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: 9MGR2

Calculation Name: 3EDU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EDU

Chain ID: A

ChEMBL ID:

UniProt ID: P11277

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1807151.325708
FMO2-HF: Nuclear repulsion 1730896.367583
FMO2-HF: Total energy -76254.958125
FMO2-MP2: Total energy -76479.435644


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:1690:GLY)


Summations of interaction energy for fragment #1(A:1690:GLY)
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.
-6.321-3.5670.615-1.452-1.9190
Interaction energy analysis for fragmet #1(A:1690:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.011
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].
3A1692LEU00.0980.0363.810-1.216-0.283-0.005-0.514-0.4140.001
4A1693PHE0-0.0180.0036.5250.1680.1680.0000.0000.0000.000
5A1694GLN0-0.009-0.0132.523-1.428-0.5920.443-0.496-0.7840.002
6A1695LEU00.0390.0434.107-0.530-0.362-0.001-0.031-0.1360.000
7A1696LYS10.9180.9775.3640.6010.652-0.001-0.001-0.0500.000
8A1697ARG10.8150.9077.4730.0050.0050.0000.0000.0000.000
9A1698GLU-1-0.938-0.9805.984-1.452-1.4520.0000.0000.0000.000
10A1699THR00.009-0.0028.2070.0610.0610.0000.0000.0000.000
11A1700ASP-1-0.801-0.88610.923-0.062-0.0620.0000.0000.0000.000
12A1701ASP-1-0.925-0.97411.3830.0600.0600.0000.0000.0000.000
13A1702LEU0-0.070-0.03412.5620.0190.0190.0000.0000.0000.000
14A1703GLU-1-0.832-0.92614.265-0.251-0.2510.0000.0000.0000.000
15A1704GLN0-0.066-0.02316.3610.0270.0270.0000.0000.0000.000
16A1705TRP0-0.011-0.00516.6660.0100.0100.0000.0000.0000.000
17A1706ILE00.0260.01217.3900.0160.0160.0000.0000.0000.000
18A1707SER00.0780.02820.1190.0160.0160.0000.0000.0000.000
19A1708GLU-1-0.931-0.95320.118-0.039-0.0390.0000.0000.0000.000
20A1709LYS10.7670.86920.3580.0920.0920.0000.0000.0000.000
21A1710GLU-1-0.802-0.91123.060-0.112-0.1120.0000.0000.0000.000
22A1711LEU0-0.0230.00826.2680.0080.0080.0000.0000.0000.000
23A1712VAL0-0.071-0.03527.7820.0060.0060.0000.0000.0000.000
24A1713ALA0-0.029-0.02028.3900.0050.0050.0000.0000.0000.000
25A1714SER00.012-0.00829.8040.0010.0010.0000.0000.0000.000
26A1715SER0-0.050-0.00932.1750.0050.0050.0000.0000.0000.000
27A1716PRO00.0300.01034.597-0.002-0.0020.0000.0000.0000.000
28A1717GLU-1-0.861-0.91737.855-0.023-0.0230.0000.0000.0000.000
29A1718MET00.0180.01537.174-0.002-0.0020.0000.0000.0000.000
30A1719GLY0-0.0060.00041.1350.0000.0000.0000.0000.0000.000
31A1720GLN0-0.073-0.05443.6570.0000.0000.0000.0000.0000.000
32A1721ASP-1-0.836-0.91446.939-0.015-0.0150.0000.0000.0000.000
33A1722PHE00.0250.00246.892-0.002-0.0020.0000.0000.0000.000
34A1723ASP-1-0.909-0.93045.896-0.017-0.0170.0000.0000.0000.000
35A1724HIS00.0380.02241.866-0.002-0.0020.0000.0000.0000.000
36A1725VAL0-0.004-0.00642.298-0.002-0.0020.0000.0000.0000.000
37A1726THR0-0.032-0.02541.621-0.003-0.0030.0000.0000.0000.000
38A1727LEU0-0.014-0.01340.298-0.002-0.0020.0000.0000.0000.000
39A1728LEU0-0.070-0.02237.784-0.002-0.0020.0000.0000.0000.000
40A1729ARG10.8130.88536.7730.0300.0300.0000.0000.0000.000
