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

tag_button

FMODB ID: RM1L8

Calculation Name: 2R8B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2R8B

Chain ID: A

ChEMBL ID:

UniProt ID: A9CHT9

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2292617.310727
FMO2-HF: Nuclear repulsion 2215907.914448
FMO2-HF: Total energy -76709.396279
FMO2-MP2: Total energy -76935.261284


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:43:PRO)


Summations of interaction energy for fragment #1(A:43:PRO)
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.
-28.932-24.5440.543-2.173-2.759-0.019
Interaction energy analysis for fragmet #1(A:43:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.911
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].
3A45THR00.0550.0253.629-1.1960.2660.010-0.645-0.828-0.001
5A47ASP-1-0.886-0.9533.611-38.938-38.6120.013-0.136-0.203-0.001
6A48SER0-0.044-0.0212.717-10.553-8.0500.521-1.405-1.619-0.017
7A49TYR00.0420.0164.0360.4290.526-0.0010.013-0.1090.000
4A46LYS10.9490.9835.87631.02431.0240.0000.0000.0000.000
8A50PHE00.0030.0136.130-1.869-1.8690.0000.0000.0000.000
9A51HIS10.8760.9296.97733.02133.0210.0000.0000.0000.000
10A52LYS10.9621.0129.95017.48617.4860.0000.0000.0000.000
11A53SER0-0.019-0.02512.440-0.343-0.3430.0000.0000.0000.000
12A54ARG10.8370.92014.29813.38513.3850.0000.0000.0000.000
13A55ALA00.0150.01317.4860.1220.1220.0000.0000.0000.000
14A56GLY00.0240.00618.6410.5830.5830.0000.0000.0000.000
15A57VAL0-0.028-0.00721.763-0.310-0.3100.0000.0000.0000.000
16A58ALA00.0350.02322.531-0.169-0.1690.0000.0000.0000.000
17A59GLY0-0.010-0.00823.2590.5890.5890.0000.0000.0000.000
18A60ALA0-0.0040.00124.2360.3890.3890.0000.0000.0000.000
19A61PRO0-0.009-0.01623.032-0.533-0.5330.0000.0000.0000.000
20A62LEU00.0140.00715.303-0.352-0.3520.0000.0000.0000.000
21A63PHE0-0.024-0.01819.2600.3850.3850.0000.0000.0000.000
22A64VAL00.0080.00215.060-0.678-0.6780.0000.0000.0000.000
23A65LEU0-0.063-0.02116.8330.8890.8890.0000.0000.0000.000
24A66LEU0-0.008-0.00614.966-1.003-1.0030.0000.0000.0000.000
25A67HIS00.0190.00615.562-0.051-0.0510.0000.0000.0000.000
26A68GLY00.0470.02319.233-0.037-0.0370.0000.0000.0000.000
27A69THR0-0.034-0.02620.285-0.737-0.7370.0000.0000.0000.000
28A70GLY0-0.022-0.00819.8370.6260.6260.0000.0000.0000.000
29A71GLY0-0.060-0.01119.8370.3380.3380.0000.0000.0000.000
30A72ASP-1-0.786-0.90415.872-16.728-16.7280.0000.0000.0000.000
31A73GLU-1-0.882-0.95912.375-19.810-19.8100.0000.0000.0000.000
32A74ASN0-0.056-0.03615.3870.6220.6220.0000.0000.0000.000
33A75GLN0-0.0170.01218.8590.5440.5440.0000.0000.0000.000
34A76PHE00.035-0.00119.6890.7070.7070.0000.0000.0000.000
35A77PHE00.0120.02716.5710.1370.1370.0000.0000.0000.000
36A78ASP-1-0.835-0.93119.499-13.165-13.1650.0000.0000.0000.000
37A79PHE0-0.061-0.04022.9240.6510.6510.0000.0000.0000.000
38A80GLY00.0720.01922.0000.4350.4350.0000.0000.0000.000
39A81ALA0-0.067-0.03721.9450.2690.2690.0000.0000.0000.000
40A82ARG10.8940.94623.59311.04711.0470.0000.0000.0000.000
41A83LEU0-0.052-0.01625.8970.4600.4600.0000.0000.0000.000
42A84LEU00.0370.03924.3560.1960.1960.0000.0000.0000.000
43A85PRO00.0110.01425.224-0.491-0.4910.0000.0000.0000.000
44A86GLN0-0.005-0.00625.349-0.369-0.3690.0000.0000.0000.000
