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: 82G3Y

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 OptAll
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 -2898563.775768
FMO2-HF: Nuclear repulsion 2806600.846539
FMO2-HF: Total energy -91962.929229
FMO2-MP2: Total energy -92233.776074


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.
-44.419-33.37624.017-12.945-22.113-0.107
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 : 0.869 / q_NPA : 0.936
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].
3A6TYR0-0.002-0.0042.800-5.508-1.6700.234-1.779-2.2940.000
4A7ARG10.7960.8605.89521.90721.9070.0000.0000.0000.000
5A8ALA0-0.0110.0139.445-0.330-0.3300.0000.0000.0000.000
6A9ASP-1-0.773-0.86912.478-17.335-17.3350.0000.0000.0000.000
7A10SER00.0430.01714.932-0.309-0.3090.0000.0000.0000.000
8A11ARG10.8190.91516.34217.01117.0110.0000.0000.0000.000
9A12PRO00.0070.02616.227-1.255-1.2550.0000.0000.0000.000
10A13PRO00.0330.00113.7240.0780.0780.0000.0000.0000.000
11A14ASP-1-0.801-0.88615.224-15.292-15.2920.0000.0000.0000.000
12A15GLU-1-0.871-0.94418.389-14.240-14.2400.0000.0000.0000.000
13A16ILE0-0.0180.00912.412-0.097-0.0970.0000.0000.0000.000
14A17LYS10.8150.89415.72018.11618.1160.0000.0000.0000.000
15A18ARG10.8270.89016.57414.14114.1410.0000.0000.0000.000
16A19SER00.0140.01117.4990.6020.6020.0000.0000.0000.000
17A20GLY00.0230.01716.8470.0790.0790.0000.0000.0000.000
18A21GLY0-0.009-0.02913.147-1.398-1.3980.0000.0000.0000.000
19A22LEU0-0.051-0.0189.9281.0161.0160.0000.0000.0000.000
20A23MET00.0010.04213.768-0.353-0.3530.0000.0000.0000.000
21A24PRO00.0570.01017.080-0.024-0.0240.0000.0000.0000.000
22A25ARG10.8120.89318.97911.82311.8230.0000.0000.0000.000
23A26GLY00.0180.01222.2740.3930.3930.0000.0000.0000.000
24A27HIS0-0.040-0.01120.5250.5940.5940.0000.0000.0000.000
25A28ASN0-0.051-0.03821.491-0.520-0.5200.0000.0000.0000.000
26A29GLU-1-0.887-0.94120.856-13.291-13.2910.0000.0000.0000.000
27A30TYR00.016-0.01115.603-0.027-0.0270.0000.0000.0000.000
28A31PHE0-0.040-0.04617.4680.1510.1510.0000.0000.0000.000
29A32ASP-1-0.727-0.82722.090-11.079-11.0790.0000.0000.0000.000
30A33ARG10.8050.87222.40312.97312.9730.0000.0000.0000.000
31A34GLY0-0.0020.02027.2700.2910.2910.0000.0000.0000.000
32A35THR0-0.037-0.04026.8670.4550.4550.0000.0000.0000.000
33A36GLN0-0.054-0.02023.951-0.539-0.5390.0000.0000.0000.000
34A37MET0-0.0050.02819.8480.1450.1450.0000.0000.0000.000
35A38ASN00.0270.01025.5820.1040.1040.0000.0000.0000.000
36A39ILE0-0.050-0.03220.411-0.637-0.6370.0000.0000.0000.000
37A40ASN00.0270.00222.457-0.133-0.1330.0000.0000.0000.000
38A41LEU00.0170.01816.903-0.280-0.2800.0000.0000.0000.000
39A42TYR00.0510.02420.486-0.230-0.2300.0000.0000.0000.000
