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: GRZ81

Calculation Name: 5B5K-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid

Ligand 3-letter code: NAG | EPE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5B5K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D9J7

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 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2677556.473135
FMO2-HF: Nuclear repulsion 2580285.308447
FMO2-HF: Total energy -97271.164688
FMO2-MP2: Total energy -97547.783949


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:22:CYS)


Summations of interaction energy for fragment #1(A:22:CYS)
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.
-154.978-135.40846.035-26.094-39.512-0.181
Interaction energy analysis for fragmet #1(A:22:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.705 / q_NPA : 0.868
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].
3A24LYS10.8820.9483.48951.82654.0270.000-0.829-1.3730.000
4A25CYS0-0.082-0.0182.041-5.939-3.8866.830-3.536-5.3460.034
5A26ASP-1-0.803-0.8725.226-27.466-27.275-0.002-0.007-0.1810.000
41A62SER0-0.056-0.0514.976-9.249-9.243-0.002-0.001-0.0040.000
43A64PHE00.0280.0112.248-3.595-2.6191.450-1.057-1.369-0.005
44A65GLY00.0460.0052.009-39.687-36.6949.185-6.338-5.840-0.075
45A66VAL0-0.099-0.0352.516-1.595-0.1221.204-0.920-1.757-0.019
46A67VAL0-0.0010.0144.6972.5172.663-0.002-0.005-0.1390.000
55A76GLY0-0.010-0.0043.180-12.923-10.1900.476-1.346-1.864-0.014
56A77ALA0-0.045-0.0281.928-19.583-20.0977.366-2.940-3.912-0.046
57A78VAL00.0320.0172.5804.6103.2286.515-1.884-3.249-0.013
58A79ASP-1-0.792-0.8805.262-29.715-29.561-0.001-0.023-0.1300.000
62A83LEU0-0.052-0.0202.238-6.910-7.0793.136-0.788-2.179-0.007
63A84GLU-1-0.877-0.9354.644-23.602-23.600-0.002-0.0060.0060.000
101A122PHE00.0470.0082.414-18.449-16.1377.277-3.886-5.703-0.053
126A147ILE0-0.004-0.0083.123-0.4453.0501.959-1.921-3.533-0.005
129A151LYS10.8640.9032.82417.23320.1930.381-1.734-1.6070.014
130A153GLU-1-0.806-0.8822.813-26.400-26.7480.2641.146-1.0620.009
131A154LYS10.8700.9323.81315.73916.0270.001-0.019-0.270-0.001
6A27GLN0-0.008-0.0166.8800.5510.5510.0000.0000.0000.000
7A28PHE00.0310.01310.4031.6521.6520.0000.0000.0000.000
8A29VAL0-0.017-0.0027.4171.4311.4310.0000.0000.0000.000
9A30THR0-0.006-0.0089.5211.0601.0600.0000.0000.0000.000
10A31ASP-1-0.832-0.90711.787-17.877-17.8770.0000.0000.0000.000
11A32ALA0-0.0050.01513.4511.4841.4840.0000.0000.0000.000
12A33LEU0-0.008-0.00910.0711.1741.1740.0000.0000.0000.000
13A34LYS10.8950.94214.52818.78518.7850.0000.0000.0000.000
14A35THR0-0.019-0.01417.3951.3081.3080.0000.0000.0000.000
15A36PHE00.001-0.01916.8150.8250.8250.0000.0000.0000.000
16A37GLU-1-0.838-0.91017.986-15.483-15.4830.0000.0000.0000.000
17A38ASN0-0.055-0.03119.7000.6900.6900.0000.0000.0000.000
18A39THR0-0.037-0.00222.3250.7960.7960.0000.0000.0000.000
19A40TYR00.0830.03219.8640.1200.1200.0000.0000.0000.000
