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: LZRM9

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 OptAll
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 -2145426.123565
FMO2-HF: Nuclear repulsion 2062962.801825
FMO2-HF: Total energy -82463.321739
FMO2-MP2: Total energy -82703.490297


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.
-52.462-46.4412.492-3.231-5.2820.026
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 : -0.883 / q_NPA : -0.952
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].
3A3VAL00.0270.0323.176-1.4760.6730.068-0.897-1.3200.004
4A4LEU00.0120.0114.593-4.432-4.391-0.001-0.009-0.0300.000
5A5THR0-0.043-0.0278.1930.2170.2170.0000.0000.0000.000
6A6GLN00.0490.00111.334-0.332-0.3320.0000.0000.0000.000
7A7SER0-0.063-0.01614.543-0.167-0.1670.0000.0000.0000.000
8A8PRO00.0520.02717.756-0.271-0.2710.0000.0000.0000.000
9A9SER00.0650.03417.3020.2410.2410.0000.0000.0000.000
10A10SER0-0.020-0.00919.3400.0660.0660.0000.0000.0000.000
11A11LEU0-0.032-0.01322.879-0.169-0.1690.0000.0000.0000.000
12A12SER0-0.016-0.02925.954-0.048-0.0480.0000.0000.0000.000
13A13ALA0-0.025-0.00329.633-0.079-0.0790.0000.0000.0000.000
14A14SER00.000-0.00932.216-0.067-0.0670.0000.0000.0000.000
15A15LEU00.003-0.00634.3920.1970.1970.0000.0000.0000.000
16A16GLY0-0.027-0.01435.768-0.206-0.2060.0000.0000.0000.000
17A17ASP-1-0.796-0.87433.2368.7198.7190.0000.0000.0000.000
18A18THR0-0.028-0.02330.7340.1090.1090.0000.0000.0000.000
19A19ILE0-0.031-0.00426.581-0.008-0.0080.0000.0000.0000.000
20A20THR00.011-0.00524.5350.0430.0430.0000.0000.0000.000
21A21ILE0-0.0010.01318.9710.1790.1790.0000.0000.0000.000
22A22THR0-0.029-0.02318.7270.1150.1150.0000.0000.0000.000
23A23CYS0-0.0330.00113.1440.4420.4420.0000.0000.0000.000
24A24HIS00.0080.02113.147-0.456-0.4560.0000.0000.0000.000
25A25ALA0-0.004-0.0029.2671.5781.5780.0000.0000.0000.000
26A26SER0-0.022-0.0256.134-0.415-0.4150.0000.0000.0000.000
27A27GLN0-0.010-0.0073.856-5.277-4.8030.002-0.198-0.2790.001
28A28ASN00.000-0.0088.619-0.738-0.7380.0000.0000.0000.000
29A29ILE00.0680.0328.8351.0041.0040.0000.0000.0000.000
30A30ASN00.000-0.01311.432-0.005-0.0050.0000.0000.0000.000
31A31VAL00.0370.01215.225-0.904-0.9040.0000.0000.0000.000
32A32TRP0-0.015-0.00112.736-0.939-0.9390.0000.0000.0000.000
33A33LEU00.0080.01212.3411.8661.8660.0000.0000.0000.000
34A34SER0-0.028-0.01914.570-1.568-1.5680.0000.0000.0000.000
35A35TRP00.0460.01515.5731.1511.1510.0000.0000.0000.000
36A36TYR0-0.003-0.02314.853-1.347-1.3470.0000.0000.0000.000
37A37GLN00.0200.01719.544-0.192-0.1920.0000.0000.0000.000
38A38GLN0-0.005-0.00520.3180.5750.5750.0000.0000.0000.000
