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: YRNN2

Calculation Name: 2B1M-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-l-fucopyranose | tetraethylene glycol | di(hydroxyethyl)ether

Ligand 3-letter code: NAG | FUC | PG4 | PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B1M

Chain ID: A

ChEMBL ID:

UniProt ID: Q3Y6U7

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2741613.885006
FMO2-HF: Nuclear repulsion 2654340.33341
FMO2-HF: Total energy -87273.551596
FMO2-MP2: Total energy -87527.795889


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:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-244.672-242.5281.023-1.125-2.041-0.009
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.821 / q_NPA : 0.903
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].
3A4GLU-1-0.851-0.9043.865-56.518-55.528-0.007-0.419-0.5630.000
127A130GLN00.0050.0192.9964.4834.7930.049-0.111-0.2480.000
131A134LEU0-0.091-0.0492.359-2.939-2.4610.976-0.463-0.991-0.008
172A175TYR0-0.039-0.0333.6281.0111.3770.005-0.132-0.239-0.001
4A5SER0-0.056-0.0216.6516.0586.0580.0000.0000.0000.000
5A6TRP00.000-0.0106.101-3.682-3.6820.0000.0000.0000.000
6A7ASP-1-0.747-0.8448.117-17.773-17.7730.0000.0000.0000.000
7A8TRP00.024-0.0079.9191.1271.1270.0000.0000.0000.000
8A9SER0-0.034-0.03813.3241.3061.3060.0000.0000.0000.000
9A10LYS10.8310.89414.36220.37520.3750.0000.0000.0000.000
10A11LYS10.8210.92910.51925.11525.1150.0000.0000.0000.000
11A12GLY00.0040.01416.1150.3570.3570.0000.0000.0000.000
12A13VAL00.0070.00815.1810.5740.5740.0000.0000.0000.000
13A14ILE0-0.0040.00815.8940.0390.0390.0000.0000.0000.000
14A15THR0-0.036-0.04219.6210.3630.3630.0000.0000.0000.000
15A16LYS10.9910.99222.8689.6149.6140.0000.0000.0000.000
16A17VAL00.0180.02423.726-0.048-0.0480.0000.0000.0000.000
17A18LYS10.7430.86425.91411.43411.4340.0000.0000.0000.000
18A19PHE00.002-0.02028.619-0.058-0.0580.0000.0000.0000.000
19A20GLN00.0540.03929.207-0.117-0.1170.0000.0000.0000.000
20A21GLY00.0040.01632.2080.2670.2670.0000.0000.0000.000
21A22GLN0-0.043-0.02934.896-0.163-0.1630.0000.0000.0000.000
22A23CYS0-0.113-0.04334.284-0.100-0.1000.0000.0000.0000.000
23A24GLY00.0290.03432.648-0.260-0.2600.0000.0000.0000.000
24A25SER00.049-0.00731.020-0.189-0.1890.0000.0000.0000.000
25A26GLY00.0230.00927.191-0.199-0.1990.0000.0000.0000.000
26A27TRP0-0.0030.03025.529-0.579-0.5790.0000.0000.0000.000
27A28ALA00.0320.02525.707-0.305-0.3050.0000.0000.0000.000
28A29PHE0-0.044-0.03725.807-0.224-0.2240.0000.0000.0000.000
29A30SER0-0.048-0.01121.205-0.477-0.4770.0000.0000.0000.000
30A31ALA00.0520.02521.233-0.644-0.6440.0000.0000.0000.000
31A32THR0-0.022-0.05222.731-0.437-0.4370.0000.0000.0000.000
32A33GLY00.0020.00821.437-0.260-0.2600.0000.0000.0000.000
33A34ALA00.0340.00318.303-0.626-0.6260.0000.0000.0000.000
