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

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FMODB ID: 821LY

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2448552.243417
FMO2-HF: Nuclear repulsion 2361121.963152
FMO2-HF: Total energy -87430.280265
FMO2-MP2: Total energy -87687.359765


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.
-65.826-59.336.189-6.197-6.4890.059
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 : -0.833 / q_NPA : -0.920
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].
3A5SER0-0.072-0.0401.998-34.719-30.0545.669-5.305-5.0300.063
4A6TYR00.0210.0062.9156.9968.7230.521-0.888-1.360-0.004
5A7ARG10.9600.9684.790-48.129-48.025-0.001-0.004-0.0990.000
6A8PRO0-0.0330.0047.350-2.741-2.7410.0000.0000.0000.000
7A9THR00.0310.0219.9180.7900.7900.0000.0000.0000.000
8A10ILE00.0100.0099.421-0.183-0.1830.0000.0000.0000.000
9A11GLY0-0.041-0.02312.495-0.804-0.8040.0000.0000.0000.000
10A12ARG10.8670.91913.308-16.721-16.7210.0000.0000.0000.000
11A13THR00.017-0.00217.085-0.278-0.2780.0000.0000.0000.000
12A14TYR00.0090.00818.5090.4360.4360.0000.0000.0000.000
13A15VAL00.005-0.00223.060-0.195-0.1950.0000.0000.0000.000
14A16TYR0-0.036-0.01924.3990.0030.0030.0000.0000.0000.000
15A17ASP-1-0.913-0.95029.3508.0918.0910.0000.0000.0000.000
16A18ASN00.0270.01231.6820.1020.1020.0000.0000.0000.000
17A19LYS10.9651.00230.817-8.626-8.6260.0000.0000.0000.000
18A20TYR00.0550.01826.6890.1950.1950.0000.0000.0000.000
19A21TYR0-0.0110.00024.283-0.238-0.2380.0000.0000.0000.000
20A22LYS10.9730.99218.618-13.801-13.8010.0000.0000.0000.000
21A23ASN0-0.022-0.03615.560-0.886-0.8860.0000.0000.0000.000
22A24LEU00.0480.00919.5630.0110.0110.0000.0000.0000.000
23A25ASP-1-0.753-0.87415.03716.99216.9920.0000.0000.0000.000
24A26ALA0-0.069-0.03716.6450.1530.1530.0000.0000.0000.000
25A27VAL0-0.0140.00318.191-0.280-0.2800.0000.0000.0000.000
26A28ILE0-0.011-0.01020.844-0.389-0.3890.0000.0000.0000.000
27A29LYS10.9110.96514.329-19.377-19.3770.0000.0000.0000.000
28A30ASN0-0.003-0.00519.8840.4670.4670.0000.0000.0000.000
29A31ALA0-0.036-0.00222.430-0.043-0.0430.0000.0000.0000.000
30A49PRO00.012-0.00115.754-0.253-0.2530.0000.0000.0000.000
31A50LEU00.018-0.00718.224-0.382-0.3820.0000.0000.0000.000
32A51ASP-1-0.837-0.93013.50918.14918.1490.0000.0000.0000.000
33A52ASN0-0.079-0.01316.1450.5800.5800.0000.0000.0000.000
34A53TYR0-0.0190.00218.088-0.546-0.5460.0000.0000.0000.000
35A54LEU0-0.019-0.00219.9760.4080.4080.0000.0000.0000.000
36A55VAL0-0.0080.00322.844-0.404-0.4040.0000.0000.0000.000
37A56ALA0-0.017-0.01125.4550.2250.2250.0000.0000.0000.000
