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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: VRV71

Calculation Name: 1LTI-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-alpha-d-galactopyranose

ligand 3-letter code: A2G

PDB ID: 1LTI

Chain ID: A

ChEMBL ID:

UniProt ID: P06717

Base Structure: X-ray

Registration Date: 2023-03-13

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087704.262909
FMO2-HF: Nuclear repulsion 2013285.398902
FMO2-HF: Total energy -74418.864007
FMO2-MP2: Total energy -74638.490561


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:4:ARG)


Summations of interaction energy for fragment #1(A:4:ARG)
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.
-33.737-18.9815.868-10.434-20.188-0.072
Interaction energy analysis for fragmet #1(A:4:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.907 / q_NPA : 0.947
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].
3A6TYR0-0.013-0.0113.519-5.517-2.3340.017-1.525-1.6750.003
4A7ARG10.8130.8726.20821.39721.3970.0000.0000.0000.000
5A8ALA0-0.0180.0089.611-0.371-0.3710.0000.0000.0000.000
6A9ASP-1-0.755-0.86312.724-16.984-16.9840.0000.0000.0000.000
7A10SER00.0390.01515.079-0.393-0.3930.0000.0000.0000.000
8A11ARG10.8240.92116.16516.72016.7200.0000.0000.0000.000
9A12PRO00.0100.02616.410-1.251-1.2510.0000.0000.0000.000
10A13PRO00.0370.00413.7700.0840.0840.0000.0000.0000.000
11A14ASP-1-0.810-0.88915.354-15.190-15.1900.0000.0000.0000.000
12A15GLU-1-0.876-0.94618.522-14.094-14.0940.0000.0000.0000.000
13A16ILE00.0040.01312.903-0.082-0.0820.0000.0000.0000.000
14A17LYS10.7950.88115.58518.18218.1820.0000.0000.0000.000
15A18ARG10.8120.88516.58314.02914.0290.0000.0000.0000.000
16A19SER00.0220.01817.8790.6400.6400.0000.0000.0000.000
17A20GLY00.0310.02116.5430.0600.0600.0000.0000.0000.000
18A21GLY0-0.014-0.03313.244-1.385-1.3850.0000.0000.0000.000
19A22LEU0-0.043-0.01110.1280.9950.9950.0000.0000.0000.000
20A23MET0-0.0010.04613.999-0.409-0.4090.0000.0000.0000.000
21A24PRO00.0510.00817.185-0.032-0.0320.0000.0000.0000.000
22A25ARG10.8170.89818.85511.81211.8120.0000.0000.0000.000
23A26GLY00.0070.00322.0290.3510.3510.0000.0000.0000.000
24A27HIS0-0.033-0.00419.6660.6930.6930.0000.0000.0000.000
25A28ASN0-0.016-0.01821.855-0.092-0.0920.0000.0000.0000.000
26A29GLU-1-0.913-0.95820.845-13.089-13.0890.0000.0000.0000.000
27A30TYR0-0.015-0.02215.228-0.148-0.1480.0000.0000.0000.000
28A31PHE0-0.035-0.03316.297-0.074-0.0740.0000.0000.0000.000
29A32ASP-1-0.756-0.84821.015-11.109-11.1090.0000.0000.0000.000
30A33ARG10.8010.87522.00812.75212.7520.0000.0000.0000.000
31A34GLY00.0150.02427.2770.2170.2170.0000.0000.0000.000
32A35THR0-0.030-0.02927.6770.4640.4640.0000.0000.0000.000
33A36GLN0-0.020-0.00626.090-0.645-0.6450.0000.0000.0000.000
34A37MET0-0.022-0.00322.4800.0540.0540.0000.0000.0000.000
35A38ASN0-0.049-0.04126.3260.0890.0890.0000.0000.0000.000
36A39ILE0-0.041-0.03020.695-0.520-0.5200.0000.0000.0000.000
