Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 492GN

Calculation Name: 4UOS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UOS

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2049091.029072
FMO2-HF: Nuclear repulsion 1969527.434507
FMO2-HF: Total energy -79563.594566
FMO2-MP2: Total energy -79783.802614


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
4.2767.3510.26-1.418-1.9190.003
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.023
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].
3A2ASN0-0.014-0.0203.621-0.2261.468-0.001-0.923-0.7700.003
4A3GLU-1-0.879-0.9562.496-0.996-0.0990.262-0.384-0.7760.000
5A4GLU-1-0.853-0.9343.957-3.679-3.195-0.001-0.111-0.3730.000
6A5VAL00.0020.0045.7031.2071.2070.0000.0000.0000.000
7A6LYS10.9200.9667.5361.0211.0210.0000.0000.0000.000
8A7LYS10.9230.9596.7361.4671.4670.0000.0000.0000.000
9A8MET00.0210.0059.2470.3780.3780.0000.0000.0000.000
10A9LEU0-0.0140.00111.7980.2380.2380.0000.0000.0000.000
11A10GLU-1-0.943-0.97611.702-0.577-0.5770.0000.0000.0000.000
12A11LYS10.8780.94211.8080.8910.8910.0000.0000.0000.000
13A12MET0-0.025-0.00215.5190.0620.0620.0000.0000.0000.000
14A13ILE0-0.010-0.01317.2660.0620.0620.0000.0000.0000.000
15A14GLU-1-0.903-0.94318.259-0.249-0.2490.0000.0000.0000.000
16A15GLU-1-0.931-0.97419.750-0.290-0.2900.0000.0000.0000.000
17A16ILE0-0.036-0.02521.6980.0360.0360.0000.0000.0000.000
18A17LYS10.9821.00222.9730.2330.2330.0000.0000.0000.000
19A18LYS11.0181.02123.9590.2770.2770.0000.0000.0000.000
20A19MET0-0.148-0.07725.7490.0180.0180.0000.0000.0000.000
21A20LEU00.0270.01826.8680.0160.0160.0000.0000.0000.000
22A21GLU-1-0.885-0.93727.473-0.166-0.1660.0000.0000.0000.000
23A22LYS10.8880.93627.4000.2240.2240.0000.0000.0000.000
24A23ALA0-0.021-0.01231.8630.0100.0100.0000.0000.0000.000
25A24ILE00.0500.02632.0570.0090.0090.0000.0000.0000.000
26A25LYS10.9490.98334.5250.1190.1190.0000.0000.0000.000
27A26LYS10.9390.97834.2790.1530.1530.0000.0000.0000.000
28A27VAL00.0080.00237.8380.0060.0060.0000.0000.0000.000
29A28LYS10.9030.94839.1710.0870.0870.0000.0000.0000.000
30A29GLU-1-0.874-0.94939.229-0.096-0.0960.0000.0000.0000.000
31A30MET0-0.081-0.04242.1090.0030.0030.0000.0000.0000.000
32A31LEU00.0370.02042.7700.0040.0040.0000.0000.0000.000
33A32GLU-1-0.849-0.90844.209-0.072-0.0720.0000.0000.0000.000
34A33LYS10.9030.95044.2610.0870.0870.0000.0000.0000.000
35A34MET0-0.003-0.02748.2900.0020.0020.0000.0000.0000.000
36A35ILE0-0.001-0.01048.7510.0030.0030.0000.0000.0000.000
37A36LYS10.9400.97150.9930.0610.0610.0000.0000.0000.000
38A37GLU-1-0.900-0.95752.693-0.054-0.0540.0000.0000.0000.000
39A38ILE0-0.017-0.00253.9040.0020.0020.0000.0000.0000.000
40A39LYS10.9350.97155.5200.0460.0460.0000.0000.0000.000
41A40LYS10.9500.97957.0280.0510.0510.0000.0000.0000.000
42A41MET0-0.029-0.01357.3240.0010.0010.0000.0000.0000.000
43A42LEU00.000-0.00559.1460.0010.0010.0000.0000.0000.000
