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: 37QML

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1806565.132816
FMO2-HF: Nuclear repulsion 1730311.665425
FMO2-HF: Total energy -76253.467391
FMO2-MP2: Total energy -76478.203024


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.
-5.84-3.4630.108-1.196-1.2870.003
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 : 0.037 / q_NPA : 0.006
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].
3A1692LEU00.1250.0493.790-1.523-0.475-0.009-0.680-0.3600.002
4A1693PHE0-0.038-0.0086.4550.2320.2320.0000.0000.0000.000
5A1694GLN0-0.019-0.0233.174-0.889-0.2400.076-0.271-0.4530.002
6A1695LEU00.0730.0594.161-0.474-0.317-0.001-0.025-0.1300.000
7A1696LYS10.8420.9255.3280.5450.601-0.001-0.001-0.0540.000
8A1697ARG10.9200.9597.875-0.183-0.1830.0000.0000.0000.000
9A1698GLU-1-0.928-0.9615.526-1.353-1.3530.0000.0000.0000.000
10A1699THR0-0.014-0.0208.3680.0120.0120.0000.0000.0000.000
11A1700ASP-1-0.813-0.89510.688-0.098-0.0980.0000.0000.0000.000
12A1701ASP-1-0.946-0.98411.5960.1760.1760.0000.0000.0000.000
13A1702LEU0-0.078-0.03412.4640.0270.0270.0000.0000.0000.000
14A1703GLU-1-0.810-0.92214.142-0.256-0.2560.0000.0000.0000.000
15A1704GLN0-0.0170.00516.2210.0120.0120.0000.0000.0000.000
16A1705TRP0-0.071-0.04816.9090.0130.0130.0000.0000.0000.000
17A1706ILE0-0.014-0.01717.2850.0110.0110.0000.0000.0000.000
18A1707SER00.0360.02520.1030.0100.0100.0000.0000.0000.000
19A1708GLU-1-0.987-0.99721.1710.0060.0060.0000.0000.0000.000
20A1709LYS10.8640.93722.0080.0520.0520.0000.0000.0000.000
21A1710GLU-1-0.818-0.91923.911-0.102-0.1020.0000.0000.0000.000
22A1711LEU0-0.016-0.00226.2500.0060.0060.0000.0000.0000.000
23A1712VAL0-0.105-0.04627.4540.0060.0060.0000.0000.0000.000
24A1713ALA0-0.052-0.03628.1480.0030.0030.0000.0000.0000.000
25A1714SER00.0480.02929.871-0.001-0.0010.0000.0000.0000.000
26A1715SER0-0.100-0.03132.1020.0040.0040.0000.0000.0000.000
27A1716PRO00.0410.00434.654-0.002-0.0020.0000.0000.0000.000
28A1717GLU-1-0.867-0.92337.909-0.018-0.0180.0000.0000.0000.000
29A1718MET00.008-0.00337.729-0.002-0.0020.0000.0000.0000.000
30A1719GLY00.0120.00441.3910.0000.0000.0000.0000.0000.000
31A1720GLN0-0.047-0.03743.669-0.001-0.0010.0000.0000.0000.000
32A1721ASP-1-0.840-0.91746.901-0.010-0.0100.0000.0000.0000.000
33A1722PHE00.030-0.00346.811-0.001-0.0010.0000.0000.0000.000
34A1723ASP-1-0.903-0.91346.422-0.010-0.0100.0000.0000.0000.000
35A1724HIS00.0370.04441.515-0.001-0.0010.0000.0000.0000.000
36A1725VAL0-0.027-0.01742.238-0.001-0.0010.0000.0000.0000.000
37A1726THR0-0.042-0.04641.551-0.003-0.0030.0000.0000.0000.000
38A1727LEU0-0.008-0.00540.335-0.001-0.0010.0000.0000.0000.000
39A1728LEU0-0.076-0.03237.651-0.001-0.0010.0000.0000.0000.000
40A1729ARG10.8760.95936.7180.0250.0250.0000.0000.0000.000
41A1730ASP-1-0.871-0.94736.521-0.027-0.0270.0000.0000.0000.000
42A1731LYS10.9650.97932.7610.0100.0100.0000.0000.0000.000
43A1732PHE00.004-0.00430.635-0.001-0.0010.0000.0000.0000.000
44A1733ARG10.9010.94231.5020.0440.0440.0000.0000.0000.000
