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: 5YJ1Z

Calculation Name: 3KEV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | s-hydroxycysteine | acetate ion

Ligand 3-letter code: SO4 | CSO | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KEV

Chain ID: A

ChEMBL ID:

UniProt ID: D1MPT4

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2117497.339654
FMO2-HF: Nuclear repulsion 2041548.720152
FMO2-HF: Total energy -75948.619502
FMO2-MP2: Total energy -76175.188255


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:4:ALA)


Summations of interaction energy for fragment #1(A:4:ALA)
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.
-74.257-67.95211.947-7.435-10.816-0.09
Interaction energy analysis for fragmet #1(A:4:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.902
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].
3A6LYS10.9100.9393.85635.43136.512-0.006-0.416-0.6590.000
6A9ILE0-0.032-0.0052.3982.0582.0141.408-0.485-0.878-0.004
67A70ALA0-0.013-0.0052.226-8.111-7.6251.234-0.834-0.887-0.004
68A71ASN0-0.057-0.0233.294-7.753-7.7090.0050.257-0.306-0.001
70A73GLN0-0.014-0.0132.087-27.337-25.8024.199-2.726-3.007-0.037
71A74VAL0-0.043-0.0282.753-0.863-0.8860.8760.268-1.120-0.006
72A75ASP-1-0.760-0.8722.170-78.285-75.3014.220-3.432-3.773-0.038
73A76SER00.0210.0043.6805.1545.2120.010-0.030-0.0380.000
76A79LYS10.7710.8623.61755.69255.8760.001-0.037-0.1480.000
4A7LYS10.9410.9745.79829.56529.5650.0000.0000.0000.000
5A8ALA00.0330.0155.6622.7882.7880.0000.0000.0000.000
7A10LEU0-0.010-0.0106.3723.1873.1870.0000.0000.0000.000
8A11GLU-1-0.922-0.9389.622-19.535-19.5350.0000.0000.0000.000
9A12LEU00.0390.0177.1871.3131.3130.0000.0000.0000.000
10A13PHE00.005-0.00110.4201.3891.3890.0000.0000.0000.000
11A14GLN0-0.072-0.05312.2472.1962.1960.0000.0000.0000.000
12A15THR0-0.011-0.00413.9981.6811.6810.0000.0000.0000.000
13A16TYR0-0.102-0.09612.9240.3660.3660.0000.0000.0000.000
14A17LYS10.8540.96316.22116.29716.2970.0000.0000.0000.000
15A18GLU-1-0.737-0.86617.745-13.057-13.0570.0000.0000.0000.000
16A19PRO0-0.040-0.03721.513-0.221-0.2210.0000.0000.0000.000
17A20LEU0-0.011-0.00123.6680.1370.1370.0000.0000.0000.000
18A21GLY0-0.062-0.01620.256-0.068-0.0680.0000.0000.0000.000
19A22ASN00.029-0.00418.209-0.769-0.7690.0000.0000.0000.000
20A23TYR0-0.022-0.02217.252-0.640-0.6400.0000.0000.0000.000
21A24ILE0-0.0090.02413.3600.1810.1810.0000.0000.0000.000
22A25GLY00.0560.02017.803-0.002-0.0020.0000.0000.0000.000
23A26ALA00.0500.01720.461-0.383-0.3830.0000.0000.0000.000
24A27GLU-1-0.928-0.95222.987-11.301-11.3010.0000.0000.0000.000
25A28GLY0-0.021-0.02418.822-0.156-0.1560.0000.0000.0000.000
26A29LEU0-0.042-0.03416.447-0.708-0.7080.0000.0000.0000.000
27A30GLN0-0.031-0.00818.633-0.009-0.0090.0000.0000.0000.000
28A31ARG10.9580.99519.07414.08414.0840.0000.0000.0000.000
29A32LEU0-0.0160.00512.277-0.591-0.5910.0000.0000.0000.000
30A33PHE0-0.031-0.04115.637-0.909-0.9090.0000.0000.0000.000
31A34GLU-1-0.894-0.93118.060-12.321-12.3210.0000.0000.0000.000
