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: QVQ2Y

Calculation Name: 4QMD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QMD

Chain ID: A

ChEMBL ID:

UniProt ID: Q92817

Base Structure: X-ray

Registration Date: 2023-09-24

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087666.066519
FMO2-HF: Nuclear repulsion 2012907.550871
FMO2-HF: Total energy -74758.515648
FMO2-MP2: Total energy -74975.474562


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:1822:ASP)


Summations of interaction energy for fragment #1(A:1822:ASP)
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.
-178.131-184.08430.907-14.301-10.6530.157
Interaction energy analysis for fragmet #1(A:1822:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.795 / q_NPA : -0.884
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].
3A1824SER0-0.049-0.0313.519-7.627-5.334-0.006-1.104-1.1830.003
4A1825PHE0-0.036-0.0273.948-5.728-5.218-0.001-0.173-0.3360.000
5A1826PRO0-0.0310.0004.8241.7641.832-0.001-0.007-0.0590.000
6A1827ILE00.0240.0016.7632.3102.3100.0000.0000.0000.000
7A1828ALA00.0010.0137.717-2.399-2.3990.0000.0000.0000.000
8A1829GLY0-0.015-0.0279.531-2.105-2.1050.0000.0000.0000.000
9A1830ILE0-0.026-0.00312.3310.6480.6480.0000.0000.0000.000
10A1831TYR0-0.039-0.04813.5060.4440.4440.0000.0000.0000.000
11A1832ASP-1-0.748-0.82615.34613.60313.6030.0000.0000.0000.000
12A1833THR0-0.022-0.03718.607-0.326-0.3260.0000.0000.0000.000
13A1834THR0-0.062-0.04820.314-0.528-0.5280.0000.0000.0000.000
14A1835THR0-0.086-0.06921.922-0.395-0.3950.0000.0000.0000.000
15A1836ASP-1-0.800-0.85117.05318.84418.8440.0000.0000.0000.000
16A1837ASN00.0040.00517.4781.2351.2350.0000.0000.0000.000
17A1838LYS10.8720.92812.620-21.621-21.6210.0000.0000.0000.000
18A1839CYS0-0.046-0.02315.836-0.954-0.9540.0000.0000.0000.000
19A1840SER00.0860.04915.6140.8060.8060.0000.0000.0000.000
20A1841ILE00.0530.01813.562-0.668-0.6680.0000.0000.0000.000
21A1842LYS10.8190.91517.413-12.582-12.5820.0000.0000.0000.000
22A1843THR0-0.025-0.02820.015-0.773-0.7730.0000.0000.0000.000
23A1844ALA00.0500.02019.053-0.462-0.4620.0000.0000.0000.000
24A1845VAL0-0.024-0.00520.987-0.529-0.5290.0000.0000.0000.000
25A1846ALA0-0.027-0.01123.281-0.508-0.5080.0000.0000.0000.000
26A1847LYS10.9200.95823.898-12.121-12.1210.0000.0000.0000.000
27A1848ASN0-0.051-0.02325.971-0.236-0.2360.0000.0000.0000.000
28A1849MET0-0.0130.01621.148-0.032-0.0320.0000.0000.0000.000
29A1850LEU00.017-0.00218.0770.6460.6460.0000.0000.0000.000
30A1851ASP-1-0.762-0.82021.84312.56112.5610.0000.0000.0000.000
31A1852PRO00.0740.00722.3630.5200.5200.0000.0000.0000.000
32A1853ILE0-0.033-0.00523.1260.2230.2230.0000.0000.0000.000
33A1854THR00.016-0.02718.1250.4700.4700.0000.0000.0000.000
34A1855GLY00.0330.00718.5150.7570.7570.0000.0000.0000.000
35A1856GLN0-0.051-0.01218.7390.0860.0860.0000.0000.0000.000
36A1857LYS10.8990.93717.907-13.415-13.4150.0000.0000.0000.000
37A1858LEU00.0000.00513.1960.6880.6880.0000.0000.0000.000
38A1859LEU0-0.0020.00414.2540.7970.7970.0000.0000.0000.000
39A1860GLU-1-0.826-0.90516.38413.27113.2710.0000.0000.0000.000
40A1861ALA00.0390.02512.339-0.003-0.0030.0000.0000.0000.000
