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: Y1912

Calculation Name: 3ST9-F-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol | calcium ion

Ligand 3-letter code: SO4 | GOL | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ST9

Chain ID: F

ChEMBL ID:

UniProt ID: P63786

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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1799620.338253
FMO2-HF: Nuclear repulsion 1731566.926217
FMO2-HF: Total energy -68053.412036
FMO2-MP2: Total energy -68251.155509


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:19:ASP)


Summations of interaction energy for fragment #1(A:19:ASP)
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.
-18.669-14.6284.611-3.982-4.669-0.039
Interaction energy analysis for fragmet #1(A:19:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.045
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].
3A21TYR00.0620.0263.451-5.495-3.4390.021-0.862-1.2150.001
4A22SER00.0260.0202.010-15.719-14.1364.590-3.031-3.142-0.040
5A23ARG10.8650.9373.8482.8593.2610.000-0.089-0.3120.000
6A24LEU00.1030.0466.3360.8070.8070.0000.0000.0000.000
7A25LEU00.0080.0227.0210.8520.8520.0000.0000.0000.000
8A26LYS10.8740.9248.3282.6872.6870.0000.0000.0000.000
9A27ASP-1-0.912-0.95210.552-0.335-0.3350.0000.0000.0000.000
10A28ARG10.7550.85212.1082.1432.1430.0000.0000.0000.000
11A29ILE0-0.0020.00910.8970.2390.2390.0000.0000.0000.000
12A30ILE0-0.014-0.00710.393-1.087-1.0870.0000.0000.0000.000
13A31MET0-0.038-0.0129.1280.7530.7530.0000.0000.0000.000
14A32LEU00.0100.00511.130-0.611-0.6110.0000.0000.0000.000
15A33GLY0-0.0080.00012.5360.4600.4600.0000.0000.0000.000
16A34SER00.010-0.00113.6880.0000.0000.0000.0000.0000.000
17A35GLN00.0450.02715.565-0.009-0.0090.0000.0000.0000.000
18A36ILE0-0.017-0.00117.051-0.296-0.2960.0000.0000.0000.000
19A37ASP-1-0.745-0.86517.351-2.249-2.2490.0000.0000.0000.000
20A38ASP-1-0.773-0.88418.552-1.813-1.8130.0000.0000.0000.000
21A39ASN0-0.099-0.03913.976-0.510-0.5100.0000.0000.0000.000
22A40VAL0-0.019-0.00313.690-0.505-0.5050.0000.0000.0000.000
23A41ALA00.0050.00414.732-0.290-0.2900.0000.0000.0000.000
24A42ASN00.003-0.00916.667-0.036-0.0360.0000.0000.0000.000
25A43SER0-0.0010.02310.186-0.400-0.4000.0000.0000.0000.000
26A44ILE00.0070.00512.486-0.462-0.4620.0000.0000.0000.000
27A45VAL00.0190.00814.2190.0230.0230.0000.0000.0000.000
28A46SER0-0.034-0.03312.9610.1700.1700.0000.0000.0000.000
29A47GLN0-0.055-0.0399.411-0.602-0.6020.0000.0000.0000.000
30A48LEU00.0350.01712.5310.2200.2200.0000.0000.0000.000
31A49LEU0-0.0030.00116.0970.2600.2600.0000.0000.0000.000
32A50PHE0-0.034-0.01710.9460.0990.0990.0000.0000.0000.000
33A51LEU00.0020.00112.0480.2600.2600.0000.0000.0000.000
34A52GLN00.0510.03715.2150.4350.4350.0000.0000.0000.000
35A53ALA0-0.052-0.02616.9900.2130.2130.0000.0000.0000.000
