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: V57L1

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2586137.954561
FMO2-HF: Nuclear repulsion 2503665.732868
FMO2-HF: Total energy -82472.221693
FMO2-MP2: Total energy -82716.47692


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.
-27.009-25.8177.111-4.27-4.032-0.055
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 : -0.048 / q_NPA : -0.038
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].
3A5LEU0-0.0010.0063.873-0.1491.019-0.015-0.572-0.5800.001
4A6PHE00.0310.0026.7480.0980.0980.0000.0000.0000.000
5A7PRO0-0.041-0.0109.4760.0510.0510.0000.0000.0000.000
6A8THR0-0.001-0.01612.4120.0420.0420.0000.0000.0000.000
7A9GLU-1-0.896-0.95215.552-0.134-0.1340.0000.0000.0000.000
8A10SER0-0.038-0.01815.810-0.042-0.0420.0000.0000.0000.000
9A11ALA0-0.015-0.00713.3540.0050.0050.0000.0000.0000.000
10A12ALA0-0.023-0.00113.199-0.005-0.0050.0000.0000.0000.000
11A13LEU0-0.027-0.0117.102-0.010-0.0100.0000.0000.0000.000
12A14THR00.006-0.0056.7450.2110.2110.0000.0000.0000.000
13A15LEU0-0.0140.0005.056-0.411-0.374-0.001-0.007-0.0300.000
14A16ASP-1-0.888-0.9421.890-26.171-26.2957.129-3.683-3.322-0.056
15A17GLY00.0390.0115.3570.9300.940-0.0010.000-0.0080.000
16A18PRO0-0.034-0.0178.908-0.219-0.2190.0000.0000.0000.000
17A19VAL0-0.033-0.01911.3670.0500.0500.0000.0000.0000.000
18A20GLY00.0000.0049.1940.1150.1150.0000.0000.0000.000
19A21PRO0-0.033-0.0207.699-0.061-0.0610.0000.0000.0000.000
20A22LEU00.0480.0388.6080.4240.4240.0000.0000.0000.000
21A23ASP-1-0.777-0.8429.722-0.982-0.9820.0000.0000.0000.000
22A24VAL00.017-0.0079.7820.1260.1260.0000.0000.0000.000
23A25ALA0-0.039-0.02112.071-0.008-0.0080.0000.0000.0000.000
24A26VAL00.0180.01711.9580.0330.0330.0000.0000.0000.000
25A27ASP-1-0.824-0.89615.226-0.308-0.3080.0000.0000.0000.000
26A28LEU00.0380.02716.8230.0150.0150.0000.0000.0000.000
27A29PRO0-0.027-0.00819.705-0.002-0.0020.0000.0000.0000.000
28A30GLU-1-0.946-0.97222.903-0.128-0.1280.0000.0000.0000.000
29A31PRO0-0.007-0.00326.3420.0080.0080.0000.0000.0000.000
30A32ASP-1-0.957-0.98127.700-0.062-0.0620.0000.0000.0000.000
31A33VAL0-0.047-0.01428.2340.0040.0040.0000.0000.0000.000
32A34ALA0-0.058-0.02527.9320.0000.0000.0000.0000.0000.000
33A35VAL00.0240.00822.243-0.006-0.0060.0000.0000.0000.000
34A36GLN00.010-0.00523.7990.0140.0140.0000.0000.0000.000
35A37PRO0-0.0310.00821.012-0.009-0.0090.0000.0000.0000.000
36A38VAL00.002-0.01020.2440.0040.0040.0000.0000.0000.000
37A39THR00.0160.01314.569-0.016-0.0160.0000.0000.0000.000
38A40ALA0-0.023-0.01417.9050.0070.0070.0000.0000.0000.000
39A41ILE00.0250.02514.406-0.020-0.0200.0000.0000.0000.000
