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: JLY59

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1683837.539407
FMO2-HF: Nuclear repulsion 1607459.987175
FMO2-HF: Total energy -76377.552232
FMO2-MP2: Total energy -76598.309284


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.
-0.7641.5220.596-1.186-1.6960.002
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 : 0.066 / q_NPA : 0.024
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].
3B1902THR00.0290.0123.810-0.7770.260-0.004-0.432-0.6000.001
4B1903ALA00.0170.0122.480-0.715-0.3410.598-0.375-0.5970.000
5B1904ASP-1-0.762-0.8803.699-2.382-1.5070.002-0.379-0.4990.001
6B1905LYS10.8410.9175.4990.6350.6350.0000.0000.0000.000
7B1906PHE0-0.028-0.0117.6520.1330.1330.0000.0000.0000.000
8B1907ARG10.9050.9245.3441.1401.1400.0000.0000.0000.000
9B1908PHE0-0.008-0.0029.5070.0750.0750.0000.0000.0000.000
10B1909PHE00.026-0.00911.5490.0660.0660.0000.0000.0000.000
11B1910SER0-0.0110.00612.6660.0580.0580.0000.0000.0000.000
12B1911MET0-0.0200.00211.5670.0290.0290.0000.0000.0000.000
13B1912ALA00.0480.02715.5750.0260.0260.0000.0000.0000.000
14B1913ARG10.8240.90815.8670.0660.0660.0000.0000.0000.000
15B1914ASP-1-0.813-0.89917.766-0.060-0.0600.0000.0000.0000.000
16B1915LEU00.006-0.00218.8190.0080.0080.0000.0000.0000.000
17B1916LEU0-0.041-0.03421.1030.0100.0100.0000.0000.0000.000
18B1917SER0-0.051-0.02122.9830.0100.0100.0000.0000.0000.000
19B1918TRP00.0170.00124.2600.0020.0020.0000.0000.0000.000
20B1919MET00.0000.00624.3890.0030.0030.0000.0000.0000.000
21B1920GLU-1-0.903-0.91727.630-0.024-0.0240.0000.0000.0000.000
22B1921SER0-0.010-0.00529.0240.0060.0060.0000.0000.0000.000
23B1922ILE00.0330.01429.7840.0030.0030.0000.0000.0000.000
24B1923ILE0-0.040-0.02530.6950.0020.0020.0000.0000.0000.000
25B1924ARG10.9000.93831.9230.0270.0270.0000.0000.0000.000
26B1925GLN0-0.0150.00334.0600.0000.0000.0000.0000.0000.000
27B1926ILE0-0.063-0.02734.9790.0020.0020.0000.0000.0000.000
28B1927GLU-1-0.881-0.94737.511-0.030-0.0300.0000.0000.0000.000
29B1928THR0-0.055-0.03938.5780.0020.0020.0000.0000.0000.000
30B1929GLN0-0.031-0.01140.9450.0010.0010.0000.0000.0000.000
31B1930GLU-1-0.860-0.91543.416-0.018-0.0180.0000.0000.0000.000
32B1931ARG0-0.0360.07045.968-0.001-0.0010.0000.0000.0000.000
33B1932PRO00.073-0.02847.0610.0000.0000.0000.0000.0000.000
34B1933ARG10.8280.89149.8620.0170.0170.0000.0000.0000.000
35B1934ASP-1-0.818-0.92048.942-0.018-0.0180.0000.0000.0000.000
36B1935VAL00.0090.05449.3330.0000.0000.0000.0000.0000.000
37B1936SER0-0.043-0.01751.6310.0000.0000.0000.0000.0000.000
38B1937SER00.0500.01655.0500.0000.0000.0000.0000.0000.000
39B1938VAL00.0310.01352.482-0.001-0.0010.0000.0000.0000.000
40B1939GLU-1-0.845-0.94447.973-0.025-0.0250.0000.0000.0000.000
41B1940LEU00.002-0.01246.971-0.001-0.0010.0000.0000.0000.000
42B1941LEU00.0460.01044.682-0.001-0.0010.0000.0000.0000.000