38A57GLU-1-0.935-0.98226.38210.58910.5890.0000.0000.0000.000
39A58ASP-1-0.870-0.94129.2098.1908.1900.0000.0000.0000.000
40A59PRO00.0340.01132.7730.0690.0690.0000.0000.0000.000
41A60PHE0-0.042-0.02934.619-0.108-0.1080.0000.0000.0000.000
42A61LEU0-0.036-0.00832.593-0.082-0.0820.0000.0000.0000.000
43A62GLY00.0290.04230.6450.2110.2110.0000.0000.0000.000
44A63PRO0-0.031-0.02528.990-0.249-0.2490.0000.0000.0000.000
45A64GLY00.0150.01031.799-0.162-0.1620.0000.0000.0000.000
46A65LYS10.8530.90135.274-7.194-7.1940.0000.0000.0000.000
47A66ASN0-0.002-0.01037.7570.0340.0340.0000.0000.0000.000
48A67GLN0-0.038-0.03840.6390.0760.0760.0000.0000.0000.000
49A68LYS10.8880.95444.341-6.411-6.4110.0000.0000.0000.000
50A69LEU00.0240.03446.657-0.093-0.0930.0000.0000.0000.000
51A70THR0-0.022-0.02850.0790.0290.0290.0000.0000.0000.000
52A71LEU0-0.022-0.00952.268-0.096-0.0960.0000.0000.0000.000
53A72PHE0-0.016-0.00454.927-0.119-0.1190.0000.0000.0000.000
54A73LYS10.8670.91654.675-5.495-5.4950.0000.0000.0000.000
55A74GLH0-0.019-0.04257.958-0.102-0.1020.0000.0000.0000.000
56A75ILE00.0240.02658.7890.0890.0890.0000.0000.0000.000
57A76ARG10.8190.92359.156-5.137-5.1370.0000.0000.0000.000
58A77ASN00.0680.05060.7420.0160.0160.0000.0000.0000.000
59A78VAL0-0.016-0.00757.604-0.067-0.0670.0000.0000.0000.000
60A79LYS10.9120.95060.913-4.799-4.7990.0000.0000.0000.000
61A80PRO00.0810.05359.5670.0660.0660.0000.0000.0000.000
62A81ASP-1-0.814-0.89857.4795.3145.3140.0000.0000.0000.000
63A82THR0-0.113-0.05358.658-0.040-0.0400.0000.0000.0000.000
64A83MET0-0.018-0.00251.7370.0900.0900.0000.0000.0000.000
65A84LYS10.8380.91757.240-5.008-5.0080.0000.0000.0000.000
66A85LEU0-0.0220.00656.6570.1190.1190.0000.0000.0000.000
67A86VAL0-0.0040.00653.927-0.076-0.0760.0000.0000.0000.000
68A87VAL00.0210.02054.106-0.074-0.0740.0000.0000.0000.000
69A88GLY00.0540.02656.9960.0480.0480.0000.0000.0000.000
70A89TRP0-0.029-0.00152.760-0.119-0.1190.0000.0000.0000.000
71A90LYS11.0190.98658.432-4.760-4.7600.0000.0000.0000.000
72A91GLY00.0660.01356.5520.0480.0480.0000.0000.0000.000
73A92LYS11.0141.00156.954-4.808-4.8080.0000.0000.0000.000
74A93GLU-1-0.843-0.89958.8745.0095.0090.0000.0000.0000.000
75A94PHE0-0.0020.01049.9570.0070.0070.0000.0000.0000.000
76A95TYR00.0360.00650.928-0.017-0.0170.0000.0000.0000.000
77A96ARG10.8310.90155.159-5.045-5.0450.0000.0000.0000.000
78A97GLU-1-0.891-0.95555.4605.3715.3710.0000.0000.0000.000
79A98THR0-0.010-0.01450.1510.0780.0780.0000.0000.0000.000
80A99TRP0-0.016-0.00652.4580.0250.0250.0000.0000.0000.000
81A100THR0-0.018-0.02853.773-0.010-0.0100.0000.0000.0000.000
82A101ARG10.9190.97353.560-5.523-5.5230.0000.0000.0000.000
