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: YZL82

Calculation Name: 2FUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FUK

Chain ID: A

ChEMBL ID:

UniProt ID: B0RM26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2586608.63345
FMO2-HF: Nuclear repulsion 2504137.179934
FMO2-HF: Total energy -82471.453517
FMO2-MP2: Total energy -82715.827855


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:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-14.933-11.8430.306-1.613-1.782-0.009
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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].
3A5LEU00.0070.0023.8730.4031.593-0.013-0.574-0.6030.000
4A6PHE00.0240.0076.749-0.059-0.0590.0000.0000.0000.000
5A7PRO0-0.040-0.0129.547-0.015-0.0150.0000.0000.0000.000
6A8THR00.002-0.01212.4120.0660.0660.0000.0000.0000.000
7A9GLU-1-0.929-0.97715.550-0.110-0.1100.0000.0000.0000.000
8A10SER0-0.025-0.01415.810-0.021-0.0210.0000.0000.0000.000
9A11ALA0-0.010-0.00513.191-0.033-0.0330.0000.0000.0000.000
10A12ALA0-0.0160.00513.0360.0510.0510.0000.0000.0000.000
11A13LEU0-0.026-0.0096.956-0.082-0.0820.0000.0000.0000.000
12A14THR00.0130.0016.6380.2620.2620.0000.0000.0000.000
13A15LEU0-0.031-0.0105.086-0.484-0.4840.0000.0000.0000.000
14A16ASP-1-0.918-0.9583.088-15.835-13.9350.319-1.039-1.179-0.009
15A17GLY00.0230.0025.9351.1901.1900.0000.0000.0000.000
16A18PRO0-0.030-0.0229.578-0.241-0.2410.0000.0000.0000.000
17A19VAL0-0.035-0.01212.128-0.004-0.0040.0000.0000.0000.000
18A20GLY0-0.0060.0009.375-0.015-0.0150.0000.0000.0000.000
19A21PRO0-0.032-0.0197.4490.0850.0850.0000.0000.0000.000
20A22LEU00.0440.0328.6830.4500.4500.0000.0000.0000.000
21A23ASP-1-0.783-0.8599.632-1.207-1.2070.0000.0000.0000.000
22A24VAL00.015-0.0069.7020.2120.2120.0000.0000.0000.000
23A25ALA0-0.045-0.02511.943-0.091-0.0910.0000.0000.0000.000
24A26VAL00.0160.01812.1090.0810.0810.0000.0000.0000.000
25A27ASP-1-0.814-0.90015.090-0.255-0.2550.0000.0000.0000.000
26A28LEU00.0200.01716.8860.0370.0370.0000.0000.0000.000
27A29PRO0-0.037-0.01419.783-0.018-0.0180.0000.0000.0000.000
28A30GLU-1-0.934-0.97222.980-0.078-0.0780.0000.0000.0000.000
29A31PRO0-0.025-0.01026.1160.0140.0140.0000.0000.0000.000
30A32ASP-1-0.940-0.97227.774-0.022-0.0220.0000.0000.0000.000
31A33VAL0-0.038-0.00928.3160.0030.0030.0000.0000.0000.000
32A34ALA0-0.063-0.02928.0020.0050.0050.0000.0000.0000.000
33A35VAL00.0240.00922.325-0.004-0.0040.0000.0000.0000.000
34A36GLN00.020-0.00823.9030.0220.0220.0000.0000.0000.000
35A37PRO0-0.0380.01021.0780.0010.0010.0000.0000.0000.000
36A38VAL00.015-0.00320.2770.0170.0170.0000.0000.0000.000
37A39THR00.0090.01014.644-0.021-0.0210.0000.0000.0000.000
