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: V6291

Calculation Name: 2RCK-A-Xray549

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: 2RCK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ITP4

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2393145.291405
FMO2-HF: Nuclear repulsion 2307931.806245
FMO2-HF: Total energy -85213.48516
FMO2-MP2: Total energy -85464.500027


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:1:SER)


Summations of interaction energy for fragment #1(A:1: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.
-41.062-39.0141.138-1.284-1.901-0.005
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.914 / q_NPA : 0.940
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].
3A3LEU00.0560.0463.9030.6811.9500.001-0.440-0.8300.001
4A4ASN0-0.0190.0072.253-0.871-0.2251.137-0.813-0.970-0.006
5A5LEU00.0370.0174.3723.5673.7000.000-0.031-0.1010.000
6A6SER0-0.027-0.0315.6803.7143.7140.0000.0000.0000.000
7A7THR0-0.031-0.0058.2290.0170.0170.0000.0000.0000.000
8A8GLU-1-0.949-0.9837.486-36.583-36.5830.0000.0000.0000.000
9A9PRO0-0.050-0.02911.8790.8680.8680.0000.0000.0000.000
10A10CYS0-0.0230.02714.092-1.067-1.0670.0000.0000.0000.000
11A11ASP-1-0.737-0.83415.272-16.366-16.3660.0000.0000.0000.000
12A12VAL0-0.043-0.04016.9280.7030.7030.0000.0000.0000.000
13A13SER0-0.079-0.07318.9651.0901.0900.0000.0000.0000.000
14A14ASP-1-0.882-0.93114.787-18.809-18.8090.0000.0000.0000.000
15A15ILE00.0090.00818.2590.1220.1220.0000.0000.0000.000
16A16GLU-1-0.898-0.95517.831-14.765-14.7650.0000.0000.0000.000
17A18ILE00.0470.01217.7040.4460.4460.0000.0000.0000.000
18A19SER0-0.0210.01120.8290.6360.6360.0000.0000.0000.000
19A20LYS10.9600.97617.78815.78015.7800.0000.0000.0000.000
20A21ALA00.013-0.00118.9440.2210.2210.0000.0000.0000.000
21A22THR0-0.023-0.01920.5180.5700.5700.0000.0000.0000.000
22A23GLN0-0.060-0.04823.1420.5090.5090.0000.0000.0000.000
23A24VAL0-0.009-0.00419.3970.3300.3300.0000.0000.0000.000
24A25PHE00.0260.02322.7570.2800.2800.0000.0000.0000.000
25A26LEU00.0010.01625.0800.4470.4470.0000.0000.0000.000
26A27ASP-1-0.830-0.92725.133-11.546-11.5460.0000.0000.0000.000
27A28ASN0-0.089-0.05223.6230.1070.1070.0000.0000.0000.000
28A29THR0-0.002-0.01226.9390.2300.2300.0000.0000.0000.000
29A30TYR00.0070.01329.8430.3910.3910.0000.0000.0000.000
30A31GLN00.0300.00829.3920.4610.4610.0000.0000.0000.000
31A32GLY0-0.043-0.01533.6380.3580.3580.0000.0000.0000.000
32A33ILE0-0.009-0.01829.148-0.162-0.1620.0000.0000.0000.000
33A34PRO00.0150.01333.541-0.029-0.0290.0000.0000.0000.000
34A35GLU-1-0.884-0.94733.722-8.992-8.9920.0000.0000.0000.000
