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: 4G33N

Calculation Name: 1MQL-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | 2-acetamido-2-deoxy-alpha-d-glucopyranose | alpha-d-mannopyranose

Ligand 3-letter code: NAG | NDG | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MQL

Chain ID: B

ChEMBL ID:

UniProt ID: P03442

Base Structure: X-ray

Registration Date: 2025-10-06

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 171
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1519474.505597
FMO2-HF: Nuclear repulsion 1448886.582268
FMO2-HF: Total energy -70587.923329
FMO2-MP2: Total energy -70792.43454


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(B:1:GLY)


Summations of interaction energy for fragment #1(B:1:GLY)
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.
-277.867-271.60610.016-8.365-7.911-0.1
Interaction energy analysis for fragmet #1(B:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.899
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].
3B3PHE0-0.034-0.0183.47214.32715.658-0.003-0.579-0.749-0.002
4B4GLY00.0140.0222.7809.97810.5420.024-0.230-0.358-0.001
5B5ALA00.0140.0204.05010.00510.167-0.001-0.018-0.1440.000
6B6ILE0-0.023-0.0314.0725.8996.039-0.001-0.023-0.1160.000
7B7ALA0-0.040-0.0203.370-18.669-17.8410.043-0.431-0.441-0.003
8B8GLY0-0.006-0.0044.760-6.301-6.276-0.001-0.006-0.0170.000
105B105GLN0-0.040-0.0134.690-0.171-0.114-0.001-0.005-0.0510.000
108B108ILE0-0.0090.0003.032-1.778-1.4740.071-0.141-0.233-0.001
109B109ASP-1-0.801-0.8992.344-80.594-79.1073.612-2.779-2.320-0.029
110B110LEU0-0.052-0.0133.8651.1781.1520.000-0.0140.0400.000
112B112ASP-1-0.734-0.8722.000-108.247-106.8616.274-4.136-3.523-0.064
113B113SER0-0.017-0.0044.9365.8525.855-0.001-0.0030.0010.000
9B9PHE0-0.045-0.0076.0115.1005.1000.0000.0000.0000.000
10B10ILE0-0.040-0.0247.9194.3404.3400.0000.0000.0000.000
11B11GLU-1-0.923-0.9568.690-27.623-27.6230.0000.0000.0000.000
12B12ASN0-0.055-0.04010.282-0.964-0.9640.0000.0000.0000.000
13B13GLY00.0190.01811.1280.4040.4040.0000.0000.0000.000
14B14TRP0-0.025-0.03212.2381.6621.6620.0000.0000.0000.000
15B15GLU-1-0.875-0.94316.033-17.013-17.0130.0000.0000.0000.000
16B16GLY0-0.027-0.00718.1030.7720.7720.0000.0000.0000.000
17B17MET0-0.077-0.01615.3720.8790.8790.0000.0000.0000.000
18B18ILE0-0.011-0.00518.610-0.469-0.4690.0000.0000.0000.000
19B19ASP-1-0.892-0.95121.017-14.369-14.3690.0000.0000.0000.000
20B20GLY0-0.015-0.02318.6970.2640.2640.0000.0000.0000.000
21B21TRP00.005-0.00511.880-0.592-0.5920.0000.0000.0000.000
22B22TYR0-0.003-0.0159.337-0.286-0.2860.0000.0000.0000.000
23B23GLY00.0270.00914.2721.4801.4800.0000.0000.0000.000
24B24PHE0-0.030-0.00216.092-0.933-0.9330.0000.0000.0000.000
25B25ARG10.8760.92918.47816.61616.6160.0000.0000.0000.000
