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: 6534Z

Calculation Name: 1CD9-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CD9

Chain ID: B

ChEMBL ID:

UniProt ID: P40223

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2275030.358107
FMO2-HF: Nuclear repulsion 2187170.188714
FMO2-HF: Total energy -87860.169393
FMO2-MP2: Total energy -88105.640735


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:ALA)


Summations of interaction energy for fragment #1(B:1:ALA)
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.
-35.325-29.5480.717-3.01-3.483-0.025
Interaction energy analysis for fragmet #1(B:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.901
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].
3B3TYR0-0.0140.0082.758-2.2870.7020.417-1.465-1.940-0.008
32B33HIS0-0.072-0.0562.727-20.786-18.0700.301-1.523-1.495-0.017
33B34LEU0-0.0120.0114.716-4.140-4.068-0.001-0.022-0.0480.000
4B4PRO00.0410.0196.2730.5800.5800.0000.0000.0000.000
5B5PRO0-0.009-0.00910.120-0.812-0.8120.0000.0000.0000.000
6B6ALA00.0270.02812.2131.0181.0180.0000.0000.0000.000
7B7SER00.0100.00314.1130.0460.0460.0000.0000.0000.000
8B8PRO0-0.070-0.01617.4240.1690.1690.0000.0000.0000.000
9B9SER00.009-0.00718.8571.0441.0440.0000.0000.0000.000
10B10ASN00.000-0.02021.2790.2600.2600.0000.0000.0000.000
11B11LEU0-0.0140.01824.2170.0280.0280.0000.0000.0000.000
12B12SER0-0.0020.00425.3700.5280.5280.0000.0000.0000.000
13B13CYS0-0.016-0.01127.543-0.073-0.0730.0000.0000.0000.000
14B14LEU00.0290.01631.0020.2600.2600.0000.0000.0000.000
15B15MET00.0010.01233.858-0.232-0.2320.0000.0000.0000.000
16B16HIS0-0.020-0.01832.7600.1740.1740.0000.0000.0000.000
17B17LEU00.0440.01237.3500.0020.0020.0000.0000.0000.000
18B18THR0-0.0040.00338.8460.0410.0410.0000.0000.0000.000
19B19THR0-0.002-0.00535.0410.1040.1040.0000.0000.0000.000
20B20ASN00.0110.00837.940-0.102-0.1020.0000.0000.0000.000
21B21SER0-0.049-0.02834.485-0.147-0.1470.0000.0000.0000.000
22B22LEU00.0630.03032.7210.0680.0680.0000.0000.0000.000
23B23VAL0-0.0310.00129.213-0.314-0.3140.0000.0000.0000.000
24B25GLN00.001-0.01724.442-0.095-0.0950.0000.0000.0000.000
25B26TRP00.0240.01218.5210.7860.7860.0000.0000.0000.000
26B27GLU-1-0.870-0.92716.560-17.785-17.7850.0000.0000.0000.000
27B28PRO0-0.044-0.02414.5220.3020.3020.0000.0000.0000.000
28B29GLY00.0220.01814.059-0.648-0.6480.0000.0000.0000.000
29B30PRO0-0.048-0.0419.064-0.595-0.5950.0000.0000.0000.000
30B31GLU-1-0.849-0.9076.504-34.657-34.6570.0000.0000.0000.000
31B32THR00.0210.0006.244-3.822-3.8220.0000.0000.0000.000
34B35PRO0-0.058-0.0327.4202.8312.8310.0000.0000.0000.000