41A1730ASP-1-0.814-0.87936.408-0.037-0.0370.0000.0000.0000.000
42A1731LYS10.9860.99332.6850.0200.0200.0000.0000.0000.000
43A1732PHE00.005-0.00231.050-0.002-0.0020.0000.0000.0000.000
44A1733ARG10.8890.93331.7070.0490.0490.0000.0000.0000.000
45A1734ASP-1-0.846-0.90830.968-0.043-0.0430.0000.0000.0000.000
46A1735PHE0-0.014-0.00726.352-0.004-0.0040.0000.0000.0000.000
47A1736ALA00.0240.01726.900-0.008-0.0080.0000.0000.0000.000
48A1737ARG10.7070.82526.7290.0420.0420.0000.0000.0000.000
49A1738GLU-1-0.826-0.89524.528-0.063-0.0630.0000.0000.0000.000
50A1739THR0-0.035-0.02322.579-0.010-0.0100.0000.0000.0000.000
51A1740GLY00.0290.01321.776-0.017-0.0170.0000.0000.0000.000
52A1741ALA0-0.028-0.01621.695-0.018-0.0180.0000.0000.0000.000
53A1742ILE0-0.010-0.01217.622-0.017-0.0170.0000.0000.0000.000
54A1743GLY00.0110.00217.050-0.025-0.0250.0000.0000.0000.000
55A1744GLN0-0.006-0.00416.930-0.020-0.0200.0000.0000.0000.000
56A1745GLU-1-0.951-0.96414.611-0.234-0.2340.0000.0000.0000.000
57A1746ARG10.8790.93411.7380.1800.1800.0000.0000.0000.000
58A1747VAL00.0550.03012.329-0.104-0.1040.0000.0000.0000.000
59A1748ASP-1-0.848-0.90314.084-0.361-0.3610.0000.0000.0000.000
60A1749ASN0-0.117-0.0689.919-0.079-0.0790.0000.0000.0000.000
61A1750VAL00.0370.0268.762-0.177-0.1770.0000.0000.0000.000
62A1751ASN0-0.001-0.00410.225-0.097-0.0970.0000.0000.0000.000
63A1752ALA00.0670.03611.517-0.038-0.0380.0000.0000.0000.000
64A1753PHE0-0.120-0.0743.019-0.7440.0220.179-0.410-0.535-0.003
65A1754ILE00.0270.0078.230-0.091-0.0910.0000.0000.0000.000
66A1755GLU-1-0.841-0.91910.189-0.400-0.4000.0000.0000.0000.000
67A1756ARG10.9490.9808.5780.7690.7690.0000.0000.0000.000
68A1757LEU0-0.057-0.0196.1710.0510.0510.0000.0000.0000.000
69A1758ILE0-0.011-0.00710.2310.0990.0990.0000.0000.0000.000
70A1759ASP-1-0.927-0.95813.928-0.356-0.3560.0000.0000.0000.000
71A1760ALA0-0.123-0.06111.7000.0590.0590.0000.0000.0000.000
72A1761GLY0-0.029-0.01113.7780.0280.0280.0000.0000.0000.000
73A1762HIS0-0.030-0.0089.6790.0610.0610.0000.0000.0000.000
74A1763SER0-0.032-0.04713.3060.0200.0200.0000.0000.0000.000
75A1764GLU-1-0.870-0.92211.820-0.336-0.3360.0000.0000.0000.000
76A1765ALA00.0010.00513.672-0.037-0.0370.0000.0000.0000.000
77A1766ALA0-0.004-0.00614.5740.0050.0050.0000.0000.0000.000
78A1767THR0-0.015-0.01814.0210.0250.0250.0000.0000.0000.000
79A1768ILE0-0.016-0.0119.737-0.030-0.0300.0000.0000.0000.000
80A1769ALA00.0100.00612.862-0.011-0.0110.0000.0000.0000.000
81A1770GLU-1-0.934-0.96315.826-0.240-0.2400.0000.0000.0000.000
82A1771TRP0-0.028-0.0288.997-0.029-0.0290.0000.0000.0000.000
83A1772LYS10.8000.90014.2060.4430.4430.0000.0000.0000.000
84A1773ASP-1-0.876-0.94614.935-0.301-0.3010.0000.0000.0000.000
85A1774GLY00.0250.02518.0050.0300.0300.0000.0000.0000.000
86A1775LEU00.0140.00413.1130.0230.0230.0000.0000.0000.000
87A1776ASN0-0.075-0.04616.9880.0210.0210.0000.0000.0000.000
88A1777GLU-1-0.979-0.97119.342-0.149-0.1490.0000.0000.0000.000
89A1778MET00.0520.02219.7680.0100.0100.0000.0000.0000.000
90A1779TRP0-0.065-0.03619.1290.0210.0210.0000.0000.0000.000
91A1780ALA0-0.012-0.00621.1960.0160.0160.0000.0000.0000.000
