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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JMZL9

Calculation Name: 3CZU-A-Xray308

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3CZU

Chain ID: A

ChEMBL ID:

UniProt ID: P20827

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 175
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1875652.202124
FMO2-HF: Nuclear repulsion 1804103.577004
FMO2-HF: Total energy -71548.62512
FMO2-MP2: Total energy -71753.171109


3D Structure
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:26:ACE )


Summations of interaction energy for fragment #1(A:26:ACE )
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.
-1.3280.9111.257-1.574-1.924-0.011
Interaction energy analysis for fragmet #1(A:26:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.028
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].
3A28GLU -1-0.874-0.9303.861-0.0600.744-0.005-0.333-0.4650.000
4A29VAL 0-0.0230.0036.9480.0100.0100.0000.0000.0000.000
5A30VAL 00.009-0.0069.6820.0970.0970.0000.0000.0000.000
6A31LEU 0-0.048-0.03013.0630.0230.0230.0000.0000.0000.000
7A32LEU 0-0.023-0.01415.8450.0260.0260.0000.0000.0000.000
8A33ASP -1-0.856-0.93917.395-0.223-0.2230.0000.0000.0000.000
9A34PHE 0-0.057-0.02119.3370.0060.0060.0000.0000.0000.000
10A35ALA 00.0260.01221.9550.0050.0050.0000.0000.0000.000
11A36ALA 0-0.020-0.00120.4460.0030.0030.0000.0000.0000.000
12A37ALA 0-0.025-0.01622.5640.0030.0030.0000.0000.0000.000
13A38GLY 00.0340.02425.0830.0080.0080.0000.0000.0000.000
14A39GLY 0-0.017-0.01927.9890.0070.0070.0000.0000.0000.000
15A40GLU -1-0.953-0.96828.755-0.081-0.0810.0000.0000.0000.000
16A41LEU 0-0.057-0.02923.9510.0030.0030.0000.0000.0000.000
17A42GLY 0-0.0200.00128.5000.0030.0030.0000.0000.0000.000
18A43TRP 00.0120.00123.7600.0030.0030.0000.0000.0000.000
19A44LEU 0-0.0090.01730.3620.0030.0030.0000.0000.0000.000
20A45THR 00.004-0.00832.2460.0000.0000.0000.0000.0000.000
21A46HIS 0-0.0270.00834.8220.0010.0010.0000.0000.0000.000
22A47PRO 00.023-0.00236.8250.0000.0000.0000.0000.0000.000
23A48TYR 0-0.001-0.02539.701-0.001-0.0010.0000.0000.0000.000
24A49GLY 00.0150.02039.8120.0010.0010.0000.0000.0000.000
25A50LYS 10.8360.92540.3290.0180.0180.0000.0000.0000.000
26A51GLY 0-0.014-0.02037.6150.0000.0000.0000.0000.0000.000
27A52TRP 0-0.027-0.03230.455-0.002-0.0020.0000.0000.0000.000
28A53ASP -1-0.854-0.91935.361-0.033-0.0330.0000.0000.0000.000
29A54LEU 0-0.068-0.04031.093-0.003-0.0030.0000.0000.0000.000
30A55MET 0-0.028-0.00433.7430.0020.0020.0000.0000.0000.000
31A56GLN 00.001-0.01333.475-0.007-0.0070.0000.0000.0000.000
32A57ASN 0-0.010-0.02633.8350.0050.0050.0000.0000.0000.000
33A58ILE 00.0000.03233.580-0.004-0.0040.0000.0000.0000.000
34A59MET 0-0.022-0.01027.5600.0050.0050.0000.0000.0000.000
35A60ASN 0-0.017-0.01028.066-0.001-0.0010.0000.0000.0000.000
