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: QY93Y

Calculation Name: 1L0B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L0B

Chain ID: A

ChEMBL ID:

UniProt ID: O54952

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2174552.610106
FMO2-HF: Nuclear repulsion 2096249.186463
FMO2-HF: Total energy -78303.423644
FMO2-MP2: Total energy -78528.982133


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:1591:ARG)


Summations of interaction energy for fragment #1(A:1591:ARG)
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.
-141.2-144.77325.692-12.57-9.55-0.147
Interaction energy analysis for fragmet #1(A:1591:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.873
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].
3A1593GLU-1-0.850-0.9211.737-137.745-141.31825.692-12.570-9.550-0.147
4A1594ARG10.9090.9496.04231.72131.7210.0000.0000.0000.000
5A1595ASP-1-0.877-0.9068.894-22.565-22.5650.0000.0000.0000.000
6A1596ILE0-0.042-0.03211.2080.2170.2170.0000.0000.0000.000
7A1597SER00.0290.02913.2661.9511.9510.0000.0000.0000.000
8A1598MET0-0.050-0.02615.236-0.457-0.4570.0000.0000.0000.000
9A1599VAL00.0310.04317.3660.8450.8450.0000.0000.0000.000
10A1600VAL00.020-0.00119.790-0.387-0.3870.0000.0000.0000.000
11A1601SER00.0350.00222.3710.5490.5490.0000.0000.0000.000
12A1602GLY00.0440.01424.072-0.106-0.1060.0000.0000.0000.000
13A1603LEU0-0.050-0.00124.4110.1420.1420.0000.0000.0000.000
14A1604THR00.003-0.02928.1490.3130.3130.0000.0000.0000.000
15A1605PRO00.0950.03030.649-0.256-0.2560.0000.0000.0000.000
16A1606LYS10.9690.98431.7998.6378.6370.0000.0000.0000.000
17A1607GLU-1-0.737-0.82028.085-10.830-10.8300.0000.0000.0000.000
18A1608VAL00.0170.01127.122-0.445-0.4450.0000.0000.0000.000
19A1609MET0-0.011-0.01327.486-0.210-0.2100.0000.0000.0000.000
20A1610ILE0-0.083-0.03426.617-0.091-0.0910.0000.0000.0000.000
21A1611VAL00.0140.00522.264-0.303-0.3030.0000.0000.0000.000
22A1612GLN00.012-0.00124.153-0.143-0.1430.0000.0000.0000.000
23A1613LYS11.0021.00025.8529.6229.6220.0000.0000.0000.000
24A1614PHE0-0.024-0.00618.5250.0140.0140.0000.0000.0000.000
25A1615ALA00.0180.00321.015-0.427-0.4270.0000.0000.0000.000
26A1616GLU-1-0.923-0.95121.659-11.373-11.3730.0000.0000.0000.000
27A1617LYS10.8590.93222.94312.58912.5890.0000.0000.0000.000
28A1618TYR0-0.040-0.02218.2720.2200.2200.0000.0000.0000.000
29A1619ARG10.9440.98217.10414.95914.9590.0000.0000.0000.000
30A1620LEU0-0.028-0.00415.580-0.845-0.8450.0000.0000.0000.000
31A1621ALA00.0390.02117.6120.9160.9160.0000.0000.0000.000
32A1622LEU0-0.034-0.02818.775-0.519-0.5190.0000.0000.0000.000
33A1623THR0-0.008-0.00320.5840.5100.5100.0000.0000.0000.000
34A1624ASP-1-0.904-0.95922.560-11.581-11.5810.0000.0000.0000.000
35A1625VAL00.0180.00823.577-0.016-0.0160.0000.0000.0000.000
36A1626ILE0-0.046-0.01117.754-0.430-0.4300.0000.0000.0000.000
37A1627THR0-0.016-0.03118.8900.3160.3160.0000.0000.0000.000
38A1628GLU-1-0.940-0.96816.694-16.854-16.8540.0000.0000.0000.000
39A1629GLU-1-0.836-0.92014.512-18.067-18.0670.0000.0000.0000.000
40A1630THR0-0.057-0.00713.857-1.002-1.0020.0000.0000.0000.000
