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: N98YQ

Calculation Name: 3LBX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LBX

Chain ID: B

ChEMBL ID:

UniProt ID: P02549

Base Structure: X-ray

Registration Date: 2023-06-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1680830.213503
FMO2-HF: Nuclear repulsion 1604454.822954
FMO2-HF: Total energy -76375.390549
FMO2-MP2: Total energy -76596.235662


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(B:1900:GLY)


Summations of interaction energy for fragment #1(B:1900:GLY)
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.
-1.2081.80.551-1.562-1.997-0.001
Interaction energy analysis for fragmet #1(B:1900:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.022
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].
3B1902THR00.0110.0003.810-1.198-0.204-0.003-0.412-0.5790.001
4B1903ALA00.0050.0082.5260.1250.5620.531-0.371-0.5970.000
5B1904ASP-1-0.873-0.9543.648-3.435-1.8580.023-0.779-0.821-0.002
6B1905LYS10.9800.9885.5000.9320.9320.0000.0000.0000.000
7B1906PHE0-0.039-0.0127.6650.2240.2240.0000.0000.0000.000
8B1907ARG10.9620.9655.6361.3761.3760.0000.0000.0000.000
9B1908PHE00.001-0.0049.5140.1430.1430.0000.0000.0000.000
10B1909PHE00.031-0.00311.5510.0820.0820.0000.0000.0000.000
11B1910SER0-0.036-0.01212.6440.0670.0670.0000.0000.0000.000
12B1911MET0-0.0120.01011.2080.0560.0560.0000.0000.0000.000
13B1912ALA00.0440.02915.5730.0440.0440.0000.0000.0000.000
14B1913ARG10.9290.97415.4970.2910.2910.0000.0000.0000.000
15B1914ASP-1-0.887-0.94118.218-0.211-0.2110.0000.0000.0000.000
16B1915LEU0-0.032-0.02518.4680.0200.0200.0000.0000.0000.000
17B1916LEU0-0.042-0.03421.4950.0190.0190.0000.0000.0000.000
18B1917SER0-0.041-0.01323.0570.0160.0160.0000.0000.0000.000
19B1918TRP00.0320.00924.2610.0070.0070.0000.0000.0000.000
20B1919MET0-0.0100.02224.9930.0070.0070.0000.0000.0000.000
21B1920GLU-1-0.952-0.94927.634-0.079-0.0790.0000.0000.0000.000
22B1921SER0-0.052-0.02829.0260.0080.0080.0000.0000.0000.000
23B1922ILE00.0550.02429.8140.0060.0060.0000.0000.0000.000
24B1923ILE0-0.017-0.01431.1990.0050.0050.0000.0000.0000.000
25B1924ARG10.9640.98332.4390.0760.0760.0000.0000.0000.000
26B1925GLN0-0.013-0.00733.8340.0010.0010.0000.0000.0000.000
27B1926ILE0-0.076-0.02135.6850.0040.0040.0000.0000.0000.000
28B1927GLU-1-0.921-0.96937.857-0.050-0.0500.0000.0000.0000.000
29B1928THR0-0.072-0.03038.2940.0020.0020.0000.0000.0000.000
30B1929GLN0-0.053-0.02940.9470.0040.0040.0000.0000.0000.000
31B1930GLU-1-0.902-0.94243.414-0.037-0.0370.0000.0000.0000.000
32B1931ARG0-0.0210.16046.0050.0010.0010.0000.0000.0000.000
33B1932PRO00.092-0.08747.0630.0000.0000.0000.0000.0000.000
34B1933ARG10.7640.82649.8670.0300.0300.0000.0000.0000.000
35B1934ASP-1-0.856-0.93949.066-0.031-0.0310.0000.0000.0000.000
36B1935VAL0-0.0070.04549.094-0.001-0.0010.0000.0000.0000.000
37B1936SER0-0.055-0.02351.6210.0010.0010.0000.0000.0000.000
38B1937SER00.0580.02255.1230.0000.0000.0000.0000.0000.000
