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: V5291

Calculation Name: 1M1L-A-Xray372

Preferred Name: Suppressor of fused homolog

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1M1L

Chain ID: A

ChEMBL ID: CHEMBL5390

UniProt ID: Q9UMX1

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 OptHSide
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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3014246.299374
FMO2-HF: Nuclear repulsion 2920826.91654
FMO2-HF: Total energy -93419.382834
FMO2-MP2: Total energy -93692.228182


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:27:ALA)


Summations of interaction energy for fragment #1(A:27: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.
-1.3840.9750.271-1.01-1.620.003
Interaction energy analysis for fragmet #1(A:27:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.005
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].
3A29LEU0-0.061-0.0072.6670.0302.3640.272-0.998-1.6080.003
4A30PHE00.0260.0064.787-0.850-0.825-0.001-0.012-0.0120.000
5A31PRO00.0290.0218.571-0.092-0.0920.0000.0000.0000.000
6A32PRO00.0270.0198.9630.0130.0130.0000.0000.0000.000
7A33GLY00.0580.03412.0750.0130.0130.0000.0000.0000.000
8A34LEU00.0070.01212.7530.0080.0080.0000.0000.0000.000
9A35HIS0-0.038-0.03912.4980.0470.0470.0000.0000.0000.000
10A36ALA0-0.0010.01614.754-0.004-0.0040.0000.0000.0000.000
11A37ILE00.0520.04317.865-0.001-0.0010.0000.0000.0000.000
12A38TYR0-0.008-0.01416.0490.0160.0160.0000.0000.0000.000
13A39GLY0-0.031-0.02618.5690.0020.0020.0000.0000.0000.000
14A40GLU-1-0.731-0.82620.0870.0720.0720.0000.0000.0000.000
15A41CYS0-0.063-0.03221.517-0.007-0.0070.0000.0000.0000.000
16A42ARG10.9110.96017.359-0.259-0.2590.0000.0000.0000.000
17A43ARG10.7780.86723.417-0.080-0.0800.0000.0000.0000.000
18A44LEU0-0.043-0.02226.146-0.007-0.0070.0000.0000.0000.000
19A45TYR0-0.043-0.03425.815-0.010-0.0100.0000.0000.0000.000
20A46PRO0-0.0040.01125.7260.0140.0140.0000.0000.0000.000
21A47ASP-1-0.934-0.96826.1480.1180.1180.0000.0000.0000.000
22A48GLN0-0.066-0.04725.585-0.002-0.0020.0000.0000.0000.000
23A49PRO00.0100.00320.9200.0050.0050.0000.0000.0000.000
24A50ASN0-0.048-0.03518.8610.0560.0560.0000.0000.0000.000
25A51PRO0-0.0100.02220.397-0.013-0.0130.0000.0000.0000.000
26A52LEU00.0260.01421.1620.0120.0120.0000.0000.0000.000
27A53GLN0-0.029-0.02816.2570.0130.0130.0000.0000.0000.000
28A54VAL00.0000.00319.6070.0020.0020.0000.0000.0000.000
29A55THR0-0.022-0.04115.473-0.001-0.0010.0000.0000.0000.000
30A56ALA00.0740.06017.780-0.001-0.0010.0000.0000.0000.000
31A57ILE0-0.024-0.01816.386-0.012-0.0120.0000.0000.0000.000
32A58VAL0-0.014-0.00515.561-0.021-0.0210.0000.0000.0000.000
33A59LYS10.8460.92312.8000.0930.0930.0000.0000.0000.000
34A60TYR00.1090.07315.806-0.022-0.0220.0000.0000.0000.000
