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: 3ML7L

Calculation Name: 3QXG-A-Xray547

Preferred Name:

Target Type:

Ligand Name: l(+)-tartaric acid | phosphate ion | acetate ion | calcium ion | magnesium ion

Ligand 3-letter code: TLA | PO4 | ACT | CA | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3QXG

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A5V9

Base Structure: X-ray

Registration Date: 2025-10-05

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2709318.251059
FMO2-HF: Nuclear repulsion 2621587.183867
FMO2-HF: Total energy -87731.067192
FMO2-MP2: Total energy -87982.548986


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-534.921-527.38512.325-8.594-11.265-0.087
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.825 / q_NPA : 1.913
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].
3A5LEU0-0.0020.0322.1293.4737.9552.878-2.783-4.578-0.012
4A6LYS10.8570.9191.91619.59619.7576.624-3.746-3.038-0.054
5A7ALA00.0180.0144.5014.7284.811-0.001-0.008-0.0730.000
103A105GLU0-0.109-0.0763.589-3.511-3.2810.002-0.032-0.2000.000
104A106GLY0-0.041-0.0163.434-20.230-19.5910.004-0.334-0.308-0.002
105A107LEU0-0.070-0.0212.024-10.408-10.3962.787-0.909-1.890-0.013
221A223MET0-0.072-0.0233.307-9.711-9.1640.017-0.120-0.445-0.001
222A224LEU-1-1.008-0.9803.542-111.559-110.1770.014-0.662-0.733-0.005
6A8VAL00.0050.0066.813-3.214-3.2140.0000.0000.0000.000
7A9LEU0-0.022-0.0179.1413.7663.7660.0000.0000.0000.000
8A10PHE00.0470.01911.5180.0650.0650.0000.0000.0000.000
9A11ASP-1-0.705-0.85115.299-26.078-26.0780.0000.0000.0000.000
10A12MET0-0.018-0.01618.826-0.582-0.5820.0000.0000.0000.000
11A13ASP-1-0.797-0.86821.490-22.354-22.3540.0000.0000.0000.000
12A14GLY00.0610.03523.105-0.345-0.3450.0000.0000.0000.000
13A15VAL0-0.0170.01417.067-0.583-0.5830.0000.0000.0000.000
14A16LEU0-0.023-0.01416.794-0.764-0.7640.0000.0000.0000.000
15A17PHE00.016-0.00720.5860.5120.5120.0000.0000.0000.000
16A18ASN0-0.020-0.00624.423-0.264-0.2640.0000.0000.0000.000
17A19SER0-0.026-0.05826.9120.7060.7060.0000.0000.0000.000
18A20MET00.0170.01826.9550.8060.8060.0000.0000.0000.000
19A21PRO00.0040.02029.5380.6140.6140.0000.0000.0000.000
20A22TYR0-0.020-0.01632.5540.6220.6220.0000.0000.0000.000
21A23HIS00.007-0.00428.3621.2511.2510.0000.0000.0000.000
22A24SER0-0.034-0.01832.8770.5900.5900.0000.0000.0000.000
23A25GLU-1-0.791-0.85734.462-14.920-14.9200.0000.0000.0000.000
24A26ALA00.007-0.00836.4470.4690.4690.0000.0000.0000.000
25A27TRP00.028-0.00432.5460.5720.5720.0000.0000.0000.000
26A28HIS0-0.021-0.01037.6410.6010.6010.0000.0000.0000.000
27A29GLN0-0.023-0.03240.0240.6830.6830.0000.0000.0000.000