41A1631THR00.033-0.00310.346-0.684-0.6840.0000.0000.0000.000
42A1632HIS00.0160.01810.194-1.165-1.1650.0000.0000.0000.000
43A1633VAL00.0290.01713.9781.2631.2630.0000.0000.0000.000
44A1634ILE0-0.032-0.01216.709-0.275-0.2750.0000.0000.0000.000
45A1635ILE00.003-0.01319.3430.8090.8090.0000.0000.0000.000
46A1636LYS10.8550.91122.02110.62210.6220.0000.0000.0000.000
47A1637THR0-0.0230.01421.793-0.325-0.3250.0000.0000.0000.000
48A1638ASP-1-0.856-0.91925.128-11.462-11.4620.0000.0000.0000.000
49A1639ALA0-0.010-0.03026.016-0.452-0.4520.0000.0000.0000.000
50A1640GLU-1-0.873-0.93025.441-12.877-12.8770.0000.0000.0000.000
51A1641PHE0-0.061-0.03320.388-0.613-0.6130.0000.0000.0000.000
52A1642VAL00.0460.03721.868-0.687-0.6870.0000.0000.0000.000
53A1643CYS0-0.058-0.03422.7960.1550.1550.0000.0000.0000.000
54A1644GLU-1-0.841-0.90924.822-10.472-10.4720.0000.0000.0000.000
55A1645ARG10.8290.89225.16011.22111.2210.0000.0000.0000.000
56A1646THR0-0.016-0.02324.1900.2730.2730.0000.0000.0000.000
57A1647LEU00.0830.03824.080-0.418-0.4180.0000.0000.0000.000
58A1648LYS10.8740.92721.02712.38312.3830.0000.0000.0000.000
59A1649TYR0-0.031-0.01819.679-1.254-1.2540.0000.0000.0000.000
60A1650PHE00.0500.01019.091-0.817-0.8170.0000.0000.0000.000
61A1651LEU00.005-0.00619.162-0.743-0.7430.0000.0000.0000.000
62A1652GLY0-0.006-0.01616.170-0.901-0.9010.0000.0000.0000.000
63A1653ILE0-0.025-0.01614.712-1.640-1.6400.0000.0000.0000.000
64A1654ALA00.0350.02814.629-1.187-1.1870.0000.0000.0000.000
65A1655GLY0-0.037-0.00614.035-0.384-0.3840.0000.0000.0000.000
66A1656GLY00.0150.01510.468-1.698-1.6980.0000.0000.0000.000
67A1657LYS10.7950.8969.58519.13319.1330.0000.0000.0000.000
68A1658TRP00.0220.0147.0820.6000.6000.0000.0000.0000.000
69A1659ILE00.0050.01311.6981.6031.6030.0000.0000.0000.000
70A1660VAL0-0.004-0.00814.189-0.311-0.3110.0000.0000.0000.000
71A1661SER00.0670.03716.7991.0101.0100.0000.0000.0000.000
72A1662TYR00.0540.00620.273-0.128-0.1280.0000.0000.0000.000
73A1663SER00.001-0.01422.427-0.033-0.0330.0000.0000.0000.000
74A1664TRP00.0420.00515.1580.3360.3360.0000.0000.0000.000
75A1665VAL0-0.0290.00719.834-0.010-0.0100.0000.0000.0000.000
76A1666ILE0-0.015-0.01121.7630.3500.3500.0000.0000.0000.000
77A1667LYS10.9500.97921.46014.16814.1680.0000.0000.0000.000
78A1668SER0-0.031-0.04519.1210.2430.2430.0000.0000.0000.000
79A1669ILE0-0.020-0.00621.1500.2720.2720.0000.0000.0000.000
80A1670GLN0-0.084-0.03524.4580.4950.4950.0000.0000.0000.000
81A1671GLU-1-0.858-0.93221.597-13.443-13.4430.0000.0000.0000.000
82A1672ARG10.8660.93423.33110.52810.5280.0000.0000.0000.000
83A1673LYS10.8960.95318.48814.36914.3690.0000.0000.0000.000
84A1674LEU00.0270.02414.8490.1770.1770.0000.0000.0000.000
85A1675LEU0-0.0090.00115.329-0.831-0.8310.0000.0000.0000.000
86A1676SER00.0490.03610.214-1.548-1.5480.0000.0000.0000.000
87A1677VAL00.0380.01810.6841.0501.0500.0000.0000.0000.000
88A1678HIS10.9120.9367.21132.62932.6290.0000.0000.0000.000
89A1679GLU-1-0.890-0.94212.396-19.631-19.6310.0000.0000.0000.000
90A1680PHE0-0.049-0.02515.5751.3971.3970.0000.0000.0000.000
91A1681GLU-1-0.814-0.89312.155-25.166-25.1660.0000.0000.0000.000
92A1682VAL0-0.051-0.03215.7310.8370.8370.0000.0000.0000.000
