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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: YVM42

Calculation Name: 2AZM-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 2AZM

Chain ID: A

ChEMBL ID:

UniProt ID: P16104

Base Structure: X-ray

Registration Date: 2023-09-23

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2000919.471695
FMO2-HF: Nuclear repulsion 1927013.190251
FMO2-HF: Total energy -73906.281444
FMO2-MP2: Total energy -74122.019166


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:1891:THR)


Summations of interaction energy for fragment #1(A:1891:THR)
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.
-1.5021.0020.004-1.283-1.2250.005
Interaction energy analysis for fragmet #1(A:1891:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.005
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].
3A1893PRO00.0050.0073.500-0.6431.8610.004-1.283-1.2250.005
4A1894LYS10.9300.9785.291-0.730-0.7300.0000.0000.0000.000
5A1895VAL00.0400.0127.6820.1570.1570.0000.0000.0000.000
6A1896LEU0-0.0150.01211.1780.0720.0720.0000.0000.0000.000
7A1897PHE00.0770.04114.275-0.050-0.0500.0000.0000.0000.000
8A1898THR0-0.012-0.02317.8240.0540.0540.0000.0000.0000.000
9A1899GLY0-0.0030.01321.053-0.019-0.0190.0000.0000.0000.000
10A1900VAL00.0240.03021.293-0.003-0.0030.0000.0000.0000.000
11A1901VAL00.0060.01422.5730.0050.0050.0000.0000.0000.000
12A1902ASP-1-0.747-0.90219.955-0.298-0.2980.0000.0000.0000.000
13A1903ALA00.0550.02720.272-0.027-0.0270.0000.0000.0000.000
14A1904ARG10.8850.95520.7520.2800.2800.0000.0000.0000.000
15A1905GLY00.0270.01418.338-0.041-0.0410.0000.0000.0000.000
16A1906GLU-1-0.903-0.96016.239-0.261-0.2610.0000.0000.0000.000
17A1907ARG10.9110.94015.9250.1940.1940.0000.0000.0000.000
18A1908ALA0-0.033-0.02116.278-0.032-0.0320.0000.0000.0000.000
19A1909VAL00.0250.02110.777-0.109-0.1090.0000.0000.0000.000
20A1910LEU00.0100.00811.502-0.155-0.1550.0000.0000.0000.000
21A1911ALA0-0.059-0.02412.893-0.042-0.0420.0000.0000.0000.000
22A1912LEU0-0.039-0.01911.4560.0350.0350.0000.0000.0000.000
23A1913GLY00.0070.0219.086-0.270-0.2700.0000.0000.0000.000
24A1914GLY0-0.006-0.0017.102-0.425-0.4250.0000.0000.0000.000
25A1915SER0-0.070-0.0407.0940.4320.4320.0000.0000.0000.000
26A1916LEU00.0250.0079.319-0.036-0.0360.0000.0000.0000.000
27A1917ALA0-0.059-0.02010.4820.0920.0920.0000.0000.0000.000
28A1918GLY0-0.001-0.01711.507-0.059-0.0590.0000.0000.0000.000
29A1919SER0-0.041-0.04113.416-0.010-0.0100.0000.0000.0000.000
30A1920ALA00.0580.00613.2800.0390.0390.0000.0000.0000.000
31A1921ALA0-0.0010.00013.1260.0350.0350.0000.0000.0000.000
32A1922GLU-1-0.832-0.8839.7360.7520.7520.0000.0000.0000.000
33A1923ALA0-0.033-0.0078.5780.2110.2110.0000.0000.0000.000
34A1924SER00.0000.0066.3760.1990.1990.0000.0000.0000.000
35A1925HIS00.0700.0337.255-0.074-0.0740.0000.0000.0000.000
36A1926LEU0-0.023-0.00111.7210.0790.0790.0000.0000.0000.000
37A1927VAL0-0.0010.01214.941-0.045-0.0450.0000.0000.0000.000
38A1928THR0-0.064-0.07817.4070.0520.0520.0000.0000.0000.000
39A1929ASP-1-0.800-0.89421.190-0.145-0.1450.0000.0000.0000.000
