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: GN891

Calculation Name: 1LT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name: beta-d-glucopyranose

ligand 3-letter code: BGC

PDB ID: 1LT4

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2887804.513921
FMO2-HF: Nuclear repulsion 2795842.154553
FMO2-HF: Total energy -91962.359369
FMO2-MP2: Total energy -92233.154825


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.
-41.207-29.35119.339-11.152-20.042-0.09
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 : 0.874 / q_NPA : 0.940
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].
3A6TYR0-0.026-0.0202.663-4.616-0.7620.401-1.703-2.5520.001
4A7ARG10.8010.8805.89321.87921.8790.0000.0000.0000.000
5A8ALA0-0.0300.0069.384-0.412-0.4120.0000.0000.0000.000
6A9ASP-1-0.753-0.87512.335-17.303-17.3030.0000.0000.0000.000
7A10SER00.0490.02314.730-0.400-0.4000.0000.0000.0000.000
8A11ARG10.8320.92816.01017.10417.1040.0000.0000.0000.000
9A12PRO00.0210.03315.998-1.380-1.3800.0000.0000.0000.000
10A13PRO00.034-0.00413.9920.2500.2500.0000.0000.0000.000
11A14ASP-1-0.803-0.88815.676-15.102-15.1020.0000.0000.0000.000
12A15GLU-1-0.889-0.94918.752-14.181-14.1810.0000.0000.0000.000
13A16ILE0-0.0130.00012.798-0.036-0.0360.0000.0000.0000.000
14A17LYS10.8020.88816.18017.82017.8200.0000.0000.0000.000
15A18ARG10.8270.90017.10913.97813.9780.0000.0000.0000.000
16A19SER00.0110.01617.9730.6560.6560.0000.0000.0000.000
17A20GLY00.0000.00717.0890.1700.1700.0000.0000.0000.000
18A21GLY00.003-0.02613.481-1.313-1.3130.0000.0000.0000.000
19A22LEU0-0.063-0.02010.3621.0321.0320.0000.0000.0000.000
20A23MET0-0.0100.03214.219-0.456-0.4560.0000.0000.0000.000
21A24PRO00.0530.01217.339-0.189-0.1890.0000.0000.0000.000
22A25ARG10.8150.89418.84611.94711.9470.0000.0000.0000.000
23A26GLY00.0060.00522.1580.2520.2520.0000.0000.0000.000
24A27HIS0-0.0070.01420.5920.4590.4590.0000.0000.0000.000
25A28ASN0-0.036-0.02321.509-0.486-0.4860.0000.0000.0000.000
26A29GLU-1-0.889-0.94421.112-13.234-13.2340.0000.0000.0000.000
27A30TYR00.019-0.01015.854-0.086-0.0860.0000.0000.0000.000
28A31PHE0-0.057-0.06317.5310.0590.0590.0000.0000.0000.000
29A32ASP-1-0.786-0.88022.125-11.083-11.0830.0000.0000.0000.000
30A33ARG10.8080.88122.45612.98112.9810.0000.0000.0000.000
31A34GLY00.0040.01427.1890.2510.2510.0000.0000.0000.000
32A35THR0-0.021-0.00627.3600.4760.4760.0000.0000.0000.000
33A36GLN0-0.041-0.00823.977-0.558-0.5580.0000.0000.0000.000
34A37MET00.0090.02619.7610.1230.1230.0000.0000.0000.000
35A38ASN00.001-0.00225.4570.2160.2160.0000.0000.0000.000
36A39ILE0-0.062-0.04720.408-0.590-0.5900.0000.0000.0000.000
37A40ASN00.0810.03722.206-0.003-0.0030.0000.0000.0000.000
38A41LEU00.0130.01116.770-0.298-0.2980.0000.0000.0000.000
39A42TYR00.0480.02120.563-0.270-0.2700.0000.0000.0000.000
