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: L7JV9

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1804995.367731
FMO2-HF: Nuclear repulsion 1728740.869936
FMO2-HF: Total energy -76254.497794
FMO2-MP2: Total energy -76479.160032


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.
-5.938-3.2910.157-1.358-1.4470.002
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 : 0.033 / q_NPA : 0.007
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].
3A1692LEU00.1260.0473.799-1.356-0.290-0.010-0.692-0.3650.003
4A1693PHE0-0.025-0.0026.5000.1910.1910.0000.0000.0000.000
5A1694GLN0-0.024-0.0253.164-0.935-0.2500.086-0.304-0.4670.002
6A1695LEU00.0680.0604.213-0.499-0.347-0.001-0.024-0.1270.000
7A1696LYS10.8360.9225.3560.4400.494-0.001-0.001-0.0520.000
8A1697ARG10.9240.9667.998-0.243-0.2430.0000.0000.0000.000
9A1698GLU-1-0.940-0.9705.628-1.321-1.3210.0000.0000.0000.000
10A1699THR0-0.012-0.0288.385-0.024-0.0240.0000.0000.0000.000
11A1700ASP-1-0.822-0.89010.702-0.057-0.0570.0000.0000.0000.000
12A1701ASP-1-0.930-0.98311.6930.2210.2210.0000.0000.0000.000
13A1702LEU0-0.086-0.03412.4050.0210.0210.0000.0000.0000.000
14A1703GLU-1-0.804-0.91514.146-0.231-0.2310.0000.0000.0000.000
15A1704GLN0-0.059-0.02316.2350.0150.0150.0000.0000.0000.000
16A1705TRP0-0.041-0.03516.9280.0070.0070.0000.0000.0000.000
17A1706ILE00.008-0.00717.2380.0100.0100.0000.0000.0000.000
18A1707SER00.0570.02920.1050.0080.0080.0000.0000.0000.000
19A1708GLU-1-0.950-0.97520.7380.0140.0140.0000.0000.0000.000
20A1709LYS10.7890.90521.0480.0400.0400.0000.0000.0000.000
21A1710GLU-1-0.802-0.91023.392-0.090-0.0900.0000.0000.0000.000
22A1711LEU0-0.0260.00626.2520.0050.0050.0000.0000.0000.000
23A1712VAL0-0.086-0.04027.5420.0040.0040.0000.0000.0000.000
24A1713ALA0-0.048-0.03328.0880.0030.0030.0000.0000.0000.000
25A1714SER00.0400.01129.761-0.002-0.0020.0000.0000.0000.000
26A1715SER0-0.070-0.02032.1030.0040.0040.0000.0000.0000.000
27A1716PRO00.0350.01534.655-0.003-0.0030.0000.0000.0000.000
28A1717GLU-1-0.862-0.91337.922-0.014-0.0140.0000.0000.0000.000
29A1718MET00.0140.01037.506-0.002-0.0020.0000.0000.0000.000
30A1719GLY0-0.003-0.00441.384-0.001-0.0010.0000.0000.0000.000
31A1720GLN0-0.073-0.06143.663-0.001-0.0010.0000.0000.0000.000
32A1721ASP-1-0.825-0.90646.900-0.008-0.0080.0000.0000.0000.000
33A1722PHE00.0330.00046.800-0.001-0.0010.0000.0000.0000.000
34A1723ASP-1-0.910-0.92446.253-0.008-0.0080.0000.0000.0000.000
35A1724HIS00.0410.03141.513-0.001-0.0010.0000.0000.0000.000
36A1725VAL0-0.020-0.01342.165-0.001-0.0010.0000.0000.0000.000
37A1726THR0-0.015-0.02741.535-0.003-0.0030.0000.0000.0000.000
38A1727LEU0-0.022-0.01040.421-0.001-0.0010.0000.0000.0000.000
39A1728LEU0-0.078-0.02937.816-0.001-0.0010.0000.0000.0000.000
40A1729ARG10.8150.90036.7040.0220.0220.0000.0000.0000.000
41A1730ASP-1-0.823-0.89736.501-0.026-0.0260.0000.0000.0000.000
42A1731LYS10.9690.98732.4830.0050.0050.0000.0000.0000.000
43A1732PHE00.004-0.00730.666-0.001-0.0010.0000.0000.0000.000
44A1733ARG10.8880.93631.4830.0410.0410.0000.0000.0000.000
