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: QLK4Y

Calculation Name: 2FKB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | acetate ion | glycerol | magnesium ion

Ligand 3-letter code: SO4 | ACT | GOL | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FKB

Chain ID: A

ChEMBL ID:

UniProt ID: P65556

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 161
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1649910.779333
FMO2-HF: Nuclear repulsion 1584651.762906
FMO2-HF: Total energy -65259.016427
FMO2-MP2: Total energy -65445.110963


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:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
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.
-195.354-193.6950-0.648-1.0110
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.906
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].
3A10GLU-1-0.762-0.8483.849-32.555-30.9770.001-0.642-0.9370.000
4A11TRP00.009-0.0124.8804.4004.481-0.001-0.006-0.0740.000
5A12VAL00.0150.0118.4010.0020.0020.0000.0000.0000.000
6A13ASP-1-0.750-0.87211.899-17.541-17.5410.0000.0000.0000.000
7A14ILE0-0.090-0.04415.1860.3450.3450.0000.0000.0000.000
8A15VAL0-0.005-0.00817.9560.4570.4570.0000.0000.0000.000
9A16ASN0-0.010-0.01921.504-0.122-0.1220.0000.0000.0000.000
10A17GLU-1-0.974-0.99025.161-10.103-10.1030.0000.0000.0000.000
11A18GLU-1-0.862-0.94628.074-10.550-10.5500.0000.0000.0000.000
12A19ASN0-0.037-0.00822.988-0.530-0.5300.0000.0000.0000.000
13A20GLU-1-0.847-0.90223.671-11.215-11.2150.0000.0000.0000.000
14A21VAL0-0.021-0.01517.215-0.074-0.0740.0000.0000.0000.000
15A22ILE0-0.038-0.01720.5230.4000.4000.0000.0000.0000.000
16A23ALA0-0.045-0.02018.0640.1490.1490.0000.0000.0000.000
17A24GLN00.0340.01910.416-1.700-1.7000.0000.0000.0000.000
18A25ALA0-0.0060.00713.1400.5390.5390.0000.0000.0000.000
19A26SER00.0370.0149.359-0.863-0.8630.0000.0000.0000.000
20A27ARG10.9170.9339.33629.50429.5040.0000.0000.0000.000
21A28GLU-1-0.943-0.96810.624-24.566-24.5660.0000.0000.0000.000
22A29GLN00.0190.00312.3793.1013.1010.0000.0000.0000.000
23A30MET0-0.0180.00814.1381.2011.2010.0000.0000.0000.000
24A31ARG10.9260.97014.53220.09920.0990.0000.0000.0000.000
25A32ALA0-0.016-0.00516.5021.2421.2420.0000.0000.0000.000
26A33GLN0-0.051-0.03718.3091.5901.5900.0000.0000.0000.000
27A34CYS0-0.055-0.00820.0270.7490.7490.0000.0000.0000.000
28A35LEU0-0.0130.00916.7980.6990.6990.0000.0000.0000.000
29A36ARG10.8670.94919.80511.94311.9430.0000.0000.0000.000
30A37HIS0-0.015-0.00816.576-0.341-0.3410.0000.0000.0000.000
31A38ARG10.8570.91217.41915.82315.8230.0000.0000.0000.000
32A39ALA00.0250.01216.841-1.185-1.1850.0000.0000.0000.000
33A40THR0-0.017-0.00217.1311.1011.1010.0000.0000.0000.000
34A41TYR0-0.034-0.03619.698-0.260-0.2600.0000.0000.0000.000
35A42ILE0-0.010-0.00619.4790.6980.6980.0000.0000.0000.000
36A43VAL00.0210.00223.733-0.061-0.0610.0000.0000.0000.000
37A44VAL00.0370.02523.7390.2650.2650.0000.0000.0000.000
38A45HIS0-0.007-0.01026.9430.3580.3580.0000.0000.0000.000
39A46ASP-1-0.694-0.85530.682-9.305-9.3050.0000.0000.0000.000
40A47GLY0-0.033-0.00733.1560.1850.1850.0000.0000.0000.000
41A48MET0-0.131-0.06935.6230.3410.3410.0000.0000.0000.000
42A49GLY00.0030.00936.6140.2470.2470.0000.0000.0000.000
43A50LYS10.7680.87933.9438.8498.8490.0000.0000.0000.000
44A51ILE00.006-0.00828.913-0.087-0.0870.0000.0000.0000.000
45A52LEU0-0.006-0.00124.5360.1700.1700.0000.0000.0000.000
46A53VAL0-0.025-0.00126.396-0.409-0.4090.0000.0000.0000.000
