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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: 53RKZ

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 OptH
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 -2082834.169682
FMO2-HF: Nuclear repulsion 2008417.533977
FMO2-HF: Total energy -74416.635705
FMO2-MP2: Total energy -74636.423548


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.
-23.159-12.69813.103-8.227-15.334-0.054
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 : 0.909 / q_NPA : 0.958
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].
3A6TYR0-0.039-0.0313.159-6.193-2.5280.127-1.601-2.1900.002
4A7ARG10.8460.9186.04022.15922.1590.0000.0000.0000.000
5A8ALA0-0.0240.0159.501-0.407-0.4070.0000.0000.0000.000
6A9ASP-1-0.739-0.90412.586-17.422-17.4220.0000.0000.0000.000
7A10SER00.0370.02014.903-0.391-0.3910.0000.0000.0000.000
8A11ARG10.8700.95716.10816.90316.9030.0000.0000.0000.000
9A12PRO00.0110.04416.130-1.414-1.4140.0000.0000.0000.000
10A13PRO00.0230.00513.9290.1250.1250.0000.0000.0000.000
11A14ASP-1-0.893-0.96115.593-15.105-15.1050.0000.0000.0000.000
12A15GLU-1-0.888-0.94418.922-13.881-13.8810.0000.0000.0000.000
13A16ILE00.0090.00013.3800.0620.0620.0000.0000.0000.000
14A17LYS10.8380.92716.42617.52717.5270.0000.0000.0000.000
15A18ARG10.9030.95517.32113.80413.8040.0000.0000.0000.000
16A19SER00.0240.02818.6770.6290.6290.0000.0000.0000.000
17A20GLY00.0320.02316.9680.2780.2780.0000.0000.0000.000
18A21GLY0-0.015-0.02613.790-1.322-1.3220.0000.0000.0000.000
19A22LEU0-0.057-0.01510.2141.0601.0600.0000.0000.0000.000
20A23MET00.0130.04014.240-0.421-0.4210.0000.0000.0000.000
21A24PRO00.0360.00516.660-0.088-0.0880.0000.0000.0000.000
22A25ARG10.8920.94518.56312.00312.0030.0000.0000.0000.000
23A26GLY0-0.033-0.01721.9920.2300.2300.0000.0000.0000.000
24A27HIS0-0.001-0.00120.2090.5960.5960.0000.0000.0000.000
25A28ASN0-0.040-0.00922.199-0.446-0.4460.0000.0000.0000.000
26A29GLU-1-0.894-0.94621.622-12.751-12.7510.0000.0000.0000.000
27A30TYR0-0.031-0.03915.225-0.317-0.3170.0000.0000.0000.000
28A31PHE0-0.063-0.05517.377-0.028-0.0280.0000.0000.0000.000
29A32ASP-1-0.892-0.92321.443-11.252-11.2520.0000.0000.0000.000
30A33ARG10.9330.96021.97312.70512.7050.0000.0000.0000.000
31A34GLY00.0120.01226.9400.1480.1480.0000.0000.0000.000
32A35THR00.0130.00128.2080.4260.4260.0000.0000.0000.000
33A36GLN0-0.034-0.01326.167-0.755-0.7550.0000.0000.0000.000
34A37MET00.0020.01420.9070.1570.1570.0000.0000.0000.000
35A38ASN0-0.047-0.03725.8860.1580.1580.0000.0000.0000.000
36A39ILE0-0.041-0.01520.509-0.465-0.4650.0000.0000.0000.000
37A40ASN00.0300.01222.493-0.106-0.1060.0000.0000.0000.000
38A41LEU00.0470.02716.838-0.270-0.2700.0000.0000.0000.000
39A42TYR00.007-0.00820.451-0.228-0.2280.0000.0000.0000.000
40A43ASP-1-0.901-0.95122.892-10.857-10.8570.0000.0000.0000.000
41A44HIS0-0.0310.02816.297-0.755-0.7550.0000.0000.0000.000
