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: 9R9Z2

Calculation Name: 4L3N-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: 4L3N

Chain ID: A

ChEMBL ID:

UniProt ID: M4SVE7

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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2294869.238813
FMO2-HF: Nuclear repulsion 2212919.005634
FMO2-HF: Total energy -81950.233179
FMO2-MP2: Total energy -82184.446884


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:380:GLY)


Summations of interaction energy for fragment #1(A:380: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.
-40.273-37.9850.201-0.979-1.509-0.006
Interaction energy analysis for fragmet #1(A:380:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.922
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].
3A382GLU-1-0.817-0.8943.849-39.353-38.541-0.003-0.335-0.474-0.001
4A383CYS0-0.116-0.0364.153-4.351-4.087-0.001-0.051-0.2110.000
27A406ASN0-0.020-0.0114.698-4.855-4.685-0.001-0.019-0.1500.000
28A408ASN0-0.029-0.0162.7753.1984.2400.206-0.574-0.674-0.005
5A384ASP-1-0.790-0.8719.146-19.938-19.9380.0000.0000.0000.000
6A385PHE00.027-0.00811.9621.1281.1280.0000.0000.0000.000
7A386SER0-0.024-0.03115.4131.7391.7390.0000.0000.0000.000
8A387PRO0-0.002-0.01716.8051.0711.0710.0000.0000.0000.000
9A388LEU0-0.050-0.00919.1230.8160.8160.0000.0000.0000.000
10A389LEU0-0.023-0.01018.6210.6310.6310.0000.0000.0000.000
11A390SER0-0.0030.01621.9770.5790.5790.0000.0000.0000.000
12A391GLY00.0220.02223.8970.0810.0810.0000.0000.0000.000
13A392THR0-0.021-0.01627.4790.0720.0720.0000.0000.0000.000
14A393PRO00.0070.00526.769-0.116-0.1160.0000.0000.0000.000
15A394PRO0-0.0340.00826.9300.4500.4500.0000.0000.0000.000
16A395GLN00.1010.04729.870-0.104-0.1040.0000.0000.0000.000
17A396VAL00.0400.02230.669-0.190-0.1900.0000.0000.0000.000
18A397TYR0-0.053-0.04030.783-0.299-0.2990.0000.0000.0000.000
19A398ASN0-0.097-0.06630.5170.1240.1240.0000.0000.0000.000
20A399PHE00.0020.01824.889-0.228-0.2280.0000.0000.0000.000
21A400LYS10.9761.00322.54111.82411.8240.0000.0000.0000.000
22A401ARG10.8360.89320.20413.45813.4580.0000.0000.0000.000
23A402LEU00.0070.00916.211-0.211-0.2110.0000.0000.0000.000
24A403VAL0-0.018-0.01814.6180.3660.3660.0000.0000.0000.000
25A404PHE0-0.007-0.00110.407-0.984-0.9840.0000.0000.0000.000
26A405THR00.046-0.0119.5210.8150.8150.0000.0000.0000.000
29A409TYR00.014-0.0166.2532.4082.4080.0000.0000.0000.000
30A410ASN00.025-0.00210.0871.2081.2080.0000.0000.0000.000
31A411LEU00.0600.04213.0940.8560.8560.0000.0000.0000.000
32A412THR00.0420.01216.2770.7700.7700.0000.0000.0000.000
33A413LYS10.9450.97714.43720.56020.5600.0000.0000.0000.000
34A414LEU00.0140.02416.1490.7170.7170.0000.0000.0000.000
35A415LEU00.029-0.00318.0950.8390.8390.0000.0000.0000.000
36A416SER0-0.081-0.04220.2700.6710.6710.0000.0000.0000.000
37A417LEU0-0.0150.00419.7190.4170.4170.0000.0000.0000.000
38A418PHE0-0.003-0.01721.6760.5740.5740.0000.0000.0000.000
39A419SER0-0.0020.01126.048-0.033-0.0330.0000.0000.0000.000
40A420VAL0-0.005-0.01124.8110.2000.2000.0000.0000.0000.000
41A421ASN0-0.042-0.01828.1580.2570.2570.0000.0000.0000.000
42A422ASP-1-0.807-0.89529.870-9.816-9.8160.0000.0000.0000.000
43A423PHE00.0380.00221.331-0.466-0.4660.0000.0000.0000.000
