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: YZQ42

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3014854.742701
FMO2-HF: Nuclear repulsion 2921436.560032
FMO2-HF: Total energy -93418.182669
FMO2-MP2: Total energy -93691.185093


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.
-1.920.550.336-1.103-1.7030.005
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 : -0.001 / 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].
3A29LEU0-0.058-0.0042.693-0.5871.8550.337-1.090-1.6890.005
4A30PHE00.0140.0034.995-0.944-0.916-0.001-0.013-0.0140.000
5A31PRO00.0240.0188.783-0.073-0.0730.0000.0000.0000.000
6A32PRO00.0370.0269.178-0.028-0.0280.0000.0000.0000.000
7A33GLY00.0610.03012.258-0.011-0.0110.0000.0000.0000.000
8A34LEU00.0000.01412.869-0.008-0.0080.0000.0000.0000.000
9A35HIS0-0.043-0.04212.7220.0220.0220.0000.0000.0000.000
10A36ALA00.0260.02514.959-0.017-0.0170.0000.0000.0000.000
11A37ILE00.0520.04118.082-0.011-0.0110.0000.0000.0000.000
12A38TYR0-0.015-0.01816.8080.0050.0050.0000.0000.0000.000
13A39GLY0-0.035-0.02818.784-0.005-0.0050.0000.0000.0000.000
14A40GLU-1-0.760-0.87320.2840.0920.0920.0000.0000.0000.000
15A41CYS0-0.036-0.01621.688-0.011-0.0110.0000.0000.0000.000
16A42ARG10.9060.95417.639-0.287-0.2870.0000.0000.0000.000
17A43ARG10.8160.91323.618-0.108-0.1080.0000.0000.0000.000
18A44LEU0-0.028-0.01426.341-0.009-0.0090.0000.0000.0000.000
19A45TYR0-0.069-0.05525.851-0.013-0.0130.0000.0000.0000.000
20A46PRO0-0.0070.01125.8470.0140.0140.0000.0000.0000.000
21A47ASP-1-0.926-0.96426.1570.1240.1240.0000.0000.0000.000
22A48GLN0-0.076-0.05325.585-0.004-0.0040.0000.0000.0000.000
23A49PRO00.004-0.00320.9620.0080.0080.0000.0000.0000.000
24A50ASN0-0.038-0.03119.0850.0480.0480.0000.0000.0000.000
25A51PRO0-0.0200.01720.417-0.016-0.0160.0000.0000.0000.000
26A52LEU00.0360.02221.0530.0110.0110.0000.0000.0000.000
27A53GLN0-0.034-0.03216.2160.0160.0160.0000.0000.0000.000
28A54VAL00.0120.01019.494-0.002-0.0020.0000.0000.0000.000
29A55THR0-0.046-0.06615.4800.0030.0030.0000.0000.0000.000
30A56ALA00.0560.04917.583-0.006-0.0060.0000.0000.0000.000
31A57ILE0-0.033-0.03016.288-0.010-0.0100.0000.0000.0000.000
32A58VAL0-0.012-0.00315.477-0.025-0.0250.0000.0000.0000.000
33A59LYS10.8970.95512.6320.0690.0690.0000.0000.0000.000
34A60TYR00.1050.07315.709-0.024-0.0240.0000.0000.0000.000
35A61TRP00.011-0.0189.760-0.065-0.0650.0000.0000.0000.000
36A62LEU0-0.125-0.06011.263-0.049-0.0490.0000.0000.0000.000
37A63GLY0-0.024-0.01515.4710.0050.0050.0000.0000.0000.000
38A64GLY0-0.044-0.00518.2920.0170.0170.0000.0000.0000.000
39A65PRO0-0.020-0.02219.9260.0000.0000.0000.0000.0000.000
40A66ASP-1-0.881-0.94821.432-0.021-0.0210.0000.0000.0000.000
