FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: KVLR3

Calculation Name: 3WH1-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | 1,2-ethanediol

Ligand 3-letter code: NAG | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3WH1

Chain ID: A

ChEMBL ID:

UniProt ID: A9ZSX9

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2348386.640516
FMO2-HF: Nuclear repulsion 2268340.769886
FMO2-HF: Total energy -80045.87063
FMO2-MP2: Total energy -80276.449673


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-143.452-141.47810.966-6.313-6.628-0.033
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.904
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].
3A4THR0-0.0080.0171.825-16.786-16.69510.853-5.587-5.357-0.030
4A5SER0-0.090-0.0473.2749.55710.6880.022-0.422-0.732-0.001
5A6PHE00.0240.0154.7715.7585.933-0.001-0.023-0.1510.000
39A40THR0-0.140-0.1072.900-12.338-11.8180.093-0.249-0.364-0.002
46A47GLN0-0.054-0.0144.238-9.219-9.162-0.001-0.032-0.0240.000
6A7VAL00.0350.0287.0554.6494.6490.0000.0000.0000.000
7A8THR00.0500.0396.940-1.672-1.6720.0000.0000.0000.000
8A9PRO00.0380.0058.3111.6741.6740.0000.0000.0000.000
9A10ALA00.0120.00611.0031.3961.3960.0000.0000.0000.000
10A11VAL0-0.0210.00911.2261.2581.2580.0000.0000.0000.000
11A12PHE00.0170.00111.0440.8830.8830.0000.0000.0000.000
12A13GLU-1-0.816-0.88113.020-15.010-15.0100.0000.0000.0000.000
13A14GLY0-0.025-0.01415.9410.9910.9910.0000.0000.0000.000
14A15TRP0-0.048-0.03111.911-0.084-0.0840.0000.0000.0000.000
15A16PHE0-0.027-0.01114.3930.6900.6900.0000.0000.0000.000
16A17PRO00.0080.01218.6940.1920.1920.0000.0000.0000.000
17A18ASN0-0.045-0.02720.9530.6290.6290.0000.0000.0000.000
18A19ARG10.7900.87417.20815.79315.7930.0000.0000.0000.000
19A20ASN00.009-0.00321.2700.2010.2010.0000.0000.0000.000
20A21PRO0-0.003-0.01120.686-0.595-0.5950.0000.0000.0000.000
21A22PHE0-0.0270.00020.287-0.479-0.4790.0000.0000.0000.000
22A23TYR0-0.013-0.03116.986-0.707-0.7070.0000.0000.0000.000
23A24THR00.0210.00414.583-0.200-0.2000.0000.0000.0000.000
24A25TYR00.001-0.0286.244-0.954-0.9540.0000.0000.0000.000
25A26ASP-1-0.843-0.9359.648-23.534-23.5340.0000.0000.0000.000
26A27GLY0-0.0080.01610.638-0.473-0.4730.0000.0000.0000.000
27A28LEU0-0.0090.0098.850-0.058-0.0580.0000.0000.0000.000
28A29VAL0-0.003-0.0085.041-1.101-1.1010.0000.0000.0000.000
29A30SER0-0.035-0.0297.401-0.780-0.7800.0000.0000.0000.000
30A31ALA0-0.020-0.00810.1500.4540.4540.0000.0000.0000.000
31A32SER0-0.044-0.0356.669-0.806-0.8060.0000.0000.0000.000
32A33ASN0-0.010-0.0086.915-3.507-3.5070.0000.0000.0000.000
33A34GLY0-0.040-0.0088.8170.6070.6070.0000.0000.0000.000
34A35TYR0-0.029-0.01810.2931.9671.9670.0000.0000.0000.000
35A36PRO00.0450.0357.336-2.219-2.2190.0000.0000.0000.000
36A37GLU-1-0.861-0.9176.568-29.362-29.3620.0000.0000.0000.000
37A38PHE00.0080.0037.579-0.901-0.9010.0000.0000.0000.000
38A39GLY0-0.026-0.0275.658-3.805-3.8050.0000.0000.0000.000
40A41THR0-0.010-0.0065.4082.7452.7450.0000.0000.0000.000
41A42GLY00.0420.0299.151-0.041-0.0410.0000.0000.0000.000
42A43SER0-0.057-0.0558.581-3.399-3.3990.0000.0000.0000.000
43A44LEU00.010-0.0065.632-1.446-1.4460.0000.0000.0000.000