35A61TRP00.007-0.0289.548-0.074-0.0740.0000.0000.0000.000
36A62LEU0-0.120-0.05611.340-0.046-0.0460.0000.0000.0000.000
37A63GLY0-0.025-0.01615.5470.0120.0120.0000.0000.0000.000
38A64GLY0-0.047-0.00618.3760.0200.0200.0000.0000.0000.000
39A65PRO0-0.024-0.02620.012-0.001-0.0010.0000.0000.0000.000
40A66ASP-1-0.862-0.92221.373-0.035-0.0350.0000.0000.0000.000
41A67PRO0-0.007-0.00420.377-0.011-0.0110.0000.0000.0000.000
42A68LEU0-0.048-0.00819.803-0.004-0.0040.0000.0000.0000.000
43A69ASP-1-0.751-0.84814.087-0.151-0.1510.0000.0000.0000.000
44A70TYR0-0.036-0.03011.4920.0320.0320.0000.0000.0000.000
45A71VAL00.0390.02618.379-0.008-0.0080.0000.0000.0000.000
46A72SER0-0.0270.00020.0970.0100.0100.0000.0000.0000.000
47A73MET0-0.043-0.00522.248-0.014-0.0140.0000.0000.0000.000
48A74TYR00.0070.00421.5410.0160.0160.0000.0000.0000.000
49A75ARG10.8610.91927.446-0.075-0.0750.0000.0000.0000.000
50A76ASN00.0300.01330.8990.0030.0030.0000.0000.0000.000
51A77VAL00.005-0.01333.001-0.004-0.0040.0000.0000.0000.000
52A78GLY00.0000.02335.752-0.004-0.0040.0000.0000.0000.000
53A79SER0-0.024-0.03937.6970.0020.0020.0000.0000.0000.000
54A80PRO00.0390.01640.729-0.003-0.0030.0000.0000.0000.000
55A81SER0-0.028-0.01343.980-0.002-0.0020.0000.0000.0000.000
56A82ALA0-0.040-0.01742.886-0.002-0.0020.0000.0000.0000.000
57A83ASN0-0.023-0.01345.011-0.002-0.0020.0000.0000.0000.000
58A84ILE00.0170.02938.838-0.001-0.0010.0000.0000.0000.000
59A85PRO00.0350.01940.7370.0030.0030.0000.0000.0000.000
60A86GLU-1-0.793-0.85936.1350.0560.0560.0000.0000.0000.000
61A87HIS0-0.032-0.02633.792-0.002-0.0020.0000.0000.0000.000
62A88TRP0-0.047-0.03731.0420.0090.0090.0000.0000.0000.000
63A89HIS0-0.0180.01128.5920.0010.0010.0000.0000.0000.000
64A90TYR0-0.042-0.05826.6260.0090.0090.0000.0000.0000.000
65A91ILE00.0420.01622.343-0.004-0.0040.0000.0000.0000.000
66A92SER0-0.018-0.01922.2360.0080.0080.0000.0000.0000.000
67A93PHE0-0.060-0.03416.9660.0160.0160.0000.0000.0000.000
68A94GLY00.017-0.02017.877-0.012-0.0120.0000.0000.0000.000
69A95LEU00.0080.03718.875-0.019-0.0190.0000.0000.0000.000
70A96SER0-0.053-0.03619.402-0.004-0.0040.0000.0000.0000.000
71A97ASP-1-0.822-0.93415.629-0.163-0.1630.0000.0000.0000.000
72A98LEU0-0.044-0.02513.3520.0230.0230.0000.0000.0000.000
73A99TYR0-0.088-0.0999.0370.0350.0350.0000.0000.0000.000
74A100GLY00.0180.02711.256-0.038-0.0380.0000.0000.0000.000
75A101ASP-1-0.858-0.9149.669-0.622-0.6220.0000.0000.0000.000
76A102ASN0-0.017-0.00812.897-0.009-0.0090.0000.0000.0000.000
77A103ARG10.7990.8957.4270.7350.7350.0000.0000.0000.000
78A104VAL0-0.057-0.03114.4900.0080.0080.0000.0000.0000.000
79A105HIS00.0000.00417.3800.0160.0160.0000.0000.0000.000
80A106GLU-1-0.955-0.97418.169-0.147-0.1470.0000.0000.0000.000