45A1734ASP-1-0.873-0.93230.767-0.032-0.0320.0000.0000.0000.000
46A1735PHE00.0130.00826.167-0.003-0.0030.0000.0000.0000.000
47A1736ALA00.0190.01626.815-0.007-0.0070.0000.0000.0000.000
48A1737ARG10.8580.94226.4500.0330.0330.0000.0000.0000.000
49A1738GLU-1-0.972-0.99224.621-0.036-0.0360.0000.0000.0000.000
50A1739THR0-0.024-0.03222.393-0.006-0.0060.0000.0000.0000.000
51A1740GLY00.0430.01821.498-0.016-0.0160.0000.0000.0000.000
52A1741ALA0-0.037-0.01721.339-0.019-0.0190.0000.0000.0000.000
53A1742ILE0-0.005-0.00817.554-0.015-0.0150.0000.0000.0000.000
54A1743GLY00.005-0.01116.983-0.023-0.0230.0000.0000.0000.000
55A1744GLN0-0.006-0.01016.734-0.011-0.0110.0000.0000.0000.000
56A1745GLU-1-0.941-0.95414.292-0.214-0.2140.0000.0000.0000.000
57A1746ARG10.8930.94712.4600.0860.0860.0000.0000.0000.000
58A1747VAL00.0530.03011.970-0.111-0.1110.0000.0000.0000.000
59A1748ASP-1-0.846-0.90113.362-0.400-0.4000.0000.0000.0000.000
60A1749ASN0-0.048-0.0219.337-0.078-0.0780.0000.0000.0000.000
61A1750VAL00.0100.0118.436-0.250-0.2500.0000.0000.0000.000
62A1751ASN0-0.043-0.0289.722-0.116-0.1160.0000.0000.0000.000
63A1752ALA00.0760.03411.089-0.034-0.0340.0000.0000.0000.000
64A1753PHE0-0.097-0.0623.357-0.572-0.1050.043-0.219-0.290-0.001
65A1754ILE00.0130.0068.251-0.111-0.1110.0000.0000.0000.000
66A1755GLU-1-0.873-0.95110.093-0.436-0.4360.0000.0000.0000.000
67A1756ARG10.9270.9818.4180.9330.9330.0000.0000.0000.000
68A1757LEU0-0.057-0.0216.0860.0990.0990.0000.0000.0000.000
69A1758ILE0-0.010-0.01110.0090.1180.1180.0000.0000.0000.000
70A1759ASP-1-0.910-0.94013.581-0.387-0.3870.0000.0000.0000.000
71A1760ALA0-0.147-0.07211.6640.0700.0700.0000.0000.0000.000
72A1761GLY0-0.025-0.01513.7510.0350.0350.0000.0000.0000.000
73A1762HIS0-0.031-0.0049.0650.1030.1030.0000.0000.0000.000
74A1763SER0-0.004-0.01512.9130.0270.0270.0000.0000.0000.000
75A1764GLU-1-0.943-0.98612.105-0.364-0.3640.0000.0000.0000.000
76A1765ALA00.009-0.00413.763-0.034-0.0340.0000.0000.0000.000
77A1766ALA0-0.006-0.00114.7040.0020.0020.0000.0000.0000.000
78A1767THR00.0300.01512.9400.0370.0370.0000.0000.0000.000
79A1768ILE0-0.049-0.0199.787-0.026-0.0260.0000.0000.0000.000
80A1769ALA00.0250.00812.674-0.013-0.0130.0000.0000.0000.000
81A1770GLU-1-0.923-0.93815.608-0.251-0.2510.0000.0000.0000.000
82A1771TRP0-0.020-0.0328.462-0.028-0.0280.0000.0000.0000.000
83A1772LYS10.9040.96613.4620.4770.4770.0000.0000.0000.000
84A1773ASP-1-0.960-0.98314.538-0.301-0.3010.0000.0000.0000.000
85A1774GLY00.0310.02317.6340.0300.0300.0000.0000.0000.000
86A1775LEU00.0300.01912.7760.0220.0220.0000.0000.0000.000
87A1776ASN0-0.084-0.07316.5180.0260.0260.0000.0000.0000.000
88A1777GLU-1-0.961-0.96818.743-0.152-0.1520.0000.0000.0000.000
89A1778MET00.0510.03519.2350.0160.0160.0000.0000.0000.000
90A1779TRP0-0.078-0.03818.7210.0270.0270.0000.0000.0000.000
91A1780ALA0-0.010-0.01120.7550.0180.0180.0000.0000.0000.000
92A1781ASP-1-0.822-0.89823.879-0.122-0.1220.0000.0000.0000.000
93A1782LEU0-0.049-0.03321.8810.0170.0170.0000.0000.0000.000