40A43ASP-1-0.845-0.91422.976-10.867-10.8670.0000.0000.0000.000
41A44HIS0-0.0390.00916.557-0.843-0.8430.0000.0000.0000.000
42A45ALA0-0.017-0.02419.085-0.210-0.2100.0000.0000.0000.000
43A46ARG10.8100.89420.14410.90510.9050.0000.0000.0000.000
44A47GLY00.0110.01223.3990.3040.3040.0000.0000.0000.000
45A48THR0-0.020-0.00622.046-0.546-0.5460.0000.0000.0000.000
46A49GLN00.007-0.00720.972-0.281-0.2810.0000.0000.0000.000
47A50THR00.0280.02222.760-0.028-0.0280.0000.0000.0000.000
48A51GLY00.0100.00122.4430.1100.1100.0000.0000.0000.000
49A52PHE00.005-0.00818.559-0.371-0.3710.0000.0000.0000.000
50A53VAL00.0240.02013.7740.3610.3610.0000.0000.0000.000
51A54ARG10.8280.88816.88314.68314.6830.0000.0000.0000.000
52A55TYR0-0.056-0.04316.211-1.022-1.0220.0000.0000.0000.000
53A56ASP-1-0.736-0.84418.015-12.204-12.2040.0000.0000.0000.000
54A57ASP-1-0.824-0.90420.416-12.320-12.3200.0000.0000.0000.000
55A58GLY00.0540.01520.326-0.239-0.2390.0000.0000.0000.000
56A59TYR00.0090.00815.120-1.110-1.1100.0000.0000.0000.000
57A60VAL0-0.048-0.01112.2950.4570.4570.0000.0000.0000.000
58A61SER0-0.028-0.02612.442-1.805-1.8050.0000.0000.0000.000
59A62THR0-0.062-0.0397.799-1.836-1.8360.0000.0000.0000.000
60A63LYS10.8750.9248.64319.46119.4610.0000.0000.0000.000
61A64LEU00.1080.0446.101-4.062-4.0620.0000.0000.0000.000
62A65SER0-0.019-0.0105.588-1.982-1.9820.0000.0000.0000.000
63A66LEU00.0580.0316.7091.1261.1260.0000.0000.0000.000
64A67ARG10.9310.9577.96419.76519.7650.0000.0000.0000.000
65A68SER00.0560.02810.5590.7820.7820.0000.0000.0000.000
66A69ALA00.0040.0118.8341.0651.0650.0000.0000.0000.000
67A70HIS00.008-0.00110.8470.8370.8370.0000.0000.0000.000
68A71LEU0-0.015-0.01013.2520.9350.9350.0000.0000.0000.000
69A72ALA00.0130.00714.1460.8910.8910.0000.0000.0000.000
70A73GLY00.0400.01214.8540.6240.6240.0000.0000.0000.000
71A74GLN00.0060.02216.1440.3280.3280.0000.0000.0000.000
72A75SER00.0150.01319.0440.7510.7510.0000.0000.0000.000
73A76ILE0-0.059-0.03117.9760.5370.5370.0000.0000.0000.000
74A77LEU0-0.056-0.02916.4820.3370.3370.0000.0000.0000.000
75A78SER00.0100.00520.4360.1290.1290.0000.0000.0000.000
76A79GLY0-0.0220.00322.6880.1970.1970.0000.0000.0000.000
77A80TYR0-0.0130.00421.0360.1910.1910.0000.0000.0000.000
78A81SER00.0110.00022.227-0.197-0.1970.0000.0000.0000.000
79A82THR0-0.060-0.03418.802-0.110-0.1100.0000.0000.0000.000
80A83TYR00.002-0.00914.339-0.185-0.1850.0000.0000.0000.000
81A84TYR00.0050.00312.596-0.293-0.2930.0000.0000.0000.000
82A85ILE00.0260.0177.8790.3090.3090.0000.0000.0000.000
83A86TYR0-0.053-0.0548.059-1.803-1.8030.0000.0000.0000.000
84A87VAL00.001-0.0012.437-2.078-1.2931.273-0.438-1.620-0.001
85A88ILE0-0.026-0.0313.655-2.962-2.1300.013-0.234-0.611-0.001
86A89ALA00.0000.0072.306-13.776-11.2846.109-3.837-4.764-0.026
87A90THR00.0060.0072.4755.6275.8640.3480.490-1.075-0.001