93A1683LYS10.8630.93617.13813.41113.4110.0000.0000.0000.000
94A1684GLY00.006-0.00119.325-0.042-0.0420.0000.0000.0000.000
95A1685ASP-1-0.743-0.84921.517-12.730-12.7300.0000.0000.0000.000
96A1686VAL00.007-0.01924.4690.1130.1130.0000.0000.0000.000
97A1687VAL0-0.049-0.00527.2590.3810.3810.0000.0000.0000.000
98A1688THR0-0.046-0.01623.1110.0070.0070.0000.0000.0000.000
99A1689GLY00.0090.02025.8800.1020.1020.0000.0000.0000.000
100A1690SER00.015-0.01622.776-0.415-0.4150.0000.0000.0000.000
101A1691ASN0-0.002-0.01421.861-0.737-0.7370.0000.0000.0000.000
102A1692HIS0-0.013-0.00720.939-0.653-0.6530.0000.0000.0000.000
103A1693GLN0-0.0180.00116.263-1.675-1.6750.0000.0000.0000.000
104A1694GLY00.0590.04015.940-1.062-1.0620.0000.0000.0000.000
105A1695PRO00.001-0.00914.952-0.953-0.9530.0000.0000.0000.000
106A1696ARG10.8340.91511.30622.60122.6010.0000.0000.0000.000
107A1697ARG10.8290.92510.90215.84315.8430.0000.0000.0000.000
108A1698SER0-0.011-0.00611.737-1.395-1.3950.0000.0000.0000.000
109A1699ARG10.7840.8757.00432.34932.3490.0000.0000.0000.000
110A1700GLU-1-0.844-0.9046.689-32.665-32.6650.0000.0000.0000.000
111A1701SER0-0.095-0.0567.284-1.444-1.4440.0000.0000.0000.000
112A1702GLN0-0.128-0.0378.8260.1600.1600.0000.0000.0000.000
113A1703GLU-1-0.693-0.7656.390-27.529-27.5290.0000.0000.0000.000
114A1704LYS10.8190.87910.50122.43222.4320.0000.0000.0000.000
115A1705LEU0-0.151-0.15015.3500.7140.7140.0000.0000.0000.000
116A1706PHE0-0.035-0.03719.3790.6570.6570.0000.0000.0000.000
117A1707GLU-1-0.911-0.94818.647-15.377-15.3770.0000.0000.0000.000
118A1708GLY00.0120.01222.2460.2730.2730.0000.0000.0000.000
119A1709LEU0-0.034-0.00625.5830.5780.5780.0000.0000.0000.000
120A1710GLN0-0.029-0.01527.448-0.217-0.2170.0000.0000.0000.000
121A1711ILE00.008-0.00426.4410.2490.2490.0000.0000.0000.000
122A1712TYR0-0.042-0.03230.473-0.092-0.0920.0000.0000.0000.000
123A1713CYS0-0.042-0.00630.236-0.015-0.0150.0000.0000.0000.000
124A1714CYS00.0160.01333.3990.2050.2050.0000.0000.0000.000
125A1715GLU-1-0.842-0.92037.136-8.131-8.1310.0000.0000.0000.000
126A1716PRO0-0.025-0.00237.672-0.084-0.0840.0000.0000.0000.000
127A1717PHE0-0.013-0.01732.136-0.176-0.1760.0000.0000.0000.000
128A1718THR0-0.028-0.00936.1070.0010.0010.0000.0000.0000.000
129A1719ASN0-0.047-0.01731.096-0.204-0.2040.0000.0000.0000.000
130A1720MET00.0240.02827.046-0.141-0.1410.0000.0000.0000.000
131A1721PRO00.0270.00830.3450.1930.1930.0000.0000.0000.000
132A1722LYS10.9040.92730.7118.8168.8160.0000.0000.0000.000
133A1723ASP-1-0.926-0.96930.430-10.588-10.5880.0000.0000.0000.000
134A1724GLU-1-0.873-0.95425.285-12.639-12.6390.0000.0000.0000.000
135A1725LEU0-0.0310.00125.688-0.559-0.5590.0000.0000.0000.000
136A1726GLU-1-0.757-0.87926.150-10.311-10.3110.0000.0000.0000.000
137A1727ARG10.9370.98920.24914.08314.0830.0000.0000.0000.000
138A1728MET0-0.026-0.01721.639-0.669-0.6690.0000.0000.0000.000
139A1729LEU00.0230.00421.392-0.606-0.6060.0000.0000.0000.000
140A1730GLN00.0390.02819.762-0.208-0.2080.0000.0000.0000.000
141A1731LEU0-0.060-0.02117.030-0.586-0.5860.0000.0000.0000.000
142A1732CYS0-0.054-0.03117.457-1.178-1.1780.0000.0000.0000.000