43B1942MET00.0380.04543.690-0.002-0.0020.0000.0000.0000.000
44B1943LYS10.9170.95841.7870.0300.0300.0000.0000.0000.000
45B1944TYR0-0.014-0.01739.111-0.002-0.0020.0000.0000.0000.000
46B1945HIS00.0460.01539.0460.0000.0000.0000.0000.0000.000
47B1946GLN0-0.005-0.00138.267-0.002-0.0020.0000.0000.0000.000
48B1947GLY0-0.026-0.01136.977-0.003-0.0030.0000.0000.0000.000
49B1948ILE00.0310.01733.797-0.003-0.0030.0000.0000.0000.000
50B1949ASN0-0.0070.00133.033-0.008-0.0080.0000.0000.0000.000
51B1950ALA0-0.012-0.00332.490-0.005-0.0050.0000.0000.0000.000
52B1951GLU-1-0.808-0.89929.509-0.056-0.0560.0000.0000.0000.000
53B1952ILE00.0050.01028.549-0.007-0.0070.0000.0000.0000.000
54B1953GLU-1-0.897-0.94427.668-0.102-0.1020.0000.0000.0000.000
55B1954THR0-0.109-0.05826.785-0.008-0.0080.0000.0000.0000.000
56B1955ARG10.8070.89223.4340.0620.0620.0000.0000.0000.000
57B1956SER0-0.0360.00122.751-0.020-0.0200.0000.0000.0000.000
58B1957LYS10.9870.97420.4000.1010.1010.0000.0000.0000.000
59B1958ASN00.0380.01918.395-0.010-0.0100.0000.0000.0000.000
60B1959PHE00.0350.02318.019-0.024-0.0240.0000.0000.0000.000
61B1960SER00.0190.02018.460-0.018-0.0180.0000.0000.0000.000
62B1961ALA00.0030.01114.650-0.027-0.0270.0000.0000.0000.000
63B1962CYS0-0.060-0.02914.229-0.045-0.0450.0000.0000.0000.000
64B1963LEU00.006-0.03514.631-0.038-0.0380.0000.0000.0000.000
65B1964GLU-1-0.916-0.93813.401-0.393-0.3930.0000.0000.0000.000
66B1965LEU0-0.065-0.0247.633-0.056-0.0560.0000.0000.0000.000
67B1966GLY00.0270.00911.313-0.077-0.0770.0000.0000.0000.000
68B1967GLU-1-0.871-0.94713.539-0.263-0.2630.0000.0000.0000.000
69B1968SER0-0.013-0.00410.308-0.079-0.0790.0000.0000.0000.000
70B1969LEU0-0.109-0.0747.227-0.086-0.0860.0000.0000.0000.000
71B1970LEU00.0110.00410.4720.0420.0420.0000.0000.0000.000
72B1971GLN0-0.048-0.00813.4890.0220.0220.0000.0000.0000.000
73B1972ARG10.7840.8955.1201.6021.6020.0000.0000.0000.000
74B1973GLN00.0610.04011.722-0.004-0.0040.0000.0000.0000.000
75B1974HIS00.004-0.0037.7920.1270.1270.0000.0000.0000.000
76B1975GLN0-0.025-0.01811.2460.0470.0470.0000.0000.0000.000
77B1976ALA00.0010.00512.3260.0490.0490.0000.0000.0000.000
78B1977SER00.030-0.01214.118-0.032-0.0320.0000.0000.0000.000
79B1978GLU-1-0.894-0.92915.595-0.103-0.1030.0000.0000.0000.000
80B1979GLU-1-0.781-0.88415.601-0.041-0.0410.0000.0000.0000.000
81B1980ILE0-0.049-0.04311.579-0.010-0.0100.0000.0000.0000.000
82B1981ARG10.9861.00315.9930.1640.1640.0000.0000.0000.000
83B1982GLU-1-0.907-0.95218.947-0.062-0.0620.0000.0000.0000.000
84B1983LYS10.8550.93217.4940.0840.0840.0000.0000.0000.000
85B1984LEU00.0380.01216.3200.0030.0030.0000.0000.0000.000
86B1985GLN00.0160.01519.507-0.001-0.0010.0000.0000.0000.000
87B1986GLN00.0160.01822.3950.0040.0040.0000.0000.0000.000
88B1987VAL0-0.004-0.01119.6940.0100.0100.0000.0000.0000.000
89B1988MET00.0130.00622.0570.0040.0040.0000.0000.0000.000
90B1989SER0-0.100-0.04324.4210.0090.0090.0000.0000.0000.000
