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: J3819

Calculation Name: 2WUX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WUX

Chain ID: A

ChEMBL ID:

UniProt ID: P04871

Base Structure: X-ray

Registration Date: 2023-06-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2451933.802589
FMO2-HF: Nuclear repulsion 2364501.83008
FMO2-HF: Total energy -87431.972509
FMO2-MP2: Total energy -87689.03767


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:3:ASP)


Summations of interaction energy for fragment #1(A:3: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.
-79.062-77.14111.944-6.632-7.2320.08
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.813 / q_NPA : -0.914
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].
3A5SER0-0.072-0.0301.839-34.673-33.68411.814-6.979-5.8240.075
4A6TYR00.0490.0173.385-1.308-0.5480.1310.363-1.2530.005
5A7ARG10.9310.9554.521-52.948-52.776-0.001-0.016-0.1550.000
6A8PRO0-0.030-0.0046.947-3.567-3.5670.0000.0000.0000.000
7A9THR00.0540.0369.6340.7590.7590.0000.0000.0000.000
8A10ILE00.0060.0009.040-0.144-0.1440.0000.0000.0000.000
9A11GLY0-0.025-0.00812.691-0.810-0.8100.0000.0000.0000.000
10A12ARG10.8170.90814.338-17.165-17.1650.0000.0000.0000.000
11A13THR00.0380.00917.065-0.265-0.2650.0000.0000.0000.000
12A14TYR0-0.027-0.01117.8780.3940.3940.0000.0000.0000.000
13A15VAL00.003-0.00423.058-0.202-0.2020.0000.0000.0000.000
14A16TYR0-0.0070.00323.8820.0120.0120.0000.0000.0000.000
15A17ASP-1-0.831-0.91029.5468.1078.1070.0000.0000.0000.000
16A18ASN00.0020.00731.7680.0500.0500.0000.0000.0000.000
17A19LYS10.8390.93031.121-8.360-8.3600.0000.0000.0000.000
18A20TYR00.023-0.00727.0840.3140.3140.0000.0000.0000.000
19A21TYR00.0060.00224.509-0.196-0.1960.0000.0000.0000.000
20A22LYS10.9180.96319.455-13.959-13.9590.0000.0000.0000.000
21A23ASN0-0.010-0.03215.831-0.876-0.8760.0000.0000.0000.000
22A24LEU00.0580.02719.6700.1080.1080.0000.0000.0000.000
23A25ASP-1-0.760-0.88315.05817.74317.7430.0000.0000.0000.000
24A26ALA0-0.065-0.03116.4300.3460.3460.0000.0000.0000.000
25A27VAL00.0050.00618.407-0.430-0.4300.0000.0000.0000.000
26A28ILE00.0310.01621.004-0.417-0.4170.0000.0000.0000.000
27A29LYS10.8530.94413.383-20.578-20.5780.0000.0000.0000.000
28A30ASN0-0.011-0.02319.9310.3720.3720.0000.0000.0000.000
29A31ALA0-0.0320.00621.9530.0230.0230.0000.0000.0000.000
30A49PRO00.0330.00616.447-0.302-0.3020.0000.0000.0000.000
31A50LEU00.0450.01718.397-0.229-0.2290.0000.0000.0000.000
32A51ASP-1-0.901-0.94514.47118.51718.5170.0000.0000.0000.000
33A52ASN0-0.039-0.02416.2200.2370.2370.0000.0000.0000.000
34A53TYR0-0.0190.00418.171-0.593-0.5930.0000.0000.0000.000
35A54LEU0-0.013-0.01020.0500.4700.4700.0000.0000.0000.000
