FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JQ4J9

Calculation Name: 2EQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EQ5

Chain ID: A

ChEMBL ID:

UniProt ID: O58781

Base Structure: X-ray

Registration Date: 2023-09-22

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2451995.206721
FMO2-HF: Nuclear repulsion 2371353.401748
FMO2-HF: Total energy -80641.804973
FMO2-MP2: Total energy -80880.698158


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:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-120.506-113.33910.991-7.867-10.294-0.074
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.908 / q_NPA : 0.948
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].
3A5THR00.001-0.0053.382-5.332-2.7490.014-1.315-1.2830.003
4A6ILE0-0.011-0.0085.7873.3613.3610.0000.0000.0000.000
5A7GLY00.0530.0398.692-0.265-0.2650.0000.0000.0000.000
6A8LEU0-0.066-0.04212.0181.0701.0700.0000.0000.0000.000
7A9ILE00.0340.01213.9350.3980.3980.0000.0000.0000.000
8A10ARG10.8670.93817.61815.36315.3630.0000.0000.0000.000
9A11VAL00.034-0.00520.1670.2160.2160.0000.0000.0000.000
10A12ILE00.003-0.00823.2050.5090.5090.0000.0000.0000.000
11A13THR0-0.052-0.06823.505-0.367-0.3670.0000.0000.0000.000
12A14LEU0-0.053-0.03620.8230.1470.1470.0000.0000.0000.000
13A15GLU-1-0.860-0.93523.030-11.859-11.8590.0000.0000.0000.000
14A16ASP-1-0.879-0.93821.809-13.780-13.7800.0000.0000.0000.000
15A17LYS10.9990.98415.97816.62716.6270.0000.0000.0000.000
16A18GLU-1-0.916-0.94917.364-17.223-17.2230.0000.0000.0000.000
17A19ILE0-0.0040.00017.473-0.738-0.7380.0000.0000.0000.000
18A20LEU0-0.020-0.01317.089-0.442-0.4420.0000.0000.0000.000
19A21ASN0-0.070-0.06613.308-1.385-1.3850.0000.0000.0000.000
20A22LEU0-0.027-0.00413.700-1.496-1.4960.0000.0000.0000.000
21A23HIS00.001-0.02014.850-0.105-0.1050.0000.0000.0000.000
22A24GLY00.0710.02711.074-0.607-0.6070.0000.0000.0000.000
23A25ARG10.9800.9879.63618.34518.3450.0000.0000.0000.000
24A26ILE0-0.0130.00910.673-1.459-1.4590.0000.0000.0000.000
25A27ILE0-0.009-0.0058.916-0.305-0.3050.0000.0000.0000.000
26A28GLU-1-0.882-0.9385.893-38.893-38.8930.0000.0000.0000.000
27A29SER0-0.100-0.0366.645-3.159-3.1590.0000.0000.0000.000
28A30ALA00.0110.0068.828-0.742-0.7420.0000.0000.0000.000
29A31PHE0-0.041-0.0337.8910.6190.6190.0000.0000.0000.000
30A32PRO00.0660.0293.952-4.073-3.7840.000-0.073-0.2170.000
31A33GLU-1-0.914-0.9602.294-60.608-57.1423.208-2.877-3.797-0.036
32A34LEU0-0.038-0.0102.270-6.847-7.2577.691-3.291-3.990-0.040
33A35LYS10.9761.0132.99732.82234.0230.079-0.295-0.985-0.001
34A36VAL0-0.054-0.0254.4293.8173.855-0.001-0.016-0.0220.000
35A37VAL0-0.040-0.0128.1460.6180.6180.0000.0000.0000.000