44A45ASP-1-0.845-0.9397.749-25.416-25.4160.0000.0000.0000.000
45A46ASP-1-0.756-0.83910.566-21.985-21.9850.0000.0000.0000.000
47A48LYS10.8490.9267.91628.05728.0570.0000.0000.0000.000
48A49ARG10.8740.9199.89022.27222.2720.0000.0000.0000.000
49A50GLU-1-0.687-0.8249.617-25.092-25.0920.0000.0000.0000.000
50A51LEU0-0.027-0.0147.1161.5301.5300.0000.0000.0000.000
51A52ALA00.0190.01010.7641.7561.7560.0000.0000.0000.000
52A53ALA00.0090.00414.1101.6211.6210.0000.0000.0000.000
53A54PHE00.0040.00012.1691.1381.1380.0000.0000.0000.000
54A55LEU0-0.003-0.00910.9901.1861.1860.0000.0000.0000.000
55A56GLY00.0550.02615.2141.0461.0460.0000.0000.0000.000
56A57ASN0-0.021-0.02618.2661.8061.8060.0000.0000.0000.000
57A58ILE00.0000.01115.2670.8080.8080.0000.0000.0000.000
58A59ASN0-0.0580.00019.1410.5870.5870.0000.0000.0000.000
59A60GLN00.0320.01320.6910.6060.6060.0000.0000.0000.000
60A61ALA0-0.048-0.00921.9530.5260.5260.0000.0000.0000.000
61A62SER00.002-0.02120.7240.3770.3770.0000.0000.0000.000
62A63GLY00.0180.01523.0990.2490.2490.0000.0000.0000.000
63A64GLY00.0300.01320.8510.1940.1940.0000.0000.0000.000
64A65LEU0-0.048-0.02716.028-0.171-0.1710.0000.0000.0000.000
65A66GLN0-0.026-0.00120.7560.4310.4310.0000.0000.0000.000
66A67PHE0-0.029-0.01324.3250.3460.3460.0000.0000.0000.000
67A68ILE0-0.0200.02023.336-0.467-0.4670.0000.0000.0000.000
68A69GLN00.0150.00524.747-0.018-0.0180.0000.0000.0000.000
69A70GLU-1-0.729-0.81827.838-9.662-9.6620.0000.0000.0000.000
70A71GLN0-0.087-0.05329.7680.4310.4310.0000.0000.0000.000
71A72ASN0-0.069-0.04132.5570.0270.0270.0000.0000.0000.000
72A73PRO00.0750.05233.1310.0970.0970.0000.0000.0000.000
73A74GLN0-0.040-0.01735.1960.0520.0520.0000.0000.0000.000
74A75SER0-0.016-0.02136.1240.2350.2350.0000.0000.0000.000
75A76ASP-1-0.800-0.90636.906-8.070-8.0700.0000.0000.0000.000
76A77TYR0-0.072-0.05132.408-0.134-0.1340.0000.0000.0000.000
77A78CYS0-0.038-0.03234.282-0.432-0.4320.0000.0000.0000.000
78A79ASP-1-0.798-0.88335.587-8.165-8.1650.0000.0000.0000.000
79A80THR0-0.010-0.02537.386-0.075-0.0750.0000.0000.0000.000
80A81SER0-0.088-0.05638.7610.1310.1310.0000.0000.0000.000
81A82SER0-0.0060.00433.694-0.019-0.0190.0000.0000.0000.000
82A83THR0-0.013-0.02436.290-0.171-0.1710.0000.0000.0000.000
83A84GLN0-0.039-0.00531.3930.0600.0600.0000.0000.0000.000
84A85TYR00.0170.00929.092-0.139-0.1390.0000.0000.0000.000
85A86PRO00.0140.01934.0750.0080.0080.0000.0000.0000.000
86A88ALA00.0350.02836.1340.2210.2210.0000.0000.0000.000
87A89ALA0-0.007-0.01737.8650.0110.0110.0000.0000.0000.000
88A90GLY0-0.015-0.00840.041-0.017-0.0170.0000.0000.0000.000
89A91LYS10.7940.91333.8328.6918.6910.0000.0000.0000.000
90A92GLN00.0300.02634.7090.1370.1370.0000.0000.0000.000
91A93TYR0-0.039-0.03530.697-0.188-0.1880.0000.0000.0000.000
92A94TYR00.019-0.00129.994-0.099-0.0990.0000.0000.0000.000
93A95GLY00.0280.01327.254-0.257-0.2570.0000.0000.0000.000
94A96ARG10.7710.86125.17510.29510.2950.0000.0000.0000.000
95A97GLY00.0470.02921.270-0.388-0.3880.0000.0000.0000.000
96A98PRO0-0.028-0.00916.7170.3520.3520.0000.0000.0000.000
97A99ILE00.028-0.00518.3560.0360.0360.0000.0000.0000.000
98A100GLN0-0.043-0.00820.7180.8360.8360.0000.0000.0000.000
99A101LEU00.0110.02222.3080.2880.2880.0000.0000.0000.000