36A54GLN0-0.092-0.02913.6310.2080.2080.0000.0000.0000.000
37A55ASP-1-0.830-0.90817.093-0.907-0.9070.0000.0000.0000.000
38A56SER00.0060.00519.755-0.112-0.1120.0000.0000.0000.000
39A57GLU-1-0.935-0.96022.475-0.717-0.7170.0000.0000.0000.000
40A58LYS10.8490.90719.2271.0441.0440.0000.0000.0000.000
41A59ASP-1-0.763-0.85220.271-1.025-1.0250.0000.0000.0000.000
42A60ILE0-0.039-0.01215.489-0.196-0.1960.0000.0000.0000.000
43A61TYR00.0060.00515.3940.2160.2160.0000.0000.0000.000
44A62LEU00.0050.00714.854-0.390-0.3900.0000.0000.0000.000
45A63TYR00.0370.00713.9050.4070.4070.0000.0000.0000.000
46A64ILE0-0.049-0.02815.089-0.363-0.3630.0000.0000.0000.000
47A65ASN00.0240.01615.8730.2760.2760.0000.0000.0000.000
48A66SER0-0.010-0.02216.869-0.113-0.1130.0000.0000.0000.000
49A67PRO00.008-0.00219.1310.1110.1110.0000.0000.0000.000
50A68GLY00.0310.02921.0890.0750.0750.0000.0000.0000.000
51A69GLY0-0.008-0.03121.440-0.095-0.0950.0000.0000.0000.000
52A70SER00.0150.02723.0530.1310.1310.0000.0000.0000.000
53A71VAL00.045-0.00924.134-0.080-0.0800.0000.0000.0000.000
54A72THR0-0.069-0.01725.617-0.012-0.0120.0000.0000.0000.000
55A73ALA00.0360.02720.667-0.057-0.0570.0000.0000.0000.000
56A74GLY00.020-0.00221.535-0.123-0.1230.0000.0000.0000.000
57A75PHE0-0.013-0.02923.225-0.009-0.0090.0000.0000.0000.000
58A76ALA00.0150.02121.836-0.003-0.0030.0000.0000.0000.000
59A77ILE00.0030.00917.915-0.112-0.1120.0000.0000.0000.000
60A78TYR00.012-0.00220.8300.0240.0240.0000.0000.0000.000
61A79ASP-1-0.868-0.94924.091-1.112-1.1120.0000.0000.0000.000
62A80THR0-0.064-0.04419.2730.0040.0040.0000.0000.0000.000
63A81ILE0-0.038-0.03119.965-0.032-0.0320.0000.0000.0000.000
64A82GLN0-0.067-0.02822.5600.1490.1490.0000.0000.0000.000
65A83HIS0-0.051-0.00423.7580.1290.1290.0000.0000.0000.000
66A84ILE0-0.086-0.03919.127-0.003-0.0030.0000.0000.0000.000
67A85LYS10.9330.96423.2281.0021.0020.0000.0000.0000.000
68A86PRO0-0.032-0.01519.8850.0750.0750.0000.0000.0000.000
69A87ASP-1-0.754-0.85122.371-0.907-0.9070.0000.0000.0000.000
70A88VAL0-0.036-0.01919.006-0.083-0.0830.0000.0000.0000.000
71A89GLN00.009-0.00220.1450.1490.1490.0000.0000.0000.000
72A90THR0-0.064-0.03519.630-0.186-0.1860.0000.0000.0000.000
73A91ILE00.0230.01718.1140.1480.1480.0000.0000.0000.000
74A92CYS0-0.053-0.01618.777-0.085-0.0850.0000.0000.0000.000
75A93ILE0-0.002-0.01815.5290.1610.1610.0000.0000.0000.000
76A94GLY00.0100.01519.111-0.087-0.0870.0000.0000.0000.000
77A95MET00.0480.02020.6010.0290.0290.0000.0000.0000.000
78A96ALA00.014-0.00220.890-0.158-0.1580.0000.0000.0000.000
79A97ALA00.0240.01323.0510.0790.0790.0000.0000.0000.000
80A98SER00.0590.03024.356-0.151-0.1510.0000.0000.0000.000
81A99MET0-0.058-0.01023.320-0.026-0.0260.0000.0000.0000.000
82A100GLY00.0390.02021.468-0.093-0.0930.0000.0000.0000.000
83A101SER0-0.009-0.02722.357-0.026-0.0260.0000.0000.0000.000
