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

tag_button

FMODB ID: 1N3MZ

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 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 -2005763.798898
FMO2-HF: Nuclear repulsion 1931856.476775
FMO2-HF: Total energy -73907.322123
FMO2-MP2: Total energy -74123.031667


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.
-0.930.8540.013-0.859-0.9380.002
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 : -0.016 / 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].
3A1893PRO0-0.0050.0013.508-2.760-0.9760.013-0.859-0.9380.002
4A1894LYS10.8960.9525.7021.8081.8080.0000.0000.0000.000
5A1895VAL00.0320.0187.6230.2250.2250.0000.0000.0000.000
6A1896LEU00.0110.01110.7740.1580.1580.0000.0000.0000.000
7A1897PHE00.0690.03013.7890.0050.0050.0000.0000.0000.000
8A1898THR0-0.016-0.03917.3520.0350.0350.0000.0000.0000.000
9A1899GLY00.0070.02120.5270.0000.0000.0000.0000.0000.000
10A1900VAL0-0.0080.01220.6370.0130.0130.0000.0000.0000.000
11A1901VAL00.0100.00322.833-0.012-0.0120.0000.0000.0000.000
12A1902ASP-1-0.742-0.86820.220-0.338-0.3380.0000.0000.0000.000
13A1903ALA00.0620.03020.329-0.037-0.0370.0000.0000.0000.000
14A1904ARG10.8460.92320.9930.2210.2210.0000.0000.0000.000
15A1905GLY00.0480.01418.020-0.011-0.0110.0000.0000.0000.000
16A1906GLU-1-0.938-0.96916.268-0.427-0.4270.0000.0000.0000.000
17A1907ARG10.9650.96915.8310.2020.2020.0000.0000.0000.000
18A1908ALA0-0.029-0.01216.6750.0240.0240.0000.0000.0000.000
19A1909VAL00.0070.00310.724-0.030-0.0300.0000.0000.0000.000
20A1910LEU0-0.0010.00111.890-0.080-0.0800.0000.0000.0000.000
21A1911ALA0-0.060-0.03013.1420.0380.0380.0000.0000.0000.000
22A1912LEU0-0.041-0.00111.6340.0930.0930.0000.0000.0000.000
23A1913GLY00.0020.0119.304-0.022-0.0220.0000.0000.0000.000
24A1914GLY0-0.007-0.0027.509-0.319-0.3190.0000.0000.0000.000
25A1915SER0-0.066-0.0447.0130.4790.4790.0000.0000.0000.000
26A1916LEU00.0360.0089.396-0.133-0.1330.0000.0000.0000.000
27A1917ALA0-0.056-0.01710.609-0.025-0.0250.0000.0000.0000.000
28A1918GLY0-0.003-0.00811.5300.0990.0990.0000.0000.0000.000
29A1919SER0-0.013-0.02013.2320.0790.0790.0000.0000.0000.000
30A1920ALA00.0410.00113.200-0.079-0.0790.0000.0000.0000.000
31A1921ALA00.0110.01113.477-0.016-0.0160.0000.0000.0000.000
32A1922GLU-1-0.833-0.8919.080-0.646-0.6460.0000.0000.0000.000
33A1923ALA0-0.0230.0018.288-0.199-0.1990.0000.0000.0000.000
34A1924SER00.026-0.0075.280-0.028-0.0280.0000.0000.0000.000
35A1925HIS00.0630.0486.776-0.047-0.0470.0000.0000.0000.000
36A1926LEU0-0.035-0.01310.4650.0410.0410.0000.0000.0000.000
37A1927VAL0-0.0050.00914.0970.0240.0240.0000.0000.0000.000
38A1928THR0-0.050-0.06416.5760.0400.0400.0000.0000.0000.000
39A1929ASP-1-0.794-0.88120.341-0.232-0.2320.0000.0000.0000.000
40A1930ARG10.7330.82023.5500.1690.1690.0000.0000.0000.000
41A1931ILE0-0.0160.00823.809-0.016-0.0160.0000.0000.0000.000
42A1932ARG10.8390.89523.5550.2480.2480.0000.0000.0000.000
43A1933ARG10.8040.88624.4370.1010.1010.0000.0000.0000.000
44A1934THR0-0.011-0.00422.652-0.001-0.0010.0000.0000.0000.000