40A43ASP-1-0.813-0.88523.284-10.845-10.8450.0000.0000.0000.000
41A44HIS0-0.041-0.01716.790-0.760-0.7600.0000.0000.0000.000
42A45ALA0-0.010-0.00919.490-0.163-0.1630.0000.0000.0000.000
43A46ARG10.8120.88820.46710.79810.7980.0000.0000.0000.000
44A47GLY00.0280.02423.7260.1860.1860.0000.0000.0000.000
45A48THR00.000-0.00422.050-0.577-0.5770.0000.0000.0000.000
46A49GLN00.010-0.00920.933-0.332-0.3320.0000.0000.0000.000
47A50THR00.0340.01822.553-0.079-0.0790.0000.0000.0000.000
48A51GLY00.0270.01322.3920.1280.1280.0000.0000.0000.000
49A52PHE00.002-0.00418.667-0.377-0.3770.0000.0000.0000.000
50A53VAL00.0210.01713.6500.4120.4120.0000.0000.0000.000
51A54ARG10.8210.88816.77914.71614.7160.0000.0000.0000.000
52A55TYR0-0.073-0.04716.181-1.020-1.0200.0000.0000.0000.000
53A56ASP-1-0.708-0.82818.196-12.046-12.0460.0000.0000.0000.000
54A57ASP-1-0.852-0.91820.455-12.303-12.3030.0000.0000.0000.000
55A58GLY00.0490.02520.586-0.186-0.1860.0000.0000.0000.000
56A59TYR00.0130.00515.373-0.986-0.9860.0000.0000.0000.000
57A60VAL0-0.057-0.02512.5050.3580.3580.0000.0000.0000.000
58A61SER0-0.024-0.01812.303-1.993-1.9930.0000.0000.0000.000
59A62THR0-0.076-0.0477.840-1.761-1.7610.0000.0000.0000.000
60A63LYS10.8450.9038.53919.55719.5570.0000.0000.0000.000
61A64LEU00.0930.0346.815-3.724-3.7240.0000.0000.0000.000
62A65SER0-0.010-0.0106.279-1.214-1.2140.0000.0000.0000.000
63A66LEU00.0340.0276.7251.5001.5000.0000.0000.0000.000
64A67ARG10.9060.9418.24519.49219.4920.0000.0000.0000.000
65A68SER00.0430.01810.6821.5001.5000.0000.0000.0000.000
66A69ALA0-0.009-0.0029.0441.0011.0010.0000.0000.0000.000
67A70HIS00.0260.01211.0660.6560.6560.0000.0000.0000.000
68A71LEU0-0.015-0.00113.5630.9530.9530.0000.0000.0000.000
69A72ALA00.0190.00914.1440.8220.8220.0000.0000.0000.000
70A73GLY00.0420.00614.9310.5990.5990.0000.0000.0000.000
71A74GLN00.0110.01016.3260.2820.2820.0000.0000.0000.000
72A75SER0-0.0030.00618.9650.7590.7590.0000.0000.0000.000
73A76ILE0-0.046-0.01417.9150.5060.5060.0000.0000.0000.000
74A77LEU0-0.051-0.02716.6900.2750.2750.0000.0000.0000.000
75A78SER0-0.0060.00220.6950.0040.0040.0000.0000.0000.000
76A79GLY00.0200.02023.0010.2410.2410.0000.0000.0000.000
77A80TYR0-0.028-0.01121.0440.2100.2100.0000.0000.0000.000
78A81SER00.0300.00522.083-0.322-0.3220.0000.0000.0000.000
79A82THR0-0.083-0.04919.105-0.174-0.1740.0000.0000.0000.000
80A83TYR0-0.006-0.00214.658-0.160-0.1600.0000.0000.0000.000
81A84TYR00.0160.00613.078-0.266-0.2660.0000.0000.0000.000
82A85ILE0-0.010-0.0018.2370.2150.2150.0000.0000.0000.000
83A86TYR0-0.008-0.0268.228-1.891-1.8910.0000.0000.0000.000
84A87VAL0-0.004-0.0062.481-1.924-1.0130.761-0.322-1.3500.000
85A88ILE0-0.021-0.0183.547-2.369-1.3950.030-0.294-0.709-0.002
86A89ALA0-0.014-0.0102.149-15.092-12.2385.899-3.891-4.862-0.026