36A38SER0-0.0020.00010.7510.9930.9930.0000.0000.0000.000
37A39ARG10.8460.89214.05417.76317.7630.0000.0000.0000.000
38A40CYS0-0.0330.02417.380-0.015-0.0150.0000.0000.0000.000
39A41ILE00.0080.03720.8630.0470.0470.0000.0000.0000.000
40A42GLU-1-0.823-0.89923.997-11.728-11.7280.0000.0000.0000.000
41A43ASP-1-0.904-0.96126.953-9.633-9.6330.0000.0000.0000.000
42A44GLN0-0.023-0.02328.1880.2770.2770.0000.0000.0000.000
43A45PRO00.0420.01428.259-0.347-0.3470.0000.0000.0000.000
44A46LYS10.9280.97029.1808.4628.4620.0000.0000.0000.000
45A47GLY00.0190.01527.963-0.016-0.0160.0000.0000.0000.000
46A48ILE0-0.036-0.01926.5160.2820.2820.0000.0000.0000.000
47A49TYR00.0210.01829.5920.0280.0280.0000.0000.0000.000
48A50ASN00.0410.03432.4330.1520.1520.0000.0000.0000.000
49A51GLU-1-0.897-0.96533.100-8.152-8.1520.0000.0000.0000.000
50A52GLU-1-0.912-0.95534.470-7.979-7.9790.0000.0000.0000.000
51A53THR00.0170.00131.596-0.238-0.2380.0000.0000.0000.000
52A54GLU-1-0.911-0.95728.872-10.453-10.4530.0000.0000.0000.000
53A55ARG10.9720.96030.1438.2308.2300.0000.0000.0000.000
54A56GLU-1-0.962-0.96231.453-9.121-9.1210.0000.0000.0000.000
55A57ALA00.006-0.01426.761-0.170-0.1700.0000.0000.0000.000
56A58GLU-1-0.879-0.92326.865-10.563-10.5630.0000.0000.0000.000
57A59PRO00.014-0.00126.639-0.392-0.3920.0000.0000.0000.000
58A60LYS10.7960.89425.8429.9199.9190.0000.0000.0000.000
59A61ILE00.0230.02321.616-0.531-0.5310.0000.0000.0000.000
60A62ILE0-0.021-0.01321.843-0.557-0.5570.0000.0000.0000.000
61A63ARG10.8730.95022.86410.83510.8350.0000.0000.0000.000
62A64LEU00.0410.01618.621-0.293-0.2930.0000.0000.0000.000
63A65ALA00.001-0.00217.904-0.690-0.6900.0000.0000.0000.000
64A66LYS10.9240.96117.88011.05911.0590.0000.0000.0000.000
65A67GLU-1-0.971-0.99518.001-14.534-14.5340.0000.0000.0000.000
66A68PHE00.0380.01613.484-0.525-0.5250.0000.0000.0000.000
67A69GLU-1-0.812-0.90914.157-15.774-15.7740.0000.0000.0000.000
68A70ARG10.9010.95215.88212.53512.5350.0000.0000.0000.000
69A71GLU-1-0.860-0.90214.063-17.697-17.6970.0000.0000.0000.000
70A72GLY0-0.030-0.00712.148-1.019-1.0190.0000.0000.0000.000
71A73VAL0-0.086-0.0189.640-1.733-1.7330.0000.0000.0000.000
72A74ASP-1-0.812-0.9206.709-30.551-30.5510.0000.0000.0000.000
73A75ALA0-0.010-0.04110.0981.5181.5180.0000.0000.0000.000
74A76ILE00.0010.02011.715-0.589-0.5890.0000.0000.0000.000
75A77ILE00.0310.01811.5530.1160.1160.0000.0000.0000.000
76A78ILE0-0.0030.00315.173-0.104-0.1040.0000.0000.0000.000
77A79SER00.0030.01017.0180.3600.3600.0000.0000.0000.000
78A80CYS0-0.010-0.00818.7880.4710.4710.0000.0000.0000.000
79A81ALA00.0440.01922.464-0.174-0.1740.0000.0000.0000.000