38A40ALA0-0.026-0.02017.9770.0170.0170.0000.0000.0000.000
39A41ILE00.0220.02514.389-0.021-0.0210.0000.0000.0000.000
40A42VAL0-0.062-0.03018.0560.0020.0020.0000.0000.0000.000
41A43CYS0-0.0080.00419.615-0.037-0.0370.0000.0000.0000.000
42A44HIS0-0.025-0.01019.331-0.012-0.0120.0000.0000.0000.000
43A45PRO0-0.031-0.02522.7280.0050.0050.0000.0000.0000.000
44A46LEU00.0850.03224.569-0.023-0.0230.0000.0000.0000.000
45A47SER00.0320.01221.4130.0060.0060.0000.0000.0000.000
46A48THR0-0.056-0.07224.066-0.015-0.0150.0000.0000.0000.000
47A49GLU-1-0.844-0.85626.810-0.206-0.2060.0000.0000.0000.000
48A50GLY0-0.040-0.01927.238-0.019-0.0190.0000.0000.0000.000
49A51GLY0-0.087-0.03624.7680.0140.0140.0000.0000.0000.000
50A52SER00.0480.01820.680-0.033-0.0330.0000.0000.0000.000
51A53MET00.0200.00914.9120.0640.0640.0000.0000.0000.000
52A54HIS00.0160.00018.9380.0700.0700.0000.0000.0000.000
53A55ASN00.0100.02422.5870.0420.0420.0000.0000.0000.000
54A56LYS10.9820.95725.4500.1910.1910.0000.0000.0000.000
55A57VAL00.0150.02828.1090.0110.0110.0000.0000.0000.000
56A58VAL00.0230.02121.7010.0150.0150.0000.0000.0000.000
57A59THR00.000-0.01022.6830.0180.0180.0000.0000.0000.000
58A60MET0-0.074-0.01424.7450.0110.0110.0000.0000.0000.000
59A61ALA00.0330.01325.6220.0150.0150.0000.0000.0000.000
60A62ALA00.0230.00922.0800.0160.0160.0000.0000.0000.000
61A63ARG10.9400.96123.9730.1370.1370.0000.0000.0000.000
62A64ALA00.0090.00326.4080.0110.0110.0000.0000.0000.000
63A65LEU00.0350.01823.3710.0110.0110.0000.0000.0000.000
64A66ARG10.9260.97522.2570.1350.1350.0000.0000.0000.000
65A67GLU-1-0.874-0.94024.676-0.051-0.0510.0000.0000.0000.000
66A68LEU0-0.100-0.04327.2470.0070.0070.0000.0000.0000.000
67A69GLY00.0250.01725.4480.0120.0120.0000.0000.0000.000
68A70ILE0-0.047-0.02021.2210.0150.0150.0000.0000.0000.000
69A71THR00.0230.01916.223-0.034-0.0340.0000.0000.0000.000
70A72VAL0-0.054-0.02818.7650.0220.0220.0000.0000.0000.000
71A73VAL00.0180.01213.058-0.034-0.0340.0000.0000.0000.000
72A74ARG10.7370.84015.9280.2910.2910.0000.0000.0000.000
73A75PHE00.033-0.00113.379-0.014-0.0140.0000.0000.0000.000
74A76ASN0-0.022-0.01214.6180.1500.1500.0000.0000.0000.000
75A77PHE00.0520.01415.066-0.061-0.0610.0000.0000.0000.000
76A78ARG10.9300.96315.6130.3610.3610.0000.0000.0000.000
77A79SER0-0.133-0.05216.5600.1150.1150.0000.0000.0000.000
78A80VAL0-0.0130.00517.9580.0380.0380.0000.0000.0000.000
79A81GLY0-0.050-0.02117.041-0.066-0.0660.0000.0000.0000.000
80A82THR0-0.082-0.07813.6830.0430.0430.0000.0000.0000.000
81A83SER0-0.0220.00212.714-0.268-0.2680.0000.0000.0000.000
82A84ALA0-0.010-0.00112.3080.1300.1300.0000.0000.0000.000
83A85GLY00.0320.00714.0050.0730.0730.0000.0000.0000.000
