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: 66ZQZ

Calculation Name: 1LTT-A-Xray372

Preferred Name:

Target Type:

Ligand Name: beta-d-glucopyranose

ligand 3-letter code: BGC

PDB ID: 1LTT

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 -2083395.053357
FMO2-HF: Nuclear repulsion 2008977.120449
FMO2-HF: Total energy -74417.932908
FMO2-MP2: Total energy -74637.409219


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.
-4.7428.24215.055-9.744-18.293-0.061
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 : 0.910 / q_NPA : 0.954
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].
3A6TYR0-0.016-0.0143.142-7.529-3.0650.259-2.076-2.6470.002
4A7ARG10.8220.8805.75921.77221.7720.0000.0000.0000.000
5A8ALA0-0.0190.0179.295-0.531-0.5310.0000.0000.0000.000
6A9ASP-1-0.766-0.89112.238-17.455-17.4550.0000.0000.0000.000
7A10SER00.0650.03214.674-0.247-0.2470.0000.0000.0000.000
8A11ARG10.8290.92815.87616.93016.9300.0000.0000.0000.000
9A12PRO00.0090.02715.968-1.394-1.3940.0000.0000.0000.000
10A13PRO00.023-0.00314.0630.1630.1630.0000.0000.0000.000
11A14ASP-1-0.835-0.91915.750-14.958-14.9580.0000.0000.0000.000
12A15GLU-1-0.881-0.96019.021-14.053-14.0530.0000.0000.0000.000
13A16ILE00.0010.01512.988-0.015-0.0150.0000.0000.0000.000
14A17LYS10.8380.92616.20318.12818.1280.0000.0000.0000.000
15A18ARG10.8910.94817.23413.70513.7050.0000.0000.0000.000
16A19SER00.0230.02518.1600.5640.5640.0000.0000.0000.000
17A20GLY00.0150.01616.9930.1660.1660.0000.0000.0000.000
18A21GLY0-0.007-0.02613.469-1.097-1.0970.0000.0000.0000.000
19A22LEU0-0.068-0.01510.4341.0581.0580.0000.0000.0000.000
20A23MET00.0100.04114.332-0.298-0.2980.0000.0000.0000.000
21A24PRO00.024-0.00317.139-0.098-0.0980.0000.0000.0000.000
22A25ARG10.9310.96618.83611.80411.8040.0000.0000.0000.000
23A26GLY00.0020.01722.1020.2650.2650.0000.0000.0000.000
24A27HIS10.8310.92420.24814.29614.2960.0000.0000.0000.000
25A28ASN00.008-0.00822.019-0.396-0.3960.0000.0000.0000.000
26A29GLU-1-0.905-0.94921.229-13.067-13.0670.0000.0000.0000.000
27A30TYR0-0.038-0.03415.5670.0140.0140.0000.0000.0000.000
28A31PHE0-0.034-0.04817.149-0.020-0.0200.0000.0000.0000.000
29A32ASP-1-0.870-0.92021.766-11.155-11.1550.0000.0000.0000.000
30A33ARG10.9610.96421.81112.79712.7970.0000.0000.0000.000
31A34GLY00.0070.01726.9890.2750.2750.0000.0000.0000.000
32A35THR0-0.0060.00427.5430.4650.4650.0000.0000.0000.000
33A36GLN0-0.060-0.02827.035-0.710-0.7100.0000.0000.0000.000
34A37MET0-0.0020.00820.160-0.117-0.1170.0000.0000.0000.000
35A38ASN0-0.035-0.01525.3350.1420.1420.0000.0000.0000.000
36A39ILE0-0.050-0.03120.292-0.549-0.5490.0000.0000.0000.000
37A40ASN00.0530.02822.2920.0700.0700.0000.0000.0000.000
38A41LEU00.0130.01816.770-0.306-0.3060.0000.0000.0000.000
39A42TYR00.0430.01120.566-0.254-0.2540.0000.0000.0000.000
40A43ASP-1-0.887-0.95522.943-10.866-10.8660.0000.0000.0000.000
