FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VNJL1

Calculation Name: 5E9G-B-Xray547

Preferred Name: Isocitrate lyase

Target Type: SINGLE PROTEIN

Ligand Name: glyoxylic acid | glycerol | magnesium ion

Ligand 3-letter code: GLV | GOL | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5E9G

Chain ID: B

ChEMBL ID: CHEMBL1075264

UniProt ID: P0CT06

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 525
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -10126242.536473
FMO2-HF: Nuclear repulsion 9918726.57445
FMO2-HF: Total energy -207515.962023
FMO2-MP2: Total energy -208117.528516


3D Structure Molmil
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:5:ASN)


Summations of interaction energy for fragment #1(A:5:ASN)
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.
-38.111-33.450.621-2.062-3.2180.002
Interaction energy analysis for fragmet #1(A:5:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.908
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].
3A7VAL00.0180.0212.9313.4427.8880.621-2.040-3.0260.002
4A8ASN0-0.025-0.0104.266-4.880-4.6650.000-0.022-0.1920.000
5A9PRO00.0380.0347.1260.9110.9110.0000.0000.0000.000
6A10ALA0-0.023-0.01910.753-0.565-0.5650.0000.0000.0000.000
7A11VAL0-0.0020.00013.6780.4780.4780.0000.0000.0000.000
8A12GLU-1-0.884-0.95011.192-24.524-24.5240.0000.0000.0000.000
9A13PRO00.0280.00814.0321.0601.0600.0000.0000.0000.000
10A14SER0-0.063-0.02516.8180.8140.8140.0000.0000.0000.000
11A15MET0-0.0010.00318.6410.3500.3500.0000.0000.0000.000
12A16GLU-1-0.902-0.95218.562-15.292-15.2920.0000.0000.0000.000
13A17ASP-1-0.884-0.94221.241-11.662-11.6620.0000.0000.0000.000
14A18ASP-1-0.912-0.95923.442-12.140-12.1400.0000.0000.0000.000
15A19LEU0-0.084-0.04019.9500.4000.4000.0000.0000.0000.000
16A20PHE00.0500.02224.4410.5940.5940.0000.0000.0000.000
17A21ALA00.013-0.00626.5760.4430.4430.0000.0000.0000.000
18A22ARG10.8790.94723.98612.68912.6890.0000.0000.0000.000
19A23GLU-1-0.768-0.86826.600-11.128-11.1280.0000.0000.0000.000
20A24VAL0-0.020-0.01929.5530.4350.4350.0000.0000.0000.000
21A25ALA0-0.037-0.01332.2280.3900.3900.0000.0000.0000.000
22A26GLU-1-0.937-0.96829.887-10.268-10.2680.0000.0000.0000.000
23A27VAL0-0.027-0.01732.4990.2840.2840.0000.0000.0000.000
24A28LYS10.8410.90435.1118.8328.8320.0000.0000.0000.000
25A29GLN0-0.0180.00637.1970.4120.4120.0000.0000.0000.000
26A30TRP0-0.045-0.02236.0010.1310.1310.0000.0000.0000.000
27A31TRP0-0.053-0.06337.0950.1880.1880.0000.0000.0000.000
28A32SER0-0.032-0.01341.0230.2370.2370.0000.0000.0000.000
29A33ASP-1-0.888-0.92642.508-7.069-7.0690.0000.0000.0000.000
30A34PRO00.012-0.00944.4370.0730.0730.0000.0000.0000.000