40A42VAL0-0.064-0.03317.9800.0230.0230.0000.0000.0000.000
41A43CYS0-0.0070.01119.714-0.041-0.0410.0000.0000.0000.000
42A44HIS0-0.020-0.01519.3560.0000.0000.0000.0000.0000.000
43A45PRO0-0.035-0.02422.816-0.001-0.0010.0000.0000.0000.000
44A46LEU00.0640.02824.582-0.024-0.0240.0000.0000.0000.000
45A47SER00.0360.01321.2190.0120.0120.0000.0000.0000.000
46A48THR0-0.038-0.02723.881-0.010-0.0100.0000.0000.0000.000
47A49GLU-1-0.866-0.91326.675-0.222-0.2220.0000.0000.0000.000
48A50GLY0-0.031-0.01027.214-0.013-0.0130.0000.0000.0000.000
49A51GLY0-0.071-0.02824.8400.0120.0120.0000.0000.0000.000
50A52SER00.0470.01520.765-0.022-0.0220.0000.0000.0000.000
51A53MET00.0040.00214.6120.0620.0620.0000.0000.0000.000
52A54HIS00.0140.00419.0860.0490.0490.0000.0000.0000.000
53A55ASN0-0.037-0.00122.7150.0420.0420.0000.0000.0000.000
54A56LYS10.9910.96825.5760.1930.1930.0000.0000.0000.000
55A57VAL00.0190.02528.2370.0080.0080.0000.0000.0000.000
56A58VAL00.0250.02221.8350.0080.0080.0000.0000.0000.000
57A59THR00.015-0.00522.7960.0100.0100.0000.0000.0000.000
58A60MET0-0.081-0.01824.8810.0090.0090.0000.0000.0000.000
59A61ALA00.0340.01525.7970.0120.0120.0000.0000.0000.000
60A62ALA00.0190.00822.1780.0080.0080.0000.0000.0000.000
61A63ARG10.9520.96823.9270.1700.1700.0000.0000.0000.000
62A64ALA00.0030.00026.3900.0120.0120.0000.0000.0000.000
63A65LEU00.0350.01723.4120.0130.0130.0000.0000.0000.000
64A66ARG10.9220.96722.1650.2110.2110.0000.0000.0000.000
65A67GLU-1-0.816-0.88824.595-0.111-0.1110.0000.0000.0000.000
66A68LEU0-0.095-0.03927.1690.0130.0130.0000.0000.0000.000
67A69GLY00.0310.02025.3710.0080.0080.0000.0000.0000.000
68A70ILE0-0.058-0.02621.1430.0030.0030.0000.0000.0000.000
69A71THR00.0260.02216.262-0.010-0.0100.0000.0000.0000.000
70A72VAL0-0.046-0.02518.6300.0020.0020.0000.0000.0000.000
71A73VAL00.0100.00912.847-0.022-0.0220.0000.0000.0000.000
72A74ARG10.7470.83616.0410.3720.3720.0000.0000.0000.000
73A75PHE00.0380.00013.518-0.035-0.0350.0000.0000.0000.000
74A76ASN0-0.022-0.02614.7190.1420.1420.0000.0000.0000.000
75A77PHE00.0440.02015.023-0.082-0.0820.0000.0000.0000.000
76A78ARG10.8990.94815.2750.6100.6100.0000.0000.0000.000
77A79SER0-0.129-0.04916.2980.1180.1180.0000.0000.0000.000
78A80VAL0-0.0260.00217.8950.0570.0570.0000.0000.0000.000
79A81GLY0-0.041-0.01717.132-0.060-0.0600.0000.0000.0000.000
80A82THR0-0.089-0.08614.1090.0660.0660.0000.0000.0000.000
81A83SER0-0.021-0.00312.796-0.192-0.1920.0000.0000.0000.000
82A84ALA0-0.016-0.00412.2580.1300.1300.0000.0000.0000.000
83A85GLY00.0380.00914.0470.0100.0100.0000.0000.0000.000
84A86SER0-0.021-0.03116.5840.0350.0350.0000.0000.0000.000
85A87PHE0-0.011-0.01320.011-0.011-0.0110.0000.0000.0000.000