42A45ALA00.013-0.01519.048-0.159-0.1590.0000.0000.0000.000
43A46ARG10.8560.92620.07211.00711.0070.0000.0000.0000.000
44A47GLY00.0460.03322.6590.3950.3950.0000.0000.0000.000
45A48THR0-0.023-0.01621.775-0.798-0.7980.0000.0000.0000.000
46A49GLN0-0.040-0.00520.5180.2890.2890.0000.0000.0000.000
47A50THR00.0340.01622.105-0.343-0.3430.0000.0000.0000.000
48A51GLY0-0.021-0.00422.8110.2160.2160.0000.0000.0000.000
49A52PHE0-0.020-0.02717.990-0.408-0.4080.0000.0000.0000.000
50A53VAL00.0330.03213.9650.3930.3930.0000.0000.0000.000
51A54ARG10.8760.91117.00114.76014.7600.0000.0000.0000.000
52A55TYR0-0.056-0.03116.287-1.157-1.1570.0000.0000.0000.000
53A56ASP-1-0.764-0.88017.994-12.060-12.0600.0000.0000.0000.000
54A57ASP-1-0.796-0.89620.245-12.422-12.4220.0000.0000.0000.000
55A58GLY00.017-0.00120.188-0.290-0.2900.0000.0000.0000.000
56A59TYR00.0270.01815.201-0.634-0.6340.0000.0000.0000.000
57A60VAL0-0.019-0.00212.2610.4600.4600.0000.0000.0000.000
58A61SER0-0.0120.00812.374-1.314-1.3140.0000.0000.0000.000
59A62THR0-0.092-0.0567.676-1.828-1.8280.0000.0000.0000.000
60A63SER00.0620.0168.4671.8121.8120.0000.0000.0000.000
61A64LEU00.0780.0335.292-4.595-4.5950.0000.0000.0000.000
62A65SER00.0000.0125.192-2.564-2.577-0.001-0.0060.0210.000
63A66LEU00.0400.0276.8131.2371.2370.0000.0000.0000.000
64A67ARG10.9790.9818.06018.60718.6070.0000.0000.0000.000
65A68SER00.052-0.00110.4341.9611.9610.0000.0000.0000.000
66A69ALA00.0360.0269.2641.2011.2010.0000.0000.0000.000
67A70HIS0-0.043-0.03311.2850.6010.6010.0000.0000.0000.000
68A71LEU0-0.032-0.00613.4681.1741.1740.0000.0000.0000.000
69A72ALA00.0480.03114.5391.0081.0080.0000.0000.0000.000
70A73GLY00.036-0.01515.1540.7860.7860.0000.0000.0000.000
71A74GLN0-0.053-0.01716.6080.2130.2130.0000.0000.0000.000
72A75SER00.0310.01319.4040.8800.8800.0000.0000.0000.000
73A76ILE0-0.044-0.00818.4420.5390.5390.0000.0000.0000.000
74A77LEU0-0.116-0.04316.7660.4830.4830.0000.0000.0000.000
75A78SER00.0020.00320.4400.1860.1860.0000.0000.0000.000
76A79GLY00.0120.01322.9920.1910.1910.0000.0000.0000.000
77A80TYR0-0.033-0.01421.2070.2230.2230.0000.0000.0000.000
78A81SER00.0200.00522.695-0.023-0.0230.0000.0000.0000.000
79A82THR0-0.029-0.03019.1640.1230.1230.0000.0000.0000.000
80A83TYR0-0.0260.00814.518-0.162-0.1620.0000.0000.0000.000
81A84TYR0-0.007-0.00812.672-0.024-0.0240.0000.0000.0000.000
82A85ILE00.0190.0228.0310.1900.1900.0000.0000.0000.000
83A86TYR0-0.044-0.0638.106-1.815-1.8150.0000.0000.0000.000
84A87VAL0-0.027-0.0131.960-0.930-3.5566.356-1.137-2.593-0.007
85A88ILE00.004-0.0103.612-2.022-1.3070.012-0.200-0.528-0.001
86A89ALA0-0.0120.0002.159-16.537-13.6354.961-3.562-4.301-0.027
87A90THR00.0260.0262.9117.2577.2810.2380.529-0.791-0.003
88A91ALA0-0.006-0.0144.957-0.527-0.484-0.001-0.003-0.0380.000
89A92PRO00.0730.0198.6830.3610.3610.0000.0000.0000.000
90A93ASN00.0230.02910.381-0.236-0.2360.0000.0000.0000.000
