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: RLG18

Calculation Name: 3WP4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3WP4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UV68

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2783513.378783
FMO2-HF: Nuclear repulsion 2696121.75616
FMO2-HF: Total energy -87391.622623
FMO2-MP2: Total energy -87646.115132


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:ALA)


Summations of interaction energy for fragment #1(A:-3: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.
-35.063-32.3050.107-1.308-1.557-0.007
Interaction energy analysis for fragmet #1(A:-3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.895
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].
3A-1PHE00.0240.0163.0574.7646.6910.027-0.917-1.037-0.004
4A1GLN00.0400.0243.243-10.712-9.8810.080-0.391-0.520-0.003
5A2SER00.005-0.0035.7692.1392.1390.0000.0000.0000.000
6A3PHE00.0550.0256.6681.2301.2300.0000.0000.0000.000
7A4CYS0-0.043-0.0187.4292.8762.8760.0000.0000.0000.000
8A5SER0-0.021-0.0086.9731.4301.4300.0000.0000.0000.000
9A6SER0-0.038-0.0249.6781.1621.1620.0000.0000.0000.000
10A7ALA0-0.0300.00312.7631.2371.2370.0000.0000.0000.000
11A8SER0-0.005-0.00814.7690.6760.6760.0000.0000.0000.000
12A9HIS10.7780.88318.48613.24813.2480.0000.0000.0000.000
13A10SER0-0.055-0.04721.1280.2650.2650.0000.0000.0000.000
14A11GLY00.0240.00923.1570.0560.0560.0000.0000.0000.000
15A12GLN0-0.005-0.00226.0210.0010.0010.0000.0000.0000.000
16A13SER00.004-0.00128.165-0.188-0.1880.0000.0000.0000.000
17A14VAL0-0.0020.00429.8660.3770.3770.0000.0000.0000.000
18A15LYS10.9340.98031.3708.7598.7590.0000.0000.0000.000
19A16VAL0-0.021-0.00533.0650.3040.3040.0000.0000.0000.000
20A17THR00.029-0.02034.944-0.200-0.2000.0000.0000.0000.000
21A18GLY00.0320.03237.6560.1480.1480.0000.0000.0000.000
22A19ASN0-0.028-0.01837.310-0.317-0.3170.0000.0000.0000.000
23A20LYS10.8610.92936.0608.4618.4610.0000.0000.0000.000
24A21VAL00.0810.05433.987-0.273-0.2730.0000.0000.0000.000
25A22GLY0-0.042-0.03533.3290.3500.3500.0000.0000.0000.000
26A23THR00.0080.01431.166-0.195-0.1950.0000.0000.0000.000
27A24ILE0-0.024-0.00427.7030.3000.3000.0000.0000.0000.000
28A25GLY00.010-0.00128.461-0.413-0.4130.0000.0000.0000.000
29A26GLY0-0.012-0.01427.9890.2740.2740.0000.0000.0000.000
30A27VAL0-0.0200.02124.284-0.152-0.1520.0000.0000.0000.000
31A28GLY00.0300.01526.9500.4780.4780.0000.0000.0000.000
32A29TYR0-0.042-0.02927.653-0.307-0.3070.0000.0000.0000.000
33A30GLU-1-0.834-0.92829.537-8.864-8.8640.0000.0000.0000.000
34A31LEU0-0.043-0.00230.611-0.357-0.3570.0000.0000.0000.000
35A32TRP00.004-0.00632.9990.2900.2900.0000.0000.0000.000
36A33ALA00.0250.00334.512-0.263-0.2630.0000.0000.0000.000
37A34ASP-1-0.788-0.85237.160-7.831-7.8310.0000.0000.0000.000
38A35SER0-0.053-0.04239.7800.2550.2550.0000.0000.0000.000