86A88ASP-1-0.899-0.97120.452-0.396-0.3960.0000.0000.0000.000
87A89HIS0-0.033-0.01922.6010.0270.0270.0000.0000.0000.000
88A90GLY00.012-0.00823.1090.0260.0260.0000.0000.0000.000
89A91ASP-1-0.898-0.92022.554-0.262-0.2620.0000.0000.0000.000
90A92GLY00.0350.00818.681-0.015-0.0150.0000.0000.0000.000
91A93GLU-1-0.804-0.91817.197-0.483-0.4830.0000.0000.0000.000
92A94GLN0-0.010-0.02617.886-0.002-0.0020.0000.0000.0000.000
93A95ASP-1-0.852-0.91615.096-0.441-0.4410.0000.0000.0000.000
94A96ASP-1-0.829-0.90813.222-0.820-0.8200.0000.0000.0000.000
95A97LEU0-0.014-0.01413.396-0.024-0.0240.0000.0000.0000.000
96A98ARG10.8000.89013.4270.4370.4370.0000.0000.0000.000
97A99ALA00.0340.0309.5990.0490.0490.0000.0000.0000.000
98A100VAL0-0.009-0.0099.5600.1040.1040.0000.0000.0000.000
99A101ALA0-0.003-0.01610.9980.0860.0860.0000.0000.0000.000
100A102GLU-1-0.889-0.93810.194-0.258-0.2580.0000.0000.0000.000
101A103TRP0-0.030-0.0114.641-0.0630.038-0.001-0.008-0.0920.000
102A104VAL00.004-0.0147.956-0.005-0.0050.0000.0000.0000.000
103A105ARG10.8540.91110.9110.1410.1410.0000.0000.0000.000
104A106ALA0-0.0290.0027.6970.0320.0320.0000.0000.0000.000
105A107GLN0-0.012-0.0075.814-0.062-0.0620.0000.0000.0000.000
106A108ARG10.7630.8609.3730.1100.1100.0000.0000.0000.000
107A109PRO00.0160.01012.169-0.003-0.0030.0000.0000.0000.000
108A110THR0-0.047-0.02314.7170.0080.0080.0000.0000.0000.000
109A111ASP-1-0.837-0.86716.559-0.097-0.0970.0000.0000.0000.000
110A112THR0-0.040-0.03718.2230.0030.0030.0000.0000.0000.000
111A113LEU00.0210.00416.015-0.011-0.0110.0000.0000.0000.000
112A114TRP0-0.030-0.02319.1250.0040.0040.0000.0000.0000.000
113A115LEU00.0440.02017.959-0.022-0.0220.0000.0000.0000.000
114A116ALA00.0230.01021.5500.0200.0200.0000.0000.0000.000
115A117GLY00.0440.03022.563-0.029-0.0290.0000.0000.0000.000
116A118PHE0-0.031-0.01624.8310.0200.0200.0000.0000.0000.000
117A119SER00.001-0.01126.926-0.019-0.0190.0000.0000.0000.000
118A120PHE00.0240.02722.0600.0090.0090.0000.0000.0000.000
119A121GLY00.0640.02723.615-0.008-0.0080.0000.0000.0000.000
120A122ALA0-0.063-0.02424.2060.0000.0000.0000.0000.0000.000
121A123TYR00.0010.00426.6590.0140.0140.0000.0000.0000.000
122A124VAL00.0230.01420.5070.0060.0060.0000.0000.0000.000
123A125SER0-0.008-0.03122.0510.0060.0060.0000.0000.0000.000
124A126LEU0-0.040-0.01423.0390.0120.0120.0000.0000.0000.000
125A127ARG10.8440.91325.0530.1860.1860.0000.0000.0000.000
126A128ALA00.0140.01220.1940.0050.0050.0000.0000.0000.000
127A129ALA0-0.038-0.01721.6130.0060.0060.0000.0000.0000.000
128A130ALA00.0160.00923.4380.0100.0100.0000.0000.0000.000
129A131ALA00.0090.00820.1310.0100.0100.0000.0000.0000.000
130A132LEU0-0.021-0.01016.3740.0050.0050.0000.0000.0000.000