39A39LYS10.8650.91123.110-10.904-10.9040.0000.0000.0000.000
40A40PRO00.0320.01126.0240.2280.2280.0000.0000.0000.000
41A41GLY00.0130.02025.898-0.396-0.3960.0000.0000.0000.000
42A42ASN0-0.031-0.00826.5010.2840.2840.0000.0000.0000.000
43A43ILE00.0560.03022.9340.5050.5050.0000.0000.0000.000
44A44PRO00.000-0.01018.754-0.497-0.4970.0000.0000.0000.000
45A45LYS10.8810.94821.676-12.403-12.4030.0000.0000.0000.000
46A46LEU00.0000.00419.6740.3590.3590.0000.0000.0000.000
47A47LEU0-0.034-0.00421.355-0.659-0.6590.0000.0000.0000.000
48A48ILE00.0160.00621.033-0.585-0.5850.0000.0000.0000.000
49A49TYR00.0420.02318.8730.9620.9620.0000.0000.0000.000
50A50LYS10.8810.93217.944-14.241-14.2410.0000.0000.0000.000
51A51ALA00.0120.01918.046-0.815-0.8150.0000.0000.0000.000
52A52SER0-0.010-0.01519.306-0.132-0.1320.0000.0000.0000.000
53A53ASN0-0.0250.00322.631-0.563-0.5630.0000.0000.0000.000
54A54LEU00.0310.01623.6160.5390.5390.0000.0000.0000.000
55A55HIS00.0000.00624.1050.0540.0540.0000.0000.0000.000
56A56THR00.019-0.01325.982-0.361-0.3610.0000.0000.0000.000
57A57GLY0-0.017-0.00429.2130.1300.1300.0000.0000.0000.000
58A58VAL0-0.046-0.00726.180-0.201-0.2010.0000.0000.0000.000
59A59PRO00.0110.00629.557-0.147-0.1470.0000.0000.0000.000
60A60SER00.027-0.00130.6980.2670.2670.0000.0000.0000.000
61A61ARG10.8530.92631.521-9.544-9.5440.0000.0000.0000.000
62A62PHE0-0.0070.00425.8150.2080.2080.0000.0000.0000.000
63A63SER0-0.005-0.01426.500-0.288-0.2880.0000.0000.0000.000
64A64GLY00.0080.01122.6000.3000.3000.0000.0000.0000.000
65A65SER0-0.010-0.01421.664-0.372-0.3720.0000.0000.0000.000
66A66GLY00.0550.02719.3250.6090.6090.0000.0000.0000.000
67A67SER0-0.012-0.01118.125-0.456-0.4560.0000.0000.0000.000
68A68GLY0-0.006-0.00115.490-0.120-0.1200.0000.0000.0000.000
69A69THR0-0.012-0.01012.0231.0931.0930.0000.0000.0000.000
70A70GLY00.0370.03813.7840.7830.7830.0000.0000.0000.000
71A71PHE0-0.020-0.01514.058-0.701-0.7010.0000.0000.0000.000
72A72THR0-0.029-0.01917.830-0.010-0.0100.0000.0000.0000.000
73A73LEU0-0.0220.00620.310-0.038-0.0380.0000.0000.0000.000
74A74THR0-0.022-0.01721.949-0.128-0.1280.0000.0000.0000.000
75A75ILE00.0050.00124.4050.0540.0540.0000.0000.0000.000
76A76SER00.011-0.00328.172-0.214-0.2140.0000.0000.0000.000
77A77SER0-0.045-0.02631.791-0.017-0.0170.0000.0000.0000.000
78A78LEU0-0.0100.01728.914-0.064-0.0640.0000.0000.0000.000
79A79GLN0-0.027-0.02132.645-0.526-0.5260.0000.0000.0000.000
80A80PRO00.0620.02332.7210.3180.3180.0000.0000.0000.000
81A81GLU-1-0.832-0.90831.7309.5979.5970.0000.0000.0000.000
82A82ASP-1-0.784-0.87728.67610.64810.6480.0000.0000.0000.000
