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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: LL819

Calculation Name: 1LTI-A-Xray307

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: 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 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2092436.098125
FMO2-HF: Nuclear repulsion 2017848.611526
FMO2-HF: Total energy -74587.4866
FMO2-MP2: Total energy -74807.796838


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:3:ACE )


Summations of interaction energy for fragment #1(A:3: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.
0.641.442-0.002-0.32-0.480.001
Interaction energy analysis for fragmet #1(A:3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.012
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].
3A5LEU 00.0580.0493.8800.9411.593-0.005-0.284-0.3630.001
4A6TYR 0-0.038-0.0286.324-0.097-0.0970.0000.0000.0000.000
5A7ARG 10.8460.91810.3020.2910.2910.0000.0000.0000.000
6A8ALA 0-0.0230.01613.910-0.009-0.0090.0000.0000.0000.000
7A9ASP -1-0.741-0.90517.167-0.175-0.1750.0000.0000.0000.000
8A10SER 00.0390.02019.924-0.005-0.0050.0000.0000.0000.000
9A11ARG 10.8700.95720.5560.1680.1680.0000.0000.0000.000
10A12PRO 00.0130.04421.573-0.024-0.0240.0000.0000.0000.000
11A13PRO 00.0200.00620.037-0.002-0.0020.0000.0000.0000.000
12A14ASP -1-0.894-0.96221.576-0.139-0.1390.0000.0000.0000.000
13A15GLU -1-0.885-0.94324.667-0.122-0.1220.0000.0000.0000.000
14A16ILE 00.006-0.00118.589-0.002-0.0020.0000.0000.0000.000
15A17LYS 10.8440.92922.0430.1760.1760.0000.0000.0000.000
16A18ARG 10.8990.95322.9390.1240.1240.0000.0000.0000.000
17A19SER 00.0290.03123.3930.0100.0100.0000.0000.0000.000
18A20GLY 00.0300.02222.4160.0040.0040.0000.0000.0000.000
19A21GLY 0-0.014-0.02718.736-0.027-0.0270.0000.0000.0000.000
20A22LEU 0-0.063-0.01614.8740.0230.0230.0000.0000.0000.000
21A23MET 00.0170.04118.459-0.009-0.0090.0000.0000.0000.000
22A24PRO 00.0370.00519.8780.0010.0010.0000.0000.0000.000
23A25ARG 10.8930.94621.9770.0760.0760.0000.0000.0000.000
24A26GLY 0-0.033-0.01725.4040.0050.0050.0000.0000.0000.000
25A27HIS 00.000-0.00123.6180.0090.0090.0000.0000.0000.000
26A28ASN 0-0.042-0.00926.031-0.008-0.0080.0000.0000.0000.000
27A29GLU -1-0.893-0.94726.259-0.112-0.1120.0000.0000.0000.000
28A30TYR 0-0.031-0.04018.812-0.007-0.0070.0000.0000.0000.000
29A31PHE 0-0.064-0.05522.4010.0010.0010.0000.0000.0000.000
30A32ASP -1-0.890-0.92225.766-0.083-0.0830.0000.0000.0000.000
31A33ARG 10.9340.96025.8510.1030.1030.0000.0000.0000.000
32A34GLY 00.0120.01330.5010.0020.0020.0000.0000.0000.000
33A35THR 00.0130.00131.5840.0070.0070.0000.0000.0000.000
34A36GLN 0-0.037-0.01328.685-0.011-0.0110.0000.0000.0000.000
35A37MET 0-0.0010.01323.9960.0010.0010.0000.0000.0000.000
36A38ASN 0-0.045-0.03628.0830.0030.0030.0000.0000.0000.000
37A39ILE 0-0.040-0.01422.685-0.007-0.0070.0000.0000.0000.000
38A40ASN 00.0330.01224.4570.0060.0060.0000.0000.0000.000
39A41LEU 00.0420.02517.791-0.005-0.0050.0000.0000.0000.000