88A91ALA0-0.006-0.0175.151-1.143-1.059-0.001-0.003-0.0800.000
89A92PRO00.0530.0288.5640.6130.6130.0000.0000.0000.000
90A93ASN00.0610.04310.4110.0220.0220.0000.0000.0000.000
91A94MET0-0.064-0.0116.6371.0641.0640.0000.0000.0000.000
92A95PHE00.0920.04010.757-0.122-0.1220.0000.0000.0000.000
93A96ASN0-0.032-0.02910.797-0.356-0.3560.0000.0000.0000.000
94A97VAL00.0190.00112.1031.0171.0170.0000.0000.0000.000
95A98ASN0-0.011-0.01514.6481.2981.2980.0000.0000.0000.000
96A99ASP-1-0.860-0.91513.450-17.059-17.0590.0000.0000.0000.000
97A100VAL0-0.019-0.00515.9160.6500.6500.0000.0000.0000.000
98A101LEU00.0060.01518.3810.6570.6570.0000.0000.0000.000
99A102GLY00.0820.04719.6830.6460.6460.0000.0000.0000.000
100A103VAL0-0.031-0.03321.216-0.215-0.2150.0000.0000.0000.000
101A104TYR0-0.077-0.05423.4990.3940.3940.0000.0000.0000.000
102A105SER0-0.053-0.03118.360-0.058-0.0580.0000.0000.0000.000
103A106PRO00.0310.00920.9090.2220.2220.0000.0000.0000.000
104A107HIS10.7900.90319.53212.89612.8960.0000.0000.0000.000
105A108PRO00.0750.04418.377-0.803-0.8030.0000.0000.0000.000
106A109TYR00.0400.00317.261-0.571-0.5710.0000.0000.0000.000
107A110GLU-1-0.890-0.94116.034-15.007-15.0070.0000.0000.0000.000
108A111GLN0-0.090-0.04012.276-1.519-1.5190.0000.0000.0000.000
109A112GLU-1-0.766-0.82011.337-18.473-18.4730.0000.0000.0000.000
110A113VAL00.0250.0147.5930.2680.2680.0000.0000.0000.000
111A114SER0-0.034-0.02910.236-1.452-1.4520.0000.0000.0000.000
112A115ALA0-0.006-0.00410.445-0.337-0.3370.0000.0000.0000.000
113A116LEU00.0210.01012.2540.9090.9090.0000.0000.0000.000
114A117GLY00.022-0.01015.738-0.417-0.4170.0000.0000.0000.000
115A118GLY00.0040.00414.7430.4470.4470.0000.0000.0000.000
116A119ILE0-0.076-0.0368.754-1.270-1.2700.0000.0000.0000.000
117A120PRO00.0460.03311.3220.5890.5890.0000.0000.0000.000
118A121TYR00.048-0.00310.806-2.416-2.4160.0000.0000.0000.000
119A122SER00.0030.00310.160-1.197-1.1970.0000.0000.0000.000
120A123GLN0-0.048-0.0196.8650.0600.0600.0000.0000.0000.000
121A124ILE0-0.0160.0005.766-6.526-6.5260.0000.0000.0000.000
122A125TYR00.0230.0052.340-6.731-4.8195.636-2.445-5.103-0.025
123A126GLY00.0370.0064.7243.7153.799-0.001-0.006-0.0770.000
124A127TRP00.0120.0117.401-1.282-1.2820.0000.0000.0000.000
125A128TYR00.0120.0276.847-1.109-1.1090.0000.0000.0000.000
126A129ARG10.9420.97111.51815.38615.3860.0000.0000.0000.000
127A130VAL0-0.019-0.00214.028-0.201-0.2010.0000.0000.0000.000
128A131ASN00.008-0.01016.5430.5120.5120.0000.0000.0000.000
129A132PHE00.0590.01020.3090.1190.1190.0000.0000.0000.000
130A133GLY00.0220.01819.2720.2740.2740.0000.0000.0000.000
131A134VAL00.0000.00618.597-0.507-0.5070.0000.0000.0000.000
132A135ILE0-0.057-0.03712.051-0.217-0.2170.0000.0000.0000.000
133A136ASP-1-0.804-0.85415.505-16.421-16.4210.0000.0000.0000.000