35B36THR00.0240.02810.9961.6621.6620.0000.0000.0000.000
36B37SER0-0.082-0.03612.6821.1181.1180.0000.0000.0000.000
37B38PHE00.0480.00614.206-0.171-0.1710.0000.0000.0000.000
38B39ILE0-0.0010.00219.1230.5770.5770.0000.0000.0000.000
39B40LEU0-0.0070.00222.7520.0030.0030.0000.0000.0000.000
40B41LYS10.8680.92625.18312.52012.5200.0000.0000.0000.000
41B42SER00.033-0.00327.8250.1810.1810.0000.0000.0000.000
42B43PHE0-0.0040.00531.3310.0280.0280.0000.0000.0000.000
43B44ARG10.9030.94434.8118.1308.1300.0000.0000.0000.000
44B45SER0-0.028-0.03437.3800.0190.0190.0000.0000.0000.000
45B46ARG10.9200.96139.5267.2947.2940.0000.0000.0000.000
46B47ALA00.0760.02940.208-0.199-0.1990.0000.0000.0000.000
47B48ASP-1-0.911-0.95638.944-7.619-7.6190.0000.0000.0000.000
48B49CYS0-0.082-0.04230.771-0.097-0.0970.0000.0000.0000.000
49B50GLN00.0280.02236.647-0.338-0.3380.0000.0000.0000.000
50B51TYR0-0.059-0.01538.6080.0890.0890.0000.0000.0000.000
51B52GLN00.0160.01234.315-0.385-0.3850.0000.0000.0000.000
52B53GLY00.0260.01838.0710.1970.1970.0000.0000.0000.000
53B54ASP-1-0.935-0.96537.885-8.042-8.0420.0000.0000.0000.000
54B55THR0-0.004-0.00832.647-0.192-0.1920.0000.0000.0000.000
55B56ILE0-0.056-0.02633.3620.2370.2370.0000.0000.0000.000
56B57PRO0-0.059-0.04032.355-0.265-0.2650.0000.0000.0000.000
57B58ASP-1-0.784-0.87226.948-11.857-11.8570.0000.0000.0000.000
58B59CYS0-0.089-0.02323.795-0.170-0.1700.0000.0000.0000.000
59B60VAL00.0070.00322.978-0.399-0.3990.0000.0000.0000.000
60B61ALA00.0370.02220.0730.3870.3870.0000.0000.0000.000
61B62LYS10.9410.96720.95112.20112.2010.0000.0000.0000.000
62B63LYS11.0451.00712.75922.30422.3040.0000.0000.0000.000
63B64ARG10.9300.95716.02418.55418.5540.0000.0000.0000.000
64B65GLN0-0.0310.00917.030-0.024-0.0240.0000.0000.0000.000
65B66ASN00.0300.02216.735-0.543-0.5430.0000.0000.0000.000
66B67ASN0-0.004-0.02520.4090.7910.7910.0000.0000.0000.000
67B69SER0-0.0010.00626.3370.3070.3070.0000.0000.0000.000
68B70ILE00.0710.03930.1770.0260.0260.0000.0000.0000.000
69B71PRO0-0.005-0.00332.7670.2840.2840.0000.0000.0000.000
70B72ARG10.9810.97135.8237.5837.5830.0000.0000.0000.000
71B73LYS10.8990.95736.7028.8068.8060.0000.0000.0000.000
72B74ASN00.0230.00934.0780.3020.3020.0000.0000.0000.000
73B75LEU00.0020.02135.413-0.006-0.0060.0000.0000.0000.000
74B76LEU0-0.027-0.00839.0280.2150.2150.0000.0000.0000.000
75B77LEU0-0.010-0.01740.502-0.113-0.1130.0000.0000.0000.000
76B78TYR00.007-0.00342.7340.1620.1620.0000.0000.0000.000
77B79GLN0-0.016-0.00742.2680.0910.0910.0000.0000.0000.000
78B80TYR00.0090.01638.857-0.118-0.1180.0000.0000.0000.000
79B81MET0-0.040-0.02533.5170.1300.1300.0000.0000.0000.000