131A133GLU-1-0.918-0.93519.518-0.066-0.0660.0000.0000.0000.000
132A134PRO0-0.056-0.01821.1680.0080.0080.0000.0000.0000.000
133A135GLN00.0230.01722.0890.0050.0050.0000.0000.0000.000
134A136VAL0-0.016-0.01223.9530.0060.0060.0000.0000.0000.000
135A137LEU00.0190.02124.165-0.014-0.0140.0000.0000.0000.000
136A138ILE0-0.014-0.02025.6910.0110.0110.0000.0000.0000.000
137A139SER00.0200.01126.714-0.013-0.0130.0000.0000.0000.000
138A140ILE0-0.015-0.00828.2010.0120.0120.0000.0000.0000.000
139A141ALA00.0180.00230.527-0.013-0.0130.0000.0000.0000.000
140A142PRO00.0320.01931.131-0.011-0.0110.0000.0000.0000.000
141A143PRO0-0.0070.00330.1310.0090.0090.0000.0000.0000.000
142A144ALA00.0530.02533.282-0.002-0.0020.0000.0000.0000.000
143A145GLY00.0120.00635.8870.0020.0020.0000.0000.0000.000
144A146ARG10.8360.91333.7990.1460.1460.0000.0000.0000.000
145A147TRP00.0090.00628.298-0.008-0.0080.0000.0000.0000.000
146A148ASP-1-0.804-0.88031.574-0.136-0.1360.0000.0000.0000.000
147A149PHE0-0.034-0.02430.574-0.012-0.0120.0000.0000.0000.000
148A150SER0-0.051-0.03532.7500.0080.0080.0000.0000.0000.000
149A151ASP-1-0.875-0.94632.160-0.122-0.1220.0000.0000.0000.000
150A152VAL0-0.0110.00828.086-0.009-0.0090.0000.0000.0000.000
151A153GLN0-0.048-0.03428.1570.0120.0120.0000.0000.0000.000
152A154PRO0-0.0060.01327.551-0.004-0.0040.0000.0000.0000.000
153A155PRO00.0040.01426.0280.0090.0090.0000.0000.0000.000
154A156ALA00.022-0.00728.4000.0000.0000.0000.0000.0000.000
155A157GLN0-0.059-0.01628.969-0.001-0.0010.0000.0000.0000.000
156A158TRP00.0570.01528.899-0.007-0.0070.0000.0000.0000.000
157A159LEU0-0.036-0.01630.1520.0070.0070.0000.0000.0000.000
158A160VAL00.0150.01530.942-0.012-0.0120.0000.0000.0000.000
159A161ILE0-0.009-0.01032.2260.0080.0080.0000.0000.0000.000
160A162GLN00.013-0.01434.248-0.015-0.0150.0000.0000.0000.000
161A163GLY0-0.0040.00836.9350.0060.0060.0000.0000.0000.000
162A164ASP-1-0.750-0.86738.906-0.094-0.0940.0000.0000.0000.000
163A165ALA0-0.0270.00141.5960.0040.0040.0000.0000.0000.000
164A166ASP-1-0.814-0.88736.497-0.149-0.1490.0000.0000.0000.000
165A167GLU-1-0.901-0.95039.616-0.109-0.1090.0000.0000.0000.000
166A168ILE0-0.104-0.04534.288-0.002-0.0020.0000.0000.0000.000
167A169VAL0-0.067-0.03634.134-0.003-0.0030.0000.0000.0000.000
168A170ASP-1-0.823-0.91237.363-0.100-0.1000.0000.0000.0000.000
169A171PRO0-0.009-0.00940.176-0.001-0.0010.0000.0000.0000.000
170A172GLN0-0.027-0.03241.2160.0010.0010.0000.0000.0000.000
171A173ALA00.0350.02739.9530.0020.0020.0000.0000.0000.000
172A174VAL0-0.061-0.03436.586-0.001-0.0010.0000.0000.0000.000
173A175TYR0-0.066-0.08138.9550.0000.0000.0000.0000.0000.000
174A176ASP-1-0.811-0.88641.680-0.084-0.0840.0000.0000.0000.000
