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: YY872

Calculation Name: 2QWU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QWU

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NEC5

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220295.292693
FMO2-HF: Nuclear repulsion 2140974.04896
FMO2-HF: Total energy -79321.243733
FMO2-MP2: Total energy -79546.124971


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:MET)


Summations of interaction energy for fragment #1(A:3:MET)
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.
-14.929-13.9228.784-5.097-4.695-0.042
Interaction energy analysis for fragmet #1(A:3:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.016
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].
3A5GLU-1-0.842-0.9041.842-14.565-13.8838.785-5.034-4.434-0.042
4A6MET0-0.015-0.0025.2110.3280.3280.0000.0000.0000.000
5A7ILE0-0.036-0.0167.9000.3940.3940.0000.0000.0000.000
6A8THR00.0370.0094.109-0.168-0.041-0.001-0.017-0.1100.000
7A9ARG10.8950.9166.3810.8710.8710.0000.0000.0000.000
8A10GLN00.0400.0267.3590.2130.2130.0000.0000.0000.000
9A11GLN00.0630.0638.389-0.210-0.2100.0000.0000.0000.000
10A12VAL0-0.038-0.02010.9630.0510.0510.0000.0000.0000.000
11A13THR0-0.060-0.04212.3050.0040.0040.0000.0000.0000.000
12A14SER0-0.061-0.05212.2300.0180.0180.0000.0000.0000.000
13A15GLY0-0.0060.01614.8320.0150.0150.0000.0000.0000.000
14A16GLU-1-0.946-0.96210.399-0.096-0.0960.0000.0000.0000.000
15A17THR0-0.026-0.01514.556-0.043-0.0430.0000.0000.0000.000
16A18ILE00.0110.01912.939-0.059-0.0590.0000.0000.0000.000
17A19HIS00.000-0.01712.4030.0640.0640.0000.0000.0000.000
18A20VAL00.0610.02511.955-0.147-0.1470.0000.0000.0000.000
19A21ARG10.8500.90513.2770.7110.7110.0000.0000.0000.000
20A22THR00.0220.00913.825-0.115-0.1150.0000.0000.0000.000
21A23ASP-1-0.875-0.93416.280-0.600-0.6000.0000.0000.0000.000
22A24PRO00.010-0.01518.8080.0100.0100.0000.0000.0000.000
23A25THR00.0260.02522.3150.0180.0180.0000.0000.0000.000
24A26ALA00.0130.01818.8010.0090.0090.0000.0000.0000.000
25A27CYS0-0.035-0.01120.798-0.010-0.0100.0000.0000.0000.000
26A28ILE00.0140.02423.0730.0230.0230.0000.0000.0000.000
27A29GLY00.0300.01123.993-0.021-0.0210.0000.0000.0000.000
28A30SER0-0.005-0.01223.904-0.008-0.0080.0000.0000.0000.000
29A31HIS0-0.036-0.01918.887-0.037-0.0370.0000.0000.0000.000
30A32PRO00.0250.00515.4340.0130.0130.0000.0000.0000.000
31A33ASN00.0210.03414.325-0.170-0.1700.0000.0000.0000.000
32A34CYS00.0260.00112.1810.1060.1060.0000.0000.0000.000
33A35ARG10.8020.89814.8200.7290.7290.0000.0000.0000.000
34A36MET00.0010.00617.004-0.036-0.0360.0000.0000.0000.000
35A37PHE00.000-0.00419.7080.0370.0370.0000.0000.0000.000
36A38ILE0-0.0040.00223.429-0.012-0.0120.0000.0000.0000.000
37A39ASP-1-0.803-0.89026.057-0.239-0.2390.0000.0000.0000.000
38A40SER0-0.036-0.03229.3270.0230.0230.0000.0000.0000.000
39A41LEU00.0370.01728.894-0.014-0.0140.0000.0000.0000.000
40A42THR0-0.048-0.00831.5750.0160.0160.0000.0000.0000.000
41A43ILE00.0600.02230.928-0.006-0.0060.0000.0000.0000.000
42A44ALA00.0500.03334.6170.0080.0080.0000.0000.0000.000
43A45GLY0-0.016-0.01037.3490.0090.0090.0000.0000.0000.000
44A46GLU-1-0.883-0.92537.820-0.120-0.1200.0000.0000.0000.000