36A61ASP -1-0.913-0.95531.398-0.068-0.0680.0000.0000.0000.000
37A62MET 0-0.029-0.01328.531-0.003-0.0030.0000.0000.0000.000
38A63PRO 0-0.0120.00131.1070.0040.0040.0000.0000.0000.000
39A64ILE 0-0.010-0.01128.371-0.007-0.0070.0000.0000.0000.000
40A65TYR 00.0510.01328.9610.0060.0060.0000.0000.0000.000
41A66MET 0-0.023-0.00728.814-0.003-0.0030.0000.0000.0000.000
42A67TYR 00.0370.03528.5260.0030.0030.0000.0000.0000.000
43A68SER 0-0.050-0.02831.0080.0000.0000.0000.0000.0000.000
44A69VAL 00.0550.03333.7010.0010.0010.0000.0000.0000.000
45A188CYS 0-0.062-0.02836.222-0.001-0.0010.0000.0000.0000.000
46A71ASN 00.0050.00938.9370.0010.0010.0000.0000.0000.000
47A72VAL 00.0360.00540.0890.0020.0020.0000.0000.0000.000
48A73MET 0-0.061-0.01842.4670.0020.0020.0000.0000.0000.000
49A74SER 0-0.034-0.01744.7790.0010.0010.0000.0000.0000.000
50A75GLY 0-0.0060.00545.7310.0010.0010.0000.0000.0000.000
51A76ASP -1-0.917-0.96742.973-0.007-0.0070.0000.0000.0000.000
52A77GLN 00.0230.04039.331-0.002-0.0020.0000.0000.0000.000
53A78ASP -1-0.796-0.89836.930-0.009-0.0090.0000.0000.0000.000
54A79ASN 0-0.041-0.00636.0870.0000.0000.0000.0000.0000.000
55A80TRP 0-0.050-0.03630.2240.0000.0000.0000.0000.0000.000
56A81LEU 00.0070.02928.428-0.001-0.0010.0000.0000.0000.000
57A82ARG 10.8550.92927.9720.0350.0350.0000.0000.0000.000
58A83THR 00.0210.00623.2310.0000.0000.0000.0000.0000.000
59A84ASN 0-0.003-0.01725.7520.0130.0130.0000.0000.0000.000
60A85TRP 0-0.033-0.01124.481-0.005-0.0050.0000.0000.0000.000
61A86VAL 00.0110.01418.399-0.009-0.0090.0000.0000.0000.000
62A87TYR 0-0.027-0.01518.3290.0180.0180.0000.0000.0000.000
63A88ARG 10.8890.91916.105-0.046-0.0460.0000.0000.0000.000
64A89GLY 0-0.006-0.01315.430-0.013-0.0130.0000.0000.0000.000
65A90GLU -1-0.866-0.9289.714-0.054-0.0540.0000.0000.0000.000
66A91ALA 0-0.0160.01411.8500.0380.0380.0000.0000.0000.000
67A92GLU -1-0.892-0.93212.0510.2060.2060.0000.0000.0000.000
68A93ARG 10.9130.95711.464-0.146-0.1460.0000.0000.0000.000
69A94ILE 0-0.044-0.00911.461-0.013-0.0130.0000.0000.0000.000
70A95PHE 0-0.034-0.0409.1920.0560.0560.0000.0000.0000.000
71A96ILE 0-0.012-0.01513.285-0.036-0.0360.0000.0000.0000.000
72A97GLU -1-0.866-0.94315.270-0.170-0.1700.0000.0000.0000.000
73A98LEU 0-0.019-0.01617.213-0.006-0.0060.0000.0000.0000.000
74A99LYS 10.9760.98919.1050.1450.1450.0000.0000.0000.000
75A100PHE 0-0.016-0.01523.0470.0000.0000.0000.0000.0000.000
76A101THR 00.0110.01626.7840.0020.0020.0000.0000.0000.000
77A102VAL 00.024-0.00130.1220.0010.0010.0000.0000.0000.000
78A103ARG 10.8620.93632.6950.0250.0250.0000.0000.0000.000
79A104ASP -1-0.808-0.90236.388-0.014-0.0140.0000.0000.0000.000
80A115CYS 0-0.0420.00838.567-0.002-0.0020.0000.0000.0000.000
81A106ASN 0-0.023-0.00940.8190.0010.0010.0000.0000.0000.000
82A107SER 0-0.118-0.06141.1430.0000.0000.0000.0000.0000.000