40A42TYR 00.008-0.00821.682-0.001-0.0010.0000.0000.0000.000
41A43ASP -1-0.903-0.95123.840-0.034-0.0340.0000.0000.0000.000
42A44HIS 0-0.0270.02818.507-0.006-0.0060.0000.0000.0000.000
43A45ALA 00.007-0.01620.117-0.002-0.0020.0000.0000.0000.000
44A46ARG 10.8600.92721.3840.0300.0300.0000.0000.0000.000
45A47GLY 00.0460.03324.3740.0030.0030.0000.0000.0000.000
46A48THR 0-0.023-0.01623.952-0.010-0.0100.0000.0000.0000.000
47A49GLN 0-0.037-0.00423.164-0.005-0.0050.0000.0000.0000.000
48A50THR 00.0300.01425.230-0.001-0.0010.0000.0000.0000.000
49A51GLY 0-0.020-0.00326.624-0.001-0.0010.0000.0000.0000.000
50A52PHE 0-0.020-0.02722.281-0.009-0.0090.0000.0000.0000.000
51A53VAL 00.0290.03017.1470.0110.0110.0000.0000.0000.000
52A54ARG 10.8840.91419.1990.0460.0460.0000.0000.0000.000
53A55TYR 0-0.063-0.03219.046-0.022-0.0220.0000.0000.0000.000
54A56ASP -1-0.761-0.88021.014-0.077-0.0770.0000.0000.0000.000
55A57ASP -1-0.800-0.89822.708-0.066-0.0660.0000.0000.0000.000
56A58GLY 00.0180.00122.828-0.002-0.0020.0000.0000.0000.000
57A59TYR 00.0250.01717.077-0.014-0.0140.0000.0000.0000.000
58A60VAL 0-0.021-0.00215.6290.0090.0090.0000.0000.0000.000
59A61SER 0-0.0100.00814.684-0.030-0.0300.0000.0000.0000.000
60A62THR 0-0.087-0.05310.222-0.068-0.0680.0000.0000.0000.000
61A63SER 00.0580.01510.9470.0630.0630.0000.0000.0000.000
62A64LEU 00.0790.0346.017-0.165-0.1650.0000.0000.0000.000
63A65SER 0-0.0040.0096.6570.0860.0860.0000.0000.0000.000
64A66LEU 00.0400.0268.835-0.049-0.0490.0000.0000.0000.000
65A67ARG 10.9780.98111.1500.0000.0000.0000.0000.0000.000
66A68SER 00.0540.00011.9450.0100.0100.0000.0000.0000.000
67A69ALA 00.0370.02712.529-0.005-0.0050.0000.0000.0000.000
68A70HIS 0-0.046-0.03414.3240.0060.0060.0000.0000.0000.000
69A71LEU 0-0.025-0.00316.5950.0090.0090.0000.0000.0000.000
70A72ALA 00.0450.02917.7250.0050.0050.0000.0000.0000.000
71A73GLY 00.036-0.01618.6230.0010.0010.0000.0000.0000.000
72A74GLN 0-0.051-0.01520.422-0.003-0.0030.0000.0000.0000.000
73A75SER 00.0320.01322.7180.0080.0080.0000.0000.0000.000
74A76ILE 0-0.044-0.00921.6800.0020.0020.0000.0000.0000.000
75A77LEU 0-0.121-0.04621.1250.0020.0020.0000.0000.0000.000
76A78SER 00.0030.00524.7250.0000.0000.0000.0000.0000.000
77A79GLY 00.0150.01426.9360.0020.0020.0000.0000.0000.000
78A80TYR 0-0.034-0.01425.9400.0000.0000.0000.0000.0000.000
79A81SER 00.0190.00527.2740.0020.0020.0000.0000.0000.000
80A82THR 0-0.028-0.03024.4100.0030.0030.0000.0000.0000.000
81A83TYR 0-0.0240.00818.910-0.005-0.0050.0000.0000.0000.000
82A84TYR 0-0.009-0.00918.1740.0030.0030.0000.0000.0000.000
83A85ILE 00.0150.02012.7480.0020.0020.0000.0000.0000.000
84A86TYR 0-0.038-0.06013.652-0.031-0.0310.0000.0000.0000.000
85A87VAL 0-0.032-0.0157.892-0.053-0.0530.0000.0000.0000.000
86A88ILE 00.003-0.0108.7820.0360.0360.0000.0000.0000.000
87A89ALA 0-0.0110.0016.173-0.687-0.6870.0000.0000.0000.000
88A90THR 00.0310.0283.9790.0330.1830.003-0.036-0.1170.000
89A91ALA 0-0.005-0.0146.4930.1080.1080.0000.0000.0000.000
