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: K9163

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2178337.662135
FMO2-HF: Nuclear repulsion 2100032.74711
FMO2-HF: Total energy -78304.915025
FMO2-MP2: Total energy -78530.302487


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.
-150.024-156.51730.408-13.496-10.42-0.147
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 : 0.813 / q_NPA : 0.862
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-1-0.843-0.8981.678-140.695-147.18830.408-13.496-10.420-0.147
4A1594ARG10.8320.9045.87331.66631.6660.0000.0000.0000.000
5A1595ASP-1-0.882-0.9278.551-23.378-23.3780.0000.0000.0000.000
6A1596ILE0-0.031-0.01511.058-0.077-0.0770.0000.0000.0000.000
7A1597SER00.0140.01412.7732.0802.0800.0000.0000.0000.000
8A1598MET0-0.046-0.01514.633-0.630-0.6300.0000.0000.0000.000
9A1599VAL00.0580.05316.8670.9970.9970.0000.0000.0000.000
10A1600VAL00.011-0.00619.512-0.356-0.3560.0000.0000.0000.000
11A1601SER00.0530.01622.2860.5750.5750.0000.0000.0000.000
12A1602GLY00.0400.00724.127-0.121-0.1210.0000.0000.0000.000
13A1603LEU0-0.054-0.00124.2390.2000.2000.0000.0000.0000.000
14A1604THR0-0.002-0.03128.1000.3110.3110.0000.0000.0000.000
15A1605PRO00.0720.01430.503-0.265-0.2650.0000.0000.0000.000
16A1606LYS10.9720.98231.4998.6778.6770.0000.0000.0000.000
17A1607GLU-1-0.755-0.82427.951-10.926-10.9260.0000.0000.0000.000
18A1608VAL00.0380.02226.732-0.453-0.4530.0000.0000.0000.000
19A1609MET00.0060.00127.061-0.214-0.2140.0000.0000.0000.000
20A1610ILE0-0.071-0.02126.185-0.098-0.0980.0000.0000.0000.000
21A1611VAL00.0220.00221.844-0.323-0.3230.0000.0000.0000.000
22A1612GLN00.0030.00323.567-0.182-0.1820.0000.0000.0000.000
23A1613LYS11.0010.99425.0809.6889.6880.0000.0000.0000.000
24A1614PHE0-0.030-0.01017.9970.0560.0560.0000.0000.0000.000
25A1615ALA00.0130.00220.402-0.412-0.4120.0000.0000.0000.000
26A1616GLU-1-0.929-0.95821.172-11.453-11.4530.0000.0000.0000.000
27A1617LYS10.8560.94022.37212.85812.8580.0000.0000.0000.000
28A1618TYR0-0.052-0.03517.9870.1670.1670.0000.0000.0000.000
29A1619ARG10.9240.96616.54715.82715.8270.0000.0000.0000.000
30A1620LEU0-0.0230.00015.123-0.789-0.7890.0000.0000.0000.000
31A1621ALA00.0350.02316.9970.9680.9680.0000.0000.0000.000
32A1622LEU0-0.036-0.02418.167-0.568-0.5680.0000.0000.0000.000
33A1623THR0-0.011-0.00619.8290.5500.5500.0000.0000.0000.000
34A1624ASP-1-0.856-0.93422.033-11.873-11.8730.0000.0000.0000.000
35A1625VAL00.0240.00022.8420.0490.0490.0000.0000.0000.000
36A1626ILE0-0.038-0.01217.144-0.455-0.4550.0000.0000.0000.000
37A1627THR0-0.025-0.02117.9780.1160.1160.0000.0000.0000.000
38A1628GLU-1-0.865-0.92816.349-17.526-17.5260.0000.0000.0000.000
39A1629GLU-1-0.792-0.89813.880-18.581-18.5810.0000.0000.0000.000
40A1630THR0-0.061-0.00912.999-1.581-1.5810.0000.0000.0000.000
41A1631THR00.035-0.0039.626-0.400-0.4000.0000.0000.0000.000
42A1632HIS00.0150.01810.157-1.264-1.2640.0000.0000.0000.000
43A1633VAL00.0150.00613.7601.2031.2030.0000.0000.0000.000
44A1634ILE0-0.0170.00516.685-0.119-0.1190.0000.0000.0000.000