26B26HIS0-0.016-0.00520.546-0.450-0.4500.0000.0000.0000.000
27B27GLN0-0.001-0.01223.494-0.082-0.0820.0000.0000.0000.000
28B28ASN00.0370.02726.119-0.257-0.2570.0000.0000.0000.000
29B29SER00.0330.00829.1530.0820.0820.0000.0000.0000.000
30B30GLU-1-0.895-0.94132.180-9.249-9.2490.0000.0000.0000.000
31B31GLY0-0.0040.01231.0800.0720.0720.0000.0000.0000.000
32B32THR0-0.041-0.03725.943-0.385-0.3850.0000.0000.0000.000
33B33GLY00.0160.01625.4500.4380.4380.0000.0000.0000.000
34B34GLN00.012-0.00420.480-0.945-0.9450.0000.0000.0000.000
35B35ALA00.0090.01221.4610.6360.6360.0000.0000.0000.000
36B36ALA00.0590.04618.973-0.823-0.8230.0000.0000.0000.000
37B37ASP-1-0.814-0.90417.004-15.904-15.9040.0000.0000.0000.000
38B38LEU00.0340.01518.083-0.844-0.8440.0000.0000.0000.000
39B39LYS10.8480.90819.60815.19515.1950.0000.0000.0000.000
40B40SER00.0340.01313.574-0.489-0.4890.0000.0000.0000.000
41B41THR0-0.027-0.01314.985-1.431-1.4310.0000.0000.0000.000
42B42GLN0-0.027-0.02616.364-0.424-0.4240.0000.0000.0000.000
43B43ALA00.0270.01915.5240.0290.0290.0000.0000.0000.000
44B44ALA00.0210.02412.079-0.252-0.2520.0000.0000.0000.000
45B45ILE00.0280.01713.6690.0970.0970.0000.0000.0000.000
46B46ASP-1-0.842-0.91016.473-14.374-14.3740.0000.0000.0000.000
47B47GLN0-0.138-0.08513.0070.4790.4790.0000.0000.0000.000
48B48ILE00.0220.01410.8640.3340.3340.0000.0000.0000.000
49B49ASN0-0.007-0.00615.0081.1991.1990.0000.0000.0000.000
50B50ARG10.8850.95618.41415.98515.9850.0000.0000.0000.000
51B51LYS10.7730.87711.71323.87723.8770.0000.0000.0000.000
52B52LEU00.0410.02217.2460.4930.4930.0000.0000.0000.000
53B53ASN0-0.013-0.03719.2701.0691.0690.0000.0000.0000.000
54B54ARG10.8270.88919.89514.09414.0940.0000.0000.0000.000
55B55VAL0-0.014-0.00219.0230.2430.2430.0000.0000.0000.000
56B56ILE0-0.0090.00522.2810.3880.3880.0000.0000.0000.000
57B57GLU-1-0.970-0.96924.785-10.005-10.0050.0000.0000.0000.000
58B58LYS0-0.0250.01124.9040.2170.2170.0000.0000.0000.000
59B59THR00.0380.02628.195-0.155-0.1550.0000.0000.0000.000
60B60ASN0-0.068-0.04330.9770.2910.2910.0000.0000.0000.000
61B61GLU-1-0.855-0.92534.091-7.871-7.8710.0000.0000.0000.000
62B62LYS10.8600.91535.9208.5218.5210.0000.0000.0000.000
63B63PHE00.0270.02939.3800.0280.0280.0000.0000.0000.000
64B64HIS0-0.012-0.00342.8530.0070.0070.0000.0000.0000.000
65B65GLN0-0.045-0.03439.479-0.286-0.2860.0000.0000.0000.000
66B66ILE00.0120.01541.5690.1600.1600.0000.0000.0000.000
67B67GLU-1-0.884-0.94343.909-6.875-6.8750.0000.0000.0000.000
68B68LYS10.7850.87338.2097.9777.9770.0000.0000.0000.000
69B69GLU-1-0.964-0.96743.166-7.371-7.3710.0000.0000.0000.000
70B70PHE00.017-0.00544.7860.0800.0800.0000.0000.0000.000
71B71SER0-0.040-0.04048.811-0.061-0.0610.0000.0000.0000.000
72B72GLU-1-0.917-0.92651.809-5.748-5.7480.0000.0000.0000.000
73B73VAL0-0.031-0.01651.258-0.126-0.1260.0000.0000.0000.000