45A1734ASP-1-0.815-0.88930.773-0.030-0.0300.0000.0000.0000.000
46A1735PHE0-0.0050.00226.112-0.003-0.0030.0000.0000.0000.000
47A1736ALA00.0140.00526.795-0.006-0.0060.0000.0000.0000.000
48A1737ARG10.7520.86326.4250.0270.0270.0000.0000.0000.000
49A1738GLU-1-0.897-0.94824.647-0.033-0.0330.0000.0000.0000.000
50A1739THR0-0.019-0.01622.361-0.006-0.0060.0000.0000.0000.000
51A1740GLY00.0440.01621.475-0.015-0.0150.0000.0000.0000.000
52A1741ALA0-0.043-0.01921.309-0.019-0.0190.0000.0000.0000.000
53A1742ILE0-0.006-0.01117.561-0.015-0.0150.0000.0000.0000.000
54A1743GLY00.009-0.00716.955-0.022-0.0220.0000.0000.0000.000
55A1744GLN0-0.0050.00016.709-0.015-0.0150.0000.0000.0000.000
56A1745GLU-1-0.936-0.95514.235-0.210-0.2100.0000.0000.0000.000
57A1746ARG10.9340.96912.2110.0670.0670.0000.0000.0000.000
58A1747VAL00.0620.03511.943-0.106-0.1060.0000.0000.0000.000
59A1748ASP-1-0.856-0.90513.333-0.393-0.3930.0000.0000.0000.000
60A1749ASN0-0.108-0.0599.312-0.123-0.1230.0000.0000.0000.000
61A1750VAL00.0280.0218.460-0.244-0.2440.0000.0000.0000.000
62A1751ASN0-0.006-0.0149.696-0.128-0.1280.0000.0000.0000.000
63A1752ALA00.0450.01911.140-0.032-0.0320.0000.0000.0000.000
64A1753PHE0-0.090-0.0543.217-0.6800.0100.083-0.337-0.436-0.003
65A1754ILE00.0280.0148.252-0.112-0.1120.0000.0000.0000.000
66A1755GLU-1-0.829-0.91910.094-0.417-0.4170.0000.0000.0000.000
67A1756ARG10.9320.9768.3930.9350.9350.0000.0000.0000.000
68A1757LEU0-0.058-0.0216.0440.1020.1020.0000.0000.0000.000
69A1758ILE0-0.011-0.01110.0090.1180.1180.0000.0000.0000.000
70A1759ASP-1-0.910-0.94213.581-0.381-0.3810.0000.0000.0000.000
71A1760ALA0-0.149-0.07111.6310.0690.0690.0000.0000.0000.000
72A1761GLY0-0.024-0.01413.7500.0350.0350.0000.0000.0000.000
73A1762HIS0-0.042-0.0159.2360.0670.0670.0000.0000.0000.000
74A1763SER0-0.026-0.04612.9130.0240.0240.0000.0000.0000.000
75A1764GLU-1-0.907-0.94212.085-0.345-0.3450.0000.0000.0000.000
76A1765ALA00.009-0.00213.765-0.031-0.0310.0000.0000.0000.000
77A1766ALA0-0.008-0.00414.7050.0030.0030.0000.0000.0000.000
78A1767THR00.0200.00713.5620.0350.0350.0000.0000.0000.000
79A1768ILE0-0.022-0.0099.764-0.027-0.0270.0000.0000.0000.000
80A1769ALA00.0260.01112.687-0.011-0.0110.0000.0000.0000.000
81A1770GLU-1-0.920-0.94415.611-0.238-0.2380.0000.0000.0000.000
82A1771TRP0-0.039-0.0368.591-0.023-0.0230.0000.0000.0000.000
83A1772LYS10.8130.91313.4610.4840.4840.0000.0000.0000.000
84A1773ASP-1-0.939-0.97614.536-0.288-0.2880.0000.0000.0000.000
85A1774GLY00.0310.02517.6380.0290.0290.0000.0000.0000.000
86A1775LEU00.0220.01212.6710.0220.0220.0000.0000.0000.000
87A1776ASN0-0.074-0.05916.5190.0290.0290.0000.0000.0000.000
88A1777GLU-1-0.962-0.97018.734-0.143-0.1430.0000.0000.0000.000
89A1778MET00.0530.03019.2290.0170.0170.0000.0000.0000.000
90A1779TRP0-0.064-0.03418.6760.0270.0270.0000.0000.0000.000
91A1780ALA0-0.010-0.00720.7450.0170.0170.0000.0000.0000.000
92A1781ASP-1-0.843-0.91123.867-0.106-0.1060.0000.0000.0000.000
93A1782LEU0-0.065-0.03621.7750.0160.0160.0000.0000.0000.000