80A82ALA00.0330.01324.4530.2060.2060.0000.0000.0000.000
81A83ASP-1-0.791-0.88123.051-12.791-12.7910.0000.0000.0000.000
82A84PRO00.0190.01523.4420.2110.2110.0000.0000.0000.000
83A85ALA00.0930.03324.181-0.407-0.4070.0000.0000.0000.000
84A86VAL0-0.0130.00421.085-0.233-0.2330.0000.0000.0000.000
85A87GLU-1-0.953-0.98123.193-10.456-10.4560.0000.0000.0000.000
86A88LYS10.8360.91425.8099.8439.8430.0000.0000.0000.000
87A89VAL00.0720.01620.0870.0590.0590.0000.0000.0000.000
88A90ARG10.8670.94120.38013.10313.1030.0000.0000.0000.000
89A91LYS10.9090.95722.4619.7469.7460.0000.0000.0000.000
90A92LEU0-0.080-0.03323.6670.2740.2740.0000.0000.0000.000
91A93LEU0-0.0390.00517.8510.0330.0330.0000.0000.0000.000
92A94SER0-0.049-0.02519.2600.4860.4860.0000.0000.0000.000
93A95ILE0-0.0370.00113.947-0.483-0.4830.0000.0000.0000.000
94A96PRO0-0.064-0.03713.5100.8770.8770.0000.0000.0000.000
95A97VAL00.0280.02915.383-0.597-0.5970.0000.0000.0000.000
96A98ILE0-0.034-0.01913.8280.8840.8840.0000.0000.0000.000
97A99GLY00.0440.03217.077-0.012-0.0120.0000.0000.0000.000
98A100ALA00.0080.00019.249-0.134-0.1340.0000.0000.0000.000
99A101GLY00.0770.03420.0560.1110.1110.0000.0000.0000.000
100A102SER0-0.060-0.08522.3080.0930.0930.0000.0000.0000.000
101A103SER0-0.064-0.03918.398-0.234-0.2340.0000.0000.0000.000
102A104VAL0-0.0040.00220.446-0.103-0.1030.0000.0000.0000.000
103A105SER0-0.009-0.00122.3890.3010.3010.0000.0000.0000.000
104A106ALA00.0110.00122.0600.2920.2920.0000.0000.0000.000
105A107LEU0-0.027-0.02417.4630.0880.0880.0000.0000.0000.000
106A108ALA00.0390.03022.0900.0570.0570.0000.0000.0000.000
107A109LEU00.0050.00225.3350.3270.3270.0000.0000.0000.000
108A110ALA0-0.102-0.03322.9780.2870.2870.0000.0000.0000.000
109A111TYR0-0.058-0.03019.945-0.192-0.1920.0000.0000.0000.000
110A112GLY00.0240.01226.4960.3080.3080.0000.0000.0000.000
111A113ARG10.9430.96729.8288.9598.9590.0000.0000.0000.000
112A114ARG10.8760.95132.1788.6738.6730.0000.0000.0000.000
113A115VAL00.0550.03629.396-0.134-0.1340.0000.0000.0000.000
114A116GLY00.0120.01931.8580.3550.3550.0000.0000.0000.000
115A117VAL0-0.034-0.02429.996-0.410-0.4100.0000.0000.0000.000
116A118LEU0-0.0020.00429.9550.3290.3290.0000.0000.0000.000
117A119ASN00.001-0.01529.636-0.813-0.8130.0000.0000.0000.000
118A120LEU00.009-0.01430.0230.0590.0590.0000.0000.0000.000
119A121THR00.014-0.01531.9830.3050.3050.0000.0000.0000.000
120A122GLU-1-0.956-0.97130.298-9.967-9.9670.0000.0000.0000.000
121A123GLU-1-0.903-0.94634.086-8.390-8.3900.0000.0000.0000.000
122A124THR0-0.007-0.04131.446-0.403-0.4030.0000.0000.0000.000
123A125PRO0-0.0120.00428.4710.1940.1940.0000.0000.0000.000
124A126LYN00.1190.03929.441-0.019-0.0190.0000.0000.0000.000
