000
139A224ASN0-0.023-0.01825.5580.0040.0040.0000.0000.0000.000
140A225GLN0-0.022-0.01622.6060.0300.0300.0000.0000.0000.000
141A226ALA00.0280.01717.753-0.016-0.0160.0000.0000.0000.000
142A227LEU0-0.017-0.00919.8920.0080.0080.0000.0000.0000.000
143A228PHE00.0070.00013.444-0.002-0.0020.0000.0000.0000.000
144A229PRO0-0.0210.00316.328-0.037-0.0370.0000.0000.0000.000
145A230ALA0-0.0040.00017.6460.0590.0590.0000.0000.0000.000
146A231CYS0-0.056-0.00919.778-0.045-0.0450.0000.0000.0000.000
147A232VAL0-0.003-0.00121.7560.0270.0270.0000.0000.0000.000
148A233LEU0-0.014-0.00121.834-0.019-0.0190.0000.0000.0000.000
149A234LYS10.8460.89925.640-0.103-0.1030.0000.0000.0000.000
150A235ASN0-0.021-0.01427.916-0.009-0.0090.0000.0000.0000.000
151A236ALA00.0050.02226.545-0.009-0.0090.0000.0000.0000.000
152A237GLU-1-0.796-0.88422.3220.0240.0240.0000.0000.0000.000
153A238LEU0-0.006-0.00321.889-0.005-0.0050.0000.0000.0000.000
154A239LYS10.8160.90316.7560.0820.0820.0000.0000.0000.000
155A240PHE0-0.006-0.01316.8640.0080.0080.0000.0000.0000.000
156A241ASN00.042-0.00517.361-0.031-0.0310.0000.0000.0000.000
157A242PHE0-0.006-0.01213.9570.0290.0290.0000.0000.0000.000
158A243GLY00.0480.02417.1280.0230.0230.0000.0000.0000.000
159A244GLU-1-0.866-0.88812.547-0.087-0.0870.0000.0000.0000.000
160A245GLU-1-0.837-0.89715.946-0.141-0.1410.0000.0000.0000.000
161A246GLU-1-0.932-0.95618.804-0.028-0.0280.0000.0000.0000.000
162A247PHE0-0.101-0.05220.6070.0090.0090.0000.0000.0000.000
163A248LYS10.9300.95524.203-0.012-0.0120.0000.0000.0000.000
164A249PHE0-0.006-0.00927.180-0.003-0.0030.0000.0000.0000.000
165A250PRO00.0180.01826.5190.0130.0130.0000.0000.0000.000
166A251PRO0-0.0380.00224.9530.0030.0030.0000.0000.0000.000
167A252LYS10.8850.92328.033-0.075-0.0750.0000.0000.0000.000
168A253ASP-1-0.836-0.92130.1380.0840.0840.0000.0000.0000.000
169A254GLY00.0290.01529.8590.0070.0070.0000.0000.0000.000
170A255PHE0-0.056-0.00925.8690.0100.0100.0000.0000.0000.000
171A256VAL00.0320.01021.720-0.015-0.0150.0000.0000.0000.000
172A257ALA00.0710.02519.0120.0180.0180.0000.0000.0000.000
173A258LEU0-0.022-0.00316.4920.0100.0100.0000.0000.0000.000
174A259SER0-0.064-0.08013.6120.0470.0470.0000.0000.0000.000
175A260LYS10.8250.90414.1280.0440.0440.0000.0000.0000.000
176A261ALA00.0000.00916.503-0.012-0.0120.0000.0000.0000.000
177A262PRO00.0100.00015.7140.0260.0260.0000.0000.0000.000
178A263ASP-1-0.872-0.93811.8930.4550.4550.0000.0000.0000.000
179A264GLY0-0.021-0.00814.7290.0580.0580.0000.0000.0000.000
180A265TYR0-0.062-0.03117.668-0.018-0.0180.0000.0000.0000.000
181A266ILE0-0.019-0.01012.728-0.001-0.0010.0000.0000.0000.000
182A267VAL0-0.0030.00713.9810.0390.0390.0000.0000.0000.000
183A268LYS10.8920.9306.094-3.172-3.1720.0000.0000.0000.000
184A269SER00.007-0.00210.760-0.157-0.1570.0000.0000.0000.000
185A270GLN0-0.008-0.03710.8970.1900.1900.0000.0000.0000.000
186A271HIS0-0.061-0.02012.214-0.010-0.0100.0000.0000.0000.000
187A272SER0-0.014-0.0157.2290.2390.2390.0000.0000.0000.000
188A273GLY00.0400.0147.012-0.411-0.4110.0000.0000.0000.000
189A274ASN00.0060.0135.9730.6970.6970.0000.0000.0000.000
190A275ALA00.0140.0333.368-0.536-0.1950.012-0.083-0.2700.000