83A102PHE00.0130.00446.1280.0390.0390.0000.0000.0000.000
84A103MET0-0.034-0.01350.3150.0910.0910.0000.0000.0000.000
85A104GLU-1-1.002-0.99853.1595.3175.3170.0000.0000.0000.000
86A105ASP-1-0.901-0.93449.5386.1496.1490.0000.0000.0000.000
87A106SER0-0.015-0.01748.7580.0900.0900.0000.0000.0000.000
88A107PHE0-0.079-0.00950.3560.0490.0490.0000.0000.0000.000
89A108PRO0-0.021-0.02151.556-0.064-0.0640.0000.0000.0000.000
90A109ILE00.018-0.00446.4120.0870.0870.0000.0000.0000.000
91A110VAL0-0.041-0.02345.863-0.038-0.0380.0000.0000.0000.000
92A111ASN0-0.043-0.03442.364-0.027-0.0270.0000.0000.0000.000
93A112ASP-1-0.876-0.92341.0746.9576.9570.0000.0000.0000.000
94A113GLN0-0.021-0.03040.2990.2040.2040.0000.0000.0000.000
95A114GLU-1-0.855-0.92036.5498.0398.0390.0000.0000.0000.000
96A115VAL0-0.031-0.02239.6340.0820.0820.0000.0000.0000.000
97A116MET0-0.066-0.02033.7670.0270.0270.0000.0000.0000.000
98A117ASP-1-0.749-0.85238.2017.5267.5260.0000.0000.0000.000
99A118VAL0-0.035-0.02040.213-0.076-0.0760.0000.0000.0000.000
100A119PHE00.006-0.00137.6680.0230.0230.0000.0000.0000.000
101A120LEU00.0040.01443.732-0.126-0.1260.0000.0000.0000.000
102A121VAL0-0.017-0.02044.2650.1100.1100.0000.0000.0000.000
103A122VAL0-0.009-0.00646.839-0.163-0.1630.0000.0000.0000.000
104A123ASN0-0.014-0.01747.918-0.017-0.0170.0000.0000.0000.000
105A124MET0-0.028-0.00148.629-0.156-0.1560.0000.0000.0000.000
106A125ARG10.8990.95451.272-5.761-5.7610.0000.0000.0000.000
107A126PRO00.0640.04053.625-0.085-0.0850.0000.0000.0000.000
108A127THR0-0.062-0.07056.8420.0320.0320.0000.0000.0000.000
109A128ARG10.9210.96359.894-4.962-4.9620.0000.0000.0000.000
110A129PRO00.0270.02158.3480.0940.0940.0000.0000.0000.000
111A130ASN0-0.039-0.05058.005-0.089-0.0890.0000.0000.0000.000
112A131ARG10.9491.00657.116-5.159-5.1590.0000.0000.0000.000
113A132CYS0-0.034-0.03153.8240.1190.1190.0000.0000.0000.000
114A133TYR00.0060.01453.187-0.076-0.0760.0000.0000.0000.000
115A134LYS10.9060.96144.355-6.736-6.7360.0000.0000.0000.000
116A135PHE00.009-0.00149.313-0.134-0.1340.0000.0000.0000.000
117A136LEU0-0.0080.00248.7740.1470.1470.0000.0000.0000.000
118A137ALA00.001-0.02447.907-0.125-0.1250.0000.0000.0000.000
119A138GLN00.0670.04146.8300.1340.1340.0000.0000.0000.000
120A139HIS00.0450.04444.664-0.169-0.1690.0000.0000.0000.000
121A140ALA0-0.006-0.00349.5820.0170.0170.0000.0000.0000.000
122A141LEU0-0.026-0.00345.021-0.057-0.0570.0000.0000.0000.000
123A142ARG10.9020.95349.521-5.642-5.6420.0000.0000.0000.000
124A143CYS00.0560.02151.7990.0950.0950.0000.0000.0000.000
125A144ASP-1-0.798-0.88953.2435.3535.3530.0000.0000.0000.000
126A145PRO0-0.191-0.12357.045-0.006-0.0060.0000.0000.0000.000