87A90THR0-0.016-0.0032.3425.5625.7010.6490.565-1.352-0.003
88A91ALA0-0.002-0.0074.892-0.900-0.805-0.001-0.005-0.0880.000
89A92PRO00.0550.0348.5930.7620.7620.0000.0000.0000.000
90A93ASN00.0630.03810.2740.0840.0840.0000.0000.0000.000
91A94MET0-0.068-0.0126.5811.2641.2640.0000.0000.0000.000
92A95PHE00.0980.04710.6390.0630.0630.0000.0000.0000.000
93A96ASN0-0.054-0.04511.201-0.287-0.2870.0000.0000.0000.000
94A97VAL00.0230.00612.4990.9590.9590.0000.0000.0000.000
95A98ASN0-0.013-0.01115.1591.2671.2670.0000.0000.0000.000
96A99ASP-1-0.841-0.90813.388-17.204-17.2040.0000.0000.0000.000
97A100VAL0-0.0100.00916.0260.5740.5740.0000.0000.0000.000
98A101LEU00.0070.01118.5340.6620.6620.0000.0000.0000.000
99A102GLY00.0550.03520.0380.6380.6380.0000.0000.0000.000
100A103VAL0-0.049-0.03921.667-0.205-0.2050.0000.0000.0000.000
101A104TYR0-0.072-0.05723.9750.3880.3880.0000.0000.0000.000
102A105SER0-0.004-0.01718.713-0.121-0.1210.0000.0000.0000.000
103A106PRO0-0.006-0.00921.3070.2200.2200.0000.0000.0000.000
104A107HIS10.8050.91019.71712.96612.9660.0000.0000.0000.000
105A108PRO00.0650.05118.839-0.757-0.7570.0000.0000.0000.000
106A109TYR00.032-0.01017.631-0.637-0.6370.0000.0000.0000.000
107A110GLU-1-0.859-0.90816.766-14.582-14.5820.0000.0000.0000.000
108A111GLN0-0.083-0.03212.794-1.502-1.5020.0000.0000.0000.000
109A112GLU-1-0.751-0.80712.017-18.499-18.4990.0000.0000.0000.000
110A113VAL00.0190.0097.8530.3660.3660.0000.0000.0000.000
111A114SER00.002-0.00310.238-1.613-1.6130.0000.0000.0000.000
112A115ALA0-0.025-0.02010.544-0.022-0.0220.0000.0000.0000.000
113A116LEU00.0420.02612.2700.9310.9310.0000.0000.0000.000
114A117GLY00.013-0.01015.679-0.506-0.5060.0000.0000.0000.000
115A118GLY00.000-0.00514.4460.4080.4080.0000.0000.0000.000
116A119ILE0-0.056-0.0258.504-1.179-1.1790.0000.0000.0000.000
117A120PRO00.0250.02211.1520.5350.5350.0000.0000.0000.000
118A121TYR00.0650.01010.334-2.776-2.7760.0000.0000.0000.000
119A122SER00.006-0.00110.050-1.561-1.5610.0000.0000.0000.000
120A123GLN0-0.042-0.0176.7580.3270.3270.0000.0000.0000.000
121A124ILE0-0.0260.0005.648-6.881-6.8810.0000.0000.0000.000
122A125TYR00.0340.0082.239-8.134-6.3417.723-3.211-6.305-0.033
123A126GLY00.011-0.0074.6163.4363.536-0.001-0.011-0.0880.000
124A127TRP00.0070.0057.062-0.884-0.8840.0000.0000.0000.000
125A128TYR00.0050.0216.960-0.701-0.7010.0000.0000.0000.000
126A129ARG10.9050.94411.60715.29515.2950.0000.0000.0000.000
127A130VAL0-0.0150.00114.199-0.386-0.3860.0000.0000.0000.000
128A131ASN00.0360.03416.7070.4750.4750.0000.0000.0000.000
129A132PHE00.039-0.00620.3960.1100.1100.0000.0000.0000.000
130A133GLY00.0420.03419.5620.3640.3640.0000.0000.0000.000
131A134VAL0-0.0060.00118.831-0.456-0.4560.0000.0000.0000.000
