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

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FMODB ID: 39G3L

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 OptHSide
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 -2144958.138711
FMO2-HF: Nuclear repulsion 2062495.85162
FMO2-HF: Total energy -82462.287092
FMO2-MP2: Total energy -82702.48217


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.
-48.136-42.5522.862-2.998-5.4450.028
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 : -0.914 / q_NPA : -0.962
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].
3A3VAL0-0.0020.0073.491-0.0272.0170.016-0.808-1.2520.005
4A4LEU00.011-0.0114.961-3.769-3.719-0.001-0.004-0.0440.000
5A5THR0-0.065-0.0498.3070.0450.0450.0000.0000.0000.000
6A6GLN00.038-0.00911.488-0.475-0.4750.0000.0000.0000.000
7A7SER0-0.071-0.01514.372-0.172-0.1720.0000.0000.0000.000
8A8PRO00.0140.00317.694-0.197-0.1970.0000.0000.0000.000
9A9SER00.0790.04117.6090.5480.5480.0000.0000.0000.000
10A10SER0-0.009-0.01419.5100.1210.1210.0000.0000.0000.000
11A11LEU0-0.021-0.00722.939-0.136-0.1360.0000.0000.0000.000
12A12SER00.007-0.00425.875-0.059-0.0590.0000.0000.0000.000
13A13ALA0-0.040-0.00929.537-0.018-0.0180.0000.0000.0000.000
14A14SER0-0.018-0.02231.898-0.067-0.0670.0000.0000.0000.000
15A15LEU00.0250.00334.0930.1700.1700.0000.0000.0000.000
16A16GLY0-0.028-0.01135.213-0.152-0.1520.0000.0000.0000.000
17A17ASP-1-0.815-0.88932.7408.8188.8180.0000.0000.0000.000
18A18THR0-0.015-0.02229.8950.1030.1030.0000.0000.0000.000
19A19ILE0-0.045-0.01726.029-0.010-0.0100.0000.0000.0000.000
20A20THR00.010-0.00724.0390.0560.0560.0000.0000.0000.000
21A21ILE0-0.0130.01418.6280.1910.1910.0000.0000.0000.000
22A22THR0-0.023-0.02118.3760.0630.0630.0000.0000.0000.000
23A23CYS0-0.0120.02212.6540.3320.3320.0000.0000.0000.000
24A24HIS00.0250.02512.746-0.504-0.5040.0000.0000.0000.000
25A25ALA00.0240.0159.1791.6151.6150.0000.0000.0000.000
26A26SER00.0210.0126.4420.0010.0010.0000.0000.0000.000
27A27GLN00.0110.0054.384-5.852-5.648-0.001-0.024-0.1780.000
28A28ASN00.0210.0048.782-0.461-0.4610.0000.0000.0000.000
29A29ILE00.0410.0118.6891.2611.2610.0000.0000.0000.000
30A30ASN0-0.007-0.02011.3440.0000.0000.0000.0000.0000.000
31A31VAL00.0540.02115.041-0.751-0.7510.0000.0000.0000.000
32A32TRP0-0.035-0.01612.401-1.093-1.0930.0000.0000.0000.000
33A33LEU00.0070.01212.0751.7571.7570.0000.0000.0000.000
34A34SER0-0.029-0.01714.091-1.292-1.2920.0000.0000.0000.000
35A35TRP00.0480.01515.5280.7340.7340.0000.0000.0000.000
36A36TYR0-0.019-0.02114.373-1.430-1.4300.0000.0000.0000.000
37A37GLN0-0.001-0.00918.833-0.119-0.1190.0000.0000.0000.000