100A102SER00.022-0.00724.5000.4710.4710.0000.0000.0000.000
101A103TRP00.0120.00728.210-0.056-0.0560.0000.0000.0000.000
102A104ASN00.0220.01329.776-0.409-0.4090.0000.0000.0000.000
103A105TYR00.0140.00529.413-0.270-0.2700.0000.0000.0000.000
104A106ASN0-0.002-0.00725.690-0.434-0.4340.0000.0000.0000.000
105A107TYR0-0.027-0.00825.860-0.430-0.4300.0000.0000.0000.000
106A108GLY00.001-0.00527.059-0.166-0.1660.0000.0000.0000.000
107A109GLU-1-0.825-0.86525.010-11.970-11.9700.0000.0000.0000.000
108A110ALA00.0450.02522.551-0.336-0.3360.0000.0000.0000.000
109A111GLY0-0.010-0.01423.297-0.343-0.3430.0000.0000.0000.000
110A112ALA0-0.037-0.01925.608-0.045-0.0450.0000.0000.0000.000
111A113ASP-1-0.802-0.86521.004-13.313-13.3130.0000.0000.0000.000
112A114LEU0-0.079-0.03418.301-0.665-0.6650.0000.0000.0000.000
113A115GLY00.0190.02621.358-0.253-0.2530.0000.0000.0000.000
114A116LEU0-0.061-0.04021.2390.0260.0260.0000.0000.0000.000
115A117ASP-1-0.830-0.91325.571-9.348-9.3480.0000.0000.0000.000
116A118LEU0-0.035-0.02423.2400.2400.2400.0000.0000.0000.000
117A119LEU00.0190.01727.9640.0430.0430.0000.0000.0000.000
118A120ASN0-0.017-0.01031.2890.4300.4300.0000.0000.0000.000
119A121ASN00.005-0.00730.3650.3480.3480.0000.0000.0000.000
120A122PRO00.0530.03428.597-0.365-0.3650.0000.0000.0000.000
121A123ASP-1-0.821-0.90927.774-9.675-9.6750.0000.0000.0000.000
122A124LEU00.0150.01125.293-0.246-0.2460.0000.0000.0000.000
123A125VAL0-0.024-0.01222.278-0.404-0.4040.0000.0000.0000.000
124A126ALA0-0.019-0.02023.116-0.400-0.4000.0000.0000.0000.000
125A127GLN0-0.063-0.02425.1600.1540.1540.0000.0000.0000.000
126A128ASP-1-0.821-0.91220.354-13.645-13.6450.0000.0000.0000.000
127A129SER00.0200.00818.070-0.262-0.2620.0000.0000.0000.000
128A130THR0-0.006-0.00815.545-1.155-1.1550.0000.0000.0000.000
129A131VAL0-0.029-0.00716.994-0.649-0.6490.0000.0000.0000.000
130A132ALA00.0100.02318.928-0.190-0.1900.0000.0000.0000.000
131A133TRP00.007-0.00613.522-0.501-0.5010.0000.0000.0000.000
132A134ARG10.9020.94015.11514.96914.9690.0000.0000.0000.000
133A135THR00.001-0.01316.175-0.027-0.0270.0000.0000.0000.000
134A136ALA0-0.0020.00416.1270.1620.1620.0000.0000.0000.000
135A137LEU0-0.018-0.00710.925-0.133-0.1330.0000.0000.0000.000
136A138TRP0-0.038-0.02414.759-0.114-0.1140.0000.0000.0000.000
137A139PHE00.0010.00617.6710.1200.1200.0000.0000.0000.000
138A140TRP0-0.010-0.03113.1020.8280.8280.0000.0000.0000.000
139A141MET0-0.033-0.01311.883-0.520-0.5200.0000.0000.0000.000
140A142LYS10.7990.87315.92113.29913.2990.0000.0000.0000.000
141A143ARG10.7700.85119.57612.79212.7920.0000.0000.0000.000
142A144ASP-1-0.823-0.90817.585-16.204-16.2040.0000.0000.0000.000
143A145CYS0-0.043-0.00617.1200.3720.3720.0000.0000.0000.000
144A146HIS10.8280.90210.07924.02024.0200.0000.0000.0000.000
145A147GLY00.0310.03214.652-0.957-0.9570.0000.0000.0000.000
146A148ALA0-0.045-0.01516.9650.1420.1420.0000.0000.0000.000
147A149ILE0-0.031-0.01613.3560.2220.2220.0000.0000.0000.000
148A150THR0-0.088-0.06310.959-0.614-0.6140.0000.0000.0000.000
149A151ALA00.0030.02314.095-0.239-0.2390.0000.0000.0000.000
150A152SER0-0.030-0.00716.416-0.569-0.5690.0000.0000.0000.000