84A86SER0-0.017-0.02916.7250.0090.0090.0000.0000.0000.000
85A87PHE0-0.020-0.01220.3180.0080.0080.0000.0000.0000.000
86A88ASP-1-0.874-0.94721.191-0.243-0.2430.0000.0000.0000.000
87A89HIS0-0.037-0.02223.0940.0400.0400.0000.0000.0000.000
88A90GLY0-0.001-0.01623.7260.0240.0240.0000.0000.0000.000
89A91ASP-1-0.905-0.92723.300-0.093-0.0930.0000.0000.0000.000
90A92GLY00.011-0.00619.4400.0120.0120.0000.0000.0000.000
91A93GLU-1-0.826-0.92917.918-0.309-0.3090.0000.0000.0000.000
92A94GLN0-0.018-0.02418.4250.0410.0410.0000.0000.0000.000
93A95ASP-1-0.917-0.94715.871-0.050-0.0500.0000.0000.0000.000
94A96ASP-1-0.827-0.92113.958-0.468-0.4680.0000.0000.0000.000
95A97LEU0-0.012-0.01713.5530.0530.0530.0000.0000.0000.000
96A98ARG10.8940.95513.830-0.185-0.1850.0000.0000.0000.000
97A99ALA00.0320.0249.7100.1300.1300.0000.0000.0000.000
98A100VAL0-0.005-0.0069.6130.3020.3020.0000.0000.0000.000
99A101ALA0-0.005-0.01511.0640.1310.1310.0000.0000.0000.000
100A102GLU-1-0.910-0.95810.2960.6770.6770.0000.0000.0000.000
101A103TRP0-0.040-0.0104.825-0.048-0.0480.0000.0000.0000.000
102A104VAL00.003-0.0138.014-0.045-0.0450.0000.0000.0000.000
103A105ARG10.8450.90110.977-0.361-0.3610.0000.0000.0000.000
104A106ALA0-0.0260.0057.709-0.020-0.0200.0000.0000.0000.000
105A107GLN00.012-0.0035.271-0.345-0.3450.0000.0000.0000.000
106A108ARG10.7700.8859.423-0.368-0.3680.0000.0000.0000.000
107A109PRO00.0140.01012.190-0.047-0.0470.0000.0000.0000.000
108A110THR0-0.043-0.02814.754-0.025-0.0250.0000.0000.0000.000
109A111ASP-1-0.819-0.86816.5650.1770.1770.0000.0000.0000.000
110A112THR0-0.054-0.03818.2740.0270.0270.0000.0000.0000.000
111A113LEU00.012-0.00415.944-0.005-0.0050.0000.0000.0000.000
112A114TRP0-0.029-0.01519.187-0.026-0.0260.0000.0000.0000.000
113A115LEU00.0360.01218.212-0.002-0.0020.0000.0000.0000.000
114A116ALA00.0260.01221.619-0.003-0.0030.0000.0000.0000.000
115A117GLY00.0350.02722.635-0.014-0.0140.0000.0000.0000.000
116A118PHE0-0.031-0.01524.8380.0080.0080.0000.0000.0000.000
117A119SER00.004-0.00926.848-0.023-0.0230.0000.0000.0000.000
118A120PHE00.0130.02422.4130.0150.0150.0000.0000.0000.000
119A121GLY00.0590.02223.6160.0040.0040.0000.0000.0000.000
120A122ALA0-0.060-0.03124.2060.0190.0190.0000.0000.0000.000
121A123TYR00.0000.00626.7500.0230.0230.0000.0000.0000.000
122A124VAL00.0340.01820.7920.0150.0150.0000.0000.0000.000
123A125SER0-0.023-0.03122.1090.0240.0240.0000.0000.0000.000
124A126LEU0-0.025-0.00423.0990.0230.0230.0000.0000.0000.000
125A127ARG10.8560.91625.1290.0380.0380.0000.0000.0000.000
126A128ALA00.0140.01420.2310.0130.0130.0000.0000.0000.000
127A129ALA0-0.040-0.01821.6580.0340.0340.0000.0000.0000.000
128A130ALA00.0250.01423.4830.0220.0220.0000.0000.0000.000