83A83ILE0-0.0080.01327.4190.5370.5370.0000.0000.0000.000
84A84ALA0-0.006-0.01124.365-0.028-0.0280.0000.0000.0000.000
85A85THR0-0.0020.00419.154-0.283-0.2830.0000.0000.0000.000
86A86TYR0-0.015-0.02119.885-0.102-0.1020.0000.0000.0000.000
87A87TYR0-0.006-0.01714.7130.4050.4050.0000.0000.0000.000
88A89GLN0-0.0050.00410.923-0.119-0.1190.0000.0000.0000.000
89A90GLN00.0200.0025.933-6.216-6.2160.0000.0000.0000.000
90A91GLY00.002-0.00610.0881.1801.1800.0000.0000.0000.000
91A92GLN0-0.096-0.0249.3410.3940.3940.0000.0000.0000.000
92A93SER00.0150.0076.205-0.718-0.7180.0000.0000.0000.000
93A94TYR0-0.0010.0126.124-0.521-0.5210.0000.0000.0000.000
94A95PRO00.0500.0212.521-5.999-3.2792.410-1.933-3.1960.020
95A96LEU0-0.034-0.0065.1570.0930.100-0.001-0.003-0.0030.000
96A97THR0-0.012-0.0143.523-1.625-0.9950.014-0.191-0.4540.001
97A98PHE00.0370.0006.904-4.353-4.3530.0000.0000.0000.000
98A99GLY00.015-0.0038.7651.8771.8770.0000.0000.0000.000
99A100GLY0-0.021-0.00210.714-1.484-1.4840.0000.0000.0000.000
100A101GLY00.011-0.00712.356-0.557-0.5570.0000.0000.0000.000
101A102THR0-0.068-0.05415.789-0.411-0.4110.0000.0000.0000.000
102A103LYS10.8230.91619.289-11.885-11.8850.0000.0000.0000.000
103A104LEU0-0.0250.00222.721-0.178-0.1780.0000.0000.0000.000
104A105GLU-1-0.781-0.85326.0939.9789.9780.0000.0000.0000.000
105A106ILE00.0300.00329.5580.0080.0080.0000.0000.0000.000
106A107LYS10.8830.94332.523-9.253-9.2530.0000.0000.0000.000
107A108ARG10.8300.91334.974-7.820-7.8200.0000.0000.0000.000
108A109ALA00.0390.01338.3130.0150.0150.0000.0000.0000.000
109A110ASP-1-0.824-0.90240.7897.7177.7170.0000.0000.0000.000
110A111ALA0-0.025-0.00441.341-0.130-0.1300.0000.0000.0000.000
111A112ALA00.0350.01742.1230.1510.1510.0000.0000.0000.000
112A113PRO0-0.0020.01141.572-0.026-0.0260.0000.0000.0000.000
113A114THR00.0050.00643.455-0.219-0.2190.0000.0000.0000.000
114A115VAL00.002-0.00445.0090.0790.0790.0000.0000.0000.000
115A116SER0-0.069-0.04145.831-0.257-0.2570.0000.0000.0000.000
116A117ILE0-0.022-0.00446.1050.1860.1860.0000.0000.0000.000
117A118PHE0-0.001-0.00346.104-0.138-0.1380.0000.0000.0000.000
118A119PRO00.0210.00847.8500.1360.1360.0000.0000.0000.000
119A120PRO00.0090.01647.9960.0560.0560.0000.0000.0000.000
120A121SER0-0.015-0.01848.713-0.094-0.0940.0000.0000.0000.000
121A122SER00.0570.01850.6230.0460.0460.0000.0000.0000.000
122A123GLU-1-0.818-0.87850.1486.2926.2920.0000.0000.0000.000
123A124GLN00.0060.00944.020-0.035-0.0350.0000.0000.0000.000
124A125LEU00.0180.00248.9480.0270.0270.0000.0000.0000.000
125A126THR0-0.063-0.04051.610-0.075-0.0750.0000.0000.0000.000
126A127SER0-0.067-0.04048.161-0.015-0.0150.0000.0000.0000.000