44A424THR0-0.043-0.00727.4610.2420.2420.0000.0000.0000.000
45A425CYS0-0.076-0.02822.092-0.299-0.2990.0000.0000.0000.000
46A426SER00.0370.02125.9960.5540.5540.0000.0000.0000.000
47A427GLN0-0.007-0.01925.408-0.446-0.4460.0000.0000.0000.000
48A428ILE00.0210.02719.155-0.344-0.3440.0000.0000.0000.000
49A429SER00.0190.00723.0530.3230.3230.0000.0000.0000.000
50A430PRO00.0740.01722.165-0.644-0.6440.0000.0000.0000.000
51A431ALA00.0090.00920.995-0.645-0.6450.0000.0000.0000.000
52A432ALA0-0.0010.02519.687-0.767-0.7670.0000.0000.0000.000
53A433ILE00.024-0.00717.800-1.012-1.0120.0000.0000.0000.000
54A434ALA0-0.028-0.01516.383-1.058-1.0580.0000.0000.0000.000
55A435SER0-0.036-0.03914.802-0.981-0.9810.0000.0000.0000.000
56A436ASN00.0070.03314.8170.0580.0580.0000.0000.0000.000
57A437CYS00.0310.0387.1662.5952.5950.0000.0000.0000.000
58A438TYR00.006-0.00511.4222.0402.0400.0000.0000.0000.000
59A439SER0-0.043-0.02511.028-1.839-1.8390.0000.0000.0000.000
60A440SER00.000-0.01411.854-0.663-0.6630.0000.0000.0000.000
61A441LEU0-0.0190.01112.8690.8660.8660.0000.0000.0000.000
62A442ILE0-0.022-0.01314.425-0.479-0.4790.0000.0000.0000.000
63A443LEU0-0.011-0.00816.7750.2480.2480.0000.0000.0000.000
64A444ASP-1-0.748-0.82818.768-13.270-13.2700.0000.0000.0000.000
65A445TYR0-0.013-0.02220.647-0.060-0.0600.0000.0000.0000.000
66A446PHE0-0.009-0.00924.1970.1690.1690.0000.0000.0000.000
67A447SER00.003-0.00627.853-0.100-0.1000.0000.0000.0000.000
68A448TYR0-0.063-0.08230.7760.1380.1380.0000.0000.0000.000
69A449PRO00.0100.03032.769-0.093-0.0930.0000.0000.0000.000
70A450LEU00.027-0.00633.1110.0270.0270.0000.0000.0000.000
71A451SER0-0.020-0.01635.442-0.024-0.0240.0000.0000.0000.000
72A452MET00.0080.02136.8240.1470.1470.0000.0000.0000.000
73A453LYS10.8730.94432.1229.5029.5020.0000.0000.0000.000
74A454SER00.017-0.00335.157-0.228-0.2280.0000.0000.0000.000
75A455ASP-1-0.863-0.92237.373-8.055-8.0550.0000.0000.0000.000
76A456LEU00.0110.00830.509-0.062-0.0620.0000.0000.0000.000
77A457SER0-0.077-0.03633.129-0.141-0.1410.0000.0000.0000.000
78A458VAL00.048-0.00332.8380.1640.1640.0000.0000.0000.000
79A459SER0-0.028-0.01235.6120.1020.1020.0000.0000.0000.000
80A460SER0-0.0080.01638.2820.3310.3310.0000.0000.0000.000
81A461ALA00.0110.00839.197-0.158-0.1580.0000.0000.0000.000
82A462GLY00.0370.01639.7140.1520.1520.0000.0000.0000.000
83A463PRO00.0070.00739.224-0.129-0.1290.0000.0000.0000.000
84A464ILE0-0.028-0.00733.632-0.149-0.1490.0000.0000.0000.000
85A465SER00.0220.01334.217-0.142-0.1420.0000.0000.0000.000
86A466GLN0-0.0210.00235.288-0.043-0.0430.0000.0000.0000.000
87A467PHE00.0120.00137.5300.0060.0060.0000.0000.0000.000
88A468ASN0-0.075-0.04533.929-0.067-0.0670.0000.0000.0000.000
89A469TYR0-0.006-0.04624.675-0.150-0.1500.0000.0000.0000.000
90A470LYS10.9740.99929.7689.5489.5480.0000.0000.0000.000
91A471GLN00.0020.00124.0100.0590.0590.0000.0000.0000.000
92A472SER00.002-0.01524.7920.5700.5700.0000.0000.0000.000
93A473PHE00.007-0.00226.6810.0180.0180.0000.0000.0000.000
94A474SER0-0.018-0.00527.1010.1950.1950.0000.0000.0000.000
95A475ASN0-0.0220.00421.812-0.049-0.0490.0000.0000.0000.000
96A476PRO00.0140.00421.3470.3010.3010.0000.0000.0000.000
97A477THR0-0.005-0.00221.660-0.484-0.4840.0000.0000.0000.000
98A479LEU00.0220.02923.920-0.215-0.2150.0000.0000.0000.000