31A35ARG10.7350.85443.7107.2467.2460.0000.0000.0000.000
32A36TRP0-0.014-0.00740.6960.0830.0830.0000.0000.0000.000
33A37ARG10.7900.87746.2546.1976.1970.0000.0000.0000.000
34A38TYR0-0.055-0.05849.5360.0770.0770.0000.0000.0000.000
35A39THR0-0.039-0.00844.5850.0190.0190.0000.0000.0000.000
36A40LYS10.9360.96946.3696.3866.3860.0000.0000.0000.000
37A41ARG10.8270.89040.1677.7507.7500.0000.0000.0000.000
38A42PRO0-0.096-0.03742.7900.0460.0460.0000.0000.0000.000
39A43PHE0-0.012-0.00838.192-0.043-0.0430.0000.0000.0000.000
40A44THR00.0370.01036.5510.0130.0130.0000.0000.0000.000
41A45ALA00.0440.02134.767-0.114-0.1140.0000.0000.0000.000
42A46GLU-1-0.783-0.87832.259-9.000-9.0000.0000.0000.0000.000
43A47GLN0-0.001-0.00131.749-0.182-0.1820.0000.0000.0000.000
44A48ILE00.0170.01632.553-0.210-0.2100.0000.0000.0000.000
45A49VAL00.0400.02327.998-0.210-0.2100.0000.0000.0000.000
46A50SER0-0.0220.00227.742-0.282-0.2820.0000.0000.0000.000
47A51LYS10.7890.88027.8219.8179.8170.0000.0000.0000.000
48A52ARG10.7660.87526.61310.36510.3650.0000.0000.0000.000
49A53GLY00.0180.01422.850-0.247-0.2470.0000.0000.0000.000
50A54ASN00.013-0.00617.8240.7500.7500.0000.0000.0000.000
51A55LEU0-0.012-0.00520.635-0.353-0.3530.0000.0000.0000.000
52A56LYS10.9210.95822.63311.36211.3620.0000.0000.0000.000
53A57ILE0-0.027-0.00926.049-0.134-0.1340.0000.0000.0000.000
54A58GLU-1-0.865-0.91228.006-9.737-9.7370.0000.0000.0000.000
55A59TYR00.0480.00730.158-0.019-0.0190.0000.0000.0000.000
56A60PRO00.009-0.00234.0340.2300.2300.0000.0000.0000.000
57A61SER0-0.001-0.00637.0540.1870.1870.0000.0000.0000.000
58A62ASN00.0730.04435.7210.4710.4710.0000.0000.0000.000
59A63ALA00.0160.01738.7630.2150.2150.0000.0000.0000.000
60A64GLN00.002-0.00940.5340.2330.2330.0000.0000.0000.000
61A65SER0-0.002-0.00641.4470.1990.1990.0000.0000.0000.000
62A66LYS10.8570.91839.0948.1438.1430.0000.0000.0000.000
63A67LYS10.7710.86744.2576.9636.9630.0000.0000.0000.000
64A68LEU00.009-0.00346.5560.1770.1770.0000.0000.0000.000
65A69TRP00.0410.01747.0290.1520.1520.0000.0000.0000.000
66A70LYS10.9570.97448.3406.6196.6190.0000.0000.0000.000
67A71ILE0-0.042-0.01250.1310.1370.1370.0000.0000.0000.000
68A72LEU00.0330.00051.5630.1410.1410.0000.0000.0000.000
69A73GLU-1-0.740-0.82651.099-6.092-6.0920.0000.0000.0000.000
70A74GLY0-0.0120.00154.1910.1180.1180.0000.0000.0000.000
71A75ARG10.7900.87856.4005.7075.7070.0000.0000.0000.000
72A76PHE00.0430.01857.3070.1170.1170.0000.0000.0000.000
73A77GLN0-0.028-0.02356.0450.0060.0060.0000.0000.0000.000
74A78LYS10.9080.96759.9955.3865.3860.0000.0000.0000.000
75A79ARG10.8440.95561.9395.2085.2080.0000.0000.0000.000
76A80ASP-1-0.894-0.93361.117-5.076-5.0760.0000.0000.0000.000
77A81ALA0-0.024-0.04459.862-0.059-0.0590.0000.0000.0000.000
