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: G5121

Calculation Name: 3BUU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BUU

Chain ID: A

ChEMBL ID:

UniProt ID: Q82SR2

Base Structure: X-ray

Registration Date: 2023-09-24

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2870621.25679
FMO2-HF: Nuclear repulsion 2780582.457457
FMO2-HF: Total energy -90038.799333
FMO2-MP2: Total energy -90302.828213


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:34:ALA)


Summations of interaction energy for fragment #1(A:34:ALA)
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.
-1.8960.7650.042-1.384-1.3190.005
Interaction energy analysis for fragmet #1(A:34:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.008
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].
3A36THR00.0190.0143.351-1.2641.3970.042-1.384-1.3190.005
4A37ALA00.0550.0115.6990.2380.2380.0000.0000.0000.000
5A38GLN00.0350.0079.166-0.057-0.0570.0000.0000.0000.000
6A39SER00.0020.0156.806-0.269-0.2690.0000.0000.0000.000
7A40ILE0-0.022-0.0097.9410.2020.2020.0000.0000.0000.000
8A41LEU0-0.012-0.01010.3800.1930.1930.0000.0000.0000.000
9A42GLU-1-0.911-0.95510.892-1.174-1.1740.0000.0000.0000.000
10A43LYS10.9480.9787.7241.6971.6970.0000.0000.0000.000
11A44ALA00.0290.01613.2830.1230.1230.0000.0000.0000.000
12A45ASP-1-0.757-0.88116.053-0.458-0.4580.0000.0000.0000.000
13A46GLU-1-0.952-0.97513.941-0.703-0.7030.0000.0000.0000.000
14A47ILE00.0100.02615.7640.0730.0730.0000.0000.0000.000
15A48ARG10.8650.93219.0940.3330.3330.0000.0000.0000.000
16A49PHE0-0.060-0.04421.4460.0520.0520.0000.0000.0000.000
17A50PRO00.0350.01721.433-0.035-0.0350.0000.0000.0000.000
18A51GLN0-0.056-0.02818.195-0.002-0.0020.0000.0000.0000.000
19A52ASP-1-0.864-0.93721.594-0.236-0.2360.0000.0000.0000.000
20A53SER0-0.066-0.02324.9640.0050.0050.0000.0000.0000.000
21A54PHE0-0.006-0.01226.0570.0120.0120.0000.0000.0000.000
22A55GLN0-0.0140.00130.1780.0080.0080.0000.0000.0000.000
23A56VAL0-0.010-0.00130.793-0.005-0.0050.0000.0000.0000.000
24A57ASN0-0.0110.00433.2900.0050.0050.0000.0000.0000.000
25A58VAL00.0260.01133.215-0.007-0.0070.0000.0000.0000.000
26A59ALA0-0.037-0.01435.7400.0090.0090.0000.0000.0000.000
27A60ILE00.0230.00135.741-0.007-0.0070.0000.0000.0000.000
28A61ARG10.9400.97238.1260.1110.1110.0000.0000.0000.000
29A62THR00.0950.05739.044-0.008-0.0080.0000.0000.0000.000
30A63ALA0-0.0040.01240.6200.0050.0050.0000.0000.0000.000
31A64ALA00.0380.02041.175-0.005-0.0050.0000.0000.0000.000
32A65PRO0-0.074-0.05342.8040.0020.0020.0000.0000.0000.000
33A66ASP-1-0.896-0.91845.802-0.059-0.0590.0000.0000.0000.000
34A67HIS0-0.077-0.04746.3210.0050.0050.0000.0000.0000.000
35A68ALA0-0.0110.00045.382-0.004-0.0040.0000.0000.0000.000