41A1862GLN0-0.042-0.00511.494-0.018-0.0180.0000.0000.0000.000
42A1863ALA0-0.016-0.01413.1370.0860.0860.0000.0000.0000.000
43A1864ALA0-0.007-0.00714.664-0.155-0.1550.0000.0000.0000.000
44A1865THR00.014-0.0119.9640.4360.4360.0000.0000.0000.000
45A1866GLY00.0130.00111.1701.4391.4390.0000.0000.0000.000
46A1867GLY0-0.052-0.00813.648-0.727-0.7270.0000.0000.0000.000
47A1868ILE0-0.010-0.01413.5061.1741.1740.0000.0000.0000.000
48A1869VAL00.0170.0039.477-0.184-0.1840.0000.0000.0000.000
49A1870ASP-1-0.835-0.88412.66516.52316.5230.0000.0000.0000.000
50A1871LEU0-0.023-0.02711.1621.0451.0450.0000.0000.0000.000
51A1872LEU0-0.047-0.02313.1090.7470.7470.0000.0000.0000.000
52A1873SER0-0.052-0.05013.7380.0530.0530.0000.0000.0000.000
53A1874ARG10.8000.8904.385-35.911-35.844-0.001-0.002-0.0630.000
54A1875GLU-1-0.882-0.93310.57418.49318.4930.0000.0000.0000.000
55A1876ARG10.7850.8889.580-22.136-22.1360.0000.0000.0000.000
56A1877TYR0-0.024-0.01214.288-1.480-1.4800.0000.0000.0000.000
57A1878SER00.0230.01017.7400.2270.2270.0000.0000.0000.000
58A1879VAL00.016-0.00420.021-0.180-0.1800.0000.0000.0000.000
59A1880HIS0-0.017-0.01021.755-0.083-0.0830.0000.0000.0000.000
60A1881LYS10.9630.97919.985-13.759-13.7590.0000.0000.0000.000
61A1882ALA00.0440.02719.3610.0930.0930.0000.0000.0000.000
62A1883MET0-0.024-0.00621.003-0.104-0.1040.0000.0000.0000.000
63A1884GLU-1-0.820-0.90024.48310.92110.9210.0000.0000.0000.000
64A1885ARG10.7940.89121.460-12.465-12.4650.0000.0000.0000.000
65A1886GLY00.0020.01622.5560.2880.2880.0000.0000.0000.000
66A1887LEU0-0.004-0.00216.9180.1100.1100.0000.0000.0000.000
67A1888ILE0-0.029-0.01619.5390.4270.4270.0000.0000.0000.000
68A1889GLU-1-0.775-0.87921.79111.11211.1120.0000.0000.0000.000
69A1890ASN00.034-0.00425.4440.3020.3020.0000.0000.0000.000
70A1891THR00.0070.01028.0860.0480.0480.0000.0000.0000.000
71A1892SER0-0.001-0.01722.997-0.036-0.0360.0000.0000.0000.000
72A1893THR0-0.040-0.03424.4840.1600.1600.0000.0000.0000.000
73A1894GLN00.0360.01725.0330.4060.4060.0000.0000.0000.000
74A1895ARG10.8610.90322.564-12.132-12.1320.0000.0000.0000.000
75A1896LEU00.0370.02419.0810.2880.2880.0000.0000.0000.000
76A1897LEU0-0.010-0.01421.1600.4350.4350.0000.0000.0000.000
77A1898ASN00.0000.00323.591-0.177-0.1770.0000.0000.0000.000
78A1899ALA00.0490.03318.4470.0400.0400.0000.0000.0000.000
79A1900GLN00.0290.01018.5540.7070.7070.0000.0000.0000.000
80A1901LYS10.8610.94019.413-10.623-10.6230.0000.0000.0000.000
81A1902ALA00.0040.00417.311-0.141-0.1410.0000.0000.0000.000
82A1903PHE00.0210.04515.1120.2960.2960.0000.0000.0000.000
83A1904THR0-0.077-0.05217.113-0.196-0.1960.0000.0000.0000.000
84A1905GLY00.0880.04520.545-0.458-0.4580.0000.0000.0000.000
85A1906ILE0-0.057-0.03222.438-0.130-0.1300.0000.0000.0000.000
86A1907GLU-1-0.848-0.92426.0889.8139.8130.0000.0000.0000.000
87A1908ASP-1-0.757-0.85229.4148.6778.6770.0000.0000.0000.000
88A1909PRO00.0180.00831.987-0.210-0.2100.0000.0000.0000.000
89A1910VAL0-0.0100.01935.015-0.230-0.2300.0000.0000.0000.000
90A1911THR0-0.065-0.07334.327-0.039-0.0390.0000.0000.0000.000
91A1912LYS10.8740.92633.562-8.040-8.0400.0000.0000.0000.000