127A128GLY0-0.0020.01248.8160.1000.1000.0000.0000.0000.000
128A129GLY0-0.050-0.02346.3090.0820.0820.0000.0000.0000.000
129A130ALA00.009-0.01246.252-0.136-0.1360.0000.0000.0000.000
130A131SER0-0.023-0.01742.6270.1210.1210.0000.0000.0000.000
131A132VAL0-0.0120.01044.536-0.114-0.1140.0000.0000.0000.000
132A133VAL00.0200.00641.7790.2030.2030.0000.0000.0000.000
133A134CYS0-0.084-0.03642.477-0.026-0.0260.0000.0000.0000.000
134A135PHE00.0030.01740.8700.2230.2230.0000.0000.0000.000
135A136LEU00.012-0.01239.798-0.235-0.2350.0000.0000.0000.000
136A137ASN00.010-0.01139.9920.3620.3620.0000.0000.0000.000
137A138ASN00.002-0.01240.2750.0160.0160.0000.0000.0000.000
138A139PHE00.0140.01635.973-0.160-0.1600.0000.0000.0000.000
139A140TYR00.016-0.01433.1650.1970.1970.0000.0000.0000.000
140A141PRO00.010-0.00334.951-0.256-0.2560.0000.0000.0000.000
141A142LYS10.9130.97528.252-10.711-10.7110.0000.0000.0000.000
142A143ASP-1-0.916-0.95832.3599.5459.5450.0000.0000.0000.000
143A144ILE0-0.0240.00134.659-0.329-0.3290.0000.0000.0000.000
144A145ASN0-0.023-0.00835.7120.2790.2790.0000.0000.0000.000
145A146VAL00.0110.00637.887-0.272-0.2720.0000.0000.0000.000
146A147LYS10.8450.90939.439-7.084-7.0840.0000.0000.0000.000
147A148TRP00.0320.01341.089-0.234-0.2340.0000.0000.0000.000
148A149LYS10.7730.86544.243-6.508-6.5080.0000.0000.0000.000
149A150ILE00.0130.02046.768-0.004-0.0040.0000.0000.0000.000
150A151ASP-1-0.731-0.84450.2325.8295.8290.0000.0000.0000.000
151A152GLY00.0520.02853.1950.0370.0370.0000.0000.0000.000
152A153SER0-0.072-0.06650.4960.0550.0550.0000.0000.0000.000
153A154GLU-1-0.863-0.92849.2366.3926.3920.0000.0000.0000.000
154A155ARG10.9210.97139.844-7.692-7.6920.0000.0000.0000.000
155A156GLN00.0790.05342.3980.0970.0970.0000.0000.0000.000
156A157ASN0-0.074-0.06537.987-0.027-0.0270.0000.0000.0000.000
157A158GLY00.0170.02738.0470.2440.2440.0000.0000.0000.000
158A159VAL0-0.039-0.03437.753-0.206-0.2060.0000.0000.0000.000
159A160LEU00.0120.02432.6200.2840.2840.0000.0000.0000.000
160A161ASN00.0120.00633.700-0.460-0.4600.0000.0000.0000.000
161A162SER00.0050.00431.9770.4170.4170.0000.0000.0000.000
162A163TRP00.0380.00331.024-0.281-0.2810.0000.0000.0000.000
163A164THR0-0.016-0.01331.3520.1500.1500.0000.0000.0000.000
164A165ASP-1-0.781-0.89628.11211.42011.4200.0000.0000.0000.000
165A166GLN0-0.068-0.02830.511-0.118-0.1180.0000.0000.0000.000
166A167ASP-1-0.806-0.90332.6948.5468.5460.0000.0000.0000.000
167A168SER0-0.083-0.04935.135-0.061-0.0610.0000.0000.0000.000
168A169LYS10.8440.91235.950-7.384-7.3840.0000.0000.0000.000
169A170ASP-1-0.819-0.89839.6327.3277.3270.0000.0000.0000.000