39B1938VAL00.0350.01052.5460.0000.0000.0000.0000.0000.000
40B1939GLU-1-0.839-0.94348.749-0.036-0.0360.0000.0000.0000.000
41B1940LEU00.019-0.01046.952-0.001-0.0010.0000.0000.0000.000
42B1941LEU00.0450.00644.671-0.002-0.0020.0000.0000.0000.000
43B1942MET00.0220.03843.674-0.002-0.0020.0000.0000.0000.000
44B1943LYS10.9180.96241.7630.0450.0450.0000.0000.0000.000
45B1944TYR0-0.016-0.01939.086-0.003-0.0030.0000.0000.0000.000
46B1945HIS00.0480.02038.984-0.003-0.0030.0000.0000.0000.000
47B1946GLN00.0020.00338.250-0.002-0.0020.0000.0000.0000.000
48B1947GLY0-0.027-0.01636.955-0.003-0.0030.0000.0000.0000.000
49B1948ILE00.0590.02933.781-0.005-0.0050.0000.0000.0000.000
50B1949ASN00.0190.01433.015-0.008-0.0080.0000.0000.0000.000
51B1950ALA0-0.035-0.01732.466-0.004-0.0040.0000.0000.0000.000
52B1951GLU-1-0.910-0.95730.058-0.094-0.0940.0000.0000.0000.000
53B1952ILE00.0130.04728.528-0.011-0.0110.0000.0000.0000.000
54B1953GLU-1-0.923-0.95127.644-0.099-0.0990.0000.0000.0000.000
55B1954THR0-0.145-0.12226.747-0.009-0.0090.0000.0000.0000.000
56B1955ARG10.9280.97323.3000.1180.1180.0000.0000.0000.000
57B1956SER0-0.0160.00922.726-0.018-0.0180.0000.0000.0000.000
58B1957LYS11.0010.98420.3030.1190.1190.0000.0000.0000.000
59B1958ASN00.0140.00918.4570.0020.0020.0000.0000.0000.000
60B1959PHE00.0400.02418.032-0.025-0.0250.0000.0000.0000.000
61B1960SER00.0220.01718.464-0.008-0.0080.0000.0000.0000.000
62B1961ALA0-0.0060.00914.656-0.011-0.0110.0000.0000.0000.000
63B1962CYS0-0.052-0.02614.233-0.029-0.0290.0000.0000.0000.000
64B1963LEU0-0.003-0.04014.627-0.024-0.0240.0000.0000.0000.000
65B1964GLU-1-0.894-0.92813.611-0.219-0.2190.0000.0000.0000.000
66B1965LEU0-0.052-0.0067.667-0.015-0.0150.0000.0000.0000.000
67B1966GLY00.0050.00311.292-0.014-0.0140.0000.0000.0000.000
68B1967GLU-1-0.876-0.94813.510-0.090-0.0900.0000.0000.0000.000
69B1968SER0-0.033-0.04110.2210.0010.0010.0000.0000.0000.000
70B1969LEU0-0.140-0.0887.2270.0510.0510.0000.0000.0000.000
71B1970LEU00.0180.01110.4350.0940.0940.0000.0000.0000.000
72B1971GLN0-0.0180.00713.0780.0160.0160.0000.0000.0000.000
73B1972ARG10.8540.9427.3390.4050.4050.0000.0000.0000.000
74B1973GLN00.0530.03111.670-0.001-0.0010.0000.0000.0000.000
75B1974HIS00.0100.0038.0040.1590.1590.0000.0000.0000.000
76B1975GLN00.0220.02511.419-0.084-0.0840.0000.0000.0000.000
77B1976ALA0-0.021-0.01212.379-0.019-0.0190.0000.0000.0000.000
78B1977SER00.012-0.03614.118-0.053-0.0530.0000.0000.0000.000
79B1978GLU-1-0.873-0.92015.5950.0020.0020.0000.0000.0000.000
80B1979GLU-1-0.907-0.96016.031-0.159-0.1590.0000.0000.0000.000
81B1980ILE0-0.052-0.03911.610-0.030-0.0300.0000.0000.0000.000
82B1981ARG10.9690.98815.9930.0210.0210.0000.0000.0000.000
83B1982GLU-1-0.915-0.95618.947-0.060-0.0600.0000.0000.0000.000
84B1983LYS10.9220.97217.5860.1590.1590.0000.0000.0000.000
85B1984LEU00.0420.00716.196-0.010-0.0100.0000.0000.0000.000
86B1985GLN00.0200.01919.4890.0040.0040.0000.0000.0000.000
87B1986GLN0-0.024-0.00822.354-0.001-0.0010.0000.0000.0000.000