37A40ASN0-0.019-0.01522.479-0.211-0.2110.0000.0000.0000.000
38A41LEU00.0370.02716.481-0.189-0.1890.0000.0000.0000.000
39A42TYR00.0290.00420.192-0.208-0.2080.0000.0000.0000.000
40A43ASP-1-0.826-0.89322.940-10.524-10.5240.0000.0000.0000.000
41A44HIS0-0.043-0.01016.492-0.679-0.6790.0000.0000.0000.000
42A45ALA00.0070.00219.154-0.133-0.1330.0000.0000.0000.000
43A46ARG10.7900.88220.22010.91010.9100.0000.0000.0000.000
44A47GLY00.0570.04423.2950.2050.2050.0000.0000.0000.000
45A48THR0-0.028-0.02721.915-0.724-0.7240.0000.0000.0000.000
46A49GLN0-0.012-0.01721.3530.3190.3190.0000.0000.0000.000
47A50THR00.0370.01122.350-0.388-0.3880.0000.0000.0000.000
48A51GLY0-0.0060.00722.8690.0890.0890.0000.0000.0000.000
49A52PHE00.0350.00718.627-0.291-0.2910.0000.0000.0000.000
50A53VAL00.0320.02013.9610.4090.4090.0000.0000.0000.000
51A54ARG10.7560.86317.07014.47514.4750.0000.0000.0000.000
52A55TYR0-0.047-0.03416.285-1.047-1.0470.0000.0000.0000.000
53A56ASP-1-0.718-0.83318.171-11.915-11.9150.0000.0000.0000.000
54A57ASP-1-0.845-0.90720.257-12.233-12.2330.0000.0000.0000.000
55A58GLY00.0680.03320.568-0.148-0.1480.0000.0000.0000.000
56A59TYR0-0.0030.00115.208-0.921-0.9210.0000.0000.0000.000
57A60VAL0-0.039-0.01612.5390.4090.4090.0000.0000.0000.000
58A61SER0-0.023-0.01412.524-1.513-1.5130.0000.0000.0000.000
59A62THR0-0.076-0.0487.872-1.777-1.7770.0000.0000.0000.000
60A63SER00.0530.0168.7311.6811.6810.0000.0000.0000.000
61A64LEU00.0630.0276.094-3.866-3.8660.0000.0000.0000.000
62A65SER0-0.014-0.0076.173-1.071-1.0710.0000.0000.0000.000
63A66LEU00.0280.0267.2941.4801.4800.0000.0000.0000.000
64A67ARG10.9070.9318.74818.22118.2210.0000.0000.0000.000
65A68SER00.0490.02811.0651.7501.7500.0000.0000.0000.000
66A69ALA00.0280.0179.7091.1101.1100.0000.0000.0000.000
67A70HIS00.0220.01111.7780.8690.8690.0000.0000.0000.000
68A71LEU0-0.036-0.00714.3480.9950.9950.0000.0000.0000.000
69A72ALA00.0460.03114.8630.9110.9110.0000.0000.0000.000
70A73GLY00.037-0.00315.5870.6360.6360.0000.0000.0000.000
71A74GLN00.0160.01116.8730.1970.1970.0000.0000.0000.000
72A75SER0-0.0010.00919.7140.8980.8980.0000.0000.0000.000
73A76ILE0-0.060-0.01519.0280.5510.5510.0000.0000.0000.000
74A77LEU0-0.065-0.03616.6210.2850.2850.0000.0000.0000.000
75A78SER0-0.030-0.01120.5280.3220.3220.0000.0000.0000.000
76A79GLY00.0210.01723.1200.2040.2040.0000.0000.0000.000
77A80TYR0-0.065-0.02621.4810.3070.3070.0000.0000.0000.000
78A81SER00.0220.00222.614-0.251-0.2510.0000.0000.0000.000
79A82THR0-0.060-0.03619.618-0.140-0.1400.0000.0000.0000.000
80A83TYR0-0.012-0.00115.052-0.135-0.1350.0000.0000.0000.000
81A84TYR00.0030.00113.257-0.249-0.2490.0000.0000.0000.000
82A85ILE0-0.010-0.0058.7560.2710.2710.0000.0000.0000.000
83A86TYR00.003-0.0168.399-2.158-2.1580.0000.0000.0000.000
84A87VAL00.0020.0002.474-1.903-1.2531.060-0.362-1.348-0.001
85A88ILE0-0.026-0.0213.149-2.068-1.2320.036-0.246-0.626-0.001
86A89ALA0-0.029-0.0122.493-13.873-10.1512.478-2.495-3.706-0.022
87A90THR00.0310.0182.5015.2876.2000.651-0.375-1.189-0.003