45A1935VAL00.0620.01821.271-0.009-0.0090.0000.0000.0000.000
46A1936LYS10.9090.95517.9280.3700.3700.0000.0000.0000.000
47A1937PHE00.0380.02117.999-0.030-0.0300.0000.0000.0000.000
48A1938LEU00.0290.01619.454-0.005-0.0050.0000.0000.0000.000
49A1939CYS0-0.032-0.00717.2890.0120.0120.0000.0000.0000.000
50A1940ALA00.012-0.00114.9340.0010.0010.0000.0000.0000.000
51A1941LEU0-0.011-0.00515.600-0.007-0.0070.0000.0000.0000.000
52A1942GLY00.0500.01518.1910.0140.0140.0000.0000.0000.000
53A1943ARG10.8270.9109.3160.4270.4270.0000.0000.0000.000
54A1944GLY00.0400.03113.8770.0020.0020.0000.0000.0000.000
55A1945ILE0-0.064-0.00910.543-0.012-0.0120.0000.0000.0000.000
56A1946PRO0-0.001-0.01010.4300.0770.0770.0000.0000.0000.000
57A1947ILE00.0020.00613.277-0.069-0.0690.0000.0000.0000.000
58A1948LEU0-0.024-0.00613.0470.0290.0290.0000.0000.0000.000
59A1949SER00.035-0.01317.171-0.009-0.0090.0000.0000.0000.000
60A1950LEU0-0.004-0.02418.364-0.044-0.0440.0000.0000.0000.000
61A1951ASP-1-0.851-0.89619.271-0.285-0.2850.0000.0000.0000.000
62A1952TRP00.0080.0109.729-0.014-0.0140.0000.0000.0000.000
63A1953LEU0-0.0140.01713.065-0.008-0.0080.0000.0000.0000.000
64A1954HIS0-0.036-0.04416.4430.0640.0640.0000.0000.0000.000
65A1955GLN00.0410.03319.1370.0450.0450.0000.0000.0000.000
66A1956SER00.015-0.00314.7380.0140.0140.0000.0000.0000.000
67A1957ARG10.8940.94816.7250.3270.3270.0000.0000.0000.000
68A1958LYS10.8100.90318.3210.2290.2290.0000.0000.0000.000
69A1959ALA00.0050.01917.2860.0300.0300.0000.0000.0000.000
70A1960GLY0-0.0040.00717.0210.0410.0410.0000.0000.0000.000
71A1961PHE0-0.025-0.01812.1130.0170.0170.0000.0000.0000.000
72A1962PHE0-0.014-0.0239.019-0.108-0.1080.0000.0000.0000.000
73A1963LEU00.0160.01511.5830.0680.0680.0000.0000.0000.000
74A1964PRO00.0120.02012.642-0.141-0.1410.0000.0000.0000.000
75A1965PRO0-0.005-0.01911.7260.0100.0100.0000.0000.0000.000
76A1966ASP-1-0.872-0.94814.257-0.299-0.2990.0000.0000.0000.000
77A1967GLU-1-0.933-0.96517.209-0.157-0.1570.0000.0000.0000.000
78A1968TYR0-0.025-0.01816.8990.0150.0150.0000.0000.0000.000
79A1969VAL0-0.0040.00017.329-0.035-0.0350.0000.0000.0000.000
80A1970VAL0-0.056-0.02619.2190.0290.0290.0000.0000.0000.000
81A1971THR00.0070.01921.6540.0140.0140.0000.0000.0000.000
82A1972ASP-1-0.753-0.86525.098-0.168-0.1680.0000.0000.0000.000
83A1973PRO00.0670.02627.6300.0070.0070.0000.0000.0000.000
84A1974GLU-1-0.849-0.88730.759-0.115-0.1150.0000.0000.0000.000
85A1975GLN00.043-0.00228.7580.0170.0170.0000.0000.0000.000
86A1976GLU-1-0.833-0.91326.355-0.157-0.1570.0000.0000.0000.000
87A1977LYS10.9660.98529.8770.0890.0890.0000.0000.0000.000
88A1978ASN0-0.085-0.03732.8760.0120.0120.0000.0000.0000.000
89A1979PHE00.0080.00030.0770.0040.0040.0000.0000.0000.000
90A1980GLY00.0030.00932.5220.0040.0040.0000.0000.0000.000
91A1981PHE0-0.090-0.05824.9500.0050.0050.0000.0000.0000.000
92A1982SER00.0390.00226.258-0.005-0.0050.0000.0000.0000.000
93A1983LEU00.018-0.00520.6680.0020.0020.0000.0000.0000.000
94A1984GLN00.1020.04719.206-0.035-0.0350.0000.0000.0000.000
