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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: YY9L2

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2083602.102629
FMO2-HF: Nuclear repulsion 2009184.117191
FMO2-HF: Total energy -74417.985439
FMO2-MP2: Total energy -74637.664809


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.
-30.619-17.5314.234-9.074-18.245-0.065
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 : 0.897 / 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].
3A6TYR0-0.040-0.0313.173-4.671-1.4550.032-1.388-1.8600.004
4A7ARG10.8250.8996.11821.72421.7240.0000.0000.0000.000
5A8ALA0-0.0290.0099.556-0.407-0.4070.0000.0000.0000.000
6A9ASP-1-0.733-0.87712.649-17.271-17.2710.0000.0000.0000.000
7A10SER00.0440.02614.940-0.422-0.4220.0000.0000.0000.000
8A11ARG10.8320.92015.92716.95416.9540.0000.0000.0000.000
9A12PRO00.0140.02816.131-1.338-1.3380.0000.0000.0000.000
10A13PRO00.0340.01113.8520.1840.1840.0000.0000.0000.000
11A14ASP-1-0.822-0.91015.601-15.038-15.0380.0000.0000.0000.000
12A15GLU-1-0.883-0.94818.871-14.107-14.1070.0000.0000.0000.000
13A16ILE00.0110.00713.112-0.006-0.0060.0000.0000.0000.000
14A17LYS10.7880.88315.75817.98017.9800.0000.0000.0000.000
15A18ARG10.8200.90516.70614.01014.0100.0000.0000.0000.000
16A19SER00.0140.01418.0890.6250.6250.0000.0000.0000.000
17A20GLY00.0310.02116.4130.2740.2740.0000.0000.0000.000
18A21GLY0-0.012-0.02313.381-1.412-1.4120.0000.0000.0000.000
19A22LEU0-0.056-0.01510.2871.1131.1130.0000.0000.0000.000
20A23MET00.0000.04114.207-0.450-0.4500.0000.0000.0000.000
21A24PRO00.0650.01717.184-0.120-0.1200.0000.0000.0000.000
22A25ARG10.8280.89218.56411.94611.9460.0000.0000.0000.000
23A26GLY0-0.018-0.01321.9940.2260.2260.0000.0000.0000.000
24A27HIS0-0.028-0.00620.0210.6330.6330.0000.0000.0000.000
25A28ASN0-0.030-0.01522.181-0.316-0.3160.0000.0000.0000.000
26A29GLU-1-0.889-0.94421.225-13.067-13.0670.0000.0000.0000.000
27A30TYR0-0.031-0.03615.291-0.360-0.3600.0000.0000.0000.000
28A31PHE0-0.055-0.04816.792-0.024-0.0240.0000.0000.0000.000
29A32ASP-1-0.829-0.90321.096-11.248-11.2480.0000.0000.0000.000
30A33ARG10.8840.94021.79912.88312.8830.0000.0000.0000.000
31A34GLY00.0170.01526.7020.1580.1580.0000.0000.0000.000
32A35THR0-0.006-0.00828.2310.4260.4260.0000.0000.0000.000
33A36GLN0-0.019-0.00226.185-0.691-0.6910.0000.0000.0000.000
34A37MET0-0.0110.00621.7820.0930.0930.0000.0000.0000.000
35A38ASN0-0.057-0.05225.9410.1120.1120.0000.0000.0000.000
36A39ILE0-0.029-0.01320.441-0.464-0.4640.0000.0000.0000.000
37A40ASN00.0190.00722.460-0.127-0.1270.0000.0000.0000.000
38A41LEU00.0470.02716.832-0.244-0.2440.0000.0000.0000.000
39A42TYR00.0160.00020.399-0.191-0.1910.0000.0000.0000.000
40A43ASP-1-0.831-0.91122.865-10.685-10.6850.0000.0000.0000.000
41A44HIS0-0.0460.02316.305-0.742-0.7420.0000.0000.0000.000
42A45ALA0-0.005-0.02319.025-0.144-0.1440.0000.0000.0000.000