88B1987VAL0-0.022-0.01519.6860.0060.0060.0000.0000.0000.000
89B1988MET00.0100.00022.0180.0060.0060.0000.0000.0000.000
90B1989SER0-0.082-0.03124.4100.0070.0070.0000.0000.0000.000
91B1990ARG11.0110.98325.8630.0910.0910.0000.0000.0000.000
92B1991ARG10.9530.96324.2440.1150.1150.0000.0000.0000.000
93B1992LYS10.9280.95727.5060.0610.0610.0000.0000.0000.000
94B1993GLU-1-0.856-0.91530.356-0.063-0.0630.0000.0000.0000.000
95B1994MET0-0.033-0.00728.1720.0010.0010.0000.0000.0000.000
96B1995ASN00.005-0.01929.6100.0020.0020.0000.0000.0000.000
97B1996GLU-1-0.913-0.94233.309-0.048-0.0480.0000.0000.0000.000
98B1997LYS10.9170.94035.2920.0570.0570.0000.0000.0000.000
99B1998TRP00.004-0.00635.1570.0020.0020.0000.0000.0000.000
100B1999GLU-1-0.932-0.98036.650-0.047-0.0470.0000.0000.0000.000
101B2000ALA0-0.043-0.00538.9490.0030.0030.0000.0000.0000.000
102B2001ARG10.9020.96040.4410.0470.0470.0000.0000.0000.000
103B2002TRP0-0.021-0.01540.7780.0020.0020.0000.0000.0000.000
104B2003GLU-1-0.895-0.94542.672-0.031-0.0310.0000.0000.0000.000
105B2004ARG10.9240.94645.1700.0340.0340.0000.0000.0000.000
106B2005LEU0-0.029-0.01243.0590.0010.0010.0000.0000.0000.000
107B2006ARG10.9911.00045.0680.0350.0350.0000.0000.0000.000
108B2007MET0-0.0280.00849.0650.0020.0020.0000.0000.0000.000
109B2008LEU0-0.052-0.02950.4630.0010.0010.0000.0000.0000.000
110B2009LEU0-0.030-0.01550.3130.0010.0010.0000.0000.0000.000
111B2010GLU-1-0.883-0.94352.782-0.025-0.0250.0000.0000.0000.000
112B2011VAL00.0180.02355.7100.0010.0010.0000.0000.0000.000
113B2012CYS0-0.048-0.01354.5960.0010.0010.0000.0000.0000.000
114B2013GLN0-0.058-0.03254.1580.0010.0010.0000.0000.0000.000
115B2014PHE00.0960.06058.5610.0010.0010.0000.0000.0000.000
116B2015SER0-0.034-0.02460.6150.0010.0010.0000.0000.0000.000
117B2016ARG10.9100.95158.5910.0240.0240.0000.0000.0000.000
118B2017ASP-1-0.932-0.97661.962-0.021-0.0210.0000.0000.0000.000
119B2018ALA00.0280.02064.5250.0010.0010.0000.0000.0000.000
120B2019SER0-0.007-0.00466.4730.0010.0010.0000.0000.0000.000
121B2020VAL0-0.049-0.01866.1780.0000.0000.0000.0000.0000.000
122B2021ALA00.0120.01168.8150.0010.0010.0000.0000.0000.000
123B2022GLU-1-0.937-0.98470.373-0.015-0.0150.0000.0000.0000.000
124B2023ALA0-0.038-0.02671.8410.0010.0010.0000.0000.0000.000
125B2024TRP0-0.010-0.01573.1380.0000.0000.0000.0000.0000.000
126B2025LEU00.012-0.00374.8970.0000.0000.0000.0000.0000.000
127B2026ILE0-0.0180.01176.4970.0000.0000.0000.0000.0000.000
128B2027ALA0-0.049-0.02877.3830.0000.0000.0000.0000.0000.000
129B2028GLN0-0.009-0.00579.0510.0000.0000.0000.0000.0000.000
130B2029GLU-1-0.917-0.94181.632-0.011-0.0110.0000.0000.0000.000
131B2030PRO0-0.029-0.02483.3020.0000.0000.0000.0000.0000.000
132B2031TYR0-0.095-0.07085.3790.0000.0000.0000.0000.0000.000
133B2032LEU0-0.001-0.00783.5620.0000.0000.0000.0000.0000.000
134B2033ALA00.0140.02487.1420.0000.0000.0000.0000.0000.000
135B2034SER0-0.126-0.04789.3730.0000.0000.0000.0000.0000.000
136B2035GLY00.0560.01892.4880.0000.0000.0000.0000.0000.000