41A67PRO0-0.005-0.00520.377-0.008-0.0080.0000.0000.0000.000
42A68LEU0-0.041-0.00519.8030.0030.0030.0000.0000.0000.000
43A69ASP-1-0.751-0.85614.521-0.066-0.0660.0000.0000.0000.000
44A70TYR0-0.039-0.01911.4400.0140.0140.0000.0000.0000.000
45A71VAL00.0430.02918.379-0.007-0.0070.0000.0000.0000.000
46A72SER0-0.030-0.00120.1600.0080.0080.0000.0000.0000.000
47A73MET0-0.042-0.00922.179-0.015-0.0150.0000.0000.0000.000
48A74TYR00.0140.00921.8280.0090.0090.0000.0000.0000.000
49A75ARG10.9330.97027.398-0.082-0.0820.0000.0000.0000.000
50A76ASN00.0520.03030.8040.0010.0010.0000.0000.0000.000
51A77VAL00.018-0.00833.047-0.004-0.0040.0000.0000.0000.000
52A78GLY0-0.0110.01535.839-0.004-0.0040.0000.0000.0000.000
53A79SER0-0.028-0.03937.8030.0020.0020.0000.0000.0000.000
54A80PRO00.0260.02040.865-0.003-0.0030.0000.0000.0000.000
55A81SER0-0.019-0.02644.067-0.003-0.0030.0000.0000.0000.000
56A82ALA0-0.041-0.01443.148-0.002-0.0020.0000.0000.0000.000
57A83ASN0-0.017-0.01345.220-0.002-0.0020.0000.0000.0000.000
58A84ILE00.0180.03638.944-0.001-0.0010.0000.0000.0000.000
59A85PRO00.0100.00840.6390.0030.0030.0000.0000.0000.000
60A86GLU-1-0.867-0.92136.4560.0590.0590.0000.0000.0000.000
61A87HIS0-0.033-0.02833.952-0.001-0.0010.0000.0000.0000.000
62A88TRP0-0.046-0.02530.7020.0100.0100.0000.0000.0000.000
63A89HIS0-0.0090.03129.0900.0000.0000.0000.0000.0000.000
64A90TYR0-0.043-0.05526.6980.0090.0090.0000.0000.0000.000
65A91ILE00.0480.02322.515-0.004-0.0040.0000.0000.0000.000
66A92SER0-0.017-0.01722.3860.0070.0070.0000.0000.0000.000
67A93PHE0-0.059-0.03217.1260.0190.0190.0000.0000.0000.000
68A94GLY00.018-0.01918.014-0.011-0.0110.0000.0000.0000.000
69A95LEU00.0030.03919.009-0.019-0.0190.0000.0000.0000.000
70A96SER0-0.055-0.03019.473-0.003-0.0030.0000.0000.0000.000
71A97ASP-1-0.791-0.91515.718-0.053-0.0530.0000.0000.0000.000
72A98LEU0-0.050-0.03413.5270.0320.0320.0000.0000.0000.000
73A99TYR0-0.097-0.1019.2520.0720.0720.0000.0000.0000.000
74A100GLY00.0240.02511.399-0.018-0.0180.0000.0000.0000.000
75A101ASP-1-0.865-0.9209.787-0.434-0.4340.0000.0000.0000.000
76A102ASN0-0.0070.00312.956-0.020-0.0200.0000.0000.0000.000
77A103ARG10.7950.8987.6940.4690.4690.0000.0000.0000.000
78A104VAL0-0.060-0.03314.4970.0020.0020.0000.0000.0000.000
79A105HIS0-0.013-0.00917.3880.0060.0060.0000.0000.0000.000
80A106GLU-1-0.924-0.96118.186-0.102-0.1020.0000.0000.0000.000
81A107PHE0-0.0400.00017.3750.0180.0180.0000.0000.0000.000
82A108THR0-0.010-0.00519.416-0.004-0.0040.0000.0000.0000.000
83A109GLY0-0.027-0.03821.2680.0070.0070.0000.0000.0000.000
84A110THR0-0.024-0.02520.0040.0020.0020.0000.0000.0000.000
85A111ASP-1-0.979-0.97822.2990.0230.0230.0000.0000.0000.000