132A135ILE0-0.067-0.04212.043-0.242-0.2420.0000.0000.0000.000
133A136ASP-1-0.770-0.85015.583-16.082-16.0820.0000.0000.0000.000
134A137GLU-1-0.900-0.96313.127-17.881-17.8810.0000.0000.0000.000
135A138ARG10.7930.85812.31016.10116.1010.0000.0000.0000.000
136A139LEU0-0.046-0.0165.532-0.588-0.5880.0000.0000.0000.000
137A140HIS0-0.0100.00510.1971.2721.2720.0000.0000.0000.000
138A141ARG10.9310.9516.20830.18230.1820.0000.0000.0000.000
139A142ASN00.0020.0097.3385.8105.8100.0000.0000.0000.000
140A143ARG10.9580.9678.32416.62116.6210.0000.0000.0000.000
141A144GLU-1-0.815-0.89510.583-19.447-19.4470.0000.0000.0000.000
142A145TYR0-0.047-0.0281.909-18.203-19.2518.722-3.396-4.279-0.039
143A146ARG10.7990.8647.26822.78422.7840.0000.0000.0000.000
144A147ASP-1-0.786-0.8613.727-53.649-53.0610.000-0.314-0.274-0.002
145A148ARG10.9320.9545.51920.04520.0450.0000.0000.0000.000
146A149TYR0-0.0100.0108.0832.3872.3870.0000.0000.0000.000
147A150TYR00.033-0.0193.9240.7450.9180.000-0.021-0.1510.000
148A151ARG10.8260.9163.67825.32325.8990.002-0.265-0.313-0.002
149A152ASN0-0.028-0.0144.6331.2371.287-0.001-0.001-0.0480.000
150A153LEU0-0.0220.0105.8634.5144.5140.0000.0000.0000.000
151A154ASN00.0450.0136.261-5.921-5.9210.0000.0000.0000.000
152A155ILE0-0.018-0.0175.7440.3120.3120.0000.0000.0000.000
153A156ALA00.0070.0258.9000.7960.7960.0000.0000.0000.000
154A157PRO00.0120.00912.717-0.161-0.1610.0000.0000.0000.000
155A158ALA00.033-0.00414.7280.3880.3880.0000.0000.0000.000
156A159GLU-1-0.919-0.96016.833-13.252-13.2520.0000.0000.0000.000
157A160ASP-1-0.847-0.91017.584-14.391-14.3910.0000.0000.0000.000
158A161GLY0-0.020-0.01217.9740.0150.0150.0000.0000.0000.000
159A162TYR0-0.029-0.01618.7800.4250.4250.0000.0000.0000.000
160A163ARG10.8760.92920.28114.18614.1860.0000.0000.0000.000
161A164LEU0-0.085-0.04019.0570.1610.1610.0000.0000.0000.000
162A165ALA0-0.022-0.00421.517-0.220-0.2200.0000.0000.0000.000
163A166GLY00.0440.00822.512-0.060-0.0600.0000.0000.0000.000
164A167PHE0-0.011-0.00124.0090.1240.1240.0000.0000.0000.000
165A168PRO00.0530.04027.8550.0570.0570.0000.0000.0000.000
166A169PRO00.0650.01131.526-0.021-0.0210.0000.0000.0000.000
167A170ASP-1-0.907-0.95233.983-8.347-8.3470.0000.0000.0000.000
168A171HIS00.0020.00628.1640.2290.2290.0000.0000.0000.000
169A172GLN00.0350.02831.349-0.085-0.0850.0000.0000.0000.000
170A173ALA00.0660.02127.4200.0860.0860.0000.0000.0000.000
171A174TRP0-0.063-0.03225.888-0.129-0.1290.0000.0000.0000.000
172A175ARG10.7590.86030.9398.8138.8130.0000.0000.0000.000
173A176GLU-1-0.856-0.89129.519-9.269-9.2690.0000.0000.0000.000
174A177GLU-1-0.837-0.89228.049-9.939-9.9390.0000.0000.0000.000
175A178PRO00.0030.00023.113-0.055-0.0550.0000.0000.0000.000
176A179TRP0-0.045-0.04522.6330.0890.0890.0000.0000.0000.000