20A41LEU0-0.0150.00219.6620.3080.3080.0000.0000.0000.000
21A42ASN0-0.036-0.02923.1740.5730.5730.0000.0000.0000.000
22A43ASP-1-0.858-0.90826.070-11.444-11.4440.0000.0000.0000.000
23A44HIS10.7250.85724.01313.23713.2370.0000.0000.0000.000
24A45LEU0-0.021-0.01222.7300.1860.1860.0000.0000.0000.000
25A46PRO00.0380.02226.7230.0800.0800.0000.0000.0000.000
26A47HIS00.0450.01626.907-0.265-0.2650.0000.0000.0000.000
27A48ASP-1-0.896-0.94326.541-10.575-10.5750.0000.0000.0000.000
28A49ILE0-0.052-0.02123.973-0.265-0.2650.0000.0000.0000.000
29A50HIS0-0.016-0.01122.583-0.877-0.8770.0000.0000.0000.000
30A51LYS10.9020.92520.83413.01313.0130.0000.0000.0000.000
31A52ASN00.0110.00219.979-0.970-0.9700.0000.0000.0000.000
32A53VAL00.0580.03418.393-0.748-0.7480.0000.0000.0000.000
33A54MET00.0320.01914.961-1.034-1.0340.0000.0000.0000.000
34A55ARG10.8720.94515.11713.21313.2130.0000.0000.0000.000
35A56MET0-0.0020.00214.430-1.033-1.0330.0000.0000.0000.000
36A57VAL00.0360.01512.402-1.600-1.6000.0000.0000.0000.000
37A58ASN00.015-0.00110.786-3.453-3.4530.0000.0000.0000.000
38A59HIS0-0.0040.0219.773-2.848-2.8480.0000.0000.0000.000
39A60GLU-1-0.831-0.9189.193-30.614-30.6140.0000.0000.0000.000
40A61VAL00.0100.0136.534-4.917-4.9170.0000.0000.0000.000
42A63SER0-0.065-0.0345.740-3.153-3.1530.0000.0000.0000.000
47A68THR0-0.052-0.0576.9973.2133.2130.0000.0000.0000.000
48A69SER0-0.061-0.03010.2522.7772.7770.0000.0000.0000.000
49A70ALA00.0470.00712.182-0.683-0.6830.0000.0000.0000.000
50A71GLU-1-0.889-0.94713.549-19.667-19.6670.0000.0000.0000.000
51A72ASP-1-0.768-0.8508.573-33.508-33.5080.0000.0000.0000.000
52A73SER0-0.058-0.0307.698-3.390-3.3900.0000.0000.0000.000
53A74TYR0-0.015-0.0077.755-2.493-2.4930.0000.0000.0000.000
54A75LEU0-0.016-0.0035.072-2.765-2.7650.0000.0000.0000.000
59A80GLU-1-0.815-0.9296.221-26.136-26.1360.0000.0000.0000.000
60A81ASN0-0.0100.0077.631-0.875-0.8750.0000.0000.0000.000
61A82THR00.010-0.0216.4250.7050.7050.0000.0000.0000.000
64A85GLN0-0.038-0.0328.1591.4541.4540.0000.0000.0000.000
65A86ALA00.0080.0095.1431.1091.1090.0000.0000.0000.000
66A87THR0-0.066-0.0496.835-1.891-1.8910.0000.0000.0000.000
67A88TRP00.009-0.0038.2832.6472.6470.0000.0000.0000.000
68A89SER0-0.043-0.0239.6811.3601.3600.0000.0000.0000.000
69A90PHE00.0230.0038.1651.6821.6820.0000.0000.0000.000
70A91LEU0-0.010-0.00710.2752.2912.2910.0000.0000.0000.000
71A92LYS10.9580.98712.96119.04219.0420.0000.0000.0000.000
72A93ASP-1-0.785-0.90113.411-18.522-18.5220.0000.0000.0000.000
73A94LEU0-0.0060.00013.1081.1161.1160.0000.0000.0000.000
74A95LYS10.8260.93415.39115.95815.9580.0000.0000.0000.000
75A96ARG10.8360.89816.82517.83717.8370.0000.0000.0000.000
76A97ILE00.0050.00516.8850.8130.8130.0000.0000.0000.000
77A98THR0-0.061-0.02818.8820.7470.7470.0000.0000.0000.000
78A99ASP-1-0.816-0.90821.288-13.102-13.1020.0000.0000.0000.000
79A100SER0-0.091-0.04223.0350.6390.6390.0000.0000.0000.000