86A112GLY00.004-0.00225.9720.0040.0040.0000.0000.0000.000
87A113PRO00.0200.01924.9070.0080.0080.0000.0000.0000.000
88A114SER00.0640.05118.946-0.012-0.0120.0000.0000.0000.000
89A115GLY00.0320.01321.2050.0040.0040.0000.0000.0000.000
90A116PHE00.018-0.00621.7760.0000.0000.0000.0000.0000.000
91A117GLY0-0.028-0.00823.8510.0020.0020.0000.0000.0000.000
92A118PHE0-0.046-0.04024.8360.0070.0070.0000.0000.0000.000
93A119GLU-1-0.664-0.78720.4130.0450.0450.0000.0000.0000.000
94A120LEU00.0140.00724.606-0.001-0.0010.0000.0000.0000.000
95A121THR0-0.023-0.04326.1810.0070.0070.0000.0000.0000.000
96A122PHE00.001-0.00128.606-0.007-0.0070.0000.0000.0000.000
97A123ARG10.8260.90331.079-0.053-0.0530.0000.0000.0000.000
98A124LEU00.0060.01933.679-0.004-0.0040.0000.0000.0000.000
99A125LYS10.9440.97235.353-0.026-0.0260.0000.0000.0000.000
100A126ARG10.7950.91335.543-0.052-0.0520.0000.0000.0000.000
101A127GLU-1-0.902-0.94937.6360.0280.0280.0000.0000.0000.000
102A128THR0-0.067-0.04538.9300.0030.0030.0000.0000.0000.000
103A129GLY0-0.001-0.00739.232-0.001-0.0010.0000.0000.0000.000
104A130GLU-1-0.780-0.87534.6890.0410.0410.0000.0000.0000.000
105A131SER0-0.026-0.03732.7420.0010.0010.0000.0000.0000.000
106A132ALA0-0.022-0.01528.7400.0070.0070.0000.0000.0000.000
107A133PRO00.0200.01327.686-0.005-0.0050.0000.0000.0000.000
108A134PRO00.0240.02329.3030.0010.0010.0000.0000.0000.000
109A135THR00.0640.00526.1400.0020.0020.0000.0000.0000.000
110A136TRP00.0670.04428.0280.0000.0000.0000.0000.0000.000
111A137PRO00.0230.01329.386-0.004-0.0040.0000.0000.0000.000
112A138ALA0-0.0010.00124.599-0.001-0.0010.0000.0000.0000.000
113A139GLU-1-0.924-0.96026.570-0.006-0.0060.0000.0000.0000.000
114A140LEU0-0.0140.00028.297-0.005-0.0050.0000.0000.0000.000
115A141MET0-0.041-0.01126.413-0.001-0.0010.0000.0000.0000.000
116A142GLN00.0460.03121.324-0.009-0.0090.0000.0000.0000.000
117A143GLY0-0.015-0.01126.192-0.007-0.0070.0000.0000.0000.000
118A144LEU00.009-0.00429.622-0.004-0.0040.0000.0000.0000.000
119A145ALA00.0140.00324.584-0.003-0.0030.0000.0000.0000.000
120A146ARG10.8680.93926.0760.0220.0220.0000.0000.0000.000
121A147TYR0-0.034-0.01927.416-0.006-0.0060.0000.0000.0000.000
122A148VAL00.0090.03526.889-0.002-0.0020.0000.0000.0000.000
123A149PHE00.004-0.01720.527-0.003-0.0030.0000.0000.0000.000
124A150GLN0-0.083-0.04126.119-0.008-0.0080.0000.0000.0000.000
125A151SER0-0.066-0.05228.754-0.001-0.0010.0000.0000.0000.000
126A152GLU-1-0.923-0.95227.312-0.052-0.0520.0000.0000.0000.000
127A153ASN0-0.052-0.00529.5680.0020.0020.0000.0000.0000.000
128A154THR0-0.018-0.01828.7680.0000.0000.0000.0000.0000.000
129A155PHE0-0.026-0.00930.952-0.001-0.0010.0000.0000.0000.000