90A92PRO 00.0720.0199.8610.0240.0240.0000.0000.0000.000
91A93ASN 00.0240.02912.624-0.008-0.0080.0000.0000.0000.000
92A94MET 0-0.053-0.0119.703-0.048-0.0480.0000.0000.0000.000
93A95PHE 00.0940.04311.8390.0250.0250.0000.0000.0000.000
94A96ASN 00.0190.00210.303-0.051-0.0510.0000.0000.0000.000
95A97VAL 00.0510.00912.5810.0180.0180.0000.0000.0000.000
96A98ASN 00.0110.00614.938-0.011-0.0110.0000.0000.0000.000
97A99ASP -1-0.924-0.95412.9720.1630.1630.0000.0000.0000.000
98A100VAL 0-0.057-0.02215.872-0.003-0.0030.0000.0000.0000.000
99A101LEU 0-0.0120.00518.305-0.001-0.0010.0000.0000.0000.000
100A102GLY 00.0380.03119.7280.0010.0010.0000.0000.0000.000
101A103VAL 00.000-0.01321.351-0.001-0.0010.0000.0000.0000.000
102A104TYR 0-0.072-0.03224.376-0.003-0.0030.0000.0000.0000.000
103A105SER 00.024-0.00718.882-0.013-0.0130.0000.0000.0000.000
104A106PRO 0-0.041-0.00321.4490.0040.0040.0000.0000.0000.000
105A107HIS 10.8520.92420.8850.0160.0160.0000.0000.0000.000
106A108PRO 00.1120.06819.359-0.001-0.0010.0000.0000.0000.000
107A109TYR 0-0.028-0.01217.7910.0090.0090.0000.0000.0000.000
108A110GLU -1-0.950-0.98717.087-0.003-0.0030.0000.0000.0000.000
109A111GLN 0-0.099-0.04511.623-0.050-0.0500.0000.0000.0000.000
110A112GLU -1-0.815-0.88012.021-0.063-0.0630.0000.0000.0000.000
111A113VAL 0-0.012-0.0088.4560.0260.0260.0000.0000.0000.000
112A114SER 0-0.019-0.03811.581-0.068-0.0680.0000.0000.0000.000
113A115ALA 0-0.048-0.01813.0930.0000.0000.0000.0000.0000.000
114A116LEU 00.0250.00514.4070.0210.0210.0000.0000.0000.000
115A117GLY 00.018-0.00217.707-0.014-0.0140.0000.0000.0000.000
116A118GLY 0-0.015-0.01418.0110.0060.0060.0000.0000.0000.000
117A119ILE 0-0.077-0.03812.472-0.037-0.0370.0000.0000.0000.000
118A120PRO 00.0500.04315.0870.0120.0120.0000.0000.0000.000
119A121TYR 00.0850.01115.638-0.060-0.0600.0000.0000.0000.000
120A122SER 0-0.059-0.02616.098-0.043-0.0430.0000.0000.0000.000
121A123GLN 0-0.012-0.0149.8440.0780.0780.0000.0000.0000.000
122A124ILE 0-0.0150.00110.916-0.190-0.1900.0000.0000.0000.000
123A125TYR 00.0050.0019.3280.0870.0870.0000.0000.0000.000
124A126GLY 00.0490.00311.4380.1130.1130.0000.0000.0000.000
125A127TRP 00.0210.00513.417-0.055-0.0550.0000.0000.0000.000
126A128TYR 00.0480.03010.6960.0260.0260.0000.0000.0000.000
127A129ARG 10.9530.99016.5800.1010.1010.0000.0000.0000.000
128A130VAL 0-0.0020.00818.8690.0060.0060.0000.0000.0000.000
129A131ASN 00.022-0.00621.4350.0000.0000.0000.0000.0000.000
130A132PHE 00.0320.01325.1290.0050.0050.0000.0000.0000.000
131A133GLY 00.0220.01323.5380.0060.0060.0000.0000.0000.000
132A134VAL 00.003-0.00122.2540.0040.0040.0000.0000.0000.000
133A135ILE 0-0.045-0.03315.551-0.010-0.0100.0000.0000.0000.000
134A136ASP -1-0.867-0.92519.563-0.107-0.1070.0000.0000.0000.000
135A137GLU -1-0.967-0.97417.031-0.103-0.1030.0000.0000.0000.000
136A138ARG 10.9490.96717.6500.1160.1160.0000.0000.0000.000
137A139LEU 0-0.076-0.02711.538-0.023-0.0230.0000.0000.0000.000
138A140HIS 0-0.091-0.03215.4940.0360.0360.0000.0000.0000.000