95A1985ASP-1-0.874-0.89021.921-0.108-0.1080.0000.0000.0000.000
96A1986ALA0-0.0070.00223.2390.0070.0070.0000.0000.0000.000
97A1987LEU0-0.004-0.01316.7480.0020.0020.0000.0000.0000.000
98A1988SER0-0.058-0.04218.658-0.003-0.0030.0000.0000.0000.000
99A1989ARG10.8320.90320.6080.1110.1110.0000.0000.0000.000
100A1990ALA0-0.0010.01618.1870.0130.0130.0000.0000.0000.000
101A1991ARG10.7890.89414.9930.2980.2980.0000.0000.0000.000
102A1992GLU-1-0.837-0.87217.380-0.005-0.0050.0000.0000.0000.000
103A1993ARG10.7970.86520.5290.0440.0440.0000.0000.0000.000
104A1994ARG10.8390.91217.7390.0770.0770.0000.0000.0000.000
105A1995LEU0-0.0050.00521.3200.0080.0080.0000.0000.0000.000
106A1996LEU0-0.050-0.03223.5070.0040.0040.0000.0000.0000.000
107A1997GLU-1-0.833-0.91122.7590.0020.0020.0000.0000.0000.000
108A1998GLY0-0.021-0.00825.168-0.001-0.0010.0000.0000.0000.000
109A1999TYR0-0.037-0.02527.4110.0000.0000.0000.0000.0000.000
110A2000GLU-1-0.819-0.88827.797-0.015-0.0150.0000.0000.0000.000
111A2001ILE00.0140.01027.4320.0000.0000.0000.0000.0000.000
112A2002TYR00.0070.00929.666-0.003-0.0030.0000.0000.0000.000
113A2003VAL0-0.010-0.01229.402-0.002-0.0020.0000.0000.0000.000
114A2004THR0-0.033-0.01632.7670.0010.0010.0000.0000.0000.000
115A2005PRO0-0.029-0.03534.978-0.005-0.0050.0000.0000.0000.000
116A2006GLY00.0290.02235.425-0.004-0.0040.0000.0000.0000.000
117A2007VAL0-0.061-0.01531.831-0.003-0.0030.0000.0000.0000.000
118A2008GLN0-0.031-0.00632.012-0.010-0.0100.0000.0000.0000.000
119A2009PRO00.018-0.00926.8490.0010.0010.0000.0000.0000.000
120A2010PRO00.0660.02428.9410.0050.0050.0000.0000.0000.000
121A2011PRO00.0240.01328.499-0.008-0.0080.0000.0000.0000.000
122A2012PRO00.0160.00725.823-0.001-0.0010.0000.0000.0000.000
123A2013GLN0-0.035-0.02722.9170.0010.0010.0000.0000.0000.000
124A2014MET0-0.0100.00724.208-0.007-0.0070.0000.0000.0000.000
125A2015GLY00.0490.01424.9220.0010.0010.0000.0000.0000.000
126A2016GLU-1-0.837-0.90919.572-0.200-0.2000.0000.0000.0000.000
127A2017ILE00.015-0.00620.025-0.010-0.0100.0000.0000.0000.000
128A2018ILE0-0.021-0.00321.6150.0010.0010.0000.0000.0000.000
129A2019SER0-0.006-0.01419.5690.0110.0110.0000.0000.0000.000
130A2020CYS0-0.102-0.03717.052-0.001-0.0010.0000.0000.0000.000
131A2021CYS0-0.045-0.01717.840-0.007-0.0070.0000.0000.0000.000
132A2022GLY0-0.027-0.01319.9540.0110.0110.0000.0000.0000.000
133A2023GLY00.0360.03320.6360.0120.0120.0000.0000.0000.000
134A2024THR0-0.028-0.02123.344-0.003-0.0030.0000.0000.0000.000
135A2025TYR00.0200.01424.468-0.003-0.0030.0000.0000.0000.000
136A2026LEU0-0.009-0.00626.2280.0070.0070.0000.0000.0000.000
137A2027PRO00.0200.01527.177-0.003-0.0030.0000.0000.0000.000
138A2028SER0-0.052-0.04129.6410.0030.0030.0000.0000.0000.000
139A2029MET0-0.0030.01833.0560.0010.0010.0000.0000.0000.000
140A2030PRO00.0160.01834.6670.0040.0040.0000.0000.0000.000
141A2031ARG10.9400.95036.6000.0220.0220.0000.0000.0000.000
142A2032SER00.0410.01838.8980.0010.0010.0000.0000.0000.000
143A2033TYR00.0600.04038.677-0.001-0.0010.0000.0000.0000.000