91B1990ARG11.0100.98225.9280.0630.0630.0000.0000.0000.000
92B1991ARG10.9570.99324.0020.1240.1240.0000.0000.0000.000
93B1992LYS10.9390.97027.5090.0850.0850.0000.0000.0000.000
94B1993GLU-1-0.844-0.91830.362-0.046-0.0460.0000.0000.0000.000
95B1994MET0-0.014-0.00128.0310.0050.0050.0000.0000.0000.000
96B1995ASN0-0.002-0.01929.9770.0050.0050.0000.0000.0000.000
97B1996GLU-1-0.909-0.94633.307-0.058-0.0580.0000.0000.0000.000
98B1997LYS10.8600.92234.8290.0430.0430.0000.0000.0000.000
99B1998TRP0-0.024-0.00635.1680.0030.0030.0000.0000.0000.000
100B1999GLU-1-0.871-0.95936.676-0.047-0.0470.0000.0000.0000.000
101B2000ALA0-0.041-0.00738.9480.0030.0030.0000.0000.0000.000
102B2001ARG10.8240.90240.4540.0310.0310.0000.0000.0000.000
103B2002TRP0-0.038-0.02340.7560.0030.0030.0000.0000.0000.000
104B2003GLU-1-0.804-0.87442.688-0.031-0.0310.0000.0000.0000.000
105B2004ARG10.8500.89145.1910.0260.0260.0000.0000.0000.000
106B2005LEU0-0.025-0.00443.1480.0010.0010.0000.0000.0000.000
107B2006ARG10.9780.99444.9270.0370.0370.0000.0000.0000.000
108B2007MET0-0.0050.03249.0730.0010.0010.0000.0000.0000.000
109B2008LEU0-0.040-0.01750.4780.0010.0010.0000.0000.0000.000
110B2009LEU00.001-0.00550.4520.0010.0010.0000.0000.0000.000
111B2010GLU-1-0.909-0.94952.799-0.023-0.0230.0000.0000.0000.000
112B2011VAL00.0210.02155.7390.0010.0010.0000.0000.0000.000
113B2012CYS0-0.035-0.00354.4390.0010.0010.0000.0000.0000.000
114B2013GLN0-0.056-0.02854.4430.0010.0010.0000.0000.0000.000
115B2014PHE00.0960.04758.5800.0010.0010.0000.0000.0000.000
116B2015SER00.002-0.01260.6380.0010.0010.0000.0000.0000.000
117B2016ARG10.7470.86059.6660.0180.0180.0000.0000.0000.000
118B2017ASP-1-0.822-0.90361.884-0.017-0.0170.0000.0000.0000.000
119B2018ALA00.0360.02864.5440.0000.0000.0000.0000.0000.000
120B2019SER0-0.023-0.01066.4610.0010.0010.0000.0000.0000.000
121B2020VAL0-0.043-0.01866.0420.0010.0010.0000.0000.0000.000
122B2021ALA00.0070.01368.8340.0000.0000.0000.0000.0000.000
123B2022GLU-1-0.926-0.97870.541-0.012-0.0120.0000.0000.0000.000
124B2023ALA0-0.034-0.02571.8580.0000.0000.0000.0000.0000.000
125B2024TRP0-0.004-0.01373.1600.0000.0000.0000.0000.0000.000
126B2025LEU00.0110.00274.9170.0000.0000.0000.0000.0000.000
127B2026ILE0-0.034-0.00676.6810.0000.0000.0000.0000.0000.000
128B2027ALA0-0.041-0.02177.4110.0000.0000.0000.0000.0000.000
129B2028GLN0-0.014-0.00379.0920.0000.0000.0000.0000.0000.000
130B2029GLU-1-0.914-0.94381.653-0.009-0.0090.0000.0000.0000.000
131B2030PRO0-0.020-0.02483.3670.0000.0000.0000.0000.0000.000
132B2031TYR0-0.067-0.03685.4550.0000.0000.0000.0000.0000.000
133B2032LEU0-0.009-0.00583.6370.0000.0000.0000.0000.0000.000
134B2033ALA00.0170.02787.1630.0000.0000.0000.0000.0000.000
135B2034SER0-0.127-0.05589.3920.0000.0000.0000.0000.0000.000
136B2035GLY00.0500.02092.5070.0000.0000.0000.0000.0000.000
137B2036ASP-1-0.955-0.97895.350-0.007-0.0070.0000.0000.0000.000