45A1635ILE0-0.018-0.01919.3350.8160.8160.0000.0000.0000.000
46A1636LYS10.8510.90722.06010.74510.7450.0000.0000.0000.000
47A1637THR0-0.0190.00022.125-0.478-0.4780.0000.0000.0000.000
48A1638ASP-1-0.819-0.90525.349-11.575-11.5750.0000.0000.0000.000
49A1639ALA0-0.027-0.02126.290-0.439-0.4390.0000.0000.0000.000
50A1640GLU-1-0.793-0.88325.334-13.175-13.1750.0000.0000.0000.000
51A1641PHE0-0.039-0.01020.438-0.639-0.6390.0000.0000.0000.000
52A1642VAL00.0260.03021.833-0.734-0.7340.0000.0000.0000.000
53A1643CYS0-0.037-0.02722.6670.1660.1660.0000.0000.0000.000
54A1644GLU-1-0.853-0.91324.740-10.523-10.5230.0000.0000.0000.000
55A1645ARG10.8440.89024.98511.19511.1950.0000.0000.0000.000
56A1646THR0-0.044-0.03424.0840.1850.1850.0000.0000.0000.000
57A1647LEU00.0620.02323.908-0.423-0.4230.0000.0000.0000.000
58A1648LYS10.8110.90321.26312.29212.2920.0000.0000.0000.000
59A1649TYR0-0.017-0.03519.705-1.282-1.2820.0000.0000.0000.000
60A1650PHE00.0300.00618.920-0.869-0.8690.0000.0000.0000.000
61A1651LEU00.0210.00218.970-0.723-0.7230.0000.0000.0000.000
62A1652GLY0-0.006-0.00715.928-0.895-0.8950.0000.0000.0000.000
63A1653ILE0-0.018-0.00414.419-1.685-1.6850.0000.0000.0000.000
64A1654ALA00.0430.01914.532-1.117-1.1170.0000.0000.0000.000
65A1655GLY0-0.0090.01513.634-0.134-0.1340.0000.0000.0000.000
66A1656GLY0-0.0010.00310.174-1.575-1.5750.0000.0000.0000.000
67A1657LYS10.8110.9099.43519.45719.4570.0000.0000.0000.000
68A1658TRP00.0150.0057.0721.0731.0730.0000.0000.0000.000
69A1659ILE00.0170.01811.7371.6591.6590.0000.0000.0000.000
70A1660VAL0-0.009-0.00614.338-0.262-0.2620.0000.0000.0000.000
71A1661SER00.0580.03116.9891.0171.0170.0000.0000.0000.000
72A1662TYR00.030-0.01220.335-0.193-0.1930.0000.0000.0000.000
73A1663SER00.004-0.02322.2510.0870.0870.0000.0000.0000.000
74A1664TRP00.019-0.00814.6590.4080.4080.0000.0000.0000.000
75A1665VAL0-0.0060.03019.7410.1510.1510.0000.0000.0000.000
76A1666ILE00.0100.00321.5720.3490.3490.0000.0000.0000.000
77A1667LYS10.9120.95021.01914.21614.2160.0000.0000.0000.000
78A1668SER0-0.003-0.03518.9250.2130.2130.0000.0000.0000.000
79A1669ILE0-0.0110.00921.0030.2340.2340.0000.0000.0000.000
80A1670GLN0-0.061-0.02924.3680.3750.3750.0000.0000.0000.000
81A1671GLU-1-0.835-0.90521.256-13.588-13.5880.0000.0000.0000.000
82A1672ARG10.8770.93423.00610.43210.4320.0000.0000.0000.000
83A1673LYS10.8770.94418.73214.45914.4590.0000.0000.0000.000
84A1674LEU00.0210.01314.5200.1330.1330.0000.0000.0000.000
85A1675LEU0-0.0080.00315.441-0.705-0.7050.0000.0000.0000.000
86A1676SER00.0150.00610.599-1.691-1.6910.0000.0000.0000.000
87A1677VAL00.0290.01610.1531.2551.2550.0000.0000.0000.000
88A1678HIS10.8910.9326.97630.33330.3330.0000.0000.0000.000
89A1679GLU-1-0.840-0.91712.181-21.038-21.0380.0000.0000.0000.000
90A1680PHE0-0.030-0.00715.4351.5011.5010.0000.0000.0000.000
91A1681GLU-1-0.814-0.89711.996-25.706-25.7060.0000.0000.0000.000
92A1682VAL0-0.061-0.03315.9090.8620.8620.0000.0000.0000.000
93A1683LYS10.8140.90617.35713.41413.4140.0000.0000.0000.000
94A1684GLY00.0040.00019.404-0.105-0.1050.0000.0000.0000.000