92A1781ASP-1-0.852-0.91724.501-0.116-0.1160.0000.0000.0000.000
93A1782LEU0-0.059-0.03221.9560.0150.0150.0000.0000.0000.000
94A1783LEU0-0.034-0.01823.5030.0150.0150.0000.0000.0000.000
95A1784GLU-1-0.919-0.95126.643-0.086-0.0860.0000.0000.0000.000
96A1785LEU0-0.0010.00527.8630.0110.0110.0000.0000.0000.000
97A1786ILE0-0.040-0.02825.9080.0110.0110.0000.0000.0000.000
98A1787ASP-1-0.889-0.92430.084-0.071-0.0710.0000.0000.0000.000
99A1788THR00.019-0.00532.5590.0080.0080.0000.0000.0000.000
100A1789ARG10.8200.89833.0340.0500.0500.0000.0000.0000.000
101A1790MET00.0010.01031.9900.0060.0060.0000.0000.0000.000
102A1791GLN0-0.058-0.04335.6300.0090.0090.0000.0000.0000.000
103A1792LEU0-0.010-0.00437.7480.0050.0050.0000.0000.0000.000
104A1793LEU0-0.007-0.00736.0320.0040.0040.0000.0000.0000.000
105A1794ALA0-0.034-0.00639.8340.0030.0030.0000.0000.0000.000
106A1795ALA00.0200.00241.6460.0030.0030.0000.0000.0000.000
107A1796SER0-0.031-0.02343.0620.0030.0030.0000.0000.0000.000
108A1797TYR00.006-0.00843.1500.0020.0020.0000.0000.0000.000
109A1798ASP-1-0.761-0.85345.071-0.030-0.0300.0000.0000.0000.000
110A1799LEU00.0140.01847.6160.0010.0010.0000.0000.0000.000
111A1800HIS0-0.031-0.02346.6690.0030.0030.0000.0000.0000.000
112A1801ARG10.8530.92648.7780.0290.0290.0000.0000.0000.000
113A1802TYR0-0.069-0.01950.6480.0010.0010.0000.0000.0000.000
114A1803PHE00.038-0.00552.4410.0010.0010.0000.0000.0000.000
115A1804TYR0-0.094-0.05653.0060.0010.0010.0000.0000.0000.000
116A1805THR0-0.016-0.04454.0350.0010.0010.0000.0000.0000.000
117A1806GLY00.0440.02056.4540.0010.0010.0000.0000.0000.000
118A1807ALA0-0.045-0.01758.4680.0010.0010.0000.0000.0000.000
119A1808GLU-1-0.904-0.92957.276-0.016-0.0160.0000.0000.0000.000
120A1809ILE00.0130.00159.5920.0010.0010.0000.0000.0000.000
121A1810LEU0-0.0100.00062.3620.0010.0010.0000.0000.0000.000
122A1811GLY0-0.0160.00063.6590.0010.0010.0000.0000.0000.000
123A1812LEU0-0.038-0.02161.8560.0010.0010.0000.0000.0000.000
124A1813ILE0-0.007-0.01465.8970.0000.0000.0000.0000.0000.000
125A1814ASP-1-0.876-0.92168.216-0.010-0.0100.0000.0000.0000.000
126A1815GLU-1-0.844-0.90768.743-0.009-0.0090.0000.0000.0000.000
127A1816LYS10.7480.85370.1530.0120.0120.0000.0000.0000.000
128A1817HIS0-0.0010.01072.0740.0000.0000.0000.0000.0000.000
129A1818ARG10.7260.82768.8820.0100.0100.0000.0000.0000.000
130A1819GLU-1-0.928-0.94273.628-0.009-0.0090.0000.0000.0000.000
131A1820LEU00.0180.00876.8750.0000.0000.0000.0000.0000.000
132A1821PRO0-0.075-0.03278.7640.0000.0000.0000.0000.0000.000
133A1835HIS00.1230.06081.3080.0000.0000.0000.0000.0000.000
134A1836ARG10.9000.92981.3360.0070.0070.0000.0000.0000.000
135A1837VAL00.0280.00576.5740.0000.0000.0000.0000.0000.000
136A1838HIS0-0.0210.00076.5870.0000.0000.0000.0000.0000.000
137A1839THR00.0500.01176.2510.0000.0000.0000.0000.0000.000
138A1840ALA0-0.073-0.03272.5220.0000.0000.0000.0000.0000.000
139A1841PHE00.0700.03572.027-0.001-0.0010.0000.0000.0000.000
140A1842GLU-1-0.856-0.91772.750-0.012-0.0120.0000.0000.0000.000
141A1843ARG10.8890.93369.7700.0120.0120.0000.0000.0000.000