35A36TYR0-0.013-0.01129.817-0.122-0.1220.0000.0000.0000.000
36A37ASN0-0.026-0.02033.3960.0400.0400.0000.0000.0000.000
37A38ILE0-0.0080.02529.9620.0770.0770.0000.0000.0000.000
38A39LYS10.9660.97934.3377.9857.9850.0000.0000.0000.000
39A40LYS10.8870.94835.6538.1678.1670.0000.0000.0000.000
40A41LEU0-0.024-0.01533.6040.1100.1100.0000.0000.0000.000
41A42ASP-1-0.851-0.90835.589-8.404-8.4040.0000.0000.0000.000
42A43PRO0-0.031-0.02236.832-0.135-0.1350.0000.0000.0000.000
43A44ILE0-0.007-0.00339.569-0.023-0.0230.0000.0000.0000.000
44A45THR0-0.026-0.02241.5810.1490.1490.0000.0000.0000.000
45A46ILE00.0080.01244.844-0.043-0.0430.0000.0000.0000.000
46A47PRO0-0.010-0.01347.5470.1190.1190.0000.0000.0000.000
47A48SER0-0.010-0.02650.7570.1310.1310.0000.0000.0000.000
48A49LEU0-0.007-0.00449.258-0.113-0.1130.0000.0000.0000.000
49A50GLU-1-0.843-0.89652.860-5.572-5.5720.0000.0000.0000.000
50A51LYS10.8600.93054.4025.7455.7450.0000.0000.0000.000
51A52SER00.0020.00058.0040.0780.0780.0000.0000.0000.000
52A53ILE00.0000.00460.001-0.069-0.0690.0000.0000.0000.000
53A54GLU-1-0.823-0.89262.807-4.607-4.6070.0000.0000.0000.000
54A55LYS10.8530.91165.4104.5374.5370.0000.0000.0000.000
55A56ILE0-0.006-0.00563.5910.0720.0720.0000.0000.0000.000
56A57ASN0-0.059-0.04867.6750.0300.0300.0000.0000.0000.000
57A58LEU00.0450.03162.4660.0330.0330.0000.0000.0000.000
58A59ASN0-0.0020.00362.447-0.064-0.0640.0000.0000.0000.000
59A60VAL0-0.023-0.01957.2280.0230.0230.0000.0000.0000.000
60A61ARG10.9140.96457.0565.3035.3030.0000.0000.0000.000
61A62TYR00.0270.02152.9270.0430.0430.0000.0000.0000.000
62A63ASN0-0.021-0.02753.826-0.017-0.0170.0000.0000.0000.000
63A64ASN0-0.020-0.02950.412-0.093-0.0930.0000.0000.0000.000
64A65LEU0-0.0060.01848.1520.0010.0010.0000.0000.0000.000
65A66LYS10.9770.99143.9126.9846.9840.0000.0000.0000.000
66A67VAL00.0040.00341.5810.0280.0280.0000.0000.0000.000
67A68THR0-0.038-0.03040.018-0.156-0.1560.0000.0000.0000.000
68A69GLY00.0370.01437.4590.1090.1090.0000.0000.0000.000
69A70PHE00.0490.00335.840-0.217-0.2170.0000.0000.0000.000
70A71LYS10.9040.96232.0838.7088.7080.0000.0000.0000.000
71A72ASN0-0.038-0.02230.971-0.496-0.4960.0000.0000.0000.000
72A73GLN00.0090.04231.131-0.030-0.0300.0000.0000.0000.000
73A74LYS10.8370.92726.43010.97010.9700.0000.0000.0000.000
74A75ILE0-0.0060.00025.4600.4320.4320.0000.0000.0000.000
75A76SER0-0.104-0.07728.382-0.229-0.2290.0000.0000.0000.000
76A77HIS0-0.0220.00029.5460.0700.0700.0000.0000.0000.000
77A78PHE00.0360.00424.9220.0820.0820.0000.0000.0000.000
78A79THR00.0080.00527.051-0.267-0.2670.0000.0000.0000.000
79A80LEU0-0.001-0.00724.5000.1910.1910.0000.0000.0000.000
80A81VAL00.0030.00326.793-0.232-0.2320.0000.0000.0000.000