43A46ARG10.8040.87620.02510.88910.8890.0000.0000.0000.000
44A47GLY00.0300.02122.5940.3950.3950.0000.0000.0000.000
45A48THR0-0.031-0.01221.749-0.766-0.7660.0000.0000.0000.000
46A49GLN0-0.021-0.01020.6580.1890.1890.0000.0000.0000.000
47A50THR00.0390.01422.167-0.445-0.4450.0000.0000.0000.000
48A51GLY0-0.0190.00022.8630.2030.2030.0000.0000.0000.000
49A52PHE0-0.006-0.02118.308-0.334-0.3340.0000.0000.0000.000
50A53VAL00.0460.03314.0180.3810.3810.0000.0000.0000.000
51A54ARG10.8320.88816.98614.74214.7420.0000.0000.0000.000
52A55TYR0-0.071-0.03616.271-1.008-1.0080.0000.0000.0000.000
53A56ASP-1-0.734-0.84517.985-11.982-11.9820.0000.0000.0000.000
54A57ASP-1-0.809-0.89420.220-12.240-12.2400.0000.0000.0000.000
55A58GLY00.0280.00820.166-0.276-0.2760.0000.0000.0000.000
56A59TYR00.0190.02014.913-1.013-1.0130.0000.0000.0000.000
57A60VAL0-0.0260.00312.2140.4410.4410.0000.0000.0000.000
58A61SER0-0.027-0.01312.311-1.306-1.3060.0000.0000.0000.000
59A62THR0-0.078-0.0537.659-1.753-1.7530.0000.0000.0000.000
60A63SER00.0340.0058.4671.7991.7990.0000.0000.0000.000
61A64LEU00.0920.0415.185-4.490-4.4900.0000.0000.0000.000
62A65SER0-0.016-0.0035.243-2.331-2.3310.0000.0000.0000.000
63A66LEU00.0380.0267.1151.2031.2030.0000.0000.0000.000
64A67ARG10.9200.9428.33618.34718.3470.0000.0000.0000.000
65A68SER00.0580.02310.5931.9301.9300.0000.0000.0000.000
66A69ALA00.0410.0289.3921.1391.1390.0000.0000.0000.000
67A70HIS0-0.005-0.00711.4120.8240.8240.0000.0000.0000.000
68A71LEU0-0.030-0.01113.7251.0631.0630.0000.0000.0000.000
69A72ALA00.0340.02314.6200.9480.9480.0000.0000.0000.000
70A73GLY00.042-0.00115.2470.7340.7340.0000.0000.0000.000
71A74GLN0-0.028-0.00416.6950.2410.2410.0000.0000.0000.000
72A75SER00.0240.01619.5030.8440.8440.0000.0000.0000.000
73A76ILE0-0.047-0.01518.6680.5190.5190.0000.0000.0000.000
74A77LEU0-0.111-0.04516.6540.4720.4720.0000.0000.0000.000
75A78SER00.0010.00420.5110.2860.2860.0000.0000.0000.000
76A79GLY00.0010.00323.0750.1990.1990.0000.0000.0000.000
77A80TYR0-0.014-0.00721.2850.2080.2080.0000.0000.0000.000
78A81SER00.0470.02622.761-0.085-0.0850.0000.0000.0000.000
79A82THR0-0.053-0.04119.343-0.123-0.1230.0000.0000.0000.000
80A83TYR0-0.0090.01214.682-0.160-0.1600.0000.0000.0000.000
81A84TYR0-0.006-0.00812.790-0.231-0.2310.0000.0000.0000.000
82A85ILE00.0220.0198.1770.2440.2440.0000.0000.0000.000
83A86TYR0-0.027-0.0368.118-1.780-1.7800.0000.0000.0000.000
84A87VAL0-0.018-0.0092.118-1.930-2.3013.075-0.669-2.034-0.004
85A88ILE0-0.002-0.0173.596-3.188-2.4540.013-0.199-0.547-0.001
86A89ALA0-0.0220.0012.107-14.323-11.7324.956-3.244-4.304-0.025
87A90THR00.0380.0242.7595.9696.5640.2990.087-0.981-0.002
88A91ALA0-0.015-0.0164.914-0.859-0.809-0.001-0.003-0.0450.000
89A92PRO00.0710.0188.6460.4620.4620.0000.0000.0000.000
90A93ASN00.0120.02010.273-0.199-0.1990.0000.0000.0000.000
91A94MET0-0.055-0.0176.208-0.612-0.6120.0000.0000.0000.000