38A38GLN00.0360.01719.7480.3950.3950.0000.0000.0000.000
39A39LYS10.8560.93222.324-10.876-10.8760.0000.0000.0000.000
40A40PRO00.001-0.00925.4810.1380.1380.0000.0000.0000.000
41A41GLY00.0260.02925.423-0.486-0.4860.0000.0000.0000.000
42A42ASN0-0.032-0.00625.6690.4160.4160.0000.0000.0000.000
43A43ILE00.0400.01222.5910.4230.4230.0000.0000.0000.000
44A44PRO0-0.006-0.00218.413-0.429-0.4290.0000.0000.0000.000
45A45LYS10.9170.96521.318-11.930-11.9300.0000.0000.0000.000
46A46LEU0-0.012-0.01219.2800.3810.3810.0000.0000.0000.000
47A47LEU0-0.016-0.00220.747-0.634-0.6340.0000.0000.0000.000
48A48ILE0-0.010-0.00620.488-0.556-0.5560.0000.0000.0000.000
49A49TYR00.0460.02418.5320.9950.9950.0000.0000.0000.000
50A50LYS10.8960.94018.138-13.925-13.9250.0000.0000.0000.000
51A51ALA00.0290.03317.978-0.886-0.8860.0000.0000.0000.000
52A52SER00.0170.00119.297-0.113-0.1130.0000.0000.0000.000
53A53ASN0-0.042-0.02322.455-0.549-0.5490.0000.0000.0000.000
54A54LEU00.0550.04223.1380.5220.5220.0000.0000.0000.000
55A55HIS0-0.032-0.00723.600-0.037-0.0370.0000.0000.0000.000
56A56THR00.031-0.00525.630-0.318-0.3180.0000.0000.0000.000
57A57GLY0-0.0240.00028.2040.2540.2540.0000.0000.0000.000
58A58VAL0-0.043-0.02725.397-0.271-0.2710.0000.0000.0000.000
59A59PRO00.0090.01928.780-0.143-0.1430.0000.0000.0000.000
60A60SER00.042-0.00830.2990.2460.2460.0000.0000.0000.000
61A61ARG10.8210.91930.655-9.531-9.5310.0000.0000.0000.000
62A62PHE00.0090.02025.3030.2200.2200.0000.0000.0000.000
63A63SER0-0.004-0.02226.098-0.212-0.2120.0000.0000.0000.000
64A64GLY00.0280.02722.1040.2640.2640.0000.0000.0000.000
65A65SER0-0.005-0.01921.192-0.463-0.4630.0000.0000.0000.000
66A66GLY00.0450.03019.5850.6810.6810.0000.0000.0000.000
67A67SER0-0.013-0.02417.928-0.443-0.4430.0000.0000.0000.000
68A68GLY0-0.0270.00015.475-0.307-0.3070.0000.0000.0000.000
69A69THR00.006-0.00612.1341.0051.0050.0000.0000.0000.000
70A70GLY00.0490.05013.7560.8540.8540.0000.0000.0000.000
71A71PHE0-0.050-0.02713.864-0.637-0.6370.0000.0000.0000.000
72A72THR0-0.014-0.01717.5520.1510.1510.0000.0000.0000.000
73A73LEU0-0.0300.00120.035-0.142-0.1420.0000.0000.0000.000
74A74THR0-0.016-0.02421.682-0.144-0.1440.0000.0000.0000.000
75A75ILE00.0140.02224.226-0.045-0.0450.0000.0000.0000.000
76A76SER0-0.0020.01027.865-0.206-0.2060.0000.0000.0000.000
77A77SER0-0.025-0.02331.572-0.029-0.0290.0000.0000.0000.000
78A78LEU0-0.0230.01228.567-0.023-0.0230.0000.0000.0000.000
79A79GLN0-0.023-0.02332.083-0.519-0.5190.0000.0000.0000.000
80A80PRO00.0700.02432.0920.2860.2860.0000.0000.0000.000
81A81GLU-1-0.885-0.92831.4129.6379.6370.0000.0000.0000.000