129A131ALA00.0050.00720.1510.0190.0190.0000.0000.0000.000
130A132LEU0-0.033-0.01716.4780.0450.0450.0000.0000.0000.000
131A133GLU-1-0.910-0.92819.5620.2390.2390.0000.0000.0000.000
132A134PRO0-0.065-0.02121.2300.0170.0170.0000.0000.0000.000
133A135GLN00.0400.01522.144-0.011-0.0110.0000.0000.0000.000
134A136VAL00.0010.00024.016-0.013-0.0130.0000.0000.0000.000
135A137LEU00.0170.01724.2300.0050.0050.0000.0000.0000.000
136A138ILE0-0.014-0.01825.758-0.007-0.0070.0000.0000.0000.000
137A139SER00.0190.01226.785-0.006-0.0060.0000.0000.0000.000
138A140ILE0-0.017-0.00628.0900.0020.0020.0000.0000.0000.000
139A141ALA00.006-0.00230.469-0.013-0.0130.0000.0000.0000.000
140A142PRO00.0220.01631.123-0.011-0.0110.0000.0000.0000.000
141A143PRO0-0.0010.00730.3550.0020.0020.0000.0000.0000.000
142A144ALA00.0550.02533.427-0.001-0.0010.0000.0000.0000.000
143A145GLY00.0080.00436.039-0.003-0.0030.0000.0000.0000.000
144A146ARG10.8550.92334.1830.0890.0890.0000.0000.0000.000
145A147TRP00.0090.00528.520-0.008-0.0080.0000.0000.0000.000
146A148ASP-1-0.806-0.86132.173-0.028-0.0280.0000.0000.0000.000
147A149PHE0-0.026-0.01730.727-0.002-0.0020.0000.0000.0000.000
148A150SER0-0.057-0.06032.7530.0110.0110.0000.0000.0000.000
149A151ASP-1-0.914-0.96532.0160.0310.0310.0000.0000.0000.000
150A152VAL0-0.0130.01428.4220.0030.0030.0000.0000.0000.000
151A153GLN0-0.021-0.02828.1280.0130.0130.0000.0000.0000.000
152A154PRO0-0.0070.00527.6100.0110.0110.0000.0000.0000.000
153A155PRO00.0080.01726.2030.0040.0040.0000.0000.0000.000
154A156ALA00.024-0.00728.453-0.010-0.0100.0000.0000.0000.000
155A157GLN0-0.057-0.01728.990-0.004-0.0040.0000.0000.0000.000
156A158TRP00.0510.01028.9620.0040.0040.0000.0000.0000.000
157A159LEU0-0.037-0.01830.219-0.003-0.0030.0000.0000.0000.000
158A160VAL00.0210.01931.012-0.006-0.0060.0000.0000.0000.000
159A161ILE0-0.013-0.01231.9830.0010.0010.0000.0000.0000.000
160A162GLN00.0550.00734.302-0.006-0.0060.0000.0000.0000.000
161A163GLY0-0.0210.00036.9720.0030.0030.0000.0000.0000.000
162A164ASP-1-0.740-0.88038.810-0.044-0.0440.0000.0000.0000.000
163A165ALA0-0.0330.00141.4960.0020.0020.0000.0000.0000.000
164A166ASP-1-0.827-0.90836.497-0.099-0.0990.0000.0000.0000.000
165A167GLU-1-0.906-0.95639.556-0.083-0.0830.0000.0000.0000.000
166A168ILE0-0.102-0.04134.314-0.004-0.0040.0000.0000.0000.000
167A169VAL0-0.072-0.04234.170-0.001-0.0010.0000.0000.0000.000
168A170ASP-1-0.833-0.92237.373-0.055-0.0550.0000.0000.0000.000
169A171PRO0-0.017-0.01140.1700.0040.0040.0000.0000.0000.000
170A172GLN0-0.035-0.03841.1830.0030.0030.0000.0000.0000.000
171A173ALA00.0440.03040.0520.0040.0040.0000.0000.0000.000
172A174VAL0-0.069-0.03436.7420.0040.0040.0000.0000.0000.000