32A35ASP-1-0.807-0.88316.356-15.606-15.6060.0000.0000.0000.000
33A36ILE0-0.133-0.07012.999-0.791-0.7910.0000.0000.0000.000
34A37GLN0-0.087-0.05716.357-0.509-0.5090.0000.0000.0000.000
35A38VAL0-0.055-0.02516.8920.0850.0850.0000.0000.0000.000
36A39ASP-1-0.787-0.86619.934-11.443-11.4430.0000.0000.0000.000
37A40PRO0-0.001-0.02221.625-0.426-0.4260.0000.0000.0000.000
38A41SER0-0.048-0.03422.690-0.017-0.0170.0000.0000.0000.000
39A42ASP-1-0.767-0.84421.204-13.662-13.6620.0000.0000.0000.000
40A43VAL00.0830.04721.595-0.569-0.5690.0000.0000.0000.000
41A44VAL0-0.047-0.03816.881-0.539-0.5390.0000.0000.0000.000
42A45THR0-0.026-0.01016.872-1.124-1.1240.0000.0000.0000.000
43A46LEU00.0400.02417.889-0.629-0.6290.0000.0000.0000.000
44A47VAL0-0.035-0.01715.801-0.486-0.4860.0000.0000.0000.000
45A48LEU0-0.011-0.00811.217-1.217-1.2170.0000.0000.0000.000
46A49ALA00.0380.02314.101-1.073-1.0730.0000.0000.0000.000
47A50TRP0-0.0180.00016.340-0.668-0.6680.0000.0000.0000.000
48A51LYS10.7830.87011.60720.37520.3750.0000.0000.0000.000
49A52LEU0-0.063-0.03010.149-1.805-1.8050.0000.0000.0000.000
50A53LYS10.8440.92912.72221.28821.2880.0000.0000.0000.000
51A54ALA0-0.0190.00516.0920.4850.4850.0000.0000.0000.000
52A55SER0-0.047-0.06117.4950.9070.9070.0000.0000.0000.000
53A56SER0-0.0030.00420.6120.9010.9010.0000.0000.0000.000
54A57THR0-0.007-0.02321.398-0.452-0.4520.0000.0000.0000.000
55A58CYS0-0.060-0.03221.3000.2100.2100.0000.0000.0000.000
56A59GLU-1-0.893-0.94419.802-12.912-12.9120.0000.0000.0000.000
57A60PHE0-0.035-0.02614.232-0.852-0.8520.0000.0000.0000.000
58A61SER00.014-0.01416.310-0.230-0.2300.0000.0000.0000.000
59A62GLU-1-0.907-0.96213.106-20.827-20.8270.0000.0000.0000.000
60A63LYS10.9220.95411.82717.34917.3490.0000.0000.0000.000
61A64GLU-1-0.759-0.83511.291-18.660-18.6600.0000.0000.0000.000
62A65PHE00.0530.0229.543-2.060-2.0600.0000.0000.0000.000
63A66VAL00.015-0.0027.482-3.238-3.2380.0000.0000.0000.000
64A67GLU-1-0.874-0.9376.196-36.876-36.8760.0000.0000.0000.000
65A68GLY00.0200.0207.020-2.816-2.8160.0000.0000.0000.000
66A69LEU00.006-0.0055.008-1.580-1.5800.0000.0000.0000.000
69A72LEU0-0.039-0.0166.1101.7391.7390.0000.0000.0000.000
74A77LEU00.1070.0577.439-0.988-0.9880.0000.0000.0000.000
75A78GLU-1-0.807-0.89010.656-18.850-18.8500.0000.0000.0000.000
77A80LEU00.0450.0308.711-0.569-0.5690.0000.0000.0000.000
78A81LYS10.9100.9729.69818.14118.1410.0000.0000.0000.000
79A82ARG10.9220.95711.20321.64721.6470.0000.0000.0000.000
80A83LYS10.9210.9758.16929.79929.7990.0000.0000.0000.000
81A84LEU00.0590.02710.6730.8270.8270.0000.0000.0000.000
82A85SER0-0.011-0.00813.8111.5521.5520.0000.0000.0000.000
83A86SER0-0.117-0.04812.3430.4310.4310.0000.0000.0000.000
84A87LEU00.027-0.00711.8680.6700.6700.0000.0000.0000.000
85A88ARG10.8340.88415.12214.93814.9380.0000.0000.0000.000
86A89LYS10.9180.95417.66016.76316.7630.0000.0000.0000.000
87A90GLU-1-0.835-0.88614.300-19.744-19.7440.0000.0000.0000.000
88A91ILE0-0.011-0.01018.0500.2350.2350.0000.0000.0000.000
89A92GLU-1-0.839-0.90520.892-11.576-11.5760.0000.0000.0000.000