134A137GLU-1-0.913-0.97113.141-17.713-17.7130.0000.0000.0000.000
135A138ARG10.8050.87812.75016.43316.4330.0000.0000.0000.000
136A139LEU0-0.060-0.0295.750-0.466-0.4660.0000.0000.0000.000
137A140HIS0-0.044-0.01610.4071.6811.6810.0000.0000.0000.000
138A141ARG10.9600.9676.20629.71629.7160.0000.0000.0000.000
139A142ASN00.0040.0057.6155.6955.6950.0000.0000.0000.000
140A143ARG10.9520.9658.42516.43416.4340.0000.0000.0000.000
141A144GLU-1-0.833-0.90511.009-19.249-19.2490.0000.0000.0000.000
142A145TYR0-0.0290.0051.999-18.668-17.8115.565-2.785-3.637-0.036
143A146ARG10.7720.8497.43223.54923.5490.0000.0000.0000.000
144A147ASP-1-0.791-0.8903.882-53.304-52.963-0.001-0.138-0.201-0.001
145A148ARG10.9570.9665.73019.54719.5470.0000.0000.0000.000
146A149TYR0-0.008-0.0038.5520.8660.8660.0000.0000.0000.000
147A150TYR00.0480.0004.1051.4211.548-0.001-0.011-0.1160.000
148A151ARG10.8270.9274.00428.32728.536-0.001-0.042-0.1660.000
149A152ASN0-0.016-0.0134.951-0.365-0.323-0.0010.000-0.0400.000
150A153LEU0-0.0470.0036.1724.0124.0120.0000.0000.0000.000
151A154ASN00.0320.0046.530-4.982-4.9820.0000.0000.0000.000
152A155ILE0-0.003-0.0065.4090.1920.1920.0000.0000.0000.000
153A156ALA0-0.0070.0138.7180.7870.7870.0000.0000.0000.000
154A157PRO00.0110.00812.541-0.174-0.1740.0000.0000.0000.000
155A158ALA00.0550.00214.3230.4480.4480.0000.0000.0000.000
156A159GLU-1-0.916-0.95716.495-13.052-13.0520.0000.0000.0000.000
157A160ASP-1-0.884-0.92017.327-14.538-14.5380.0000.0000.0000.000
158A161GLY0-0.047-0.03217.943-0.045-0.0450.0000.0000.0000.000
159A162TYR0-0.0030.01218.8090.3550.3550.0000.0000.0000.000
160A163ARG10.9240.95020.66013.86813.8680.0000.0000.0000.000
161A164LEU0-0.085-0.04719.1200.2130.2130.0000.0000.0000.000
162A165ALA0-0.022-0.00621.381-0.171-0.1710.0000.0000.0000.000
163A166GLY00.0250.00022.397-0.108-0.1080.0000.0000.0000.000
164A167PHE0-0.0130.00423.8580.1640.1640.0000.0000.0000.000
165A168PRO00.0770.04427.3750.0800.0800.0000.0000.0000.000
166A169PRO00.0750.01830.9720.0030.0030.0000.0000.0000.000
167A170ASP-1-0.945-0.96433.655-8.276-8.2760.0000.0000.0000.000
168A171HIS00.0230.01428.0420.2420.2420.0000.0000.0000.000
169A172GLN00.0320.01931.166-0.151-0.1510.0000.0000.0000.000
170A173ALA00.0690.04027.2180.0740.0740.0000.0000.0000.000
171A174TRP0-0.060-0.04025.873-0.201-0.2010.0000.0000.0000.000
172A175ARG10.7740.87230.7668.7168.7160.0000.0000.0000.000
173A176GLU-1-0.857-0.90229.073-9.315-9.3150.0000.0000.0000.000
174A177GLU-1-0.859-0.87928.149-9.908-9.9080.0000.0000.0000.000
175A178PRO00.014-0.00823.259-0.011-0.0110.0000.0000.0000.000
176A179TRP0-0.041-0.04822.388-0.091-0.0910.0000.0000.0000.000
177A180ILE0-0.0120.00026.6770.0270.0270.0000.0000.0000.000
178A181HIS0-0.087-0.05528.0080.2050.2050.0000.0000.0000.000
179A182HIS0-0.098-0.06224.876-0.333-0.3330.0000.0000.0000.000