81A107PHE0-0.009-0.00817.2330.0180.0180.0000.0000.0000.000
82A108THR0-0.010-0.00919.3010.0010.0010.0000.0000.0000.000
83A109GLY0-0.037-0.01921.1800.0110.0110.0000.0000.0000.000
84A110THR0-0.024-0.01620.091-0.001-0.0010.0000.0000.0000.000
85A111ASP-1-0.962-0.98022.176-0.012-0.0120.0000.0000.0000.000
86A112GLY00.0140.00725.8420.0050.0050.0000.0000.0000.000
87A113PRO00.0230.02424.7530.0060.0060.0000.0000.0000.000
88A114SER00.0310.03018.825-0.007-0.0070.0000.0000.0000.000
89A115GLY00.0310.01321.0260.0050.0050.0000.0000.0000.000
90A116PHE00.022-0.00321.6000.0040.0040.0000.0000.0000.000
91A117GLY0-0.019-0.00523.6600.0060.0060.0000.0000.0000.000
92A118PHE0-0.047-0.04024.6370.0090.0090.0000.0000.0000.000
93A119GLU-1-0.662-0.77420.189-0.010-0.0100.0000.0000.0000.000
94A120LEU00.0120.00424.3830.0020.0020.0000.0000.0000.000
95A121THR0-0.032-0.06825.9480.0060.0060.0000.0000.0000.000
96A122PHE00.0020.00428.373-0.006-0.0060.0000.0000.0000.000
97A123ARG10.8170.89130.938-0.038-0.0380.0000.0000.0000.000
98A124LEU0-0.0080.01433.625-0.004-0.0040.0000.0000.0000.000
99A125LYS10.7970.87935.408-0.020-0.0200.0000.0000.0000.000
100A126ARG10.7660.88135.378-0.048-0.0480.0000.0000.0000.000
101A127GLU-1-0.817-0.89137.7570.0230.0230.0000.0000.0000.000
102A128THR0-0.030-0.02139.0430.0020.0020.0000.0000.0000.000
103A129GLY0-0.023-0.02339.335-0.002-0.0020.0000.0000.0000.000
104A130GLU-1-0.769-0.85834.8110.0370.0370.0000.0000.0000.000
105A131SER0-0.019-0.02633.0730.0010.0010.0000.0000.0000.000
106A132ALA0-0.021-0.01528.8500.0070.0070.0000.0000.0000.000
107A133PRO00.0400.02527.673-0.005-0.0050.0000.0000.0000.000
108A134PRO00.0090.02329.4170.0010.0010.0000.0000.0000.000
109A135THR00.0640.00226.3650.0000.0000.0000.0000.0000.000
110A136TRP00.0530.02928.148-0.002-0.0020.0000.0000.0000.000
111A137PRO00.0320.02129.535-0.005-0.0050.0000.0000.0000.000
112A138ALA0-0.0010.00124.709-0.002-0.0020.0000.0000.0000.000
113A139GLU-1-0.837-0.90826.606-0.026-0.0260.0000.0000.0000.000
114A140LEU0-0.0040.00328.358-0.005-0.0050.0000.0000.0000.000
115A141MET0-0.032-0.01226.343-0.003-0.0030.0000.0000.0000.000
116A142GLN00.0390.02921.380-0.012-0.0120.0000.0000.0000.000
117A143GLY00.003-0.00326.192-0.008-0.0080.0000.0000.0000.000
118A144LEU00.003-0.00829.602-0.004-0.0040.0000.0000.0000.000
119A145ALA00.0180.00024.598-0.003-0.0030.0000.0000.0000.000
120A146ARG10.7680.86726.0830.0300.0300.0000.0000.0000.000
121A147TYR0-0.023-0.01427.416-0.005-0.0050.0000.0000.0000.000
122A148VAL00.0040.02527.065-0.002-0.0020.0000.0000.0000.000
123A149PHE00.002-0.01620.438-0.003-0.0030.0000.0000.0000.000
124A150GLN0-0.082-0.03526.114-0.008-0.0080.0000.0000.0000.000
125A151SER0-0.073-0.04428.7530.0000.0000.0000.0000.0000.000
126A152GLU-1-0.926-0.95427.355-0.077-0.0770.0000.0000.0000.000