81A82ARG10.8960.92620.85413.50013.5000.0000.0000.0000.000
82A83ASP-1-0.899-0.94727.447-10.100-10.1000.0000.0000.0000.000
83A84THR00.005-0.01530.768-0.003-0.0030.0000.0000.0000.000
84A85LYS10.9380.98624.82912.28212.2820.0000.0000.0000.000
85A86ALA00.0100.00730.0280.0510.0510.0000.0000.0000.000
86A87VAL0-0.0080.00528.401-0.322-0.3220.0000.0000.0000.000
87A88ASN0-0.024-0.01930.6660.3730.3730.0000.0000.0000.000
88A89PHE00.0250.01929.579-0.326-0.3260.0000.0000.0000.000
89A90LYS10.9120.93531.3039.1369.1360.0000.0000.0000.000
90A91THR00.0170.00130.178-0.309-0.3090.0000.0000.0000.000
91A92LYS10.9420.98632.6869.3749.3740.0000.0000.0000.000
92A93VAL0-0.002-0.01133.829-0.277-0.2770.0000.0000.0000.000
93A94ASN00.0330.03736.4500.2860.2860.0000.0000.0000.000
94A95PHE0-0.034-0.02138.743-0.124-0.1240.0000.0000.0000.000
95A96THR00.0760.03641.1740.1070.1070.0000.0000.0000.000
96A97ALA0-0.033-0.02543.990-0.120-0.1200.0000.0000.0000.000
97A98GLU-1-0.896-0.93546.493-6.394-6.3940.0000.0000.0000.000
98A99GLY00.0210.00349.156-0.078-0.0780.0000.0000.0000.000
99A100LYS10.8130.90751.9515.9665.9660.0000.0000.0000.000
100A101LEU00.0050.00755.313-0.072-0.0720.0000.0000.0000.000
101A102VAL0-0.025-0.01057.6060.0820.0820.0000.0000.0000.000
102A103ILE00.0120.00460.463-0.056-0.0560.0000.0000.0000.000
103A104GLU-1-0.832-0.91463.161-4.989-4.9890.0000.0000.0000.000
104A105LEU00.0150.00666.048-0.030-0.0300.0000.0000.0000.000
105A106PRO00.0250.00468.0150.0870.0870.0000.0000.0000.000
106A107LYS10.9000.94770.8904.3844.3840.0000.0000.0000.000
107A108SER0-0.031-0.03073.0090.0440.0440.0000.0000.0000.000
108A109SER0-0.033-0.00872.8790.0360.0360.0000.0000.0000.000
109A110LYS10.8260.90871.0394.4314.4310.0000.0000.0000.000
110A111THR0-0.005-0.01565.618-0.076-0.0760.0000.0000.0000.000
111A112TYR0-0.030-0.02865.3200.0500.0500.0000.0000.0000.000
112A113THR0-0.031-0.04060.644-0.068-0.0680.0000.0000.0000.000
113A114GLY00.0290.02760.3700.0750.0750.0000.0000.0000.000
114A115GLU-1-0.904-0.94055.448-5.856-5.8560.0000.0000.0000.000
115A116VAL0-0.017-0.00852.9690.0700.0700.0000.0000.0000.000
116A117THR00.006-0.00548.687-0.126-0.1260.0000.0000.0000.000
117A118ILE0-0.032-0.00648.0150.1120.1120.0000.0000.0000.000
118A119GLU-1-0.854-0.88745.629-6.897-6.8970.0000.0000.0000.000
119A120ALA0-0.008-0.01544.3120.1470.1470.0000.0000.0000.000
120A121SER0-0.0020.00240.908-0.138-0.1380.0000.0000.0000.000
121A122ALA0-0.007-0.01039.8670.1840.1840.0000.0000.0000.000
122A123GLU-1-0.808-0.87435.300-9.204-9.2040.0000.0000.0000.000
123A124GLY00.0380.02737.0230.2370.2370.0000.0000.0000.000
124A125GLY0-0.007-0.01735.219-0.313-0.3130.0000.0000.0000.000