175A177TRP0-0.013-0.00632.696-0.001-0.0010.0000.0000.0000.000
176A178LEU0-0.028-0.03135.4830.0020.0020.0000.0000.0000.000
177A179GLU-1-0.985-0.97639.236-0.071-0.0710.0000.0000.0000.000
178A180THR0-0.082-0.04840.7100.0040.0040.0000.0000.0000.000
179A181LEU0-0.060-0.02235.4520.0010.0010.0000.0000.0000.000
180A182GLU-1-0.920-0.95638.686-0.063-0.0630.0000.0000.0000.000
181A183GLN0-0.088-0.04835.7620.0060.0060.0000.0000.0000.000
182A184GLN0-0.0090.00336.424-0.003-0.0030.0000.0000.0000.000
183A185PRO00.0020.02433.6140.0030.0030.0000.0000.0000.000
184A186THR0-0.013-0.01534.8960.0040.0040.0000.0000.0000.000
185A187LEU00.0090.00735.501-0.007-0.0070.0000.0000.0000.000
186A188VAL0-0.040-0.02236.7270.0060.0060.0000.0000.0000.000
187A189ARG10.8930.93738.0790.0800.0800.0000.0000.0000.000
188A190MET0-0.053-0.02437.1260.0020.0020.0000.0000.0000.000
189A191PRO00.0690.03440.994-0.003-0.0030.0000.0000.0000.000
190A192ASP-1-0.906-0.95143.516-0.085-0.0850.0000.0000.0000.000
191A193THR0-0.087-0.03438.077-0.003-0.0030.0000.0000.0000.000
192A194SER00.0370.01038.361-0.003-0.0030.0000.0000.0000.000
193A195HIS10.8790.92431.8000.1670.1670.0000.0000.0000.000
194A196PHE0-0.008-0.01630.417-0.007-0.0070.0000.0000.0000.000
195A197PHE00.0280.00532.895-0.001-0.0010.0000.0000.0000.000
196A198HIS00.0300.01135.945-0.004-0.0040.0000.0000.0000.000
197A199ARG10.8640.92337.3950.1250.1250.0000.0000.0000.000
198A200LYS10.9670.98737.4040.1010.1010.0000.0000.0000.000
199A201LEU00.0080.01031.4630.0000.0000.0000.0000.0000.000
200A202ILE00.0050.00534.076-0.003-0.0030.0000.0000.0000.000
201A203ASP-1-0.809-0.91136.216-0.097-0.0970.0000.0000.0000.000
202A204LEU0-0.0080.00031.0500.0020.0020.0000.0000.0000.000
203A205ARG10.8490.90931.1060.1110.1110.0000.0000.0000.000
204A206GLY00.0200.01132.9960.0020.0020.0000.0000.0000.000
205A207ALA00.0080.00435.2750.0040.0040.0000.0000.0000.000
206A208LEU00.0000.00428.8810.0020.0020.0000.0000.0000.000
207A209GLN0-0.070-0.05230.2220.0090.0090.0000.0000.0000.000
208A210HIS0-0.064-0.03832.4160.0050.0050.0000.0000.0000.000
209A211GLY0-0.009-0.00633.9430.0050.0050.0000.0000.0000.000
210A212VAL00.0270.01828.5040.0020.0020.0000.0000.0000.000
211A213ARG10.9510.99230.9310.0830.0830.0000.0000.0000.000
212A214ARG10.9190.93532.4820.0570.0570.0000.0000.0000.000
213A215TRP00.0040.00229.3920.0040.0040.0000.0000.0000.000
214A216LEU0-0.046-0.00127.426-0.002-0.0020.0000.0000.0000.000
215A217PRO0-0.0020.00924.9010.0070.0070.0000.0000.0000.000
216A218ALA00.0100.01327.4620.0090.0090.0000.0000.0000.000
217A219THR0-0.021-0.01429.232-0.004-0.0040.0000.0000.0000.000
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