39A36GLY00.0360.01939.437-0.226-0.2260.0000.0000.0000.000
40A37ASN0-0.113-0.05839.6260.0830.0830.0000.0000.0000.000
41A38ASN00.023-0.00935.424-0.351-0.3510.0000.0000.0000.000
42A39SER0-0.064-0.06033.3530.1310.1310.0000.0000.0000.000
43A40ALA00.0490.04029.543-0.262-0.2620.0000.0000.0000.000
44A41THR0-0.054-0.02228.6460.4620.4620.0000.0000.0000.000
45A42PHE00.0410.01726.604-0.450-0.4500.0000.0000.0000.000
46A43TYR00.0360.00424.1700.5200.5200.0000.0000.0000.000
47A44SER0-0.004-0.00725.290-0.343-0.3430.0000.0000.0000.000
48A45ASP-1-0.767-0.82220.603-13.964-13.9640.0000.0000.0000.000
49A46GLY00.021-0.00220.563-0.742-0.7420.0000.0000.0000.000
50A47SER0-0.046-0.02320.0940.2090.2090.0000.0000.0000.000
51A48PHE0-0.013-0.03821.5660.6260.6260.0000.0000.0000.000
52A49SER0-0.0060.00723.390-0.361-0.3610.0000.0000.0000.000
53A50CYS0-0.057-0.00925.9290.4150.4150.0000.0000.0000.000
54A51THR0-0.014-0.00328.362-0.033-0.0330.0000.0000.0000.000
55A52PHE00.0430.03728.9840.1560.1560.0000.0000.0000.000
56A53GLN00.0180.01033.8530.1130.1130.0000.0000.0000.000
57A54ASN0-0.024-0.01737.0800.1020.1020.0000.0000.0000.000
58A55ALA00.0230.02336.1480.1950.1950.0000.0000.0000.000
59A56GLY00.0340.03437.424-0.131-0.1310.0000.0000.0000.000
60A57ASP-1-0.819-0.89734.580-9.374-9.3740.0000.0000.0000.000
61A58TYR0-0.016-0.02329.6710.0460.0460.0000.0000.0000.000
62A59LEU00.0260.01830.262-0.397-0.3970.0000.0000.0000.000
63A61ARG10.8310.87225.9749.5599.5590.0000.0000.0000.000
64A62SER0-0.033-0.02523.5700.6170.6170.0000.0000.0000.000
65A63GLY00.005-0.00523.550-0.661-0.6610.0000.0000.0000.000
66A64LEU00.0170.01923.5690.4490.4490.0000.0000.0000.000
67A65SER00.015-0.01026.6290.0020.0020.0000.0000.0000.000
68A66PHE0-0.021-0.00626.674-0.067-0.0670.0000.0000.0000.000
69A67ASP-1-0.790-0.87632.404-8.749-8.7490.0000.0000.0000.000
70A68SER0-0.0030.01334.8360.2670.2670.0000.0000.0000.000
71A69THR0-0.060-0.05436.2650.1680.1680.0000.0000.0000.000
72A70LYS10.9240.96432.6919.7909.7900.0000.0000.0000.000
73A71THR00.0540.03132.296-0.198-0.1980.0000.0000.0000.000
74A72PRO00.0650.01127.074-0.069-0.0690.0000.0000.0000.000
75A73SER0-0.0180.00027.874-0.193-0.1930.0000.0000.0000.000
76A74GLN00.0080.00929.040-0.060-0.0600.0000.0000.0000.000
77A75ILE0-0.074-0.02526.8380.1990.1990.0000.0000.0000.000
78A76GLY00.0350.01625.400-0.097-0.0970.0000.0000.0000.000
79A77ARG10.7860.86619.82914.79214.7920.0000.0000.0000.000
80A78MET00.002-0.00221.0790.0950.0950.0000.0000.0000.000
81A79LYS10.8030.90114.91918.78418.7840.0000.0000.0000.000
82A80ALA00.0370.01216.7400.9070.9070.0000.0000.0000.000
83A81ASP-1-0.816-0.85712.829-23.836-23.8360.0000.0000.0000.000
84A82PHE0-0.046-0.04213.6371.6251.6250.0000.0000.0000.000
85A83LYS10.9160.93711.98019.37819.3780.0000.0000.0000.000
86A84LEU0-0.0260.00014.9001.1111.1110.0000.0000.0000.000
