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: P89LY

Calculation Name: 2J23-A-Xray23

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J23

Chain ID: A

ChEMBL ID:

UniProt ID: Q1RQI9

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1091719.132036
FMO2-HF: Nuclear repulsion 1041208.839317
FMO2-HF: Total energy -50510.292719
FMO2-MP2: Total energy -50655.273422


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:-9:ACE)


Summations of interaction energy for fragment #1(A:-9:ACE)
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.
-0.6421.28-0.01-0.888-1.023-0.001
Interaction energy analysis for fragmet #1(A:-9:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.016
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].
3A-7HIS0-0.010-0.0093.684-0.6531.024-0.008-0.853-0.815-0.001
4A-6HIS00.0700.0554.439-0.188-0.126-0.001-0.007-0.0540.000
5A-5HIS0-0.0020.0104.3070.3430.526-0.001-0.028-0.1540.000
6A-4LEU00.005-0.0136.145-0.086-0.0860.0000.0000.0000.000
7A-3VAL0-0.022-0.0168.922-0.048-0.0480.0000.0000.0000.000
8A-2PRO0-0.016-0.01212.011-0.010-0.0100.0000.0000.0000.000
9A-1ARG10.9390.96314.709-0.108-0.1080.0000.0000.0000.000
10A0GLY00.0770.07017.987-0.016-0.0160.0000.0000.0000.000
11A1SER0-0.072-0.04319.998-0.009-0.0090.0000.0000.0000.000
12A2VAL00.0560.02823.038-0.003-0.0030.0000.0000.0000.000
13A3GLN0-0.048-0.03025.218-0.008-0.0080.0000.0000.0000.000
14A4VAL00.0110.01028.3870.0000.0000.0000.0000.0000.000
15A5ILE0-0.0090.00131.268-0.004-0.0040.0000.0000.0000.000
16A6SER0-0.014-0.01434.660-0.001-0.0010.0000.0000.0000.000
17A7SER00.0180.02237.149-0.003-0.0030.0000.0000.0000.000
18A8TYR0-0.010-0.06539.8610.0020.0020.0000.0000.0000.000
19A9ASP-1-0.855-0.93542.0410.0310.0310.0000.0000.0000.000
20A10GLN0-0.0170.00133.549-0.001-0.0010.0000.0000.0000.000
21A11PHE00.0010.00237.7760.0020.0020.0000.0000.0000.000
22A12LYS10.8490.94338.850-0.036-0.0360.0000.0000.0000.000
23A13GLN00.0290.03736.7660.0020.0020.0000.0000.0000.000
24A14VAL0-0.008-0.00534.0550.0000.0000.0000.0000.0000.000
25A15THR0-0.019-0.01635.7520.0010.0010.0000.0000.0000.000
26A16GLY00.0270.02237.824-0.001-0.0010.0000.0000.0000.000
27A17GLY00.0010.00838.241-0.003-0.0030.0000.0000.0000.000
28A18ASP-1-0.905-0.96737.3110.0420.0420.0000.0000.0000.000
29A19LYS10.8710.94528.006-0.064-0.0640.0000.0000.0000.000
30A20VAL0-0.0020.00032.078-0.001-0.0010.0000.0000.0000.000
31A21VAL0-0.024-0.00431.2380.0040.0040.0000.0000.0000.000
32A22VAL0-0.026-0.01328.201-0.002-0.0020.0000.0000.0000.000
33A23ILE0-0.007-0.01130.4530.0030.0030.0000.0000.0000.000
34A24ASP-1-0.844-0.92528.9450.0970.0970.0000.0000.0000.000
35A25PHE0-0.020-0.02631.427-0.003-0.0030.0000.0000.0000.000
36A26TRP00.0440.00031.9790.0030.0030.0000.0000.0000.000
37A27ALA00.0820.02734.098-0.005-0.0050.0000.0000.0000.000
38A28THR00.002-0.01234.0620.0040.0040.0000.0000.0000.000
39A29TRP0-0.116-0.05135.0120.0030.0030.0000.0000.0000.000
40A30CYS-1-0.838-0.87434.3390.0780.0780.0000.0000.0000.000
41A31GLY00.002-0.00733.1680.0050.0050.0000.0000.0000.000
42A32PRO00.003-0.03631.2970.0080.0080.0000.0000.0000.000