94A1783LEU0-0.046-0.03322.9390.0150.0150.0000.0000.0000.000
95A1784GLU-1-0.926-0.94926.192-0.081-0.0810.0000.0000.0000.000
96A1785LEU00.0170.00927.7090.0110.0110.0000.0000.0000.000
97A1786ILE0-0.049-0.03225.7350.0110.0110.0000.0000.0000.000
98A1787ASP-1-0.901-0.92929.848-0.065-0.0650.0000.0000.0000.000
99A1788THR00.024-0.00332.0930.0070.0070.0000.0000.0000.000
100A1789ARG10.8390.90832.9040.0380.0380.0000.0000.0000.000
101A1790MET0-0.0060.00831.5900.0060.0060.0000.0000.0000.000
102A1791GLN0-0.044-0.02835.2420.0080.0080.0000.0000.0000.000
103A1792LEU0-0.011-0.00537.4740.0040.0040.0000.0000.0000.000
104A1793LEU0-0.008-0.01135.8720.0040.0040.0000.0000.0000.000
105A1794ALA0-0.026-0.00239.5770.0030.0030.0000.0000.0000.000
106A1795ALA00.0090.00441.3560.0020.0020.0000.0000.0000.000
107A1796SER0-0.028-0.03042.8850.0030.0030.0000.0000.0000.000
108A1797TYR0-0.003-0.00642.9220.0020.0020.0000.0000.0000.000
109A1798ASP-1-0.753-0.86344.879-0.026-0.0260.0000.0000.0000.000
110A1799LEU0-0.0160.00647.3620.0010.0010.0000.0000.0000.000
111A1800HIS0-0.017-0.02146.4330.0030.0030.0000.0000.0000.000
112A1801ARG10.8590.93648.6690.0240.0240.0000.0000.0000.000
113A1802TYR0-0.062-0.03150.4850.0010.0010.0000.0000.0000.000
114A1803PHE00.0360.00252.4280.0010.0010.0000.0000.0000.000
115A1804TYR0-0.086-0.04552.6810.0010.0010.0000.0000.0000.000
116A1805THR0-0.015-0.03553.9350.0000.0000.0000.0000.0000.000
117A1806GLY00.0400.01956.3000.0010.0010.0000.0000.0000.000
118A1807ALA0-0.043-0.01458.2970.0010.0010.0000.0000.0000.000
119A1808GLU-1-0.885-0.92657.055-0.011-0.0110.0000.0000.0000.000
120A1809ILE00.000-0.01659.4990.0000.0000.0000.0000.0000.000
121A1810LEU0-0.042-0.01262.1670.0000.0000.0000.0000.0000.000
122A1811GLY0-0.007-0.00363.5510.0010.0010.0000.0000.0000.000
123A1812LEU0-0.031-0.01961.6010.0000.0000.0000.0000.0000.000
124A1813ILE0-0.005-0.00865.7150.0000.0000.0000.0000.0000.000
125A1814ASP-1-0.868-0.91668.086-0.007-0.0070.0000.0000.0000.000
126A1815GLU-1-0.882-0.93168.434-0.005-0.0050.0000.0000.0000.000
127A1816LYS10.7690.86769.8540.0090.0090.0000.0000.0000.000
128A1817HIS0-0.009-0.00271.8510.0000.0000.0000.0000.0000.000
129A1818ARG10.7500.83769.1050.0070.0070.0000.0000.0000.000
130A1819GLU-1-0.919-0.94073.416-0.007-0.0070.0000.0000.0000.000
131A1820LEU00.0130.01676.8070.0000.0000.0000.0000.0000.000
132A1821PRO0-0.073-0.03678.7910.0000.0000.0000.0000.0000.000
133A1835HIS00.1060.05881.1280.0000.0000.0000.0000.0000.000
134A1836ARG10.9020.92181.1280.0050.0050.0000.0000.0000.000
135A1837VAL00.0090.00176.1190.0000.0000.0000.0000.0000.000
136A1838HIS00.0260.01676.5030.0000.0000.0000.0000.0000.000
137A1839THR00.0340.01375.9060.0000.0000.0000.0000.0000.000
138A1840ALA0-0.062-0.03472.4070.0000.0000.0000.0000.0000.000
139A1841PHE00.0620.02971.7530.0000.0000.0000.0000.0000.000
140A1842GLU-1-0.892-0.94072.810-0.010-0.0100.0000.0000.0000.000
141A1843ARG10.8940.93569.3360.0090.0090.0000.0000.0000.000
142A1844GLU-1-0.879-0.90867.442-0.009-0.0090.0000.0000.0000.000