139A141ARG 10.9280.96913.0840.3450.3450.0000.0000.0000.000
140A142ASN 0-0.0030.00014.9820.0980.0980.0000.0000.0000.000
141A143ARG 10.9390.93716.3520.1430.1430.0000.0000.0000.000
142A144GLU -1-0.913-0.96418.645-0.192-0.1920.0000.0000.0000.000
143A145TYR 0-0.0120.0279.013-0.092-0.0920.0000.0000.0000.000
144A146ARG 10.9020.93914.3880.2840.2840.0000.0000.0000.000
145A147ASP -1-0.851-0.94411.349-0.484-0.4840.0000.0000.0000.000
146A148ARG 10.9450.96011.8150.1380.1380.0000.0000.0000.000
147A149TYR 0-0.050-0.02913.1220.0150.0150.0000.0000.0000.000
148A150TYR 00.1010.0309.1940.0380.0380.0000.0000.0000.000
149A151ARG 10.8730.9698.2690.0970.0970.0000.0000.0000.000
150A152ASN 00.010-0.0047.593-0.060-0.0600.0000.0000.0000.000
151A153LEU 0-0.0260.0168.8300.0990.0990.0000.0000.0000.000
152A154ASN 0-0.004-0.0295.126-0.019-0.0190.0000.0000.0000.000
153A155ILE 0-0.042-0.0126.347-0.088-0.0880.0000.0000.0000.000
154A156ALA 0-0.0040.0258.8910.0710.0710.0000.0000.0000.000
155A157PRO 00.0280.01512.4970.0220.0220.0000.0000.0000.000
156A158ALA 00.029-0.00913.855-0.025-0.0250.0000.0000.0000.000
157A159GLU -1-0.936-0.96316.1410.0490.0490.0000.0000.0000.000
158A160ASP -1-0.914-0.95817.025-0.025-0.0250.0000.0000.0000.000
159A161GLY 0-0.067-0.03718.019-0.015-0.0150.0000.0000.0000.000
160A162TYR 00.0270.01418.815-0.003-0.0030.0000.0000.0000.000
161A163ARG 10.9951.00221.8220.0330.0330.0000.0000.0000.000
162A164LEU 0-0.113-0.06119.572-0.004-0.0040.0000.0000.0000.000
163A165ALA 00.0130.00521.935-0.007-0.0070.0000.0000.0000.000
164A166GLY 0-0.025-0.01422.9340.0000.0000.0000.0000.0000.000
165A167PHE 00.0060.00724.222-0.001-0.0010.0000.0000.0000.000
166A168PRO 00.0110.01627.733-0.002-0.0020.0000.0000.0000.000
167A169PRO 00.033-0.01031.3360.0030.0030.0000.0000.0000.000
168A170ASP -1-0.880-0.95033.775-0.001-0.0010.0000.0000.0000.000
169A171HIS 00.046-0.00128.811-0.001-0.0010.0000.0000.0000.000
170A172GLN 0-0.0250.00730.6770.0010.0010.0000.0000.0000.000
171A173ALA 00.0610.01326.9760.0020.0020.0000.0000.0000.000
172A174TRP 0-0.0350.01626.1700.0030.0030.0000.0000.0000.000
173A175ARG 10.7230.86730.654-0.006-0.0060.0000.0000.0000.000
174A176GLU -1-0.829-0.90028.8250.0310.0310.0000.0000.0000.000
175A177GLU -1-0.884-0.92327.0350.0350.0350.0000.0000.0000.000
176A178PRO 00.0360.00322.6040.0020.0020.0000.0000.0000.000
177A179TRP 0-0.010-0.02822.279-0.004-0.0040.0000.0000.0000.000
178A180ILE 00.0190.01226.429-0.006-0.0060.0000.0000.0000.000
179A181HIS 0-0.102-0.05126.905-0.004-0.0040.0000.0000.0000.000
180A182HIS 0-0.063-0.03523.880-0.002-0.0020.0000.0000.0000.000
181A183ALA 00.0180.01527.117-0.006-0.0060.0000.0000.0000.000
182A184PRO 0-0.022-0.00327.681-0.001-0.0010.0000.0000.0000.000
183A185GLN 00.007-0.01630.2230.0040.0040.0000.0000.0000.000
184A186GLY 0-0.029-0.00633.929-0.002-0.0020.0000.0000.0000.000
185A187CYS 0-0.070-0.00131.216-0.002-0.0020.0000.0000.0000.000
186A188GLY 00.0830.01733.1510.0020.0020.0000.0000.0000.000
187A189NME 0-0.031-0.00233.825-0.001-0.0010.0000.0000.0000.000