43A33CYS-1-0.759-0.85229.8860.0920.0920.0000.0000.0000.000
44A34LYS10.8530.92027.824-0.088-0.0880.0000.0000.0000.000
45A35MET0-0.0570.02124.5390.0110.0110.0000.0000.0000.000
46A36ILE00.0420.00024.9470.0160.0160.0000.0000.0000.000
47A37GLY00.0680.05825.2960.0070.0070.0000.0000.0000.000
48A38PRO0-0.039-0.02620.8750.0080.0080.0000.0000.0000.000
49A39VAL0-0.011-0.00520.6140.0210.0210.0000.0000.0000.000
50A40PHE00.0060.00421.5200.0100.0100.0000.0000.0000.000
51A41GLU-1-0.739-0.83020.5490.1560.1560.0000.0000.0000.000
52A42LYS10.8920.97015.048-0.304-0.3040.0000.0000.0000.000
53A43ILE0-0.002-0.00518.1640.0090.0090.0000.0000.0000.000
54A44SER0-0.0260.00120.609-0.008-0.0080.0000.0000.0000.000
55A45ASP-1-0.769-0.88715.8360.2250.2250.0000.0000.0000.000
56A46THR0-0.091-0.04016.9170.0060.0060.0000.0000.0000.000
57A47PRO00.0920.02417.468-0.013-0.0130.0000.0000.0000.000
58A48ALA00.0250.03220.456-0.014-0.0140.0000.0000.0000.000
59A49GLY0-0.0050.00122.016-0.011-0.0110.0000.0000.0000.000
60A50ASP-1-0.917-0.95121.4200.0940.0940.0000.0000.0000.000
61A51LYS10.7910.90024.257-0.075-0.0750.0000.0000.0000.000
62A52VAL0-0.037-0.00626.628-0.008-0.0080.0000.0000.0000.000
63A53GLY0-0.0190.00026.7000.0060.0060.0000.0000.0000.000
64A54PHE0-0.015-0.01024.5070.0010.0010.0000.0000.0000.000
65A55TYR0-0.007-0.02527.523-0.001-0.0010.0000.0000.0000.000
66A56LYS10.8340.89527.200-0.094-0.0940.0000.0000.0000.000
67A57VAL0-0.022-0.01631.149-0.004-0.0040.0000.0000.0000.000
68A58ASP-1-0.738-0.83734.7560.0610.0610.0000.0000.0000.000
69A59VAL00.044-0.01535.962-0.004-0.0040.0000.0000.0000.000
70A60ASP-1-0.768-0.82038.8880.0480.0480.0000.0000.0000.000
71A61GLU-1-0.809-0.87437.2530.0490.0490.0000.0000.0000.000
72A62GLN0-0.0280.02038.095-0.004-0.0040.0000.0000.0000.000
73A63SER00.0730.06341.1890.0010.0010.0000.0000.0000.000
74A64GLN00.0100.02644.3490.0000.0000.0000.0000.0000.000
75A65ILE00.0480.01738.8830.0000.0000.0000.0000.0000.000
76A66ALA00.0100.00941.1810.0010.0010.0000.0000.0000.000
77A67GLN0-0.037-0.03042.2860.0000.0000.0000.0000.0000.000
78A68GLU-1-0.826-0.86144.5260.0360.0360.0000.0000.0000.000
79A69VAL0-0.031-0.01239.5610.0000.0000.0000.0000.0000.000
80A70GLY0-0.024-0.00642.9810.0000.0000.0000.0000.0000.000
81A71ILE0-0.045-0.01638.6670.0010.0010.0000.0000.0000.000
82A72ARG10.9220.94841.662-0.044-0.0440.0000.0000.0000.000
83A73ALA0-0.014-0.00639.068-0.001-0.0010.0000.0000.0000.000
84A74MET0-0.0160.04636.2460.0000.0000.0000.0000.0000.000
85A75PRO00.1820.06331.5220.0000.0000.0000.0000.0000.000
86A76THR0-0.106-0.07134.245-0.002-0.0020.0000.0000.0000.000
87A77PHE00.0150.01728.4890.0000.0000.0000.0000.0000.000
88A78VAL0-0.021-0.00733.111-0.003-0.0030.0000.0000.0000.000
89A79PHE00.003-0.00230.0820.0030.0030.0000.0000.0000.000
90A80PHE00.035-0.00334.940-0.004-0.0040.0000.0000.0000.000
91A81LYS10.9630.97935.871-0.042-0.0420.0000.0000.0000.000
92A82ASN0-0.0090.00838.258-0.002-0.0020.0000.0000.0000.000
93A83GLY00.0430.02740.565-0.002-0.0020.0000.0000.0000.000
94A84GLN0-0.136-0.05941.505-0.001-0.0010.0000.0000.0000.000
95A85LYS10.9190.96439.639-0.044-0.0440.0000.0000.0000.000