94A1783LEU0-0.050-0.03723.0570.0170.0170.0000.0000.0000.000
95A1784GLU-1-0.927-0.94926.208-0.088-0.0880.0000.0000.0000.000
96A1785LEU00.0150.00127.5180.0120.0120.0000.0000.0000.000
97A1786ILE0-0.064-0.04025.6870.0120.0120.0000.0000.0000.000
98A1787ASP-1-0.913-0.93729.862-0.069-0.0690.0000.0000.0000.000
99A1788THR00.0470.01532.1110.0080.0080.0000.0000.0000.000
100A1789ARG10.8660.93932.8880.0430.0430.0000.0000.0000.000
101A1790MET0-0.033-0.00731.6150.0060.0060.0000.0000.0000.000
102A1791GLN0-0.045-0.02735.2600.0080.0080.0000.0000.0000.000
103A1792LEU0-0.008-0.00437.5780.0050.0050.0000.0000.0000.000
104A1793LEU0-0.004-0.01235.9250.0040.0040.0000.0000.0000.000
105A1794ALA0-0.037-0.00639.6020.0030.0030.0000.0000.0000.000
106A1795ALA00.0270.01841.3750.0020.0020.0000.0000.0000.000
107A1796SER0-0.032-0.04342.8230.0030.0030.0000.0000.0000.000
108A1797TYR0-0.005-0.00242.9630.0020.0020.0000.0000.0000.000
109A1798ASP-1-0.886-0.96444.897-0.030-0.0300.0000.0000.0000.000
110A1799LEU0-0.035-0.00547.3760.0020.0020.0000.0000.0000.000
111A1800HIS0-0.008-0.01446.3600.0030.0030.0000.0000.0000.000
112A1801ARG10.9020.98048.5730.0260.0260.0000.0000.0000.000
113A1802TYR0-0.077-0.04750.5040.0010.0010.0000.0000.0000.000
114A1803PHE00.0430.00152.5390.0010.0010.0000.0000.0000.000
115A1804TYR0-0.029-0.00452.6190.0010.0010.0000.0000.0000.000
116A1805THR0-0.004-0.01754.0240.0010.0010.0000.0000.0000.000
117A1806GLY00.0360.02156.3210.0010.0010.0000.0000.0000.000
118A1807ALA0-0.032-0.01058.3110.0010.0010.0000.0000.0000.000
119A1808GLU-1-0.940-0.96457.008-0.012-0.0120.0000.0000.0000.000
120A1809ILE0-0.004-0.02059.6320.0010.0010.0000.0000.0000.000
121A1810LEU0-0.042-0.01362.2760.0000.0000.0000.0000.0000.000
122A1811GLY00.0060.00463.5690.0010.0010.0000.0000.0000.000
123A1812LEU0-0.036-0.02261.5450.0010.0010.0000.0000.0000.000
124A1813ILE0-0.017-0.01265.7380.0000.0000.0000.0000.0000.000
125A1814ASP-1-0.909-0.94568.106-0.008-0.0080.0000.0000.0000.000
126A1815GLU-1-0.897-0.95968.404-0.006-0.0060.0000.0000.0000.000
127A1816LYS10.8410.95469.5710.0100.0100.0000.0000.0000.000
128A1817HIS0-0.023-0.01171.8750.0000.0000.0000.0000.0000.000
129A1818ARG10.7880.88569.1630.0070.0070.0000.0000.0000.000
130A1819GLU-1-0.960-0.96472.900-0.008-0.0080.0000.0000.0000.000
131A1820LEU00.0070.01276.8310.0000.0000.0000.0000.0000.000
132A1821PRO0-0.073-0.03678.7900.0000.0000.0000.0000.0000.000
133A1835HIS00.0850.03381.1560.0000.0000.0000.0000.0000.000
134A1836ARG10.9260.94681.1170.0050.0050.0000.0000.0000.000
135A1837VAL00.0140.00776.1760.0000.0000.0000.0000.0000.000
136A1838HIS00.0190.01376.5350.0000.0000.0000.0000.0000.000
137A1839THR00.015-0.00175.9070.0000.0000.0000.0000.0000.000
138A1840ALA0-0.058-0.02972.4070.0000.0000.0000.0000.0000.000
139A1841PHE00.0980.04271.7840.0000.0000.0000.0000.0000.000
140A1842GLU-1-0.886-0.93972.840-0.011-0.0110.0000.0000.0000.000
141A1843ARG10.9170.94169.3660.0100.0100.0000.0000.0000.000
142A1844GLU-1-0.926-0.94467.689-0.010-0.0100.0000.0000.0000.000