41A44HIS10.7650.89615.67415.90415.9040.0000.0000.0000.000
42A45ALA0-0.022-0.03519.186-0.130-0.1300.0000.0000.0000.000
43A46ARG10.9040.97220.13710.83410.8340.0000.0000.0000.000
44A47GLY00.0210.03623.2630.2610.2610.0000.0000.0000.000
45A48THR00.0100.00521.923-0.451-0.4510.0000.0000.0000.000
46A49GLN00.0190.00720.892-0.308-0.3080.0000.0000.0000.000
47A50THR00.0340.02222.449-0.311-0.3110.0000.0000.0000.000
48A51GLY00.0260.01721.8460.0440.0440.0000.0000.0000.000
49A52PHE0-0.052-0.03717.843-0.569-0.5690.0000.0000.0000.000
50A53VAL00.0490.03813.4200.3020.3020.0000.0000.0000.000
51A54ARG10.8720.91616.65114.16314.1630.0000.0000.0000.000
52A55TYR0-0.071-0.04316.270-1.006-1.0060.0000.0000.0000.000
53A56ASP-1-0.799-0.90318.016-11.995-11.9950.0000.0000.0000.000
54A57ASP-1-0.816-0.90420.310-12.330-12.3300.0000.0000.0000.000
55A58GLY00.0500.01220.147-0.243-0.2430.0000.0000.0000.000
56A59TYR00.0290.00815.180-0.576-0.5760.0000.0000.0000.000
57A60VAL0-0.031-0.01112.3010.5350.5350.0000.0000.0000.000
58A61SER0-0.027-0.01612.322-1.169-1.1690.0000.0000.0000.000
59A62THR0-0.084-0.0497.426-1.498-1.4980.0000.0000.0000.000
60A63SER00.0350.0208.2692.1862.1860.0000.0000.0000.000
61A64LEU00.0940.0396.069-4.327-4.3270.0000.0000.0000.000
62A65SER00.0110.0195.617-1.985-1.9850.0000.0000.0000.000
63A66LEU00.0540.0366.4771.1811.1810.0000.0000.0000.000
64A67ARG10.9951.0017.78919.78019.7800.0000.0000.0000.000
65A68SER0-0.005-0.03610.2271.7931.7930.0000.0000.0000.000
66A69ALA00.0250.0238.8161.0131.0130.0000.0000.0000.000
67A70HIS0-0.033-0.02510.8220.7870.7870.0000.0000.0000.000
68A71LEU0-0.047-0.02213.2871.0851.0850.0000.0000.0000.000
69A72ALA00.0420.02613.8820.9380.9380.0000.0000.0000.000
70A73GLY00.0250.00314.6630.6900.6900.0000.0000.0000.000
71A74GLN00.0310.02616.0460.6380.6380.0000.0000.0000.000
72A75SER0-0.0130.00118.9340.9210.9210.0000.0000.0000.000
73A76ILE0-0.017-0.01217.9890.5440.5440.0000.0000.0000.000
74A77LEU0-0.059-0.03616.6710.2210.2210.0000.0000.0000.000
75A78SER00.0140.00520.5560.0790.0790.0000.0000.0000.000
76A79GLY0-0.0250.00922.106-0.076-0.0760.0000.0000.0000.000
77A80TYR00.0250.02121.0540.2510.2510.0000.0000.0000.000
78A81SER0-0.023-0.02222.110-0.268-0.2680.0000.0000.0000.000
79A82THR0-0.069-0.04618.301-0.170-0.1700.0000.0000.0000.000
80A83TYR0-0.0070.00114.427-0.159-0.1590.0000.0000.0000.000
81A84TYR00.016-0.00212.670-0.293-0.2930.0000.0000.0000.000
82A85ILE00.0230.0227.7140.1010.1010.0000.0000.0000.000
83A86TYR0-0.050-0.0527.946-1.741-1.7410.0000.0000.0000.000
84A87VAL00.0060.0082.402-2.119-1.3641.695-0.504-1.946-0.001
85A88ILE0-0.025-0.0303.232-2.220-1.1850.040-0.342-0.732-0.002
86A89ALA0-0.0070.0032.205-14.312-11.2595.068-3.683-4.438-0.024
87A90THR00.0070.0072.4466.4866.9910.4080.102-1.015-0.002
88A91ALA0-0.001-0.0125.122-1.012-0.958-0.001-0.005-0.0480.000
89A92PRO00.0540.0248.6320.3870.3870.0000.0000.0000.000
90A93ASN00.0350.02910.351-0.097-0.0970.0000.0000.0000.000