34A35ILE0-0.0020.00118.990-0.470-0.4700.0000.0000.0000.000
35A36GLU-1-0.765-0.84921.589-12.047-12.0470.0000.0000.0000.000
36A37ALA00.0150.01416.603-0.102-0.1020.0000.0000.0000.000
37A38ALA00.0330.01717.103-0.516-0.5160.0000.0000.0000.000
38A39HIS00.0230.00518.1010.1620.1620.0000.0000.0000.000
39A40ALA0-0.048-0.00919.3740.1540.1540.0000.0000.0000.000
40A41ILE0-0.047-0.02913.452-0.092-0.0920.0000.0000.0000.000
41A42ALA0-0.0060.01317.079-0.294-0.2940.0000.0000.0000.000
42A43THR0-0.024-0.03119.3360.4340.4340.0000.0000.0000.000
43A44GLY0-0.023-0.00320.8180.4340.4340.0000.0000.0000.000
44A45ASN0-0.076-0.04421.8220.6370.6370.0000.0000.0000.000
45A46LEU0-0.0130.00421.223-0.053-0.0530.0000.0000.0000.000
46A47VAL0-0.006-0.00823.8350.5130.5130.0000.0000.0000.000
47A48SER0-0.023-0.00925.761-0.353-0.3530.0000.0000.0000.000
48A49LEU0-0.009-0.01025.1440.3900.3900.0000.0000.0000.000
49A50SER0-0.024-0.02928.632-0.036-0.0360.0000.0000.0000.000
50A51GLU-1-0.676-0.77927.743-10.595-10.5950.0000.0000.0000.000
51A52GLN0-0.066-0.05330.7300.0300.0300.0000.0000.0000.000
52A53GLU-1-0.771-0.90232.799-8.813-8.8130.0000.0000.0000.000
53A54LEU00.0090.00627.6160.0860.0860.0000.0000.0000.000
54A55ILE0-0.025-0.01932.1560.1210.1210.0000.0000.0000.000
55A56ASP-1-0.792-0.87634.615-7.701-7.7010.0000.0000.0000.000
56A57CYS0-0.0520.01135.1180.2890.2890.0000.0000.0000.000
57A58VAL00.0290.02530.906-0.013-0.0130.0000.0000.0000.000
58A59ASP-1-0.931-0.97034.122-7.978-7.9780.0000.0000.0000.000
59A60GLU-1-0.974-0.97532.693-9.148-9.1480.0000.0000.0000.000
60A61SER0-0.039-0.02131.541-0.298-0.2980.0000.0000.0000.000
61A62GLU-1-0.951-0.96433.919-7.779-7.7790.0000.0000.0000.000
62A63GLY00.0600.02735.5390.0560.0560.0000.0000.0000.000
63A65TYR0-0.058-0.01036.1690.0240.0240.0000.0000.0000.000
64A66ASN0-0.042-0.04630.497-0.412-0.4120.0000.0000.0000.000
65A67GLY00.0610.02730.6870.2590.2590.0000.0000.0000.000
66A68TRP0-0.003-0.00425.900-0.493-0.4930.0000.0000.0000.000
67A69HIS0-0.0010.01121.0220.6010.6010.0000.0000.0000.000
68A70TYR00.0550.00723.7480.0610.0610.0000.0000.0000.000
69A71GLN00.0440.03724.7140.0500.0500.0000.0000.0000.000
70A72SER0-0.017-0.01226.0390.3600.3600.0000.0000.0000.000
71A73PHE0-0.014-0.01220.7590.0670.0670.0000.0000.0000.000
72A74GLU-1-0.851-0.90525.325-10.091-10.0910.0000.0000.0000.000
73A75TRP0-0.014-0.01727.9440.2250.2250.0000.0000.0000.000
74A76VAL00.003-0.00226.4660.2810.2810.0000.0000.0000.000
75A77VAL0-0.0010.01326.1300.1350.1350.0000.0000.0000.000
76A78LYS10.8620.93428.7868.8638.8630.0000.0000.0000.000
77A79HIS0-0.046-0.02532.1900.6140.6140.0000.0000.0000.000
78A80GLY0-0.022-0.00632.0030.2000.2000.0000.0000.0000.000
79A81GLY00.025-0.00229.0470.0060.0060.0000.0000.0000.000
80A82ILE0-0.076-0.02427.2210.2670.2670.0000.0000.0000.000
81A83ALA00.0380.01230.372-0.060-0.0600.0000.0000.0000.000