40A1930ARG10.8280.94224.3840.0840.0840.0000.0000.0000.000
41A1931ILE0-0.023-0.00224.8250.0040.0040.0000.0000.0000.000
42A1932ARG10.8420.89924.4850.0880.0880.0000.0000.0000.000
43A1933ARG10.8300.88725.586-0.018-0.0180.0000.0000.0000.000
44A1934THR0-0.014-0.01523.2540.0110.0110.0000.0000.0000.000
45A1935VAL00.0570.01821.6020.0000.0000.0000.0000.0000.000
46A1936LYS10.9210.96718.122-0.014-0.0140.0000.0000.0000.000
47A1937PHE00.0550.03219.1240.0110.0110.0000.0000.0000.000
48A1938LEU00.0350.01320.5790.0030.0030.0000.0000.0000.000
49A1939CYS0-0.043-0.00918.0110.0170.0170.0000.0000.0000.000
50A1940ALA0-0.010-0.01015.9880.0370.0370.0000.0000.0000.000
51A1941LEU00.0050.00116.5780.0020.0020.0000.0000.0000.000
52A1942GLY00.0260.01819.0570.0020.0020.0000.0000.0000.000
53A1943ARG10.8580.9329.606-0.730-0.7300.0000.0000.0000.000
54A1944GLY00.0440.04114.9860.0250.0250.0000.0000.0000.000
55A1945ILE0-0.065-0.00511.258-0.032-0.0320.0000.0000.0000.000
56A1946PRO0-0.025-0.02410.856-0.011-0.0110.0000.0000.0000.000
57A1947ILE00.0080.00913.9960.0160.0160.0000.0000.0000.000
58A1948LEU0-0.035-0.01413.321-0.016-0.0160.0000.0000.0000.000
59A1949SER00.0840.03517.6160.0190.0190.0000.0000.0000.000
60A1950LEU0-0.012-0.02818.864-0.039-0.0390.0000.0000.0000.000
61A1951ASP-1-0.889-0.94120.353-0.308-0.3080.0000.0000.0000.000
62A1952TRP0-0.021-0.00810.0770.0360.0360.0000.0000.0000.000
63A1953LEU00.0150.01113.210-0.074-0.0740.0000.0000.0000.000
64A1954HIS0-0.071-0.04116.510-0.011-0.0110.0000.0000.0000.000
65A1955GLN00.0160.00418.8560.0170.0170.0000.0000.0000.000
66A1956SER00.0340.00614.326-0.060-0.0600.0000.0000.0000.000
67A1957ARG10.9010.95516.2680.4320.4320.0000.0000.0000.000
68A1958LYS10.8630.93417.8800.3510.3510.0000.0000.0000.000
69A1959ALA00.0060.02116.7460.0330.0330.0000.0000.0000.000
70A1960GLY00.0010.01216.5580.0170.0170.0000.0000.0000.000
71A1961PHE0-0.034-0.02611.496-0.066-0.0660.0000.0000.0000.000
72A1962PHE0-0.022-0.0228.4980.1140.1140.0000.0000.0000.000
73A1963LEU00.0140.01611.172-0.081-0.0810.0000.0000.0000.000
74A1964PRO00.0120.01711.907-0.145-0.1450.0000.0000.0000.000
75A1965PRO0-0.007-0.02111.1360.0830.0830.0000.0000.0000.000
76A1966ASP-1-0.901-0.95313.918-0.482-0.4820.0000.0000.0000.000
77A1967GLU-1-0.899-0.94816.807-0.252-0.2520.0000.0000.0000.000
78A1968TYR0-0.046-0.02516.3560.0350.0350.0000.0000.0000.000
79A1969VAL0-0.0040.00417.9490.0150.0150.0000.0000.0000.000
80A1970VAL0-0.028-0.01219.6110.0140.0140.0000.0000.0000.000
81A1971THR00.0230.00622.1350.0140.0140.0000.0000.0000.000
82A1972ASP-1-0.749-0.87925.545-0.085-0.0850.0000.0000.0000.000
83A1973PRO00.0700.03428.2530.0130.0130.0000.0000.0000.000
84A1974GLU-1-0.903-0.95531.297-0.057-0.0570.0000.0000.0000.000
85A1975GLN00.008-0.01529.7140.0140.0140.0000.0000.0000.000
86A1976GLU-1-0.855-0.92226.934-0.081-0.0810.0000.0000.0000.000
87A1977LYS10.9280.96930.8330.0570.0570.0000.0000.0000.000
88A1978ASN0-0.079-0.03733.8850.0090.0090.0000.0000.0000.000
89A1979PHE0-0.026-0.01430.8230.0080.0080.0000.0000.0000.000
90A1980GLY0-0.038-0.00833.4500.0070.0070.0000.0000.0000.000
91A1981PHE0-0.067-0.05125.7080.0070.0070.0000.0000.0000.000