74B74GLU-1-0.856-0.91951.673-6.007-6.0070.0000.0000.0000.000
75B75GLY0-0.024-0.00150.6670.0900.0900.0000.0000.0000.000
76B76ARG10.9530.95549.5856.0776.0770.0000.0000.0000.000
77B77ILE0-0.0170.00548.707-0.099-0.0990.0000.0000.0000.000
78B78GLN00.0540.00647.011-0.252-0.2520.0000.0000.0000.000
79B79ASP-1-0.932-0.97245.452-6.795-6.7950.0000.0000.0000.000
80B80LEU0-0.061-0.02743.281-0.200-0.2000.0000.0000.0000.000
81B81GLU-1-0.905-0.96442.841-6.842-6.8420.0000.0000.0000.000
82B82LYS10.9320.97041.5816.7996.7990.0000.0000.0000.000
83B83TYR00.0090.01237.121-0.162-0.1620.0000.0000.0000.000
84B84VAL0-0.020-0.00738.137-0.252-0.2520.0000.0000.0000.000
85B85GLU-1-0.746-0.85537.140-8.699-8.6990.0000.0000.0000.000
86B86ASP-1-0.937-0.96135.595-9.005-9.0050.0000.0000.0000.000
87B87THR00.011-0.00433.751-0.351-0.3510.0000.0000.0000.000
88B88LYS10.7980.88332.3388.3208.3200.0000.0000.0000.000
89B89ILE00.0090.00131.280-0.353-0.3530.0000.0000.0000.000
90B90ASP-1-0.848-0.90129.191-10.582-10.5820.0000.0000.0000.000
91B91LEU0-0.066-0.03927.585-0.511-0.5110.0000.0000.0000.000
92B92TRP0-0.051-0.03026.195-0.579-0.5790.0000.0000.0000.000
93B93SER0-0.001-0.00825.588-0.470-0.4700.0000.0000.0000.000
94B94TYR0-0.025-0.01021.396-0.770-0.7700.0000.0000.0000.000
95B95ASN0-0.037-0.03121.768-0.892-0.8920.0000.0000.0000.000
96B96ALA0-0.0140.00221.264-0.615-0.6150.0000.0000.0000.000
97B97GLU-1-0.917-0.95417.932-16.821-16.8210.0000.0000.0000.000
98B98LEU0-0.015-0.01116.696-1.167-1.1670.0000.0000.0000.000
99B99LEU0-0.0060.00216.355-1.108-1.1080.0000.0000.0000.000
100B100VAL00.0140.00215.697-1.212-1.2120.0000.0000.0000.000
101B101ALA00.0030.01413.056-1.785-1.7850.0000.0000.0000.000
102B102LEU0-0.021-0.02011.444-2.349-2.3490.0000.0000.0000.000
103B103GLU-1-0.824-0.90311.102-21.852-21.8520.0000.0000.0000.000
104B104ASN00.0080.01410.628-1.602-1.6020.0000.0000.0000.000
106B106HIS00.0460.0246.135-4.511-4.5110.0000.0000.0000.000
107B107THR0-0.020-0.0417.619-0.693-0.6930.0000.0000.0000.000
111B111ALA00.0350.0136.7911.5571.5570.0000.0000.0000.000
114B114GLU-1-0.868-0.9317.451-20.607-20.6070.0000.0000.0000.000
115B115MET00.0180.0297.3133.1513.1510.0000.0000.0000.000
116B116ASN00.0140.0057.3391.8211.8210.0000.0000.0000.000
117B117LYS10.8320.9069.29927.85127.8510.0000.0000.0000.000
118B118LEU0-0.0010.01012.4782.1262.1260.0000.0000.0000.000
119B119PHE00.0160.02211.7681.5861.5860.0000.0000.0000.000
120B120GLU-1-0.835-0.92313.082-20.473-20.4730.0000.0000.0000.000
121B121LYS10.8100.91315.07017.32117.3210.0000.0000.0000.000
122B122THR0-0.026-0.02216.9731.4851.4850.0000.0000.0000.000
123B123ARG10.8490.90314.50921.30921.3090.0000.0000.0000.000
124B124ARG10.8960.94216.90818.53518.5350.0000.0000.0000.000
125B125GLN0-0.0190.01221.1840.0680.0680.0000.0000.0000.000