36A55VAL0-0.032-0.01022.883-0.371-0.3710.0000.0000.0000.000
37A56ALA00.0090.00425.6350.2270.2270.0000.0000.0000.000
38A57GLU-1-0.917-0.96825.99110.87810.8780.0000.0000.0000.000
39A58ASP-1-0.860-0.93829.4928.1758.1750.0000.0000.0000.000
40A59PRO00.0300.00633.2350.0560.0560.0000.0000.0000.000
41A60PHE0-0.034-0.02334.941-0.089-0.0890.0000.0000.0000.000
42A61LEU0-0.054-0.01432.790-0.096-0.0960.0000.0000.0000.000
43A62GLY00.0500.04630.4420.2250.2250.0000.0000.0000.000
44A63PRO0-0.024-0.02128.703-0.312-0.3120.0000.0000.0000.000
45A64GLY00.0170.01331.657-0.178-0.1780.0000.0000.0000.000
46A65LYS10.8260.89835.058-7.224-7.2240.0000.0000.0000.000
47A66ASN00.011-0.01437.6720.1090.1090.0000.0000.0000.000
48A67GLN0-0.034-0.04040.5680.0540.0540.0000.0000.0000.000
49A68LYS10.8440.92744.366-6.523-6.5230.0000.0000.0000.000
50A69LEU00.0740.05746.571-0.108-0.1080.0000.0000.0000.000
51A70THR0-0.056-0.04749.840-0.005-0.0050.0000.0000.0000.000
52A71LEU0-0.032-0.00452.007-0.094-0.0940.0000.0000.0000.000
53A72PHE00.004-0.00354.854-0.112-0.1120.0000.0000.0000.000
54A73LYS10.8560.90654.106-5.596-5.5960.0000.0000.0000.000
55A74GLH0-0.014-0.02757.970-0.091-0.0910.0000.0000.0000.000
56A75ILE00.0310.02358.7590.0850.0850.0000.0000.0000.000
57A76ARG10.7510.83259.180-5.183-5.1830.0000.0000.0000.000
58A77ASN00.0100.00061.2690.0030.0030.0000.0000.0000.000
59A78VAL0-0.0160.00357.702-0.051-0.0510.0000.0000.0000.000
60A79LYS10.8360.89761.088-4.816-4.8160.0000.0000.0000.000
61A80PRO00.0880.05459.7880.0730.0730.0000.0000.0000.000
62A81ASP-1-0.800-0.87757.9215.3245.3240.0000.0000.0000.000
63A82THR0-0.090-0.05358.994-0.053-0.0530.0000.0000.0000.000
64A83MET0-0.0060.00451.5630.0930.0930.0000.0000.0000.000
65A84LYS10.8490.92457.270-5.071-5.0710.0000.0000.0000.000
66A85LEU0-0.0190.00856.6600.1120.1120.0000.0000.0000.000
67A86VAL00.0040.01153.332-0.074-0.0740.0000.0000.0000.000
68A87VAL0-0.0060.00454.078-0.074-0.0740.0000.0000.0000.000
69A88GLY00.0540.02556.7500.0520.0520.0000.0000.0000.000
70A89TRP0-0.028-0.00352.595-0.124-0.1240.0000.0000.0000.000
71A90LYS11.0191.00158.369-4.823-4.8230.0000.0000.0000.000
72A91GLY00.0860.03256.2120.0390.0390.0000.0000.0000.000
73A92LYS11.0191.00056.559-4.864-4.8640.0000.0000.0000.000
74A93GLU-1-0.886-0.92158.6445.0725.0720.0000.0000.0000.000
75A94PHE00.0220.01149.6830.0080.0080.0000.0000.0000.000
76A95TYR00.016-0.00250.639-0.019-0.0190.0000.0000.0000.000
77A96ARG10.7870.88254.759-5.148-5.1480.0000.0000.0000.000
78A97GLU-1-0.829-0.90155.2765.4035.4030.0000.0000.0000.000
79A98THR0-0.019-0.02649.8880.0780.0780.0000.0000.0000.000
80A99TRP0-0.012-0.00652.1520.0200.0200.0000.0000.0000.000
