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: 145ZZ

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2886104.311729
FMO2-HF: Nuclear repulsion 2794143.157903
FMO2-HF: Total energy -91961.153826
FMO2-MP2: Total energy -92231.971114


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.
-28.178-15.20813.522-8.889-17.602-0.061
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 : 0.908 / q_NPA : 0.955
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].
3A6TYR0-0.028-0.0172.914-5.715-1.7980.471-1.760-2.6290.000
4A7ARG10.8190.8925.84321.89621.8960.0000.0000.0000.000
5A8ALA0-0.0370.0039.350-0.408-0.4080.0000.0000.0000.000
6A9ASP-1-0.767-0.90612.296-17.422-17.4220.0000.0000.0000.000
7A10SER00.0380.01514.711-0.350-0.3500.0000.0000.0000.000
8A11ARG10.8630.96216.20716.93116.9310.0000.0000.0000.000
9A12PRO00.0350.04316.007-1.428-1.4280.0000.0000.0000.000
10A13PRO00.025-0.00214.1060.1770.1770.0000.0000.0000.000
11A14ASP-1-0.872-0.94115.710-15.016-15.0160.0000.0000.0000.000
12A15GLU-1-0.900-0.94518.828-13.818-13.8180.0000.0000.0000.000
13A16ILE0-0.016-0.01212.965-0.005-0.0050.0000.0000.0000.000
14A17LYS10.8860.94616.42017.13117.1310.0000.0000.0000.000
15A18ARG10.8900.94617.27113.59413.5940.0000.0000.0000.000
16A19SER00.0200.02918.3290.6350.6350.0000.0000.0000.000
17A20GLY00.0020.01017.1750.1670.1670.0000.0000.0000.000
18A21GLY00.002-0.02313.746-1.261-1.2610.0000.0000.0000.000
19A22LEU0-0.065-0.02010.5431.0201.0200.0000.0000.0000.000
20A23MET0-0.0110.02214.484-0.502-0.5020.0000.0000.0000.000
21A24PRO00.0540.00717.163-0.185-0.1850.0000.0000.0000.000
22A25ARG10.9040.94918.85111.87511.8750.0000.0000.0000.000
23A26GLY0-0.014-0.00322.1600.2670.2670.0000.0000.0000.000
24A27HIS0-0.0070.01620.1010.5280.5280.0000.0000.0000.000
25A28ASN0-0.013-0.01821.756-0.557-0.5570.0000.0000.0000.000
26A29GLU-1-0.895-0.94821.412-13.001-13.0010.0000.0000.0000.000
27A30TYR00.025-0.00215.237-0.026-0.0260.0000.0000.0000.000
28A31PHE0-0.076-0.07517.1890.0260.0260.0000.0000.0000.000
29A32ASP-1-0.843-0.91321.861-11.025-11.0250.0000.0000.0000.000
30A33ARG10.8240.88421.98212.82712.8270.0000.0000.0000.000
31A34GLY00.0090.01927.0440.2380.2380.0000.0000.0000.000
32A35THR00.0030.01927.4430.4690.4690.0000.0000.0000.000
33A36GLN0-0.016-0.01623.946-0.431-0.4310.0000.0000.0000.000
34A37MET00.0050.01120.1520.0520.0520.0000.0000.0000.000
35A38ASN00.0030.01325.4770.2640.2640.0000.0000.0000.000
36A39ILE0-0.087-0.05920.463-0.579-0.5790.0000.0000.0000.000
37A40ASN00.0780.03322.2440.0850.0850.0000.0000.0000.000
38A41LEU00.0190.01716.812-0.290-0.2900.0000.0000.0000.000
39A42TYR00.0260.01020.588-0.251-0.2510.0000.0000.0000.000
40A43ASP-1-0.918-0.95523.012-10.835-10.8350.0000.0000.0000.000
41A44HIS0-0.043-0.01116.679-0.841-0.8410.0000.0000.0000.000