138B2037PHE00.0150.00193.7300.0000.0000.0000.0000.0000.000
139B2038GLY00.000-0.00197.8150.0000.0000.0000.0000.0000.000
140B2039HIS0-0.015-0.009100.4250.0000.0000.0000.0000.0000.000
141B2040THR0-0.044-0.033103.1970.0000.0000.0000.0000.0000.000
142B2041VAL00.0380.030102.5090.0000.0000.0000.0000.0000.000
143B2042ASP-1-0.742-0.844101.086-0.007-0.0070.0000.0000.0000.000
144B2043SER0-0.052-0.02999.5920.0000.0000.0000.0000.0000.000
145B2044VAL00.0430.01297.9220.0000.0000.0000.0000.0000.000
146B2045GLU-1-0.910-0.95796.560-0.008-0.0080.0000.0000.0000.000
147B2046LYS10.7660.85695.1620.0070.0070.0000.0000.0000.000
148B2047LEU0-0.015-0.00193.3750.0000.0000.0000.0000.0000.000
149B2048ILE00.0380.02591.9490.0000.0000.0000.0000.0000.000
150B2049LYS10.9911.01690.4590.0090.0090.0000.0000.0000.000
151B2050ARG10.9020.95087.8200.0080.0080.0000.0000.0000.000
152B2051HIS00.0230.01386.6660.0000.0000.0000.0000.0000.000
153B2052GLU-1-0.885-0.94286.297-0.010-0.0100.0000.0000.0000.000
154B2053ALA0-0.106-0.05384.5680.0000.0000.0000.0000.0000.000
155B2054PHE00.000-0.00782.6660.0000.0000.0000.0000.0000.000
156B2055GLU-1-0.826-0.91981.905-0.011-0.0110.0000.0000.0000.000
157B2056LYS10.9590.99479.0250.0120.0120.0000.0000.0000.000
158B2057SER0-0.094-0.05577.9240.0000.0000.0000.0000.0000.000
159B2058THR00.012-0.01176.8900.0000.0000.0000.0000.0000.000
160B2059ALA0-0.012-0.01376.5020.0000.0000.0000.0000.0000.000
161B2060SER0-0.078-0.02172.6210.0000.0000.0000.0000.0000.000
162B2061TRP00.035-0.00869.870-0.001-0.0010.0000.0000.0000.000
163B2062ALA00.0080.01771.4070.0000.0000.0000.0000.0000.000
164B2063GLU-1-0.929-0.96267.599-0.017-0.0170.0000.0000.0000.000
165B2064ARG10.8960.95267.0150.0140.0140.0000.0000.0000.000
166B2065PHE00.0310.00567.2420.0000.0000.0000.0000.0000.000
167B2066ALA00.0420.02468.4760.0000.0000.0000.0000.0000.000
168B2067ALA0-0.070-0.03363.291-0.001-0.0010.0000.0000.0000.000
169B2068LEU0-0.066-0.03963.781-0.001-0.0010.0000.0000.0000.000
170B2069GLU-1-0.951-0.95165.456-0.016-0.0160.0000.0000.0000.000
171B2070LYS10.9090.96359.0700.0210.0210.0000.0000.0000.000
172B2071PRO00.0190.01160.3590.0000.0000.0000.0000.0000.000
173B2072THR0-0.040-0.03456.048-0.001-0.0010.0000.0000.0000.000
174B2073THR00.0550.00152.1350.0000.0000.0000.0000.0000.000
175B2074LEU0-0.015-0.02453.5340.0000.0000.0000.0000.0000.000
176B2075GLU-1-0.795-0.88555.014-0.019-0.0190.0000.0000.0000.000
177B2076LEU0-0.061-0.02155.3480.0000.0000.0000.0000.0000.000
178B2077LYS10.7710.82948.2600.0290.0290.0000.0000.0000.000
179B2078GLU-1-0.837-0.90853.785-0.020-0.0200.0000.0000.0000.000
180B2079ARG10.9240.96155.8950.0230.0230.0000.0000.0000.000
181B2080GLN0-0.047-0.02050.246-0.001-0.0010.0000.0000.0000.000
182B2081ILE0-0.061-0.01952.9720.0000.0000.0000.0000.0000.000
183B2082ALA0-0.038-0.01854.9780.0010.0010.0000.0000.0000.000
184B2083GLU-1-1.031-1.00355.221-0.023-0.0230.0000.0000.0000.000