81A100THR0-0.029-0.04553.635-0.016-0.0160.0000.0000.0000.000
82A101ARG10.8300.90153.346-5.560-5.5600.0000.0000.0000.000
83A102PHE00.0240.01345.9460.0480.0480.0000.0000.0000.000
84A103MET0-0.049-0.00750.6290.1030.1030.0000.0000.0000.000
85A104GLU-1-0.909-0.94453.0295.4165.4160.0000.0000.0000.000
86A105ASP-1-0.904-0.93849.2676.1836.1830.0000.0000.0000.000
87A106SER0-0.003-0.00948.4390.1250.1250.0000.0000.0000.000
88A107PHE0-0.071-0.02149.9900.0560.0560.0000.0000.0000.000
89A108PRO0-0.041-0.02551.714-0.056-0.0560.0000.0000.0000.000
90A109ILE00.0200.00246.3600.0920.0920.0000.0000.0000.000
91A110VAL0-0.049-0.02545.994-0.020-0.0200.0000.0000.0000.000
92A111ASN0-0.021-0.01842.3330.0080.0080.0000.0000.0000.000
93A112ASP-1-0.873-0.92741.3106.8956.8950.0000.0000.0000.000
94A113GLN00.008-0.01340.1980.2680.2680.0000.0000.0000.000
95A114GLU-1-0.795-0.86735.9628.1948.1940.0000.0000.0000.000
96A115VAL0-0.003-0.01239.3670.1050.1050.0000.0000.0000.000
97A116MET0-0.088-0.01333.4830.0020.0020.0000.0000.0000.000
98A117ASP-1-0.778-0.88037.7017.7727.7720.0000.0000.0000.000
99A118VAL0-0.022-0.00639.767-0.081-0.0810.0000.0000.0000.000
100A119PHE00.0300.00937.592-0.003-0.0030.0000.0000.0000.000
101A120LEU0-0.0040.00843.600-0.124-0.1240.0000.0000.0000.000
102A121VAL0-0.017-0.01544.1700.1190.1190.0000.0000.0000.000
103A122VAL0-0.0010.00646.893-0.159-0.1590.0000.0000.0000.000
104A123ASN0-0.022-0.01647.3100.0070.0070.0000.0000.0000.000
105A124MET0-0.043-0.01448.622-0.155-0.1550.0000.0000.0000.000
106A125ARG10.9120.94851.373-5.857-5.8570.0000.0000.0000.000
107A126PRO00.0600.03553.969-0.090-0.0900.0000.0000.0000.000
108A127THR0-0.074-0.07257.1550.0380.0380.0000.0000.0000.000
109A128ARG10.9040.94660.021-5.022-5.0220.0000.0000.0000.000
110A129PRO00.0320.02158.5740.0920.0920.0000.0000.0000.000
111A130ASN0-0.032-0.04158.107-0.068-0.0680.0000.0000.0000.000
112A131ARG10.8100.91057.572-5.178-5.1780.0000.0000.0000.000
113A132CYS0-0.051-0.03754.2030.1200.1200.0000.0000.0000.000
114A133TYR0-0.0180.00053.264-0.046-0.0460.0000.0000.0000.000
115A134LYS10.8500.92145.455-6.660-6.6600.0000.0000.0000.000
116A135PHE00.0310.00049.520-0.128-0.1280.0000.0000.0000.000
117A136LEU0-0.046-0.01348.9040.1550.1550.0000.0000.0000.000
118A137ALA00.014-0.00947.638-0.132-0.1320.0000.0000.0000.000
119A138GLN00.0490.02447.3800.1350.1350.0000.0000.0000.000
120A139HIS00.0090.01544.450-0.161-0.1610.0000.0000.0000.000
121A140ALA00.0070.00849.4660.0310.0310.0000.0000.0000.000
122A141LEU0-0.0040.00744.978-0.044-0.0440.0000.0000.0000.000
123A142ARG10.8640.93449.578-5.703-5.7030.0000.0000.0000.000
124A143CYS00.0710.04651.2710.0880.0880.0000.0000.0000.000
125A144ASP-1-0.864-0.93753.2815.4255.4250.0000.0000.0000.000