127A146ASP-1-0.920-0.93759.2524.8754.8750.0000.0000.0000.000
128A147TYR00.0360.00457.1640.0560.0560.0000.0000.0000.000
129A148VAL0-0.048-0.01160.6540.0380.0380.0000.0000.0000.000
130A149PRO0-0.0230.00158.282-0.010-0.0100.0000.0000.0000.000
131A150HIS00.0490.02759.987-0.104-0.1040.0000.0000.0000.000
132A151ASP-1-0.784-0.90060.4885.0185.0180.0000.0000.0000.000
133A152VAL0-0.076-0.04060.9150.0590.0590.0000.0000.0000.000
134A153ILE0-0.0060.01055.052-0.053-0.0530.0000.0000.0000.000
135A154ARG10.8820.91658.722-5.110-5.1100.0000.0000.0000.000
136A155ILE0-0.0110.00352.9230.0720.0720.0000.0000.0000.000
137A156VAL0-0.009-0.01152.436-0.040-0.0400.0000.0000.0000.000
138A157GLU-1-0.951-0.96248.1236.3776.3770.0000.0000.0000.000
139A158PRO0-0.039-0.00248.3020.0630.0630.0000.0000.0000.000
140A159SER00.008-0.00243.8280.1690.1690.0000.0000.0000.000
141A160TRP00.017-0.00844.222-0.114-0.1140.0000.0000.0000.000
142A161VAL0-0.0140.00343.8400.1750.1750.0000.0000.0000.000
143A162GLY0-0.010-0.01242.267-0.015-0.0150.0000.0000.0000.000
144A163SER00.0330.00242.808-0.091-0.0910.0000.0000.0000.000
145A164ASN00.0020.00941.493-0.167-0.1670.0000.0000.0000.000
146A165ASN0-0.012-0.00744.175-0.050-0.0500.0000.0000.0000.000
147A166GLU-1-0.802-0.89244.2346.6576.6570.0000.0000.0000.000
148A167TYR0-0.058-0.03644.2470.1740.1740.0000.0000.0000.000
149A168ARG10.8460.90539.344-7.469-7.4690.0000.0000.0000.000
150A169ILE00.0110.00542.1610.1250.1250.0000.0000.0000.000
151A170SER0-0.080-0.05439.751-0.112-0.1120.0000.0000.0000.000
152A171LEU0-0.008-0.02641.902-0.101-0.1010.0000.0000.0000.000
153A172ALA00.0360.04140.458-0.132-0.1320.0000.0000.0000.000
154A173LYS10.9590.98740.012-7.196-7.1960.0000.0000.0000.000
155A187TYR00.0640.02347.924-0.040-0.0400.0000.0000.0000.000
156A188THR0-0.020-0.01549.996-0.084-0.0840.0000.0000.0000.000
157A189ASN00.0530.02153.4300.0540.0540.0000.0000.0000.000
158A190SER0-0.002-0.00456.713-0.041-0.0410.0000.0000.0000.000
159A191PHE00.0360.01456.3460.0370.0370.0000.0000.0000.000
160A192GLU-1-0.937-0.97258.0324.9044.9040.0000.0000.0000.000
161A193GLN00.0630.02856.3490.1130.1130.0000.0000.0000.000
162A194PHE0-0.039-0.01350.4120.0720.0720.0000.0000.0000.000
163A195ILE0-0.033-0.03154.2160.0760.0760.0000.0000.0000.000
164A196ASP-1-0.846-0.91056.5425.1375.1370.0000.0000.0000.000
165A197ARG10.7930.90651.580-5.718-5.7180.0000.0000.0000.000
166A198VAL00.023-0.01551.4620.1110.1110.0000.0000.0000.000
167A199ILE00.0010.00848.3130.1050.1050.0000.0000.0000.000
168A200TRP0-0.083-0.02749.2600.1230.1230.0000.0000.0000.000
169A201GLU-1-0.901-0.95149.3495.9595.9590.0000.0000.0000.000
