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: 46LQN

Calculation Name: 3MW4-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG | BMA | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MW4

Chain ID: A

ChEMBL ID:

UniProt ID: Q6P9K9

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 -1834058.902797
FMO2-HF: Nuclear repulsion 1767429.863341
FMO2-HF: Total energy -66629.039457
FMO2-MP2: Total energy -66828.296111


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:79:GLY)


Summations of interaction energy for fragment #1(A:79: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.
68.81370.7825.293-3.679-3.584-0.041
Interaction energy analysis for fragmet #1(A:79:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.905
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].
3A81GLY00.0660.0493.6535.1676.2970.001-0.490-0.641-0.002
4A82SER0-0.071-0.0312.027-21.311-20.7575.290-3.031-2.814-0.038
5A83ALA00.0570.0463.7904.3864.6710.002-0.158-0.129-0.001
6A84THR00.0140.0057.059-2.038-2.0380.0000.0000.0000.000
7A85TYR00.0180.0059.2792.9552.9550.0000.0000.0000.000
8A86ILE00.0030.00612.927-0.227-0.2270.0000.0000.0000.000
9A87PHE00.0090.00414.5750.8480.8480.0000.0000.0000.000
10A88GLY00.0570.02118.5760.0390.0390.0000.0000.0000.000
11A89LYS10.9720.97921.91211.68811.6880.0000.0000.0000.000
12A90SER0-0.0070.00025.0050.2620.2620.0000.0000.0000.000
13A91GLY00.0350.03223.1520.4000.4000.0000.0000.0000.000
14A92GLY0-0.016-0.01321.7910.5400.5400.0000.0000.0000.000
15A93LEU0-0.039-0.01420.853-0.171-0.1710.0000.0000.0000.000
16A94ILE00.0010.00615.016-0.031-0.0310.0000.0000.0000.000
17A95LEU0-0.003-0.00818.870-0.141-0.1410.0000.0000.0000.000
18A96TYR00.0280.01117.887-0.166-0.1660.0000.0000.0000.000
19A97THR0-0.027-0.01620.0010.5930.5930.0000.0000.0000.000
20A98TRP00.0250.00319.824-0.410-0.4100.0000.0000.0000.000
21A99PRO00.0250.01423.3140.5880.5880.0000.0000.0000.000
22A100ALA0-0.038-0.02526.482-0.021-0.0210.0000.0000.0000.000
23A101ASN0-0.012-0.01029.1630.4230.4230.0000.0000.0000.000
24A102ASP-1-0.873-0.93424.114-12.349-12.3490.0000.0000.0000.000
25A103ARG10.8970.95524.43610.39510.3950.0000.0000.0000.000
26A104PRO0-0.0060.02221.9360.4090.4090.0000.0000.0000.000
27A105SER00.0390.02125.1450.2620.2620.0000.0000.0000.000
28A106THR0-0.043-0.03822.2620.2690.2690.0000.0000.0000.000
29A107ARG10.9780.99525.48510.70610.7060.0000.0000.0000.000
30A108SER00.0100.00822.3900.2490.2490.0000.0000.0000.000
31A109ASP-1-0.721-0.78319.708-14.469-14.4690.0000.0000.0000.000
32A110ARG10.9210.95811.59222.54622.5460.0000.0000.0000.000
33A111LEU00.0200.01914.105-0.727-0.7270.0000.0000.0000.000
34A112ALA0-0.046-0.02510.2660.2090.2090.0000.0000.0000.000
35A113VAL00.0140.0109.113-1.123-1.1230.0000.0000.0000.000
36A114GLY00.0300.0357.3731.3301.3300.0000.0000.0000.000
37A115PHE0-0.023-0.0348.3600.8500.8500.0000.0000.0000.000