127A153ASN0-0.064-0.02129.5590.0040.0040.0000.0000.0000.000
128A154THR0-0.005-0.00728.3570.0000.0000.0000.0000.0000.000
129A155PHE0-0.030-0.01430.5950.0010.0010.0000.0000.0000.000
130A156CYS0-0.053-0.03031.9840.0010.0010.0000.0000.0000.000
131A157SER0-0.016-0.03834.4590.0010.0010.0000.0000.0000.000
132A158GLY0-0.036-0.03136.155-0.001-0.0010.0000.0000.0000.000
133A159ASP-1-0.816-0.89636.124-0.012-0.0120.0000.0000.0000.000
134A160HIS0-0.016-0.02038.5660.0020.0020.0000.0000.0000.000
135A161VAL00.0130.00135.131-0.003-0.0030.0000.0000.0000.000
136A162SER0-0.008-0.01338.5960.0020.0020.0000.0000.0000.000
137A163TRP0-0.047-0.03332.412-0.002-0.0020.0000.0000.0000.000
138A164HIS0-0.022-0.02439.011-0.001-0.0010.0000.0000.0000.000
139A165SER00.0210.00939.264-0.001-0.0010.0000.0000.0000.000
140A166PRO0-0.0080.01940.0180.0010.0010.0000.0000.0000.000
141A167LEU0-0.024-0.02136.035-0.001-0.0010.0000.0000.0000.000
142A168ASP-1-0.855-0.90235.5470.0100.0100.0000.0000.0000.000
143A169ASN0-0.112-0.05834.810-0.001-0.0010.0000.0000.0000.000
144A170SER0-0.049-0.04538.6380.0000.0000.0000.0000.0000.000
145A171GLU-1-0.913-0.97241.3200.0010.0010.0000.0000.0000.000
146A172SER0-0.093-0.05942.148-0.001-0.0010.0000.0000.0000.000
147A173ARG10.8330.87444.189-0.007-0.0070.0000.0000.0000.000
148A174ILE0-0.036-0.01340.130-0.001-0.0010.0000.0000.0000.000
149A175GLN0-0.021-0.02441.189-0.001-0.0010.0000.0000.0000.000
150A176HIS00.0100.02640.166-0.003-0.0030.0000.0000.0000.000
151A177MET0-0.0080.00634.3520.0030.0030.0000.0000.0000.000
152A178LEU00.0310.03338.350-0.002-0.0020.0000.0000.0000.000
153A179LEU00.0090.01232.9980.0030.0030.0000.0000.0000.000
154A180THR00.0060.01034.948-0.001-0.0010.0000.0000.0000.000
155A181GLU-1-0.809-0.87032.7460.0130.0130.0000.0000.0000.000
156A182ASP-1-0.735-0.83130.1250.0460.0460.0000.0000.0000.000
157A183PRO0-0.047-0.00732.1870.0010.0010.0000.0000.0000.000
158A184GLN0-0.020-0.01431.2480.0030.0030.0000.0000.0000.000
159A185MET0-0.057-0.01823.5810.0070.0070.0000.0000.0000.000
160A186GLN0-0.009-0.00827.844-0.011-0.0110.0000.0000.0000.000
161A187PRO00.005-0.01026.4310.0040.0040.0000.0000.0000.000
162A188VAL0-0.0170.00020.7400.0060.0060.0000.0000.0000.000
163A189GLN0-0.016-0.01222.632-0.008-0.0080.0000.0000.0000.000
164A190THR00.0120.00217.0650.0220.0220.0000.0000.0000.000
165A191PRO0-0.054-0.02314.757-0.008-0.0080.0000.0000.0000.000
166A192PHE0-0.003-0.02811.959-0.020-0.0200.0000.0000.0000.000
167A193GLY00.0910.06418.138-0.010-0.0100.0000.0000.0000.000
168A194VAL0-0.071-0.03421.3960.0130.0130.0000.0000.0000.000
169A195VAL00.0060.01420.363-0.009-0.0090.0000.0000.0000.000
170A196THR0-0.038-0.02623.8120.0100.0100.0000.0000.0000.000
171A197PHE00.040-0.00122.5810.0010.0010.0000.0000.0000.000
172A198LEU00.0220.02427.7930.0010.0010.0000.0000.0000.000