28A30VAL0-0.0120.01640.9570.4330.4330.0000.0000.0000.000
29A31MET0-0.0190.00039.6630.4490.4490.0000.0000.0000.000
30A32LYS10.9801.00643.17613.61313.6130.0000.0000.0000.000
31A33THR0-0.086-0.05745.6110.4300.4300.0000.0000.0000.000
32A34HIS10.7680.85045.57313.87713.8770.0000.0000.0000.000
33A35GLY0-0.0340.00147.6850.1260.1260.0000.0000.0000.000
34A36LEU0-0.044-0.01944.2160.0990.0990.0000.0000.0000.000
35A37ASP-1-0.956-0.98744.170-14.330-14.3300.0000.0000.0000.000
36A38LEU0-0.0080.01036.596-0.335-0.3350.0000.0000.0000.000
37A39SER00.006-0.03438.700-0.087-0.0870.0000.0000.0000.000
38A40ARG10.8290.86036.19015.08915.0890.0000.0000.0000.000
39A41GLU-1-0.906-0.94834.202-17.767-17.7670.0000.0000.0000.000
40A42GLU-1-0.758-0.84333.408-16.492-16.4920.0000.0000.0000.000
41A43ALA0-0.033-0.01733.571-0.412-0.4120.0000.0000.0000.000
42A44TYR00.007-0.00128.349-0.248-0.2480.0000.0000.0000.000
43A45MET0-0.009-0.00128.984-0.928-0.9280.0000.0000.0000.000
44A46HIS0-0.022-0.00629.951-0.781-0.7810.0000.0000.0000.000
45A47GLU-1-0.792-0.89925.417-23.340-23.3400.0000.0000.0000.000
46A48GLY00.007-0.00425.125-0.591-0.5910.0000.0000.0000.000
47A49ARG10.8730.94425.79519.45519.4550.0000.0000.0000.000
48A50THR00.0310.02028.8840.2590.2590.0000.0000.0000.000
49A51GLY00.014-0.00230.6080.3930.3930.0000.0000.0000.000
50A52ALA00.0440.01833.9220.3780.3780.0000.0000.0000.000
51A53SER0-0.021-0.00132.2730.2420.2420.0000.0000.0000.000
52A54THR00.009-0.01732.7520.1440.1440.0000.0000.0000.000
53A55ILE0-0.022-0.00634.9290.3490.3490.0000.0000.0000.000
54A56ASN00.0650.02337.7220.6750.6750.0000.0000.0000.000
55A57ILE0-0.0140.00833.8770.2850.2850.0000.0000.0000.000
56A58VAL00.0080.00838.2550.2610.2610.0000.0000.0000.000
57A59PHE0-0.013-0.00940.7330.4110.4110.0000.0000.0000.000
58A60GLN0-0.019-0.01539.0550.0970.0970.0000.0000.0000.000
59A61ARG10.7510.86439.63715.46315.4630.0000.0000.0000.000
60A62GLU-1-0.815-0.89843.314-13.883-13.8830.0000.0000.0000.000
61A63LEU0-0.050-0.02846.1340.3930.3930.0000.0000.0000.000
62A64GLY0-0.0150.00946.6400.2500.2500.0000.0000.0000.000
63A65LYS10.8290.92846.34313.13113.1310.0000.0000.0000.000
64A66GLU-1-0.914-0.96440.581-15.752-15.7520.0000.0000.0000.000
65A67ALA0-0.052-0.01842.0910.3800.3800.0000.0000.0000.000
66A68THR0-0.038-0.04343.500-0.149-0.1490.0000.0000.0000.000
67A69GLN0-0.032-0.03038.771-0.307-0.3070.0000.0000.0000.000
68A70GLU-1-0.849-0.93942.857-13.602-13.6020.0000.0000.0000.000
69A71GLU-1-0.827-0.89245.148-13.328-13.3280.0000.0000.0000.000
70A72ILE00.000-0.00238.550-0.236-0.2360.0000.0000.0000.000
71A73GLU-1-0.893-0.93739.999-15.322-15.3220.0000.0000.0000.000