91A94MET0-0.101-0.0396.5281.3111.3110.0000.0000.0000.000
92A95PHE00.1090.06010.5990.0470.0470.0000.0000.0000.000
93A96ASN00.0380.00610.3100.2660.2660.0000.0000.0000.000
94A97VAL00.0400.00311.8930.9810.9810.0000.0000.0000.000
95A98ASN00.0140.00714.5131.2341.2340.0000.0000.0000.000
96A99ASP-1-0.902-0.93513.421-16.621-16.6210.0000.0000.0000.000
97A100VAL0-0.053-0.02315.7340.6040.6040.0000.0000.0000.000
98A101LEU0-0.014-0.00718.2980.7000.7000.0000.0000.0000.000
99A102GLY00.0490.03319.5010.6510.6510.0000.0000.0000.000
100A103VAL0-0.005-0.00521.055-0.187-0.1870.0000.0000.0000.000
101A104TYR0-0.044-0.01723.7280.3590.3590.0000.0000.0000.000
102A105SER0-0.073-0.04718.174-0.129-0.1290.0000.0000.0000.000
103A106PRO00.023-0.00220.8490.1920.1920.0000.0000.0000.000
104A107HIS0-0.0390.00019.1820.7000.7000.0000.0000.0000.000
105A108PRO00.0170.01318.293-0.781-0.7810.0000.0000.0000.000
106A109TYR0-0.008-0.02117.090-0.712-0.7120.0000.0000.0000.000
107A110GLU-1-0.919-0.95415.818-15.125-15.1250.0000.0000.0000.000
108A111GLN0-0.125-0.05811.992-1.571-1.5710.0000.0000.0000.000
109A112GLU-1-0.778-0.88311.213-18.416-18.4160.0000.0000.0000.000
110A113VAL0-0.018-0.0107.4190.4200.4200.0000.0000.0000.000
111A114SER0-0.0280.00210.216-0.479-0.4790.0000.0000.0000.000
112A115ALA00.0220.00510.480-0.399-0.3990.0000.0000.0000.000
113A116LEU0-0.0040.00412.1500.9390.9390.0000.0000.0000.000
114A117GLY00.0370.00515.447-0.443-0.4430.0000.0000.0000.000
115A118GLY0-0.027-0.01014.5740.4800.4800.0000.0000.0000.000
116A119ILE0-0.048-0.0198.789-1.086-1.0860.0000.0000.0000.000
117A120PRO00.0410.02211.2940.4140.4140.0000.0000.0000.000
118A121TYR00.0530.00510.856-2.424-2.4240.0000.0000.0000.000
119A122SER0-0.029-0.01910.061-1.970-1.9700.0000.0000.0000.000
120A123GLN00.0010.0086.513-0.057-0.0570.0000.0000.0000.000
121A124ILE0-0.0190.0035.801-6.434-6.4340.0000.0000.0000.000
122A125TYR00.013-0.0032.960-4.240-2.0213.321-1.242-4.299-0.007
123A126GLY00.0310.0005.3673.3293.394-0.001-0.001-0.0620.000
124A127TRP00.0260.0187.500-1.555-1.5550.0000.0000.0000.000
125A128TYR00.0250.0276.811-1.541-1.5410.0000.0000.0000.000
126A129ARG10.9340.96311.40315.94015.9400.0000.0000.0000.000
127A130VAL0-0.0040.01214.019-0.222-0.2220.0000.0000.0000.000
128A131ASN00.017-0.00116.4810.7620.7620.0000.0000.0000.000
129A132PHE00.0390.01020.2570.1090.1090.0000.0000.0000.000
130A133GLY00.0350.02119.0690.2720.2720.0000.0000.0000.000
131A134VAL0-0.017-0.00118.617-0.497-0.4970.0000.0000.0000.000
132A135ILE0-0.037-0.02911.938-0.167-0.1670.0000.0000.0000.000
133A136ASP-1-0.909-0.94515.483-17.072-17.0720.0000.0000.0000.000
134A137GLU-1-0.926-0.97912.894-18.455-18.4550.0000.0000.0000.000
135A138ARG10.9260.96812.17116.68316.6830.0000.0000.0000.000
136A139LEU0-0.069-0.0285.597-1.005-1.0050.0000.0000.0000.000
137A140HIS0-0.021-0.00210.0582.1732.1730.0000.0000.0000.000
138A141ARG10.9150.9485.23936.22536.2250.0000.0000.0000.000