91A94MET0-0.050-0.0116.569-0.610-0.6100.0000.0000.0000.000
92A95PHE00.0920.04310.752-0.005-0.0050.0000.0000.0000.000
93A96ASN00.0190.00310.3860.2150.2150.0000.0000.0000.000
94A97VAL00.0510.00912.1371.0101.0100.0000.0000.0000.000
95A98ASN00.0070.00514.5151.3301.3300.0000.0000.0000.000
96A99ASP-1-0.920-0.95213.420-16.710-16.7100.0000.0000.0000.000
97A100VAL0-0.055-0.02115.6760.6390.6390.0000.0000.0000.000
98A101LEU0-0.0150.00418.1720.7090.7090.0000.0000.0000.000
99A102GLY00.0350.03019.5980.6670.6670.0000.0000.0000.000
100A103VAL00.001-0.01321.327-0.169-0.1690.0000.0000.0000.000
101A104TYR0-0.074-0.03424.1490.3020.3020.0000.0000.0000.000
102A105SER00.023-0.00818.416-0.186-0.1860.0000.0000.0000.000
103A106PRO0-0.039-0.00320.6430.2230.2230.0000.0000.0000.000
104A107HIS10.8520.92419.83413.07413.0740.0000.0000.0000.000
105A108PRO00.1130.07018.696-0.713-0.7130.0000.0000.0000.000
106A109TYR0-0.030-0.01317.277-0.668-0.6680.0000.0000.0000.000
107A110GLU-1-0.952-0.98816.043-14.737-14.7370.0000.0000.0000.000
108A111GLN0-0.096-0.04410.515-1.658-1.6580.0000.0000.0000.000
109A112GLU-1-0.815-0.88011.205-18.208-18.2080.0000.0000.0000.000
110A113VAL0-0.010-0.0077.5860.2520.2520.0000.0000.0000.000
111A114SER0-0.020-0.03810.174-1.532-1.5320.0000.0000.0000.000
112A115ALA0-0.057-0.02110.246-0.096-0.0960.0000.0000.0000.000
113A116LEU00.0380.00811.9900.9330.9330.0000.0000.0000.000
114A117GLY00.014-0.00215.379-0.432-0.4320.0000.0000.0000.000
115A118GLY0-0.014-0.01414.7040.4630.4630.0000.0000.0000.000
116A119ILE0-0.076-0.0388.708-1.425-1.4250.0000.0000.0000.000
117A120PRO00.0510.04410.7210.3240.3240.0000.0000.0000.000
118A121TYR00.0880.01310.470-2.655-2.6550.0000.0000.0000.000
119A122SER0-0.064-0.02910.095-2.238-2.2380.0000.0000.0000.000
120A123GLN0-0.012-0.0146.2950.2690.2690.0000.0000.0000.000
121A124ILE0-0.0180.0005.417-6.999-6.9990.0000.0000.0000.000
122A125TYR00.0160.0043.332-3.107-0.1381.161-0.989-3.140-0.003
123A126GLY00.0420.0005.4823.7003.7000.0000.0000.0000.000
124A127TRP00.0230.0077.175-1.474-1.4740.0000.0000.0000.000
125A128TYR00.0440.0276.842-1.354-1.3540.0000.0000.0000.000
126A129ARG10.9500.99011.17515.04715.0470.0000.0000.0000.000
127A130VAL00.0010.00914.219-0.196-0.1960.0000.0000.0000.000
128A131ASN00.021-0.00616.8570.7750.7750.0000.0000.0000.000
129A132PHE00.0320.01320.6350.0260.0260.0000.0000.0000.000
130A133GLY00.0200.01119.5790.1890.1890.0000.0000.0000.000
131A134VAL00.0040.00018.629-0.352-0.3520.0000.0000.0000.000
132A135ILE0-0.042-0.03211.852-0.138-0.1380.0000.0000.0000.000
133A136ASP-1-0.868-0.92415.205-17.556-17.5560.0000.0000.0000.000
134A137GLU-1-0.969-0.97612.509-18.873-18.8730.0000.0000.0000.000
135A138ARG10.9470.96712.55216.85716.8570.0000.0000.0000.000
136A139LEU0-0.082-0.0295.728-0.643-0.6430.0000.0000.0000.000
137A140HIS0-0.087-0.0309.8081.8871.8870.0000.0000.0000.000