80A101ASP-1-0.848-0.93024.994-11.047-11.0470.0000.0000.0000.000
81A102LEU0-0.018-0.01223.2870.2340.2340.0000.0000.0000.000
82A103LYS10.8960.95426.13010.69710.6970.0000.0000.0000.000
83A104GLY00.0230.00527.1630.0720.0720.0000.0000.0000.000
84A105GLU-1-0.823-0.91025.248-12.606-12.6060.0000.0000.0000.000
85A106LEU00.0090.00124.702-0.493-0.4930.0000.0000.0000.000
86A107PHE00.0120.01520.726-0.596-0.5960.0000.0000.0000.000
87A108ILE00.0230.00420.696-0.838-0.8380.0000.0000.0000.000
88A109LYS10.8270.91219.75211.82911.8290.0000.0000.0000.000
89A110GLU-1-0.787-0.88219.716-16.148-16.1480.0000.0000.0000.000
90A111LEU0-0.0110.00215.440-1.086-1.0860.0000.0000.0000.000
91A112LEU0-0.015-0.02415.339-1.551-1.5510.0000.0000.0000.000
92A113TRP0-0.040-0.02515.181-0.821-0.8210.0000.0000.0000.000
93A114MET0-0.0160.01713.248-1.749-1.7490.0000.0000.0000.000
94A115LEU00.000-0.00610.488-1.775-1.7750.0000.0000.0000.000
95A116ARG10.9430.97810.08317.62217.6220.0000.0000.0000.000
96A117HIS00.0490.03711.420-1.491-1.4910.0000.0000.0000.000
97A118GLN00.013-0.0178.918-2.759-2.7590.0000.0000.0000.000
98A119LYS10.8240.9186.83329.59829.5980.0000.0000.0000.000
99A120ASP-1-0.878-0.9477.774-26.998-26.9980.0000.0000.0000.000
100A121ILE0-0.051-0.0259.0280.2970.2970.0000.0000.0000.000
102A123ASN00.013-0.0096.245-5.056-5.0560.0000.0000.0000.000
103A124ASN0-0.013-0.0098.2402.1262.1260.0000.0000.0000.000
104A125LEU00.0090.0107.7491.3111.3110.0000.0000.0000.000
105A126ALA0-0.0050.0076.3411.5271.5270.0000.0000.0000.000
106A127ARG10.9440.9608.17624.45524.4550.0000.0000.0000.000
107A128GLN0-0.019-0.00311.5771.5491.5490.0000.0000.0000.000
108A129PHE00.031-0.0018.2201.2181.2180.0000.0000.0000.000
109A130GLN0-0.012-0.0239.1473.1023.1020.0000.0000.0000.000
110A131LYS10.8270.91812.12218.11718.1170.0000.0000.0000.000
111A132GLU-1-0.887-0.93315.010-16.406-16.4060.0000.0000.0000.000
112A133VAL0-0.014-0.00412.3750.9330.9330.0000.0000.0000.000
113A134LEU0-0.0150.01410.4200.3590.3590.0000.0000.0000.000
114A135CYS0-0.080-0.01313.6890.8160.8160.0000.0000.0000.000
115A136PRO00.0730.03216.1350.9730.9730.0000.0000.0000.000
116A137ASN0-0.061-0.03718.7150.1690.1690.0000.0000.0000.000
117A138LYS10.9910.98321.16311.81411.8140.0000.0000.0000.000
118A139CYS0-0.061-0.02523.804-0.013-0.0130.0000.0000.0000.000
119A140GLY00.0300.01223.002-0.447-0.4470.0000.0000.0000.000
120A141VAL0-0.061-0.04418.393-0.375-0.3750.0000.0000.0000.000
121A142MET0-0.0060.02416.2580.2050.2050.0000.0000.0000.000
122A143SER0-0.012-0.00814.420-0.436-0.4360.0000.0000.0000.000
123A144GLN00.015-0.01311.5280.4020.4020.0000.0000.0000.000
124A145THR0-0.050-0.0179.054-0.003-0.0030.0000.0000.0000.000
125A146LEU00.0080.0125.417-0.206-0.2060.0000.0000.0000.000
132A155GLN0-0.030-0.0115.7072.8192.8190.0000.0000.0000.000
133A156LEU0-0.030-0.0157.400-0.857-0.8570.0000.0000.0000.000
134A157HIS00.0540.0248.3220.0280.0280.0000.0000.0000.000