95A1685ASP-1-0.734-0.85021.438-12.740-12.7400.0000.0000.0000.000
96A1686VAL00.011-0.01124.5510.1300.1300.0000.0000.0000.000
97A1687VAL0-0.0340.00227.4220.4030.4030.0000.0000.0000.000
98A1688THR0-0.047-0.01823.1080.0310.0310.0000.0000.0000.000
99A1689GLY00.0110.01026.0200.1580.1580.0000.0000.0000.000
100A1690SER0-0.015-0.03523.028-0.418-0.4180.0000.0000.0000.000
101A1691ASN0-0.018-0.01822.046-0.788-0.7880.0000.0000.0000.000
102A1692HIS0-0.008-0.00221.247-0.692-0.6920.0000.0000.0000.000
103A1693GLN0-0.024-0.00216.437-1.694-1.6940.0000.0000.0000.000
104A1694GLY00.0490.04616.003-1.209-1.2090.0000.0000.0000.000
105A1695PRO00.007-0.00815.137-0.908-0.9080.0000.0000.0000.000
106A1696ARG10.8040.89411.54622.70722.7070.0000.0000.0000.000
107A1697ARG10.8370.91211.19316.24116.2410.0000.0000.0000.000
108A1698SER0-0.0100.00412.042-1.295-1.2950.0000.0000.0000.000
109A1699ARG10.7950.8656.96632.96532.9650.0000.0000.0000.000
110A1700GLU-1-0.842-0.8856.981-34.004-34.0040.0000.0000.0000.000
111A1701SER0-0.085-0.0638.2570.2000.2000.0000.0000.0000.000
112A1702GLN0-0.041-0.0198.8411.2601.2600.0000.0000.0000.000
113A1703GLU-1-0.933-0.9657.981-27.292-27.2920.0000.0000.0000.000
114A1704LYS10.7620.90111.53220.61520.6150.0000.0000.0000.000
115A1705LEU0-0.027-0.00115.0980.0250.0250.0000.0000.0000.000
116A1706PHE0-0.008-0.03018.4160.5820.5820.0000.0000.0000.000
117A1707GLU-1-0.904-0.95018.268-15.581-15.5810.0000.0000.0000.000
118A1708GLY00.0040.00921.8350.3180.3180.0000.0000.0000.000
119A1709LEU0-0.023-0.01025.1960.6040.6040.0000.0000.0000.000
120A1710GLN0-0.026-0.02327.094-0.205-0.2050.0000.0000.0000.000
121A1711ILE0-0.010-0.00526.0540.1780.1780.0000.0000.0000.000
122A1712TYR0-0.032-0.02630.039-0.105-0.1050.0000.0000.0000.000
123A1713CYS0-0.047-0.00829.4880.0290.0290.0000.0000.0000.000
124A1714CYS0-0.016-0.00832.7940.2020.2020.0000.0000.0000.000
125A1715GLU-1-0.793-0.89536.598-8.362-8.3620.0000.0000.0000.000
126A1716PRO0-0.020-0.00237.630-0.053-0.0530.0000.0000.0000.000
127A1717PHE0-0.013-0.01331.602-0.161-0.1610.0000.0000.0000.000
128A1718THR0-0.023-0.02735.2660.0700.0700.0000.0000.0000.000
129A1719ASN0-0.053-0.01530.707-0.191-0.1910.0000.0000.0000.000
130A1720MET00.0130.01426.775-0.279-0.2790.0000.0000.0000.000
131A1721PRO00.0150.01029.9440.1700.1700.0000.0000.0000.000
132A1722LYS10.8980.93930.1498.8298.8290.0000.0000.0000.000
133A1723ASP-1-0.880-0.94929.728-10.780-10.7800.0000.0000.0000.000
134A1724GLU-1-0.858-0.93925.006-12.854-12.8540.0000.0000.0000.000
135A1725LEU0-0.0170.00025.186-0.587-0.5870.0000.0000.0000.000
136A1726GLU-1-0.755-0.87725.704-10.314-10.3140.0000.0000.0000.000
137A1727ARG10.8750.93919.50914.57814.5780.0000.0000.0000.000
138A1728MET0-0.032-0.01221.299-0.700-0.7000.0000.0000.0000.000
139A1729LEU00.0290.00320.955-0.655-0.6550.0000.0000.0000.000
140A1730GLN00.0460.02919.091-0.252-0.2520.0000.0000.0000.000
141A1731LEU0-0.070-0.03116.540-0.570-0.5700.0000.0000.0000.000
142A1732CYS0-0.020-0.00216.844-1.264-1.2640.0000.0000.0000.000
143A1733GLY00.0330.00818.799-0.174-0.1740.0000.0000.0000.000