82A82ASP-1-0.717-0.85528.00910.63010.6300.0000.0000.0000.000
83A83ILE0-0.036-0.00826.6150.5920.5920.0000.0000.0000.000
84A84ALA0-0.009-0.00823.880-0.056-0.0560.0000.0000.0000.000
85A85THR0-0.0160.00018.639-0.334-0.3340.0000.0000.0000.000
86A86TYR0-0.008-0.01919.1660.0140.0140.0000.0000.0000.000
87A87TYR0-0.019-0.00813.9470.2370.2370.0000.0000.0000.000
88A89GLN00.001-0.00310.289-0.019-0.0190.0000.0000.0000.000
89A90GLN00.0460.0345.621-6.205-6.2050.0000.0000.0000.000
90A91GLY0-0.001-0.0109.7251.3221.3220.0000.0000.0000.000
91A92GLN0-0.111-0.0408.9460.2320.2320.0000.0000.0000.000
92A93SER00.0180.0046.014-1.135-1.1350.0000.0000.0000.000
93A94TYR0-0.0190.0236.3370.7210.7210.0000.0000.0000.000
94A95PRO00.0370.0062.616-6.471-3.9862.755-1.946-3.2940.022
95A96LEU0-0.014-0.0055.0820.1900.232-0.001-0.004-0.0370.000
96A97THR0-0.016-0.0102.885-1.409-0.6500.094-0.212-0.6400.001
97A98PHE00.017-0.0186.321-4.412-4.4120.0000.0000.0000.000
98A99GLY00.0090.0018.2162.2442.2440.0000.0000.0000.000
99A100GLY0-0.025-0.00110.443-1.724-1.7240.0000.0000.0000.000
100A101GLY00.025-0.00312.4220.0300.0300.0000.0000.0000.000
101A102THR0-0.040-0.03615.833-0.452-0.4520.0000.0000.0000.000
102A103LYS10.7990.89919.115-12.179-12.1790.0000.0000.0000.000
103A104LEU0-0.024-0.00522.272-0.174-0.1740.0000.0000.0000.000
104A105GLU-1-0.828-0.89625.5509.9629.9620.0000.0000.0000.000
105A106ILE00.0370.02028.881-0.032-0.0320.0000.0000.0000.000
106A107LYS10.8930.95432.339-9.082-9.0820.0000.0000.0000.000
107A108ARG10.8920.93634.803-7.793-7.7930.0000.0000.0000.000
108A109ALA00.0130.01238.2930.0230.0230.0000.0000.0000.000
109A110ASP-1-0.824-0.90740.2207.7687.7680.0000.0000.0000.000
110A111ALA0-0.052-0.02641.359-0.175-0.1750.0000.0000.0000.000
111A112ALA00.0270.00342.2100.1390.1390.0000.0000.0000.000
112A113PRO00.0140.02241.404-0.048-0.0480.0000.0000.0000.000
113A114THR0-0.034-0.00243.364-0.222-0.2220.0000.0000.0000.000
114A115VAL00.0080.00144.6500.1170.1170.0000.0000.0000.000
115A116SER0-0.065-0.04445.518-0.237-0.2370.0000.0000.0000.000
116A117ILE0-0.0070.01345.9650.1840.1840.0000.0000.0000.000
117A118PHE0-0.006-0.00345.926-0.130-0.1300.0000.0000.0000.000
118A119PRO00.0070.00547.5990.1390.1390.0000.0000.0000.000
119A120PRO00.0170.01648.0160.0320.0320.0000.0000.0000.000
120A121SER00.0570.03748.532-0.121-0.1210.0000.0000.0000.000
121A122SER00.0480.01550.4270.0670.0670.0000.0000.0000.000
122A123GLU-1-0.926-0.96050.2036.3266.3260.0000.0000.0000.000
123A124GLN00.012-0.01244.037-0.039-0.0390.0000.0000.0000.000
124A125LEU0-0.008-0.01448.7950.0260.0260.0000.0000.0000.000
125A126THR0-0.051-0.02651.325-0.044-0.0440.0000.0000.0000.000