45A47LYS10.9200.95436.5690.1320.1320.0000.0000.0000.000
46A48LEU00.0030.00232.8010.0060.0060.0000.0000.0000.000
47A49ASP-1-0.911-0.94835.496-0.161-0.1610.0000.0000.0000.000
48A50LYS10.8760.94531.2600.2250.2250.0000.0000.0000.000
49A51ASN0-0.011-0.02933.650-0.005-0.0050.0000.0000.0000.000
50A52ILE00.0220.01728.3430.0020.0020.0000.0000.0000.000
51A53VAL00.0360.01630.471-0.006-0.0060.0000.0000.0000.000
52A54ALA0-0.040-0.00825.419-0.011-0.0110.0000.0000.0000.000
53A55ILE00.0170.01023.6730.0140.0140.0000.0000.0000.000
54A56ASP-1-0.755-0.87421.089-0.561-0.5610.0000.0000.0000.000
55A57GLY00.0220.00918.5130.0040.0040.0000.0000.0000.000
56A58GLY0-0.042-0.03019.5210.0210.0210.0000.0000.0000.000
57A59GLU-1-0.937-0.95221.058-0.317-0.3170.0000.0000.0000.000
58A60ASP-1-0.810-0.87524.496-0.275-0.2750.0000.0000.0000.000
59A61VAL00.040-0.01126.2770.0140.0140.0000.0000.0000.000
60A62THR0-0.103-0.06028.7760.0190.0190.0000.0000.0000.000
61A63LYS10.8570.91531.0120.2590.2590.0000.0000.0000.000
62A64ALA0-0.0080.01829.5820.0050.0050.0000.0000.0000.000
63A65ASP-1-0.867-0.92331.692-0.193-0.1930.0000.0000.0000.000
64A66SER0-0.083-0.04734.6910.0030.0030.0000.0000.0000.000
65A67ALA0-0.025-0.00732.819-0.013-0.0130.0000.0000.0000.000
66A68THR0-0.022-0.03128.1960.0070.0070.0000.0000.0000.000
67A69ALA0-0.044-0.02927.452-0.009-0.0090.0000.0000.0000.000
68A70ALA0-0.0140.00729.4200.0140.0140.0000.0000.0000.000
69A71ALA0-0.029-0.01527.6140.0110.0110.0000.0000.0000.000
70A72SER00.000-0.00823.230-0.015-0.0150.0000.0000.0000.000
71A73VAL0-0.003-0.01920.0970.0300.0300.0000.0000.0000.000
72A74ILE0-0.0210.00119.956-0.042-0.0420.0000.0000.0000.000
73A75ARG10.9670.97017.8040.3300.3300.0000.0000.0000.000
74A76MET0-0.0160.00517.3940.0470.0470.0000.0000.0000.000
75A77SER00.0080.01916.793-0.081-0.0810.0000.0000.0000.000
76A78ILE00.0080.00417.4040.0460.0460.0000.0000.0000.000
77A79THR00.016-0.00117.758-0.026-0.0260.0000.0000.0000.000
78A80PRO0-0.013-0.00618.1100.0160.0160.0000.0000.0000.000
79A81GLY00.0350.02821.0370.0200.0200.0000.0000.0000.000
80A82SER0-0.060-0.03524.286-0.006-0.0060.0000.0000.0000.000
81A83ILE0-0.010-0.00926.6430.0000.0000.0000.0000.0000.000
82A84ASN00.0260.01327.705-0.010-0.0100.0000.0000.0000.000
83A85PRO00.0330.03823.0660.0100.0100.0000.0000.0000.000
84A86THR0-0.0220.01023.3370.0140.0140.0000.0000.0000.000
85A87ILE0-0.024-0.02622.056-0.019-0.0190.0000.0000.0000.000
86A88SER0-0.0010.02321.8530.0130.0130.0000.0000.0000.000
87A89ILE0-0.033-0.03021.681-0.036-0.0360.0000.0000.0000.000
88A90THR00.0150.00422.0570.0200.0200.0000.0000.0000.000
89A91LEU0-0.002-0.00622.942-0.035-0.0350.0000.0000.0000.000
90A92GLY00.0400.03725.5760.0180.0180.0000.0000.0000.000
91A93VAL00.0110.00027.023-0.003-0.0030.0000.0000.0000.000
92A94LEU00.0090.01530.5230.0040.0040.0000.0000.0000.000
93A95ILE00.0450.01933.3040.0090.0090.0000.0000.0000.000
94A96LYS10.9670.98136.5570.1300.1300.0000.0000.0000.000
95A97SER00.0520.00539.325-0.003-0.0030.0000.0000.0000.000
96A98ASN0-0.001-0.01040.502-0.003-0.0030.0000.0000.0000.000
97A99VAL00.0270.01738.1070.0040.0040.0000.0000.0000.000
98A100ARG10.8500.90836.3270.1400.1400.0000.0000.0000.000
99A101THR00.0090.00738.1550.0000.0000.0000.0000.0000.000
100A102LYS10.7770.86841.0480.1040.1040.0000.0000.0000.000