143A1845LEU00.0590.03067.782-0.001-0.0010.0000.0000.0000.000
144A1846HIS0-0.003-0.00567.3980.0000.0000.0000.0000.0000.000
145A1847LEU0-0.019-0.00861.795-0.001-0.0010.0000.0000.0000.000
146A1848LEU00.0630.03563.883-0.001-0.0010.0000.0000.0000.000
147A1849GLY00.0560.03364.645-0.001-0.0010.0000.0000.0000.000
148A1850VAL0-0.054-0.03461.313-0.001-0.0010.0000.0000.0000.000
149A1851GLN00.0110.00459.102-0.001-0.0010.0000.0000.0000.000
150A1852VAL0-0.023-0.01360.5200.0000.0000.0000.0000.0000.000
151A1853GLN0-0.053-0.02161.0700.0000.0000.0000.0000.0000.000
152A1854GLN0-0.044-0.02255.726-0.001-0.0010.0000.0000.0000.000
153A1855PHE0-0.012-0.00156.966-0.001-0.0010.0000.0000.0000.000
154A1856GLN00.026-0.00457.922-0.001-0.0010.0000.0000.0000.000
155A1857ASP-1-0.863-0.91056.796-0.023-0.0230.0000.0000.0000.000
156A1858VAL0-0.098-0.05252.371-0.001-0.0010.0000.0000.0000.000
157A1859ALA00.0420.02254.124-0.001-0.0010.0000.0000.0000.000
158A1860THR0-0.048-0.02055.909-0.001-0.0010.0000.0000.0000.000
159A1861ARG10.8540.91748.4530.0280.0280.0000.0000.0000.000
160A1862LEU0-0.014-0.00449.584-0.001-0.0010.0000.0000.0000.000
161A1863GLN0-0.004-0.01051.5340.0000.0000.0000.0000.0000.000
162A1864THR0-0.100-0.04851.410-0.001-0.0010.0000.0000.0000.000
163A1865ALA0-0.024-0.01347.498-0.002-0.0020.0000.0000.0000.000
164A1866TYR0-0.042-0.02846.9860.0000.0000.0000.0000.0000.000
165A1867ALA00.0570.02050.9820.0000.0000.0000.0000.0000.000
166A1868GLY0-0.025-0.02153.5980.0000.0000.0000.0000.0000.000
167A1869GLU-1-0.860-0.93854.600-0.015-0.0150.0000.0000.0000.000
168A1870LYS10.9380.97947.1400.0230.0230.0000.0000.0000.000
169A1871ALA0-0.0020.00853.6040.0000.0000.0000.0000.0000.000
170A1872GLU-1-0.783-0.88655.322-0.016-0.0160.0000.0000.0000.000
171A1873ALA0-0.0040.01155.5590.0010.0010.0000.0000.0000.000
172A1874ILE0-0.059-0.03252.2250.0000.0000.0000.0000.0000.000
173A1875GLN0-0.0130.00456.7250.0000.0000.0000.0000.0000.000
174A1876ASN0-0.063-0.04260.0010.0010.0010.0000.0000.0000.000
175A1877LYS10.8160.89758.5040.0130.0130.0000.0000.0000.000
176A1878GLU-1-0.851-0.91459.903-0.016-0.0160.0000.0000.0000.000
177A1879GLN00.0160.00861.5680.0010.0010.0000.0000.0000.000
178A1880GLU-1-0.843-0.89663.547-0.011-0.0110.0000.0000.0000.000
179A1881VAL0-0.007-0.00961.6510.0010.0010.0000.0000.0000.000
180A1882SER0-0.026-0.03564.8860.0000.0000.0000.0000.0000.000
181A1883ALA0-0.0090.00166.9070.0000.0000.0000.0000.0000.000
182A1884ALA0-0.0020.00767.5960.0010.0010.0000.0000.0000.000
183A1885TRP00.0170.00567.5110.0000.0000.0000.0000.0000.000
184A1886GLN0-0.031-0.01669.5830.0000.0000.0000.0000.0000.000
185A1887ALA0-0.002-0.00372.3720.0000.0000.0000.0000.0000.000
186A1888LEU00.0150.02170.8120.0000.0000.0000.0000.0000.000
187A1889LEU0-0.052-0.04671.7510.0000.0000.0000.0000.0000.000
188A1890ASP-1-0.999-0.98375.022-0.009-0.0090.0000.0000.0000.000
189A1891ALA00.0100.01277.1220.0000.0000.0000.0000.0000.000
190A1892CYS0-0.130-0.03976.7210.0000.0000.0000.0000.0000.000
191A1893ALA0-0.039-0.02879.0200.0000.0000.0000.0000.0000.000