135A158ILE0-0.022-0.01710.1691.0051.0050.0000.0000.0000.000
136A160ARG10.9340.96515.81614.18914.1890.0000.0000.0000.000
137A161LYS10.8490.93518.90714.80914.8090.0000.0000.0000.000
138A162SER00.0300.00822.2440.1050.1050.0000.0000.0000.000
139A163LEU0-0.0020.00825.125-0.096-0.0960.0000.0000.0000.000
140A164ASP-1-0.809-0.87326.719-8.968-8.9680.0000.0000.0000.000
141A166GLY00.0060.01929.592-0.036-0.0360.0000.0000.0000.000
142A167GLU-1-0.915-0.96633.369-7.717-7.7170.0000.0000.0000.000
143A168ARG10.8100.90332.1549.0629.0620.0000.0000.0000.000
144A169HIS00.0390.02038.225-0.026-0.0260.0000.0000.0000.000
145A170ILE0-0.066-0.03439.620-0.122-0.1220.0000.0000.0000.000
146A171GLU-1-0.911-0.95243.528-6.277-6.2770.0000.0000.0000.000
147A172VAL0-0.020-0.01146.784-0.095-0.0950.0000.0000.0000.000
148A173HIS00.0320.02948.7100.0240.0240.0000.0000.0000.000
149A174ARG10.9250.96151.7505.5085.5080.0000.0000.0000.000
150A175SER0-0.050-0.04153.4050.1070.1070.0000.0000.0000.000
151A176GLU-1-0.902-0.92949.541-6.168-6.1680.0000.0000.0000.000
152A177ASP-1-0.867-0.92245.701-6.632-6.6320.0000.0000.0000.000
153A178LEU0-0.0160.00243.043-0.078-0.0780.0000.0000.0000.000
154A179VAL0-0.019-0.02338.643-0.082-0.0820.0000.0000.0000.000
155A180LEU0-0.0150.00737.848-0.041-0.0410.0000.0000.0000.000
156A181ASP-1-0.770-0.89333.138-9.597-9.5970.0000.0000.0000.000
157A182CYS0-0.0920.01630.999-0.065-0.0650.0000.0000.0000.000
158A183LEU00.0230.01227.099-0.440-0.4400.0000.0000.0000.000
159A184LEU0-0.005-0.00725.5230.0840.0840.0000.0000.0000.000
160A185SER0-0.010-0.01824.351-0.248-0.2480.0000.0000.0000.000
161A186TRP00.0210.00520.119-0.580-0.5800.0000.0000.0000.000
162A187HIS00.0330.01520.503-0.533-0.5330.0000.0000.0000.000
163A188ARG10.9730.98121.51612.38812.3880.0000.0000.0000.000
164A189ALA00.0110.00817.096-0.260-0.2600.0000.0000.0000.000
165A190SER0-0.0150.00416.788-1.168-1.1680.0000.0000.0000.000
166A191LYS10.8950.94013.12920.57520.5750.0000.0000.0000.000
167A192GLY00.010-0.00916.9240.1470.1470.0000.0000.0000.000
168A193LEU0-0.0150.00218.9790.3900.3900.0000.0000.0000.000
169A194THR0-0.077-0.05222.1200.1290.1290.0000.0000.0000.000
170A195ASP-1-0.903-0.96225.461-9.790-9.7900.0000.0000.0000.000
171A196TYR0-0.029-0.02027.098-0.096-0.0960.0000.0000.0000.000
172A197SER0-0.013-0.02030.3710.2940.2940.0000.0000.0000.000
173A198PHE00.0110.00633.140-0.073-0.0730.0000.0000.0000.000
174A199TYR00.006-0.00934.0990.0620.0620.0000.0000.0000.000
175A200ARG10.8600.93438.7856.4566.4560.0000.0000.0000.000
176A201VAL0-0.026-0.03639.461-0.011-0.0110.0000.0000.0000.000
177A202TRP00.005-0.00942.5590.1260.1260.0000.0000.0000.000
178A203GLU-1-0.894-0.95545.927-6.022-6.0220.0000.0000.0000.000
179A204ASN0-0.044-0.00147.384-0.081-0.0810.0000.0000.0000.000
180A205SER0-0.012-0.00443.766-0.023-0.0230.0000.0000.0000.000
181A206SER0-0.049-0.02843.165-0.077-0.0770.0000.0000.0000.000
182A207GLU-1-0.809-0.90437.077-7.924-7.9240.0000.0000.0000.000