92A1913LYS10.9801.00830.418-8.544-8.5440.0000.0000.0000.000
93A1914ARG10.8380.90824.721-10.804-10.8040.0000.0000.0000.000
94A1915LEU0-0.049-0.00725.8410.0030.0030.0000.0000.0000.000
95A1916SER00.041-0.00920.9770.3560.3560.0000.0000.0000.000
96A1917VAL00.012-0.00819.889-0.446-0.4460.0000.0000.0000.000
97A1918GLY00.0540.03321.825-0.302-0.3020.0000.0000.0000.000
98A1919GLU-1-0.728-0.83023.06910.67610.6760.0000.0000.0000.000
99A1920ALA0-0.045-0.02525.510-0.446-0.4460.0000.0000.0000.000
100A1921VAL0-0.0170.00024.904-0.347-0.3470.0000.0000.0000.000
101A1922GLN0-0.077-0.04625.967-0.530-0.5300.0000.0000.0000.000
102A1923LYS10.8130.90628.612-10.231-10.2310.0000.0000.0000.000
103A1924GLY00.0120.01831.115-0.257-0.2570.0000.0000.0000.000
104A1925TRP0-0.058-0.04229.588-0.172-0.1720.0000.0000.0000.000
105A1926MET0-0.044-0.03023.8600.1910.1910.0000.0000.0000.000
106A1927PRO00.0420.02628.057-0.006-0.0060.0000.0000.0000.000
107A1928ARG10.8410.87125.702-9.705-9.7050.0000.0000.0000.000
108A1929GLU-1-0.816-0.90724.37810.60110.6010.0000.0000.0000.000
109A1930SER0-0.078-0.04124.0040.2380.2380.0000.0000.0000.000
110A1931VAL0-0.024-0.01721.1410.3690.3690.0000.0000.0000.000
111A1932LEU00.0250.02319.7640.6440.6440.0000.0000.0000.000
112A1933PRO00.0570.02818.1140.7510.7510.0000.0000.0000.000
113A1934HIS0-0.007-0.00316.0171.5441.5440.0000.0000.0000.000
114A1935LEU0-0.011-0.00314.8580.9400.9400.0000.0000.0000.000
115A1936GLN00.0260.00714.6160.8710.8710.0000.0000.0000.000
116A1937VAL0-0.016-0.00110.9721.3721.3720.0000.0000.0000.000
117A1938GLN0-0.048-0.02610.1681.6531.6530.0000.0000.0000.000
118A1939HIS0-0.020-0.02510.2231.6261.6260.0000.0000.0000.000
119A1940LEU0-0.008-0.0069.0311.5751.5750.0000.0000.0000.000
120A1941THR0-0.050-0.0205.7702.5162.5160.0000.0000.0000.000
121A1942GLY00.0200.0116.6442.0972.0970.0000.0000.0000.000
122A1943GLY00.0010.0108.336-1.433-1.4330.0000.0000.0000.000
123A1944LEU00.003-0.00211.9450.3870.3870.0000.0000.0000.000
124A1945ILE00.001-0.00412.0080.3670.3670.0000.0000.0000.000
125A1946ASP-1-0.813-0.89515.34812.49312.4930.0000.0000.0000.000
126A1947PRO0-0.013-0.01618.3490.2860.2860.0000.0000.0000.000
127A1948LYS10.8120.89219.407-12.937-12.9370.0000.0000.0000.000
128A1949ARG10.8550.94318.308-13.490-13.4900.0000.0000.0000.000
129A1950THR00.0030.00413.4210.3770.3770.0000.0000.0000.000
130A1951GLY00.0300.02312.202-0.669-0.6690.0000.0000.0000.000
131A1952ARG10.7760.8868.318-25.186-25.1860.0000.0000.0000.000
132A1953ILE00.0150.00913.072-0.202-0.2020.0000.0000.0000.000
133A1954PRO00.0170.00714.5180.1800.1800.0000.0000.0000.000
134A1955ILE00.0360.02715.810-1.004-1.0040.0000.0000.0000.000
135A1956GLN00.0290.00518.090-1.167-1.1670.0000.0000.0000.000
136A1957GLN00.0240.01818.640-0.022-0.0220.0000.0000.0000.000
137A1958ALA00.0240.01519.043-0.545-0.5450.0000.0000.0000.000
138A1959LEU0-0.0030.00321.028-0.508-0.5080.0000.0000.0000.000
139A1960LEU0-0.040-0.02423.893-0.510-0.5100.0000.0000.0000.000
140A1961SER0-0.060-0.04023.180-0.286-0.2860.0000.0000.0000.000
141A1962GLY00.0220.01825.916-0.246-0.2460.0000.0000.0000.000
142A1963MET0-0.0490.00118.133-0.038-0.0380.0000.0000.0000.000
143A1964ILE0-0.060-0.03720.0390.2040.2040.0000.0000.0000.000