36A69GLU-1-0.915-0.95543.004-0.084-0.0840.0000.0000.0000.000
37A70ASP-1-0.913-0.94845.726-0.075-0.0750.0000.0000.0000.000
38A71LEU0-0.114-0.06841.521-0.005-0.0050.0000.0000.0000.000
39A72TYR00.0370.01840.9060.0010.0010.0000.0000.0000.000
40A73ARG10.8500.92640.1190.0940.0940.0000.0000.0000.000
41A74TYR00.0410.01837.2890.0040.0040.0000.0000.0000.000
42A75GLN0-0.0050.00237.506-0.003-0.0030.0000.0000.0000.000
43A76VAL0-0.007-0.00632.1060.0030.0030.0000.0000.0000.000
44A77LEU0-0.054-0.02233.816-0.001-0.0010.0000.0000.0000.000
45A78SER00.0400.00527.8860.0000.0000.0000.0000.0000.000
46A79LYS10.9080.95328.5480.1790.1790.0000.0000.0000.000
47A80GLY00.1040.05324.994-0.003-0.0030.0000.0000.0000.000
48A81ASN00.012-0.01323.1170.0230.0230.0000.0000.0000.000
49A82GLU-1-0.946-0.96426.223-0.212-0.2120.0000.0000.0000.000
50A83ASN0-0.021-0.01928.4590.0260.0260.0000.0000.0000.000
51A84SER00.008-0.00130.780-0.004-0.0040.0000.0000.0000.000
52A85ILE0-0.023-0.01433.0510.0110.0110.0000.0000.0000.000
53A86VAL00.0180.02434.845-0.004-0.0040.0000.0000.0000.000
54A87MET0-0.022-0.01637.4080.0090.0090.0000.0000.0000.000
55A88ILE00.0010.02440.739-0.004-0.0040.0000.0000.0000.000
56A89THR0-0.015-0.02642.3900.0050.0050.0000.0000.0000.000
57A90GLU-1-0.909-0.94044.171-0.084-0.0840.0000.0000.0000.000
58A91PRO00.1660.07944.252-0.005-0.0050.0000.0000.0000.000
59A92ALA0-0.026-0.03147.799-0.001-0.0010.0000.0000.0000.000
60A93SER0-0.017-0.00249.8960.0010.0010.0000.0000.0000.000
61A94GLU-1-0.875-0.94245.879-0.088-0.0880.0000.0000.0000.000
62A95ARG10.8460.90846.8660.0750.0750.0000.0000.0000.000
63A96GLY00.0100.01146.4600.0040.0040.0000.0000.0000.000
64A97GLN0-0.042-0.01044.4080.0030.0030.0000.0000.0000.000
65A98ALA00.004-0.00741.883-0.003-0.0030.0000.0000.0000.000
66A99ILE00.0090.00237.2240.0030.0030.0000.0000.0000.000
67A100LEU0-0.0410.00037.046-0.004-0.0040.0000.0000.0000.000
68A101MET00.0080.02829.2730.0030.0030.0000.0000.0000.000
69A102LYS10.9450.97733.5440.1210.1210.0000.0000.0000.000
70A103GLY00.0370.01730.0470.0050.0050.0000.0000.0000.000
71A104ARG10.8740.91624.5120.2400.2400.0000.0000.0000.000
72A105ASP-1-0.915-0.92331.287-0.134-0.1340.0000.0000.0000.000
73A106LEU00.0120.00633.922-0.003-0.0030.0000.0000.0000.000
74A107TRP0-0.044-0.04237.1500.0090.0090.0000.0000.0000.000
75A108VAL00.0400.01340.419-0.004-0.0040.0000.0000.0000.000
76A109PHE0-0.014-0.02041.8100.0060.0060.0000.0000.0000.000
77A110MET00.0680.03045.791-0.003-0.0030.0000.0000.0000.000
78A111PRO00.0680.03048.5840.0020.0020.0000.0000.0000.000
79A112SER0-0.031-0.00351.9880.0020.0020.0000.0000.0000.000
80A113VAL0-0.030-0.01549.3210.0020.0020.0000.0000.0000.000
81A114SER00.006-0.00151.754-0.001-0.0010.0000.0000.0000.000