144A1734ALA0-0.0210.00320.0300.3730.3730.0000.0000.0000.000
145A1735SER00.004-0.00123.766-0.218-0.2180.0000.0000.0000.000
146A1736VAL0-0.039-0.02825.2190.4460.4460.0000.0000.0000.000
147A1737VAL0-0.028-0.00827.9150.1730.1730.0000.0000.0000.000
148A1738LYS10.8560.91029.66110.33110.3310.0000.0000.0000.000
149A1739GLU-1-0.957-0.97233.500-7.735-7.7350.0000.0000.0000.000
150A1740LEU0-0.0130.00036.466-0.131-0.1310.0000.0000.0000.000
151A1741PRO0-0.020-0.01339.1820.1610.1610.0000.0000.0000.000
152A1742LEU00.0630.02333.6870.0190.0190.0000.0000.0000.000
153A1743LEU00.0090.00537.716-0.023-0.0230.0000.0000.0000.000
154A1744THR0-0.012-0.01138.765-0.203-0.2030.0000.0000.0000.000
155A1745ARG10.8800.93633.6578.7098.7090.0000.0000.0000.000
156A1746ASP-1-0.822-0.89033.438-9.041-9.0410.0000.0000.0000.000
157A1747THR0-0.034-0.03029.677-0.126-0.1260.0000.0000.0000.000
158A1748GLY0-0.029-0.00632.401-0.127-0.1270.0000.0000.0000.000
159A1749ALA0-0.0020.00930.2750.1420.1420.0000.0000.0000.000
160A1750HIS00.0170.00932.3100.1580.1580.0000.0000.0000.000
161A1751PRO0-0.0090.00832.863-0.182-0.1820.0000.0000.0000.000
162A1752ILE0-0.003-0.00829.1730.2670.2670.0000.0000.0000.000
163A1753VAL0-0.031-0.01232.625-0.171-0.1710.0000.0000.0000.000
164A1754LEU00.0220.01228.8810.0670.0670.0000.0000.0000.000
165A1755VAL00.012-0.00133.5510.1610.1610.0000.0000.0000.000
166A1756GLN00.0170.02635.009-0.078-0.0780.0000.0000.0000.000
167A1776ARG10.9360.96036.3838.1948.1940.0000.0000.0000.000
168A1777LEU0-0.0100.00236.607-0.119-0.1190.0000.0000.0000.000
169A1778VAL00.0180.00432.0520.0990.0990.0000.0000.0000.000
170A1779MET00.0100.00533.9000.0260.0260.0000.0000.0000.000
171A1780TRP00.0480.00828.863-0.498-0.4980.0000.0000.0000.000
172A1781ASP-1-0.859-0.93429.091-10.143-10.1430.0000.0000.0000.000
173A1782TRP00.0040.00126.733-0.427-0.4270.0000.0000.0000.000
174A1783VAL0-0.0060.00724.362-0.517-0.5170.0000.0000.0000.000
175A1784LEU00.0060.00123.907-0.687-0.6870.0000.0000.0000.000
176A1785ASP-1-0.748-0.85123.742-11.809-11.8090.0000.0000.0000.000
177A1786SER0-0.023-0.00622.742-0.494-0.4940.0000.0000.0000.000
178A1787ILE0-0.0010.00618.673-0.799-0.7990.0000.0000.0000.000
179A1788SER0-0.059-0.02819.017-0.692-0.6920.0000.0000.0000.000
180A1789VAL0-0.008-0.01619.838-0.370-0.3700.0000.0000.0000.000
181A1790TYR00.0200.00613.7820.0340.0340.0000.0000.0000.000
182A1791ARG10.9260.96117.61813.92113.9210.0000.0000.0000.000
183A1792CYS00.0160.02020.3840.6140.6140.0000.0000.0000.000
184A1793ARG10.8740.94323.12211.40011.4000.0000.0000.0000.000
185A1794ASP-1-0.850-0.92626.296-9.715-9.7150.0000.0000.0000.000
186A1795LEU00.0280.00629.743-0.014-0.0140.0000.0000.0000.000
187A1796ASP-1-0.870-0.94631.893-8.393-8.3930.0000.0000.0000.000
188A1797ALA0-0.088-0.03832.4440.2180.2180.0000.0000.0000.000
189A1798TYR0-0.047-0.04929.253-0.077-0.0770.0000.0000.0000.000
190A1799LEU0-0.0450.00534.3560.0440.0440.0000.0000.0000.000
191A1800VAL0-0.004-0.01236.8250.1230.1230.0000.0000.0000.000
192A1801GLN0-0.050-0.01239.8280.1950.1950.0000.0000.0000.000