72A74SER0-0.054-0.03641.320-0.025-0.0250.0000.0000.0000.000
73A75ILE00.0250.01140.112-0.078-0.0780.0000.0000.0000.000
74A76TYR00.001-0.00532.952-0.420-0.4200.0000.0000.0000.000
75A77HIS0-0.0090.00138.233-0.526-0.5260.0000.0000.0000.000
76A78GLU-1-0.835-0.89940.433-13.884-13.8840.0000.0000.0000.000
77A79LYS10.8570.93832.75718.35018.3500.0000.0000.0000.000
78A80SER0-0.026-0.01135.973-0.464-0.4640.0000.0000.0000.000
79A81ILE0-0.006-0.00437.124-0.146-0.1460.0000.0000.0000.000
80A82LEU0-0.0210.00139.949-0.014-0.0140.0000.0000.0000.000
81A83PHE0-0.0050.00230.767-0.138-0.1380.0000.0000.0000.000
82A84ASN0-0.052-0.01734.765-0.668-0.6680.0000.0000.0000.000
83A85SER0-0.049-0.02637.1710.3110.3110.0000.0000.0000.000
84A86TYR0-0.0130.00036.1540.2840.2840.0000.0000.0000.000
85A87PRO00.001-0.00435.690-0.155-0.1550.0000.0000.0000.000
86A88GLU-1-0.809-0.88431.485-19.487-19.4870.0000.0000.0000.000
87A89ALA00.0230.01428.858-0.181-0.1810.0000.0000.0000.000
88A90GLU-1-0.907-0.94227.788-20.176-20.1760.0000.0000.0000.000
89A91ARG10.8770.92821.93523.32823.3280.0000.0000.0000.000
90A92MET0-0.0180.00620.9550.8460.8460.0000.0000.0000.000
91A93PRO00.002-0.01720.827-1.152-1.1520.0000.0000.0000.000
92A94GLY00.0790.03818.132-0.491-0.4910.0000.0000.0000.000
93A95ALA0-0.030-0.00516.226-2.016-2.0160.0000.0000.0000.000
94A96TRP00.0200.00215.569-1.893-1.8930.0000.0000.0000.000
95A97GLU-1-0.869-0.92514.748-35.206-35.2060.0000.0000.0000.000
96A98LEU00.0450.01410.130-2.417-2.4170.0000.0000.0000.000
97A99LEU00.0010.00110.784-3.998-3.9980.0000.0000.0000.000
98A100GLN0-0.014-0.02011.459-1.872-1.8720.0000.0000.0000.000
99A101LYS10.8380.9398.29343.99343.9930.0000.0000.0000.000
100A102VAL00.0190.0026.678-5.462-5.4620.0000.0000.0000.000
101A103LYS10.8950.9396.73131.33431.3340.0000.0000.0000.000
102A104SER0-0.073-0.0548.485-0.086-0.0860.0000.0000.0000.000
106A108THR00.000-0.0145.5349.9129.9120.0000.0000.0000.000
107A109PRO0-0.0050.0018.859-1.439-1.4390.0000.0000.0000.000
108A110MET0-0.052-0.01411.3371.3821.3820.0000.0000.0000.000
109A111VAL00.0050.01713.888-0.358-0.3580.0000.0000.0000.000
110A112VAL0-0.007-0.01215.8860.8220.8220.0000.0000.0000.000
111A113THR00.0030.00318.7360.6190.6190.0000.0000.0000.000
112A114GLY00.0360.02222.3360.2970.2970.0000.0000.0000.000
113A115SER00.0130.00625.4141.4011.4010.0000.0000.0000.000
114A116GLY00.0610.01627.050-0.407-0.4070.0000.0000.0000.000
115A117GLN0-0.016-0.00529.0620.8030.8030.0000.0000.0000.000
116A118LEU00.0370.01329.098-0.580-0.5800.0000.0000.0000.000
117A119SER0-0.015-0.02429.444-0.628-0.6280.0000.0000.0000.000