143A1733GLY00.0420.01019.1600.0190.0190.0000.0000.0000.000
144A1734ALA0-0.0160.01420.5470.3650.3650.0000.0000.0000.000
145A1735SER0-0.0120.00224.200-0.240-0.2400.0000.0000.0000.000
146A1736VAL0-0.041-0.03825.9770.3120.3120.0000.0000.0000.000
147A1737VAL0-0.032-0.02328.5900.1800.1800.0000.0000.0000.000
148A1738LYS10.8790.91529.88410.27710.2770.0000.0000.0000.000
149A1739GLU-1-0.942-0.96834.282-7.646-7.6460.0000.0000.0000.000
150A1740LEU0-0.0300.00836.886-0.099-0.0990.0000.0000.0000.000
151A1741PRO0-0.008-0.01839.7700.1400.1400.0000.0000.0000.000
152A1742LEU00.0820.03534.285-0.022-0.0220.0000.0000.0000.000
153A1743LEU00.0070.00238.242-0.042-0.0420.0000.0000.0000.000
154A1744THR00.003-0.00739.011-0.200-0.2000.0000.0000.0000.000
155A1745ARG10.8710.93034.0548.6688.6680.0000.0000.0000.000
156A1746ASP-1-0.848-0.90433.825-8.979-8.9790.0000.0000.0000.000
157A1747THR0-0.024-0.03229.641-0.056-0.0560.0000.0000.0000.000
158A1748GLY0-0.0100.00632.776-0.059-0.0590.0000.0000.0000.000
159A1749ALA0-0.0320.00130.7070.1170.1170.0000.0000.0000.000
160A1750HIS00.0310.00932.7790.2450.2450.0000.0000.0000.000
161A1751PRO0-0.009-0.00433.412-0.169-0.1690.0000.0000.0000.000
162A1752ILE00.0010.01029.4770.1830.1830.0000.0000.0000.000
163A1753VAL0-0.036-0.02033.033-0.129-0.1290.0000.0000.0000.000
164A1754LEU00.0100.01329.0970.0690.0690.0000.0000.0000.000
165A1755VAL00.009-0.00933.7260.1750.1750.0000.0000.0000.000
166A1756GLN00.0230.01335.425-0.105-0.1050.0000.0000.0000.000
167A1776ARG10.9360.96635.9938.1028.1020.0000.0000.0000.000
168A1777LEU0-0.0100.00436.402-0.141-0.1410.0000.0000.0000.000
169A1778VAL00.000-0.01231.8680.0460.0460.0000.0000.0000.000
170A1779MET00.0290.02133.9660.0380.0380.0000.0000.0000.000
171A1780TRP00.0880.02329.089-0.497-0.4970.0000.0000.0000.000
172A1781ASP-1-0.874-0.93129.299-10.067-10.0670.0000.0000.0000.000
173A1782TRP00.000-0.00926.532-0.375-0.3750.0000.0000.0000.000
174A1783VAL0-0.024-0.01324.709-0.520-0.5200.0000.0000.0000.000
175A1784LEU00.001-0.00124.204-0.673-0.6730.0000.0000.0000.000
176A1785ASP-1-0.744-0.84823.949-11.707-11.7070.0000.0000.0000.000
177A1786SER0-0.030-0.01422.802-0.436-0.4360.0000.0000.0000.000
178A1787ILE00.0120.00618.845-0.778-0.7780.0000.0000.0000.000
179A1788SER0-0.061-0.01619.161-0.682-0.6820.0000.0000.0000.000
180A1789VAL0-0.017-0.01819.778-0.495-0.4950.0000.0000.0000.000
181A1790TYR00.0020.00314.110-0.299-0.2990.0000.0000.0000.000
182A1791ARG10.9290.95517.81714.01614.0160.0000.0000.0000.000
183A1792CYS00.0170.03020.4330.5500.5500.0000.0000.0000.000
184A1793ARG10.8730.94423.12511.53311.5330.0000.0000.0000.000
185A1794ASP-1-0.862-0.92626.198-9.779-9.7790.0000.0000.0000.000
186A1795LEU00.032-0.00529.5330.1090.1090.0000.0000.0000.000
187A1796ASP-1-0.875-0.92431.751-8.412-8.4120.0000.0000.0000.000
188A1797ALA0-0.064-0.02932.7440.2200.2200.0000.0000.0000.000
189A1798TYR0-0.053-0.06629.294-0.067-0.0670.0000.0000.0000.000
190A1799LEU0-0.0290.01034.3930.0440.0440.0000.0000.0000.000
191A1800VAL00.005-0.00137.0630.1470.1470.0000.0000.0000.000
192A1801GLN0-0.045-0.01439.9020.1950.1950.0000.0000.0000.000