125A126ALA0-0.016-0.00134.1140.2900.2900.0000.0000.0000.000
126A127ALA00.0140.01434.090-0.304-0.3040.0000.0000.0000.000
127A128TYR00.004-0.00329.7050.2740.2740.0000.0000.0000.000
128A129SER00.0340.01832.987-0.132-0.1320.0000.0000.0000.000
129A130TYR0-0.043-0.01328.0610.0380.0380.0000.0000.0000.000
130A131SER00.0060.01432.1350.0310.0310.0000.0000.0000.000
131A132VAL00.0220.00829.820-0.232-0.2320.0000.0000.0000.000
132A133LYS10.8080.88532.0329.1129.1120.0000.0000.0000.000
133A134THR00.0300.01633.291-0.270-0.2700.0000.0000.0000.000
134A135ASP-1-0.948-0.95633.603-9.252-9.2520.0000.0000.0000.000
135A136ASP-1-0.812-0.93135.288-8.293-8.2930.0000.0000.0000.000
136A137LYS10.8600.92136.1788.4638.4630.0000.0000.0000.000
137A138GLY00.0160.01233.463-0.067-0.0670.0000.0000.0000.000
138A139VAL0-0.029-0.00630.080-0.387-0.3870.0000.0000.0000.000
139A140GLU-1-0.893-0.93429.290-10.132-10.1320.0000.0000.0000.000
140A141HIS10.8300.91828.82810.35910.3590.0000.0000.0000.000
141A142TYR0-0.0060.00224.4160.3430.3430.0000.0000.0000.000
142A143GLU-1-0.774-0.85430.221-8.835-8.8350.0000.0000.0000.000
143A144ALA0-0.007-0.00132.3410.0390.0390.0000.0000.0000.000
144A145GLY00.0600.03633.9650.2320.2320.0000.0000.0000.000
145A146PRO0-0.026-0.01737.152-0.135-0.1350.0000.0000.0000.000
146A147GLU-1-0.807-0.89937.126-8.312-8.3120.0000.0000.0000.000
147A148THR0-0.047-0.01238.8770.3120.3120.0000.0000.0000.000
148A149VAL0-0.020-0.01138.758-0.225-0.2250.0000.0000.0000.000
149A150SER0-0.010-0.00139.0340.1420.1420.0000.0000.0000.000
150A151CYS0-0.030-0.02940.071-0.323-0.3230.0000.0000.0000.000
151A152GLU-1-0.896-0.92940.695-7.577-7.5770.0000.0000.0000.000
152A153ILE0-0.016-0.03241.861-0.102-0.1020.0000.0000.0000.000
153A154PHE0-0.028-0.01138.1420.0650.0650.0000.0000.0000.000
154A155GLY00.0190.01743.7820.0420.0420.0000.0000.0000.000
155A156GLU-1-0.846-0.93647.202-5.933-5.9330.0000.0000.0000.000
156A157PRO0-0.0030.01147.651-0.034-0.0340.0000.0000.0000.000
157A158THR0-0.040-0.03748.7190.1770.1770.0000.0000.0000.000
158A159LEU0-0.021-0.02650.583-0.061-0.0610.0000.0000.0000.000
159A160SER00.0060.01252.7600.1450.1450.0000.0000.0000.000
160A161VAL00.037-0.00554.553-0.042-0.0420.0000.0000.0000.000
161A162SER00.0190.03057.3740.0160.0160.0000.0000.0000.000
162A163SER00.0910.02659.3690.0450.0450.0000.0000.0000.000
163A164THR00.0390.01662.3480.0450.0450.0000.0000.0000.000
164A165LEU0-0.029-0.00260.1860.0770.0770.0000.0000.0000.000
165A166GLU-1-0.871-0.93861.171-5.154-5.1540.0000.0000.0000.000
166A167ASP-1-0.849-0.92463.782-4.795-4.7950.0000.0000.0000.000
167A168ALA0-0.015-0.00466.9540.0790.0790.0000.0000.0000.000