126A145PRO0-0.102-0.08357.0630.0080.0080.0000.0000.0000.000
127A146ASP-1-0.942-0.93859.4284.8644.8640.0000.0000.0000.000
128A147TYR00.022-0.01157.5990.0830.0830.0000.0000.0000.000
129A148VAL0-0.0070.00860.1600.0460.0460.0000.0000.0000.000
130A149PRO0-0.017-0.00658.2460.0000.0000.0000.0000.0000.000
131A150HIS00.0410.03260.326-0.115-0.1150.0000.0000.0000.000
132A151ASP-1-0.774-0.85560.5105.0785.0780.0000.0000.0000.000
133A152VAL0-0.022-0.02460.8370.0600.0600.0000.0000.0000.000
134A153ILE0-0.0130.00655.000-0.047-0.0470.0000.0000.0000.000
135A154ARG10.8620.89458.812-5.143-5.1430.0000.0000.0000.000
136A155ILE0-0.019-0.00153.0260.0730.0730.0000.0000.0000.000
137A156VAL00.006-0.00352.539-0.039-0.0390.0000.0000.0000.000
138A157GLU-1-0.945-0.96647.9186.3846.3840.0000.0000.0000.000
139A158PRO0-0.0280.00148.3780.0590.0590.0000.0000.0000.000
140A159SER00.0160.00444.0560.1930.1930.0000.0000.0000.000
141A160TRP00.007-0.00744.304-0.118-0.1180.0000.0000.0000.000
142A161VAL0-0.0170.00243.9450.1770.1770.0000.0000.0000.000
143A162GLY00.0500.03542.520-0.002-0.0020.0000.0000.0000.000
144A163SER00.028-0.00142.715-0.117-0.1170.0000.0000.0000.000
145A164ASN0-0.022-0.01342.190-0.085-0.0850.0000.0000.0000.000
146A165ASN0-0.027-0.00744.329-0.098-0.0980.0000.0000.0000.000
147A166GLU-1-0.803-0.89743.8576.8236.8230.0000.0000.0000.000
148A167TYR0-0.019-0.01744.2180.2030.2030.0000.0000.0000.000
149A168ARG10.8500.91538.686-7.705-7.7050.0000.0000.0000.000
150A169ILE0-0.0040.00042.2840.1180.1180.0000.0000.0000.000
151A170SER0-0.063-0.04139.835-0.118-0.1180.0000.0000.0000.000
152A171LEU0-0.007-0.01941.983-0.108-0.1080.0000.0000.0000.000
153A172ALA00.0150.02740.377-0.124-0.1240.0000.0000.0000.000
154A173LYS10.9510.98439.849-7.165-7.1650.0000.0000.0000.000
155A187TYR00.0790.03147.930-0.024-0.0240.0000.0000.0000.000
156A188THR0-0.005-0.01150.065-0.074-0.0740.0000.0000.0000.000
157A189ASN00.0250.01153.5070.0820.0820.0000.0000.0000.000
158A190SER0-0.028-0.04056.782-0.039-0.0390.0000.0000.0000.000
159A191PHE00.0100.01056.0060.0350.0350.0000.0000.0000.000
160A192GLU-1-0.842-0.90257.6585.0015.0010.0000.0000.0000.000
161A193GLN00.0790.03756.0410.1420.1420.0000.0000.0000.000
162A194PHE0-0.034-0.01250.1180.0780.0780.0000.0000.0000.000
163A195ILE0-0.055-0.03053.9610.0730.0730.0000.0000.0000.000
164A196ASP-1-0.853-0.92356.1815.1685.1680.0000.0000.0000.000
165A197ARG10.7660.87851.313-5.733-5.7330.0000.0000.0000.000
166A198VAL00.0130.00051.2800.1230.1230.0000.0000.0000.000
167A199ILE0-0.0030.00448.1730.1010.1010.0000.0000.0000.000
168A200TRP0-0.048-0.02049.0300.1270.1270.0000.0000.0000.000
169A201GLU-1-0.908-0.94649.1036.0016.0010.0000.0000.0000.000
