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: LQRM9

Calculation Name: 1DE4-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG | GOL | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DE4

Chain ID: A

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2025-09-02

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 270
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3659429.238943
FMO2-HF: Nuclear repulsion 3546598.715983
FMO2-HF: Total energy -112830.52296
FMO2-MP2: Total energy -113157.390861


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:4:ARG)


Summations of interaction energy for fragment #1(A:4:ARG)
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.
-539.127-541.47134.929-16.123-16.46-0.167
Interaction energy analysis for fragmet #1(A:4:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.654 / q_NPA : 1.804
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].
3A6HIS00.0160.0263.825-1.9120.004-0.018-0.699-1.198-0.001
102A105GLN00.019-0.0085.039-21.483-21.412-0.001-0.018-0.0520.000
103A106GLU-1-0.834-0.9141.783-224.492-229.39834.947-15.275-14.765-0.166
104A107ASP-1-0.881-0.9244.066-72.956-72.3810.001-0.131-0.4450.000
4A7SER00.000-0.0076.4804.3744.3740.0000.0000.0000.000
5A8LEU0-0.0150.00310.0861.2511.2510.0000.0000.0000.000
6A9HIS10.8240.89513.02538.28038.2800.0000.0000.0000.000
7A10TYR0-0.004-0.01416.2530.6170.6170.0000.0000.0000.000
8A11LEU0-0.025-0.00618.487-0.231-0.2310.0000.0000.0000.000
9A12PHE00.016-0.00622.0250.4540.4540.0000.0000.0000.000
10A13MET0-0.043-0.01725.829-0.324-0.3240.0000.0000.0000.000
11A14GLY00.1110.06428.6340.2320.2320.0000.0000.0000.000
12A15ALA0-0.025-0.02132.416-0.094-0.0940.0000.0000.0000.000
13A16SER00.013-0.00335.7200.0090.0090.0000.0000.0000.000
14A17GLU-1-0.901-0.92139.114-13.936-13.9360.0000.0000.0000.000
15A18GLN0-0.051-0.03438.2460.1170.1170.0000.0000.0000.000
16A19ASP-1-0.749-0.88637.746-16.479-16.4790.0000.0000.0000.000
17A20LEU0-0.117-0.05740.8080.4620.4620.0000.0000.0000.000
18A21GLY0-0.029-0.01141.5730.3290.3290.0000.0000.0000.000
19A22LEU0-0.053-0.03440.071-0.166-0.1660.0000.0000.0000.000
20A23SER0-0.051-0.04834.868-0.061-0.0610.0000.0000.0000.000
21A24LEU00.0280.01835.2540.0140.0140.0000.0000.0000.000
22A25PHE0-0.062-0.03829.210-0.158-0.1580.0000.0000.0000.000
23A26GLU-1-0.859-0.91928.974-19.429-19.4290.0000.0000.0000.000
24A27ALA0-0.056-0.04625.055-0.491-0.4910.0000.0000.0000.000
25A28LEU0-0.0090.00221.7030.1220.1220.0000.0000.0000.000
26A29GLY00.009-0.00819.530-0.724-0.7240.0000.0000.0000.000
27A30TYR0-0.005-0.01715.0470.4730.4730.0000.0000.0000.000
28A31VAL00.0230.00211.145-0.479-0.4790.0000.0000.0000.000