183A208THR0-0.0240.00141.9540.0700.0700.0000.0000.0000.000
184A209LEU0-0.056-0.02035.843-0.055-0.0550.0000.0000.0000.000
185A210ILE0-0.028-0.01739.5320.1550.1550.0000.0000.0000.000
186A211ALA00.0220.01237.8510.0730.0730.0000.0000.0000.000
187A212LYS10.8370.91930.2869.1119.1110.0000.0000.0000.000
188A213GLY00.0530.04132.9780.1810.1810.0000.0000.0000.000
189A214LYS10.9220.95527.7069.9959.9950.0000.0000.0000.000
190A215GLU-1-0.873-0.92930.067-9.068-9.0680.0000.0000.0000.000
191A216PRO0-0.025-0.01729.4080.0450.0450.0000.0000.0000.000
192A217TYR0-0.010-0.01931.348-0.105-0.1050.0000.0000.0000.000
193A218LEU00.0160.02535.0340.0300.0300.0000.0000.0000.000
194A219THR00.010-0.00438.163-0.040-0.0400.0000.0000.0000.000
195A220LYS10.8050.92241.5276.3506.3500.0000.0000.0000.000
196A221SER0-0.015-0.02844.7960.0780.0780.0000.0000.0000.000
197A222MET0-0.027-0.01847.8860.1120.1120.0000.0000.0000.000
198A223VAL0-0.0280.00647.6940.0570.0570.0000.0000.0000.000
199A224GLY00.0710.03750.7450.1200.1200.0000.0000.0000.000
200A225PRO0-0.059-0.04152.060-0.094-0.0940.0000.0000.0000.000
201A226GLU-1-0.845-0.92752.223-5.801-5.8010.0000.0000.0000.000
202A227ASP-1-0.827-0.91947.998-6.379-6.3790.0000.0000.0000.000
203A228ALA00.0170.02647.377-0.178-0.1780.0000.0000.0000.000
204A229GLY00.0150.01846.8680.0550.0550.0000.0000.0000.000
205A230ASN00.0090.00342.048-0.130-0.1300.0000.0000.0000.000
206A231TYR0-0.029-0.03339.7250.0010.0010.0000.0000.0000.000
207A232ARG10.8210.89432.6968.2648.2640.0000.0000.0000.000
208A234VAL0-0.031-0.02929.042-0.153-0.1530.0000.0000.0000.000
209A235LEU00.0400.03524.4050.0460.0460.0000.0000.0000.000
210A236ASP-1-0.759-0.86526.029-9.892-9.8920.0000.0000.0000.000
211A237THR0-0.050-0.04720.534-0.483-0.4830.0000.0000.0000.000
212A238ILE0-0.006-0.00720.1370.2410.2410.0000.0000.0000.000
213A239ASN0-0.023-0.01518.4800.4320.4320.0000.0000.0000.000
214A240GLN00.0300.02015.5630.3930.3930.0000.0000.0000.000
215A241GLY00.0380.03319.7240.1420.1420.0000.0000.0000.000
216A242HIS10.8570.92423.4169.7819.7810.0000.0000.0000.000
217A243ALA00.0500.03422.077-0.254-0.2540.0000.0000.0000.000
218A244THR0-0.009-0.02323.296-0.350-0.3500.0000.0000.0000.000
219A245VAL00.0050.01526.4520.1810.1810.0000.0000.0000.000
220A246ILE00.0140.01529.949-0.212-0.2120.0000.0000.0000.000
221A247ARG10.8150.88832.7708.4518.4510.0000.0000.0000.000
222A248TYR0-0.025-0.06334.405-0.173-0.1730.0000.0000.0000.000
223A249ASP-1-0.844-0.90439.432-6.769-6.7690.0000.0000.0000.000
224A250VAL0-0.005-0.00442.900-0.046-0.0460.0000.0000.0000.000
225A251THR00.0570.02945.2390.1930.1930.0000.0000.0000.000
226A252VAL0-0.034-0.01948.775-0.043-0.0430.0000.0000.0000.000
227A253LEU0-0.0040.00851.0770.1530.1530.0000.0000.0000.000
228A254PRO0-0.016-0.03253.6610.0580.0580.0000.0000.0000.000
229A255PRO0-0.006-0.02155.533-0.084-0.0840.0000.0000.0000.000
230A256LYS00.0250.03956.536-0.141-0.1410.0000.0000.0000.000