82A84SER00.011-0.03531.020-0.306-0.3060.0000.0000.0000.000
83A85GLU0-0.117-0.10930.2960.3400.3400.0000.0000.0000.000
84A86ALA0-0.058-0.03132.5880.2150.2150.0000.0000.0000.000
85A87ASP-1-0.836-0.88335.468-8.269-8.2690.0000.0000.0000.000
86A88TYR0-0.081-0.06435.0460.3070.3070.0000.0000.0000.000
87A89PRO0-0.0200.00735.347-0.201-0.2010.0000.0000.0000.000
88A90TYR0-0.001-0.01733.1740.1220.1220.0000.0000.0000.000
89A91LYS10.8840.93036.0397.5487.5480.0000.0000.0000.000
90A92ALA0-0.018-0.00536.4720.2050.2050.0000.0000.0000.000
91A93ARG10.9320.95637.5137.2437.2430.0000.0000.0000.000
92A94ASP-1-0.750-0.86638.678-7.957-7.9570.0000.0000.0000.000
93A95GLY0-0.049-0.03739.9970.2100.2100.0000.0000.0000.000
94A96LYS10.9370.97740.9756.6326.6320.0000.0000.0000.000
95A98LYS10.8250.90339.4727.7357.7350.0000.0000.0000.000
96A99ALA00.1080.04836.5890.0390.0390.0000.0000.0000.000
97A100ASN0-0.097-0.04838.207-0.145-0.1450.0000.0000.0000.000
98A101GLU-1-0.987-0.99641.123-6.905-6.9050.0000.0000.0000.000
99A102ILE0-0.053-0.00835.2190.0410.0410.0000.0000.0000.000
100A103GLN0-0.050-0.02538.2040.1070.1070.0000.0000.0000.000
101A104ASP-1-0.911-0.95034.044-8.635-8.6350.0000.0000.0000.000
102A105LYS10.8650.93531.6378.7048.7040.0000.0000.0000.000
103A106VAL0-0.0270.00125.079-0.104-0.1040.0000.0000.0000.000
104A107THR00.0250.00626.6140.1430.1430.0000.0000.0000.000
105A108ILE0-0.051-0.03022.687-0.441-0.4410.0000.0000.0000.000
106A109ASP-1-0.836-0.90822.425-12.543-12.5430.0000.0000.0000.000
107A110ASN0-0.045-0.03121.6720.5500.5500.0000.0000.0000.000
108A111TYR0-0.066-0.05620.669-0.370-0.3700.0000.0000.0000.000
109A112GLY00.0440.04517.9640.1110.1110.0000.0000.0000.000
110A113VAL0-0.026-0.02019.0430.2850.2850.0000.0000.0000.000
111A114GLN0-0.030-0.02414.270-0.506-0.5060.0000.0000.0000.000
112A115ILE00.0010.00418.8050.1020.1020.0000.0000.0000.000
113A116LEU0-0.030-0.00116.978-0.068-0.0680.0000.0000.0000.000
114A117SER0-0.002-0.02421.0290.4720.4720.0000.0000.0000.000
115A118ASN0-0.035-0.04222.496-0.536-0.5360.0000.0000.0000.000
116A119GLU-1-0.917-0.93423.482-11.761-11.7610.0000.0000.0000.000
117A120SER0-0.0300.00918.294-0.506-0.5060.0000.0000.0000.000
118A121THR0-0.044-0.06116.3950.0770.0770.0000.0000.0000.000
119A122GLU-1-0.800-0.91414.838-17.931-17.9310.0000.0000.0000.000
120A123SER0-0.034-0.00412.444-1.680-1.6800.0000.0000.0000.000
121A124GLU-1-0.811-0.88511.387-19.394-19.3940.0000.0000.0000.000
122A125ALA00.0180.03612.475-0.937-0.9370.0000.0000.0000.000
123A126GLU-1-0.728-0.85910.522-23.013-23.0130.0000.0000.0000.000
124A127SER0-0.062-0.0227.636-3.521-3.5210.0000.0000.0000.000
125A128SER0-0.014-0.0247.967-1.999-1.9990.0000.0000.0000.000
126A129LEU00.0290.0149.982-0.488-0.4880.0000.0000.0000.000
128A131SER0-0.054-0.0255.950-3.890-3.8900.0000.0000.0000.000