88A91ALA0-0.018-0.0134.654-0.774-0.711-0.001-0.007-0.0550.000
89A92PRO00.0690.0208.4450.8080.8080.0000.0000.0000.000
90A93ASN00.0090.02010.341-0.134-0.1340.0000.0000.0000.000
91A94MET0-0.064-0.0216.259-0.579-0.5790.0000.0000.0000.000
92A95PHE00.0900.04910.7490.0490.0490.0000.0000.0000.000
93A96ASN0-0.043-0.04011.123-0.303-0.3030.0000.0000.0000.000
94A97VAL00.0250.00812.4930.9340.9340.0000.0000.0000.000
95A98ASN00.002-0.00514.9711.4681.4680.0000.0000.0000.000
96A99ASP-1-0.849-0.91213.196-16.726-16.7260.0000.0000.0000.000
97A100VAL00.0010.01016.0870.5790.5790.0000.0000.0000.000
98A101LEU0-0.0080.00418.5020.6610.6610.0000.0000.0000.000
99A102GLY00.0460.02419.9400.6030.6030.0000.0000.0000.000
100A103VAL0-0.032-0.02921.571-0.181-0.1810.0000.0000.0000.000
101A104TYR0-0.065-0.04724.0920.3180.3180.0000.0000.0000.000
102A105SER0-0.022-0.02618.760-0.173-0.1730.0000.0000.0000.000
103A106PRO0-0.015-0.01121.0850.2290.2290.0000.0000.0000.000
104A107HIS10.8200.91120.05712.74212.7420.0000.0000.0000.000
105A108PRO00.0880.06518.952-0.669-0.6690.0000.0000.0000.000
106A109TYR0-0.015-0.01617.433-0.634-0.6340.0000.0000.0000.000
107A110GLU-1-0.848-0.92016.696-14.021-14.0210.0000.0000.0000.000
108A111GLN0-0.092-0.05411.191-2.345-2.3450.0000.0000.0000.000
109A112GLU-1-0.763-0.83411.549-17.878-17.8780.0000.0000.0000.000
110A113VAL0-0.010-0.0058.1200.2720.2720.0000.0000.0000.000
111A114SER0-0.009-0.01010.227-1.479-1.4790.0000.0000.0000.000
112A115ALA0-0.052-0.02610.438-0.088-0.0880.0000.0000.0000.000
113A116LEU00.0580.02712.2930.8310.8310.0000.0000.0000.000
114A117GLY00.002-0.00215.543-0.584-0.5840.0000.0000.0000.000
115A118GLY00.004-0.00714.7960.4600.4600.0000.0000.0000.000
116A119ILE0-0.055-0.0188.803-1.250-1.2500.0000.0000.0000.000
117A120PRO00.0500.03410.8440.1200.1200.0000.0000.0000.000
118A121TYR00.053-0.00310.115-2.786-2.7860.0000.0000.0000.000
119A122SER0-0.052-0.0329.032-1.468-1.4680.0000.0000.0000.000
120A123GLN0-0.003-0.0066.119-0.466-0.4660.0000.0000.0000.000
121A124ILE0-0.0230.0044.964-8.183-8.087-0.0010.000-0.0940.000
122A125TYR00.004-0.0092.628-5.522-1.4663.306-1.482-5.879-0.004
123A126GLY00.003-0.0094.7383.2313.304-0.001-0.014-0.0580.000
124A127TRP00.0220.0157.203-1.518-1.5180.0000.0000.0000.000
125A128TYR00.0240.0307.092-1.203-1.2030.0000.0000.0000.000
126A129ARG10.9330.95611.54414.92314.9230.0000.0000.0000.000
127A130VAL0-0.0140.00314.895-0.289-0.2890.0000.0000.0000.000
128A131ASN00.0210.00417.3450.5340.5340.0000.0000.0000.000
129A132PHE00.028-0.00521.1370.1020.1020.0000.0000.0000.000
130A133GLY00.0380.03120.2960.3580.3580.0000.0000.0000.000
131A134VAL0-0.0070.00119.355-0.515-0.5150.0000.0000.0000.000
132A135ILE0-0.037-0.02412.779-0.146-0.1460.0000.0000.0000.000
133A136ASP-1-0.821-0.89115.709-17.020-17.0200.0000.0000.0000.000
134A137GLU-1-0.855-0.93713.725-18.517-18.5170.0000.0000.0000.000
135A138ARG10.7970.88412.59116.24016.2400.0000.0000.0000.000
136A139LEU0-0.041-0.0115.141-0.592-0.5920.0000.0000.0000.000