38A116SER00.0410.02511.4580.3060.3060.0000.0000.0000.000
39A117THR00.024-0.01514.0660.6730.6730.0000.0000.0000.000
40A118THR00.0410.02117.7960.0390.0390.0000.0000.0000.000
41A119VAL0-0.038-0.00320.7540.8480.8480.0000.0000.0000.000
42A120LYS10.9780.97022.96211.12711.1270.0000.0000.0000.000
43A121ASP-1-0.796-0.87925.135-11.770-11.7700.0000.0000.0000.000
44A122GLY00.0410.03322.475-0.161-0.1610.0000.0000.0000.000
45A123ILE0-0.043-0.01321.347-0.373-0.3730.0000.0000.0000.000
46A124LEU0-0.030-0.00914.838-0.265-0.2650.0000.0000.0000.000
47A125VAL00.003-0.01814.992-0.738-0.7380.0000.0000.0000.000
48A126ARG10.7570.85518.30812.47512.4750.0000.0000.0000.000
49A127ILE0-0.0170.01318.555-0.152-0.1520.0000.0000.0000.000
50A128ASP-1-0.781-0.86922.342-11.545-11.5450.0000.0000.0000.000
51A129SER00.0410.00225.915-0.454-0.4540.0000.0000.0000.000
52A130ALA0-0.033-0.01528.3040.0890.0890.0000.0000.0000.000
53A131PRO00.001-0.01530.9020.1590.1590.0000.0000.0000.000
54A132GLY00.0150.01633.7390.1790.1790.0000.0000.0000.000
55A133LEU0-0.061-0.01831.5680.1740.1740.0000.0000.0000.000
56A134GLY00.0130.00433.036-0.084-0.0840.0000.0000.0000.000
57A135ASP-1-0.858-0.92628.914-10.538-10.5380.0000.0000.0000.000
58A136PHE0-0.056-0.04025.801-0.258-0.2580.0000.0000.0000.000
59A137LEU0-0.0130.00220.059-0.003-0.0030.0000.0000.0000.000
60A138GLN00.0220.01722.002-0.301-0.3010.0000.0000.0000.000
61A139LEU0-0.0060.00915.2310.1760.1760.0000.0000.0000.000
62A140HIS00.016-0.00119.731-0.119-0.1190.0000.0000.0000.000
63A141ILE00.0010.00618.267-0.166-0.1660.0000.0000.0000.000
64A142GLU-1-0.824-0.91422.300-11.149-11.1490.0000.0000.0000.000
65A143GLN0-0.010-0.01326.0150.1740.1740.0000.0000.0000.000
66A144GLY00.0070.00123.5450.0630.0630.0000.0000.0000.000
67A145LYS10.8740.93722.30310.83010.8300.0000.0000.0000.000
68A146ILE00.0020.00016.4870.2380.2380.0000.0000.0000.000
69A147GLY00.0410.01220.7980.3510.3510.0000.0000.0000.000
70A148VAL0-0.069-0.02219.246-0.608-0.6080.0000.0000.0000.000
71A149VAL0-0.0010.00922.1270.4690.4690.0000.0000.0000.000
72A150PHE00.008-0.01424.508-0.490-0.4900.0000.0000.0000.000
73A151ASN00.0030.00326.5090.4440.4440.0000.0000.0000.000
74A152ILE0-0.013-0.00827.805-0.349-0.3490.0000.0000.0000.000
75A153GLY00.0640.03930.6480.2020.2020.0000.0000.0000.000
76A154THR0-0.077-0.03933.9130.2230.2230.0000.0000.0000.000
77A155VAL0-0.001-0.00634.1430.2590.2590.0000.0000.0000.000
78A156ASP-1-0.848-0.92330.717-10.449-10.4490.0000.0000.0000.000
79A157ILE0-0.034-0.00128.1120.2000.2000.0000.0000.0000.000
80A158SER0-0.013-0.01726.765-0.610-0.6100.0000.0000.0000.000
81A159ILE0-0.0020.00522.5940.2250.2250.0000.0000.0000.000
82A160LYS10.8570.91823.32011.81011.8100.0000.0000.0000.000
83A161GLU-1-0.819-0.89420.421-13.702-13.7020.0000.0000.0000.000
84A162GLU-1-0.881-0.95722.913-10.877-10.8770.0000.0000.0000.000