80B82ALA00.0450.03032.719-0.081-0.0810.0000.0000.0000.000
81B83ILE0-0.029-0.03528.393-0.109-0.1090.0000.0000.0000.000
82B84TRP0-0.029-0.02724.3980.2720.2720.0000.0000.0000.000
83B85VAL00.0090.00920.5300.0600.0600.0000.0000.0000.000
84B86GLN00.0190.01220.3230.3870.3870.0000.0000.0000.000
85B87ALA0-0.002-0.00615.418-0.114-0.1140.0000.0000.0000.000
86B88GLU-1-0.947-0.97216.554-16.530-16.5300.0000.0000.0000.000
87B89ASN00.0530.0098.920-0.810-0.8100.0000.0000.0000.000
88B90MET0-0.013-0.0018.3500.9640.9640.0000.0000.0000.000
89B91LEU0-0.032-0.0136.9400.0270.0270.0000.0000.0000.000
90B92GLY00.0130.01311.2860.7710.7710.0000.0000.0000.000
91B93SER00.007-0.01714.387-1.082-1.0820.0000.0000.0000.000
92B94SER0-0.065-0.03616.1550.3390.3390.0000.0000.0000.000
93B95GLU-1-0.823-0.91318.097-12.444-12.4440.0000.0000.0000.000
94B96SER00.0100.02021.110-0.257-0.2570.0000.0000.0000.000
95B97PRO0-0.013-0.00922.6060.3040.3040.0000.0000.0000.000
96B98LYS10.8850.95125.95911.34811.3480.0000.0000.0000.000
97B99LEU00.0190.02228.8770.2740.2740.0000.0000.0000.000
98B101LEU00.0120.00232.9270.0680.0680.0000.0000.0000.000
99B102ASP-1-0.703-0.83936.631-7.661-7.6610.0000.0000.0000.000
100B103PRO0-0.017-0.03437.040-0.078-0.0780.0000.0000.0000.000
101B104MET0-0.079-0.04338.325-0.099-0.0990.0000.0000.0000.000
102B105ASP-1-0.839-0.91339.706-7.444-7.4440.0000.0000.0000.000
103B106VAL0-0.046-0.01735.038-0.062-0.0620.0000.0000.0000.000
104B107VAL0-0.0010.00136.960-0.229-0.2290.0000.0000.0000.000
105B108LYS10.8930.96133.8579.2259.2250.0000.0000.0000.000
106B109LEU0-0.0020.00338.4700.0690.0690.0000.0000.0000.000
107B110GLU-1-0.921-0.97740.612-7.981-7.9810.0000.0000.0000.000
108B111PRO0-0.042-0.02242.8520.1310.1310.0000.0000.0000.000
109B112PRO00.0090.01045.8010.0140.0140.0000.0000.0000.000
110B113MET0-0.045-0.02649.492-0.047-0.0470.0000.0000.0000.000
111B114LEU0-0.018-0.01651.5440.1370.1370.0000.0000.0000.000
112B115GLN0-0.031-0.02053.5190.0210.0210.0000.0000.0000.000
113B116ALA00.0280.00856.4620.0410.0410.0000.0000.0000.000
114B117LEU0-0.053-0.03059.752-0.016-0.0160.0000.0000.0000.000
115B118ASP-1-0.921-0.96563.141-4.903-4.9030.0000.0000.0000.000
116B119ILE00.0160.01564.8830.0400.0400.0000.0000.0000.000
117B120GLY0-0.018-0.00467.1290.0480.0480.0000.0000.0000.000
118B121PRO0-0.010-0.01367.5560.0520.0520.0000.0000.0000.000
119B122ASP-1-0.922-0.96470.484-4.483-4.4830.0000.0000.0000.000
120B123VAL0-0.063-0.02571.3890.0730.0730.0000.0000.0000.000
121B124VAL0-0.0340.00271.4440.0290.0290.0000.0000.0000.000
122B125SER0-0.006-0.00674.4470.0410.0410.0000.0000.0000.000