42A45ALA0-0.001-0.01919.038-0.217-0.2170.0000.0000.0000.000
43A46ARG10.8630.93620.19110.87610.8760.0000.0000.0000.000
44A47GLY00.0280.02123.4520.2950.2950.0000.0000.0000.000
45A48THR0-0.027-0.01322.015-0.542-0.5420.0000.0000.0000.000
46A49GLN00.021-0.00421.079-0.210-0.2100.0000.0000.0000.000
47A50THR00.0200.02022.716-0.052-0.0520.0000.0000.0000.000
48A51GLY00.003-0.00222.4070.1140.1140.0000.0000.0000.000
49A52PHE0-0.013-0.01518.325-0.419-0.4190.0000.0000.0000.000
50A53VAL00.0250.02413.6580.3540.3540.0000.0000.0000.000
51A54ARG10.8690.94416.84414.10514.1050.0000.0000.0000.000
52A55TYR0-0.044-0.03616.223-1.093-1.0930.0000.0000.0000.000
53A56ASP-1-0.795-0.87618.026-12.156-12.1560.0000.0000.0000.000
54A57ASP-1-0.813-0.90620.442-12.475-12.4750.0000.0000.0000.000
55A58GLY00.0540.01320.353-0.247-0.2470.0000.0000.0000.000
56A59TYR00.0110.00415.263-0.715-0.7150.0000.0000.0000.000
57A60VAL0-0.041-0.01012.2870.4670.4670.0000.0000.0000.000
58A61SER0-0.0140.00012.466-1.839-1.8390.0000.0000.0000.000
59A62THR0-0.063-0.0317.845-1.947-1.9470.0000.0000.0000.000
60A63LYS10.9320.9618.58219.65819.6580.0000.0000.0000.000
61A64LEU00.1100.0426.008-4.105-4.1050.0000.0000.0000.000
62A65SER0-0.008-0.0045.534-1.839-1.8390.0000.0000.0000.000
63A66LEU00.0500.0316.4881.3051.3050.0000.0000.0000.000
64A67ARG10.9660.9797.79620.17720.1770.0000.0000.0000.000
65A68SER00.0430.02410.3031.5711.5710.0000.0000.0000.000
66A69ALA00.0000.0098.7471.0931.0930.0000.0000.0000.000
67A70HIS0-0.020-0.03010.7730.9370.9370.0000.0000.0000.000
68A71LEU0-0.012-0.00813.1780.9840.9840.0000.0000.0000.000
69A72ALA00.0050.00514.1000.9190.9190.0000.0000.0000.000
70A73GLY00.0350.00814.7890.6440.6440.0000.0000.0000.000
71A74GLN00.0270.02716.0850.4380.4380.0000.0000.0000.000
72A75SER0-0.031-0.00618.9730.8630.8630.0000.0000.0000.000
73A76ILE0-0.024-0.01417.7350.5060.5060.0000.0000.0000.000
74A77LEU0-0.059-0.03616.4860.3400.3400.0000.0000.0000.000
75A78SER00.0040.00120.3900.1390.1390.0000.0000.0000.000
76A79GLY0-0.0040.01322.6330.1890.1890.0000.0000.0000.000
77A80TYR0-0.0170.00320.9890.2150.2150.0000.0000.0000.000
78A81SER00.004-0.00622.189-0.206-0.2060.0000.0000.0000.000
79A82THR0-0.038-0.02118.713-0.088-0.0880.0000.0000.0000.000
80A83TYR0-0.007-0.00714.553-0.210-0.2100.0000.0000.0000.000
81A84TYR00.0050.00312.593-0.080-0.0800.0000.0000.0000.000
82A85ILE00.0300.0227.7430.2660.2660.0000.0000.0000.000
83A86TYR0-0.061-0.0688.064-1.793-1.7930.0000.0000.0000.000
84A87VAL0-0.006-0.0012.370-1.968-1.3061.552-0.456-1.758-0.001
85A88ILE0-0.013-0.0233.685-2.174-1.4240.010-0.222-0.539-0.001
86A89ALA0-0.0070.0032.112-15.323-13.2976.673-3.955-4.743-0.023
87A90THR00.0110.0132.5627.1517.1870.2930.610-0.938-0.002
88A91ALA00.000-0.0155.203-0.782-0.715-0.001-0.003-0.0630.000