130A156CYS0-0.047-0.02832.1890.0020.0020.0000.0000.0000.000
131A157SER00.005-0.00834.6670.0000.0000.0000.0000.0000.000
132A158GLY0-0.038-0.02936.370-0.002-0.0020.0000.0000.0000.000
133A159ASP-1-0.819-0.90236.4580.0040.0040.0000.0000.0000.000
134A160HIS0-0.024-0.03238.7870.0010.0010.0000.0000.0000.000
135A161VAL00.0100.00235.202-0.002-0.0020.0000.0000.0000.000
136A162SER0-0.007-0.01438.6240.0010.0010.0000.0000.0000.000
137A163TRP0-0.052-0.03432.702-0.002-0.0020.0000.0000.0000.000
138A164HIS0-0.022-0.01539.011-0.002-0.0020.0000.0000.0000.000
139A165SER0-0.001-0.00539.179-0.002-0.0020.0000.0000.0000.000
140A166PRO00.0020.02440.0180.0010.0010.0000.0000.0000.000
141A167LEU0-0.024-0.02236.0850.0000.0000.0000.0000.0000.000
142A168ASP-1-0.844-0.89935.4950.0170.0170.0000.0000.0000.000
143A169ASN0-0.099-0.04534.753-0.002-0.0020.0000.0000.0000.000
144A170SER0-0.056-0.04438.519-0.001-0.0010.0000.0000.0000.000
145A171GLU-1-0.913-0.97541.2020.0050.0050.0000.0000.0000.000
146A172SER0-0.092-0.03441.967-0.001-0.0010.0000.0000.0000.000
147A173ARG10.8260.87744.063-0.012-0.0120.0000.0000.0000.000
148A174ILE0-0.041-0.01640.220-0.001-0.0010.0000.0000.0000.000
149A175GLN0-0.014-0.02141.190-0.001-0.0010.0000.0000.0000.000
150A176HIS00.0040.01240.163-0.003-0.0030.0000.0000.0000.000
151A177MET0-0.0100.00134.3650.0030.0030.0000.0000.0000.000
152A178LEU00.0280.03438.556-0.003-0.0030.0000.0000.0000.000
153A179LEU00.0100.01433.1320.0030.0030.0000.0000.0000.000
154A180THR00.0360.02835.169-0.003-0.0030.0000.0000.0000.000
155A181GLU-1-0.880-0.92932.9700.0310.0310.0000.0000.0000.000
156A182ASP-1-0.762-0.85630.3480.0640.0640.0000.0000.0000.000
157A183PRO0-0.045-0.01132.4120.0010.0010.0000.0000.0000.000
158A184GLN0-0.051-0.04331.4500.0030.0030.0000.0000.0000.000
159A185MET0-0.060-0.02423.8970.0070.0070.0000.0000.0000.000
160A186GLN0-0.018-0.01128.043-0.012-0.0120.0000.0000.0000.000
161A187PRO0-0.001-0.01426.6360.0070.0070.0000.0000.0000.000
162A188VAL0-0.021-0.00121.2060.0050.0050.0000.0000.0000.000
163A189GLN00.000-0.00122.633-0.004-0.0040.0000.0000.0000.000
164A190THR00.0130.01516.8240.0290.0290.0000.0000.0000.000
165A191PRO0-0.063-0.03514.969-0.014-0.0140.0000.0000.0000.000
166A192PHE0-0.023-0.03712.184-0.015-0.0150.0000.0000.0000.000
167A193GLY00.0870.06418.283-0.013-0.0130.0000.0000.0000.000
168A194VAL0-0.059-0.02921.5640.0160.0160.0000.0000.0000.000
169A195VAL00.0070.01620.605-0.008-0.0080.0000.0000.0000.000
170A196THR0-0.033-0.02824.0100.0070.0070.0000.0000.0000.000
171A197PHE00.029-0.00722.8690.0030.0030.0000.0000.0000.000
172A198LEU00.0270.02528.013-0.002-0.0020.0000.0000.0000.000
173A199GLN00.0070.00530.0630.0060.0060.0000.0000.0000.000