99A480ILE0-0.007-0.00622.0720.1390.1390.0000.0000.0000.000
100A481LEU00.0050.01526.3590.0990.0990.0000.0000.0000.000
101A482ALA00.0030.00026.874-0.040-0.0400.0000.0000.0000.000
102A483THR00.014-0.00428.8900.2700.2700.0000.0000.0000.000
103A484VAL00.003-0.01327.738-0.350-0.3500.0000.0000.0000.000
104A485PRO0-0.0090.00627.9150.4360.4360.0000.0000.0000.000
105A486HIS00.007-0.00530.268-0.458-0.4580.0000.0000.0000.000
106A487ASN0-0.037-0.01629.314-0.019-0.0190.0000.0000.0000.000
107A488LEU0-0.0100.00723.688-0.364-0.3640.0000.0000.0000.000
108A489THR0-0.012-0.02327.506-0.110-0.1100.0000.0000.0000.000
109A490THR0-0.035-0.01924.1880.2770.2770.0000.0000.0000.000
110A491ILE0-0.0130.01524.226-0.100-0.1000.0000.0000.0000.000
111A492THR00.000-0.00727.7150.3320.3320.0000.0000.0000.000
112A493LYS10.8700.91931.2238.5478.5470.0000.0000.0000.000
113A494PRO00.0110.01732.7040.1560.1560.0000.0000.0000.000
114A495LEU00.017-0.01335.5250.0890.0890.0000.0000.0000.000
115A496LYS10.8060.92038.1547.6867.6860.0000.0000.0000.000
116A497TYR00.0490.00633.588-0.369-0.3690.0000.0000.0000.000
117A498SER0-0.045-0.04236.5340.3160.3160.0000.0000.0000.000
118A499TYR00.001-0.00736.402-0.270-0.2700.0000.0000.0000.000
119A500ILE00.0250.01336.8140.2320.2320.0000.0000.0000.000
120A501ASN0-0.028-0.03839.667-0.086-0.0860.0000.0000.0000.000
121A502LYS10.8850.92442.5516.5826.5820.0000.0000.0000.000
122A503CYS0-0.0290.00337.1710.1050.1050.0000.0000.0000.000
123A504SER0-0.038-0.04142.246-0.017-0.0170.0000.0000.0000.000
124A505ARG10.8700.92043.5356.9546.9540.0000.0000.0000.000
125A506LEU0-0.0250.01746.9360.0480.0480.0000.0000.0000.000
126A507LEU00.004-0.00549.333-0.055-0.0550.0000.0000.0000.000
127A508SER00.0430.00352.2240.0320.0320.0000.0000.0000.000
128A509ASP-1-0.812-0.86955.173-5.640-5.6400.0000.0000.0000.000
129A510ASP-1-0.956-0.97755.943-5.527-5.5270.0000.0000.0000.000
130A511ARG10.8460.92056.2575.2825.2820.0000.0000.0000.000
131A512THR0-0.042-0.04951.777-0.051-0.0510.0000.0000.0000.000
132A513GLU-1-0.792-0.85749.292-6.497-6.4970.0000.0000.0000.000
133A514VAL0-0.014-0.00745.3640.0020.0020.0000.0000.0000.000
134A515PRO00.011-0.00143.783-0.119-0.1190.0000.0000.0000.000
135A516GLN0-0.082-0.05140.444-0.108-0.1080.0000.0000.0000.000
136A517LEU00.0110.00337.946-0.110-0.1100.0000.0000.0000.000
137A518VAL0-0.037-0.00932.206-0.077-0.0770.0000.0000.0000.000
138A519ASN0-0.023-0.01831.6170.0640.0640.0000.0000.0000.000
139A520ALA00.002-0.00428.182-0.193-0.1930.0000.0000.0000.000
140A521ASN0-0.041-0.01724.031-0.522-0.5220.0000.0000.0000.000
141A522GLN0-0.0060.01226.4510.0840.0840.0000.0000.0000.000
142A523TYR0-0.002-0.00526.255-0.003-0.0030.0000.0000.0000.000
143A524SER00.0280.01531.1320.2220.2220.0000.0000.0000.000
144A525PRO00.0640.02734.877-0.039-0.0390.0000.0000.0000.000
145A527VAL00.0130.00533.1700.1090.1090.0000.0000.0000.000
146A528SER0-0.101-0.04836.3910.0550.0550.0000.0000.0000.000
147A529ILE0-0.047-0.02538.4080.1610.1610.0000.0000.0000.000
148A530VAL0-0.0220.00538.8110.1640.1640.0000.0000.0000.000
149A531PRO00.0440.03737.995-0.261-0.2610.0000.0000.0000.000
150A532SER00.0240.01733.9250.0850.0850.0000.0000.0000.000
151A533THR0-0.083-0.05535.417-0.221-0.2210.0000.0000.0000.000