139A142ASN0-0.002-0.0028.2985.1155.1150.0000.0000.0000.000
140A143ARG10.9680.9639.21415.69615.6960.0000.0000.0000.000
141A144GLU-1-0.931-0.96911.419-19.414-19.4140.0000.0000.0000.000
142A145TYR0-0.0020.0352.048-13.005-12.4724.269-1.977-2.826-0.027
143A146ARG10.9220.9447.66323.54023.5400.0000.0000.0000.000
144A147ASP-1-0.821-0.9134.632-45.633-45.548-0.001-0.004-0.0790.000
145A148ARG10.9410.9566.39319.79119.7910.0000.0000.0000.000
146A149TYR0-0.047-0.0188.7550.8250.8250.0000.0000.0000.000
147A150TYR00.0890.0194.2591.0961.197-0.001-0.009-0.0900.000
148A151ARG10.7940.9124.62728.21728.332-0.001-0.003-0.1110.000
149A152ASN00.0390.0145.549-2.292-2.2920.0000.0000.0000.000
150A153LEU0-0.0300.0186.8823.1883.1880.0000.0000.0000.000
151A154ASN00.022-0.0026.349-4.050-4.0500.0000.0000.0000.000
152A155ILE0-0.005-0.0145.7060.4490.4490.0000.0000.0000.000
153A156ALA0-0.0010.0128.5820.8550.8550.0000.0000.0000.000
154A157PRO0-0.012-0.00412.446-0.256-0.2560.0000.0000.0000.000
155A158ALA00.0450.00614.2820.4700.4700.0000.0000.0000.000
156A159GLU-1-0.930-0.97416.341-12.941-12.9410.0000.0000.0000.000
157A160ASP-1-0.913-0.94116.894-14.851-14.8510.0000.0000.0000.000
158A161GLY0-0.046-0.03817.8870.0240.0240.0000.0000.0000.000
159A162TYR00.0150.01818.7630.3930.3930.0000.0000.0000.000
160A163ARG10.9930.99820.72313.29413.2940.0000.0000.0000.000
161A164LEU0-0.124-0.06418.8880.2120.2120.0000.0000.0000.000
162A165ALA00.0050.01221.329-0.194-0.1940.0000.0000.0000.000
163A166GLY00.005-0.00422.342-0.106-0.1060.0000.0000.0000.000
164A167PHE00.0170.01124.0740.1260.1260.0000.0000.0000.000
165A168PRO00.0580.02827.2540.1020.1020.0000.0000.0000.000
166A169PRO00.0610.01530.850-0.002-0.0020.0000.0000.0000.000
167A170ASP-1-0.957-0.95833.384-8.274-8.2740.0000.0000.0000.000
168A171HIS00.0140.01428.2290.2240.2240.0000.0000.0000.000
169A172GLN00.0260.00831.542-0.054-0.0540.0000.0000.0000.000
170A173ALA00.0850.04527.1380.0410.0410.0000.0000.0000.000
171A174TRP0-0.054-0.02925.809-0.140-0.1400.0000.0000.0000.000
172A175ARG10.7610.86930.4538.6658.6650.0000.0000.0000.000
173A176GLU-1-0.870-0.94428.968-9.227-9.2270.0000.0000.0000.000
174A177GLU-1-0.914-0.93928.159-9.635-9.6350.0000.0000.0000.000
175A178PRO0-0.016-0.02922.830-0.019-0.0190.0000.0000.0000.000
176A179TRP0-0.028-0.03322.3400.1630.1630.0000.0000.0000.000
177A180ILE0-0.0020.01126.4510.0250.0250.0000.0000.0000.000
178A181HIS0-0.038-0.01027.6820.2060.2060.0000.0000.0000.000
179A182HIS0-0.065-0.03123.867-0.182-0.1820.0000.0000.0000.000
180A183ALA00.0200.00927.131-0.261-0.2610.0000.0000.0000.000
181A184PRO0-0.021-0.01327.4340.1790.1790.0000.0000.0000.000
182A185GLN0-0.009-0.00730.1340.1570.1570.0000.0000.0000.000
183A186GLY0-0.006-0.00533.9480.0490.0490.0000.0000.0000.000
184A187CYS0-0.065-0.01329.8280.0720.0720.0000.0000.0000.000
185A188GLY00.0040.01232.9940.1590.1590.0000.0000.0000.000