Manual

About

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

tag_button

FMODB ID: JLK69

Calculation Name: 1IGT-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1IGT

Chain ID: A

ChEMBL ID:

UniProt ID: P01863

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2143767.438451
FMO2-HF: Nuclear repulsion 2061306.882533
FMO2-HF: Total energy -82460.555918
FMO2-MP2: Total energy -82700.891077


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-45.759-39.8971.136-2.55-4.4490.02
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.922 / q_NPA : -0.963
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].
3A3VAL0-0.010-0.0023.339-0.6191.5010.020-0.851-1.2900.005
4A4LEU00.009-0.0195.050-3.712-3.659-0.001-0.004-0.0480.000
5A5THR0-0.039-0.0338.3470.1460.1460.0000.0000.0000.000
6A6GLN00.038-0.02711.563-0.199-0.1990.0000.0000.0000.000
7A7SER0-0.073-0.01614.419-0.067-0.0670.0000.0000.0000.000
8A8PRO00.0030.00317.761-0.212-0.2120.0000.0000.0000.000
9A9SER00.0770.02317.8310.5110.5110.0000.0000.0000.000
10A10SER0-0.011-0.01519.5750.1570.1570.0000.0000.0000.000
11A11LEU0-0.033-0.01622.991-0.112-0.1120.0000.0000.0000.000
12A12SER00.0400.03325.920-0.107-0.1070.0000.0000.0000.000
13A13ALA0-0.025-0.01329.577-0.036-0.0360.0000.0000.0000.000
14A14SER00.0000.00331.929-0.045-0.0450.0000.0000.0000.000
15A15LEU00.0510.01334.1050.1690.1690.0000.0000.0000.000
16A16GLY0-0.029-0.00735.202-0.151-0.1510.0000.0000.0000.000
17A17ASP-1-0.875-0.93932.5618.8038.8030.0000.0000.0000.000
18A18THR0-0.031-0.02729.9400.0640.0640.0000.0000.0000.000
19A19ILE0-0.021-0.00625.3050.0020.0020.0000.0000.0000.000
20A20THR0-0.024-0.01724.0080.0540.0540.0000.0000.0000.000
21A21ILE0-0.0120.01318.6380.1730.1730.0000.0000.0000.000
22A22THR0-0.023-0.02418.2190.0830.0830.0000.0000.0000.000
23A23CYS0-0.0060.02412.3870.4080.4080.0000.0000.0000.000
24A24HIS00.0180.02512.791-0.432-0.4320.0000.0000.0000.000
25A25ALA00.0150.0119.1121.5671.5670.0000.0000.0000.000
26A26SER00.0170.0126.3770.0090.0090.0000.0000.0000.000
27A27GLN00.0110.0044.850-4.584-4.5840.0000.0000.0000.000
28A28ASN00.0470.0208.782-0.477-0.4770.0000.0000.0000.000
29A29ILE00.025-0.0048.6821.2631.2630.0000.0000.0000.000
30A30ASN00.0170.00211.3210.0370.0370.0000.0000.0000.000
31A31VAL00.0570.02015.019-0.716-0.7160.0000.0000.0000.000
32A32TRP0-0.043-0.01512.295-1.117-1.1170.0000.0000.0000.000
33A33LEU00.0140.01212.1811.6951.6950.0000.0000.0000.000
34A34SER0-0.049-0.02314.002-1.449-1.4490.0000.0000.0000.000
35A35TRP00.0510.01415.4540.7450.7450.0000.0000.0000.000
36A36TYR0-0.009-0.02414.350-1.320-1.3200.0000.0000.0000.000