45A87ALA00.0390.03522.319-0.199-0.1990.0000.0000.0000.000
46A88THR0-0.049-0.01017.237-0.388-0.3880.0000.0000.0000.000
47A89ILE00.0140.01017.989-0.031-0.0310.0000.0000.0000.000
48A90LEU0-0.024-0.01211.371-0.914-0.9140.0000.0000.0000.000
49A91SER0-0.026-0.02613.7990.7540.7540.0000.0000.0000.000
50A92PRO0-0.005-0.01710.327-1.114-1.1140.0000.0000.0000.000
51A93VAL00.0110.01010.3231.6391.6390.0000.0000.0000.000
52A94GLY0-0.043-0.02610.848-1.694-1.6940.0000.0000.0000.000
53A95ASP-1-0.800-0.8898.707-26.401-26.4010.0000.0000.0000.000
54A96VAL0-0.0140.00310.515-0.236-0.2360.0000.0000.0000.000
55A97SER00.0220.00113.6950.9040.9040.0000.0000.0000.000
56A98GLU-1-0.815-0.90915.885-12.853-12.8530.0000.0000.0000.000
57A99HIS0-0.034-0.02819.5830.6710.6710.0000.0000.0000.000
58A100GLY00.0170.01818.4390.4960.4960.0000.0000.0000.000
59A101ALA0-0.010-0.00118.418-0.467-0.4670.0000.0000.0000.000
60A102ALA00.0420.03314.849-0.180-0.1800.0000.0000.0000.000
61A103ARG10.8020.89815.46715.41915.4190.0000.0000.0000.000
62A104PHE00.034-0.00412.775-1.196-1.1960.0000.0000.0000.000
63A105PHE00.0220.02014.453-0.591-0.5910.0000.0000.0000.000
64A106ARG10.8350.91316.45314.93214.9320.0000.0000.0000.000
65A107ARG10.8530.92318.42112.41012.4100.0000.0000.0000.000
66A108THR0-0.042-0.04121.953-0.398-0.3980.0000.0000.0000.000
67A109GLY00.0440.02324.417-0.014-0.0140.0000.0000.0000.000
68A110GLU-1-0.913-0.96326.893-9.903-9.9030.0000.0000.0000.000
69A111GLY0-0.0270.00126.7310.2280.2280.0000.0000.0000.000
70A112VAL00.0080.00726.421-0.243-0.2430.0000.0000.0000.000
71A113TYR0-0.036-0.04523.181-0.457-0.4570.0000.0000.0000.000
72A114ASP-1-0.787-0.87619.792-14.081-14.0810.0000.0000.0000.000
73A115MET00.015-0.00220.660-0.363-0.3630.0000.0000.0000.000
74A116VAL00.0710.03918.716-0.311-0.3110.0000.0000.0000.000
75A117ASP-1-0.798-0.87514.680-19.876-19.8760.0000.0000.0000.000
76A118LEU00.0160.01015.848-0.928-0.9280.0000.0000.0000.000
77A119GLU-1-0.938-0.94317.602-15.078-15.0780.0000.0000.0000.000
78A120ARG10.7720.84310.49221.69321.6930.0000.0000.0000.000
79A121ALA00.002-0.00312.848-1.385-1.3850.0000.0000.0000.000
80A122THR0-0.006-0.01813.706-0.428-0.4280.0000.0000.0000.000
81A123GLY00.0300.02014.449-0.008-0.0080.0000.0000.0000.000
82A124LYS10.8230.9116.40333.11833.1180.0000.0000.0000.000
83A125MET0-0.052-0.02710.391-1.543-1.5430.0000.0000.0000.000
84A126ALA00.0150.01612.811-0.016-0.0160.0000.0000.0000.000
85A127ASP-1-0.874-0.94210.566-21.348-21.3480.0000.0000.0000.000
86A128PHE0-0.042-0.0137.173-0.471-0.4710.0000.0000.0000.000
87A129ILE00.0130.00810.0270.0720.0720.0000.0000.0000.000
88A130LYS10.8890.95213.57618.39218.3920.0000.0000.0000.000
89A131ALA00.0190.0089.8330.4550.4550.0000.0000.0000.000
90A132ASN0-0.074-0.0799.0300.0050.0050.0000.0000.0000.000
91A133ARG10.8410.93112.63415.34215.3420.0000.0000.0000.000
92A134GLU-1-0.905-0.95014.300-16.625-16.6250.0000.0000.0000.000
93A135HIS0-0.046-0.01312.432-0.102-0.1020.0000.0000.0000.000
94A136TYR0-0.057-0.04212.651-0.010-0.0100.0000.0000.0000.000
95A137GLN00.0090.01417.1031.3541.3540.0000.0000.0000.000
96A138ALA00.0120.01218.7830.7740.7740.0000.0000.0000.000
97A139GLY00.0380.02620.5190.0290.0290.0000.0000.0000.000
98A140PRO0-0.0060.00322.848-0.359-0.3590.0000.0000.0000.000