87A85VAL0-0.026-0.01916.728-0.733-0.7330.0000.0000.0000.000
88A86LYS10.8930.94419.21914.96114.9610.0000.0000.0000.000
89A87GLN00.0050.02121.9870.3000.3000.0000.0000.0000.000
90A88ASN00.0010.00525.223-0.179-0.1790.0000.0000.0000.000
91A89SER0-0.012-0.00928.4330.1740.1740.0000.0000.0000.000
92A90SER0-0.031-0.02230.3490.1930.1930.0000.0000.0000.000
93A91ASN0-0.010-0.02533.6940.0080.0080.0000.0000.0000.000
94A92VAL00.0020.01929.8170.1370.1370.0000.0000.0000.000
95A93GLY0-0.010-0.00132.756-0.107-0.1070.0000.0000.0000.000
96A94TYR0-0.091-0.06131.446-0.031-0.0310.0000.0000.0000.000
97A95SER0-0.035-0.04827.012-0.127-0.1270.0000.0000.0000.000
98A96TYR00.0160.01425.684-0.197-0.1970.0000.0000.0000.000
99A97VAL0-0.013-0.00520.2710.1270.1270.0000.0000.0000.000
100A98GLY00.0030.00819.395-0.519-0.5190.0000.0000.0000.000
101A99VAL0-0.032-0.01619.4540.0700.0700.0000.0000.0000.000
102A100TYR00.007-0.01422.0740.1480.1480.0000.0000.0000.000
103A101GLY0-0.009-0.01825.863-0.201-0.2010.0000.0000.0000.000
104A102TRP00.0590.01728.6380.2440.2440.0000.0000.0000.000
105A103THR0-0.041-0.02031.627-0.244-0.2440.0000.0000.0000.000
106A104ARG10.8360.88533.9338.5138.5130.0000.0000.0000.000
107A105SER0-0.066-0.01937.4510.0080.0080.0000.0000.0000.000
108A106PRO00.0660.02636.175-0.018-0.0180.0000.0000.0000.000
109A107LEU0-0.031-0.01837.012-0.208-0.2080.0000.0000.0000.000
110A108VAL0-0.033-0.00932.4260.1000.1000.0000.0000.0000.000
111A109GLU-1-0.720-0.81631.488-9.671-9.6710.0000.0000.0000.000
112A110TYR0-0.054-0.05824.980-0.257-0.2570.0000.0000.0000.000
113A111TYR0-0.028-0.03725.892-0.253-0.2530.0000.0000.0000.000
114A112ILE0-0.040-0.01519.758-0.064-0.0640.0000.0000.0000.000
115A113VAL0-0.0050.00721.680-0.278-0.2780.0000.0000.0000.000
116A114ASP-1-0.694-0.83115.853-19.408-19.4080.0000.0000.0000.000
117A115ASN0-0.019-0.03417.2330.2130.2130.0000.0000.0000.000
118A116TRP00.0580.02820.5010.3310.3310.0000.0000.0000.000
119A117LEU00.017-0.00423.446-0.375-0.3750.0000.0000.0000.000
120A118SER00.0390.02325.8140.3290.3290.0000.0000.0000.000
121A119PRO0-0.039-0.02126.498-0.431-0.4310.0000.0000.0000.000
122A120PHE0-0.012-0.01326.876-0.230-0.2300.0000.0000.0000.000
123A121PRO00.0100.02124.4330.0830.0830.0000.0000.0000.000
124A122PRO00.0190.00625.8790.4340.4340.0000.0000.0000.000
125A123GLY00.0290.02128.066-0.337-0.3370.0000.0000.0000.000
126A124ASP-1-0.804-0.88930.745-10.136-10.1360.0000.0000.0000.000
127A125TRP00.0120.01131.2220.1690.1690.0000.0000.0000.000
128A126VAL0-0.042-0.01129.8230.1840.1840.0000.0000.0000.000
129A127GLY00.006-0.00433.1550.0260.0260.0000.0000.0000.000
130A128ASN0-0.033-0.00335.195-0.062-0.0620.0000.0000.0000.000
131A129LYS10.9070.97434.5839.2969.2960.0000.0000.0000.000
132A130LYS10.8830.92430.36610.18110.1810.0000.0000.0000.000
133A131HIS0-0.043-0.04730.2150.1790.1790.0000.0000.0000.000