78A82SER0-0.069-0.03955.7880.0370.0370.0000.0000.0000.000
79A83TYR0-0.020-0.01857.8920.0050.0050.0000.0000.0000.000
80A84THR0-0.027-0.04054.456-0.011-0.0110.0000.0000.0000.000
81A85TYR00.035-0.00456.6030.1270.1270.0000.0000.0000.000
82A86GLY00.0140.01954.406-0.119-0.1190.0000.0000.0000.000
83A87CYS0-0.038-0.01651.5720.1020.1020.0000.0000.0000.000
84A88LEU0-0.0050.00352.266-0.079-0.0790.0000.0000.0000.000
85A89GLU-1-0.770-0.87149.770-6.322-6.3220.0000.0000.0000.000
86A90PRO00.046-0.00147.0780.0730.0730.0000.0000.0000.000
87A91THR0-0.014-0.02049.6670.0110.0110.0000.0000.0000.000
88A92MET00.0000.04153.0840.0430.0430.0000.0000.0000.000
89A93VAL00.0350.00448.7130.0550.0550.0000.0000.0000.000
90A94THR0-0.116-0.05650.4570.0330.0330.0000.0000.0000.000
91A95GLN00.012-0.00152.8120.1570.1570.0000.0000.0000.000
92A96MET0-0.0040.00754.4000.0320.0320.0000.0000.0000.000
93A97ALA00.0000.00652.0390.0560.0560.0000.0000.0000.000
94A98LYS10.8200.90254.0195.5565.5560.0000.0000.0000.000
95A99TYR0-0.007-0.00657.0260.0490.0490.0000.0000.0000.000
96A100LEU0-0.0410.00256.0990.0460.0460.0000.0000.0000.000
97A101ASP-1-0.781-0.87453.892-5.937-5.9370.0000.0000.0000.000
98A102THR00.0060.00751.377-0.128-0.1280.0000.0000.0000.000
99A103VAL00.0030.02149.8150.1140.1140.0000.0000.0000.000
100A104TYR00.0060.00250.681-0.049-0.0490.0000.0000.0000.000
101A105VAL0-0.023-0.00847.1390.0410.0410.0000.0000.0000.000
102A106SER00.0190.00850.247-0.017-0.0170.0000.0000.0000.000
103A107GLY00.0600.03250.264-0.058-0.0580.0000.0000.0000.000
104A108TRP00.0490.01751.218-0.008-0.0080.0000.0000.0000.000
105A109GLN0-0.009-0.03053.7180.1190.1190.0000.0000.0000.000
106A110SER0-0.023-0.01248.760-0.043-0.0430.0000.0000.0000.000
107A111SER00.003-0.01250.632-0.106-0.1060.0000.0000.0000.000
108A112SER0-0.053-0.01552.2420.0350.0350.0000.0000.0000.000
109A113THR0-0.092-0.06152.8820.0400.0400.0000.0000.0000.000
110A114ALA0-0.052-0.03647.886-0.055-0.0550.0000.0000.0000.000
111A115SER00.0500.04047.012-0.227-0.2270.0000.0000.0000.000
112A116SER0-0.074-0.05942.0130.0220.0220.0000.0000.0000.000
113A117SER0-0.031-0.01643.038-0.189-0.1890.0000.0000.0000.000
114A118ASP-1-0.913-0.94545.162-6.803-6.8030.0000.0000.0000.000
115A119GLU-1-0.973-0.98248.218-5.942-5.9420.0000.0000.0000.000
116A120PRO0-0.028-0.00750.491-0.068-0.0680.0000.0000.0000.000
117A121GLY00.0530.01653.0030.0680.0680.0000.0000.0000.000
118A122PRO0-0.007-0.00555.2020.0240.0240.0000.0000.0000.000
119A123ASP-1-0.856-0.93754.510-5.996-5.9960.0000.0000.0000.000
120A124LEU0-0.008-0.00654.3200.1080.1080.0000.0000.0000.000
121A125ALA0-0.072-0.02749.509-0.047-0.0470.0000.0000.0000.000