44A43GLU-1-0.962-0.98060.209-0.041-0.0410.0000.0000.0000.000
45A44ASN0-0.099-0.04763.2640.0020.0020.0000.0000.0000.000
46A45GLY00.0040.01765.3370.0010.0010.0000.0000.0000.000
47A46GLU-1-0.894-0.95162.970-0.044-0.0440.0000.0000.0000.000
48A47ASP-1-0.818-0.90765.532-0.041-0.0410.0000.0000.0000.000
49A48SER00.0670.00963.436-0.002-0.0020.0000.0000.0000.000
50A49GLU-1-0.907-0.95262.370-0.043-0.0430.0000.0000.0000.000
51A50LYS10.8580.93961.3850.0450.0450.0000.0000.0000.000
52A51ILE00.0190.00058.578-0.003-0.0030.0000.0000.0000.000
53A52LEU00.009-0.00557.885-0.003-0.0030.0000.0000.0000.000
54A53LYS10.9240.97356.9860.0530.0530.0000.0000.0000.000
55A54LYS10.9370.98054.1920.0590.0590.0000.0000.0000.000
56A55ALA00.0340.01353.354-0.003-0.0030.0000.0000.0000.000
57A56LYS10.9820.98352.1560.0560.0560.0000.0000.0000.000
58A57GLU-1-0.969-0.97551.446-0.071-0.0710.0000.0000.0000.000
59A58MET00.0120.02949.307-0.004-0.0040.0000.0000.0000.000
60A59ALA00.0030.00547.589-0.005-0.0050.0000.0000.0000.000
61A60GLU-1-0.831-0.91146.768-0.092-0.0920.0000.0000.0000.000
62A61LYS10.9370.96045.9320.0750.0750.0000.0000.0000.000
63A62ILE0-0.016-0.00642.266-0.006-0.0060.0000.0000.0000.000
64A63LEU00.0200.01141.908-0.006-0.0060.0000.0000.0000.000
65A64LYS10.8500.91341.3860.0880.0880.0000.0000.0000.000
66A65MET00.0210.02738.437-0.008-0.0080.0000.0000.0000.000
67A66VAL0-0.023-0.02037.060-0.009-0.0090.0000.0000.0000.000
68A67ILE00.006-0.00336.495-0.008-0.0080.0000.0000.0000.000
69A68GLU-1-0.873-0.91935.584-0.152-0.1520.0000.0000.0000.000
70A69LEU0-0.053-0.05633.402-0.013-0.0130.0000.0000.0000.000
71A70ALA00.0160.01231.900-0.014-0.0140.0000.0000.0000.000
72A71GLU-1-0.906-0.95131.328-0.168-0.1680.0000.0000.0000.000
73A72LYS10.8710.92929.8040.1660.1660.0000.0000.0000.000
74A73ILE00.0030.00226.541-0.021-0.0210.0000.0000.0000.000
75A74LEU00.0190.00626.406-0.023-0.0230.0000.0000.0000.000
76A75LYS10.9340.97626.7400.2160.2160.0000.0000.0000.000
77A76LYS10.9680.98821.5680.3600.3600.0000.0000.0000.000
78A77ALA00.0080.00022.153-0.037-0.0370.0000.0000.0000.000
79A78LYS10.9760.97621.7040.2350.2350.0000.0000.0000.000
80A79GLU-1-0.892-0.94022.196-0.360-0.3600.0000.0000.0000.000
81A80MET0-0.082-0.04617.803-0.059-0.0590.0000.0000.0000.000
82A81ALA00.0400.01917.380-0.070-0.0700.0000.0000.0000.000
83A82GLU-1-0.948-0.97617.953-0.523-0.5230.0000.0000.0000.000
84A83LYS10.9500.97715.6620.5470.5470.0000.0000.0000.000
85A84ILE00.0080.00812.875-0.097-0.0970.0000.0000.0000.000
86A85LEU00.0180.01113.592-0.067-0.0670.0000.0000.0000.000
87A86LYS10.9520.96814.8250.6790.6790.0000.0000.0000.000
88A87LYS10.8000.8885.8713.1573.1570.0000.0000.0000.000
89A88VAL00.015-0.00610.726-0.078-0.0780.0000.0000.0000.000
90A89LYS10.8880.95812.1900.5480.5480.0000.0000.0000.000
91A90GLU-1-0.890-0.9348.609-1.436-1.4360.0000.0000.0000.000
92A91LEU0-0.042-0.0317.4620.0540.0540.0000.0000.0000.000