101A103ILE00.0400.02835.2330.0020.0020.0000.0000.0000.000
102A104GLU-1-0.780-0.86536.593-0.132-0.1320.0000.0000.0000.000
103A105GLU-1-0.810-0.89238.504-0.094-0.0940.0000.0000.0000.000
104A106LYS10.8350.92240.0420.1210.1210.0000.0000.0000.000
105A107VAL00.021-0.00535.1490.0030.0030.0000.0000.0000.000
106A108SER00.0070.00938.3780.0050.0050.0000.0000.0000.000
107A109SER0-0.010-0.02640.3160.0070.0070.0000.0000.0000.000
108A110ILE0-0.035-0.01239.7190.0040.0040.0000.0000.0000.000
109A111LEU0-0.038-0.01735.9660.0030.0030.0000.0000.0000.000
110A112GLN0-0.067-0.04339.5210.0080.0080.0000.0000.0000.000
111A113ALA0-0.0520.01142.8310.0050.0050.0000.0000.0000.000
112A114SER0-0.036-0.04842.2850.0050.0050.0000.0000.0000.000
113A115ALA00.0390.01737.221-0.005-0.0050.0000.0000.0000.000
114A116THR00.0120.00735.696-0.006-0.0060.0000.0000.0000.000
115A117ASP-1-0.865-0.90636.724-0.099-0.0990.0000.0000.0000.000
116A118MET0-0.086-0.02433.035-0.005-0.0050.0000.0000.0000.000
117A119LYS10.8820.93633.7870.1190.1190.0000.0000.0000.000
118A120ILE00.0100.00629.0830.0000.0000.0000.0000.0000.000
119A121LYS10.8170.91030.3980.1800.1800.0000.0000.0000.000
120A122LEU00.008-0.00924.581-0.001-0.0010.0000.0000.0000.000
121A123GLY00.0330.03228.4440.0100.0100.0000.0000.0000.000
122A124ASN0-0.065-0.06726.333-0.017-0.0170.0000.0000.0000.000
123A125SER00.0370.02321.379-0.002-0.0020.0000.0000.0000.000
124A126ASN0-0.044-0.02719.3410.0180.0180.0000.0000.0000.000
125A127LYS10.8720.90819.7190.3680.3680.0000.0000.0000.000
126A128LYS10.7930.89817.3800.4420.4420.0000.0000.0000.000
127A129GLN00.0170.00415.184-0.050-0.0500.0000.0000.0000.000
128A130GLU-1-0.756-0.8778.744-2.219-2.2190.0000.0000.0000.000
129A131TYR0-0.063-0.04911.9900.0750.0750.0000.0000.0000.000
130A132LYS10.7500.8638.9351.4601.4600.0000.0000.0000.000
131A133THR00.017-0.0064.3550.1930.259-0.001-0.007-0.0570.000
132A134ASP-1-0.804-0.8607.824-0.889-0.8890.0000.0000.0000.000
133A135GLU-1-0.917-0.93310.979-0.558-0.5580.0000.0000.0000.000
134A136ALA00.0160.01912.9800.1620.1620.0000.0000.0000.000
135A137TRP0-0.015-0.00313.216-0.164-0.1640.0000.0000.0000.000
136A138GLY00.002-0.00113.6110.0800.0800.0000.0000.0000.000
137A139ILE0-0.044-0.00814.430-0.021-0.0210.0000.0000.0000.000
138A140MET0-0.0110.00711.384-0.163-0.1630.0000.0000.0000.000
139A141ILE00.0580.00113.0690.0270.0270.0000.0000.0000.000
140A142ASP-1-0.845-0.87516.143-0.397-0.3970.0000.0000.0000.000
141A143LEU00.018-0.00719.5280.0360.0360.0000.0000.0000.000
142A144SER0-0.039-0.04122.1040.0340.0340.0000.0000.0000.000
143A145ASN0-0.071-0.02625.0540.0210.0210.0000.0000.0000.000
144A146LEU00.0250.03523.1520.0200.0200.0000.0000.0000.000
145A147GLU-1-0.865-0.93826.941-0.153-0.1530.0000.0000.0000.000
146A148LEU0-0.0180.00525.0440.0020.0020.0000.0000.0000.000
147A149TYR0-0.017-0.01929.1770.0090.0090.0000.0000.0000.000
148A150PRO00.0050.00630.738-0.005-0.0050.0000.0000.0000.000
149A151ILE0-0.0030.01527.8830.0080.0080.0000.0000.0000.000
150A152SER0-0.013-0.02532.3570.0110.0110.0000.0000.0000.000
151A153ALA00.0600.01934.745-0.006-0.0060.0000.0000.0000.000
152A154LYS10.9210.95136.0910.0540.0540.0000.0000.0000.000
153A155ALA0-0.0150.00230.7050.0000.0000.0000.0000.0000.000