47A54GLN00.001-0.02121.520-0.615-0.6150.0000.0000.0000.000
48A55ARG10.8210.91423.94411.73911.7390.0000.0000.0000.000
49A56ARG10.8130.88218.45615.29715.2970.0000.0000.0000.000
50A57THR0-0.006-0.02016.3170.9070.9070.0000.0000.0000.000
51A58GLU-1-0.975-1.00919.524-12.958-12.9580.0000.0000.0000.000
52A59THR0-0.021-0.01815.4020.5720.5720.0000.0000.0000.000
53A60LYS10.8430.93913.67920.32820.3280.0000.0000.0000.000
54A61ASP-1-0.888-0.95714.172-21.601-21.6010.0000.0000.0000.000
55A62PHE0-0.075-0.03617.2360.9710.9710.0000.0000.0000.000
56A63LEU00.003-0.00119.507-0.146-0.1460.0000.0000.0000.000
57A64PRO00.0540.04220.366-0.021-0.0210.0000.0000.0000.000
58A65GLY00.0220.01921.5430.6730.6730.0000.0000.0000.000
59A66MET0-0.074-0.03023.8460.3830.3830.0000.0000.0000.000
60A67LEU0-0.016-0.00724.186-0.501-0.5010.0000.0000.0000.000
61A68ASP-1-0.753-0.83621.180-14.689-14.6890.0000.0000.0000.000
62A69ALA0-0.038-0.03624.6890.2330.2330.0000.0000.0000.000
63A70THR0-0.083-0.05122.9560.4590.4590.0000.0000.0000.000
64A71ALA00.0590.05220.128-0.283-0.2830.0000.0000.0000.000
65A72GLY00.018-0.01418.1030.7220.7220.0000.0000.0000.000
66A73GLY00.0460.04115.220-0.342-0.3420.0000.0000.0000.000
67A74VAL0-0.069-0.03012.6591.1501.1500.0000.0000.0000.000
68A75VAL0-0.0090.00612.882-0.932-0.9320.0000.0000.0000.000
69A76GLN0-0.010-0.0276.397-0.311-0.3110.0000.0000.0000.000
70A77ALA0-0.065-0.0509.7041.5911.5910.0000.0000.0000.000
71A78ASP-1-0.945-0.97311.100-20.178-20.1780.0000.0000.0000.000
72A79GLU-1-0.770-0.81411.799-22.644-22.6440.0000.0000.0000.000
73A80GLN0-0.043-0.03814.4011.4851.4850.0000.0000.0000.000
74A81LEU00.000-0.01517.590-0.422-0.4220.0000.0000.0000.000
75A82LEU00.0050.00419.214-0.318-0.3180.0000.0000.0000.000
76A83GLU-1-0.895-0.94115.583-17.986-17.9860.0000.0000.0000.000
77A84SER0-0.017-0.01413.983-0.276-0.2760.0000.0000.0000.000
78A85ALA00.0080.00115.467-0.456-0.4560.0000.0000.0000.000
79A86ARG10.8050.88318.02913.81713.8170.0000.0000.0000.000
80A87ARG10.7580.8619.67926.12926.1290.0000.0000.0000.000
81A88GLU-1-0.835-0.90612.942-23.128-23.1280.0000.0000.0000.000
82A89ALA0-0.017-0.02015.0150.2450.2450.0000.0000.0000.000
83A90GLU-1-1.005-0.99814.944-19.246-19.2460.0000.0000.0000.000
84A91GLU-1-0.826-0.9209.747-29.113-29.1130.0000.0000.0000.000
85A92GLU0-0.029-0.03114.0570.7630.7630.0000.0000.0000.000
86A93LEU0-0.022-0.02016.4780.9640.9640.0000.0000.0000.000
87A94GLY00.0480.04218.1550.9480.9480.0000.0000.0000.000
88A95ILE0-0.090-0.03719.3930.9170.9170.0000.0000.0000.000
89A96ALA00.0830.03419.802-0.472-0.4720.0000.0000.0000.000
90A97GLY0-0.055-0.03421.3910.6240.6240.0000.0000.0000.000
91A98VAL00.0140.01824.2750.5320.5320.0000.0000.0000.000
92A99PRO0-0.001-0.00125.302-0.356-0.3560.0000.0000.0000.000
93A100PHE00.015-0.00220.9650.0380.0380.0000.0000.0000.000
94A101ALA0-0.026-0.00726.7480.2480.2480.0000.0000.0000.000
95A102GLU-1-0.851-0.93725.619-11.968-11.9680.0000.0000.0000.000
96A103HIS10.8360.90428.26110.56810.5680.0000.0000.0000.000
97A104GLY00.0140.01628.7950.3230.3230.0000.0000.0000.000
98A105GLN00.0310.00724.293-0.838-0.8380.0000.0000.0000.000
99A106PHE0-0.049-0.02225.2260.6280.6280.0000.0000.0000.000
100A107TYR00.028-0.00325.023-0.525-0.5250.0000.0000.0000.000
101A108PHE0-0.017-0.02725.1070.6110.6110.0000.0000.0000.000
102A109GLU-1-0.817-0.87225.546-11.690-11.6900.0000.0000.0000.000
103A110ASP-1-0.831-0.92025.370-12.220-12.2200.0000.0000.0000.000
104A111LYS10.8880.94327.30410.39210.3920.0000.0000.0000.000