122A126ASP-1-0.890-0.94449.102-6.246-6.2460.0000.0000.0000.000
123A127TYR0-0.033-0.02546.524-0.058-0.0580.0000.0000.0000.000
124A128PRO00.0470.02042.254-0.104-0.1040.0000.0000.0000.000
125A129TYR00.0360.01536.530-0.066-0.0660.0000.0000.0000.000
126A130THR0-0.007-0.00838.0020.0230.0230.0000.0000.0000.000
127A131THR0-0.0040.00740.789-0.031-0.0310.0000.0000.0000.000
128A132VAL00.0510.03344.289-0.017-0.0170.0000.0000.0000.000
129A133PRO0-0.012-0.01140.1430.0070.0070.0000.0000.0000.000
130A134ASN00.019-0.00539.024-0.233-0.2330.0000.0000.0000.000
131A135LYS10.8710.94641.7896.6956.6950.0000.0000.0000.000
132A136VAL00.014-0.00242.5600.0800.0800.0000.0000.0000.000
133A137SER0-0.007-0.00339.089-0.097-0.0970.0000.0000.0000.000
134A138HIS00.0000.01341.290-0.001-0.0010.0000.0000.0000.000
135A139LEU00.0090.01443.9660.0730.0730.0000.0000.0000.000
136A140PHE00.0380.01138.7420.0060.0060.0000.0000.0000.000
137A141MET00.012-0.00236.446-0.060-0.0600.0000.0000.0000.000
138A142ALA00.0110.01641.250-0.009-0.0090.0000.0000.0000.000
139A143GLN0-0.038-0.03244.663-0.037-0.0370.0000.0000.0000.000
140A144LEU00.0200.00238.5700.0430.0430.0000.0000.0000.000
141A145PHE0-0.053-0.00942.044-0.142-0.1420.0000.0000.0000.000
142A146HIS00.0710.04143.3980.0640.0640.0000.0000.0000.000
143A147ASP-1-0.905-0.95743.606-7.110-7.1100.0000.0000.0000.000
144A148ARG10.8910.94839.4628.0968.0960.0000.0000.0000.000
145A149LYS10.8150.92243.8276.4596.4590.0000.0000.0000.000
146A150GLN00.0130.00646.6890.2200.2200.0000.0000.0000.000
147A151ARG10.9460.96240.6447.6087.6080.0000.0000.0000.000
148A152HIS00.0490.03044.830-0.051-0.0510.0000.0000.0000.000
149A153GLU-1-0.807-0.87146.452-5.931-5.9310.0000.0000.0000.000
150A154ARG10.8280.90349.9756.1016.1010.0000.0000.0000.000
151A155LEU0-0.085-0.05244.7970.0830.0830.0000.0000.0000.000
152A156SER00.0160.00448.0370.0020.0020.0000.0000.0000.000
153A157ALA00.0030.02249.7480.1040.1040.0000.0000.0000.000
154A158PRO00.0630.02453.004-0.058-0.0580.0000.0000.0000.000
155A159LYS10.9620.97054.4465.8265.8260.0000.0000.0000.000
156A160SER00.008-0.00655.642-0.021-0.0210.0000.0000.0000.000
157A161GLU-1-0.815-0.88957.171-5.218-5.2180.0000.0000.0000.000
158A162ARG10.8700.93450.5016.2416.2410.0000.0000.0000.000
159A163SER0-0.067-0.02656.567-0.017-0.0170.0000.0000.0000.000
160A164LYS10.8930.93259.7475.2355.2350.0000.0000.0000.000
161A165LEU0-0.0330.00754.391-0.006-0.0060.0000.0000.0000.000
162A166GLN00.003-0.01454.8720.0870.0870.0000.0000.0000.000
163A167ASN0-0.013-0.02552.342-0.188-0.1880.0000.0000.0000.000
164A168ILE00.0110.02452.3810.0350.0350.0000.0000.0000.000
165A169ASP-1-0.787-0.86748.877-6.695-6.6950.0000.0000.0000.000
166A170TYR00.0590.00847.9680.0130.0130.0000.0000.0000.000