29A32ASP-1-0.819-0.9287.848-60.080-60.0800.0000.0000.0000.000
30A33ASP-1-0.896-0.9299.844-42.580-42.5800.0000.0000.0000.000
31A34GLN0-0.004-0.00212.8304.2614.2610.0000.0000.0000.000
32A35LEU0-0.041-0.00914.694-0.036-0.0360.0000.0000.0000.000
33A36PHE0-0.010-0.00816.5480.7840.7840.0000.0000.0000.000
34A37VAL0-0.027-0.01519.0791.1991.1990.0000.0000.0000.000
35A38PHE0-0.0050.00022.271-0.705-0.7050.0000.0000.0000.000
36A39TYR0-0.111-0.07725.3000.3940.3940.0000.0000.0000.000
37A40ASP-1-0.776-0.88128.280-18.505-18.5050.0000.0000.0000.000
38A41HIS00.0810.03031.417-0.314-0.3140.0000.0000.0000.000
39A42GLU-1-0.935-0.96534.691-16.198-16.1980.0000.0000.0000.000
40A43SER0-0.107-0.06335.741-0.247-0.2470.0000.0000.0000.000
41A44ARG10.8690.95233.00117.72317.7230.0000.0000.0000.000
42A45ARG10.8300.91032.15917.55717.5570.0000.0000.0000.000
43A46VAL0-0.008-0.00426.185-0.354-0.3540.0000.0000.0000.000
44A47GLU-1-0.820-0.89127.673-19.137-19.1370.0000.0000.0000.000
45A48PRO00.002-0.00323.767-0.826-0.8260.0000.0000.0000.000
46A49ARG10.8180.90021.41223.01523.0150.0000.0000.0000.000
47A50THR00.0780.02317.593-0.357-0.3570.0000.0000.0000.000
48A51PRO00.0140.00120.7600.1120.1120.0000.0000.0000.000
49A52TRP00.0300.02614.5000.9980.9980.0000.0000.0000.000
50A53VAL00.0410.02718.1100.0680.0680.0000.0000.0000.000
51A54SER0-0.040-0.02220.5330.9040.9040.0000.0000.0000.000
52A55SER0-0.070-0.05222.8050.7100.7100.0000.0000.0000.000
53A56ARG10.8490.92115.86632.42832.4280.0000.0000.0000.000
54A57ILE00.0000.01819.441-0.287-0.2870.0000.0000.0000.000
55A58SER00.0320.01822.3401.1551.1550.0000.0000.0000.000
56A59SER00.032-0.00225.141-0.162-0.1620.0000.0000.0000.000
57A60GLN00.0040.00524.813-0.580-0.5800.0000.0000.0000.000
58A61MET00.0300.02220.245-0.273-0.2730.0000.0000.0000.000
59A62TRP00.0560.02922.365-0.705-0.7050.0000.0000.0000.000
60A63LEU0-0.0110.01325.6270.4450.4450.0000.0000.0000.000
61A64GLN00.009-0.01024.4250.7170.7170.0000.0000.0000.000
62A65LEU00.0170.03121.2090.0350.0350.0000.0000.0000.000
63A66SER00.003-0.01724.5200.4820.4820.0000.0000.0000.000
64A67GLN0-0.070-0.03227.9810.3010.3010.0000.0000.0000.000
65A68SER0-0.011-0.01324.8760.3140.3140.0000.0000.0000.000
66A69LEU0-0.0020.00023.2430.2130.2130.0000.0000.0000.000
67A70LYS10.9280.97727.04219.67219.6720.0000.0000.0000.000
68A71GLY0-0.0040.00430.0850.5190.5190.0000.0000.0000.000
69A72TRP00.018-0.00622.0150.2790.2790.0000.0000.0000.000
70A73ASP-1-0.722-0.79728.792-18.200-18.2000.0000.0000.0000.000
71A74HIS0-0.045-0.01231.2320.8080.8080.0000.0000.0000.000
72A75MET0-0.057-0.01728.5410.2510.2510.0000.0000.0000.000
73A76PHE00.010-0.01525.8590.2200.2200.0000.0000.0000.000
74A77THR00.0330.01231.5350.4120.4120.0000.0000.0000.000