90A93ASP-1-0.867-0.89621.696-12.964-12.9640.0000.0000.0000.000
91A94PRO00.0660.02523.602-0.201-0.2010.0000.0000.0000.000
92A95SER0-0.074-0.05323.9000.1090.1090.0000.0000.0000.000
93A96LYS10.8400.89916.81416.90616.9060.0000.0000.0000.000
94A97PHE00.0100.01121.945-0.243-0.2430.0000.0000.0000.000
95A98ARG10.8150.88524.07510.15210.1520.0000.0000.0000.000
96A99ALA0-0.034-0.02521.9570.0910.0910.0000.0000.0000.000
97A100PHE0-0.020-0.01120.423-0.145-0.1450.0000.0000.0000.000
98A101TYR00.038-0.00122.126-0.016-0.0160.0000.0000.0000.000
99A102GLN0-0.001-0.00925.7350.4920.4920.0000.0000.0000.000
100A103PHE0-0.049-0.01219.1610.1260.1260.0000.0000.0000.000
101A104VAL00.0350.01522.8000.0460.0460.0000.0000.0000.000
102A105PHE00.0070.02824.6380.1760.1760.0000.0000.0000.000
103A106GLN00.011-0.00224.7350.6010.6010.0000.0000.0000.000
104A107TYR00.0120.01320.116-0.075-0.0750.0000.0000.0000.000
105A108SER00.000-0.00223.892-0.109-0.1090.0000.0000.0000.000
106A109LYS10.8170.91526.67210.67510.6750.0000.0000.0000.000
107A110GLU-1-0.846-0.92628.051-10.114-10.1140.0000.0000.0000.000
108A111PRO0-0.010-0.00826.6200.2000.2000.0000.0000.0000.000
109A112SER0-0.031-0.02229.1220.0640.0640.0000.0000.0000.000
110A113GLN00.0320.03132.4700.3960.3960.0000.0000.0000.000
111A114ARG10.9430.96432.9557.8117.8110.0000.0000.0000.000
112A115SER0-0.022-0.01134.784-0.078-0.0780.0000.0000.0000.000
113A116LEU0-0.0110.02130.033-0.063-0.0630.0000.0000.0000.000
114A117PRO00.0310.00732.8940.2500.2500.0000.0000.0000.000
115A118ALA00.0540.03135.068-0.190-0.1900.0000.0000.0000.000
116A119GLU-1-0.900-0.94936.608-8.125-8.1250.0000.0000.0000.000
117A120THR0-0.001-0.00630.370-0.060-0.0600.0000.0000.0000.000
118A121ALA0-0.020-0.01131.764-0.283-0.2830.0000.0000.0000.000
119A122MET00.0110.00833.118-0.090-0.0900.0000.0000.0000.000
120A123ALA00.0270.01931.721-0.072-0.0720.0000.0000.0000.000
121A124LEU0-0.019-0.01726.575-0.265-0.2650.0000.0000.0000.000
122A125TRP00.033-0.00929.443-0.107-0.1070.0000.0000.0000.000
123A126ASP-1-0.824-0.87032.084-9.029-9.0290.0000.0000.0000.000
124A127VAL0-0.011-0.00925.725-0.146-0.1460.0000.0000.0000.000
125A128LEU0-0.085-0.04024.682-0.392-0.3920.0000.0000.0000.000
126A129LEU00.012-0.00927.936-0.137-0.1370.0000.0000.0000.000
127A130ARG10.7880.85231.2348.9438.9430.0000.0000.0000.000
128A131GLY0-0.048-0.02331.114-0.277-0.2770.0000.0000.0000.000
129A132ARG10.8440.91625.21611.41211.4120.0000.0000.0000.000
130A133PHE00.0550.03032.4570.1100.1100.0000.0000.0000.000
131A134SER00.010-0.00435.599-0.018-0.0180.0000.0000.0000.000
132A135LEU00.0300.02838.8100.1370.1370.0000.0000.0000.000
133A136LEU00.0030.01834.2070.0920.0920.0000.0000.0000.000
134A137ASP-1-0.824-0.89738.158-7.985-7.9850.0000.0000.0000.000
135A138SER00.0270.00740.5800.0880.0880.0000.0000.0000.000
136A139TRP00.0210.01537.0950.1620.1620.0000.0000.0000.000
137A140LEU0-0.015-0.02236.4250.0600.0600.0000.0000.0000.000
138A141GLU-1-1.018-1.00640.584-6.605-6.6050.0000.0000.0000.000
139A142PHE00.0420.02143.2570.1010.1010.0000.0000.0000.000
