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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: VQ691

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2002525.827201
FMO2-HF: Nuclear repulsion 1928618.72176
FMO2-HF: Total energy -73907.105442
FMO2-MP2: Total energy -74122.842898


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.
-0.6610.9630.003-0.784-0.8430
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 : -0.010 / q_NPA : -0.019
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].
3A1893PRO00.0010.0083.640-2.590-0.9660.003-0.784-0.8430.000
4A1894LYS10.8960.9425.6101.9391.9390.0000.0000.0000.000
5A1895VAL00.0200.0037.4420.2660.2660.0000.0000.0000.000
6A1896LEU0-0.0020.01010.6780.1850.1850.0000.0000.0000.000
7A1897PHE00.0710.03613.6490.0050.0050.0000.0000.0000.000
8A1898THR0-0.009-0.04017.1980.0350.0350.0000.0000.0000.000
9A1899GLY0-0.0070.00920.2730.0040.0040.0000.0000.0000.000
10A1900VAL00.0150.02220.8230.0180.0180.0000.0000.0000.000
11A1901VAL00.0100.01722.200-0.022-0.0220.0000.0000.0000.000
12A1902ASP-1-0.740-0.88120.015-0.388-0.3880.0000.0000.0000.000
13A1903ALA00.0520.02520.220-0.040-0.0400.0000.0000.0000.000
14A1904ARG10.8470.92720.8380.2470.2470.0000.0000.0000.000
15A1905GLY00.0280.00818.195-0.013-0.0130.0000.0000.0000.000
16A1906GLU-1-0.935-0.97316.362-0.507-0.5070.0000.0000.0000.000
17A1907ARG10.9320.95015.9960.2430.2430.0000.0000.0000.000
18A1908ALA0-0.034-0.01816.3570.0020.0020.0000.0000.0000.000
19A1909VAL00.0160.02010.804-0.039-0.0390.0000.0000.0000.000
20A1910LEU00.0080.00611.552-0.131-0.1310.0000.0000.0000.000
21A1911ALA0-0.055-0.02212.9090.0260.0260.0000.0000.0000.000
22A1912LEU0-0.040-0.01811.5180.0930.0930.0000.0000.0000.000
23A1913GLY00.0080.0209.121-0.016-0.0160.0000.0000.0000.000
24A1914GLY0-0.0080.0007.145-0.425-0.4250.0000.0000.0000.000
25A1915SER0-0.068-0.0407.0400.5500.5500.0000.0000.0000.000
26A1916LEU00.0280.0079.379-0.181-0.1810.0000.0000.0000.000
27A1917ALA0-0.046-0.01210.1750.0260.0260.0000.0000.0000.000
28A1918GLY0-0.013-0.01611.4570.1130.1130.0000.0000.0000.000
29A1919SER0-0.022-0.02813.1750.0910.0910.0000.0000.0000.000
30A1920ALA00.0560.00712.673-0.092-0.0920.0000.0000.0000.000
31A1921ALA0-0.0010.00012.326-0.070-0.0700.0000.0000.0000.000
32A1922GLU-1-0.821-0.8729.443-0.707-0.7070.0000.0000.0000.000
33A1923ALA0-0.0240.0027.960-0.254-0.2540.0000.0000.0000.000
34A1924SER00.002-0.0165.282-0.080-0.0800.0000.0000.0000.000
35A1925HIS00.0660.0527.213-0.109-0.1090.0000.0000.0000.000
36A1926LEU0-0.0310.00010.4990.0440.0440.0000.0000.0000.000
37A1927VAL0-0.0110.00513.9850.0280.0280.0000.0000.0000.000
38A1928THR0-0.066-0.07616.4170.0440.0440.0000.0000.0000.000
39A1929ASP-1-0.783-0.88620.185-0.266-0.2660.0000.0000.0000.000
40A1930ARG10.7150.83123.5000.1950.1950.0000.0000.0000.000
41A1931ILE0-0.0220.00823.682-0.024-0.0240.0000.0000.0000.000
42A1932ARG10.8460.90223.3690.2810.2810.0000.0000.0000.000
43A1933ARG10.8270.88824.4850.1210.1210.0000.0000.0000.000
44A1934THR0-0.0050.01322.504-0.002-0.0020.0000.0000.0000.000