85A163ARG10.9010.97025.23112.00112.0010.0000.0000.0000.000
86A164THR0-0.013-0.01021.7850.5250.5250.0000.0000.0000.000
87A165PRO0-0.034-0.02222.148-0.473-0.4730.0000.0000.0000.000
88A166VAL00.0200.00517.277-0.407-0.4070.0000.0000.0000.000
89A167ASN0-0.088-0.02318.080-0.777-0.7770.0000.0000.0000.000
90A168ASP-1-0.801-0.90118.219-16.460-16.4600.0000.0000.0000.000
91A169GLY0-0.009-0.00918.4360.1840.1840.0000.0000.0000.000
92A170LYS10.9050.96615.40415.30415.3040.0000.0000.0000.000
93A171TYR0-0.028-0.0166.075-1.604-1.6040.0000.0000.0000.000
94A172HIS10.8120.88111.64620.76820.7680.0000.0000.0000.000
95A173VAL0-0.047-0.0247.755-2.913-2.9130.0000.0000.0000.000
96A174VAL0-0.0050.01910.4882.1472.1470.0000.0000.0000.000
97A175ARG10.9200.9488.21727.41027.4100.0000.0000.0000.000
98A176PHE00.0630.03014.1081.1271.1270.0000.0000.0000.000
99A177THR0-0.070-0.04616.716-0.766-0.7660.0000.0000.0000.000
100A178ARG10.7990.88219.29213.19313.1930.0000.0000.0000.000
101A179ASN0-0.017-0.03022.058-0.194-0.1940.0000.0000.0000.000
102A180GLY00.0090.01025.2770.4590.4590.0000.0000.0000.000
103A181ALA00.0610.03127.663-0.299-0.2990.0000.0000.0000.000
104A182ASN00.0000.00527.0580.1810.1810.0000.0000.0000.000
105A183ALA0-0.016-0.01223.445-0.410-0.4100.0000.0000.0000.000
106A184THR00.0100.01420.2600.1410.1410.0000.0000.0000.000
107A185LEU0-0.006-0.00218.012-0.693-0.6930.0000.0000.0000.000
108A186GLN0-0.023-0.01615.627-0.265-0.2650.0000.0000.0000.000
109A187VAL00.0270.00914.930-1.044-1.0440.0000.0000.0000.000
110A188ASP-1-0.799-0.88912.583-22.250-22.2500.0000.0000.0000.000
111A189ASN0-0.039-0.02513.672-0.577-0.5770.0000.0000.0000.000
112A190TRP00.0040.00916.0201.1141.1140.0000.0000.0000.000
113A191PRO00.010-0.00819.183-0.356-0.3560.0000.0000.0000.000
114A192VAL0-0.025-0.00119.060-0.204-0.2040.0000.0000.0000.000
115A193ASN0-0.025-0.00621.4531.2301.2300.0000.0000.0000.000
116A194GLU-1-0.872-0.94122.869-12.351-12.3510.0000.0000.0000.000
117A195HIS00.002-0.00225.4440.3980.3980.0000.0000.0000.000
118A196TYR0-0.019-0.02826.820-0.287-0.2870.0000.0000.0000.000
119A197PRO0-0.033-0.00229.9330.3920.3920.0000.0000.0000.000
120A198THR00.0390.02433.1610.0450.0450.0000.0000.0000.000
121A199GLY00.0180.01436.6210.0430.0430.0000.0000.0000.000
122A200ARG10.9220.95337.6937.4137.4130.0000.0000.0000.000
123A201GLN00.0270.01033.563-0.162-0.1620.0000.0000.0000.000
124A202LEU00.0040.01933.7720.1020.1020.0000.0000.0000.000
125A203THR0-0.013-0.02830.253-0.289-0.2890.0000.0000.0000.000
126A204ILE0-0.027-0.02028.727-0.453-0.4530.0000.0000.0000.000
127A205PHE00.0210.03522.8250.2360.2360.0000.0000.0000.000
128A206ASN00.0350.00927.256-0.429-0.4290.0000.0000.0000.000
129A207THR0-0.006-0.00728.462-0.018-0.0180.0000.0000.0000.000
130A208GLN00.0260.02722.446-0.523-0.5230.0000.0000.0000.000
131A209ALA0-0.012-0.01725.568-0.036-0.0360.0000.0000.0000.000