89A92PRO00.0530.0278.5790.4980.4980.0000.0000.0000.000
90A93ASN00.0520.04010.4830.1660.1660.0000.0000.0000.000
91A94MET0-0.065-0.0206.4661.2901.2900.0000.0000.0000.000
92A95PHE00.0940.04610.750-0.064-0.0640.0000.0000.0000.000
93A96ASN00.0230.00310.6980.2800.2800.0000.0000.0000.000
94A97VAL00.0340.00512.1410.9740.9740.0000.0000.0000.000
95A98ASN0-0.005-0.01014.6841.2431.2430.0000.0000.0000.000
96A99ASP-1-0.919-0.95013.681-16.738-16.7380.0000.0000.0000.000
97A100VAL0-0.031-0.01115.9460.6650.6650.0000.0000.0000.000
98A101LEU00.0080.01318.4120.6600.6600.0000.0000.0000.000
99A102GLY00.0760.04919.7230.6520.6520.0000.0000.0000.000
100A103VAL0-0.027-0.03121.265-0.218-0.2180.0000.0000.0000.000
101A104TYR0-0.032-0.00523.5400.4240.4240.0000.0000.0000.000
102A105SER0-0.035-0.02118.325-0.089-0.0890.0000.0000.0000.000
103A106PRO00.0350.00821.2120.1980.1980.0000.0000.0000.000
104A107HIS10.8180.92619.50512.99112.9910.0000.0000.0000.000
105A108PRO00.0640.03518.449-0.809-0.8090.0000.0000.0000.000
106A109TYR00.0390.00417.288-0.634-0.6340.0000.0000.0000.000
107A110GLU-1-0.954-0.98615.890-15.195-15.1950.0000.0000.0000.000
108A111GLN0-0.069-0.02912.214-1.462-1.4620.0000.0000.0000.000
109A112GLU-1-0.869-0.93011.412-18.533-18.5330.0000.0000.0000.000
110A113VAL00.0050.0057.6040.2380.2380.0000.0000.0000.000
111A114SER0-0.024-0.02010.278-1.422-1.4220.0000.0000.0000.000
112A115ALA0-0.004-0.00510.561-0.330-0.3300.0000.0000.0000.000
113A116LEU00.0120.01612.2910.8630.8630.0000.0000.0000.000
114A117GLY0-0.007-0.02415.771-0.365-0.3650.0000.0000.0000.000
115A118GLY0-0.0120.00014.7490.4480.4480.0000.0000.0000.000
116A119ILE0-0.078-0.0358.909-1.168-1.1680.0000.0000.0000.000
117A120PRO00.0470.03410.9850.6740.6740.0000.0000.0000.000
118A121TYR00.043-0.00510.913-2.548-2.5480.0000.0000.0000.000
119A122SER0-0.020-0.00810.081-2.005-2.0050.0000.0000.0000.000
120A123GLN0-0.005-0.0066.4560.1590.1590.0000.0000.0000.000
121A124ILE0-0.021-0.0045.727-6.689-6.6890.0000.0000.0000.000
122A125TYR00.0130.0022.903-3.280-0.9602.690-1.170-3.841-0.008
123A126GLY00.0250.0005.4123.4253.4250.0000.0000.0000.000
124A127TRP00.0120.0127.399-1.316-1.3160.0000.0000.0000.000
125A128TYR00.0330.0336.757-1.220-1.2200.0000.0000.0000.000
126A129ARG10.9480.97211.50815.73015.7300.0000.0000.0000.000
127A130VAL0-0.0130.00613.930-0.255-0.2550.0000.0000.0000.000
128A131ASN00.003-0.01316.5100.6930.6930.0000.0000.0000.000
129A132PHE00.0450.00620.2750.1170.1170.0000.0000.0000.000
130A133GLY00.0210.01619.2260.2570.2570.0000.0000.0000.000
131A134VAL0-0.0060.00318.537-0.546-0.5460.0000.0000.0000.000
132A135ILE0-0.051-0.03411.878-0.213-0.2130.0000.0000.0000.000
133A136ASP-1-0.852-0.90915.462-16.636-16.6360.0000.0000.0000.000
134A137GLU-1-0.952-0.98712.940-17.897-17.8970.0000.0000.0000.000