93A92GLY00.0120.01811.4800.0940.0940.0000.0000.0000.000
94A93VAL0-0.016-0.00515.279-0.037-0.0370.0000.0000.0000.000
95A94ASP-1-0.930-0.96118.666-0.237-0.2370.0000.0000.0000.000
96A95ASN00.0430.03515.1040.0570.0570.0000.0000.0000.000
97A96GLU-1-0.815-0.93518.550-0.265-0.2650.0000.0000.0000.000
98A97GLU-1-0.853-0.91419.276-0.208-0.2080.0000.0000.0000.000
99A98VAL00.019-0.00114.8150.0000.0000.0000.0000.0000.000
100A99LYS10.9500.98518.0080.2420.2420.0000.0000.0000.000
101A100LYS10.9330.97320.4530.2070.2070.0000.0000.0000.000
102A101MET0-0.108-0.05118.6120.0190.0190.0000.0000.0000.000
103A102LEU00.0310.01816.5800.0080.0080.0000.0000.0000.000
104A103GLU-1-0.891-0.95220.636-0.247-0.2470.0000.0000.0000.000
105A104LYS10.9460.96924.1560.2270.2270.0000.0000.0000.000
106A105MET0-0.057-0.01018.3490.0060.0060.0000.0000.0000.000
107A106ILE0-0.004-0.01522.5410.0120.0120.0000.0000.0000.000
108A107GLU-1-0.895-0.94725.084-0.167-0.1670.0000.0000.0000.000
109A108GLU-1-0.870-0.93126.274-0.164-0.1640.0000.0000.0000.000
110A109ILE0-0.027-0.00323.2250.0110.0110.0000.0000.0000.000
111A110LYS10.9490.97727.7760.1850.1850.0000.0000.0000.000
112A111LYS10.9250.96030.5830.1690.1690.0000.0000.0000.000
113A112MET0-0.068-0.04030.3650.0170.0170.0000.0000.0000.000
114A113LEU00.0090.00329.3820.0090.0090.0000.0000.0000.000
115A114GLU-1-0.893-0.94733.206-0.138-0.1380.0000.0000.0000.000
116A115LYS10.8800.95135.7480.1180.1180.0000.0000.0000.000
117A116ALA00.0200.00035.3310.0080.0080.0000.0000.0000.000
118A117ILE00.0330.02536.5270.0070.0070.0000.0000.0000.000
119A118LYS10.9380.97139.2540.1030.1030.0000.0000.0000.000
120A119LYS10.9450.95339.6170.0980.0980.0000.0000.0000.000
121A120VAL00.0410.03339.7660.0050.0050.0000.0000.0000.000
122A121LYS10.9680.99242.5930.0890.0890.0000.0000.0000.000
123A122GLU-1-0.933-0.97045.226-0.073-0.0730.0000.0000.0000.000
124A123MET00.0330.00643.8630.0020.0020.0000.0000.0000.000
125A124LEU0-0.0040.00444.8990.0030.0030.0000.0000.0000.000
126A125GLU-1-0.945-0.97748.240-0.069-0.0690.0000.0000.0000.000
127A126LYS10.8280.91649.8820.0680.0680.0000.0000.0000.000
128A127MET00.0270.02049.3590.0010.0010.0000.0000.0000.000
129A128ILE00.0020.00251.9510.0020.0020.0000.0000.0000.000
130A129LYS10.9290.95654.2750.0550.0550.0000.0000.0000.000
131A130GLU-1-0.908-0.95354.920-0.046-0.0460.0000.0000.0000.000
132A131ILE0-0.007-0.00353.6780.0020.0020.0000.0000.0000.000
133A132LYS10.9450.97057.5660.0480.0480.0000.0000.0000.000
134A133LYS10.9440.97959.9310.0440.0440.0000.0000.0000.000
135A134MET0-0.108-0.04458.4750.0000.0000.0000.0000.0000.000
136A135LEU0-0.0100.00260.3830.0010.0010.0000.0000.0000.000
137A136GLU-1-0.966-0.97963.501-0.040-0.0400.0000.0000.0000.000
138A137ASN0-0.065-0.04763.7630.0010.0010.0000.0000.0000.000
139A138GLY00.0400.03666.5910.0010.0010.0000.0000.0000.000
140A139GLU-1-0.912-0.95361.870-0.039-0.0390.0000.0000.0000.000