174A200ILE00.002-0.01330.508-0.004-0.0040.0000.0000.0000.000
175A201VAL0-0.037-0.01834.0160.0040.0040.0000.0000.0000.000
176A202GLY00.021-0.00937.598-0.003-0.0030.0000.0000.0000.000
177A203VAL0-0.036-0.01439.3790.0010.0010.0000.0000.0000.000
178A204CYS00.010-0.00943.024-0.001-0.0010.0000.0000.0000.000
179A205THR00.0630.02646.0820.0000.0000.0000.0000.0000.000
180A206GLU-1-0.826-0.90447.3130.0080.0080.0000.0000.0000.000
181A207GLU-1-0.755-0.86146.1990.0150.0150.0000.0000.0000.000
182A208LEU0-0.0150.00442.7840.0000.0000.0000.0000.0000.000
183A209HIS0-0.045-0.03445.928-0.001-0.0010.0000.0000.0000.000
184A210SER00.0170.01649.1910.0000.0000.0000.0000.0000.000
185A211ALA00.005-0.01144.9170.0000.0000.0000.0000.0000.000
186A212GLN0-0.058-0.02245.5060.0000.0000.0000.0000.0000.000
187A213GLN0-0.070-0.03147.974-0.001-0.0010.0000.0000.0000.000
188A214TRP00.0180.03750.1180.0000.0000.0000.0000.0000.000
189A215ASN00.0410.01445.8420.0010.0010.0000.0000.0000.000
190A216GLY00.0350.01942.6900.0010.0010.0000.0000.0000.000
191A217GLN00.007-0.01839.3420.0020.0020.0000.0000.0000.000
192A218GLY00.0780.05843.7610.0020.0020.0000.0000.0000.000
193A219ILE0-0.002-0.00745.2790.0010.0010.0000.0000.0000.000
194A220LEU0-0.0080.00039.6710.0020.0020.0000.0000.0000.000
195A221GLU-1-0.984-0.99643.5310.0190.0190.0000.0000.0000.000
196A222LEU0-0.034-0.01645.8990.0010.0010.0000.0000.0000.000
197A223LEU00.0370.03842.7710.0010.0010.0000.0000.0000.000
198A224ARG10.9190.96939.463-0.026-0.0260.0000.0000.0000.000
199A225THR0-0.174-0.10644.8690.0010.0010.0000.0000.0000.000
200A226VAL00.0260.02047.5250.0000.0000.0000.0000.0000.000
201A227PRO00.0600.01345.6560.0000.0000.0000.0000.0000.000
202A228ILE0-0.042-0.02444.8110.0010.0010.0000.0000.0000.000
203A229ALA0-0.046-0.03645.2100.0000.0000.0000.0000.0000.000
204A230GLY00.0360.02141.753-0.001-0.0010.0000.0000.0000.000
205A231GLY0-0.0030.03441.6830.0030.0030.0000.0000.0000.000
206A232PRO00.003-0.01041.6680.0000.0000.0000.0000.0000.000
207A233TRP0-0.048-0.04235.9070.0020.0020.0000.0000.0000.000
208A234LEU00.0020.01837.3040.0020.0020.0000.0000.0000.000
209A235ILE0-0.011-0.00837.1730.0010.0010.0000.0000.0000.000
210A236THR00.0470.02637.351-0.004-0.0040.0000.0000.0000.000
211A237ASP-1-0.831-0.92138.8340.0290.0290.0000.0000.0000.000
212A238MET0-0.016-0.00938.001-0.001-0.0010.0000.0000.0000.000
213A239ARG10.9050.94941.148-0.028-0.0280.0000.0000.0000.000
214A240ARG10.8180.92544.318-0.019-0.0190.0000.0000.0000.000
215A241GLY00.0040.00346.443-0.001-0.0010.0000.0000.0000.000
216A242GLU-1-0.954-0.96949.5980.0140.0140.0000.0000.0000.000
217A243THR0-0.053-0.01949.6050.0010.0010.0000.0000.0000.000
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