135A138ARG10.8820.95012.58516.46316.4630.0000.0000.0000.000
136A139LEU0-0.076-0.0345.842-0.417-0.4170.0000.0000.0000.000
137A140HIS0-0.053-0.02710.4041.7731.7730.0000.0000.0000.000
138A141ARG10.9790.9726.31529.63129.6310.0000.0000.0000.000
139A142ASN0-0.0200.0018.5265.1915.1910.0000.0000.0000.000
140A143ARG10.9420.9579.28716.58516.5850.0000.0000.0000.000
141A144GLU-1-0.887-0.95511.620-18.810-18.8100.0000.0000.0000.000
142A145TYR0-0.0110.0262.254-15.148-12.3041.837-1.902-2.779-0.026
143A146ARG10.8150.9007.55323.71523.7150.0000.0000.0000.000
144A147ASP-1-0.812-0.9224.347-47.899-47.787-0.001-0.015-0.0960.000
145A148ARG10.9520.9606.19619.49619.4960.0000.0000.0000.000
146A149TYR0-0.019-0.0028.8170.9640.9640.0000.0000.0000.000
147A150TYR00.046-0.0024.0721.4231.536-0.001-0.011-0.1000.000
148A151ARG10.8210.9364.68427.92428.047-0.001-0.005-0.1160.000
149A152ASN00.007-0.0045.558-0.847-0.8470.0000.0000.0000.000
150A153LEU0-0.061-0.0056.7643.5723.5720.0000.0000.0000.000
151A154ASN00.041-0.0056.723-4.830-4.8300.0000.0000.0000.000
152A155ILE0-0.024-0.0025.7310.1120.1120.0000.0000.0000.000
153A156ALA0-0.0030.0108.7000.7460.7460.0000.0000.0000.000
154A157PRO00.0050.00812.523-0.263-0.2630.0000.0000.0000.000
155A158ALA00.0560.00314.3180.4500.4500.0000.0000.0000.000
156A159GLU-1-0.917-0.95716.506-12.758-12.7580.0000.0000.0000.000
157A160ASP-1-0.951-0.96017.179-14.794-14.7940.0000.0000.0000.000
158A161GLY0-0.051-0.04517.951-0.034-0.0340.0000.0000.0000.000
159A162TYR00.0090.02018.8130.3560.3560.0000.0000.0000.000
160A163ARG11.0051.00021.20413.37513.3750.0000.0000.0000.000
161A164LEU0-0.096-0.04919.3880.2250.2250.0000.0000.0000.000
162A165ALA0-0.0120.00121.404-0.165-0.1650.0000.0000.0000.000
163A166GLY00.019-0.00322.418-0.114-0.1140.0000.0000.0000.000
164A167PHE0-0.0040.00624.1140.1520.1520.0000.0000.0000.000
165A168PRO00.0690.04227.4050.0930.0930.0000.0000.0000.000
166A169PRO00.0950.02431.0010.0010.0010.0000.0000.0000.000
167A170ASP-1-0.970-0.96833.679-8.194-8.1940.0000.0000.0000.000
168A171HIS00.0190.01128.4590.1960.1960.0000.0000.0000.000
169A172GLN00.0480.02931.221-0.198-0.1980.0000.0000.0000.000
170A173ALA00.0700.03927.2710.0750.0750.0000.0000.0000.000
171A174TRP0-0.052-0.03426.036-0.171-0.1710.0000.0000.0000.000
172A175ARG10.7620.85930.7928.7588.7580.0000.0000.0000.000
173A176GLU-1-0.901-0.95329.209-9.191-9.1910.0000.0000.0000.000
174A177GLU-1-0.928-0.92728.238-9.765-9.7650.0000.0000.0000.000
175A178PRO00.014-0.01023.347-0.012-0.0120.0000.0000.0000.000
176A179TRP0-0.034-0.03922.560-0.065-0.0650.0000.0000.0000.000
177A180ILE0-0.007-0.00526.6980.0290.0290.0000.0000.0000.000
178A181HIS0-0.043-0.01927.9940.1910.1910.0000.0000.0000.000
179A182HIS0-0.084-0.04624.654-0.330-0.3300.0000.0000.0000.000
180A183ALA0-0.0060.00327.389-0.259-0.2590.0000.0000.0000.000