105A112ASN0-0.0270.00022.230-0.231-0.2310.0000.0000.0000.000
106A113CYS0-0.058-0.04021.321-0.870-0.8700.0000.0000.0000.000
107A114ARG10.9690.97521.73213.58713.5870.0000.0000.0000.000
108A115VAL0-0.0040.00420.020-0.606-0.6060.0000.0000.0000.000
109A116TRP0-0.010-0.00721.8840.8410.8410.0000.0000.0000.000
110A117GLY00.0170.01721.577-0.757-0.7570.0000.0000.0000.000
111A118ALA0-0.011-0.01421.6500.7580.7580.0000.0000.0000.000
112A119LEU0-0.029-0.01023.058-0.342-0.3420.0000.0000.0000.000
113A120PHE0-0.008-0.01421.5560.4240.4240.0000.0000.0000.000
114A121SER00.0090.01725.8580.2190.2190.0000.0000.0000.000
115A122CYS0-0.064-0.02024.2910.0730.0730.0000.0000.0000.000
116A123VAL00.0240.02427.7980.0560.0560.0000.0000.0000.000
117A124SER00.004-0.01526.526-0.061-0.0610.0000.0000.0000.000
118A125HIS0-0.015-0.02029.145-0.124-0.1240.0000.0000.0000.000
119A126GLY00.0010.04026.9890.0610.0610.0000.0000.0000.000
120A127PRO0-0.078-0.06526.4360.3670.3670.0000.0000.0000.000
121A128PHE00.0150.00222.689-0.055-0.0550.0000.0000.0000.000
122A129ALA0-0.056-0.01819.2290.3110.3110.0000.0000.0000.000
123A130LEU00.0090.00518.670-0.260-0.2600.0000.0000.0000.000
124A131GLN00.0120.01311.894-1.279-1.2790.0000.0000.0000.000
125A132GLU-1-0.914-0.95315.767-16.613-16.6130.0000.0000.0000.000
126A133ASP-1-0.910-0.95113.014-22.319-22.3190.0000.0000.0000.000
127A134GLU-1-0.956-0.96912.402-24.645-24.6450.0000.0000.0000.000
128A135VAL0-0.021-0.02015.6260.8410.8410.0000.0000.0000.000
129A136SER00.0110.00519.1600.0750.0750.0000.0000.0000.000
130A137GLU-1-0.873-0.92521.818-10.649-10.6490.0000.0000.0000.000
131A138VAL00.0170.01123.263-0.324-0.3240.0000.0000.0000.000
132A139CYS0-0.054-0.02126.0150.4090.4090.0000.0000.0000.000
133A140TRP00.0220.01929.443-0.123-0.1230.0000.0000.0000.000
134A141LEU0-0.014-0.00531.7970.3780.3780.0000.0000.0000.000
135A142THR00.017-0.00533.669-0.110-0.1100.0000.0000.0000.000
136A143PRO00.0500.00035.402-0.092-0.0920.0000.0000.0000.000
137A144GLU-1-0.951-0.94736.481-7.581-7.5810.0000.0000.0000.000
138A145GLU-1-0.812-0.89836.278-8.678-8.6780.0000.0000.0000.000
139A146ILE0-0.0040.00631.561-0.127-0.1270.0000.0000.0000.000
140A147THR0-0.050-0.05134.5580.0250.0250.0000.0000.0000.000
141A148ALA0-0.046-0.02137.0040.0620.0620.0000.0000.0000.000
142A149ARG10.8270.89032.0789.7719.7710.0000.0000.0000.000
143A150CYS0-0.043-0.02333.205-0.269-0.2690.0000.0000.0000.000
144A151ASP-1-0.919-0.95632.529-9.372-9.3720.0000.0000.0000.000
145A152GLU-1-0.802-0.87430.306-10.179-10.1790.0000.0000.0000.000
146A153PHE0-0.027-0.01728.146-0.449-0.4490.0000.0000.0000.000
147A154THR00.0160.01223.0130.3560.3560.0000.0000.0000.000
148A155PRO0-0.017-0.02726.3540.1490.1490.0000.0000.0000.000
149A156ASP-1-0.835-0.88822.635-13.525-13.5250.0000.0000.0000.000
150A157SER00.0430.01024.2860.3550.3550.0000.0000.0000.000
151A158LEU00.0270.02025.9330.3590.3590.0000.0000.0000.000
152A159LYS10.8440.91828.62710.82610.8260.0000.0000.0000.000
153A160ALA0-0.010-0.00325.9910.3030.3030.0000.0000.0000.000
154A161LEU00.0410.02028.0930.2790.2790.0000.0000.0000.000
155A162ALA00.0140.00430.3980.3360.3360.0000.0000.0000.000
156A163LEU0-0.064-0.04129.8630.3970.3970.0000.0000.0000.000
157A164TRP0-0.028-0.00330.2880.1280.1280.0000.0000.0000.000
158A165MET00.0360.01332.3190.2020.2020.0000.0000.0000.000
159A166LYS10.8930.96435.5448.6478.6470.0000.0000.0000.000
160A167ARG10.7530.86032.5519.4639.4630.0000.0000.0000.000
161A168ASN-1-0.887-0.92534.478-8.784-8.7840.0000.0000.0000.000