129A132PHE00.0540.0176.9190.1900.1900.0000.0000.0000.000
130A133VAL00.0200.0188.3180.6290.6290.0000.0000.0000.000
132A135GLU-1-0.954-0.9586.758-25.698-25.6980.0000.0000.0000.000
133A136GLN0-0.034-0.0329.8961.9891.9890.0000.0000.0000.000
134A137PRO0-0.036-0.01512.346-0.294-0.2940.0000.0000.0000.000
135A138ILE00.0030.01912.5130.8800.8800.0000.0000.0000.000
136A139SER0-0.012-0.00615.3550.2300.2300.0000.0000.0000.000
137A140VAL0-0.014-0.00916.463-0.356-0.3560.0000.0000.0000.000
138A141SER00.0060.01319.4330.2920.2920.0000.0000.0000.000
139A142ILE0-0.041-0.03220.760-0.491-0.4910.0000.0000.0000.000
140A143ASP-1-0.795-0.88623.654-9.831-9.8310.0000.0000.0000.000
141A144ALA00.024-0.01426.038-0.261-0.2610.0000.0000.0000.000
142A145LYS10.8460.92527.4049.9839.9830.0000.0000.0000.000
143A146ASP-1-0.739-0.83528.095-9.927-9.9270.0000.0000.0000.000
144A147PHE00.0290.00722.956-0.083-0.0830.0000.0000.0000.000
145A148HIS0-0.051-0.01328.509-0.141-0.1410.0000.0000.0000.000
146A149PHE0-0.046-0.03230.8500.3630.3630.0000.0000.0000.000
147A150TYR0-0.049-0.01922.190-0.041-0.0410.0000.0000.0000.000
148A151SER00.002-0.00927.8860.0970.0970.0000.0000.0000.000
149A152GLY00.0310.01824.8620.0290.0290.0000.0000.0000.000
150A153GLY00.0010.01322.8230.1020.1020.0000.0000.0000.000
151A154ILE0-0.025-0.00617.801-0.349-0.3490.0000.0000.0000.000
152A155TYR0-0.032-0.04420.9290.4060.4060.0000.0000.0000.000
153A156ASP-1-0.826-0.92421.012-12.652-12.6520.0000.0000.0000.000
154A157GLY00.011-0.00222.639-0.216-0.2160.0000.0000.0000.000
155A158GLY0-0.018-0.00324.5750.3900.3900.0000.0000.0000.000
156A159ASN0-0.084-0.06228.1860.3500.3500.0000.0000.0000.000
157A160CYS0-0.141-0.05220.8910.2480.2480.0000.0000.0000.000
158A161SER0-0.005-0.00728.1440.0040.0040.0000.0000.0000.000
159A162SER0-0.0240.01128.493-0.034-0.0340.0000.0000.0000.000
160A163PRO0-0.050-0.03129.8510.2790.2790.0000.0000.0000.000
161A164TYR00.0270.00124.4440.2250.2250.0000.0000.0000.000
162A165GLY0-0.012-0.00428.3120.0570.0570.0000.0000.0000.000
163A166ILE0-0.015-0.00926.001-0.286-0.2860.0000.0000.0000.000
164A167ASN0-0.056-0.03428.2180.1470.1470.0000.0000.0000.000
165A168HIS00.0090.01125.8700.4150.4150.0000.0000.0000.000
166A169PHE00.0130.00023.074-0.255-0.2550.0000.0000.0000.000
167A170VAL0-0.025-0.00119.1790.2420.2420.0000.0000.0000.000
168A171LEU00.0030.01217.017-0.302-0.3020.0000.0000.0000.000
169A172ILE0-0.0080.00312.260-0.022-0.0220.0000.0000.0000.000
170A173VAL00.027-0.00213.598-0.499-0.4990.0000.0000.0000.000
171A174GLY00.006-0.0139.921-1.098-1.0980.0000.0000.0000.000
173A176GLY00.015-0.0079.611-1.777-1.7770.0000.0000.0000.000
174A177SER0-0.023-0.02111.0530.8690.8690.0000.0000.0000.000
175A178GLU-1-0.931-0.96113.473-15.506-15.5060.0000.0000.0000.000
176A179ASP-1-0.930-0.96217.177-14.684-14.6840.0000.0000.0000.000