142A1844GLU-1-0.864-0.91567.708-0.012-0.0120.0000.0000.0000.000
143A1845LEU00.0590.03667.945-0.001-0.0010.0000.0000.0000.000
144A1846HIS0-0.018-0.01267.8250.0000.0000.0000.0000.0000.000
145A1847LEU0-0.038-0.02262.142-0.001-0.0010.0000.0000.0000.000
146A1848LEU00.0470.02164.314-0.001-0.0010.0000.0000.0000.000
147A1849GLY00.0550.02865.0570.0000.0000.0000.0000.0000.000
148A1850VAL0-0.076-0.03561.468-0.001-0.0010.0000.0000.0000.000
149A1851GLN0-0.010-0.00759.336-0.001-0.0010.0000.0000.0000.000
150A1852VAL00.0120.00260.718-0.001-0.0010.0000.0000.0000.000
151A1853GLN0-0.045-0.02061.3100.0000.0000.0000.0000.0000.000
152A1854GLN0-0.035-0.02055.904-0.001-0.0010.0000.0000.0000.000
153A1855PHE00.0010.00457.317-0.001-0.0010.0000.0000.0000.000
154A1856GLN00.0370.00558.192-0.001-0.0010.0000.0000.0000.000
155A1857ASP-1-0.869-0.91157.024-0.026-0.0260.0000.0000.0000.000
156A1858VAL0-0.077-0.04152.801-0.002-0.0020.0000.0000.0000.000
157A1859ALA00.0480.02354.268-0.001-0.0010.0000.0000.0000.000
158A1860THR0-0.044-0.01956.0930.0000.0000.0000.0000.0000.000
159A1861ARG10.8460.89849.1310.0320.0320.0000.0000.0000.000
160A1862LEU0-0.0130.00449.641-0.002-0.0020.0000.0000.0000.000
161A1863GLN0-0.023-0.03151.8560.0000.0000.0000.0000.0000.000
162A1864THR0-0.109-0.05551.579-0.001-0.0010.0000.0000.0000.000
163A1865ALA0-0.0110.00047.539-0.002-0.0020.0000.0000.0000.000
164A1866TYR0-0.043-0.03346.889-0.001-0.0010.0000.0000.0000.000
165A1867ALA00.0430.01650.8650.0000.0000.0000.0000.0000.000
166A1868GLY0-0.015-0.01553.4120.0000.0000.0000.0000.0000.000
167A1869GLU-1-0.871-0.93754.459-0.019-0.0190.0000.0000.0000.000
168A1870LYS10.9260.97747.1240.0300.0300.0000.0000.0000.000
169A1871ALA0-0.0070.00953.6570.0000.0000.0000.0000.0000.000
170A1872GLU-1-0.783-0.88255.663-0.019-0.0190.0000.0000.0000.000
171A1873ALA0-0.0030.00855.7890.0010.0010.0000.0000.0000.000
172A1874ILE0-0.065-0.03052.5810.0010.0010.0000.0000.0000.000
173A1875GLN0-0.011-0.00457.0850.0000.0000.0000.0000.0000.000
174A1876ASN0-0.065-0.04760.4590.0010.0010.0000.0000.0000.000
175A1877LYS10.8130.88458.5890.0170.0170.0000.0000.0000.000
176A1878GLU-1-0.846-0.90360.257-0.019-0.0190.0000.0000.0000.000
177A1879GLN00.0170.01261.8400.0010.0010.0000.0000.0000.000
178A1880GLU-1-0.837-0.89563.480-0.014-0.0140.0000.0000.0000.000
179A1881VAL0-0.004-0.00161.9200.0010.0010.0000.0000.0000.000
180A1882SER0-0.034-0.04265.1060.0000.0000.0000.0000.0000.000
181A1883ALA0-0.0110.00067.1850.0000.0000.0000.0000.0000.000
182A1884ALA00.0080.00867.8640.0010.0010.0000.0000.0000.000
183A1885TRP00.0170.00767.6940.0010.0010.0000.0000.0000.000
184A1886GLN0-0.022-0.01569.7660.0000.0000.0000.0000.0000.000
185A1887ALA0-0.007-0.00672.7600.0000.0000.0000.0000.0000.000
186A1888LEU00.0200.01870.7430.0000.0000.0000.0000.0000.000
187A1889LEU0-0.028-0.02672.1100.0000.0000.0000.0000.0000.000
188A1890ASP-1-0.990-0.98275.370-0.011-0.0110.0000.0000.0000.000
189A1891ALA0-0.013-0.00477.4360.0000.0000.0000.0000.0000.000
190A1892CYS0-0.123-0.04976.5030.0000.0000.0000.0000.0000.000
191A1893ALA0-0.069-0.03079.0970.0000.0000.0000.0000.0000.000