125A127VAL0-0.0100.03725.8630.1340.1340.0000.0000.0000.000
126A128ILE00.012-0.00126.546-0.135-0.1350.0000.0000.0000.000
127A129ARG10.9150.95929.0638.8128.8120.0000.0000.0000.000
128A130SER0-0.091-0.07130.6330.2350.2350.0000.0000.0000.000
129A131ILE0-0.061-0.00325.2660.0840.0840.0000.0000.0000.000
130A132LEU0-0.0020.00628.4960.0030.0030.0000.0000.0000.000
131A133GLY00.0700.05431.2760.1900.1900.0000.0000.0000.000
132A134ASN0-0.090-0.05734.631-0.053-0.0530.0000.0000.0000.000
133A135ASN0-0.006-0.00932.5710.3030.3030.0000.0000.0000.000
134A136LEU0-0.0470.00233.065-0.221-0.2210.0000.0000.0000.000
135A137ILE0-0.050-0.02534.7910.2700.2700.0000.0000.0000.000
136A138ALA0-0.024-0.02536.1940.2730.2730.0000.0000.0000.000
137A139GLU-1-0.835-0.88735.116-8.975-8.9750.0000.0000.0000.000
138A140ASP-1-0.847-0.89934.908-7.944-7.9440.0000.0000.0000.000
139A141HIS0-0.006-0.00134.309-0.379-0.3790.0000.0000.0000.000
140A142PRO0-0.030-0.00332.9210.2180.2180.0000.0000.0000.000
141A143SER00.0200.00335.9340.0380.0380.0000.0000.0000.000
142A144GLY00.0420.01139.3670.0200.0200.0000.0000.0000.000
143A145VAL0-0.052-0.01633.161-0.024-0.0240.0000.0000.0000.000
144A146SER0-0.0020.00735.411-0.010-0.0100.0000.0000.0000.000
145A147ASN0-0.0060.00830.863-0.500-0.5000.0000.0000.0000.000
146A148THR00.0650.02725.992-0.055-0.0550.0000.0000.0000.000
147A149LEU0-0.014-0.02827.019-0.102-0.1020.0000.0000.0000.000
148A150ASP-1-0.797-0.90029.825-8.929-8.9290.0000.0000.0000.000
149A151LEU0-0.079-0.01428.3880.1970.1970.0000.0000.0000.000
150A152LEU0-0.028-0.01426.404-0.122-0.1220.0000.0000.0000.000
151A153THR0-0.057-0.04430.4010.2030.2030.0000.0000.0000.000
152A154ASP-1-0.845-0.93633.994-8.811-8.8110.0000.0000.0000.000
153A155TRP0-0.080-0.04036.1830.0550.0550.0000.0000.0000.000
154A156GLY00.0760.02734.8570.0420.0420.0000.0000.0000.000
155A157ARG10.9620.99529.20910.01210.0120.0000.0000.0000.000
156A158ARG10.9420.96133.1967.6027.6020.0000.0000.0000.000
157A159GLU-1-0.899-0.94135.836-7.957-7.9570.0000.0000.0000.000
158A160VAL0-0.006-0.00730.0880.0440.0440.0000.0000.0000.000
159A161ILE00.0320.00931.938-0.057-0.0570.0000.0000.0000.000
160A162ASN0-0.040-0.04133.6740.0330.0330.0000.0000.0000.000
161A163ALA00.0120.01734.4440.1510.1510.0000.0000.0000.000
162A164ALA00.0290.01931.926-0.005-0.0050.0000.0000.0000.000
163A165LYS10.8800.94333.6358.5988.5980.0000.0000.0000.000
164A166ARG10.8120.89336.5578.2778.2770.0000.0000.0000.000
165A167LEU00.0010.01132.9670.1410.1410.0000.0000.0000.000
166A168LYS10.9510.98434.1009.0339.0330.0000.0000.0000.000
167A169GLU-1-0.963-0.97836.152-7.338-7.3380.0000.0000.0000.000