173A199GLN0-0.013-0.00829.8350.0050.0050.0000.0000.0000.000
174A200ILE00.005-0.01330.272-0.003-0.0030.0000.0000.0000.000
175A201VAL0-0.031-0.01833.7850.0040.0040.0000.0000.0000.000
176A202GLY00.019-0.00637.365-0.003-0.0030.0000.0000.0000.000
177A203VAL0-0.033-0.01439.2920.0010.0010.0000.0000.0000.000
178A204CYS00.0120.00642.932-0.001-0.0010.0000.0000.0000.000
179A205THR00.0400.00146.082-0.001-0.0010.0000.0000.0000.000
180A206GLU-1-0.824-0.89647.3130.0010.0010.0000.0000.0000.000
181A207GLU-1-0.741-0.86146.0400.0080.0080.0000.0000.0000.000
182A208LEU0-0.0320.00242.8930.0000.0000.0000.0000.0000.000
183A209HIS0-0.050-0.03845.812-0.001-0.0010.0000.0000.0000.000
184A210SER00.0440.02649.0680.0000.0000.0000.0000.0000.000
185A211ALA00.005-0.01444.6920.0000.0000.0000.0000.0000.000
186A212GLN0-0.079-0.03644.8030.0000.0000.0000.0000.0000.000
187A213GLN0-0.070-0.03047.758-0.001-0.0010.0000.0000.0000.000
188A214TRP00.0050.02949.9680.0000.0000.0000.0000.0000.000
189A215ASN00.0100.00345.7540.0000.0000.0000.0000.0000.000
190A216GLY00.0400.02042.4710.0010.0010.0000.0000.0000.000
191A217GLN0-0.007-0.02538.9640.0030.0030.0000.0000.0000.000
192A218GLY00.0580.04343.5420.0020.0020.0000.0000.0000.000
193A219ILE0-0.002-0.01045.1620.0010.0010.0000.0000.0000.000
194A220LEU0-0.0010.00539.6330.0020.0020.0000.0000.0000.000
195A221GLU-1-0.975-0.98943.3040.0100.0100.0000.0000.0000.000
196A222LEU0-0.047-0.02145.6740.0020.0020.0000.0000.0000.000
197A223LEU00.0350.02242.6510.0010.0010.0000.0000.0000.000
198A224ARG10.9120.96938.890-0.014-0.0140.0000.0000.0000.000
199A225THR0-0.159-0.09144.6400.0010.0010.0000.0000.0000.000
200A226VAL00.0150.01547.2870.0000.0000.0000.0000.0000.000
201A227PRO00.0730.01445.4430.0000.0000.0000.0000.0000.000
202A228ILE0-0.042-0.01844.6480.0010.0010.0000.0000.0000.000
203A229ALA0-0.042-0.03645.0590.0000.0000.0000.0000.0000.000
204A230GLY00.0430.02541.550-0.001-0.0010.0000.0000.0000.000
205A231GLY0-0.0070.03441.4680.0030.0030.0000.0000.0000.000
206A232PRO00.013-0.01141.416-0.001-0.0010.0000.0000.0000.000
207A233TRP0-0.056-0.04635.7020.0010.0010.0000.0000.0000.000
208A234LEU0-0.0010.02037.0720.0010.0010.0000.0000.0000.000
209A235ILE0-0.011-0.00536.9140.0000.0000.0000.0000.0000.000
210A236THR00.0530.02937.228-0.003-0.0030.0000.0000.0000.000
211A237ASP-1-0.769-0.87838.8270.0230.0230.0000.0000.0000.000
212A238MET0-0.012-0.00438.132-0.001-0.0010.0000.0000.0000.000
213A239ARG10.8580.93841.150-0.024-0.0240.0000.0000.0000.000
214A240ARG10.7790.89544.445-0.012-0.0120.0000.0000.0000.000
215A241GLY00.0290.01846.573-0.001-0.0010.0000.0000.0000.000
216A242GLU-1-0.970-0.97049.7250.0100.0100.0000.0000.0000.000
217A243THR0-0.014-0.02449.5040.0010.0010.0000.0000.0000.000
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