141A140ASP-1-0.824-0.91163.376-0.036-0.0360.0000.0000.0000.000
142A141SER00.030-0.01160.931-0.001-0.0010.0000.0000.0000.000
143A142GLU-1-0.910-0.94859.336-0.037-0.0370.0000.0000.0000.000
144A143LYS10.9290.95858.3310.0340.0340.0000.0000.0000.000
145A144ILE00.0310.01857.514-0.002-0.0020.0000.0000.0000.000
146A145LEU00.000-0.01055.032-0.003-0.0030.0000.0000.0000.000
147A146LYS10.9180.97153.8010.0390.0390.0000.0000.0000.000
148A147LYS10.9270.96553.0190.0440.0440.0000.0000.0000.000
149A148ALA00.0220.01152.341-0.002-0.0020.0000.0000.0000.000
150A149LYS10.9720.97748.5480.0500.0500.0000.0000.0000.000
151A150GLU-1-0.924-0.96448.164-0.051-0.0510.0000.0000.0000.000
152A151MET0-0.057-0.03047.793-0.003-0.0030.0000.0000.0000.000
153A152ALA00.0200.01646.111-0.003-0.0030.0000.0000.0000.000
154A153GLU-1-0.873-0.94441.839-0.081-0.0810.0000.0000.0000.000
155A154LYS10.9110.94942.8190.0550.0550.0000.0000.0000.000
156A155ILE00.0070.00941.755-0.004-0.0040.0000.0000.0000.000
157A156LEU00.0060.00138.556-0.006-0.0060.0000.0000.0000.000
158A157LYS10.9680.97738.2830.0650.0650.0000.0000.0000.000
159A158MET0-0.0330.01037.888-0.002-0.0020.0000.0000.0000.000
160A159VAL0-0.030-0.02434.926-0.006-0.0060.0000.0000.0000.000
161A160ILE00.0310.01533.516-0.009-0.0090.0000.0000.0000.000
162A161GLU-1-0.871-0.92932.955-0.102-0.1020.0000.0000.0000.000
163A162LEU0-0.060-0.05632.902-0.005-0.0050.0000.0000.0000.000
164A163ALA00.0170.00929.970-0.011-0.0110.0000.0000.0000.000
165A164GLU-1-0.886-0.94328.504-0.135-0.1350.0000.0000.0000.000
166A165LYS10.8980.95227.9970.1030.1030.0000.0000.0000.000
167A166ILE0-0.034-0.00825.802-0.010-0.0100.0000.0000.0000.000
168A167LEU00.0030.00123.344-0.019-0.0190.0000.0000.0000.000
169A168LYS10.9310.97623.2000.1150.1150.0000.0000.0000.000
170A169LYS10.9360.96823.7400.1980.1980.0000.0000.0000.000
171A170ALA00.005-0.00121.231-0.015-0.0150.0000.0000.0000.000
172A171LYS11.0130.99818.2960.1830.1830.0000.0000.0000.000
173A172GLU-1-0.886-0.94818.812-0.185-0.1850.0000.0000.0000.000
174A173MET0-0.025-0.02820.0160.0040.0040.0000.0000.0000.000
175A174ALA00.0200.03115.424-0.028-0.0280.0000.0000.0000.000
176A175GLU-1-0.940-0.96315.285-0.276-0.2760.0000.0000.0000.000
177A176LYS10.8590.92115.7510.2600.2600.0000.0000.0000.000
178A177ILE00.0110.00514.1690.0150.0150.0000.0000.0000.000
179A178LEU00.0210.0068.781-0.018-0.0180.0000.0000.0000.000
180A179LYS10.9340.97511.5960.1560.1560.0000.0000.0000.000
181A180LYS10.8430.89513.5370.2860.2860.0000.0000.0000.000
182A181VAL0-0.0060.0059.0130.0150.0150.0000.0000.0000.000
183A182LYS10.9190.9458.0940.2560.2560.0000.0000.0000.000
184A183GLU-1-0.937-0.96510.251-0.077-0.0770.0000.0000.0000.000
185A184LEU0-0.057-0.01511.5910.0310.0310.0000.0000.0000.000
186A185GLY0-0.0140.0179.6030.0010.0010.0000.0000.0000.000
187A186VAL00.001-0.00410.5980.0330.0330.0000.0000.0000.000
188A187GLY0-0.0030.00711.0490.0670.0670.0000.0000.0000.000