167A171LEU00.0020.03043.314-0.038-0.0380.0000.0000.0000.000
168A172ARG10.8360.94246.6386.0526.0520.0000.0000.0000.000
169A173PRO00.0030.00346.404-0.078-0.0780.0000.0000.0000.000
170A174ILE00.0090.01144.9390.1550.1550.0000.0000.0000.000
171A175ILE0-0.0060.00646.395-0.150-0.1500.0000.0000.0000.000
172A176ALA0-0.008-0.01345.7310.0840.0840.0000.0000.0000.000
173A177ASP-1-0.780-0.88847.888-6.313-6.3130.0000.0000.0000.000
174A178ALA00.014-0.00645.245-0.137-0.1370.0000.0000.0000.000
175A179ASP-1-0.702-0.81146.716-6.551-6.5510.0000.0000.0000.000
176A180THR0-0.018-0.01949.321-0.023-0.0230.0000.0000.0000.000
177A181GLY0-0.013-0.01845.004-0.046-0.0460.0000.0000.0000.000
178A182HIS0-0.054-0.04943.628-0.299-0.2990.0000.0000.0000.000
179A183GLY00.0180.01043.912-0.096-0.0960.0000.0000.0000.000
180A184GLY00.0340.02742.9820.0950.0950.0000.0000.0000.000
181A185LEU00.0470.00540.440-0.126-0.1260.0000.0000.0000.000
182A186THR00.0100.00236.334-0.057-0.0570.0000.0000.0000.000
183A187ALA0-0.0110.01137.295-0.245-0.2450.0000.0000.0000.000
184A188VAL00.0540.03639.760-0.076-0.0760.0000.0000.0000.000
185A189MET0-0.050-0.00335.068-0.013-0.0130.0000.0000.0000.000
186A190LYS10.9690.98033.0629.1289.1280.0000.0000.0000.000
187A191LEU00.0080.01836.380-0.130-0.1300.0000.0000.0000.000
188A192THR0-0.002-0.01838.5190.0820.0820.0000.0000.0000.000
189A193LYS10.8770.91729.79910.32910.3290.0000.0000.0000.000
190A194LEU0-0.0090.00134.781-0.087-0.0870.0000.0000.0000.000
191A195PHE00.027-0.00436.828-0.004-0.0040.0000.0000.0000.000
192A196ILE0-0.0130.00535.2360.0800.0800.0000.0000.0000.000
193A197GLU-1-0.870-0.93731.071-10.202-10.2020.0000.0000.0000.000
194A198LYS10.8610.94135.1358.6598.6590.0000.0000.0000.000
195A199GLY0-0.018-0.00538.2620.1710.1710.0000.0000.0000.000
196A200ALA0-0.016-0.00439.6640.1780.1780.0000.0000.0000.000
197A201ALA0-0.0060.01241.827-0.154-0.1540.0000.0000.0000.000
198A202GLY00.025-0.00944.3580.0010.0010.0000.0000.0000.000
199A203ILE0-0.024-0.00442.4660.0130.0130.0000.0000.0000.000
200A204HIS00.0100.03146.4340.0880.0880.0000.0000.0000.000
201A205ILE0-0.0080.00745.717-0.060-0.0600.0000.0000.0000.000
202A206GLU-1-0.801-0.90649.418-5.866-5.8660.0000.0000.0000.000
203A207ASP-1-0.729-0.82451.781-5.753-5.7530.0000.0000.0000.000
204A208GLN00.000-0.02153.7870.1490.1490.0000.0000.0000.000
205A209ALA00.0520.02452.211-0.156-0.1560.0000.0000.0000.000
206A210PRO0-0.006-0.00948.0880.0460.0460.0000.0000.0000.000
207A211GLY00.0320.01250.5450.0560.0560.0000.0000.0000.000
208A212THR0-0.033-0.01652.1890.1250.1250.0000.0000.0000.000
209A213LYS10.7670.90852.4436.1606.1600.0000.0000.0000.000
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