154A156PHE0-0.0060.00430.840-0.009-0.0090.0000.0000.0000.000
155A157SER00.0130.01730.1500.0120.0120.0000.0000.0000.000
156A158ILE0-0.005-0.01030.569-0.013-0.0130.0000.0000.0000.000
157A159SER0-0.029-0.01230.4820.0080.0080.0000.0000.0000.000
158A160ILE00.0100.00130.934-0.015-0.0150.0000.0000.0000.000
159A161GLU-1-0.893-0.93330.461-0.171-0.1710.0000.0000.0000.000
160A162PRO0-0.041-0.00831.778-0.013-0.0130.0000.0000.0000.000
161A163THR0-0.018-0.03228.823-0.005-0.0050.0000.0000.0000.000
162A164GLU-1-0.783-0.89332.133-0.154-0.1540.0000.0000.0000.000
163A165LEU0-0.034-0.01226.254-0.002-0.0020.0000.0000.0000.000
164A166MET0-0.023-0.00429.418-0.016-0.0160.0000.0000.0000.000
165A167GLY0-0.0090.01031.7090.0090.0090.0000.0000.0000.000
166A168VAL0-0.032-0.01835.0970.0000.0000.0000.0000.0000.000
167A169SER0-0.022-0.02837.2030.0030.0030.0000.0000.0000.000
168A170LYS10.9660.95938.6960.1480.1480.0000.0000.0000.000
169A171ASP-1-0.818-0.87740.385-0.146-0.1460.0000.0000.0000.000
170A172GLY0-0.040-0.01641.7110.0040.0040.0000.0000.0000.000
171A173MET0-0.078-0.02336.7490.0000.0000.0000.0000.0000.000
172A174ARG10.8810.91634.8080.1490.1490.0000.0000.0000.000
173A175TYR00.0220.01624.7040.0000.0000.0000.0000.0000.000
174A176HIS0-0.037-0.03231.4130.0150.0150.0000.0000.0000.000
175A177ILE00.0180.00325.397-0.017-0.0170.0000.0000.0000.000
176A178ILE0-0.018-0.00828.0070.0190.0190.0000.0000.0000.000
177A179SER00.0020.00626.271-0.035-0.0350.0000.0000.0000.000
178A180ILE0-0.006-0.00726.3130.0220.0220.0000.0000.0000.000
179A181ASP-1-0.876-0.94825.039-0.231-0.2310.0000.0000.0000.000
180A182GLY00.0320.01126.8220.0120.0120.0000.0000.0000.000
181A183LEU0-0.033-0.01426.6240.0130.0130.0000.0000.0000.000
182A184THR00.001-0.03126.7320.0000.0000.0000.0000.0000.000
183A185THR0-0.012-0.03325.256-0.009-0.0090.0000.0000.0000.000
184A186SER00.0310.01428.4000.0070.0070.0000.0000.0000.000
185A187GLN0-0.061-0.01623.7220.0180.0180.0000.0000.0000.000
186A188GLY00.0780.02725.717-0.003-0.0030.0000.0000.0000.000
187A189SER0-0.021-0.01821.2110.0060.0060.0000.0000.0000.000
188A190LEU00.0440.03219.0760.0050.0050.0000.0000.0000.000
189A191PRO0-0.0060.01118.085-0.011-0.0110.0000.0000.0000.000
190A192VAL00.0170.00112.895-0.020-0.0200.0000.0000.0000.000
191A193CYS0-0.067-0.03110.5430.1530.1530.0000.0000.0000.000
192A194CYS0-0.077-0.0106.6820.0970.0970.0000.0000.0000.000
193A195ALA00.0690.0313.715-0.1040.0280.001-0.039-0.0940.000
194A196ALA00.0410.0355.4030.1010.1010.0000.0000.0000.000
195A197SER0-0.059-0.0838.4740.1820.1820.0000.0000.0000.000
196A198THR0-0.003-0.01511.6480.1210.1210.0000.0000.0000.000
197A199ASP-1-0.879-0.9227.420-1.135-1.1350.0000.0000.0000.000
198A200LYS10.9490.95710.7570.5000.5000.0000.0000.0000.000
199A201GLY0-0.0030.00213.6810.0800.0800.0000.0000.0000.000
200A202VAL0-0.042-0.01414.964-0.022-0.0220.0000.0000.0000.000
201A203ALA00.0480.03915.5240.0380.0380.0000.0000.0000.000
202A204LYS10.8610.91417.2660.1080.1080.0000.0000.0000.000
203A205ILE0-0.005-0.02319.4690.0020.0020.0000.0000.0000.000
204A206GLY00.0580.03321.9110.0100.0100.0000.0000.0000.000
205A207TYR0-0.018-0.00325.5390.0030.0030.0000.0000.0000.000
206A208ILE0-0.0100.00225.087-0.012-0.0120.0000.0000.0000.000
207A209ALA0-0.0090.00929.4580.0080.0080.0000.0000.0000.000