170A202ASN0-0.046-0.00945.1130.1100.1100.0000.0000.0000.000
171A203PHE0-0.042-0.02444.9340.1400.1400.0000.0000.0000.000
172A204TYR00.0160.02144.453-0.198-0.1980.0000.0000.0000.000
173A205LYS10.9230.97748.746-5.442-5.4420.0000.0000.0000.000
174A206PRO0-0.0200.00749.092-0.031-0.0310.0000.0000.0000.000
175A207ILE0-0.040-0.01151.107-0.130-0.1300.0000.0000.0000.000
176A208VAL00.039-0.00150.2110.1150.1150.0000.0000.0000.000
177A209TYR0-0.041-0.03352.349-0.112-0.1120.0000.0000.0000.000
178A210ILE00.019-0.00450.7270.1370.1370.0000.0000.0000.000
179A211GLY00.0330.00453.211-0.150-0.1500.0000.0000.0000.000
180A212THR0-0.035-0.00453.3170.0930.0930.0000.0000.0000.000
181A213ASP-1-0.808-0.90451.3925.9785.9780.0000.0000.0000.000
182A214SER0-0.019-0.01854.039-0.035-0.0350.0000.0000.0000.000
183A215ALA0-0.012-0.00957.145-0.026-0.0260.0000.0000.0000.000
184A216GLU-1-0.934-0.97360.2694.9604.9600.0000.0000.0000.000
185A217GLU-1-0.972-1.00161.1334.7784.7780.0000.0000.0000.000
186A218GLU-1-0.786-0.88857.9425.2875.2870.0000.0000.0000.000
187A219GLU-1-0.921-0.93160.6064.8844.8840.0000.0000.0000.000
188A220ILE0-0.037-0.01855.6530.0800.0800.0000.0000.0000.000
189A221LEU0-0.006-0.01056.873-0.073-0.0730.0000.0000.0000.000
190A222LEU0-0.016-0.02553.7880.1120.1120.0000.0000.0000.000
191A223GLU-1-0.865-0.93651.0415.8595.8590.0000.0000.0000.000
192A224VAL00.0110.01451.5720.1280.1280.0000.0000.0000.000
193A225SER0-0.008-0.01348.462-0.092-0.0920.0000.0000.0000.000
194A226LEU00.0130.02147.5120.0500.0500.0000.0000.0000.000
195A227VAL0-0.029-0.00941.818-0.030-0.0300.0000.0000.0000.000
196A228PHE00.0370.01343.1400.0740.0740.0000.0000.0000.000
197A229LYS10.8210.91535.491-8.190-8.1900.0000.0000.0000.000
198A230VAL00.0030.00139.486-0.028-0.0280.0000.0000.0000.000
199A231LYS10.8660.92732.748-8.524-8.5240.0000.0000.0000.000
200A232GLU-1-0.818-0.88637.1977.0997.0990.0000.0000.0000.000
201A233PHE0-0.036-0.02533.8830.2850.2850.0000.0000.0000.000
202A234ALA00.0200.01438.258-0.168-0.1680.0000.0000.0000.000
203A235PRO0-0.0020.00338.6740.2000.2000.0000.0000.0000.000
204A236ASP-1-0.949-0.96637.4337.8547.8540.0000.0000.0000.000
205A237ALA0-0.024-0.02439.531-0.063-0.0630.0000.0000.0000.000
206A238PRO0-0.0220.01043.275-0.022-0.0220.0000.0000.0000.000
207A239LEU00.0270.01446.023-0.069-0.0690.0000.0000.0000.000
208A240PHE0-0.032-0.02448.616-0.031-0.0310.0000.0000.0000.000
209A241THR0-0.012-0.00952.238-0.065-0.0650.0000.0000.0000.000
210A242GLY0-0.0270.01555.9290.0280.0280.0000.0000.0000.000
211A243PRO0-0.012-0.02557.734-0.074-0.0740.0000.0000.0000.000
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