144A1965SER00.0900.04623.775-0.095-0.0950.0000.0000.0000.000
145A1966GLU-1-0.846-0.93825.01710.60010.6000.0000.0000.0000.000
146A1967GLU-1-0.803-0.85825.53310.56010.5600.0000.0000.0000.000
147A1968LEU00.008-0.00122.2190.3750.3750.0000.0000.0000.000
148A1969ALA00.0210.00621.0890.6650.6650.0000.0000.0000.000
149A1970GLN0-0.060-0.04421.0380.6140.6140.0000.0000.0000.000
150A1971LEU0-0.009-0.00921.9230.3890.3890.0000.0000.0000.000
151A1972LEU0-0.029-0.00116.3150.5980.5980.0000.0000.0000.000
152A1973GLN00.0070.02117.0430.6960.6960.0000.0000.0000.000
153A1974ASP-1-0.752-0.83018.49614.27214.2720.0000.0000.0000.000
154A1975GLU-1-0.843-0.91213.09021.35821.3580.0000.0000.0000.000
155A1976SER0-0.138-0.07916.6640.4490.4490.0000.0000.0000.000
156A1977SER0-0.019-0.04619.290-0.277-0.2770.0000.0000.0000.000
157A1978TYR0-0.081-0.05514.0410.1530.1530.0000.0000.0000.000
158A1979GLU-1-0.920-0.96119.38312.47512.4750.0000.0000.0000.000
159A1980LYS10.8370.90119.383-14.233-14.2330.0000.0000.0000.000
160A1981ASP-1-0.778-0.89318.29714.83714.8370.0000.0000.0000.000
161A1982LEU0-0.051-0.01515.123-0.308-0.3080.0000.0000.0000.000
162A1983THR0-0.008-0.03019.531-0.466-0.4660.0000.0000.0000.000
163A1984ASP-1-0.784-0.84918.84316.91516.9150.0000.0000.0000.000
164A1985PRO00.0110.00318.400-0.854-0.8540.0000.0000.0000.000
165A1986ILE0-0.0210.01419.427-0.792-0.7920.0000.0000.0000.000
166A1987SER0-0.034-0.04020.856-0.960-0.9600.0000.0000.0000.000
167A1988LYS10.8020.88723.036-13.169-13.1690.0000.0000.0000.000
168A1989GLU-1-0.773-0.84621.49414.55914.5590.0000.0000.0000.000
169A1990ARG10.8190.91322.018-12.626-12.6260.0000.0000.0000.000
170A1991LEU0-0.0110.00016.8620.0490.0490.0000.0000.0000.000
171A1992SER00.007-0.01716.1770.1780.1780.0000.0000.0000.000
172A1993TYR00.0610.0049.2361.3841.3840.0000.0000.0000.000
173A1994LYS10.9160.94411.113-20.026-20.0260.0000.0000.0000.000
174A1995GLU-1-0.784-0.84611.65617.81117.8110.0000.0000.0000.000
175A1996ALA00.0050.00613.3840.4840.4840.0000.0000.0000.000
176A1997MET0-0.014-0.0165.776-0.145-0.1450.0000.0000.0000.000
177A1998GLY0-0.0200.0009.3782.6392.6390.0000.0000.0000.000
178A1999ARG10.7530.83811.175-17.947-17.9470.0000.0000.0000.000
179A2000CYS0-0.103-0.0328.737-1.476-1.4760.0000.0000.0000.000
180A2001ARG10.8380.9249.623-20.651-20.6510.0000.0000.0000.000
181A2002LYS10.8540.8951.755-145.966-155.30030.918-12.988-8.5970.154
182A2003ASP-1-0.763-0.8637.40221.55821.5580.0000.0000.0000.000
183A2004PRO0-0.012-0.0148.8102.4412.4410.0000.0000.0000.000
184A2005LEU0-0.0330.00710.989-0.652-0.6520.0000.0000.0000.000
185A2006SER0-0.015-0.0358.9260.0260.0260.0000.0000.0000.000
186A2007GLY00.0260.0085.2091.8381.8380.0000.0000.0000.000
187A2008LEU0-0.025-0.0114.7027.5757.731-0.001-0.007-0.1480.000
188A2009LEU00.0250.0214.019-1.518-1.231-0.001-0.020-0.2670.000
189A2010LEU0-0.044-0.0276.555-3.819-3.8190.0000.0000.0000.000
190A2011LEU00.0570.02510.3860.3590.3590.0000.0000.0000.000
191A2012PRO0-0.010-0.00713.062-1.031-1.0310.0000.0000.0000.000
192A2013ALA00.0290.00916.004-0.495-0.4950.0000.0000.0000.000
193A2014ALA0-0.0120.00819.298-0.159-0.1590.0000.0000.0000.000