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: LG4G9

Calculation Name: 5YW2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | magnesium ion | chloride ion

Ligand 3-letter code: SO4 | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5YW2

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NII9

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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1763111.38447
FMO2-HF: Nuclear repulsion 1696673.014441
FMO2-HF: Total energy -66438.370029
FMO2-MP2: Total energy -66634.260931


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:-2:ASP)


Summations of interaction energy for fragment #1(A:-2: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.
-25.913-25.65812.803-6.461-6.5960.052
Interaction energy analysis for fragmet #1(A:-2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.007
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].
3A0LYS10.9310.9473.85611.36013.248-0.011-0.789-1.088-0.001
4A1MET0-0.026-0.0113.151-1.2250.0990.335-0.588-1.070-0.003
5A2ASN00.0430.0201.747-8.342-11.96012.473-4.781-4.0750.054
41A38LYS10.9340.9483.648-32.276-31.6150.006-0.303-0.3630.002
6A3LEU00.0680.0355.874-0.508-0.5080.0000.0000.0000.000
7A4ASP-1-0.854-0.9048.240-2.878-2.8780.0000.0000.0000.000
8A5PHE0-0.038-0.0108.2800.3470.3470.0000.0000.0000.000
9A6ILE00.0410.0338.910-0.350-0.3500.0000.0000.0000.000
10A7LYS10.8870.92911.5110.5970.5970.0000.0000.0000.000
11A8SER0-0.122-0.07412.915-0.035-0.0350.0000.0000.0000.000
12A9LYS10.8670.94513.302-2.952-2.9520.0000.0000.0000.000
13A10ILE0-0.013-0.00115.828-0.009-0.0090.0000.0000.0000.000
14A11ALA00.0160.02218.415-0.194-0.1940.0000.0000.0000.000
15A12ALA0-0.016-0.01521.784-0.021-0.0210.0000.0000.0000.000
16A13VAL0-0.023-0.01424.408-0.009-0.0090.0000.0000.0000.000
17A14PRO00.021-0.00927.898-0.018-0.0180.0000.0000.0000.000
18A15ASP-1-0.874-0.92331.1400.2120.2120.0000.0000.0000.000
19A16PHE00.0160.03230.1390.0230.0230.0000.0000.0000.000
20A17PRO0-0.023-0.02631.371-0.004-0.0040.0000.0000.0000.000
21A18LYS10.8600.91633.741-0.198-0.1980.0000.0000.0000.000
22A19PRO00.026-0.00635.415-0.003-0.0030.0000.0000.0000.000
23A20GLY0-0.0110.00336.121-0.011-0.0110.0000.0000.0000.000
24A21ILE0-0.040-0.01230.705-0.026-0.0260.0000.0000.0000.000
25A22MET0-0.0170.00326.6630.0080.0080.0000.0000.0000.000
26A23PHE00.0100.00626.3130.0180.0180.0000.0000.0000.000
27A24ARG10.9610.98421.821-0.257-0.2570.0000.0000.0000.000
28A25ASP-1-0.780-0.87823.2571.1741.1740.0000.0000.0000.000
29A26ILE00.0210.00619.1060.0520.0520.0000.0000.0000.000
30A27THR0-0.049-0.04119.3650.2570.2570.0000.0000.0000.000
31A28PRO0-0.015-0.00818.5930.1640.1640.0000.0000.0000.000
32A29LEU0-0.028-0.00412.7340.3200.3200.0000.0000.0000.000
33A30LEU0-0.048-0.03815.5580.4050.4050.0000.0000.0000.000
34A31ALA00.0000.01018.1710.0800.0800.0000.0000.0000.000