118A120LEU0-0.029-0.01026.512-0.085-0.0850.0000.0000.0000.000
119A121LEU00.011-0.01224.192-0.763-0.7630.0000.0000.0000.000
120A122GLU-1-0.973-0.99624.901-20.395-20.3950.0000.0000.0000.000
121A123ARG10.7550.87126.97320.55220.5520.0000.0000.0000.000
122A124LEU0-0.0040.01420.471-0.437-0.4370.0000.0000.0000.000
123A125GLU-1-0.821-0.89820.970-27.909-27.9090.0000.0000.0000.000
124A126HIS0-0.009-0.02122.868-0.672-0.6720.0000.0000.0000.000
125A127ASN0-0.069-0.02722.9330.5150.5150.0000.0000.0000.000
126A128PHE0-0.017-0.01817.902-0.727-0.7270.0000.0000.0000.000
127A129PRO00.0300.02118.972-1.130-1.1300.0000.0000.0000.000
128A130GLY00.003-0.01118.257-1.315-1.3150.0000.0000.0000.000
129A131MET0-0.098-0.01914.328-3.186-3.1860.0000.0000.0000.000
130A132PHE00.0110.00314.463-2.011-2.0110.0000.0000.0000.000
131A133HIS00.0570.02615.4192.3752.3750.0000.0000.0000.000
132A134LYS10.9860.99018.70921.89821.8980.0000.0000.0000.000
133A135GLU-1-0.906-0.96218.911-26.748-26.7480.0000.0000.0000.000
134A136LEU0-0.037-0.02813.573-0.858-0.8580.0000.0000.0000.000
135A137MET0-0.0220.00516.267-1.150-1.1500.0000.0000.0000.000
136A138VAL0-0.042-0.01518.7430.7230.7230.0000.0000.0000.000
137A139THR0-0.013-0.01021.0250.1150.1150.0000.0000.0000.000
138A140ALA00.030-0.00224.3740.1120.1120.0000.0000.0000.000
139A141PHE0-0.041-0.02427.5270.6150.6150.0000.0000.0000.000
140A142ASP-1-0.827-0.88024.110-24.662-24.6620.0000.0000.0000.000
141A143VAL0-0.056-0.01924.866-0.208-0.2080.0000.0000.0000.000
142A144LYS10.8990.95227.39419.48519.4850.0000.0000.0000.000
143A145TYR0-0.069-0.04528.3570.8150.8150.0000.0000.0000.000
144A146GLY00.0180.00525.9000.3180.3180.0000.0000.0000.000
145A147LYS10.7440.87720.12228.83028.8300.0000.0000.0000.000
146A148PRO00.0420.02724.5450.8870.8870.0000.0000.0000.000
147A149ASN0-0.045-0.02424.409-1.237-1.2370.0000.0000.0000.000
148A150PRO00.0690.02820.375-0.302-0.3020.0000.0000.0000.000
149A151GLU-1-0.792-0.88920.700-23.798-23.7980.0000.0000.0000.000
150A152PRO00.0280.00621.120-0.782-0.7820.0000.0000.0000.000
151A153TYR00.020-0.03015.868-1.567-1.5670.0000.0000.0000.000
152A154LEU0-0.010-0.00816.734-1.827-1.8270.0000.0000.0000.000
153A155MET0-0.072-0.03718.367-0.503-0.5030.0000.0000.0000.000
154A156ALA00.0360.02815.327-0.282-0.2820.0000.0000.0000.000
155A157LEU0-0.0090.00112.466-1.445-1.4450.0000.0000.0000.000
156A158LYS10.8790.93814.73628.79028.7900.0000.0000.0000.000
157A159LYS10.8080.89117.20727.21327.2130.0000.0000.0000.000
158A160GLY00.0400.02212.8190.2030.2030.0000.0000.0000.000
159A161GLY0-0.057-0.01412.352-2.161-2.1610.0000.0000.0000.000
160A162LEU0-0.061-0.0248.630-2.718-2.7180.0000.0000.0000.000