82A115GLN0-0.067-0.03348.922-0.004-0.0040.0000.0000.0000.000
83A116PRO0-0.0070.01544.2010.0000.0000.0000.0000.0000.000
84A117ILE00.0110.00243.6950.0020.0020.0000.0000.0000.000
85A118ARG10.8360.89837.1140.1180.1180.0000.0000.0000.000
86A119LEU00.0390.03839.4540.0040.0040.0000.0000.0000.000
87A120SER0-0.007-0.01735.093-0.004-0.0040.0000.0000.0000.000
88A121LEU00.0690.02629.3650.0020.0020.0000.0000.0000.000
89A122SER00.0100.01332.096-0.001-0.0010.0000.0000.0000.000
90A123GLN0-0.0270.00133.1690.0040.0040.0000.0000.0000.000
91A124ARG10.9480.97635.8450.1110.1110.0000.0000.0000.000
92A125LEU0-0.0220.00935.8880.0040.0040.0000.0000.0000.000
93A126THR00.005-0.00837.9200.0070.0070.0000.0000.0000.000
94A127GLY00.0420.04237.866-0.007-0.0070.0000.0000.0000.000
95A128GLN0-0.059-0.05234.283-0.006-0.0060.0000.0000.0000.000
96A129VAL0-0.0190.00232.946-0.013-0.0130.0000.0000.0000.000
97A130ALA0-0.012-0.01131.6940.0100.0100.0000.0000.0000.000
98A131ASN00.013-0.01733.235-0.004-0.0040.0000.0000.0000.000
99A132GLY0-0.010-0.02430.271-0.004-0.0040.0000.0000.0000.000
100A133ASP-1-0.774-0.86028.865-0.216-0.2160.0000.0000.0000.000
101A134ILE0-0.047-0.02329.573-0.005-0.0050.0000.0000.0000.000
102A135ALA0-0.025-0.00931.291-0.003-0.0030.0000.0000.0000.000
103A136ARG10.7410.82925.9360.2480.2480.0000.0000.0000.000
104A137ALA0-0.0040.01224.7210.0040.0040.0000.0000.0000.000
105A138ASN00.0180.00720.326-0.018-0.0180.0000.0000.0000.000
106A139PHE00.001-0.00218.9210.0410.0410.0000.0000.0000.000
107A140THR00.004-0.02416.073-0.012-0.0120.0000.0000.0000.000
108A141GLY0-0.036-0.01118.2000.0420.0420.0000.0000.0000.000
109A142ASP-1-0.792-0.86520.156-0.249-0.2490.0000.0000.0000.000
110A143TYR0-0.010-0.00819.1390.0470.0470.0000.0000.0000.000
111A144HIS0-0.0080.00514.179-0.065-0.0650.0000.0000.0000.000
112A145PRO0-0.0180.00012.5430.0490.0490.0000.0000.0000.000
113A146GLN0-0.006-0.01112.040-0.057-0.0570.0000.0000.0000.000
114A147LEU0-0.021-0.0039.0320.0120.0120.0000.0000.0000.000
115A148LEU0-0.051-0.01211.9910.0680.0680.0000.0000.0000.000
116A149ARG10.8150.86814.5370.2570.2570.0000.0000.0000.000
117A150ASN00.0610.02510.406-0.127-0.1270.0000.0000.0000.000
118A151GLU-1-0.792-0.87414.582-0.154-0.1540.0000.0000.0000.000
119A152SER00.0410.02817.657-0.023-0.0230.0000.0000.0000.000
120A153ILE0-0.105-0.05119.7240.0110.0110.0000.0000.0000.000
121A154ASP-1-0.932-0.97722.491-0.093-0.0930.0000.0000.0000.000
122A155ASP-1-0.979-0.97921.576-0.085-0.0850.0000.0000.0000.000
123A156GLU-1-0.872-0.91518.673-0.212-0.2120.0000.0000.0000.000
124A157ASP-1-0.894-0.94514.604-0.129-0.1290.0000.0000.0000.000
125A158TYR0-0.059-0.03915.270-0.060-0.0600.0000.0000.0000.000
126A159TYR00.0500.0167.887-0.030-0.0300.0000.0000.0000.000