170A202ASN0-0.099-0.04644.7850.2400.2400.0000.0000.0000.000
171A203PHE0-0.005-0.01944.5800.1500.1500.0000.0000.0000.000
172A204TYR00.0260.03244.230-0.102-0.1020.0000.0000.0000.000
173A205LYS10.9100.96548.686-5.508-5.5080.0000.0000.0000.000
174A206PRO0-0.0120.00149.046-0.012-0.0120.0000.0000.0000.000
175A207ILE0-0.043-0.02050.956-0.155-0.1550.0000.0000.0000.000
176A208VAL00.0330.00250.1850.1150.1150.0000.0000.0000.000
177A209TYR0-0.030-0.02252.327-0.119-0.1190.0000.0000.0000.000
178A210ILE00.009-0.00750.4720.1430.1430.0000.0000.0000.000
179A211GLY00.0580.01953.284-0.154-0.1540.0000.0000.0000.000
180A212THR0-0.046-0.01653.3760.0890.0890.0000.0000.0000.000
181A213ASP-1-0.791-0.89450.8516.1176.1170.0000.0000.0000.000
182A214SER0-0.027-0.03554.119-0.033-0.0330.0000.0000.0000.000
183A215ALA0-0.004-0.00157.306-0.030-0.0300.0000.0000.0000.000
184A216GLU-1-0.882-0.93460.3254.9254.9250.0000.0000.0000.000
185A217GLU-1-0.813-0.89061.2314.8344.8340.0000.0000.0000.000
186A218GLU-1-0.769-0.85457.8955.3765.3760.0000.0000.0000.000
187A219GLU-1-0.891-0.90360.7984.9124.9120.0000.0000.0000.000
188A220ILE0-0.009-0.00355.8160.0720.0720.0000.0000.0000.000
189A221LEU00.000-0.00256.790-0.075-0.0750.0000.0000.0000.000
190A222LEU0-0.006-0.00653.9680.1320.1320.0000.0000.0000.000
191A223GLU-1-0.833-0.90450.4805.9925.9920.0000.0000.0000.000
192A224VAL00.0100.01451.7050.1210.1210.0000.0000.0000.000
193A225SER00.0110.00248.442-0.090-0.0900.0000.0000.0000.000
194A226LEU00.0080.02147.4830.0440.0440.0000.0000.0000.000
195A227VAL0-0.021-0.01041.784-0.037-0.0370.0000.0000.0000.000
196A228PHE00.0410.01742.9160.1070.1070.0000.0000.0000.000
197A229LYS10.7890.90434.990-8.358-8.3580.0000.0000.0000.000
198A230VAL0-0.013-0.01539.055-0.047-0.0470.0000.0000.0000.000
199A231LYS10.8410.89832.684-8.595-8.5950.0000.0000.0000.000
200A232GLU-1-0.833-0.90436.8087.0547.0540.0000.0000.0000.000
201A233PHE0-0.042-0.02533.9800.2680.2680.0000.0000.0000.000
202A234ALA00.0180.01338.052-0.121-0.1210.0000.0000.0000.000
203A235PRO0-0.014-0.00638.4880.1930.1930.0000.0000.0000.000
204A236ASP-1-0.942-0.95537.1777.9257.9250.0000.0000.0000.000
205A237ALA0-0.016-0.01839.308-0.075-0.0750.0000.0000.0000.000
206A238PRO0-0.0380.00043.082-0.013-0.0130.0000.0000.0000.000
207A239LEU00.0160.01045.834-0.083-0.0830.0000.0000.0000.000
208A240PHE0-0.020-0.02248.430-0.018-0.0180.0000.0000.0000.000
209A241THR0-0.004-0.00852.113-0.013-0.0130.0000.0000.0000.000
210A242GLY0-0.0070.02255.8710.0350.0350.0000.0000.0000.000
211A243PRO0-0.014-0.01357.767-0.077-0.0770.0000.0000.0000.000
212A244ALA00.0710.02752.3700.0190.0190.0000.0000.0000.000
213A245TYR0-0.049-0.02347.722-0.087-0.0870.0000.0000.0000.000