92A95PHE00.0960.04510.698-0.042-0.0420.0000.0000.0000.000
93A96ASN0-0.027-0.02210.707-0.281-0.2810.0000.0000.0000.000
94A97VAL00.0350.00512.1111.0281.0280.0000.0000.0000.000
95A98ASN00.0050.00814.4731.4541.4540.0000.0000.0000.000
96A99ASP-1-0.865-0.92813.054-16.854-16.8540.0000.0000.0000.000
97A100VAL0-0.033-0.00615.7170.6140.6140.0000.0000.0000.000
98A101LEU0-0.0120.00318.1520.6820.6820.0000.0000.0000.000
99A102GLY00.0380.02619.5680.6370.6370.0000.0000.0000.000
100A103VAL00.002-0.02021.291-0.164-0.1640.0000.0000.0000.000
101A104TYR0-0.068-0.05024.1280.2020.2020.0000.0000.0000.000
102A105SER0-0.021-0.02518.463-0.158-0.1580.0000.0000.0000.000
103A106PRO0-0.015-0.00120.6040.2220.2220.0000.0000.0000.000
104A107HIS10.8530.92719.78512.89112.8910.0000.0000.0000.000
105A108PRO00.0960.07118.636-0.704-0.7040.0000.0000.0000.000
106A109TYR0-0.019-0.00817.215-0.697-0.6970.0000.0000.0000.000
107A110GLU-1-0.898-0.96216.141-14.362-14.3620.0000.0000.0000.000
108A111GLN0-0.104-0.05810.851-2.432-2.4320.0000.0000.0000.000
109A112GLU-1-0.760-0.82511.143-18.111-18.1110.0000.0000.0000.000
110A113VAL00.003-0.0037.6780.2190.2190.0000.0000.0000.000
111A114SER0-0.018-0.02910.128-1.538-1.5380.0000.0000.0000.000
112A115ALA0-0.057-0.01710.148-0.080-0.0800.0000.0000.0000.000
113A116LEU00.0430.01011.9580.9110.9110.0000.0000.0000.000
114A117GLY00.010-0.00915.356-0.471-0.4710.0000.0000.0000.000
115A118GLY0-0.013-0.00614.7150.4150.4150.0000.0000.0000.000
116A119ILE0-0.069-0.0398.778-1.421-1.4210.0000.0000.0000.000
117A120PRO00.0530.04210.6620.2360.2360.0000.0000.0000.000
118A121TYR00.0700.00210.082-2.569-2.5690.0000.0000.0000.000
119A122SER0-0.075-0.0419.386-2.666-2.6660.0000.0000.0000.000
120A123GLN00.0150.0086.186-0.261-0.2610.0000.0000.0000.000
121A124ILE0-0.0220.0005.097-7.550-7.457-0.0010.000-0.0910.000
122A125TYR0-0.003-0.0112.770-3.894-0.6392.437-1.209-4.482-0.002
123A126GLY00.0450.0044.8854.1564.226-0.001-0.013-0.0560.000
124A127TRP00.0170.0107.152-1.530-1.5300.0000.0000.0000.000
125A128TYR00.0310.0217.155-1.147-1.1470.0000.0000.0000.000
126A129ARG10.9480.97011.48114.83914.8390.0000.0000.0000.000
127A130VAL0-0.0180.00114.338-0.159-0.1590.0000.0000.0000.000
128A131ASN00.003-0.00216.9200.6270.6270.0000.0000.0000.000
129A132PHE00.0360.00420.6980.0530.0530.0000.0000.0000.000
130A133GLY00.0230.01619.6650.2030.2030.0000.0000.0000.000
131A134VAL00.0020.00018.815-0.323-0.3230.0000.0000.0000.000
132A135ILE0-0.048-0.03712.243-0.137-0.1370.0000.0000.0000.000
133A136ASP-1-0.812-0.87315.646-17.023-17.0230.0000.0000.0000.000
134A137GLU-1-0.929-0.96112.958-18.601-18.6010.0000.0000.0000.000
135A138ARG10.8370.89312.85617.10617.1060.0000.0000.0000.000
136A139LEU0-0.064-0.0215.636-0.593-0.5930.0000.0000.0000.000
137A140HIS0-0.058-0.02310.0691.7271.7270.0000.0000.0000.000
138A141ARG10.9060.9586.11335.48935.4890.0000.0000.0000.000