123B126HIS00.0250.01674.739-0.075-0.0750.0000.0000.0000.000
124B127GLN0-0.022-0.03271.1330.0670.0670.0000.0000.0000.000
125B128PRO00.0160.00771.164-0.059-0.0590.0000.0000.0000.000
126B129GLY00.003-0.00266.975-0.009-0.0090.0000.0000.0000.000
127B130CYS0-0.0110.00463.625-0.003-0.0030.0000.0000.0000.000
128B131LEU00.0220.01060.208-0.023-0.0230.0000.0000.0000.000
129B132TRP00.0340.00463.695-0.009-0.0090.0000.0000.0000.000
130B133LEU0-0.060-0.03057.465-0.077-0.0770.0000.0000.0000.000
131B134SER00.0050.01158.9670.0580.0580.0000.0000.0000.000
132B135TRP0-0.009-0.02754.193-0.077-0.0770.0000.0000.0000.000
133B136LYS10.9670.98654.2465.6285.6280.0000.0000.0000.000
134B137PRO00.0840.05150.224-0.092-0.0920.0000.0000.0000.000
135B138TRP00.0440.01541.4030.0650.0650.0000.0000.0000.000
136B139LYS10.9100.93948.1345.9965.9960.0000.0000.0000.000
137B140PRO0-0.033-0.01544.7290.0620.0620.0000.0000.0000.000
138B141SER0-0.025-0.02445.635-0.057-0.0570.0000.0000.0000.000
139B142GLU-1-0.843-0.90747.329-6.024-6.0240.0000.0000.0000.000
140B143TYR0-0.036-0.01344.8350.0880.0880.0000.0000.0000.000
141B144MET0-0.073-0.02444.219-0.002-0.0020.0000.0000.0000.000
142B145GLU-1-0.862-0.92249.921-5.813-5.8130.0000.0000.0000.000
143B146GLN0-0.090-0.06148.075-0.206-0.2060.0000.0000.0000.000
144B147GLU-1-0.866-0.91050.173-6.008-6.0080.0000.0000.0000.000
145B148CYS0-0.022-0.02246.4900.0100.0100.0000.0000.0000.000
146B149GLU-1-0.825-0.89148.208-6.547-6.5470.0000.0000.0000.000
147B150LEU0-0.027-0.00950.753-0.096-0.0960.0000.0000.0000.000
148B151ARG10.8480.93245.3996.8406.8400.0000.0000.0000.000
149B152TYR00.051-0.00452.4790.0030.0030.0000.0000.0000.000
150B153GLN00.0350.02150.8600.0140.0140.0000.0000.0000.000
151B154PRO00.0110.02355.754-0.016-0.0160.0000.0000.0000.000
152B155GLN0-0.031-0.03553.836-0.032-0.0320.0000.0000.0000.000
153B156LEU0-0.007-0.00755.8490.0920.0920.0000.0000.0000.000
154B157LYS10.9280.95454.8585.3365.3360.0000.0000.0000.000
155B158GLY00.0100.01052.3160.0600.0600.0000.0000.0000.000
156B159ALA0-0.043-0.00253.4010.0560.0560.0000.0000.0000.000
157B160ASN00.0340.01052.369-0.225-0.2250.0000.0000.0000.000
158B161TRP0-0.035-0.01548.1440.1020.1020.0000.0000.0000.000
159B162THR00.0170.02252.8620.0420.0420.0000.0000.0000.000
160B163LEU0-0.029-0.02849.857-0.081-0.0810.0000.0000.0000.000
161B164VAL0-0.025-0.00554.4980.1170.1170.0000.0000.0000.000
162B165PHE00.0340.00750.403-0.095-0.0950.0000.0000.0000.000
163B166HIS0-0.035-0.03652.6390.1390.1390.0000.0000.0000.000
164B167LEU0-0.0030.01654.4500.1240.1240.0000.0000.0000.000
165B168PRO00.0280.01254.564-0.097-0.0970.0000.0000.0000.000