45A1935VAL00.0660.01820.943-0.008-0.0080.0000.0000.0000.000
46A1936LYS10.9160.96717.4590.4330.4330.0000.0000.0000.000
47A1937PHE00.0360.01718.117-0.033-0.0330.0000.0000.0000.000
48A1938LEU00.0320.01519.576-0.007-0.0070.0000.0000.0000.000
49A1939CYS0-0.036-0.01317.1700.0100.0100.0000.0000.0000.000
50A1940ALA0-0.016-0.01215.056-0.004-0.0040.0000.0000.0000.000
51A1941LEU00.0010.00015.670-0.019-0.0190.0000.0000.0000.000
52A1942GLY00.0430.01618.2530.0140.0140.0000.0000.0000.000
53A1943ARG10.8570.9189.0340.5790.5790.0000.0000.0000.000
54A1944GLY00.0360.03714.3600.0060.0060.0000.0000.0000.000
55A1945ILE0-0.056-0.00510.347-0.011-0.0110.0000.0000.0000.000
56A1946PRO0-0.019-0.01910.5620.1020.1020.0000.0000.0000.000
57A1947ILE00.0060.00513.457-0.077-0.0770.0000.0000.0000.000
58A1948LEU0-0.038-0.01313.2710.0400.0400.0000.0000.0000.000
59A1949SER00.054-0.00717.122-0.017-0.0170.0000.0000.0000.000
60A1950LEU0-0.005-0.02418.426-0.050-0.0500.0000.0000.0000.000
61A1951ASP-1-0.874-0.90820.052-0.295-0.2950.0000.0000.0000.000
62A1952TRP0-0.0050.0039.730-0.022-0.0220.0000.0000.0000.000
63A1953LEU00.0070.02012.9330.0010.0010.0000.0000.0000.000
64A1954HIS0-0.015-0.02416.4150.0670.0670.0000.0000.0000.000
65A1955GLN00.0790.04518.9580.0290.0290.0000.0000.0000.000
66A1956SER00.0250.00114.3250.0150.0150.0000.0000.0000.000
67A1957ARG10.9080.95616.2970.3700.3700.0000.0000.0000.000
68A1958LYS10.8030.90117.8800.2450.2450.0000.0000.0000.000
69A1959ALA0-0.0010.01717.0600.0310.0310.0000.0000.0000.000
70A1960GLY00.0030.01116.7190.0440.0440.0000.0000.0000.000
71A1961PHE0-0.038-0.02612.1120.0140.0140.0000.0000.0000.000
72A1962PHE0-0.011-0.0208.681-0.105-0.1050.0000.0000.0000.000
73A1963LEU00.0070.01011.3550.1180.1180.0000.0000.0000.000
74A1964PRO00.0050.01311.920-0.153-0.1530.0000.0000.0000.000
75A1965PRO0-0.009-0.02411.1810.0000.0000.0000.0000.0000.000
76A1966ASP-1-0.883-0.95013.934-0.264-0.2640.0000.0000.0000.000
77A1967GLU-1-0.906-0.95016.818-0.156-0.1560.0000.0000.0000.000
78A1968TYR0-0.043-0.02916.3660.0080.0080.0000.0000.0000.000
79A1969VAL0-0.0070.00417.866-0.038-0.0380.0000.0000.0000.000
80A1970VAL0-0.025-0.01019.5410.0300.0300.0000.0000.0000.000
81A1971THR00.0240.01421.7030.0150.0150.0000.0000.0000.000
82A1972ASP-1-0.743-0.85625.254-0.182-0.1820.0000.0000.0000.000
83A1973PRO00.0850.03827.6850.0070.0070.0000.0000.0000.000
84A1974GLU-1-0.847-0.90330.851-0.131-0.1310.0000.0000.0000.000
85A1975GLN00.038-0.00528.7890.0190.0190.0000.0000.0000.000
86A1976GLU-1-0.857-0.91726.598-0.168-0.1680.0000.0000.0000.000
87A1977LYS10.9300.96630.1150.0980.0980.0000.0000.0000.000
88A1978ASN0-0.075-0.03632.8330.0140.0140.0000.0000.0000.000
89A1979PHE00.0110.00829.8170.0030.0030.0000.0000.0000.000
90A1980GLY0-0.0110.00232.4130.0040.0040.0000.0000.0000.000
91A1981PHE0-0.069-0.04624.7740.0050.0050.0000.0000.0000.000
92A1982SER00.0390.00426.808-0.007-0.0070.0000.0000.0000.000
93A1983LEU00.0210.00020.8960.0000.0000.0000.0000.0000.000
94A1984GLN00.0830.03219.725-0.041-0.0410.0000.0000.0000.000