92A1982SER00.0800.05326.992-0.010-0.0100.0000.0000.0000.000
93A1983LEU00.0120.00321.3940.0140.0140.0000.0000.0000.000
94A1984GLN00.0520.01919.641-0.011-0.0110.0000.0000.0000.000
95A1985ASP-1-0.879-0.94022.470-0.051-0.0510.0000.0000.0000.000
96A1986ALA0-0.045-0.03724.3320.0150.0150.0000.0000.0000.000
97A1987LEU0-0.021-0.02317.5840.0230.0230.0000.0000.0000.000
98A1988SER0-0.049-0.02619.5030.0090.0090.0000.0000.0000.000
99A1989ARG10.8620.92521.1600.0090.0090.0000.0000.0000.000
100A1990ALA00.0180.02219.2070.0170.0170.0000.0000.0000.000
101A1991ARG10.8180.89115.0680.1430.1430.0000.0000.0000.000
102A1992GLU-1-0.962-0.95018.0100.0880.0880.0000.0000.0000.000
103A1993ARG10.9260.95120.797-0.060-0.0600.0000.0000.0000.000
104A1994ARG10.8230.88917.728-0.264-0.2640.0000.0000.0000.000
105A1995LEU0-0.013-0.00521.423-0.009-0.0090.0000.0000.0000.000
106A1996LEU0-0.065-0.03823.702-0.015-0.0150.0000.0000.0000.000
107A1997GLU-1-0.869-0.92523.4430.2400.2400.0000.0000.0000.000
108A1998GLY0-0.001-0.00125.089-0.019-0.0190.0000.0000.0000.000
109A1999TYR0-0.070-0.04227.366-0.017-0.0170.0000.0000.0000.000
110A2000GLU-1-0.857-0.90827.6110.1770.1770.0000.0000.0000.000
111A2001ILE0-0.002-0.00727.921-0.016-0.0160.0000.0000.0000.000
112A2002TYR00.0020.01529.7540.0070.0070.0000.0000.0000.000
113A2003VAL0-0.0050.00429.690-0.008-0.0080.0000.0000.0000.000
114A2004THR0-0.042-0.05632.9000.0020.0020.0000.0000.0000.000
115A2005PRO0-0.009-0.02735.1360.0010.0010.0000.0000.0000.000
116A2006GLY00.0070.01335.7580.0000.0000.0000.0000.0000.000
117A2007VAL0-0.075-0.01932.535-0.007-0.0070.0000.0000.0000.000
118A2008GLN0-0.0120.00632.6670.0020.0020.0000.0000.0000.000
119A2009PRO00.004-0.02327.838-0.005-0.0050.0000.0000.0000.000
120A2010PRO00.0710.03329.1830.0050.0050.0000.0000.0000.000
121A2011PRO00.0260.01428.9100.0090.0090.0000.0000.0000.000
122A2012PRO00.0220.01126.2570.0100.0100.0000.0000.0000.000
123A2013GLN00.0490.02024.3470.0070.0070.0000.0000.0000.000
124A2014MET0-0.0130.00224.4830.0030.0030.0000.0000.0000.000
125A2015GLY00.0320.00325.1760.0050.0050.0000.0000.0000.000
126A2016GLU-1-0.922-0.96019.9490.2310.2310.0000.0000.0000.000
127A2017ILE00.021-0.01620.4140.0210.0210.0000.0000.0000.000
128A2018ILE0-0.024-0.00422.2110.0030.0030.0000.0000.0000.000
129A2019SER0-0.008-0.00519.5640.0090.0090.0000.0000.0000.000
130A2020CYS0-0.082-0.03517.4690.0490.0490.0000.0000.0000.000
131A2021CYS0-0.0340.00818.253-0.006-0.0060.0000.0000.0000.000
132A2022GLY0-0.007-0.00220.074-0.017-0.0170.0000.0000.0000.000
133A2023GLY00.0360.04120.952-0.010-0.0100.0000.0000.0000.000
134A2024THR0-0.024-0.02323.0860.0320.0320.0000.0000.0000.000
135A2025TYR00.000-0.00124.703-0.028-0.0280.0000.0000.0000.000
136A2026LEU0-0.004-0.01826.3850.0090.0090.0000.0000.0000.000
137A2027PRO00.0210.01627.886-0.013-0.0130.0000.0000.0000.000
138A2028SER0-0.037-0.01930.344-0.011-0.0110.0000.0000.0000.000
139A2029MET00.0020.00933.6680.0010.0010.0000.0000.0000.000
140A2030PRO00.0140.01634.9990.0000.0000.0000.0000.0000.000
141A2031ARG10.9350.94936.921-0.105-0.1050.0000.0000.0000.000
142A2032SER00.0210.01039.223-0.003-0.0030.0000.0000.0000.000