134A132GLY0-0.0160.00129.3250.1330.1330.0000.0000.0000.000
135A133SER0-0.054-0.03724.287-0.065-0.0650.0000.0000.0000.000
136A134PHE00.002-0.00523.3670.1840.1840.0000.0000.0000.000
137A135THR0-0.037-0.03717.271-0.164-0.1640.0000.0000.0000.000
138A136ILE0-0.023-0.01618.4780.3770.3770.0000.0000.0000.000
139A137ASP-1-0.845-0.93713.792-23.223-23.2230.0000.0000.0000.000
140A138GLY0-0.0050.00712.418-1.352-1.3520.0000.0000.0000.000
141A139ALA0-0.038-0.01513.345-0.916-0.9160.0000.0000.0000.000
142A140GLN00.0320.03715.6150.3550.3550.0000.0000.0000.000
143A141TYR0-0.001-0.03217.033-0.506-0.5060.0000.0000.0000.000
144A142THR0-0.036-0.02421.7420.4830.4830.0000.0000.0000.000
145A143VAL0-0.0260.00325.043-0.060-0.0600.0000.0000.0000.000
146A144TYR0-0.029-0.06027.2600.2590.2590.0000.0000.0000.000
147A145GLU-1-0.834-0.91430.520-9.527-9.5270.0000.0000.0000.000
148A146ASN00.019-0.00633.3680.3340.3340.0000.0000.0000.000
149A147THR0-0.022-0.00336.167-0.012-0.0120.0000.0000.0000.000
150A148ARG10.9230.97936.5438.8018.8010.0000.0000.0000.000
151A149THR00.002-0.01239.6800.0530.0530.0000.0000.0000.000
152A150GLY0-0.001-0.00341.391-0.052-0.0520.0000.0000.0000.000
153A151PRO00.0250.01539.5900.0250.0250.0000.0000.0000.000
154A152SER0-0.021-0.01638.021-0.230-0.2300.0000.0000.0000.000
155A153ILE0-0.029-0.01534.9330.1250.1250.0000.0000.0000.000
156A154ASP-1-0.852-0.90638.218-7.821-7.8210.0000.0000.0000.000
157A155GLY0-0.0200.00141.5220.2300.2300.0000.0000.0000.000
158A156ASP-1-0.910-0.95242.570-7.380-7.3800.0000.0000.0000.000
159A157THR0-0.024-0.00942.1860.2120.2120.0000.0000.0000.000
160A158THR0-0.022-0.01142.472-0.043-0.0430.0000.0000.0000.000
161A159PHE0-0.0140.00436.0250.0450.0450.0000.0000.0000.000
162A160ASN0-0.018-0.00736.0590.1340.1340.0000.0000.0000.000
163A161GLN0-0.015-0.02032.5800.0280.0280.0000.0000.0000.000
164A162TYR0-0.038-0.03229.3700.0900.0900.0000.0000.0000.000
165A163PHE00.0490.01227.308-0.267-0.2670.0000.0000.0000.000
166A164SER0-0.014-0.00922.6840.3080.3080.0000.0000.0000.000
167A165ILE00.0110.00723.363-0.430-0.4300.0000.0000.0000.000
168A166ARG10.8680.94813.18421.49721.4970.0000.0000.0000.000
169A167GLN00.0090.00720.5510.4300.4300.0000.0000.0000.000
170A168GLN0-0.0090.00014.6890.6750.6750.0000.0000.0000.000
171A169ALA0-0.016-0.00417.161-0.734-0.7340.0000.0000.0000.000
172A170ARG10.7920.89211.00122.87022.8700.0000.0000.0000.000
173A171ASP-1-0.889-0.93512.722-20.609-20.6090.0000.0000.0000.000
174A173GLY00.003-0.0019.507-2.507-2.5070.0000.0000.0000.000
175A174THR0-0.020-0.03010.4260.6960.6960.0000.0000.0000.000
176A175ILE0-0.039-0.00512.142-0.890-0.8900.0000.0000.0000.000
177A176ASP-1-0.805-0.91115.321-17.100-17.1000.0000.0000.0000.000
178A177ILE00.019-0.00916.8630.5550.5550.0000.0000.0000.000
179A178SER00.0100.01120.4790.5990.5990.0000.0000.0000.000
180A179ALA00.0150.01818.3530.5520.5520.0000.0000.0000.000