96A86ILE0-0.075-0.04835.520-0.002-0.0020.0000.0000.0000.000
97A87ASP-1-0.834-0.90135.4200.0650.0650.0000.0000.0000.000
98A88THR0-0.030-0.02436.3810.0000.0000.0000.0000.0000.000
99A89VAL0-0.029-0.00431.4800.0000.0000.0000.0000.0000.000
100A90VAL00.0210.00634.3640.0010.0010.0000.0000.0000.000
101A91GLY00.0310.02633.9630.0010.0010.0000.0000.0000.000
102A92ALA00.0180.00229.4800.0040.0040.0000.0000.0000.000
103A93ASP-1-0.820-0.92930.0580.0980.0980.0000.0000.0000.000
104A94PRO00.0360.01124.6250.0000.0000.0000.0000.0000.000
105A95SER0-0.043-0.02126.2200.0010.0010.0000.0000.0000.000
106A96LYS10.9871.00627.351-0.080-0.0800.0000.0000.0000.000
107A97LEU00.0260.03026.047-0.004-0.0040.0000.0000.0000.000
108A98GLN00.007-0.01921.900-0.013-0.0130.0000.0000.0000.000
109A99ALA00.0160.01126.011-0.003-0.0030.0000.0000.0000.000
110A100ALA00.0350.02728.847-0.005-0.0050.0000.0000.0000.000
111A101ILE00.007-0.00724.909-0.005-0.0050.0000.0000.0000.000
112A102THR00.0000.00925.736-0.001-0.0010.0000.0000.0000.000
113A103GLN0-0.048-0.01227.484-0.004-0.0040.0000.0000.0000.000
114A104HIS10.7390.83230.833-0.072-0.0720.0000.0000.0000.000
115A105SER0-0.0200.00226.984-0.003-0.0030.0000.0000.0000.000
116A106ALA-1-0.866-0.91428.5360.0590.0590.0000.0000.0000.000
117A2003HOH00.0360.0285.544-0.120-0.1200.0000.0000.0000.000
118A2005HOH0-0.017-0.00924.991-0.004-0.0040.0000.0000.0000.000
119A2006HOH0-0.014-0.01132.966-0.001-0.0010.0000.0000.0000.000
120A2007HOH0-0.014-0.01635.3220.0020.0020.0000.0000.0000.000
121A2009HOH0-0.021-0.01541.5630.0000.0000.0000.0000.0000.000
122A2010HOH0-0.013-0.01043.3850.0000.0000.0000.0000.0000.000
123A2011HOH00.0240.01844.2770.0010.0010.0000.0000.0000.000
124A2012HOH0-0.044-0.02346.6470.0000.0000.0000.0000.0000.000
125A2013HOH00.0210.01533.185-0.001-0.0010.0000.0000.0000.000
126A2014HOH00.0040.00037.199-0.001-0.0010.0000.0000.0000.000
127A2015HOH0-0.028-0.02741.607-0.001-0.0010.0000.0000.0000.000
128A2016HOH0-0.035-0.03236.149-0.001-0.0010.0000.0000.0000.000
129A2017HOH0-0.046-0.03335.633-0.001-0.0010.0000.0000.0000.000
130A2019HOH00.0100.00941.157-0.001-0.0010.0000.0000.0000.000
131A2020HOH0-0.029-0.01542.903-0.001-0.0010.0000.0000.0000.000
132A2021HOH0-0.0070.00425.947-0.004-0.0040.0000.0000.0000.000
133A2024HOH0-0.030-0.02028.9420.0010.0010.0000.0000.0000.000
134A2025HOH00.0390.01832.6600.0020.0020.0000.0000.0000.000
135A2026HOH0-0.062-0.04132.1620.0020.0020.0000.0000.0000.000
136A2027HOH00.0280.02238.5260.0010.0010.0000.0000.0000.000
137A2029HOH0-0.048-0.03338.681-0.001-0.0010.0000.0000.0000.000
138A2030HOH0-0.056-0.06124.294-0.004-0.0040.0000.0000.0000.000
139A2032HOH0-0.037-0.02822.3060.0030.0030.0000.0000.0000.000
140A2034HOH0-0.040-0.02219.4170.0100.0100.0000.0000.0000.000
141A2035HOH0-0.016-0.01424.755-0.003-0.0030.0000.0000.0000.000
142A2036HOH0-0.021-0.01325.206-0.005-0.0050.0000.0000.0000.000
143A2037HOH0-0.050-0.03321.452-0.006-0.0060.0000.0000.0000.000
144A2038HOH0-0.021-0.03925.071-0.004-0.0040.0000.0000.0000.000
145A2039HOH00.000-0.00222.275-0.003-0.0030.0000.0000.0000.000
146A2041HOH0-0.011-0.00521.501-0.001-0.0010.0000.0000.0000.000