143A2033TYR00.0690.03838.9530.0050.0050.0000.0000.0000.000
144A2034LYS10.9430.97131.952-0.142-0.1420.0000.0000.0000.000
145A2035PRO00.0350.01335.691-0.001-0.0010.0000.0000.0000.000
146A2036GLN00.0100.00431.6480.0080.0080.0000.0000.0000.000
147A2037ARG10.7920.91032.182-0.122-0.1220.0000.0000.0000.000
148A2038VAL00.003-0.01132.303-0.009-0.0090.0000.0000.0000.000
149A2039VAL0-0.013-0.01033.8180.0080.0080.0000.0000.0000.000
150A2040ILE0-0.0210.00231.485-0.007-0.0070.0000.0000.0000.000
151A2041THR00.032-0.01634.7890.0010.0010.0000.0000.0000.000
152A2042CYS0-0.008-0.01137.738-0.004-0.0040.0000.0000.0000.000
153A2043PRO00.0530.02540.1030.0020.0020.0000.0000.0000.000
154A2044GLN00.0480.01640.174-0.002-0.0020.0000.0000.0000.000
155A2045ASP-1-0.773-0.84538.5260.0710.0710.0000.0000.0000.000
156A2046PHE00.0340.01442.1410.0040.0040.0000.0000.0000.000
157A2047PRO0-0.022-0.01444.4720.0020.0020.0000.0000.0000.000
158A2048HIS0-0.013-0.01140.0340.0050.0050.0000.0000.0000.000
159A2049CYS0-0.0180.00641.3160.0050.0050.0000.0000.0000.000
160A2050SER00.0020.00342.8070.0000.0000.0000.0000.0000.000
161A2051ILE00.000-0.01041.621-0.001-0.0010.0000.0000.0000.000
162A2052PRO00.0380.00839.503-0.001-0.0010.0000.0000.0000.000
163A2053LEU00.0400.01441.775-0.001-0.0010.0000.0000.0000.000
164A2054ARG10.8770.95645.168-0.062-0.0620.0000.0000.0000.000
165A2055VAL0-0.047-0.02141.276-0.001-0.0010.0000.0000.0000.000
166A2056GLY00.0190.02543.6390.0020.0020.0000.0000.0000.000
167A2057LEU0-0.053-0.03437.7070.0020.0020.0000.0000.0000.000
168A2058PRO0-0.0080.01337.401-0.004-0.0040.0000.0000.0000.000
169A2059LEU00.003-0.00438.3940.0060.0060.0000.0000.0000.000
170A2060LEU00.0060.00734.550-0.005-0.0050.0000.0000.0000.000
171A2061SER00.0590.03636.8370.0040.0040.0000.0000.0000.000
172A2062PRO00.0770.01533.0060.0040.0040.0000.0000.0000.000
173A2063GLU-1-0.795-0.84532.0160.0360.0360.0000.0000.0000.000
174A2064PHE00.0020.01730.735-0.002-0.0020.0000.0000.0000.000
175A2065LEU0-0.007-0.00627.0500.0030.0030.0000.0000.0000.000
176A2066LEU0-0.030-0.01628.160-0.001-0.0010.0000.0000.0000.000
177A2067THR0-0.038-0.03929.163-0.011-0.0110.0000.0000.0000.000
178A2068GLY00.0100.01329.594-0.006-0.0060.0000.0000.0000.000
179A2069VAL00.009-0.01823.2140.0000.0000.0000.0000.0000.000
180A2070LEU0-0.040-0.01024.807-0.003-0.0030.0000.0000.0000.000
181A2071LYS10.9480.98426.101-0.020-0.0200.0000.0000.0000.000
182A2072GLN00.0000.00822.6920.0050.0050.0000.0000.0000.000
183A2073GLU-1-0.945-0.98426.0820.0150.0150.0000.0000.0000.000
184A2074ALA0-0.0140.00128.981-0.001-0.0010.0000.0000.0000.000
185A2075LYS10.9770.98730.724-0.029-0.0290.0000.0000.0000.000
186A2076PRO00.007-0.00133.514-0.002-0.0020.0000.0000.0000.000
187A2077GLU-1-0.876-0.95835.7690.0500.0500.0000.0000.0000.000
188A2078ALA0-0.034-0.00237.666-0.003-0.0030.0000.0000.0000.000
189A2079PHE0-0.038-0.02134.612-0.003-0.0030.0000.0000.0000.000
190A2080VAL00.0170.00738.3760.0040.0040.0000.0000.0000.000
191A2081LEU0-0.047-0.02639.723-0.004-0.0040.0000.0000.0000.000
192A2082SER00.0090.01442.6070.0000.0000.0000.0000.0000.000
193A2083PRO0-0.020-0.00946.3790.0000.0000.0000.0000.0000.000