180A183ALA0-0.0090.00127.387-0.266-0.2660.0000.0000.0000.000
181A184PRO00.0050.01127.5370.1880.1880.0000.0000.0000.000
182A185GLN0-0.011-0.00830.2060.4900.4900.0000.0000.0000.000
183A186GLY00.0060.00233.9130.0320.0320.0000.0000.0000.000
184A187CYS0-0.0770.02231.218-0.261-0.2610.0000.0000.0000.000
185A188GLY0-0.0010.00333.2970.0380.0380.0000.0000.0000.000
186A196GLY00.003-0.01438.3130.0530.0530.0000.0000.0000.000
187A197ASP-1-0.846-0.92835.179-8.929-8.9290.0000.0000.0000.000
188A198THR00.0340.01734.623-0.178-0.1780.0000.0000.0000.000
189A200ASN0-0.020-0.04830.372-0.656-0.6560.0000.0000.0000.000
190A201GLU-1-0.965-0.98430.071-9.247-9.2470.0000.0000.0000.000
191A202GLU-1-0.810-0.91530.632-10.112-10.1120.0000.0000.0000.000
192A203THR0-0.026-0.00225.282-0.459-0.4590.0000.0000.0000.000
193A204GLN00.0340.03325.839-0.802-0.8020.0000.0000.0000.000
194A205ASN0-0.044-0.01426.365-0.548-0.5480.0000.0000.0000.000
195A206LEU00.0350.01325.261-0.406-0.4060.0000.0000.0000.000
196A207SER0-0.026-0.02921.980-0.746-0.7460.0000.0000.0000.000
197A208THR0-0.061-0.05021.868-0.734-0.7340.0000.0000.0000.000
198A209ILE0-0.011-0.00123.733-0.343-0.3430.0000.0000.0000.000
199A210TYR00.0220.00515.241-0.155-0.1550.0000.0000.0000.000
200A211LEU0-0.0280.00117.834-0.861-0.8610.0000.0000.0000.000
201A212ARG10.8840.92419.63211.57511.5750.0000.0000.0000.000
202A213GLU-1-0.912-0.94420.444-13.907-13.9070.0000.0000.0000.000
203A214TYR0-0.021-0.02410.822-0.819-0.8190.0000.0000.0000.000
204A215GLN00.0260.00416.2680.0130.0130.0000.0000.0000.000
205A216SER0-0.0030.00718.263-0.055-0.0550.0000.0000.0000.000
206A217LYS10.9210.95914.83317.13517.1350.0000.0000.0000.000
207A218VAL00.0240.01413.044-0.496-0.4960.0000.0000.0000.000
208A219LYS10.9340.98615.09713.81413.8140.0000.0000.0000.000
209A220ARG10.9520.97617.56315.23115.2310.0000.0000.0000.000
210A221GLN0-0.0370.00712.320-0.340-0.3400.0000.0000.0000.000
211A222ILE00.012-0.01214.1140.3020.3020.0000.0000.0000.000
212A223PHE00.003-0.00716.4240.5490.5490.0000.0000.0000.000
213A224SER0-0.010-0.02118.4540.9810.9810.0000.0000.0000.000
214A225ASP-1-0.837-0.86916.205-18.182-18.1820.0000.0000.0000.000
215A226TYR0-0.054-0.03119.3950.2600.2600.0000.0000.0000.000
216A227GLN0-0.075-0.02622.7390.5810.5810.0000.0000.0000.000
217A228SER00.0050.00124.678-0.176-0.1760.0000.0000.0000.000
218A229GLU-1-0.900-0.94326.823-10.822-10.8220.0000.0000.0000.000
219A230VAL0-0.043-0.02629.3910.2190.2190.0000.0000.0000.000
220A231ASP-1-0.849-0.91333.176-8.238-8.2380.0000.0000.0000.000
221A232ILE0-0.019-0.03934.5790.2310.2310.0000.0000.0000.000
222A233TYR00.0230.00437.8960.2380.2380.0000.0000.0000.000
223A234ASN0-0.033-0.00239.3960.3380.3380.0000.0000.0000.000
224A235ARG10.9140.96735.5398.5718.5710.0000.0000.0000.000
225A236ILE0-0.045-0.00640.7450.1700.1700.0000.0000.0000.000