144A2034LYS10.8130.90231.5000.0170.0170.0000.0000.0000.000
145A2035PRO00.0510.03135.579-0.003-0.0030.0000.0000.0000.000
146A2036GLN00.0340.01331.4790.0040.0040.0000.0000.0000.000
147A2037ARG10.7890.89632.1730.0140.0140.0000.0000.0000.000
148A2038VAL0-0.005-0.01632.2610.0010.0010.0000.0000.0000.000
149A2039VAL0-0.021-0.01334.000-0.001-0.0010.0000.0000.0000.000
150A2040ILE00.0060.01930.7680.0000.0000.0000.0000.0000.000
151A2041THR00.015-0.03434.2460.0010.0010.0000.0000.0000.000
152A2042CYS0-0.031-0.01437.156-0.003-0.0030.0000.0000.0000.000
153A2043PRO00.0610.02639.5090.0020.0020.0000.0000.0000.000
154A2044GLN00.0700.02139.5650.0050.0050.0000.0000.0000.000
155A2045ASP-1-0.778-0.86837.995-0.059-0.0590.0000.0000.0000.000
156A2046PHE00.0400.01141.6010.0020.0020.0000.0000.0000.000
157A2047PRO0-0.016-0.00744.0280.0020.0020.0000.0000.0000.000
158A2048HIS00.0090.00639.8040.0040.0040.0000.0000.0000.000
159A2049CYS0-0.016-0.00741.5760.0010.0010.0000.0000.0000.000
160A2050SER00.0150.01842.7130.0030.0030.0000.0000.0000.000
161A2051ILE0-0.011-0.00441.1850.0020.0020.0000.0000.0000.000
162A2052PRO00.0410.00339.2760.0020.0020.0000.0000.0000.000
163A2053LEU00.0430.02541.6530.0020.0020.0000.0000.0000.000
164A2054ARG10.8370.92045.0990.0250.0250.0000.0000.0000.000
165A2055VAL0-0.050-0.01940.9580.0020.0020.0000.0000.0000.000
166A2056GLY00.0230.01842.7020.0010.0010.0000.0000.0000.000
167A2057LEU0-0.045-0.02237.0370.0000.0000.0000.0000.0000.000
168A2058PRO0-0.0300.00537.317-0.001-0.0010.0000.0000.0000.000
169A2059LEU00.0200.00137.938-0.002-0.0020.0000.0000.0000.000
170A2060LEU0-0.0040.00333.8730.0010.0010.0000.0000.0000.000
171A2061SER00.0620.01736.250-0.004-0.0040.0000.0000.0000.000
172A2062PRO00.0470.01132.144-0.001-0.0010.0000.0000.0000.000
173A2063GLU-1-0.787-0.82431.275-0.106-0.1060.0000.0000.0000.000
174A2064PHE00.0160.01030.299-0.004-0.0040.0000.0000.0000.000
175A2065LEU0-0.034-0.01926.740-0.002-0.0020.0000.0000.0000.000
176A2066LEU0-0.013-0.02027.424-0.010-0.0100.0000.0000.0000.000
177A2067THR0-0.013-0.02428.653-0.009-0.0090.0000.0000.0000.000
178A2068GLY00.0090.01428.677-0.004-0.0040.0000.0000.0000.000
179A2069VAL00.002-0.01122.5000.0000.0000.0000.0000.0000.000
180A2070LEU0-0.050-0.00523.896-0.013-0.0130.0000.0000.0000.000
181A2071LYS10.8780.94025.0040.0850.0850.0000.0000.0000.000
182A2072GLN0-0.003-0.01121.5910.0110.0110.0000.0000.0000.000
183A2073GLU-1-0.887-0.94425.083-0.072-0.0720.0000.0000.0000.000
184A2074ALA0-0.0030.00328.0530.0000.0000.0000.0000.0000.000
185A2075LYS10.9020.94729.7920.0720.0720.0000.0000.0000.000
186A2076PRO00.0100.00532.997-0.002-0.0020.0000.0000.0000.000
187A2077GLU-1-0.851-0.94935.163-0.043-0.0430.0000.0000.0000.000
188A2078ALA0-0.048-0.01636.5080.0010.0010.0000.0000.0000.000
189A2079PHE0-0.012-0.00733.519-0.003-0.0030.0000.0000.0000.000
190A2080VAL00.0160.01237.834-0.001-0.0010.0000.0000.0000.000
191A2081LEU0-0.059-0.02538.8690.0000.0000.0000.0000.0000.000
192A2082SER00.0060.01442.0680.0020.0020.0000.0000.0000.000
193A2083PRO0-0.017-0.00845.797-0.001-0.0010.0000.0000.0000.000