37A37GLN00.0590.02418.755-0.030-0.0300.0000.0000.0000.000
38A38GLN00.0260.01219.5360.2090.2090.0000.0000.0000.000
39A39LYS10.9000.95722.268-10.589-10.5890.0000.0000.0000.000
40A40PRO0-0.006-0.01725.5700.1480.1480.0000.0000.0000.000
41A41GLY00.0540.04225.481-0.484-0.4840.0000.0000.0000.000
42A42ASN0-0.027-0.00525.7730.3060.3060.0000.0000.0000.000
43A43ILE00.0250.01022.6970.4090.4090.0000.0000.0000.000
44A44PRO0-0.026-0.00918.554-0.426-0.4260.0000.0000.0000.000
45A45LYS10.9300.96421.229-11.813-11.8130.0000.0000.0000.000
46A46LEU00.000-0.00919.1180.3530.3530.0000.0000.0000.000
47A47LEU0-0.019-0.00420.651-0.630-0.6300.0000.0000.0000.000
48A48ILE00.0050.00019.833-0.540-0.5400.0000.0000.0000.000
49A49TYR00.0040.00318.4210.9690.9690.0000.0000.0000.000
50A50LYS10.9160.95318.130-13.792-13.7920.0000.0000.0000.000
51A51ALA00.0310.03817.962-0.812-0.8120.0000.0000.0000.000
52A52SER00.0160.00119.222-0.086-0.0860.0000.0000.0000.000
53A53ASN0-0.050-0.02822.465-0.431-0.4310.0000.0000.0000.000
54A54LEU00.0650.04623.0370.5100.5100.0000.0000.0000.000
55A55HIS0-0.026-0.00123.522-0.020-0.0200.0000.0000.0000.000
56A56THR00.036-0.00525.516-0.282-0.2820.0000.0000.0000.000
57A57GLY0-0.030-0.00428.0930.2470.2470.0000.0000.0000.000
58A58VAL0-0.038-0.02125.311-0.266-0.2660.0000.0000.0000.000
59A59PRO0-0.0050.01028.692-0.155-0.1550.0000.0000.0000.000
60A60SER00.039-0.00930.2310.2380.2380.0000.0000.0000.000
61A61ARG10.8640.95630.597-9.439-9.4390.0000.0000.0000.000
62A62PHE0-0.0060.01625.0020.1910.1910.0000.0000.0000.000
63A63SER00.011-0.01026.033-0.208-0.2080.0000.0000.0000.000
64A64GLY00.0090.01822.0410.2710.2710.0000.0000.0000.000
65A65SER0-0.001-0.01821.182-0.420-0.4200.0000.0000.0000.000
66A66GLY00.0490.03219.5670.6730.6730.0000.0000.0000.000
67A67SER0-0.037-0.03717.863-0.333-0.3330.0000.0000.0000.000
68A68GLY0-0.0150.00515.533-0.251-0.2510.0000.0000.0000.000
69A69THR00.010-0.00312.0980.9730.9730.0000.0000.0000.000
70A70GLY00.0510.05013.7820.8450.8450.0000.0000.0000.000
71A71PHE0-0.036-0.02813.637-0.594-0.5940.0000.0000.0000.000
72A72THR0-0.046-0.03217.5450.2310.2310.0000.0000.0000.000
73A73LEU00.0250.03120.031-0.073-0.0730.0000.0000.0000.000
74A74THR0-0.057-0.03721.660-0.220-0.2200.0000.0000.0000.000
75A75ILE00.0570.03424.354-0.043-0.0430.0000.0000.0000.000
76A76SER00.0030.00327.843-0.224-0.2240.0000.0000.0000.000
77A77SER0-0.044-0.03231.552-0.061-0.0610.0000.0000.0000.000
78A78LEU0-0.0180.00328.636-0.031-0.0310.0000.0000.0000.000
79A79GLN0-0.039-0.01332.034-0.485-0.4850.0000.0000.0000.000
80A80PRO00.0700.02732.0590.2780.2780.0000.0000.0000.000
81A81GLU-1-0.941-0.97831.3889.5939.5930.0000.0000.0000.000