75A78VAL00.0000.00935.0190.4690.4690.0000.0000.0000.000
76A79ASP-1-0.773-0.84831.026-19.228-19.2280.0000.0000.0000.000
77A80PHE0-0.032-0.01633.8920.1660.1660.0000.0000.0000.000
78A81TRP00.009-0.00735.1690.3090.3090.0000.0000.0000.000
79A82THR0-0.036-0.02336.4690.3700.3700.0000.0000.0000.000
80A83ILE0-0.046-0.02632.3830.2140.2140.0000.0000.0000.000
81A84MET0-0.060-0.01536.8200.1730.1730.0000.0000.0000.000
82A85GLU-1-0.926-0.94939.499-13.739-13.7390.0000.0000.0000.000
83A86ASN00.012-0.01338.2820.5650.5650.0000.0000.0000.000
84A87HIS10.7580.88635.94716.49616.4960.0000.0000.0000.000
85A88ASN0-0.063-0.03741.2150.4110.4110.0000.0000.0000.000
86A89HIS0-0.0200.01839.373-0.019-0.0190.0000.0000.0000.000
87A90SER00.0560.00843.0650.0180.0180.0000.0000.0000.000
88A91LYS10.8910.95244.66511.94811.9480.0000.0000.0000.000
89A92GLU-1-0.857-0.92442.765-13.914-13.9140.0000.0000.0000.000
90A93SER0-0.013-0.01340.521-0.151-0.1510.0000.0000.0000.000
91A94HIS10.7590.85537.19115.44715.4470.0000.0000.0000.000
92A95THR00.023-0.00232.436-0.228-0.2280.0000.0000.0000.000
93A96LEU0-0.040-0.00130.161-0.019-0.0190.0000.0000.0000.000
94A97GLN00.0060.01126.355-0.691-0.6910.0000.0000.0000.000
95A98VAL0-0.014-0.00824.3950.0390.0390.0000.0000.0000.000
96A99ILE0-0.0110.00417.489-0.363-0.3630.0000.0000.0000.000
97A100LEU0-0.0130.00119.902-0.041-0.0410.0000.0000.0000.000
98A101GLY00.008-0.01116.206-0.132-0.1320.0000.0000.0000.000
99A102CYS0-0.0330.00913.9540.1320.1320.0000.0000.0000.000
100A103GLU-1-0.845-0.9237.377-64.290-64.2900.0000.0000.0000.000
101A104MET0-0.0420.0107.6860.6710.6710.0000.0000.0000.000
105A108ASN0-0.064-0.0486.00514.49814.4980.0000.0000.0000.000
106A109SER0-0.043-0.0208.4346.2816.2810.0000.0000.0000.000
107A110THR0-0.037-0.0399.675-5.136-5.1360.0000.0000.0000.000
108A111GLU-1-0.862-0.90811.160-37.238-37.2380.0000.0000.0000.000
109A112GLY0-0.007-0.01212.827-0.512-0.5120.0000.0000.0000.000
110A113TYR0-0.021-0.01212.9292.6862.6860.0000.0000.0000.000
111A114TRP00.051-0.00418.218-0.024-0.0240.0000.0000.0000.000
112A115LYS10.8820.94619.37529.39529.3950.0000.0000.0000.000
113A116TYR0-0.034-0.03723.541-0.287-0.2870.0000.0000.0000.000
114A117GLY00.0440.01226.9290.0380.0380.0000.0000.0000.000
115A118TYR00.013-0.02427.9930.2380.2380.0000.0000.0000.000
116A119ASP-1-0.826-0.90431.779-16.708-16.7080.0000.0000.0000.000
117A120GLY00.0010.00829.3290.1580.1580.0000.0000.0000.000
118A121GLN0-0.043-0.01628.944-0.353-0.3530.0000.0000.0000.000
119A122ASP-1-0.890-0.94224.820-24.019-24.0190.0000.0000.0000.000
120A123HIS0-0.012-0.00327.6821.2261.2260.0000.0000.0000.000
121A124LEU0-0.052-0.03428.2240.4200.4200.0000.0000.0000.000