83A108PHE 0-0.005-0.03439.910-0.001-0.0010.0000.0000.0000.000
84A109PRO 0-0.012-0.00845.4460.0010.0010.0000.0000.0000.000
85A110GLY 0-0.020-0.00248.8130.0010.0010.0000.0000.0000.000
86A111GLY 00.0720.02445.7140.0000.0000.0000.0000.0000.000
87A112ALA 00.0350.03746.5900.0010.0010.0000.0000.0000.000
88A113SER 0-0.007-0.00745.2060.0000.0000.0000.0000.0000.000
89A114SER 0-0.054-0.04743.6000.0010.0010.0000.0000.0000.000
90A116LYS 10.8970.95036.3810.0090.0090.0000.0000.0000.000
91A117GLU -1-0.770-0.90734.387-0.016-0.0160.0000.0000.0000.000
92A118THR 0-0.044-0.01730.885-0.001-0.0010.0000.0000.0000.000
93A119PHE 00.0010.00626.052-0.001-0.0010.0000.0000.0000.000
94A120ASN 0-0.047-0.02628.5350.0040.0040.0000.0000.0000.000
95A121LEU 00.0560.04521.017-0.004-0.0040.0000.0000.0000.000
96A122TYR 0-0.017-0.02225.6890.0090.0090.0000.0000.0000.000
97A123TYR 00.0360.00622.429-0.007-0.0070.0000.0000.0000.000
98A124ALA 00.0290.01924.5630.0060.0060.0000.0000.0000.000
99A125GLU -1-0.803-0.89721.9040.0210.0210.0000.0000.0000.000
100A126SER 0-0.023-0.02724.6570.0030.0030.0000.0000.0000.000
101A127ASP -1-0.864-0.93725.0800.0050.0050.0000.0000.0000.000
102A128LEU 0-0.036-0.03826.990-0.004-0.0040.0000.0000.0000.000
103A129ASP -1-0.819-0.89428.321-0.039-0.0390.0000.0000.0000.000
104A130TYR 0-0.036-0.02829.4080.0020.0020.0000.0000.0000.000
105A131GLY 00.0390.02331.6060.0010.0010.0000.0000.0000.000
106A132THR 00.004-0.01933.184-0.001-0.0010.0000.0000.0000.000
107A133ASN 0-0.0160.01335.2070.0010.0010.0000.0000.0000.000
108A134PHE 00.004-0.00730.934-0.001-0.0010.0000.0000.0000.000
109A135GLN 00.0370.01734.2060.0010.0010.0000.0000.0000.000
110A136LYS 10.9860.98833.3370.0080.0080.0000.0000.0000.000
111A137ARG 10.8520.92532.8890.0010.0010.0000.0000.0000.000
112A138LEU 00.0190.02031.2330.0030.0030.0000.0000.0000.000
113A139PHE 0-0.042-0.01327.0010.0000.0000.0000.0000.0000.000
114A140THR 0-0.021-0.00626.1610.0030.0030.0000.0000.0000.000
115A141LYS 10.8540.92226.473-0.006-0.0060.0000.0000.0000.000
116A142ILE 0-0.036-0.02120.6990.0050.0050.0000.0000.0000.000
117A143ASP -1-0.777-0.87823.4460.0180.0180.0000.0000.0000.000
118A144THR 0-0.070-0.03725.434-0.005-0.0050.0000.0000.0000.000
119A145ILE 0-0.033-0.00323.2770.0020.0020.0000.0000.0000.000
120A146ALA 00.016-0.02126.6200.0000.0000.0000.0000.0000.000
121A147PRO 0-0.026-0.00126.971-0.002-0.0020.0000.0000.0000.000
122A148ASP -1-0.867-0.91624.982-0.017-0.0170.0000.0000.0000.000
123A149GLU -1-0.993-1.00928.318-0.038-0.0380.0000.0000.0000.000
124A150ILE 0-0.030-0.00430.580-0.003-0.0030.0000.0000.0000.000
125A151THR 0-0.029-0.01733.242-0.002-0.0020.0000.0000.0000.000
126A152VAL 00.0310.00135.4080.0020.0020.0000.0000.0000.000
127A153SER 0-0.005-0.01839.017-0.002-0.0020.0000.0000.0000.000
128A154SER 00.0460.01040.5870.0000.0000.0000.0000.0000.000
129A155ASP -1-0.797-0.88136.439-0.031-0.0310.0000.0000.0000.000