82A82ASP-1-0.688-0.84627.94510.47810.4780.0000.0000.0000.000
83A83ILE0-0.054-0.00826.5850.5960.5960.0000.0000.0000.000
84A84ALA00.002-0.01623.772-0.064-0.0640.0000.0000.0000.000
85A85THR0-0.033-0.00418.877-0.363-0.3630.0000.0000.0000.000
86A86TYR0-0.017-0.03519.1390.1010.1010.0000.0000.0000.000
87A87TYR0-0.0280.00113.8230.2630.2630.0000.0000.0000.000
88A89GLN0-0.006-0.00510.214-0.162-0.1620.0000.0000.0000.000
89A90GLN00.0370.0385.244-6.327-6.3270.0000.0000.0000.000
90A91GLY00.022-0.0099.5941.2321.2320.0000.0000.0000.000
91A92GLN0-0.167-0.0668.7480.1180.1180.0000.0000.0000.000
92A93SER00.0370.0145.993-0.918-0.9180.0000.0000.0000.000
93A94TYR0-0.0290.0216.3380.2370.2370.0000.0000.0000.000
94A95PRO00.0350.0002.747-5.609-2.5551.021-1.559-2.5150.015
95A96LEU0-0.0020.0055.0810.0680.106-0.001-0.003-0.0340.000
96A97THR0-0.018-0.0102.859-1.327-0.7300.097-0.133-0.5620.000
97A98PHE00.022-0.0176.215-4.161-4.1610.0000.0000.0000.000
98A99GLY00.001-0.0028.2062.2572.2570.0000.0000.0000.000
99A100GLY0-0.0170.00410.452-1.597-1.5970.0000.0000.0000.000
100A101GLY00.0450.00912.4520.0060.0060.0000.0000.0000.000
101A102THR0-0.054-0.02015.846-0.387-0.3870.0000.0000.0000.000
102A103LYS10.8800.94719.140-12.423-12.4230.0000.0000.0000.000
103A104LEU0-0.011-0.00122.290-0.145-0.1450.0000.0000.0000.000
104A105GLU-1-0.947-0.97925.56210.14010.1400.0000.0000.0000.000
105A106ILE00.0180.00928.903-0.036-0.0360.0000.0000.0000.000
106A107LYS10.9080.95632.356-8.921-8.9210.0000.0000.0000.000
107A108ARG10.9150.95734.835-7.732-7.7320.0000.0000.0000.000
108A109ALA0-0.0010.00338.3250.0210.0210.0000.0000.0000.000
109A110ASP-1-0.882-0.95640.1637.7477.7470.0000.0000.0000.000
110A111ALA0-0.054-0.02741.409-0.176-0.1760.0000.0000.0000.000
111A112ALA00.0220.00042.2630.1410.1410.0000.0000.0000.000
112A113PRO00.0030.02141.517-0.048-0.0480.0000.0000.0000.000
113A114THR0-0.0060.01143.415-0.224-0.2240.0000.0000.0000.000
114A115VAL00.008-0.00344.6020.1160.1160.0000.0000.0000.000
115A116SER0-0.081-0.05345.553-0.204-0.2040.0000.0000.0000.000
116A117ILE00.0010.02045.8740.1790.1790.0000.0000.0000.000
117A118PHE0-0.025-0.01346.202-0.130-0.1300.0000.0000.0000.000
118A119PRO00.0040.00347.4460.1370.1370.0000.0000.0000.000
119A120PRO00.0190.01547.7090.0270.0270.0000.0000.0000.000
120A121SER00.0570.04147.840-0.128-0.1280.0000.0000.0000.000
121A122SER00.0510.01350.2730.0690.0690.0000.0000.0000.000
122A123GLU-1-0.918-0.95649.8176.2656.2650.0000.0000.0000.000
123A124GLN00.023-0.01443.977-0.045-0.0450.0000.0000.0000.000
124A125LEU0-0.016-0.01648.6170.0250.0250.0000.0000.0000.000
125A126THR0-0.049-0.02851.128-0.043-0.0430.0000.0000.0000.000