168A169LEU0-0.030-0.01863.1670.0640.0640.0000.0000.0000.000
169A170LYS10.7550.86164.8464.9744.9740.0000.0000.0000.000
170A171LEU00.0110.00468.9890.0650.0650.0000.0000.0000.000
171A172ASP-1-0.745-0.81070.022-4.448-4.4480.0000.0000.0000.000
172A173SER00.029-0.00371.514-0.017-0.0170.0000.0000.0000.000
173A174ASP-1-0.848-0.90072.269-4.320-4.3200.0000.0000.0000.000
174A175PHE00.0470.01663.090-0.041-0.0410.0000.0000.0000.000
175A176LYS10.9630.98768.3334.6204.6200.0000.0000.0000.000
176A177LYS10.8920.97170.2314.2804.2800.0000.0000.0000.000
177A178ILE00.0200.01066.038-0.017-0.0170.0000.0000.0000.000
178A179PHE0-0.014-0.01161.584-0.048-0.0480.0000.0000.0000.000
179A180THR0-0.047-0.03466.344-0.053-0.0530.0000.0000.0000.000
180A181GLU-1-0.898-0.94468.529-4.512-4.5120.0000.0000.0000.000
181A182TYR0-0.001-0.02765.213-0.030-0.0300.0000.0000.0000.000
182A183GLY00.0210.01963.317-0.091-0.0910.0000.0000.0000.000
183A184LYS10.8490.94260.8254.7854.7850.0000.0000.0000.000
184A185GLN00.1150.04159.469-0.075-0.0750.0000.0000.0000.000
185A186LEU0-0.042-0.00759.072-0.085-0.0850.0000.0000.0000.000
186A187THR0-0.028-0.01956.382-0.125-0.1250.0000.0000.0000.000
187A188GLU-1-0.921-0.94755.144-5.686-5.6860.0000.0000.0000.000
188A189GLY00.022-0.00154.183-0.128-0.1280.0000.0000.0000.000
189A190ARG10.7900.87352.0645.9325.9320.0000.0000.0000.000
190A191LYS10.8940.94349.4826.1836.1830.0000.0000.0000.000
191A192GLN00.0300.01649.336-0.139-0.1390.0000.0000.0000.000
192A193THR0-0.009-0.00949.645-0.058-0.0580.0000.0000.0000.000
193A194ALA00.0310.02346.157-0.098-0.0980.0000.0000.0000.000
194A196ARG10.9150.96945.1336.0576.0570.0000.0000.0000.000
195A197ILE0-0.0240.00743.322-0.065-0.0650.0000.0000.0000.000
196A198VAL0-0.012-0.00439.983-0.170-0.1700.0000.0000.0000.000
197A199GLU-1-0.899-0.96740.930-7.054-7.0540.0000.0000.0000.000
198A200THR0-0.050-0.03541.909-0.092-0.0920.0000.0000.0000.000
199A201VAL0-0.019-0.01437.927-0.106-0.1060.0000.0000.0000.000
200A202TYR00.001-0.00334.886-0.112-0.1120.0000.0000.0000.000
201A203ALA00.0790.05736.725-0.257-0.2570.0000.0000.0000.000
202A204VAL0-0.063-0.02637.295-0.110-0.1100.0000.0000.0000.000
203A205SER0-0.054-0.03733.072-0.260-0.2600.0000.0000.0000.000
204A206VAL00.0270.01032.936-0.324-0.3240.0000.0000.0000.000
205A207HIS0-0.060-0.03133.917-0.046-0.0460.0000.0000.0000.000
206A208ASN00.0390.00831.8530.0810.0810.0000.0000.0000.000
207A209ILE00.0030.00528.556-0.270-0.2700.0000.0000.0000.000
208A210ARG10.7490.84929.9578.3628.3620.0000.0000.0000.000
209A211ALA0-0.017-0.00532.668-0.006-0.0060.0000.0000.0000.000
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