95A1985ASP-1-0.861-0.89322.288-0.117-0.1170.0000.0000.0000.000
96A1986ALA0-0.028-0.02623.6270.0080.0080.0000.0000.0000.000
97A1987LEU0-0.015-0.02117.024-0.007-0.0070.0000.0000.0000.000
98A1988SER0-0.053-0.03519.047-0.004-0.0040.0000.0000.0000.000
99A1989ARG10.8460.92020.9320.1230.1230.0000.0000.0000.000
100A1990ALA00.0170.02618.5140.0140.0140.0000.0000.0000.000
101A1991ARG10.8190.90914.9610.3540.3540.0000.0000.0000.000
102A1992GLU-1-0.852-0.87917.726-0.005-0.0050.0000.0000.0000.000
103A1993ARG10.8000.87220.7290.0520.0520.0000.0000.0000.000
104A1994ARG10.8310.90017.5530.1170.1170.0000.0000.0000.000
105A1995LEU0-0.004-0.00121.0930.0120.0120.0000.0000.0000.000
106A1996LEU0-0.063-0.04223.2940.0090.0090.0000.0000.0000.000
107A1997GLU-1-0.865-0.92123.103-0.004-0.0040.0000.0000.0000.000
108A1998GLY00.0040.00324.8940.0000.0000.0000.0000.0000.000
109A1999TYR0-0.065-0.03927.1490.0010.0010.0000.0000.0000.000
110A2000GLU-1-0.804-0.87327.410-0.020-0.0200.0000.0000.0000.000
111A2001ILE00.004-0.00627.6220.0000.0000.0000.0000.0000.000
112A2002TYR00.0120.02029.421-0.002-0.0020.0000.0000.0000.000
113A2003VAL0-0.010-0.00129.146-0.002-0.0020.0000.0000.0000.000
114A2004THR0-0.024-0.02432.4200.0020.0020.0000.0000.0000.000
115A2005PRO0-0.022-0.03334.594-0.006-0.0060.0000.0000.0000.000
116A2006GLY00.0190.01935.154-0.004-0.0040.0000.0000.0000.000
117A2007VAL0-0.067-0.02031.787-0.002-0.0020.0000.0000.0000.000
118A2008GLN0-0.0290.00131.882-0.011-0.0110.0000.0000.0000.000
119A2009PRO00.013-0.01626.8850.0010.0010.0000.0000.0000.000
120A2010PRO00.0760.02928.6670.0060.0060.0000.0000.0000.000
121A2011PRO00.0150.00828.270-0.009-0.0090.0000.0000.0000.000
122A2012PRO00.0310.01825.740-0.003-0.0030.0000.0000.0000.000
123A2013GLN0-0.014-0.01522.8150.0010.0010.0000.0000.0000.000
124A2014MET0-0.016-0.00123.806-0.010-0.0100.0000.0000.0000.000
125A2015GLY00.0340.00624.6900.0010.0010.0000.0000.0000.000
126A2016GLU-1-0.849-0.91519.353-0.228-0.2280.0000.0000.0000.000
127A2017ILE00.009-0.01719.836-0.015-0.0150.0000.0000.0000.000
128A2018ILE0-0.0200.00021.6100.0000.0000.0000.0000.0000.000
129A2019SER0-0.015-0.01519.4070.0120.0120.0000.0000.0000.000
130A2020CYS0-0.090-0.03216.916-0.006-0.0060.0000.0000.0000.000
131A2021CYS0-0.041-0.00817.733-0.016-0.0160.0000.0000.0000.000
132A2022GLY0-0.008-0.00119.6930.0140.0140.0000.0000.0000.000
133A2023GLY00.0380.04320.6850.0150.0150.0000.0000.0000.000
134A2024THR0-0.030-0.02522.8580.0000.0000.0000.0000.0000.000
135A2025TYR0-0.002-0.00224.481-0.003-0.0030.0000.0000.0000.000
136A2026LEU0-0.003-0.01826.1180.0080.0080.0000.0000.0000.000
137A2027PRO00.0170.01527.684-0.003-0.0030.0000.0000.0000.000
138A2028SER0-0.027-0.01530.1240.0010.0010.0000.0000.0000.000
139A2029MET00.0000.00833.5170.0000.0000.0000.0000.0000.000
140A2030PRO00.0110.01434.6640.0040.0040.0000.0000.0000.000
141A2031ARG10.9410.95336.7740.0240.0240.0000.0000.0000.000
142A2032SER00.0340.01739.1760.0020.0020.0000.0000.0000.000
143A2033TYR00.0610.03938.834-0.002-0.0020.0000.0000.0000.000
144A2034LYS10.8470.92031.6880.0200.0200.0000.0000.0000.000