139A142ASN00.0200.0228.0705.8235.8230.0000.0000.0000.000
140A143ARG10.9550.9509.07916.33716.3370.0000.0000.0000.000
141A144GLU-1-0.861-0.92111.154-19.461-19.4610.0000.0000.0000.000
142A145TYR00.0140.0382.127-18.246-15.6083.427-2.413-3.652-0.035
143A146ARG10.9040.9407.33624.51524.5150.0000.0000.0000.000
144A147ASP-1-0.808-0.9034.280-48.591-48.455-0.001-0.020-0.1150.000
145A148ARG10.9530.9635.86820.09520.0950.0000.0000.0000.000
146A149TYR0-0.042-0.0258.6850.2590.2590.0000.0000.0000.000
147A150TYR00.0900.0284.5971.3131.395-0.001-0.003-0.0780.000
148A151ARG10.8150.9264.90829.58629.5860.0000.0000.0000.000
149A152ASN0-0.001-0.0145.900-1.462-1.4620.0000.0000.0000.000
150A153LEU0-0.0130.0247.7902.7142.7140.0000.0000.0000.000
151A154ASN0-0.006-0.0246.045-2.024-2.0240.0000.0000.0000.000
152A155ILE0-0.033-0.0115.8210.0560.0560.0000.0000.0000.000
153A156ALA00.0070.0298.9380.9570.9570.0000.0000.0000.000
154A157PRO00.0220.01612.656-0.223-0.2230.0000.0000.0000.000
155A158ALA00.034-0.00714.3870.4020.4020.0000.0000.0000.000
156A159GLU-1-0.919-0.96316.429-13.564-13.5640.0000.0000.0000.000
157A160ASP-1-0.865-0.92017.495-13.910-13.9100.0000.0000.0000.000
158A161GLY0-0.006-0.00617.7830.0800.0800.0000.0000.0000.000
159A162TYR00.0070.00518.5990.4250.4250.0000.0000.0000.000
160A163ARG10.8850.93620.77513.48513.4850.0000.0000.0000.000
161A164LEU0-0.091-0.04918.8720.3320.3320.0000.0000.0000.000
162A165ALA00.001-0.00221.356-0.190-0.1900.0000.0000.0000.000
163A166GLY0-0.033-0.01422.3810.0160.0160.0000.0000.0000.000
164A167PHE00.0190.01223.4630.2450.2450.0000.0000.0000.000
165A168PRO00.0180.02127.0600.1190.1190.0000.0000.0000.000
166A169PRO00.030-0.01730.5620.0440.0440.0000.0000.0000.000
167A170ASP-1-0.849-0.92233.250-8.429-8.4290.0000.0000.0000.000
168A171HIS00.0490.02027.706-0.037-0.0370.0000.0000.0000.000
169A172GLN0-0.0210.01130.3390.0060.0060.0000.0000.0000.000
170A173ALA00.0440.01626.8840.0830.0830.0000.0000.0000.000
171A174TRP0-0.044-0.03125.682-0.117-0.1170.0000.0000.0000.000
172A175ARG10.7340.86230.5158.4528.4520.0000.0000.0000.000
173A176GLU-1-0.807-0.86428.860-9.225-9.2250.0000.0000.0000.000
174A177GLU-1-0.860-0.89827.570-9.711-9.7110.0000.0000.0000.000
175A178PRO00.0250.00122.985-0.052-0.0520.0000.0000.0000.000
176A179TRP0-0.026-0.03422.1420.0130.0130.0000.0000.0000.000
177A180ILE00.0140.01426.5200.0650.0650.0000.0000.0000.000
178A181HIS0-0.107-0.06427.3890.1340.1340.0000.0000.0000.000
179A182HIS0-0.078-0.05324.423-0.324-0.3240.0000.0000.0000.000
180A183ALA00.0000.01127.250-0.247-0.2470.0000.0000.0000.000
181A184PRO0-0.0010.00827.2720.1960.1960.0000.0000.0000.000
182A185GLN00.001-0.01729.9110.1770.1770.0000.0000.0000.000
183A186GLY0-0.024-0.00533.6050.1350.1350.0000.0000.0000.000
184A187CYS0-0.071-0.00530.791-0.023-0.0230.0000.0000.0000.000
185A188GLY00.0310.01932.8020.1770.1770.0000.0000.0000.000