137B2036ASP-1-0.944-0.97895.319-0.009-0.0090.0000.0000.0000.000
138B2037PHE00.0090.00494.0170.0000.0000.0000.0000.0000.000
139B2038GLY00.008-0.00297.7910.0000.0000.0000.0000.0000.000
140B2039HIS0-0.022-0.013100.4000.0000.0000.0000.0000.0000.000
141B2040THR0-0.058-0.040103.1880.0000.0000.0000.0000.0000.000
142B2041VAL00.0480.031102.4460.0000.0000.0000.0000.0000.000
143B2042ASP-1-0.835-0.913100.859-0.008-0.0080.0000.0000.0000.000
144B2043SER0-0.073-0.03699.6030.0000.0000.0000.0000.0000.000
145B2044VAL00.0650.02097.7210.0000.0000.0000.0000.0000.000
146B2045GLU-1-0.914-0.95596.576-0.008-0.0080.0000.0000.0000.000
147B2046LYS10.8620.93095.1900.0090.0090.0000.0000.0000.000
148B2047LEU0-0.020-0.00393.3750.0000.0000.0000.0000.0000.000
149B2048ILE00.0530.03391.9600.0000.0000.0000.0000.0000.000
150B2049LYS10.9811.01290.4090.0100.0100.0000.0000.0000.000
151B2050ARG10.9010.94987.7910.0100.0100.0000.0000.0000.000
152B2051HIS00.0750.05187.2200.0000.0000.0000.0000.0000.000
153B2052GLU-1-0.864-0.97386.312-0.010-0.0100.0000.0000.0000.000
154B2053ALA0-0.110-0.05484.5910.0000.0000.0000.0000.0000.000
155B2054PHE0-0.008-0.01682.3720.0000.0000.0000.0000.0000.000
156B2055GLU-1-0.857-0.88381.920-0.011-0.0110.0000.0000.0000.000
157B2056LYS10.9470.98778.7630.0120.0120.0000.0000.0000.000
158B2057SER0-0.072-0.04777.9330.0000.0000.0000.0000.0000.000
159B2058THR00.006-0.00976.9050.0000.0000.0000.0000.0000.000
160B2059ALA0-0.016-0.01876.5150.0000.0000.0000.0000.0000.000
161B2060SER0-0.043-0.01372.7040.0000.0000.0000.0000.0000.000
162B2061TRP0-0.022-0.02469.593-0.001-0.0010.0000.0000.0000.000
163B2062ALA00.0250.02671.4190.0000.0000.0000.0000.0000.000
164B2063GLU-1-0.929-0.96467.287-0.017-0.0170.0000.0000.0000.000
165B2064ARG10.8860.94867.0250.0170.0170.0000.0000.0000.000
166B2065PHE00.0310.00267.2530.0000.0000.0000.0000.0000.000
167B2066ALA00.0380.02668.4210.0000.0000.0000.0000.0000.000
168B2067ALA0-0.089-0.04363.2770.0000.0000.0000.0000.0000.000
169B2068LEU0-0.040-0.02863.7870.0000.0000.0000.0000.0000.000
170B2069GLU-1-0.950-0.94865.464-0.014-0.0140.0000.0000.0000.000
171B2070LYS10.9010.95559.0280.0200.0200.0000.0000.0000.000
172B2071PRO00.0430.02460.4150.0000.0000.0000.0000.0000.000
173B2072THR0-0.0020.01256.004-0.001-0.0010.0000.0000.0000.000
174B2073THR00.047-0.00452.0540.0000.0000.0000.0000.0000.000
175B2074LEU0-0.017-0.02853.6040.0000.0000.0000.0000.0000.000
176B2075GLU-1-0.848-0.93355.014-0.019-0.0190.0000.0000.0000.000
177B2076LEU0-0.056-0.01255.1200.0010.0010.0000.0000.0000.000
178B2077LYS10.9100.93747.5050.0300.0300.0000.0000.0000.000
179B2078GLU-1-0.809-0.89853.780-0.019-0.0190.0000.0000.0000.000
180B2079ARG10.9240.96255.9740.0180.0180.0000.0000.0000.000
181B2080GLN0-0.0110.00750.2350.0010.0010.0000.0000.0000.000
182B2081ILE0-0.096-0.04152.9920.0000.0000.0000.0000.0000.000
183B2082ALA0-0.055-0.02554.9670.0010.0010.0000.0000.0000.000
184B2083GLU-1-1.041-1.00755.151-0.015-0.0150.0000.0000.0000.000