152A534VAL00.0040.03038.2370.1100.1100.0000.0000.0000.000
153A535TRP00.0160.02341.528-0.127-0.1270.0000.0000.0000.000
154A536GLU-1-0.969-1.00444.519-6.328-6.3280.0000.0000.0000.000
155A537ASP-1-0.850-0.92245.519-7.087-7.0870.0000.0000.0000.000
156A538GLY00.0390.01846.4450.1550.1550.0000.0000.0000.000
157A539ASP-1-0.821-0.89445.625-6.765-6.7650.0000.0000.0000.000
158A540TYR0-0.055-0.03546.454-0.105-0.1050.0000.0000.0000.000
159A541TYR00.0240.01043.5610.0140.0140.0000.0000.0000.000
160A542ARG10.9340.95646.4456.1636.1630.0000.0000.0000.000
161A543LYS10.8990.95441.5857.4357.4350.0000.0000.0000.000
162A544GLN00.0240.02146.6380.0900.0900.0000.0000.0000.000
163A545LEU0-0.049-0.01944.340-0.121-0.1210.0000.0000.0000.000
164A546SER0-0.004-0.03345.6350.1600.1600.0000.0000.0000.000
165A547PRO00.025-0.01847.708-0.073-0.0730.0000.0000.0000.000
166A548LEU00.0060.01344.282-0.023-0.0230.0000.0000.0000.000
167A549GLU-1-0.796-0.85142.322-7.403-7.4030.0000.0000.0000.000
168A550GLY00.0170.01644.393-0.063-0.0630.0000.0000.0000.000
169A551GLY0-0.034-0.00647.1320.1170.1170.0000.0000.0000.000
170A552GLY00.0350.02548.780-0.090-0.0900.0000.0000.0000.000
171A553TRP00.010-0.00448.816-0.087-0.0870.0000.0000.0000.000
172A554LEU00.0150.01641.126-0.031-0.0310.0000.0000.0000.000
173A555VAL0-0.040-0.03845.6620.0870.0870.0000.0000.0000.000
174A556ALA00.0230.00042.505-0.120-0.1200.0000.0000.0000.000
175A557SER0-0.037-0.02043.9920.1830.1830.0000.0000.0000.000
176A558GLY00.0040.01242.180-0.208-0.2080.0000.0000.0000.000
177A559SER00.0190.01641.9210.2030.2030.0000.0000.0000.000
178A560THR0-0.096-0.05841.151-0.237-0.2370.0000.0000.0000.000
179A561VAL00.0060.00639.7040.1050.1050.0000.0000.0000.000
180A562ALA00.0300.01740.626-0.137-0.1370.0000.0000.0000.000
181A563MET0-0.0200.00635.201-0.195-0.1950.0000.0000.0000.000
182A564THR00.000-0.00536.1810.1740.1740.0000.0000.0000.000
183A565GLU-1-0.877-0.95238.271-8.382-8.3820.0000.0000.0000.000
184A566GLN00.0430.04033.718-0.308-0.3080.0000.0000.0000.000
185A567LEU00.0280.02729.8750.1910.1910.0000.0000.0000.000
186A568GLN00.0040.01931.599-0.050-0.0500.0000.0000.0000.000
187A569MET00.0300.01325.155-0.009-0.0090.0000.0000.0000.000
188A570GLY00.0240.01927.8880.1420.1420.0000.0000.0000.000
189A571PHE0-0.006-0.02222.205-0.356-0.3560.0000.0000.0000.000
190A572GLY00.0130.02123.5420.3530.3530.0000.0000.0000.000
191A573ILE0-0.010-0.01417.950-0.651-0.6510.0000.0000.0000.000
192A574THR0-0.010-0.01519.4141.0211.0210.0000.0000.0000.000
193A575VAL0-0.0100.00615.868-0.900-0.9000.0000.0000.0000.000
194A576GLN00.0190.00316.3721.6951.6950.0000.0000.0000.000
195A577TYR00.002-0.00815.659-1.160-1.1600.0000.0000.0000.000
196A578GLY00.0130.00915.4900.7800.7800.0000.0000.0000.000
197A579THR0-0.013-0.01116.6310.5480.5480.0000.0000.0000.000
198A580ASP-1-0.896-0.95214.631-18.970-18.9700.0000.0000.0000.000
199A581THR00.0250.00711.955-1.590-1.5900.0000.0000.0000.000
200A582ASN0-0.048-0.02211.161-0.991-0.9910.0000.0000.0000.000
201A583SER00.0160.0056.429-1.439-1.4390.0000.0000.0000.000
202A584VAL0-0.065-0.0166.236-4.834-4.8340.0000.0000.0000.000
203A586PRO00.0050.0148.407-2.196-2.1960.0000.0000.0000.000
204A587LYS10.7900.8676.09738.81838.8180.0000.0000.0000.000
205A588LEU-1-0.920-0.9418.597-25.147-25.1470.0000.0000.0000.000