161A163LYS10.8780.92911.14142.72342.7230.0000.0000.0000.000
162A164ALA00.0870.03310.688-3.443-3.4430.0000.0000.0000.000
163A165ASP-1-0.796-0.9027.857-57.370-57.3700.0000.0000.0000.000
164A166GLU-1-0.902-0.9526.358-67.096-67.0960.0000.0000.0000.000
165A167ALA00.000-0.0036.607-5.611-5.6110.0000.0000.0000.000
166A168VAL00.0200.0116.311-2.031-2.0310.0000.0000.0000.000
167A169VAL0-0.025-0.0048.8651.2391.2390.0000.0000.0000.000
168A170ILE0-0.028-0.00510.684-0.899-0.8990.0000.0000.0000.000
169A171GLU-1-0.718-0.84514.014-27.951-27.9510.0000.0000.0000.000
170A172ASN0-0.006-0.01817.688-1.027-1.0270.0000.0000.0000.000
171A173ALA00.0650.06320.9270.9330.9330.0000.0000.0000.000
172A174PRO00.0190.00822.476-1.025-1.0250.0000.0000.0000.000
173A175LEU00.0200.00423.214-0.703-0.7030.0000.0000.0000.000
174A176GLY00.0290.00121.735-0.170-0.1700.0000.0000.0000.000
175A177VAL00.0100.00118.020-1.501-1.5010.0000.0000.0000.000
176A178GLU-1-0.835-0.89218.813-24.303-24.3030.0000.0000.0000.000
177A179ALA0-0.042-0.02020.746-0.297-0.2970.0000.0000.0000.000
178A180GLY00.0140.00016.509-0.594-0.5940.0000.0000.0000.000
179A181HIS00.0040.00515.897-0.255-0.2550.0000.0000.0000.000
180A182LYS10.8410.89617.10123.84723.8470.0000.0000.0000.000
181A183ALA0-0.064-0.02916.4790.8440.8440.0000.0000.0000.000
182A184GLY0-0.053-0.02215.132-1.122-1.1220.0000.0000.0000.000
183A185ILE0-0.088-0.03410.411-2.839-2.8390.0000.0000.0000.000
184A186PHE00.0230.0348.4271.2861.2860.0000.0000.0000.000
185A187THR0-0.012-0.03010.515-1.594-1.5940.0000.0000.0000.000
186A188ILE0-0.028-0.0139.4801.1281.1280.0000.0000.0000.000
187A189ALA00.0400.01913.8700.9530.9530.0000.0000.0000.000
188A190VAL0-0.033-0.03316.370-0.658-0.6580.0000.0000.0000.000
189A191ASN0-0.011-0.02318.8830.7900.7900.0000.0000.0000.000
190A192THR0-0.049-0.04721.5100.8230.8230.0000.0000.0000.000
191A193GLY0-0.0030.01224.2440.7240.7240.0000.0000.0000.000
192A194PRO0-0.067-0.03227.346-0.131-0.1310.0000.0000.0000.000
193A195LEU00.0160.01127.3260.5570.5570.0000.0000.0000.000
194A196ASP-1-0.862-0.92228.027-20.146-20.1460.0000.0000.0000.000
195A197GLY0-0.008-0.01524.723-0.474-0.4740.0000.0000.0000.000
196A198GLN00.0270.00423.842-1.445-1.4450.0000.0000.0000.000
197A199VAL00.0520.03124.925-0.578-0.5780.0000.0000.0000.000
198A200LEU0-0.028-0.01221.007-0.495-0.4950.0000.0000.0000.000
199A201LEU0-0.023-0.01519.516-1.258-1.2580.0000.0000.0000.000
200A202ASP-1-0.920-0.96221.612-23.085-23.0850.0000.0000.0000.000
201A203ALA0-0.076-0.03022.0830.1910.1910.0000.0000.0000.000
202A204GLY0-0.003-0.00619.373-0.564-0.5640.0000.0000.0000.000
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