137A140HIS0-0.048-0.0249.5941.0861.0860.0000.0000.0000.000
138A141ARG10.8790.9336.15237.14937.1490.0000.0000.0000.000
139A142ASN00.0300.0228.0895.5525.5520.0000.0000.0000.000
140A143ARG10.9530.9658.95716.38716.3870.0000.0000.0000.000
141A144GLU-1-0.828-0.89910.872-19.903-19.9030.0000.0000.0000.000
142A145TYR0-0.034-0.0201.941-17.663-17.7918.316-3.348-4.840-0.040
143A146ARG10.9230.9707.05424.28024.2800.0000.0000.0000.000
144A147ASP-1-0.780-0.8693.352-57.251-56.2470.009-0.558-0.455-0.004
145A148ARG10.9220.9485.43920.65020.6500.0000.0000.0000.000
146A149TYR0-0.0120.0068.2841.7101.7100.0000.0000.0000.000
147A150TYR00.0820.0164.0060.6460.791-0.001-0.019-0.1240.000
148A151ARG10.8080.9044.49732.85132.995-0.001-0.003-0.1390.000
149A152ASN00.0060.0005.427-0.276-0.2760.0000.0000.0000.000
150A153LEU0-0.0150.0177.5703.0203.0200.0000.0000.0000.000
151A154ASN0-0.012-0.0285.561-1.578-1.5780.0000.0000.0000.000
152A155ILE0-0.025-0.0075.9540.1280.1280.0000.0000.0000.000
153A156ALA00.0060.0249.2730.7810.7810.0000.0000.0000.000
154A157PRO0-0.0100.00113.050-0.169-0.1690.0000.0000.0000.000
155A158ALA00.0470.00715.0590.2850.2850.0000.0000.0000.000
156A159GLU-1-0.874-0.95117.105-14.045-14.0450.0000.0000.0000.000
157A160ASP-1-0.873-0.90017.761-14.103-14.1030.0000.0000.0000.000
158A161GLY00.0340.00818.0200.2410.2410.0000.0000.0000.000
159A162TYR0-0.033-0.01618.8000.4520.4520.0000.0000.0000.000
160A163ARG10.8460.89420.74513.47213.4720.0000.0000.0000.000
161A164LEU0-0.087-0.03918.6920.2780.2780.0000.0000.0000.000
162A165ALA00.0060.00721.249-0.225-0.2250.0000.0000.0000.000
163A166GLY00.0040.00122.245-0.002-0.0020.0000.0000.0000.000
164A167PHE00.0170.00423.8020.1750.1750.0000.0000.0000.000
165A168PRO00.0170.01027.3370.1170.1170.0000.0000.0000.000
166A169PRO00.035-0.01330.8390.0030.0030.0000.0000.0000.000
167A170ASP-1-0.822-0.89333.410-8.214-8.2140.0000.0000.0000.000
168A171HIS00.0090.00428.003-0.073-0.0730.0000.0000.0000.000
169A172GLN0-0.035-0.00131.0550.0320.0320.0000.0000.0000.000
170A173ALA00.0530.01927.3150.0670.0670.0000.0000.0000.000
171A174TRP0-0.060-0.03225.823-0.159-0.1590.0000.0000.0000.000
172A175ARG10.7890.87030.9228.4028.4020.0000.0000.0000.000
173A176GLU-1-0.797-0.85829.246-9.134-9.1340.0000.0000.0000.000
174A177GLU-1-0.867-0.90127.818-9.694-9.6940.0000.0000.0000.000
175A178PRO00.0180.00422.968-0.049-0.0490.0000.0000.0000.000
176A179TRP0-0.024-0.03522.4970.1110.1110.0000.0000.0000.000
177A180ILE0-0.0030.01126.8150.0570.0570.0000.0000.0000.000
178A181HIS0-0.100-0.06427.7760.1920.1920.0000.0000.0000.000
179A182HIS0-0.090-0.05724.456-0.380-0.3800.0000.0000.0000.000
180A183ALA00.0210.01727.312-0.270-0.2700.0000.0000.0000.000
181A184PRO0-0.004-0.00427.4530.1520.1520.0000.0000.0000.000
182A185GLN00.0300.01730.0740.1970.1970.0000.0000.0000.000
183A186GLY0-0.057-0.03333.5700.1650.1650.0000.0000.0000.000
184A187CYS0-0.084-0.01731.319-0.055-0.0550.0000.0000.0000.000
185A188GLY00.0330.03133.2820.1190.1190.0000.0000.0000.000