181A180HIS0-0.0020.01018.3221.1481.1480.0000.0000.0000.000
182A181PHE00.0170.00622.3850.5470.5470.0000.0000.0000.000
183A182ASP-1-0.796-0.87222.341-13.414-13.4140.0000.0000.0000.000
184A183GLN0-0.100-0.05523.330-0.001-0.0010.0000.0000.0000.000
185A184TRP00.035-0.00325.2060.4440.4440.0000.0000.0000.000
186A185GLU-1-0.759-0.88528.233-9.886-9.8860.0000.0000.0000.000
187A186LYS10.8470.92724.14913.27713.2770.0000.0000.0000.000
188A187LEU0-0.051-0.02028.1700.1670.1670.0000.0000.0000.000
189A188GLY0-0.0090.00631.8140.2840.2840.0000.0000.0000.000
190A189MET0-0.0500.00729.3010.1550.1550.0000.0000.0000.000
191A190THR0-0.033-0.01631.347-0.242-0.2420.0000.0000.0000.000
192A191MET0-0.058-0.01628.2280.1340.1340.0000.0000.0000.000
193A192GLY00.0200.02332.1140.1430.1430.0000.0000.0000.000
194A193LYS10.8530.90833.3167.8937.8930.0000.0000.0000.000
195A194LEU0-0.009-0.00227.5250.0930.0930.0000.0000.0000.000
196A195HIS00.0470.03132.2010.2930.2930.0000.0000.0000.000
197A196GLU-1-0.836-0.89328.750-10.321-10.3210.0000.0000.0000.000
198A197ALA00.0370.03424.119-0.083-0.0830.0000.0000.0000.000
199A198LYS10.7680.88923.89010.63710.6370.0000.0000.0000.000
200A199VAL00.0320.01618.915-0.253-0.2530.0000.0000.0000.000
201A200LEU0-0.023-0.01521.9130.5530.5530.0000.0000.0000.000
202A201GLY00.015-0.00723.171-0.631-0.6310.0000.0000.0000.000
203A202GLU-1-0.779-0.88325.520-10.013-10.0130.0000.0000.0000.000
204A203ALA0-0.061-0.02328.241-0.361-0.3610.0000.0000.0000.000
205A204GLY00.0810.05030.7920.2100.2100.0000.0000.0000.000
206A205ASN0-0.092-0.06634.304-0.016-0.0160.0000.0000.0000.000
207A206VAL00.0340.03337.1040.1010.1010.0000.0000.0000.000
208A207ASN0-0.026-0.00940.0760.2060.2060.0000.0000.0000.000
209A208GLY0-0.050-0.02340.3190.1530.1530.0000.0000.0000.000
210A209GLY00.0680.03439.517-0.040-0.0400.0000.0000.0000.000
211A210ALA0-0.023-0.00333.951-0.011-0.0110.0000.0000.0000.000
212A211SER00.002-0.01534.8050.1290.1290.0000.0000.0000.000
213A212GLY0-0.002-0.00730.928-0.125-0.1250.0000.0000.0000.000
214A213THR0-0.048-0.02827.6770.2600.2600.0000.0000.0000.000
215A214ALA0-0.005-0.00123.815-0.262-0.2620.0000.0000.0000.000
216A215ASP-1-0.829-0.90421.562-13.018-13.0180.0000.0000.0000.000
217A216PHE00.0430.02119.400-0.654-0.6540.0000.0000.0000.000
218A217PRO0-0.022-0.01416.6640.1930.1930.0000.0000.0000.000
219A218TYR00.011-0.00713.3930.0800.0800.0000.0000.0000.000
220A219ALA00.0060.00516.790-0.182-0.1820.0000.0000.0000.000
221A220LYS10.8900.96016.07317.79617.7960.0000.0000.0000.000
222A221VAL00.0050.00717.844-0.722-0.7220.0000.0000.0000.000
223A222TYR0-0.059-0.04313.5860.9020.9020.0000.0000.0000.000
224A223ILE0-0.011-0.01020.506-0.183-0.1830.0000.0000.0000.000
225A224GLY0-0.027-0.01619.2620.2190.2190.0000.0000.0000.000
226A225ASP-2-1.782-1.86514.627-38.411-38.4110.0000.0000.0000.000