122A125GLU-1-0.825-0.90321.244-27.892-27.8920.0000.0000.0000.000
123A126PHE0-0.035-0.02122.5570.7430.7430.0000.0000.0000.000
124A127CYS00.0020.00722.356-1.286-1.2860.0000.0000.0000.000
125A128PRO00.0450.01419.4681.1231.1230.0000.0000.0000.000
126A129ASP-1-0.895-0.94920.218-29.076-29.0760.0000.0000.0000.000
127A130THR0-0.092-0.07623.1870.4930.4930.0000.0000.0000.000
128A131LEU0-0.134-0.05825.9451.1651.1650.0000.0000.0000.000
129A132ASP-1-0.870-0.90627.255-21.002-21.0020.0000.0000.0000.000
130A133TRP00.0320.00326.941-0.624-0.6240.0000.0000.0000.000
131A134ARG10.8960.94222.89725.36325.3630.0000.0000.0000.000
132A135ALA00.006-0.00828.510-0.263-0.2630.0000.0000.0000.000
133A136ALA0-0.0160.00028.3240.0550.0550.0000.0000.0000.000
134A137GLU-1-0.855-0.93730.141-17.231-17.2310.0000.0000.0000.000
135A138PRO0-0.008-0.02733.8770.0350.0350.0000.0000.0000.000
136A139ARG10.9300.96637.08515.52315.5230.0000.0000.0000.000
137A140ALA00.0350.03632.6560.1070.1070.0000.0000.0000.000
138A141TRP0-0.003-0.01834.000-0.158-0.1580.0000.0000.0000.000
139A142PRO0-0.0140.00036.327-0.065-0.0650.0000.0000.0000.000
140A143THR00.1190.05633.7210.1290.1290.0000.0000.0000.000
141A144LYS10.7800.90831.60519.06419.0640.0000.0000.0000.000
142A145LEU0-0.037-0.02233.791-0.070-0.0700.0000.0000.0000.000
143A146GLU-1-0.891-0.93936.708-16.051-16.0510.0000.0000.0000.000
144A147TRP00.004-0.01129.770-0.092-0.0920.0000.0000.0000.000
145A148GLU-1-0.758-0.86831.641-19.306-19.3060.0000.0000.0000.000
146A149ARG10.8560.93434.55716.40816.4080.0000.0000.0000.000
147A150HIS00.0640.03935.283-0.213-0.2130.0000.0000.0000.000
148A151LYS10.8900.96133.52217.86317.8630.0000.0000.0000.000
149A152ILE0-0.031-0.02832.206-0.710-0.7100.0000.0000.0000.000
150A153ARG10.9240.95829.96018.33118.3310.0000.0000.0000.000
151A154ALA00.0300.03528.130-0.715-0.7150.0000.0000.0000.000
152A155ARG10.9360.96326.89219.76219.7620.0000.0000.0000.000
153A156GLN0-0.014-0.00927.084-0.545-0.5450.0000.0000.0000.000
154A157ASN00.0460.01624.921-0.351-0.3510.0000.0000.0000.000
155A158ARG10.9090.96122.22124.69224.6920.0000.0000.0000.000
156A159ALA0-0.033-0.01122.153-1.167-1.1670.0000.0000.0000.000
157A160TYR00.0510.01519.211-0.854-0.8540.0000.0000.0000.000
158A161LEU0-0.057-0.02618.245-1.247-1.2470.0000.0000.0000.000
159A162GLU-1-0.890-0.95217.601-30.695-30.6950.0000.0000.0000.000
160A163ARG10.7840.86418.10525.07425.0740.0000.0000.0000.000
161A164ASP-1-0.825-0.87818.341-27.804-27.8040.0000.0000.0000.000
162A166PRO00.0600.01413.624-1.527-1.5270.0000.0000.0000.000
163A167ALA0-0.0060.00613.830-1.801-1.8010.0000.0000.0000.000
164A168GLN00.0420.02715.873-0.611-0.6110.0000.0000.0000.000