130A156PHE 0-0.063-0.03238.478-0.003-0.0030.0000.0000.0000.000
131A157GLU -1-1.002-0.99840.702-0.027-0.0270.0000.0000.0000.000
132A158ALA 00.0470.03239.520-0.001-0.0010.0000.0000.0000.000
133A159ARG 10.8630.93237.8010.0410.0410.0000.0000.0000.000
134A160HIS 00.0110.01632.074-0.005-0.0050.0000.0000.0000.000
135A161VAL 0-0.008-0.01229.9200.0020.0020.0000.0000.0000.000
136A162LYS 10.8910.94230.0150.0280.0280.0000.0000.0000.000
137A163LEU 0-0.044-0.02424.5070.0000.0000.0000.0000.0000.000
138A164ASN 00.0410.03525.2560.0000.0000.0000.0000.0000.000
139A165VAL 00.003-0.01518.560-0.011-0.0110.0000.0000.0000.000
140A166GLU -1-0.827-0.90120.505-0.013-0.0130.0000.0000.0000.000
141A167GLU -1-0.876-0.93912.712-0.114-0.1140.0000.0000.0000.000
142A168ARG 10.7440.85717.2360.0260.0260.0000.0000.0000.000
143A169SER 00.0020.00613.913-0.002-0.0020.0000.0000.0000.000
144A170VAL 0-0.0130.00515.8050.0090.0090.0000.0000.0000.000
145A171GLY 00.0030.00815.9700.0030.0030.0000.0000.0000.000
146A172PRO 0-0.064-0.02416.4820.0030.0030.0000.0000.0000.000
147A173LEU 0-0.012-0.02616.618-0.012-0.0120.0000.0000.0000.000
148A174THR 0-0.046-0.03018.1810.0070.0070.0000.0000.0000.000
149A175ARG 10.9210.97520.831-0.021-0.0210.0000.0000.0000.000
150A176LYS 10.9370.99421.0400.0200.0200.0000.0000.0000.000
151A177GLY 00.0450.00321.166-0.011-0.0110.0000.0000.0000.000
152A178PHE 0-0.0090.00317.4610.0120.0120.0000.0000.0000.000
153A179TYR 0-0.036-0.00422.749-0.008-0.0080.0000.0000.0000.000
154A180LEU 00.0200.00419.6000.0070.0070.0000.0000.0000.000
155A181ALA 0-0.015-0.01323.969-0.002-0.0020.0000.0000.0000.000
156A182PHE 00.0180.01223.2520.0030.0030.0000.0000.0000.000
157A183GLN 0-0.006-0.01028.4740.0010.0010.0000.0000.0000.000
158A184ASP -1-0.722-0.87331.763-0.020-0.0200.0000.0000.0000.000
159A185ILE 0-0.046-0.02734.0150.0020.0020.0000.0000.0000.000
160A186GLY 0-0.024-0.01536.7830.0020.0020.0000.0000.0000.000
161A187ALA 0-0.0130.00834.5810.0010.0010.0000.0000.0000.000
162A189VAL 00.0220.01430.055-0.001-0.0010.0000.0000.0000.000
163A190ALA 00.0190.00531.3290.0000.0000.0000.0000.0000.000
164A191LEU 00.002-0.00824.674-0.002-0.0020.0000.0000.0000.000
165A192LEU 0-0.011-0.01825.815-0.002-0.0020.0000.0000.0000.000
166A193SER 00.0070.00220.189-0.013-0.0130.0000.0000.0000.000
167A194VAL 0-0.0020.00020.3110.0100.0100.0000.0000.0000.000
168A195ARG 10.9080.97211.1780.3340.3340.0000.0000.0000.000
169A196VAL 0-0.020-0.00615.2840.0160.0160.0000.0000.0000.000
170A197TYR 0-0.007-0.0058.571-0.053-0.0530.0000.0000.0000.000
171A198TYR 00.0270.0158.5340.0530.0530.0000.0000.0000.000
172A199LYS 10.9500.9734.199-0.266-0.2450.000-0.010-0.0120.000
173A200LYS 10.8930.9454.5000.3960.5170.000-0.026-0.0960.000
174A201CYS 0-0.075-0.0562.607-1.662-0.4401.262-1.198-1.287-0.011
175A202NME 00.0690.0554.6940.2550.3260.000-0.007-0.0640.000