151A153PRO0-0.045-0.03918.7410.5740.5740.0000.0000.0000.000
152A154PRO00.0180.02416.6990.2140.2140.0000.0000.0000.000
153A155SER0-0.029-0.05318.7450.8040.8040.0000.0000.0000.000
154A156PHE00.0020.00918.372-0.324-0.3240.0000.0000.0000.000
155A157SER0-0.012-0.03120.4430.0310.0310.0000.0000.0000.000
156A158GLY00.0130.00522.6090.4060.4060.0000.0000.0000.000
157A159THR0-0.035-0.03417.6520.1110.1110.0000.0000.0000.000
158A160ILE00.0250.00820.8850.2410.2410.0000.0000.0000.000
159A161ARG10.8890.91824.03712.08612.0860.0000.0000.0000.000
160A162ILE0-0.051-0.01321.3090.4540.4540.0000.0000.0000.000
161A163ILE0-0.039-0.01819.6160.0940.0940.0000.0000.0000.000
162A164ASN0-0.010-0.03124.0660.4800.4800.0000.0000.0000.000
163A165GLY00.0440.01827.6950.3380.3380.0000.0000.0000.000
164A166GLY0-0.049-0.01829.2470.2550.2550.0000.0000.0000.000
165A167LEU0-0.031-0.01631.5790.3530.3530.0000.0000.0000.000
166A168GLU-1-0.760-0.83927.781-11.273-11.2730.0000.0000.0000.000
167A205CYS-1-0.919-0.91827.567-10.363-10.3630.0000.0000.0000.000
168A170ASN0-0.060-0.04731.1450.3550.3550.0000.0000.0000.000
169A171GLN0-0.0530.00133.6370.5160.5160.0000.0000.0000.000
170A172PRO00.000-0.00635.945-0.038-0.0380.0000.0000.0000.000
171A173ALA00.0310.02336.856-0.159-0.1590.0000.0000.0000.000
172A174GLY0-0.006-0.00136.5810.2330.2330.0000.0000.0000.000
173A175SER0-0.044-0.03437.1280.0670.0670.0000.0000.0000.000
174A176ILE00.0420.00234.292-0.216-0.2160.0000.0000.0000.000
175A177GLY00.0820.04532.690-0.268-0.2680.0000.0000.0000.000
176A178ASN00.0230.01631.521-0.205-0.2050.0000.0000.0000.000
177A179MET0-0.009-0.01031.531-0.183-0.1830.0000.0000.0000.000
178A180GLN0-0.0180.00628.894-0.334-0.3340.0000.0000.0000.000
179A181MET0-0.0040.03427.242-0.692-0.6920.0000.0000.0000.000
180A182GLU-1-0.715-0.84526.630-11.259-11.2590.0000.0000.0000.000
181A183ASN0-0.055-0.00926.559-0.235-0.2350.0000.0000.0000.000
182A184ARG10.7780.85022.69112.07012.0700.0000.0000.0000.000
183A185VAL00.0030.00522.195-0.770-0.7700.0000.0000.0000.000
184A186THR0-0.030-0.00423.109-0.414-0.4140.0000.0000.0000.000
185A187TYR0-0.005-0.00320.594-0.355-0.3550.0000.0000.0000.000
186A188TYR0-0.010-0.01415.919-1.180-1.1800.0000.0000.0000.000
187A189THR0-0.019-0.02818.480-0.744-0.7440.0000.0000.0000.000
188A190GLN00.0280.01620.232-0.634-0.6340.0000.0000.0000.000
189A191PHE0-0.028-0.00115.456-0.536-0.5360.0000.0000.0000.000
190A192CYS0-0.024-0.01415.482-1.620-1.6200.0000.0000.0000.000
191A193GLN0-0.006-0.00416.319-0.532-0.5320.0000.0000.0000.000
192A194THR0-0.057-0.03415.146-0.011-0.0110.0000.0000.0000.000
193A195LEU0-0.042-0.01010.592-1.073-1.0730.0000.0000.0000.000
194A196GLY0-0.0160.00213.016-1.469-1.4690.0000.0000.0000.000
195A197VAL0-0.075-0.03113.016-0.530-0.5300.0000.0000.0000.000
196A198ASP-1-0.865-0.92715.324-14.416-14.4160.0000.0000.0000.000
197A199PRO00.0330.01516.986-0.962-0.9620.0000.0000.0000.000
198A200GLY00.0360.03318.828-0.143-0.1430.0000.0000.0000.000
199A201THR0-0.003-0.02520.8270.2140.2140.0000.0000.0000.000
200A202ASP-1-0.798-0.82823.355-12.031-12.0310.0000.0000.0000.000
201A203LEU0-0.031-0.01421.983-0.424-0.4240.0000.0000.0000.000
202A204ARG10.8530.85724.52010.86710.8670.0000.0000.0000.000