84A102PHE0-0.031-0.01525.5500.0200.0200.0000.0000.0000.000
85A103LEU0-0.011-0.02120.063-0.007-0.0070.0000.0000.0000.000
86A104LEU0-0.0190.00322.214-0.041-0.0410.0000.0000.0000.000
87A105ALA00.0390.03423.5370.0240.0240.0000.0000.0000.000
88A106ALA0-0.012-0.01223.9420.0490.0490.0000.0000.0000.000
89A107GLY00.0310.02923.761-0.045-0.0450.0000.0000.0000.000
90A108ALA00.0060.00824.4400.0850.0850.0000.0000.0000.000
91A109LYS10.8410.91026.4170.6170.6170.0000.0000.0000.000
92A110GLY0-0.023-0.00929.6920.0160.0160.0000.0000.0000.000
93A111LYS10.7420.83924.4510.7880.7880.0000.0000.0000.000
94A112ARG10.7430.87624.0960.5390.5390.0000.0000.0000.000
95A113PHE00.0550.02322.9540.0830.0830.0000.0000.0000.000
96A114ALA00.0080.00123.291-0.093-0.0930.0000.0000.0000.000
97A115LEU00.0410.02920.1110.0720.0720.0000.0000.0000.000
98A116PRO00.024-0.00324.410-0.034-0.0340.0000.0000.0000.000
99A117ASN0-0.075-0.03125.264-0.034-0.0340.0000.0000.0000.000
100A118ALA0-0.0200.00623.8280.0010.0010.0000.0000.0000.000
101A119GLU-1-0.953-0.97424.769-0.149-0.1490.0000.0000.0000.000
102A120VAL00.003-0.00325.431-0.097-0.0970.0000.0000.0000.000
103A121MET0-0.0300.00027.1750.0220.0220.0000.0000.0000.000
104A122ILE00.0110.01628.229-0.082-0.0820.0000.0000.0000.000
105A123HIS00.0130.00930.735-0.035-0.0350.0000.0000.0000.000
106A124GLN0-0.043-0.03928.933-0.107-0.1070.0000.0000.0000.000
107A125PRO0-0.0020.01031.979-0.040-0.0400.0000.0000.0000.000
108A126LEU00.0020.00630.405-0.017-0.0170.0000.0000.0000.000
109A127GLY00.0500.01629.001-0.041-0.0410.0000.0000.0000.000
110A128GLY0-0.058-0.03129.185-0.061-0.0610.0000.0000.0000.000
111A129ALA0-0.007-0.01430.168-0.016-0.0160.0000.0000.0000.000
112A130GLN00.0100.03525.537-0.025-0.0250.0000.0000.0000.000
113A131GLY00.005-0.00923.554-0.073-0.0730.0000.0000.0000.000
114A132GLN0-0.026-0.01322.730-0.050-0.0500.0000.0000.0000.000
115A133ALA00.0120.01724.822-0.071-0.0710.0000.0000.0000.000
116A134THR0-0.014-0.00326.5150.0810.0810.0000.0000.0000.000
117A135GLU-1-0.809-0.91728.389-0.871-0.8710.0000.0000.0000.000
118A136ILE0-0.007-0.01130.7160.0410.0410.0000.0000.0000.000
119A137GLU0-0.052-0.06224.6780.0410.0410.0000.0000.0000.000
120A138ILE00.0020.01330.1940.0410.0410.0000.0000.0000.000
121A139ALA0-0.016-0.00632.6330.0430.0430.0000.0000.0000.000
122A140ALA00.008-0.00132.1090.0380.0380.0000.0000.0000.000
123A141ASN00.0440.00729.5300.0060.0060.0000.0000.0000.000
124A142HIS0-0.042-0.02233.6000.0290.0290.0000.0000.0000.000
125A143ILE0-0.004-0.00437.3350.0260.0260.0000.0000.0000.000
126A144LEU0-0.028-0.01434.0840.0250.0250.0000.0000.0000.000
127A145LYS10.8280.90436.5220.4780.4780.0000.0000.0000.000
128A146THR00.0460.02031.3670.0370.0370.0000.0000.0000.000
129A147ARG10.9560.99033.6840.5770.5770.0000.0000.0000.000
130A148GLU-1-0.864-0.92634.934-0.476-0.4760.0000.0000.0000.000