170A171SER0-0.0090.00236.289-0.035-0.0350.0000.0000.0000.000
171A172THR0-0.041-0.00436.5820.0460.0460.0000.0000.0000.000
172A173TYR0-0.041-0.04630.2630.2930.2930.0000.0000.0000.000
173A174SER00.0330.02135.671-0.412-0.4120.0000.0000.0000.000
174A175MET0-0.043-0.00835.2750.2550.2550.0000.0000.0000.000
175A176SER00.0030.01236.407-0.379-0.3790.0000.0000.0000.000
176A177SER00.004-0.00936.7460.2030.2030.0000.0000.0000.000
177A178THR0-0.019-0.02638.717-0.202-0.2020.0000.0000.0000.000
178A179LEU00.0230.04239.5230.2030.2030.0000.0000.0000.000
179A180THR0-0.002-0.00139.687-0.150-0.1500.0000.0000.0000.000
180A181LEU0-0.031-0.00542.5920.0760.0760.0000.0000.0000.000
181A182THR00.0420.01645.2920.0300.0300.0000.0000.0000.000
182A183LYS10.8630.91347.571-5.918-5.9180.0000.0000.0000.000
183A184ASP-1-0.830-0.91350.8646.0386.0380.0000.0000.0000.000
184A185GLU-1-0.826-0.88547.9026.3736.3730.0000.0000.0000.000
185A186TYR00.016-0.00749.642-0.049-0.0490.0000.0000.0000.000
186A187GLU-1-0.860-0.93551.2425.7255.7250.0000.0000.0000.000
187A188ARG10.7920.88051.063-6.312-6.3120.0000.0000.0000.000
188A189HIS10.8030.92050.690-6.303-6.3030.0000.0000.0000.000
189A190ASN0-0.005-0.01454.927-0.035-0.0350.0000.0000.0000.000
190A191SER0-0.011-0.01154.3340.0420.0420.0000.0000.0000.000
191A192TYR0-0.014-0.01648.8610.1750.1750.0000.0000.0000.000
192A193THR00.0100.00948.960-0.090-0.0900.0000.0000.0000.000
193A195GLU-1-0.785-0.87345.0956.6656.6650.0000.0000.0000.000
194A196ALA00.0170.00442.3850.2100.2100.0000.0000.0000.000
195A197THR0-0.073-0.04741.020-0.161-0.1610.0000.0000.0000.000
196A198HIS00.0820.02938.360-0.001-0.0010.0000.0000.0000.000
197A199LYS10.8820.92839.209-7.778-7.7780.0000.0000.0000.000
198A200THR0-0.026-0.03541.697-0.174-0.1740.0000.0000.0000.000
199A201SER0-0.047-0.03444.645-0.233-0.2330.0000.0000.0000.000
200A202THR00.0050.00545.8950.1100.1100.0000.0000.0000.000
201A203SER0-0.0140.00947.948-0.043-0.0430.0000.0000.0000.000
202A204PRO00.000-0.00946.4430.0660.0660.0000.0000.0000.000
203A205ILE00.0130.03545.315-0.145-0.1450.0000.0000.0000.000
204A206VAL0-0.009-0.01246.7030.1500.1500.0000.0000.0000.000
205A207LYS10.9130.96448.552-6.372-6.3720.0000.0000.0000.000
206A208SER00.003-0.02149.7570.0710.0710.0000.0000.0000.000
207A209PHE00.0050.00749.785-0.054-0.0540.0000.0000.0000.000
208A210ASN00.0340.02354.2780.1430.1430.0000.0000.0000.000
209A211ARG10.8790.94454.420-5.752-5.7520.0000.0000.0000.000
210A212ASN0-0.069-0.04456.8710.0130.0130.0000.0000.0000.000
211A213GLU-1-0.917-0.93959.5814.9924.9920.0000.0000.0000.000
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