126A127SER0-0.042-0.02647.4360.0080.0080.0000.0000.0000.000
127A128GLY0-0.0100.01148.7570.0480.0480.0000.0000.0000.000
128A129GLY0-0.059-0.02945.6470.0940.0940.0000.0000.0000.000
129A130ALA0-0.017-0.01545.755-0.138-0.1380.0000.0000.0000.000
130A131SER0-0.0050.01942.5450.1540.1540.0000.0000.0000.000
131A132VAL00.0040.02844.322-0.132-0.1320.0000.0000.0000.000
132A133VAL00.0220.00541.3710.1960.1960.0000.0000.0000.000
133A134CYS0-0.066-0.02942.156-0.053-0.0530.0000.0000.0000.000
134A135PHE00.021-0.00340.1410.2350.2350.0000.0000.0000.000
135A136LEU0-0.026-0.01039.689-0.216-0.2160.0000.0000.0000.000
136A137ASN00.0570.00439.8870.3790.3790.0000.0000.0000.000
137A138ASN0-0.003-0.00740.0600.0550.0550.0000.0000.0000.000
138A139PHE0-0.0090.02036.130-0.157-0.1570.0000.0000.0000.000
139A140TYR00.1110.06933.7100.2030.2030.0000.0000.0000.000
140A141PRO0-0.002-0.02334.802-0.249-0.2490.0000.0000.0000.000
141A142LYS11.0201.00627.619-11.072-11.0720.0000.0000.0000.000
142A143ASP-1-0.970-0.97132.2899.5649.5640.0000.0000.0000.000
143A144ILE00.0080.00034.521-0.308-0.3080.0000.0000.0000.000
144A145ASN0-0.047-0.01035.9040.2740.2740.0000.0000.0000.000
145A146VAL00.0280.02838.050-0.264-0.2640.0000.0000.0000.000
146A147LYS10.8890.94439.328-7.256-7.2560.0000.0000.0000.000
147A148TRP00.0270.00540.657-0.244-0.2440.0000.0000.0000.000
148A149LYS10.8250.90744.252-6.515-6.5150.0000.0000.0000.000
149A150ILE00.0270.02646.812-0.039-0.0390.0000.0000.0000.000
150A151ASP-1-0.710-0.84349.7965.8415.8410.0000.0000.0000.000
151A152GLY00.0410.01552.5610.0450.0450.0000.0000.0000.000
152A153SER0-0.089-0.07350.3770.0240.0240.0000.0000.0000.000
153A154GLU-1-0.916-0.93748.7286.3386.3380.0000.0000.0000.000
154A155ARG10.9230.96938.807-7.839-7.8390.0000.0000.0000.000
155A156GLN00.0540.03742.069-0.105-0.1050.0000.0000.0000.000
156A157ASN0-0.043-0.05237.656-0.008-0.0080.0000.0000.0000.000
157A158GLY00.0380.03537.2800.2410.2410.0000.0000.0000.000
158A159VAL0-0.050-0.02436.945-0.187-0.1870.0000.0000.0000.000
159A160LEU00.0140.01133.1260.2850.2850.0000.0000.0000.000
160A161ASN00.0060.00533.276-0.403-0.4030.0000.0000.0000.000
161A162SER00.0160.00731.7020.3910.3910.0000.0000.0000.000
162A163TRP00.0400.01730.908-0.274-0.2740.0000.0000.0000.000
163A164THR00.0180.01431.1520.1660.1660.0000.0000.0000.000
164A165ASP-1-0.937-0.97127.18411.58311.5830.0000.0000.0000.000
165A166GLN0-0.091-0.04930.1380.0100.0100.0000.0000.0000.000
166A167ASP-1-0.865-0.94132.2098.5598.5590.0000.0000.0000.000
167A168SER0-0.050-0.02734.454-0.114-0.1140.0000.0000.0000.000
168A169LYS10.9610.98335.298-7.216-7.2160.0000.0000.0000.000
169A170ASP-1-0.898-0.94339.0267.5017.5010.0000.0000.0000.000