138A141ARG10.9300.9705.70535.15335.1530.0000.0000.0000.000
139A142ASN0-0.0030.0018.5675.5465.5460.0000.0000.0000.000
140A143ARG10.9390.9369.29516.65316.6530.0000.0000.0000.000
141A144GLU-1-0.912-0.96411.475-18.864-18.8640.0000.0000.0000.000
142A145TYR0-0.0010.0302.716-9.724-7.0170.251-1.256-1.702-0.015
143A146ARG10.8950.9377.98823.64423.6440.0000.0000.0000.000
144A147ASP-1-0.853-0.9444.785-45.677-45.602-0.001-0.002-0.0720.000
145A148ARG10.9430.9606.33419.59719.5970.0000.0000.0000.000
146A149TYR0-0.047-0.0289.0900.2800.2800.0000.0000.0000.000
147A150TYR00.1010.0294.8021.6651.6650.0000.0000.0000.000
148A151ARG10.8680.9665.18626.22926.2290.0000.0000.0000.000
149A152ASN00.012-0.0036.186-1.968-1.9680.0000.0000.0000.000
150A153LEU0-0.0240.0177.5562.6202.6200.0000.0000.0000.000
151A154ASN0-0.004-0.0296.748-2.858-2.8580.0000.0000.0000.000
152A155ILE0-0.043-0.0126.2670.0660.0660.0000.0000.0000.000
153A156ALA0-0.0040.0258.9100.9430.9430.0000.0000.0000.000
154A157PRO00.0300.01512.644-0.294-0.2940.0000.0000.0000.000
155A158ALA00.031-0.00814.3730.4130.4130.0000.0000.0000.000
156A159GLU-1-0.938-0.96416.430-13.163-13.1630.0000.0000.0000.000
157A160ASP-1-0.912-0.95717.117-14.600-14.6000.0000.0000.0000.000
158A161GLY0-0.068-0.03617.7830.0950.0950.0000.0000.0000.000
159A162TYR00.0270.01318.5960.4650.4650.0000.0000.0000.000
160A163ARG10.9941.00121.74913.08013.0800.0000.0000.0000.000
161A164LEU0-0.113-0.06118.9170.3490.3490.0000.0000.0000.000
162A165ALA00.0170.00521.370-0.190-0.1900.0000.0000.0000.000
163A166GLY0-0.034-0.01722.3930.0110.0110.0000.0000.0000.000
164A167PHE00.0130.01023.8890.2330.2330.0000.0000.0000.000
165A168PRO00.0090.01527.0810.1240.1240.0000.0000.0000.000
166A169PRO00.032-0.01130.5840.0390.0390.0000.0000.0000.000
167A170ASP-1-0.882-0.95233.266-8.581-8.5810.0000.0000.0000.000
168A171HIS00.0500.00028.334-0.165-0.1650.0000.0000.0000.000
169A172GLN0-0.0290.00730.3680.1350.1350.0000.0000.0000.000
170A173ALA00.0670.01826.8590.0840.0840.0000.0000.0000.000
171A174TRP0-0.034-0.00925.835-0.094-0.0940.0000.0000.0000.000
172A175ARG10.7380.87030.5318.5608.5600.0000.0000.0000.000
173A176GLU-1-0.831-0.89928.963-9.321-9.3210.0000.0000.0000.000
174A177GLU-1-0.883-0.92227.628-9.749-9.7490.0000.0000.0000.000
175A178PRO00.0370.00423.117-0.065-0.0650.0000.0000.0000.000
176A179TRP0-0.011-0.03022.2300.0480.0480.0000.0000.0000.000
177A180ILE00.0190.01226.5300.0620.0620.0000.0000.0000.000
178A181HIS0-0.096-0.04927.3520.0890.0890.0000.0000.0000.000
179A182HIS0-0.066-0.03724.394-0.296-0.2960.0000.0000.0000.000
180A183ALA00.0150.01527.246-0.253-0.2530.0000.0000.0000.000
181A184PRO0-0.0140.00027.3050.2120.2120.0000.0000.0000.000
182A185GLN00.005-0.01829.9070.1300.1300.0000.0000.0000.000
183A186GLY0-0.029-0.00733.5980.1390.1390.0000.0000.0000.000
184A187CYS0-0.0680.00130.755-0.036-0.0360.0000.0000.0000.000
185A188GLY00.0310.03032.8090.1170.1170.0000.0000.0000.000