181A184PRO00.0050.00927.6740.1930.1930.0000.0000.0000.000
182A185GLN0-0.006-0.00930.2080.5370.5370.0000.0000.0000.000
183A186GLY00.0130.00633.9120.0300.0300.0000.0000.0000.000
184A187CYS0-0.0780.01431.241-0.270-0.2700.0000.0000.0000.000
185A188GLY00.0010.00433.3110.0440.0440.0000.0000.0000.000
186A196GLY00.010-0.01238.2810.0580.0580.0000.0000.0000.000
187A197ASP-1-0.883-0.95435.490-8.852-8.8520.0000.0000.0000.000
188A198THR00.0400.01734.655-0.177-0.1770.0000.0000.0000.000
189A200ASN00.006-0.01630.535-0.652-0.6520.0000.0000.0000.000
190A201GLU-1-0.966-0.99130.121-9.287-9.2870.0000.0000.0000.000
191A202GLU-1-0.852-0.93530.684-9.947-9.9470.0000.0000.0000.000
192A203THR0-0.028-0.00125.136-0.462-0.4620.0000.0000.0000.000
193A204GLN00.0290.02825.891-0.672-0.6720.0000.0000.0000.000
194A205ASN0-0.024-0.00726.408-0.552-0.5520.0000.0000.0000.000
195A206LEU00.0310.00625.210-0.403-0.4030.0000.0000.0000.000
196A207SER0-0.008-0.01422.148-0.752-0.7520.0000.0000.0000.000
197A208THR0-0.061-0.03921.913-0.726-0.7260.0000.0000.0000.000
198A209ILE00.0050.00723.771-0.321-0.3210.0000.0000.0000.000
199A210TYR00.0170.00515.226-0.080-0.0800.0000.0000.0000.000
200A211LEU0-0.026-0.00417.983-0.792-0.7920.0000.0000.0000.000
201A212ARG10.8810.94419.31211.67311.6730.0000.0000.0000.000
202A213GLU-1-0.917-0.94920.693-13.404-13.4040.0000.0000.0000.000
203A214TYR0-0.0010.00010.732-0.920-0.9200.0000.0000.0000.000
204A215GLN00.0420.01416.119-0.002-0.0020.0000.0000.0000.000
205A216SER00.0020.00918.015-0.059-0.0590.0000.0000.0000.000
206A217LYS10.9100.95614.69517.25917.2590.0000.0000.0000.000
207A218VAL00.0350.02012.753-0.453-0.4530.0000.0000.0000.000
208A219LYS10.9450.98514.84713.52113.5210.0000.0000.0000.000
209A220ARG10.9620.97917.49415.01715.0170.0000.0000.0000.000
210A221GLN0-0.0590.00412.235-0.586-0.5860.0000.0000.0000.000
211A222ILE0-0.010-0.02714.0110.2140.2140.0000.0000.0000.000
212A223PHE00.0100.00016.3660.4800.4800.0000.0000.0000.000
213A224SER0-0.013-0.02618.5040.9310.9310.0000.0000.0000.000
214A225ASP-1-0.840-0.90316.709-17.603-17.6030.0000.0000.0000.000
215A226TYR0-0.072-0.03819.7720.2000.2000.0000.0000.0000.000
216A227GLN0-0.066-0.00623.0100.4870.4870.0000.0000.0000.000
217A228SER0-0.023-0.01125.042-0.166-0.1660.0000.0000.0000.000
218A229GLU-1-0.893-0.95826.686-10.812-10.8120.0000.0000.0000.000
219A230VAL0-0.031-0.01829.8240.2130.2130.0000.0000.0000.000
220A231ASP-1-0.875-0.92933.599-8.198-8.1980.0000.0000.0000.000
221A232ILE0-0.013-0.03435.0300.2270.2270.0000.0000.0000.000
222A233TYR00.0270.00238.2530.2340.2340.0000.0000.0000.000
223A234ASN0-0.0180.00439.8780.3680.3680.0000.0000.0000.000
224A235ARG10.9120.97535.5248.4838.4830.0000.0000.0000.000
225A236ILE0-0.049-0.01440.9660.1940.1940.0000.0000.0000.000