165A169LEU00.0060.0039.7560.1930.1930.0000.0000.0000.000
166A170GLN00.0220.0139.821-2.924-2.9240.0000.0000.0000.000
167A171GLN00.002-0.00212.5130.0720.0720.0000.0000.0000.000
168A172LEU0-0.024-0.01714.0720.9950.9950.0000.0000.0000.000
169A173LEU0-0.0120.0017.636-0.399-0.3990.0000.0000.0000.000
170A174GLU-1-0.984-0.99411.363-38.822-38.8220.0000.0000.0000.000
171A175LEU0-0.059-0.01813.0311.1651.1650.0000.0000.0000.000
172A176GLY00.0750.03313.0281.9731.9730.0000.0000.0000.000
173A177ARG10.8090.9046.26861.62361.6230.0000.0000.0000.000
174A178GLY0-0.0070.00012.1303.2523.2520.0000.0000.0000.000
175A179VAL0-0.064-0.04414.0691.9041.9040.0000.0000.0000.000
176A180LEU00.0050.0229.9260.9780.9780.0000.0000.0000.000
177A181ASP-1-0.765-0.8778.191-50.644-50.6440.0000.0000.0000.000
178A182GLN0-0.085-0.0249.874-0.106-0.1060.0000.0000.0000.000
179A183GLN0-0.035-0.0259.729-0.602-0.6020.0000.0000.0000.000
180A184VAL00.0060.00212.7651.0811.0810.0000.0000.0000.000
181A185PRO00.0170.00716.313-0.318-0.3180.0000.0000.0000.000
182A186PRO0-0.0180.00217.2331.4031.4030.0000.0000.0000.000
183A187LEU0-0.012-0.00520.1490.7340.7340.0000.0000.0000.000
184A188VAL0-0.002-0.00921.9740.5130.5130.0000.0000.0000.000
185A189LYS10.8970.94524.61820.71720.7170.0000.0000.0000.000
186A190VAL00.0240.02528.286-0.154-0.1540.0000.0000.0000.000
187A191THR0-0.028-0.01630.2310.7020.7020.0000.0000.0000.000
188A192HIS10.8690.93933.46715.80415.8040.0000.0000.0000.000
189A193HIS00.0120.02036.1240.1610.1610.0000.0000.0000.000
190A194VAL00.0260.01638.922-0.147-0.1470.0000.0000.0000.000
191A195THR0-0.052-0.03741.9710.3080.3080.0000.0000.0000.000
192A196SER00.018-0.00344.520-0.142-0.1420.0000.0000.0000.000
193A197SER0-0.018-0.00743.9580.1410.1410.0000.0000.0000.000
194A198VAL00.0040.00139.259-0.079-0.0790.0000.0000.0000.000
195A199THR0-0.029-0.00537.7650.2180.2180.0000.0000.0000.000
196A200THR0-0.0180.00134.471-0.298-0.2980.0000.0000.0000.000
197A201LEU00.0130.00132.5410.1820.1820.0000.0000.0000.000
198A202ARG10.9650.97329.65618.00218.0020.0000.0000.0000.000
199A203CYS0-0.0180.00125.138-0.409-0.4090.0000.0000.0000.000
200A204ARG10.8950.94225.71119.97419.9740.0000.0000.0000.000
201A205ALA00.0600.03120.8380.1080.1080.0000.0000.0000.000
202A206LEU0-0.046-0.03922.9460.0940.0940.0000.0000.0000.000
203A207ASN00.013-0.00822.165-0.415-0.4150.0000.0000.0000.000
204A208TYR00.0150.03616.0140.6290.6290.0000.0000.0000.000
205A209TYR00.0380.00612.1301.2841.2840.0000.0000.0000.000
206A210PRO00.0380.0269.585-0.257-0.2570.0000.0000.0000.000
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208A212ASN0-0.084-0.03010.2241.6051.6050.0000.0000.0000.000
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