140A143LEU00.018-0.00639.0620.0890.0890.0000.0000.0000.000
141A144LYS10.8680.95243.2397.0887.0880.0000.0000.0000.000
142A145ASN0-0.048-0.02045.4100.1740.1740.0000.0000.0000.000
143A146ASN0-0.058-0.02744.6520.1500.1500.0000.0000.0000.000
144A147THR00.0130.01242.665-0.159-0.1590.0000.0000.0000.000
145A148HIS00.0140.01142.280-0.179-0.1790.0000.0000.0000.000
146A149SER0-0.026-0.01637.382-0.206-0.2060.0000.0000.0000.000
147A150ILE00.0140.01535.4200.1120.1120.0000.0000.0000.000
148A151SER00.0420.02335.615-0.260-0.2600.0000.0000.0000.000
149A152ARG10.9160.93828.67110.21210.2120.0000.0000.0000.000
150A153ASP-1-0.894-0.95033.776-8.785-8.7850.0000.0000.0000.000
151A154THR00.004-0.00436.2010.0750.0750.0000.0000.0000.000
152A155TRP0-0.016-0.00828.4050.1080.1080.0000.0000.0000.000
153A156ASN0-0.042-0.02530.948-0.328-0.3280.0000.0000.0000.000
154A157LEU00.0360.01632.816-0.127-0.1270.0000.0000.0000.000
155A158LEU00.0590.04534.8600.1510.1510.0000.0000.0000.000
156A159TYR0-0.035-0.00428.732-0.062-0.0620.0000.0000.0000.000
157A160ASP-1-0.773-0.85333.228-9.293-9.2930.0000.0000.0000.000
158A161PHE00.0330.01935.5680.1050.1050.0000.0000.0000.000
159A162SER0-0.089-0.05634.1070.0210.0210.0000.0000.0000.000
160A163GLN0-0.072-0.05032.451-0.047-0.0470.0000.0000.0000.000
161A164LEU0-0.0120.01735.917-0.014-0.0140.0000.0000.0000.000
162A165SER0-0.052-0.04838.6830.1620.1620.0000.0000.0000.000
163A166GLU-1-0.939-0.94240.421-7.045-7.0450.0000.0000.0000.000
164A167LYS10.8350.89243.4656.6416.6410.0000.0000.0000.000
165A168ASP-1-0.906-0.96742.555-7.194-7.1940.0000.0000.0000.000
166A169LEU0-0.0090.00642.754-0.018-0.0180.0000.0000.0000.000
167A170SER0-0.050-0.02845.0290.1520.1520.0000.0000.0000.000
168A171ASP-1-0.925-0.94948.007-6.239-6.2390.0000.0000.0000.000
169A172TYR0-0.021-0.02344.087-0.105-0.1050.0000.0000.0000.000
170A173ASP-1-0.907-0.94545.577-6.830-6.8300.0000.0000.0000.000
171A174GLU-1-0.805-0.92046.898-6.251-6.2510.0000.0000.0000.000
172A175ASN0-0.109-0.06846.175-0.014-0.0140.0000.0000.0000.000
173A176GLY0-0.052-0.01547.8670.0130.0130.0000.0000.0000.000
174A177ALA0-0.027-0.01143.476-0.051-0.0510.0000.0000.0000.000
175A178TRP0-0.026-0.00739.052-0.375-0.3750.0000.0000.0000.000
176A179PRO0-0.021-0.02039.3180.1580.1580.0000.0000.0000.000
177A180VAL00.0320.01442.622-0.019-0.0190.0000.0000.0000.000
178A181LEU0-0.0070.00740.3790.0430.0430.0000.0000.0000.000
179A182ILE0-0.009-0.00738.664-0.010-0.0100.0000.0000.0000.000
180A183ASP-1-0.750-0.85143.146-6.438-6.4380.0000.0000.0000.000
181A184ASP-1-0.893-0.95246.741-6.416-6.4160.0000.0000.0000.000
182A185PHE0-0.071-0.02941.9680.0670.0670.0000.0000.0000.000
183A186VAL00.0090.00045.2000.0730.0730.0000.0000.0000.000
184A187LYS10.8140.91047.6316.3366.3360.0000.0000.0000.000
185A188TRP00.0400.00946.5310.0360.0360.0000.0000.0000.000
186A189LEU0-0.042-0.03044.8460.0580.0580.0000.0000.0000.000
187A190LYS10.7880.90749.4656.0596.0590.0000.0000.0000.000
188A191HIS0-0.121-0.05452.8280.0630.0630.0000.0000.0000.000
189A192GLU-2-1.818-1.89654.413-11.397-11.3970.0000.0000.0000.000