126A127SER0-0.041-0.02347.6400.0080.0080.0000.0000.0000.000
127A128GLY0-0.0060.01448.9760.0470.0470.0000.0000.0000.000
128A129GLY0-0.062-0.03145.8650.0930.0930.0000.0000.0000.000
129A130ALA0-0.020-0.01445.976-0.136-0.1360.0000.0000.0000.000
130A131SER00.0120.01542.6580.1540.1540.0000.0000.0000.000
131A132VAL0-0.0080.01744.525-0.129-0.1290.0000.0000.0000.000
132A133VAL00.0110.00241.3210.1990.1990.0000.0000.0000.000
133A134CYS0-0.033-0.01042.294-0.037-0.0370.0000.0000.0000.000
134A135PHE0-0.003-0.01440.6230.2170.2170.0000.0000.0000.000
135A136LEU0-0.021-0.00739.670-0.218-0.2180.0000.0000.0000.000
136A137ASN00.046-0.00139.8430.3690.3690.0000.0000.0000.000
137A138ASN00.005-0.00540.0160.0500.0500.0000.0000.0000.000
138A139PHE00.0020.02235.913-0.161-0.1610.0000.0000.0000.000
139A140TYR00.0750.02833.0240.1920.1920.0000.0000.0000.000
140A141PRO00.000-0.01334.730-0.256-0.2560.0000.0000.0000.000
141A142LYS10.9420.97728.074-10.709-10.7090.0000.0000.0000.000
142A143ASP-1-0.935-0.96132.1789.5399.5390.0000.0000.0000.000
143A144ILE0-0.0060.00234.441-0.315-0.3150.0000.0000.0000.000
144A145ASN0-0.056-0.02035.8190.2610.2610.0000.0000.0000.000
145A146VAL00.0390.02337.981-0.262-0.2620.0000.0000.0000.000
146A147LYS10.8290.90539.339-7.054-7.0540.0000.0000.0000.000
147A148TRP00.0290.00440.906-0.242-0.2420.0000.0000.0000.000
148A149LYS10.7930.87844.315-6.493-6.4930.0000.0000.0000.000
149A150ILE00.0140.01746.469-0.029-0.0290.0000.0000.0000.000
150A151ASP-1-0.709-0.83449.9525.8315.8310.0000.0000.0000.000
151A152GLY00.0280.00752.6220.0450.0450.0000.0000.0000.000
152A153SER0-0.053-0.05450.5270.0470.0470.0000.0000.0000.000
153A154GLU-1-0.903-0.92748.8016.3746.3740.0000.0000.0000.000
154A155ARG10.9130.96439.140-7.800-7.8000.0000.0000.0000.000
155A156GLN00.0660.04142.179-0.033-0.0330.0000.0000.0000.000
156A157ASN0-0.046-0.04937.645-0.031-0.0310.0000.0000.0000.000
157A158GLY00.0260.03037.4450.2440.2440.0000.0000.0000.000
158A159VAL0-0.053-0.03037.243-0.189-0.1890.0000.0000.0000.000
159A160LEU00.0210.02032.4770.2820.2820.0000.0000.0000.000
160A161ASN00.0140.00933.387-0.409-0.4090.0000.0000.0000.000
161A162SER00.0230.01231.8240.4000.4000.0000.0000.0000.000
162A163TRP00.0320.01330.870-0.254-0.2540.0000.0000.0000.000
163A164THR00.0100.01231.1630.1740.1740.0000.0000.0000.000
164A165ASP-1-0.812-0.91427.29511.53911.5390.0000.0000.0000.000
165A166GLN0-0.069-0.03630.123-0.057-0.0570.0000.0000.0000.000
166A167ASP-1-0.807-0.92232.1948.5828.5820.0000.0000.0000.000
167A168SER0-0.067-0.02634.420-0.102-0.1020.0000.0000.0000.000
168A169LYS10.8670.92735.314-7.401-7.4010.0000.0000.0000.000