35A32ASP-1-0.813-0.90313.0894.7084.7080.0000.0000.0000.000
36A33PRO00.002-0.00714.3800.3020.3020.0000.0000.0000.000
37A34GLN00.0040.0038.6250.1050.1050.0000.0000.0000.000
38A35GLY0-0.0090.01110.0811.0091.0090.0000.0000.0000.000
39A36LEU00.0500.02311.5960.2160.2160.0000.0000.0000.000
40A37ARG10.8880.9588.804-6.662-6.6620.0000.0000.0000.000
42A39THR0-0.029-0.0277.816-0.443-0.4430.0000.0000.0000.000
43A40ALA00.0530.02810.795-0.506-0.5060.0000.0000.0000.000
44A41GLU-1-0.900-0.9686.50312.71812.7180.0000.0000.0000.000
45A42ALA0-0.040-0.0197.349-0.693-0.6930.0000.0000.0000.000
46A43MET0-0.025-0.0118.357-1.354-1.3540.0000.0000.0000.000
47A44ALA00.0550.03010.552-0.648-0.6480.0000.0000.0000.000
48A45GLN0-0.044-0.0205.657-0.828-0.8280.0000.0000.0000.000
49A46GLU-1-0.848-0.9159.900-1.691-1.6910.0000.0000.0000.000
50A47LEU00.001-0.00512.485-0.332-0.3320.0000.0000.0000.000
51A48LYS10.9470.98210.446-0.163-0.1630.0000.0000.0000.000
52A49ASN0-0.058-0.0409.587-0.275-0.2750.0000.0000.0000.000
53A50LYS10.8030.90013.6750.3100.3100.0000.0000.0000.000
54A51GLY0-0.0030.01316.7200.0390.0390.0000.0000.0000.000
55A52ILE0-0.050-0.01718.0510.0660.0660.0000.0000.0000.000
56A53GLN0-0.061-0.04218.6630.1800.1800.0000.0000.0000.000
57A54PRO00.0010.01419.681-0.056-0.0560.0000.0000.0000.000
58A55THR0-0.023-0.03622.3690.0760.0760.0000.0000.0000.000
59A56ILE0-0.037-0.00924.2740.0690.0690.0000.0000.0000.000
60A57VAL00.0200.01819.876-0.058-0.0580.0000.0000.0000.000
61A58ALA00.0170.00723.173-0.021-0.0210.0000.0000.0000.000
62A59GLY00.0600.02523.9850.0240.0240.0000.0000.0000.000
63A60THR0-0.032-0.02224.957-0.003-0.0030.0000.0000.0000.000
64A61GLU-1-0.750-0.83726.4840.7290.7290.0000.0000.0000.000
65A62SER0-0.014-0.03527.183-0.095-0.0950.0000.0000.0000.000
66A63ARG10.8180.89722.699-0.848-0.8480.0000.0000.0000.000
67A64GLY00.1060.05321.9350.1540.1540.0000.0000.0000.000
68A65PHE0-0.091-0.03022.5560.0570.0570.0000.0000.0000.000
69A66ILE0-0.0090.01019.2620.1070.1070.0000.0000.0000.000
70A67PHE00.025-0.01015.9370.2020.2020.0000.0000.0000.000
71A68GLY00.0430.02617.6900.1560.1560.0000.0000.0000.000
72A69VAL00.0050.00119.8610.0430.0430.0000.0000.0000.000
73A70ALA0-0.027-0.01015.3740.1270.1270.0000.0000.0000.000
74A71LEU0-0.016-0.01813.7830.3650.3650.0000.0000.0000.000
75A72ALA0-0.0130.00016.0700.0050.0050.0000.0000.0000.000
76A73GLU-1-0.911-0.95717.3281.8431.8430.0000.0000.0000.000
77A74VAL0-0.079-0.03811.5360.1390.1390.0000.0000.0000.000
78A75LEU0-0.046-0.02514.5430.0350.0350.0000.0000.0000.000
79A76GLY0-0.0170.01416.667-0.212-0.2120.0000.0000.0000.000
80A77LEU0-0.074-0.03119.532-0.218-0.2180.0000.0000.0000.000
81A78GLY00.0330.01821.9980.0680.0680.0000.0000.0000.000
82A79PHE00.014-0.00622.8170.0110.0110.0000.0000.0000.000
83A80VAL0-0.020-0.00124.960-0.052-0.0520.0000.0000.0000.000
84A81PRO0-0.036-0.01827.3080.0080.0080.0000.0000.0000.000