145A2035PRO00.0470.02535.631-0.004-0.0040.0000.0000.0000.000
146A2036GLN00.0270.00731.4110.0050.0050.0000.0000.0000.000
147A2037ARG10.7850.89431.9210.0170.0170.0000.0000.0000.000
148A2038VAL00.006-0.00931.8760.0010.0010.0000.0000.0000.000
149A2039VAL0-0.016-0.00833.452-0.001-0.0010.0000.0000.0000.000
150A2040ILE0-0.020-0.00130.8150.0000.0000.0000.0000.0000.000
151A2041THR00.032-0.02434.2380.0010.0010.0000.0000.0000.000
152A2042CYS0-0.017-0.01037.145-0.004-0.0040.0000.0000.0000.000
153A2043PRO00.0590.02839.4270.0030.0030.0000.0000.0000.000
154A2044GLN00.0560.02139.3230.0060.0060.0000.0000.0000.000
155A2045ASP-1-0.794-0.87537.905-0.067-0.0670.0000.0000.0000.000
156A2046PHE00.0570.02241.5600.0020.0020.0000.0000.0000.000
157A2047PRO0-0.025-0.01443.9860.0020.0020.0000.0000.0000.000
158A2048HIS0-0.015-0.00939.5880.0040.0040.0000.0000.0000.000
159A2049CYS0-0.0220.00440.9260.0000.0000.0000.0000.0000.000
160A2050SER00.0020.00342.3770.0030.0030.0000.0000.0000.000
161A2051ILE0-0.004-0.01341.3840.0020.0020.0000.0000.0000.000
162A2052PRO00.0490.01439.0910.0020.0020.0000.0000.0000.000
163A2053LEU00.0430.01841.4660.0020.0020.0000.0000.0000.000
164A2054ARG10.8620.94844.8170.0280.0280.0000.0000.0000.000
165A2055VAL0-0.049-0.02341.0660.0020.0020.0000.0000.0000.000
166A2056GLY00.0200.02643.4430.0020.0020.0000.0000.0000.000
167A2057LEU0-0.065-0.03637.0630.0000.0000.0000.0000.0000.000
168A2058PRO0-0.0100.01036.989-0.001-0.0010.0000.0000.0000.000
169A2059LEU00.0090.00437.962-0.002-0.0020.0000.0000.0000.000
170A2060LEU00.0130.00833.9180.0010.0010.0000.0000.0000.000
171A2061SER00.0660.02836.361-0.004-0.0040.0000.0000.0000.000
172A2062PRO00.0580.01132.138-0.001-0.0010.0000.0000.0000.000
173A2063GLU-1-0.789-0.83631.260-0.121-0.1210.0000.0000.0000.000
174A2064PHE00.0100.02030.354-0.004-0.0040.0000.0000.0000.000
175A2065LEU0-0.020-0.01126.823-0.003-0.0030.0000.0000.0000.000
176A2066LEU0-0.025-0.01427.377-0.012-0.0120.0000.0000.0000.000
177A2067THR0-0.023-0.03628.263-0.011-0.0110.0000.0000.0000.000
178A2068GLY00.0170.01928.838-0.004-0.0040.0000.0000.0000.000
179A2069VAL00.004-0.02122.430-0.002-0.0020.0000.0000.0000.000
180A2070LEU0-0.046-0.00323.979-0.015-0.0150.0000.0000.0000.000
181A2071LYS10.8710.93825.1840.0970.0970.0000.0000.0000.000
182A2072GLN0-0.013-0.01221.8670.0130.0130.0000.0000.0000.000
183A2073GLU-1-0.896-0.94225.346-0.078-0.0780.0000.0000.0000.000
184A2074ALA00.0000.00328.393-0.002-0.0020.0000.0000.0000.000
185A2075LYS10.8990.94130.1390.0830.0830.0000.0000.0000.000
186A2076PRO00.0130.00733.052-0.002-0.0020.0000.0000.0000.000
187A2077GLU-1-0.857-0.95235.228-0.049-0.0490.0000.0000.0000.000
188A2078ALA0-0.042-0.00836.9040.0010.0010.0000.0000.0000.000
189A2079PHE0-0.021-0.01633.734-0.003-0.0030.0000.0000.0000.000
190A2080VAL00.0020.00237.702-0.002-0.0020.0000.0000.0000.000
191A2081LEU0-0.050-0.02338.876-0.001-0.0010.0000.0000.0000.000
192A2082SER00.0120.01641.9660.0020.0020.0000.0000.0000.000
193A2083PRO0-0.021-0.01145.725-0.002-0.0020.0000.0000.0000.000