143A1845LEU00.0320.00867.812-0.001-0.0010.0000.0000.0000.000
144A1846HIS00.021-0.00367.4730.0000.0000.0000.0000.0000.000
145A1847LEU0-0.026-0.01061.901-0.001-0.0010.0000.0000.0000.000
146A1848LEU00.0610.03463.838-0.001-0.0010.0000.0000.0000.000
147A1849GLY00.0440.03164.672-0.001-0.0010.0000.0000.0000.000
148A1850VAL0-0.040-0.02761.296-0.001-0.0010.0000.0000.0000.000
149A1851GLN00.0250.01159.459-0.001-0.0010.0000.0000.0000.000
150A1852VAL0-0.030-0.01860.5460.0000.0000.0000.0000.0000.000
151A1853GLN0-0.046-0.00861.4540.0000.0000.0000.0000.0000.000
152A1854GLN0-0.0060.00154.833-0.001-0.0010.0000.0000.0000.000
153A1855PHE0-0.036-0.02256.803-0.001-0.0010.0000.0000.0000.000
154A1856GLN00.021-0.00457.943-0.001-0.0010.0000.0000.0000.000
155A1857ASP-1-0.862-0.91956.816-0.024-0.0240.0000.0000.0000.000
156A1858VAL0-0.130-0.06852.418-0.002-0.0020.0000.0000.0000.000
157A1859ALA00.0530.02454.144-0.001-0.0010.0000.0000.0000.000
158A1860THR0-0.044-0.00755.927-0.001-0.0010.0000.0000.0000.000
159A1861ARG10.9460.97348.5140.0300.0300.0000.0000.0000.000
160A1862LEU0-0.029-0.01549.617-0.002-0.0020.0000.0000.0000.000
161A1863GLN00.013-0.00651.5490.0000.0000.0000.0000.0000.000
162A1864THR0-0.101-0.04051.219-0.001-0.0010.0000.0000.0000.000
163A1865ALA0-0.011-0.00747.521-0.002-0.0020.0000.0000.0000.000
164A1866TYR0-0.040-0.02747.240-0.001-0.0010.0000.0000.0000.000
165A1867ALA00.0550.01950.9910.0000.0000.0000.0000.0000.000
166A1868GLY0-0.028-0.02353.6040.0000.0000.0000.0000.0000.000
167A1869GLU-1-0.861-0.93554.643-0.017-0.0170.0000.0000.0000.000
168A1870LYS10.9330.97247.0830.0260.0260.0000.0000.0000.000
169A1871ALA00.0030.00953.6100.0000.0000.0000.0000.0000.000
170A1872GLU-1-0.858-0.92655.331-0.018-0.0180.0000.0000.0000.000
171A1873ALA0-0.019-0.00455.5480.0010.0010.0000.0000.0000.000
172A1874ILE0-0.056-0.03852.2720.0010.0010.0000.0000.0000.000
173A1875GLN00.0000.02056.7380.0000.0000.0000.0000.0000.000
174A1876ASN00.0250.01660.0140.0010.0010.0000.0000.0000.000
175A1877LYS10.8500.94058.4080.0150.0150.0000.0000.0000.000
176A1878GLU-1-0.805-0.88759.898-0.017-0.0170.0000.0000.0000.000
177A1879GLN00.0360.01261.5840.0010.0010.0000.0000.0000.000
178A1880GLU-1-0.936-0.95963.708-0.012-0.0120.0000.0000.0000.000
179A1881VAL0-0.003-0.01061.6700.0010.0010.0000.0000.0000.000
180A1882SER0-0.048-0.06264.8960.0000.0000.0000.0000.0000.000
181A1883ALA0-0.0030.00466.9260.0000.0000.0000.0000.0000.000
182A1884ALA00.0000.00967.6400.0010.0010.0000.0000.0000.000
183A1885TRP00.0150.00167.5650.0010.0010.0000.0000.0000.000
184A1886GLN0-0.018-0.01269.6050.0000.0000.0000.0000.0000.000
185A1887ALA00.000-0.00472.3930.0000.0000.0000.0000.0000.000
186A1888LEU00.0050.01770.7070.0000.0000.0000.0000.0000.000
187A1889LEU0-0.069-0.05571.5720.0000.0000.0000.0000.0000.000
188A1890ASP-1-1.002-0.98275.046-0.010-0.0100.0000.0000.0000.000
189A1891ALA00.0330.02177.1770.0000.0000.0000.0000.0000.000
190A1892CYS0-0.129-0.04277.0430.0000.0000.0000.0000.0000.000
191A1893ALA0-0.045-0.02979.0450.0000.0000.0000.0000.0000.000