85A82VAL00.0260.00728.408-0.066-0.0660.0000.0000.0000.000
86A83ARG10.8110.86630.368-0.658-0.6580.0000.0000.0000.000
87A84LYS10.9440.96531.454-0.614-0.6140.0000.0000.0000.000
88A85PRO00.0260.00035.6980.0140.0140.0000.0000.0000.000
89A86GLY0-0.0200.00139.2840.0070.0070.0000.0000.0000.000
90A87LYS10.8550.93435.528-0.543-0.5430.0000.0000.0000.000
91A88LEU0-0.036-0.00534.0790.0380.0380.0000.0000.0000.000
92A89PRO0-0.0080.00337.700-0.027-0.0270.0000.0000.0000.000
93A90ARG10.8070.87236.999-0.527-0.5270.0000.0000.0000.000
94A91ALA00.0380.01740.8610.0020.0020.0000.0000.0000.000
95A92THR0-0.0010.00438.5450.0130.0130.0000.0000.0000.000
96A93TYR0-0.0020.02037.365-0.029-0.0290.0000.0000.0000.000
97A94SER00.028-0.00237.9920.0190.0190.0000.0000.0000.000
98A95VAL0-0.004-0.00636.491-0.031-0.0310.0000.0000.0000.000
99A96LYS10.8720.95437.859-0.150-0.1500.0000.0000.0000.000
100A97TYR0-0.029-0.03033.212-0.013-0.0130.0000.0000.0000.000
101A98ASP-1-0.790-0.89738.4190.1560.1560.0000.0000.0000.000
102A99LEU0-0.070-0.05234.1080.0030.0030.0000.0000.0000.000
103A100GLU-1-0.870-0.92535.2680.2190.2190.0000.0000.0000.000
104A101TYR0-0.057-0.04235.325-0.009-0.0090.0000.0000.0000.000
105A102GLY00.0060.00739.5720.0000.0000.0000.0000.0000.000
106A103SER0-0.059-0.03139.806-0.016-0.0160.0000.0000.0000.000
107A104ASP-1-0.830-0.87437.0570.3780.3780.0000.0000.0000.000
108A105SER0-0.025-0.03438.344-0.031-0.0310.0000.0000.0000.000
109A106LEU0-0.0330.00431.5950.0340.0340.0000.0000.0000.000
110A107GLU-1-0.846-0.93835.0400.3560.3560.0000.0000.0000.000
111A108ILE00.0410.02031.8740.0520.0520.0000.0000.0000.000
112A109HIS00.004-0.00534.808-0.044-0.0440.0000.0000.0000.000
113A110GLN0-0.038-0.03636.0380.0020.0020.0000.0000.0000.000
114A111ASP-1-0.819-0.88237.1940.4850.4850.0000.0000.0000.000
115A112ALA0-0.054-0.01632.1320.0240.0240.0000.0000.0000.000
116A113PHE00.027-0.00228.2850.0510.0510.0000.0000.0000.000
117A114LYS10.8550.92230.340-0.607-0.6070.0000.0000.0000.000
118A115VAL00.0590.02133.4220.0030.0030.0000.0000.0000.000
119A116THR0-0.038-0.02331.374-0.021-0.0210.0000.0000.0000.000
120A117ASP-1-0.808-0.86829.0710.5750.5750.0000.0000.0000.000
121A118GLU-1-0.822-0.90326.0270.1780.1780.0000.0000.0000.000
122A119VAL00.0100.00325.3580.0870.0870.0000.0000.0000.000
123A120LEU0-0.0130.00418.380-0.075-0.0750.0000.0000.0000.000
124A121VAL0-0.004-0.00522.9780.0730.0730.0000.0000.0000.000
125A122VAL0-0.009-0.01118.4900.0100.0100.0000.0000.0000.000
126A123ASP-1-0.806-0.91720.8260.7640.7640.0000.0000.0000.000
127A124ASP-1-0.866-0.93319.7460.9660.9660.0000.0000.0000.000
128A125LEU0-0.040-0.02320.127-0.028-0.0280.0000.0000.0000.000
129A126LEU0-0.0120.01522.407-0.028-0.0280.0000.0000.0000.000
130A127ALA00.0410.00524.265-0.067-0.0670.0000.0000.0000.000
131A128THR00.0480.01327.459-0.031-0.0310.0000.0000.0000.000