126B126LEU00.0240.01221.0710.6070.6070.0000.0000.0000.000
127B127ARG10.8810.94523.55111.78711.7870.0000.0000.0000.000
128B128GLU-1-0.898-0.94724.445-12.229-12.2290.0000.0000.0000.000
129B129ASN0-0.011-0.02126.6850.2960.2960.0000.0000.0000.000
130B130ALA0-0.002-0.00822.8270.1270.1270.0000.0000.0000.000
131B131GLU-1-0.808-0.85222.093-12.572-12.5720.0000.0000.0000.000
132B132ASP-1-0.830-0.91115.396-20.762-20.7620.0000.0000.0000.000
133B133MET0-0.046-0.02318.0790.6960.6960.0000.0000.0000.000
134B134GLY0-0.023-0.00414.6900.1400.1400.0000.0000.0000.000
135B135ASN00.0220.00513.241-1.504-1.5040.0000.0000.0000.000
136B136GLY00.0410.02012.609-0.341-0.3410.0000.0000.0000.000
137B137CYS0-0.077-0.02313.1940.9110.9110.0000.0000.0000.000
138B138PHE00.012-0.00515.9930.1800.1800.0000.0000.0000.000
139B139LYS10.9000.95419.64912.39312.3930.0000.0000.0000.000
140B140ILE00.012-0.00423.0820.1000.1000.0000.0000.0000.000
141B141TYR0-0.051-0.04725.2350.3120.3120.0000.0000.0000.000
142B142HIS00.0390.03128.8380.0250.0250.0000.0000.0000.000
143B143LYS00.0100.01830.506-0.319-0.3190.0000.0000.0000.000
144B144CYS0-0.087-0.02428.484-0.390-0.3900.0000.0000.0000.000
145B145ASP-1-0.801-0.89930.117-9.764-9.7640.0000.0000.0000.000
146B146ASN0-0.004-0.03029.777-0.730-0.7300.0000.0000.0000.000
147B147ALA0-0.038-0.00529.843-0.278-0.2780.0000.0000.0000.000
148B149ILE00.0330.00425.199-0.473-0.4730.0000.0000.0000.000
149B150GLU-1-0.866-0.90925.640-12.314-12.3140.0000.0000.0000.000
150B151SER0-0.056-0.03226.385-0.353-0.3530.0000.0000.0000.000
151B152ILE00.006-0.00221.856-0.279-0.2790.0000.0000.0000.000
152B153ARG10.8110.90321.95812.05312.0530.0000.0000.0000.000
153B154ASN0-0.048-0.04122.750-0.382-0.3820.0000.0000.0000.000
154B155GLY0-0.036-0.02124.3500.2540.2540.0000.0000.0000.000
155B156THR0-0.024-0.01925.2030.0580.0580.0000.0000.0000.000
156B157TYR0-0.058-0.03026.2940.3040.3040.0000.0000.0000.000
157B158ASP-1-0.855-0.92228.358-9.771-9.7710.0000.0000.0000.000
158B159HIS0-0.035-0.04528.078-0.186-0.1860.0000.0000.0000.000
159B160ASP-1-0.841-0.91229.920-9.555-9.5550.0000.0000.0000.000
160B161ILE0-0.046-0.01833.6180.2020.2020.0000.0000.0000.000
161B162TYR00.0360.00830.9350.2450.2450.0000.0000.0000.000
162B163ARG10.9180.98629.87110.03510.0350.0000.0000.0000.000
163B164ASP-1-0.926-0.97033.118-8.705-8.7050.0000.0000.0000.000
164B165GLU-1-0.893-0.94234.434-9.219-9.2190.0000.0000.0000.000
165B166ALA00.0060.00329.705-0.063-0.0630.0000.0000.0000.000
166B167LEU0-0.029-0.02630.970-0.159-0.1590.0000.0000.0000.000
167B168ASN0-0.026-0.01032.8100.0660.0660.0000.0000.0000.000
168B169ASN0-0.023-0.01832.1740.1540.1540.0000.0000.0000.000
169B170ARG10.7370.85225.97611.74411.7440.0000.0000.0000.000
170B171PHE0-0.118-0.05228.964-0.245-0.2450.0000.0000.0000.000
171B172GLN-1-0.937-0.94933.523-8.774-8.7740.0000.0000.0000.000