168A170LYS10.8780.94838.8857.9427.9420.0000.0000.0000.000
169A171GLY0-0.001-0.00338.5830.0440.0440.0000.0000.0000.000
170A172VAL0-0.058-0.01533.054-0.057-0.0570.0000.0000.0000.000
171A173GLU-1-0.931-0.99632.216-9.251-9.2510.0000.0000.0000.000
172A174VAL0-0.0080.00426.616-0.276-0.2760.0000.0000.0000.000
173A175ILE0-0.0090.00228.4220.2950.2950.0000.0000.0000.000
174A176ALA00.0000.02226.024-0.528-0.5280.0000.0000.0000.000
175A177LEU0-0.008-0.01423.8670.4360.4360.0000.0000.0000.000
176A178GLY00.0380.01225.223-0.425-0.4250.0000.0000.0000.000
177A179CYS00.0120.00426.0870.0730.0730.0000.0000.0000.000
178A180THR00.013-0.00720.618-0.023-0.0230.0000.0000.0000.000
179A181GLY00.0270.01421.680-0.512-0.5120.0000.0000.0000.000
180A182MET0-0.009-0.01424.074-0.007-0.0070.0000.0000.0000.000
181A183SER0-0.006-0.02318.7890.1750.1750.0000.0000.0000.000
182A184THR0-0.083-0.03719.688-0.648-0.6480.0000.0000.0000.000
183A185ILE0-0.042-0.01220.751-0.189-0.1890.0000.0000.0000.000
184A186GLY00.0110.02221.2410.0940.0940.0000.0000.0000.000
185A187ILE00.017-0.00321.8980.2060.2060.0000.0000.0000.000
186A188ALA00.0390.01222.1600.3270.3270.0000.0000.0000.000
187A189PRO00.0250.01721.4020.3130.3130.0000.0000.0000.000
188A190VAL00.0030.01023.8350.3700.3700.0000.0000.0000.000
189A191LEU0-0.011-0.01327.1900.4470.4470.0000.0000.0000.000
190A192GLU-1-0.863-0.93524.385-12.402-12.4020.0000.0000.0000.000
191A193GLU-1-0.982-0.97727.512-10.630-10.6300.0000.0000.0000.000
192A194GLU-1-0.968-0.97728.885-8.736-8.7360.0000.0000.0000.000
193A195VAL0-0.079-0.06030.7320.3500.3500.0000.0000.0000.000
194A196GLY0-0.019-0.00530.3290.2240.2240.0000.0000.0000.000
195A197ILE0-0.086-0.04229.6280.1490.1490.0000.0000.0000.000
196A198PRO00.0340.01724.772-0.096-0.0960.0000.0000.0000.000
197A199VAL0-0.0150.01225.0110.4190.4190.0000.0000.0000.000
198A200ILE0-0.021-0.03021.285-0.623-0.6230.0000.0000.0000.000
199A201ASP-1-0.733-0.86118.617-15.778-15.7780.0000.0000.0000.000
200A202PRO00.022-0.00419.610-0.702-0.7020.0000.0000.0000.000
201A203VAL0-0.027-0.00614.860-0.482-0.4820.0000.0000.0000.000
202A204ILE00.0210.01314.198-1.288-1.2880.0000.0000.0000.000
203A205ALA00.0260.01414.945-1.008-1.0080.0000.0000.0000.000
204A206SER0-0.043-0.04415.175-0.540-0.5400.0000.0000.0000.000
205A207GLY00.0410.01911.717-0.657-0.6570.0000.0000.0000.000
206A208ALA00.0370.02311.359-1.371-1.3710.0000.0000.0000.000
207A209VAL0-0.043-0.01913.050-0.180-0.1800.0000.0000.0000.000
208A210ALA0-0.010-0.01310.7280.1170.1170.0000.0000.0000.000
209A211LEU00.0240.0086.758-0.764-0.7640.0000.0000.0000.000
210A212HIS00.0150.0159.666-0.451-0.4510.0000.0000.0000.000
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