132A129GLY00.0460.02428.372-0.026-0.0260.0000.0000.0000.000
133A130GLY0-0.0060.01129.3730.0220.0220.0000.0000.0000.000
134A131THR00.0250.00129.230-0.014-0.0140.0000.0000.0000.000
135A132ALA00.0260.02626.7790.0350.0350.0000.0000.0000.000
136A133LYS10.8870.94028.574-0.097-0.0970.0000.0000.0000.000
137A134ALA00.0460.01331.5860.0010.0010.0000.0000.0000.000
138A135THR0-0.015-0.02527.9220.0310.0310.0000.0000.0000.000
139A136VAL0-0.016-0.00428.6970.0240.0240.0000.0000.0000.000
140A137ASP-1-0.816-0.90330.9960.1590.1590.0000.0000.0000.000
141A138LEU0-0.085-0.04033.099-0.006-0.0060.0000.0000.0000.000
142A139ILE0-0.0050.00628.1920.0080.0080.0000.0000.0000.000
143A140GLU-1-0.808-0.86832.5870.1490.1490.0000.0000.0000.000
144A141LYS10.8230.91434.991-0.257-0.2570.0000.0000.0000.000
145A142THR0-0.041-0.03934.3150.0020.0020.0000.0000.0000.000
146A143GLN0-0.071-0.03736.7950.0130.0130.0000.0000.0000.000
147A144ALA00.0020.03131.357-0.014-0.0140.0000.0000.0000.000
148A145LYS10.8520.91528.172-0.188-0.1880.0000.0000.0000.000
149A146VAL0-0.0040.00026.5470.0550.0550.0000.0000.0000.000
150A147ALA0-0.020-0.00823.549-0.063-0.0630.0000.0000.0000.000
151A148GLY0-0.016-0.01822.569-0.093-0.0930.0000.0000.0000.000
152A149LEU0-0.027-0.00722.3730.0890.0890.0000.0000.0000.000
153A150ILE0-0.030-0.01314.519-0.126-0.1260.0000.0000.0000.000
154A151PHE00.0260.01318.3500.1090.1090.0000.0000.0000.000
155A152VAL00.000-0.00414.8900.0400.0400.0000.0000.0000.000
156A153MET0-0.071-0.03216.231-0.125-0.1250.0000.0000.0000.000
157A154GLU-1-0.759-0.85119.058-0.370-0.3700.0000.0000.0000.000
158A155LEU0-0.028-0.01421.657-0.073-0.0730.0000.0000.0000.000
159A156ASP-1-0.847-0.92823.455-0.577-0.5770.0000.0000.0000.000
160A157GLY0-0.014-0.00325.1150.0470.0470.0000.0000.0000.000
161A158LEU0-0.038-0.02327.9930.0310.0310.0000.0000.0000.000
162A159GLY00.0260.02229.7320.0510.0510.0000.0000.0000.000
163A160GLY00.0100.00528.0800.0090.0090.0000.0000.0000.000
164A161ARG10.7870.85320.3090.4120.4120.0000.0000.0000.000
165A162GLU-1-0.898-0.95626.849-0.306-0.3060.0000.0000.0000.000
166A163VAL0-0.039-0.02230.1910.0110.0110.0000.0000.0000.000
167A164LEU0-0.037-0.01425.8410.0400.0400.0000.0000.0000.000
168A165ALA00.0290.01628.313-0.015-0.0150.0000.0000.0000.000
169A166GLY0-0.038-0.01729.2230.0310.0310.0000.0000.0000.000
170A167TYR0-0.068-0.05026.7670.0130.0130.0000.0000.0000.000
171A168ASN0-0.012-0.01520.795-0.068-0.0680.0000.0000.0000.000
172A169VAL00.0480.03522.2110.1160.1160.0000.0000.0000.000
173A170SER0-0.002-0.00716.754-0.267-0.2670.0000.0000.0000.000
174A171ALA00.0310.01017.0300.1980.1980.0000.0000.0000.000
175A172LEU0-0.0500.00211.002-0.249-0.2490.0000.0000.0000.000
176A173ILE0-0.040-0.02513.577-0.420-0.4200.0000.0000.0000.000
177A174LYS10.8320.91116.0190.6830.6830.0000.0000.0000.000
178A175PHE-1-0.874-0.94618.602-0.246-0.2460.0000.0000.0000.000