166B169SER00.0670.01952.592-0.045-0.0450.0000.0000.0000.000
167B170SER0-0.074-0.03753.919-0.032-0.0320.0000.0000.0000.000
168B171LYS10.9290.96756.6995.2125.2120.0000.0000.0000.000
169B172ASP-1-0.908-0.94359.805-5.268-5.2680.0000.0000.0000.000
170B173GLN0-0.005-0.00762.353-0.018-0.0180.0000.0000.0000.000
171B174PHE0-0.024-0.01860.2640.0130.0130.0000.0000.0000.000
172B175GLU-1-0.827-0.89862.986-4.728-4.7280.0000.0000.0000.000
173B176LEU0-0.039-0.01759.416-0.043-0.0430.0000.0000.0000.000
174B178GLY00.0460.03065.309-0.038-0.0380.0000.0000.0000.000
175B179LEU0-0.096-0.04561.279-0.047-0.0470.0000.0000.0000.000
176B180HIS00.025-0.00664.3900.0080.0080.0000.0000.0000.000
177B181GLN0-0.039-0.01860.815-0.014-0.0140.0000.0000.0000.000
178B182ALA00.012-0.00260.652-0.029-0.0290.0000.0000.0000.000
179B183PRO00.0290.02662.4060.0010.0010.0000.0000.0000.000
180B184VAL00.003-0.01057.5560.0040.0040.0000.0000.0000.000
181B185TYR00.0590.03657.844-0.008-0.0080.0000.0000.0000.000
182B186THR0-0.038-0.02251.232-0.066-0.0660.0000.0000.0000.000
183B187LEU00.0150.00353.5790.0120.0120.0000.0000.0000.000
184B188GLN0-0.057-0.02445.630-0.066-0.0660.0000.0000.0000.000
185B189MET00.0110.01049.7070.0600.0600.0000.0000.0000.000
186B190ARG10.8670.93142.7016.9666.9660.0000.0000.0000.000
187B192ILE00.0410.01743.797-0.231-0.2310.0000.0000.0000.000
188B193ARG10.8640.91443.7537.3727.3720.0000.0000.0000.000
189B194SER00.0220.01046.967-0.028-0.0280.0000.0000.0000.000
190B195SER0-0.033-0.02249.8670.0150.0150.0000.0000.0000.000
191B196LEU0-0.0140.00046.269-0.001-0.0010.0000.0000.0000.000
192B197PRO00.0000.00941.582-0.032-0.0320.0000.0000.0000.000
193B198GLY00.0640.03240.7390.0110.0110.0000.0000.0000.000
194B199PHE0-0.043-0.01635.177-0.013-0.0130.0000.0000.0000.000
195B200TRP00.0170.01140.3530.0920.0920.0000.0000.0000.000
196B201SER00.0010.00240.793-0.151-0.1510.0000.0000.0000.000
197B202PRO0-0.031-0.02539.3550.0360.0360.0000.0000.0000.000
198B203TRP00.0210.02041.9010.1720.1720.0000.0000.0000.000
199B204SER00.0260.02044.384-0.112-0.1120.0000.0000.0000.000
200B205PRO00.0080.00345.900-0.038-0.0380.0000.0000.0000.000
201B206GLY0-0.003-0.00647.3120.1080.1080.0000.0000.0000.000
202B207LEU00.0130.02249.9890.0280.0280.0000.0000.0000.000
203B208GLN0-0.011-0.00751.7160.0850.0850.0000.0000.0000.000
204B209LEU00.0210.01355.6120.0430.0430.0000.0000.0000.000
205B210ARG10.9590.97259.2045.1635.1630.0000.0000.0000.000
206B211PRO0-0.036-0.01062.1150.0120.0120.0000.0000.0000.000
207B212THR0-0.018-0.00364.7660.0350.0350.0000.0000.0000.000
208B213MET-1-0.935-0.95168.460-4.652-4.6520.0000.0000.0000.000