147A2042HOH0-0.022-0.01319.8490.0030.0030.0000.0000.0000.000
148A2045HOH0-0.033-0.03531.004-0.002-0.0020.0000.0000.0000.000
149A2046HOH0-0.023-0.02026.442-0.003-0.0030.0000.0000.0000.000
150A2047HOH00.0300.04231.4470.0010.0010.0000.0000.0000.000
151A2048HOH00.004-0.01231.0420.0010.0010.0000.0000.0000.000
152A2049HOH00.0620.05527.554-0.002-0.0020.0000.0000.0000.000
153A2050HOH00.0220.02728.8120.0010.0010.0000.0000.0000.000
154A2051HOH0-0.077-0.04834.5250.0020.0020.0000.0000.0000.000
155A2052HOH0-0.072-0.04736.5680.0000.0000.0000.0000.0000.000
156A2053HOH0-0.011-0.00942.748-0.001-0.0010.0000.0000.0000.000
157A2054HOH0-0.025-0.02437.3320.0010.0010.0000.0000.0000.000
158A2055HOH0-0.054-0.03543.750-0.001-0.0010.0000.0000.0000.000
159A2056HOH0-0.052-0.04540.023-0.001-0.0010.0000.0000.0000.000
160A2057HOH0-0.018-0.02143.688-0.001-0.0010.0000.0000.0000.000
161A2058HOH0-0.029-0.03242.4460.0000.0000.0000.0000.0000.000
162A2059HOH00.0160.01036.2790.0000.0000.0000.0000.0000.000
163A2060HOH00.0140.00141.8770.0000.0000.0000.0000.0000.000
164A2061HOH0-0.009-0.01241.821-0.001-0.0010.0000.0000.0000.000
165A2062HOH0-0.015-0.03044.5960.0000.0000.0000.0000.0000.000
166A2065HOH0-0.030-0.01946.986-0.001-0.0010.0000.0000.0000.000
167A2066HOH00.008-0.00845.8990.0010.0010.0000.0000.0000.000
168A2067HOH0-0.022-0.02043.1510.0010.0010.0000.0000.0000.000
169A2068HOH00.002-0.00339.363-0.001-0.0010.0000.0000.0000.000
170A2069HOH0-0.020-0.02041.4690.0000.0000.0000.0000.0000.000
171A2071HOH0-0.028-0.02041.591-0.001-0.0010.0000.0000.0000.000
172A2072HOH00.0200.01747.8070.0010.0010.0000.0000.0000.000
173A2073HOH00.0410.02444.4040.0010.0010.0000.0000.0000.000
174A2074HOH00.0250.01740.5290.0000.0000.0000.0000.0000.000
175A2075HOH0-0.056-0.02936.6040.0000.0000.0000.0000.0000.000
176A2076HOH00.0230.01836.5000.0000.0000.0000.0000.0000.000
177A2077HOH0-0.053-0.04034.351-0.001-0.0010.0000.0000.0000.000
178A2078HOH00.0130.00823.2920.0060.0060.0000.0000.0000.000
179A2079HOH0-0.015-0.01230.208-0.003-0.0030.0000.0000.0000.000
180A2080HOH00.0140.01228.4320.0040.0040.0000.0000.0000.000
181A2081HOH0-0.029-0.02132.0070.0000.0000.0000.0000.0000.000
182A2082HOH00.0030.00620.447-0.004-0.0040.0000.0000.0000.000
183A2083HOH0-0.038-0.02930.2120.0010.0010.0000.0000.0000.000
184A2084HOH0-0.013-0.00623.210-0.005-0.0050.0000.0000.0000.000
185A2085HOH00.0420.02636.9860.0010.0010.0000.0000.0000.000
186A2087HOH00.0220.02135.6130.0010.0010.0000.0000.0000.000
187A2088HOH00.0050.00131.6970.0000.0000.0000.0000.0000.000
188A2089HOH0-0.045-0.04024.605-0.001-0.0010.0000.0000.0000.000
189B2005HOH00.0090.01921.515-0.005-0.0050.0000.0000.0000.000
190B2009HOH0-0.019-0.02016.3530.0100.0100.0000.0000.0000.000
191B2010HOH0-0.063-0.03416.021-0.001-0.0010.0000.0000.0000.000
192B2028HOH0-0.038-0.02739.486-0.001-0.0010.0000.0000.0000.000
193B2031HOH0-0.042-0.02635.6490.0000.0000.0000.0000.0000.000
194B2036HOH00.007-0.00138.666-0.001-0.0010.0000.0000.0000.000
195B2046HOH00.006-0.00729.5190.0020.0020.0000.0000.0000.000
196B2050HOH00.0450.04126.974-0.003-0.0030.0000.0000.0000.000