170A171SER0-0.036-0.01735.638-0.039-0.0390.0000.0000.0000.000
171A172THR0-0.010-0.00635.8540.0720.0720.0000.0000.0000.000
172A173TYR0-0.0210.00029.9880.2050.2050.0000.0000.0000.000
173A174SER00.004-0.00935.231-0.391-0.3910.0000.0000.0000.000
174A175MET00.0050.00534.8470.2830.2830.0000.0000.0000.000
175A176SER0-0.030-0.00536.249-0.355-0.3550.0000.0000.0000.000
176A177SER0-0.020-0.00136.6560.1790.1790.0000.0000.0000.000
177A178THR00.0260.00238.132-0.297-0.2970.0000.0000.0000.000
178A179LEU00.0010.00839.0730.2040.2040.0000.0000.0000.000
179A180THR0-0.018-0.01438.856-0.161-0.1610.0000.0000.0000.000
180A181LEU0-0.0080.00042.0340.0830.0830.0000.0000.0000.000
181A182THR00.0520.02944.8920.0220.0220.0000.0000.0000.000
182A183LYS10.9570.97247.081-5.945-5.9450.0000.0000.0000.000
183A184ASP-1-0.853-0.92650.4306.0996.0990.0000.0000.0000.000
184A185GLU-1-0.941-0.99547.2296.6186.6180.0000.0000.0000.000
185A186TYR0-0.0120.00249.077-0.038-0.0380.0000.0000.0000.000
186A187GLU-1-0.896-0.97050.5835.7145.7140.0000.0000.0000.000
187A188ARG10.8890.95651.138-6.273-6.2730.0000.0000.0000.000
188A189HIS10.8110.92450.421-6.310-6.3100.0000.0000.0000.000
189A190ASN0-0.061-0.04254.558-0.014-0.0140.0000.0000.0000.000
190A191SER0-0.009-0.00254.2540.0290.0290.0000.0000.0000.000
191A192TYR00.016-0.00448.3820.1630.1630.0000.0000.0000.000
192A193THR0-0.012-0.01248.393-0.095-0.0950.0000.0000.0000.000
193A195GLU-1-0.889-0.95844.9926.6266.6260.0000.0000.0000.000
194A196ALA00.0360.00442.5270.2240.2240.0000.0000.0000.000
195A197THR0-0.062-0.03540.901-0.117-0.1170.0000.0000.0000.000
196A198HIS00.0800.02538.331-0.004-0.0040.0000.0000.0000.000
197A199LYS10.9290.98438.938-7.791-7.7910.0000.0000.0000.000
198A200THR0-0.030-0.04441.837-0.176-0.1760.0000.0000.0000.000
199A201SER0-0.035-0.01244.444-0.224-0.2240.0000.0000.0000.000
200A202THR00.0030.00945.8510.1210.1210.0000.0000.0000.000
201A203SER0-0.023-0.01547.7430.0150.0150.0000.0000.0000.000
202A204PRO0-0.004-0.01346.3280.0360.0360.0000.0000.0000.000
203A205ILE00.0340.03845.908-0.155-0.1550.0000.0000.0000.000
204A206VAL00.0140.00446.9120.1450.1450.0000.0000.0000.000
205A207LYS10.9260.97048.698-6.325-6.3250.0000.0000.0000.000
206A208SER0-0.021-0.01149.6650.0780.0780.0000.0000.0000.000
207A209PHE00.005-0.00449.275-0.051-0.0510.0000.0000.0000.000
208A210ASN00.0650.02853.8020.1630.1630.0000.0000.0000.000
209A211ARG10.8810.94854.549-5.765-5.7650.0000.0000.0000.000
210A212ASN0-0.089-0.05756.356-0.012-0.0120.0000.0000.0000.000
211A213GLU-1-0.901-0.91559.2665.0285.0280.0000.0000.0000.000
212A214CYS0-0.015-0.00154.942-0.023-0.0230.0000.0000.0000.000