132A210GLN0-0.015-0.01023.1330.0310.0310.0000.0000.0000.000
133A211ILE00.001-0.00316.945-0.174-0.1740.0000.0000.0000.000
134A212ALA00.0280.03119.816-0.307-0.3070.0000.0000.0000.000
135A213ILE0-0.013-0.01614.556-0.597-0.5970.0000.0000.0000.000
136A214GLY00.0550.01418.3050.2490.2490.0000.0000.0000.000
137A215GLY00.0540.02719.4960.5370.5370.0000.0000.0000.000
138A216LYS10.8450.91322.78712.47412.4740.0000.0000.0000.000
139A217ASP-1-0.894-0.95524.733-12.374-12.3740.0000.0000.0000.000
140A218LYS10.9150.96126.27011.73311.7330.0000.0000.0000.000
141A219GLY0-0.0030.00728.0350.2330.2330.0000.0000.0000.000
142A220ARG10.7920.87125.62312.15612.1560.0000.0000.0000.000
143A221LEU0-0.019-0.00723.644-0.584-0.5840.0000.0000.0000.000
144A222PHE00.0080.00715.3800.1190.1190.0000.0000.0000.000
145A223GLN0-0.002-0.01519.9880.3660.3660.0000.0000.0000.000
146A224GLY0-0.0120.01717.0110.1090.1090.0000.0000.0000.000
147A225GLN0-0.009-0.0049.0791.9061.9060.0000.0000.0000.000
148A226LEU00.0030.00011.1250.0340.0340.0000.0000.0000.000
149A227SER0-0.015-0.0285.746-3.578-3.5780.0000.0000.0000.000
150A228GLY0-0.003-0.0045.299-0.766-0.7660.0000.0000.0000.000
151A229LEU0-0.033-0.0056.1290.4090.4090.0000.0000.0000.000
152A230TYR0-0.059-0.0209.104-0.149-0.1490.0000.0000.0000.000
153A231TYR00.038-0.02310.7450.7560.7560.0000.0000.0000.000
154A232ASP0-0.030-0.04914.5550.0220.0220.0000.0000.0000.000
155A233GLY00.0090.01213.4020.8490.8490.0000.0000.0000.000
156A234LEU00.0040.01012.927-1.341-1.3410.0000.0000.0000.000
157A235LYS10.9650.9777.06336.58336.5830.0000.0000.0000.000
158A236VAL00.0660.02510.397-0.484-0.4840.0000.0000.0000.000
159A237LEU00.0070.0129.2970.9910.9910.0000.0000.0000.000
160A238ASN0-0.006-0.0166.058-2.327-2.3270.0000.0000.0000.000
161A239MET00.0400.0269.8161.3171.3170.0000.0000.0000.000
162A240ALA0-0.011-0.00113.2621.5051.5050.0000.0000.0000.000
163A241ALA0-0.021-0.00611.1880.9960.9960.0000.0000.0000.000
164A242GLU-1-0.965-0.98011.345-24.898-24.8980.0000.0000.0000.000
165A243ASN0-0.059-0.01914.7221.5001.5000.0000.0000.0000.000
166A244ASN00.0520.02716.8411.7021.7020.0000.0000.0000.000
167A245PRO00.0410.01218.6060.0890.0890.0000.0000.0000.000
168A246ASN0-0.051-0.02421.1411.1461.1460.0000.0000.0000.000
169A247ILE0-0.043-0.01716.490-0.129-0.1290.0000.0000.0000.000
170A248LYS10.9410.97620.07012.47212.4720.0000.0000.0000.000
171A249ILE00.0390.01417.286-0.552-0.5520.0000.0000.0000.000
172A250ASN0-0.028-0.00921.2600.4180.4180.0000.0000.0000.000
173A251GLY00.0530.02923.068-0.331-0.3310.0000.0000.0000.000
174A252SER0-0.062-0.03723.237-0.325-0.3250.0000.0000.0000.000
175A253VAL0-0.001-0.00517.190-0.377-0.3770.0000.0000.0000.000
176A254ARG10.9250.97217.47117.06217.0620.0000.0000.0000.000
177A255LEU00.0180.01711.372-0.772-0.7720.0000.0000.0000.000
178A256VAL-1-0.921-0.96810.719-27.561-27.5610.0000.0000.0000.000