169A170ASP-1-0.851-0.91939.0407.3957.3950.0000.0000.0000.000
170A171SER0-0.0110.00635.633-0.068-0.0680.0000.0000.0000.000
171A172THR0-0.085-0.02935.8310.1070.1070.0000.0000.0000.000
172A173TYR0-0.029-0.02430.2050.3430.3430.0000.0000.0000.000
173A174SER00.0270.00435.200-0.397-0.3970.0000.0000.0000.000
174A175MET0-0.017-0.00634.9140.2660.2660.0000.0000.0000.000
175A176SER00.0040.01536.335-0.377-0.3770.0000.0000.0000.000
176A177SER0-0.024-0.01336.7890.1790.1790.0000.0000.0000.000
177A178THR00.014-0.00438.310-0.279-0.2790.0000.0000.0000.000
178A179LEU0-0.0060.00639.2650.1980.1980.0000.0000.0000.000
179A180THR00.004-0.00639.192-0.161-0.1610.0000.0000.0000.000
180A181LEU0-0.033-0.00742.2510.0820.0820.0000.0000.0000.000
181A182THR00.0520.02645.1280.0280.0280.0000.0000.0000.000
182A183LYS10.8930.92447.327-5.949-5.9490.0000.0000.0000.000
183A184ASP-1-0.799-0.89750.6636.0716.0710.0000.0000.0000.000
184A185GLU-1-0.800-0.86547.5556.4166.4160.0000.0000.0000.000
185A186TYR0-0.021-0.01949.190-0.027-0.0270.0000.0000.0000.000
186A187GLU-1-0.858-0.93550.8155.7545.7540.0000.0000.0000.000
187A188ARG10.7770.87650.974-6.315-6.3150.0000.0000.0000.000
188A189HIS10.7990.90750.360-6.333-6.3330.0000.0000.0000.000
189A190ASN0-0.024-0.02354.793-0.006-0.0060.0000.0000.0000.000
190A191SER0-0.016-0.00754.4540.0310.0310.0000.0000.0000.000
191A192TYR0-0.006-0.01148.4500.1750.1750.0000.0000.0000.000
192A193THR0-0.019-0.01048.724-0.097-0.0970.0000.0000.0000.000
193A195GLU-1-0.827-0.90544.9396.6886.6880.0000.0000.0000.000
194A196ALA00.0430.01042.4600.2170.2170.0000.0000.0000.000
195A197THR0-0.065-0.03340.923-0.132-0.1320.0000.0000.0000.000
196A198HIS00.0840.02338.218-0.014-0.0140.0000.0000.0000.000
197A199LYS10.8720.92939.062-7.815-7.8150.0000.0000.0000.000
198A200THR0-0.017-0.02441.754-0.179-0.1790.0000.0000.0000.000
199A201SER0-0.053-0.02644.372-0.227-0.2270.0000.0000.0000.000
200A202THR0-0.0010.00245.7630.1110.1110.0000.0000.0000.000
201A203SER0-0.0030.00247.6740.0210.0210.0000.0000.0000.000
202A204PRO0-0.009-0.01546.1540.0380.0380.0000.0000.0000.000
203A205ILE00.0220.03245.468-0.153-0.1530.0000.0000.0000.000
204A206VAL0-0.003-0.00546.8330.1430.1430.0000.0000.0000.000
205A207LYS10.9440.98548.567-6.352-6.3520.0000.0000.0000.000
206A208SER0-0.022-0.02749.6280.0820.0820.0000.0000.0000.000
207A209PHE00.007-0.00449.777-0.055-0.0550.0000.0000.0000.000
208A210ASN00.0510.03353.9790.1490.1490.0000.0000.0000.000
209A211ARG10.8740.92754.163-5.784-5.7840.0000.0000.0000.000
210A212ASN0-0.054-0.03556.5450.0120.0120.0000.0000.0000.000
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