99A141VAL0-0.026-0.00218.912-0.572-0.5720.0000.0000.0000.000
100A142ILE00.0220.01121.1100.5300.5300.0000.0000.0000.000
101A143GLY00.0180.00720.356-0.721-0.7210.0000.0000.0000.000
102A144LEU0-0.024-0.00920.6660.7570.7570.0000.0000.0000.000
103A145GLY00.0290.01920.501-0.811-0.8110.0000.0000.0000.000
104A146PHE00.0110.00521.9490.6540.6540.0000.0000.0000.000
105A147SER0-0.013-0.01422.691-0.670-0.6700.0000.0000.0000.000
106A148ASN0-0.018-0.00618.722-0.713-0.7130.0000.0000.0000.000
107A149GLY00.0660.03618.925-0.435-0.4350.0000.0000.0000.000
108A150ALA0-0.025-0.01419.908-0.213-0.2130.0000.0000.0000.000
109A151ASN00.0450.02122.5850.2620.2620.0000.0000.0000.000
110A152ILE0-0.0080.01115.9620.0780.0780.0000.0000.0000.000
111A153LEU0-0.0120.00919.444-0.085-0.0850.0000.0000.0000.000
112A154ALA00.015-0.00620.4400.1790.1790.0000.0000.0000.000
113A155ASN00.028-0.00220.1380.8620.8620.0000.0000.0000.000
114A156VAL0-0.004-0.00317.2790.0120.0120.0000.0000.0000.000
115A157LEU0-0.050-0.01920.2430.2100.2100.0000.0000.0000.000
116A158ILE00.0030.01023.5690.5460.5460.0000.0000.0000.000
117A159GLU-1-0.818-0.91120.514-12.487-12.4870.0000.0000.0000.000
118A160GLN0-0.078-0.04818.178-1.060-1.0600.0000.0000.0000.000
119A161PRO00.0190.02521.749-0.169-0.1690.0000.0000.0000.000
120A162GLU-1-0.944-0.98524.868-10.631-10.6310.0000.0000.0000.000
121A163LEU0-0.079-0.02617.495-0.103-0.1030.0000.0000.0000.000
122A164PHE00.011-0.01918.465-0.158-0.1580.0000.0000.0000.000
123A165ASP-1-0.872-0.92923.365-11.337-11.3370.0000.0000.0000.000
124A166ALA00.0170.00224.9820.4930.4930.0000.0000.0000.000
125A167ALA00.0120.00624.158-0.636-0.6360.0000.0000.0000.000
126A168VAL0-0.0030.00724.8370.4810.4810.0000.0000.0000.000
127A169LEU0-0.018-0.01624.285-0.558-0.5580.0000.0000.0000.000
128A170MET00.0130.00025.8830.3500.3500.0000.0000.0000.000
129A171HIS10.7310.84326.8169.3159.3150.0000.0000.0000.000
130A172PRO00.0380.02526.942-0.275-0.2750.0000.0000.0000.000
131A173LEU0-0.033-0.02927.0800.4190.4190.0000.0000.0000.000
132A174ILE00.0130.01524.925-0.521-0.5210.0000.0000.0000.000
133A175PRO0-0.026-0.01227.1970.3340.3340.0000.0000.0000.000
134A176PHE0-0.0070.00424.9650.2320.2320.0000.0000.0000.000
135A177GLU-1-0.892-0.95330.538-8.551-8.5510.0000.0000.0000.000
136A178PRO0-0.066-0.03728.834-0.210-0.2100.0000.0000.0000.000
137A179LYS10.8920.95225.23011.92311.9230.0000.0000.0000.000
138A180ILE0-0.017-0.00529.585-0.312-0.3120.0000.0000.0000.000
139A181SER00.0150.00828.0040.2230.2230.0000.0000.0000.000
140A182PRO00.0050.00329.675-0.126-0.1260.0000.0000.0000.000
141A183ALA00.0270.01228.530-0.397-0.3970.0000.0000.0000.000
142A184LYS10.8890.95125.24412.09312.0930.0000.0000.0000.000
143A185PRO00.011-0.00730.3150.0160.0160.0000.0000.0000.000
144A186THR0-0.013-0.00830.2180.1860.1860.0000.0000.0000.000
145A187ARG10.8380.93826.80110.54310.5430.0000.0000.0000.000
146A188ARG10.8470.94129.4509.6799.6790.0000.0000.0000.000
147A189VAL0-0.013-0.02028.241-0.424-0.4240.0000.0000.0000.000
148A190LEU00.0150.01929.2460.3510.3510.0000.0000.0000.000
149A191ILE00.0040.00429.335-0.429-0.4290.0000.0000.0000.000
150A192THR0-0.022-0.04130.3880.2090.2090.0000.0000.0000.000
151A193ALA00.0460.01431.358-0.268-0.2680.0000.0000.0000.000