127A160VAL0-0.026-0.00613.2040.0080.0080.0000.0000.0000.000
128A161LEU0-0.001-0.01011.289-0.011-0.0110.0000.0000.0000.000
129A162GLU-1-0.913-0.97114.967-0.200-0.2000.0000.0000.0000.000
130A163LEU0-0.036-0.01816.266-0.045-0.0450.0000.0000.0000.000
131A164THR0-0.001-0.00718.6770.0550.0550.0000.0000.0000.000
132A165GLY0-0.011-0.00720.914-0.023-0.0230.0000.0000.0000.000
133A166ILE0-0.008-0.00620.0740.0150.0150.0000.0000.0000.000
134A167ASP-1-0.822-0.91823.458-0.183-0.1830.0000.0000.0000.000
135A168ARG10.9320.94527.2920.1260.1260.0000.0000.0000.000
136A169SER0-0.094-0.03329.8130.0070.0070.0000.0000.0000.000
137A170VAL00.0020.02825.1380.0010.0010.0000.0000.0000.000
138A171THR0-0.019-0.02327.6570.0140.0140.0000.0000.0000.000
139A172TYR0-0.011-0.03525.7490.0230.0230.0000.0000.0000.000
140A173GLN0-0.052-0.04326.064-0.006-0.0060.0000.0000.0000.000
141A174LYS10.9821.00622.3480.1920.1920.0000.0000.0000.000
142A175VAL0-0.0120.00621.4990.0210.0210.0000.0000.0000.000
143A176LEU0-0.053-0.00219.337-0.023-0.0230.0000.0000.0000.000
144A177LEU00.0250.00816.7680.0270.0270.0000.0000.0000.000
145A178TRP0-0.071-0.03716.919-0.051-0.0510.0000.0000.0000.000
146A179VAL0-0.015-0.01313.5110.0130.0130.0000.0000.0000.000
147A180ASN0-0.0030.00914.586-0.027-0.0270.0000.0000.0000.000
148A181GLN00.007-0.01611.136-0.102-0.1020.0000.0000.0000.000
149A182SER0-0.028-0.00611.247-0.068-0.0680.0000.0000.0000.000
150A183ASN00.003-0.02613.234-0.042-0.0420.0000.0000.0000.000
151A184PHE00.0200.0007.891-0.095-0.0950.0000.0000.0000.000
152A185ARG10.9691.00113.7850.2980.2980.0000.0000.0000.000
153A186PRO0-0.0140.01117.478-0.003-0.0030.0000.0000.0000.000
154A187TYR00.0210.00419.1910.0370.0370.0000.0000.0000.000
155A188LYS10.9560.97121.1660.2290.2290.0000.0000.0000.000
156A189ALA0-0.040-0.01321.379-0.037-0.0370.0000.0000.0000.000
157A190GLU-1-0.849-0.90323.182-0.164-0.1640.0000.0000.0000.000
158A191PHE0-0.009-0.00324.266-0.020-0.0200.0000.0000.0000.000
159A192TYR0-0.012-0.03624.3450.0260.0260.0000.0000.0000.000
160A193SER00.001-0.00528.029-0.006-0.0060.0000.0000.0000.000
161A194VAL00.018-0.00629.434-0.005-0.0050.0000.0000.0000.000
162A195SER0-0.046-0.01930.7820.0000.0000.0000.0000.0000.000
163A196GLY00.0290.00928.3050.0070.0070.0000.0000.0000.000
164A197ARG10.8770.94629.2560.1040.1040.0000.0000.0000.000
165A198LEU00.0550.03127.613-0.007-0.0070.0000.0000.0000.000
166A199LEU0-0.068-0.04430.1370.0110.0110.0000.0000.0000.000
167A200LYS10.8830.94829.9490.1820.1820.0000.0000.0000.000
168A201THR0-0.0060.01127.781-0.012-0.0120.0000.0000.0000.000
169A202SER0-0.008-0.00325.7380.0060.0060.0000.0000.0000.000
170A203ARG10.9500.97725.9450.1380.1380.0000.0000.0000.000
171A204TYR00.0000.00022.7190.0030.0030.0000.0000.0000.000