131A149LYS10.9350.96833.7770.7500.7500.0000.0000.0000.000
132A150LEU00.0190.02429.0150.0050.0050.0000.0000.0000.000
133A151ASN00.0550.01132.548-0.011-0.0110.0000.0000.0000.000
134A152ARG10.9020.95835.5630.5460.5460.0000.0000.0000.000
135A153ILE00.0730.04530.0520.0210.0210.0000.0000.0000.000
136A154LEU00.0130.00029.8220.0080.0080.0000.0000.0000.000
137A155SER0-0.061-0.01033.1620.0320.0320.0000.0000.0000.000
138A156GLU-1-0.917-0.97534.974-0.591-0.5910.0000.0000.0000.000
139A157ARG10.7870.88628.0870.8700.8700.0000.0000.0000.000
140A158THR0-0.028-0.02232.4060.0080.0080.0000.0000.0000.000
141A159GLY0-0.0120.00534.4800.0290.0290.0000.0000.0000.000
142A160GLN00.0120.02337.3460.0600.0600.0000.0000.0000.000
143A161SER0-0.009-0.01639.138-0.022-0.0220.0000.0000.0000.000
144A162ILE00.0580.02039.049-0.009-0.0090.0000.0000.0000.000
145A163GLU-1-0.873-0.92040.612-0.351-0.3510.0000.0000.0000.000
146A164LYS10.8380.92739.5810.2960.2960.0000.0000.0000.000
147A165ILE00.0450.02635.5260.0000.0000.0000.0000.0000.000
148A166GLN0-0.0190.00837.4710.0080.0080.0000.0000.0000.000
149A167LYS10.9290.96639.1480.2840.2840.0000.0000.0000.000
150A168ASP-1-0.814-0.88836.630-0.302-0.3020.0000.0000.0000.000
151A169THR0-0.035-0.03033.337-0.014-0.0140.0000.0000.0000.000
152A170ASP-1-0.947-0.98234.952-0.469-0.4690.0000.0000.0000.000
153A171ARG10.8030.88736.4360.3230.3230.0000.0000.0000.000
154A172ASP-1-0.844-0.92133.287-0.410-0.4100.0000.0000.0000.000
155A173ASN0-0.054-0.01633.9570.0670.0670.0000.0000.0000.000
156A174PHE00.012-0.01528.487-0.046-0.0460.0000.0000.0000.000
157A175LEU0-0.0140.00330.9190.0240.0240.0000.0000.0000.000
158A176THR00.007-0.02830.019-0.016-0.0160.0000.0000.0000.000
159A177ALA00.0290.01327.508-0.039-0.0390.0000.0000.0000.000
160A178GLU-1-0.801-0.90529.153-0.138-0.1380.0000.0000.0000.000
161A179GLU-1-0.801-0.87032.637-0.188-0.1880.0000.0000.0000.000
162A180ALA0-0.023-0.01829.539-0.030-0.0300.0000.0000.0000.000
163A181LYS10.8070.89231.1670.1390.1390.0000.0000.0000.000
164A182GLU-1-0.921-0.95732.252-0.169-0.1690.0000.0000.0000.000
165A183TYR0-0.115-0.08533.577-0.014-0.0140.0000.0000.0000.000
166A184GLY00.0500.03133.671-0.018-0.0180.0000.0000.0000.000
167A185LEU0-0.069-0.04329.023-0.053-0.0530.0000.0000.0000.000
168A186ILE0-0.051-0.01926.000-0.078-0.0780.0000.0000.0000.000
169A187ASP-1-0.793-0.88328.440-0.525-0.5250.0000.0000.0000.000
170A188GLU-1-0.914-0.96228.507-0.142-0.1420.0000.0000.0000.000
171A189VAL0-0.036-0.01027.658-0.049-0.0490.0000.0000.0000.000
172A190MET0-0.004-0.00722.4410.0330.0330.0000.0000.0000.000
173A191VAL0-0.005-0.00626.2650.0480.0480.0000.0000.0000.000
174A192PRO0-0.064-0.02624.652-0.003-0.0030.0000.0000.0000.000
175A193GLU-1-0.949-0.97724.7150.5510.5510.0000.0000.0000.000
176A194THR-1-0.985-0.98527.5600.3870.3870.0000.0000.0000.000