177A180GLY0-0.032-0.01015.5720.5160.5160.0000.0000.0000.000
178A181VAL0-0.041-0.01116.271-0.139-0.1390.0000.0000.0000.000
179A182ASP-1-0.787-0.87111.730-24.857-24.8570.0000.0000.0000.000
180A183TYR0-0.035-0.04113.0571.2751.2750.0000.0000.0000.000
181A184TRP00.0410.0058.934-2.663-2.6630.0000.0000.0000.000
182A185ILE0-0.045-0.02812.5651.3431.3430.0000.0000.0000.000
183A186ALA00.0130.00514.720-0.568-0.5680.0000.0000.0000.000
184A187LYS10.8670.94117.44913.61213.6120.0000.0000.0000.000
185A188ASN00.0280.02620.1590.1120.1120.0000.0000.0000.000
186A189SER0-0.024-0.02923.669-0.145-0.1450.0000.0000.0000.000
187A190TRP0-0.024-0.02226.9530.4830.4830.0000.0000.0000.000
188A191GLY0-0.007-0.00228.8030.3240.3240.0000.0000.0000.000
189A192GLU-1-0.936-0.98426.589-11.194-11.1940.0000.0000.0000.000
190A193ASP-1-0.950-0.97228.082-9.566-9.5660.0000.0000.0000.000
191A194TRP0-0.034-0.01423.6820.0130.0130.0000.0000.0000.000
192A195GLY0-0.011-0.01125.431-0.375-0.3750.0000.0000.0000.000
193A196ILE0-0.025-0.01620.9100.1920.1920.0000.0000.0000.000
194A197ASP-1-0.890-0.93722.917-12.701-12.7010.0000.0000.0000.000
195A198GLY00.0090.00224.331-0.177-0.1770.0000.0000.0000.000
196A199TYR0-0.065-0.04618.315-0.542-0.5420.0000.0000.0000.000
197A200ILE00.003-0.00320.2620.4830.4830.0000.0000.0000.000
198A201ARG10.8270.93216.94915.67015.6700.0000.0000.0000.000
199A202ILE00.0220.00917.0910.8540.8540.0000.0000.0000.000
200A203GLN0-0.0040.00016.258-0.540-0.5400.0000.0000.0000.000
201A204ARG10.7840.8697.42628.85328.8530.0000.0000.0000.000
202A205ASN0-0.073-0.05310.1590.2160.2160.0000.0000.0000.000
203A206THR0-0.019-0.00814.5080.4820.4820.0000.0000.0000.000
204A207GLY00.0060.00617.7420.9000.9000.0000.0000.0000.000
205A208ASN0-0.069-0.03219.2570.5920.5920.0000.0000.0000.000
206A209LEU00.0190.01418.244-0.568-0.5680.0000.0000.0000.000
207A210LEU00.005-0.01418.347-0.543-0.5430.0000.0000.0000.000
208A211GLY00.0410.03118.204-0.073-0.0730.0000.0000.0000.000
209A212VAL00.0080.01118.8300.8820.8820.0000.0000.0000.000
210A214GLY00.0430.02022.6060.3150.3150.0000.0000.0000.000
211A215MET0-0.0290.00114.912-0.085-0.0850.0000.0000.0000.000
212A216ASN0-0.013-0.01515.618-0.721-0.7210.0000.0000.0000.000
213A217TYR0-0.056-0.01517.588-0.095-0.0950.0000.0000.0000.000
214A218PHE00.0410.00120.7080.1340.1340.0000.0000.0000.000
215A219ALA00.0460.04116.1180.1670.1670.0000.0000.0000.000
216A220SER0-0.052-0.04818.1830.5640.5640.0000.0000.0000.000
217A221TYR00.0140.00214.440-0.183-0.1830.0000.0000.0000.000
218A222PRO00.0040.02017.9850.3460.3460.0000.0000.0000.000
219A223ILE0-0.007-0.00817.080-0.894-0.8940.0000.0000.0000.000
220A224ILE0-0.044-0.03218.2760.9010.9010.0000.0000.0000.000
221A225GLU-1-0.974-0.96818.347-15.302-15.3020.0000.0000.0000.000
222A226LYS0-0.030-0.01016.8010.8350.8350.0000.0000.0000.000