172A205GLU-1-0.849-0.94425.465-0.155-0.1550.0000.0000.0000.000
173A206ASN0-0.012-0.01627.615-0.005-0.0050.0000.0000.0000.000
174A207PHE0-0.006-0.00921.586-0.001-0.0010.0000.0000.0000.000
175A208ASP-1-0.882-0.94226.455-0.143-0.1430.0000.0000.0000.000
176A209ASN0-0.014-0.00725.129-0.034-0.0340.0000.0000.0000.000
177A210ILE00.0140.00325.3810.0160.0160.0000.0000.0000.000
178A211LEU0-0.049-0.03024.847-0.020-0.0200.0000.0000.0000.000
179A212GLY00.0250.01522.118-0.019-0.0190.0000.0000.0000.000
180A213GLU-1-0.885-0.91817.757-0.476-0.4760.0000.0000.0000.000
181A214MET0-0.070-0.02221.0020.0380.0380.0000.0000.0000.000
182A215ARG10.8340.89621.0880.3040.3040.0000.0000.0000.000
183A216PRO0-0.058-0.00322.7910.0230.0230.0000.0000.0000.000
184A217THR0-0.017-0.01925.8130.0040.0040.0000.0000.0000.000
185A218ARG10.8640.91329.0100.1460.1460.0000.0000.0000.000
186A219ILE0-0.042-0.01526.440-0.015-0.0150.0000.0000.0000.000
187A220ILE0-0.064-0.01729.5980.0140.0140.0000.0000.0000.000
188A221MET0-0.018-0.01228.733-0.009-0.0090.0000.0000.0000.000
189A222GLU-1-0.930-0.95731.683-0.115-0.1150.0000.0000.0000.000
190A223ASP-1-0.749-0.85932.744-0.118-0.1180.0000.0000.0000.000
191A224ALA0-0.027-0.00631.9710.0020.0020.0000.0000.0000.000
192A225LEU0-0.099-0.05034.0960.0080.0080.0000.0000.0000.000
193A226LYS10.9240.93837.3680.0740.0740.0000.0000.0000.000
194A227SER0-0.049-0.03639.4150.0040.0040.0000.0000.0000.000
195A228GLY00.0360.02040.1330.0030.0030.0000.0000.0000.000
196A229GLU-1-0.903-0.94239.127-0.103-0.1030.0000.0000.0000.000
197A230VAL00.007-0.00235.209-0.007-0.0070.0000.0000.0000.000
198A231SER0-0.031-0.02935.2090.0050.0050.0000.0000.0000.000
199A232VAL0-0.024-0.01434.467-0.010-0.0100.0000.0000.0000.000
200A233LEU0-0.031-0.01631.4470.0060.0060.0000.0000.0000.000
201A234ASP-1-0.800-0.88332.578-0.143-0.1430.0000.0000.0000.000
202A235TYR00.0020.00130.121-0.001-0.0010.0000.0000.0000.000
203A236SER0-0.009-0.01932.7070.0050.0050.0000.0000.0000.000
204A237ASP-1-0.833-0.93034.431-0.128-0.1280.0000.0000.0000.000
205A238MET0-0.0130.01426.951-0.003-0.0030.0000.0000.0000.000
206A239LYS10.8400.92731.1250.1270.1270.0000.0000.0000.000
207A240LEU00.0540.02526.366-0.002-0.0020.0000.0000.0000.000
208A241ARG10.8700.92530.4500.1420.1420.0000.0000.0000.000
209A242ASP-1-0.862-0.92731.930-0.153-0.1530.0000.0000.0000.000
210A243LEU0-0.034-0.01031.5030.0110.0110.0000.0000.0000.000
211A244PRO00.0430.01233.480-0.007-0.0070.0000.0000.0000.000
212A245ASP-1-0.890-0.96134.202-0.141-0.1410.0000.0000.0000.000
213A246LYS10.9480.96135.4770.1040.1040.0000.0000.0000.000
214A247ILE00.0020.01536.3600.0070.0070.0000.0000.0000.000
215A248PHE00.0010.01633.5740.0020.0020.0000.0000.0000.000
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