152A194GLY0-0.0040.01533.8650.2020.2020.0000.0000.0000.000
153A195GLU-1-0.850-0.93636.191-7.359-7.3590.0000.0000.0000.000
154A196ARG10.8070.87338.6797.2837.2830.0000.0000.0000.000
155A197ASP-1-0.695-0.82832.418-9.558-9.5580.0000.0000.0000.000
156A198PRO0-0.056-0.01833.9480.0140.0140.0000.0000.0000.000
157A199ILE0-0.022-0.00828.399-0.074-0.0740.0000.0000.0000.000
158A200CYS0-0.048-0.00530.398-0.318-0.3180.0000.0000.0000.000
159A201PRO00.0500.02432.4800.2690.2690.0000.0000.0000.000
160A202VAL00.0320.02135.497-0.104-0.1040.0000.0000.0000.000
161A203GLN00.0420.00137.5740.0220.0220.0000.0000.0000.000
162A204LEU00.0270.02832.2440.0180.0180.0000.0000.0000.000
163A205THR00.0030.00732.997-0.259-0.2590.0000.0000.0000.000
164A206LYS10.8920.93634.0617.4727.4720.0000.0000.0000.000
165A207ALA00.0590.03735.2270.0030.0030.0000.0000.0000.000
166A208LEU00.0110.02328.220-0.121-0.1210.0000.0000.0000.000
167A209GLU-1-0.802-0.86932.221-8.373-8.3730.0000.0000.0000.000
168A210GLU-1-0.883-0.95734.248-7.967-7.9670.0000.0000.0000.000
169A211SER0-0.051-0.03631.700-0.009-0.0090.0000.0000.0000.000
170A212LEU0-0.009-0.01527.556-0.136-0.1360.0000.0000.0000.000
171A213LYS10.7910.87831.4198.0528.0520.0000.0000.0000.000
172A214ALA0-0.014-0.00634.6570.1310.1310.0000.0000.0000.000
173A215GLN0-0.040-0.01227.232-0.014-0.0140.0000.0000.0000.000
174A216GLY00.0240.02832.600-0.054-0.0540.0000.0000.0000.000
175A217GLY00.0010.00632.629-0.298-0.2980.0000.0000.0000.000
176A218THR0-0.047-0.03633.6200.2650.2650.0000.0000.0000.000
177A219VAL0-0.034-0.02032.141-0.310-0.3100.0000.0000.0000.000
178A220GLU-1-0.934-0.95333.688-8.143-8.1430.0000.0000.0000.000
179A221THR0-0.032-0.04033.783-0.405-0.4050.0000.0000.0000.000
180A222VAL0-0.017-0.00234.7870.2730.2730.0000.0000.0000.000
181A223TRP00.0330.00435.491-0.244-0.2440.0000.0000.0000.000
182A224HIS10.7860.88634.4018.6318.6310.0000.0000.0000.000
183A225PRO00.0610.04439.195-0.086-0.0860.0000.0000.0000.000
184A226GLY0-0.016-0.00239.333-0.109-0.1090.0000.0000.0000.000
185A227GLY00.0280.00536.3290.0060.0060.0000.0000.0000.000
186A228HIS0-0.029-0.03928.269-0.422-0.4220.0000.0000.0000.000
187A229GLU-1-0.758-0.85930.991-8.720-8.7200.0000.0000.0000.000
188A230ILE00.0300.00827.1520.1540.1540.0000.0000.0000.000
189A231ARG10.8180.89731.8388.0798.0790.0000.0000.0000.000
190A232SER00.0470.01534.185-0.165-0.1650.0000.0000.0000.000
191A233GLY00.0660.03035.313-0.116-0.1160.0000.0000.0000.000
192A234GLU-1-0.736-0.82631.520-9.494-9.4940.0000.0000.0000.000
193A235ILE0-0.003-0.00130.399-0.211-0.2110.0000.0000.0000.000
194A236ASP-1-0.888-0.92332.300-8.355-8.3550.0000.0000.0000.000
195A237ALA00.0130.01533.9860.0060.0060.0000.0000.0000.000
196A238VAL00.010-0.00727.937-0.083-0.0830.0000.0000.0000.000
197A239ARG10.8780.91630.8168.7588.7580.0000.0000.0000.000
198A240GLY00.0010.00532.606-0.017-0.0170.0000.0000.0000.000
199A241PHE0-0.024-0.00428.1150.0330.0330.0000.0000.0000.000
200A242LEU00.019-0.00326.437-0.099-0.0990.0000.0000.0000.000
201A243ALA00.0220.01030.157-0.136-0.1360.0000.0000.0000.000
202A244ALA0-0.051-0.01532.4070.1740.1740.0000.0000.0000.000
203A245TYR0-0.047-0.03727.8460.0230.0230.0000.0000.0000.000
204A246GLY-1-0.884-0.93328.795-10.584-10.5840.0000.0000.0000.000