173A175TYR0-0.080-0.09038.9660.0050.0050.0000.0000.0000.000
174A176ASP-1-0.777-0.86541.744-0.027-0.0270.0000.0000.0000.000
175A177TRP0-0.018-0.00732.7190.0010.0010.0000.0000.0000.000
176A178LEU0-0.035-0.03735.6070.0060.0060.0000.0000.0000.000
177A179GLU-1-0.979-0.97139.297-0.011-0.0110.0000.0000.0000.000
178A180THR0-0.097-0.05340.5970.0030.0030.0000.0000.0000.000
179A181LEU0-0.051-0.02235.5120.0040.0040.0000.0000.0000.000
180A182GLU-1-0.946-0.97238.7920.0330.0330.0000.0000.0000.000
181A183GLN0-0.054-0.02735.7910.0040.0040.0000.0000.0000.000
182A184GLN00.0000.00836.480-0.001-0.0010.0000.0000.0000.000
183A185PRO0-0.0120.01533.7440.0030.0030.0000.0000.0000.000
184A186THR0-0.002-0.01034.960-0.003-0.0030.0000.0000.0000.000
185A187LEU00.0090.00735.570-0.004-0.0040.0000.0000.0000.000
186A188VAL0-0.045-0.02336.8000.0010.0010.0000.0000.0000.000
187A189ARG10.8850.94238.1540.0280.0280.0000.0000.0000.000
188A190MET0-0.047-0.02237.3320.0010.0010.0000.0000.0000.000
189A191PRO00.0690.03541.064-0.004-0.0040.0000.0000.0000.000
190A192ASP-1-0.911-0.95643.405-0.055-0.0550.0000.0000.0000.000
191A193THR0-0.081-0.02637.960-0.005-0.0050.0000.0000.0000.000
192A194SER00.0360.01238.3370.0000.0000.0000.0000.0000.000
193A195HIS10.8860.93931.7570.1160.1160.0000.0000.0000.000
194A196PHE0-0.006-0.01230.329-0.002-0.0020.0000.0000.0000.000
195A197PHE00.0310.00432.862-0.003-0.0030.0000.0000.0000.000
196A198HIS00.0190.01035.830-0.006-0.0060.0000.0000.0000.000
197A199ARG10.8680.92037.2430.1140.1140.0000.0000.0000.000
198A200LYS11.0291.02437.2890.0660.0660.0000.0000.0000.000
199A201LEU00.0190.01231.4940.0030.0030.0000.0000.0000.000
200A202ILE00.0050.00933.9430.0020.0020.0000.0000.0000.000
201A203ASP-1-0.872-0.95036.078-0.054-0.0540.0000.0000.0000.000
202A204LEU0-0.0120.00030.7070.0050.0050.0000.0000.0000.000
203A205ARG10.9220.96131.4200.0630.0630.0000.0000.0000.000
204A206GLY00.0090.00433.0780.0070.0070.0000.0000.0000.000
205A207ALA00.0150.00735.3340.0070.0070.0000.0000.0000.000
206A208LEU0-0.0040.00128.9030.0070.0070.0000.0000.0000.000
207A209GLN0-0.068-0.03830.2770.0110.0110.0000.0000.0000.000
208A210HIS0-0.058-0.03432.4940.0090.0090.0000.0000.0000.000
209A211GLY0-0.016-0.00934.0150.0060.0060.0000.0000.0000.000
210A212VAL00.0270.02028.5940.0060.0060.0000.0000.0000.000
211A213ARG10.9640.99631.0020.0010.0010.0000.0000.0000.000
212A214ARG10.9030.92632.552-0.023-0.0230.0000.0000.0000.000
213A215TRP00.0110.01129.3620.0050.0050.0000.0000.0000.000
214A216LEU0-0.055-0.00827.5840.0080.0080.0000.0000.0000.000
215A217PRO0-0.0010.01124.921-0.001-0.0010.0000.0000.0000.000
216A218ALA00.0100.01527.5170.0040.0040.0000.0000.0000.000
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