177A180ILE0-0.0040.00926.8470.0490.0490.0000.0000.0000.000
178A181HIS0-0.096-0.05927.9890.2100.2100.0000.0000.0000.000
179A182HIS0-0.093-0.06124.598-0.395-0.3950.0000.0000.0000.000
180A183ALA00.0100.01127.219-0.296-0.2960.0000.0000.0000.000
181A184PRO0-0.0060.00427.3690.1790.1790.0000.0000.0000.000
182A185GLN0-0.010-0.01230.1030.4670.4670.0000.0000.0000.000
183A186GLY00.007-0.00233.7860.1310.1310.0000.0000.0000.000
184A187CYS0-0.118-0.01631.145-0.188-0.1880.0000.0000.0000.000
185A188GLY00.0120.01133.3330.1130.1130.0000.0000.0000.000
186A196GLY00.019-0.00538.6780.0640.0640.0000.0000.0000.000
187A197ASP-1-0.851-0.92435.162-8.960-8.9600.0000.0000.0000.000
188A198THR00.0270.01634.592-0.161-0.1610.0000.0000.0000.000
189A200ASN0-0.053-0.03830.399-0.710-0.7100.0000.0000.0000.000
190A201GLU-1-0.887-0.94529.855-9.107-9.1070.0000.0000.0000.000
191A202GLU-1-0.810-0.91030.387-10.327-10.3270.0000.0000.0000.000
192A203THR0-0.0200.00225.363-0.488-0.4880.0000.0000.0000.000
193A204GLN00.0280.01825.536-0.854-0.8540.0000.0000.0000.000
194A205ASN0-0.060-0.02426.104-0.563-0.5630.0000.0000.0000.000
195A206LEU00.0220.00825.207-0.467-0.4670.0000.0000.0000.000
196A207SER0-0.006-0.01821.758-0.785-0.7850.0000.0000.0000.000
197A208THR0-0.052-0.04021.674-0.706-0.7060.0000.0000.0000.000
198A209ILE0-0.021-0.01123.279-0.499-0.4990.0000.0000.0000.000
199A210TYR00.0200.00315.273-0.109-0.1090.0000.0000.0000.000
200A211LEU00.0020.01517.752-0.970-0.9700.0000.0000.0000.000
201A212ARG10.8370.90019.73811.55611.5560.0000.0000.0000.000
202A213GLU-1-0.815-0.89519.958-14.737-14.7370.0000.0000.0000.000
203A214TYR0-0.024-0.02610.693-0.707-0.7070.0000.0000.0000.000
204A215GLN00.0300.01116.3260.0190.0190.0000.0000.0000.000
205A216SER0-0.0120.00418.361-0.024-0.0240.0000.0000.0000.000
206A217LYS10.8220.89315.02016.40916.4090.0000.0000.0000.000
207A218VAL00.0100.00612.902-0.564-0.5640.0000.0000.0000.000
208A219LYS10.9210.97515.00513.91313.9130.0000.0000.0000.000
209A220ARG10.9560.97817.69215.19415.1940.0000.0000.0000.000
210A221GLN0-0.0180.02011.975-0.376-0.3760.0000.0000.0000.000
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212A223PHE00.008-0.00816.0200.5910.5910.0000.0000.0000.000
213A224SER0-0.019-0.01417.9481.0481.0480.0000.0000.0000.000
214A225ASP-1-0.852-0.88815.952-18.355-18.3550.0000.0000.0000.000
215A226TYR0-0.047-0.02919.1060.2840.2840.0000.0000.0000.000
216A227GLN0-0.040-0.01422.5810.6100.6100.0000.0000.0000.000
217A228SER0-0.033-0.01724.498-0.201-0.2010.0000.0000.0000.000
218A229GLU-1-0.899-0.93326.623-10.863-10.8630.0000.0000.0000.000
219A230VAL0-0.040-0.03229.2340.1900.1900.0000.0000.0000.000
220A231ASP-1-0.843-0.91733.044-8.171-8.1710.0000.0000.0000.000
221A232ILE00.000-0.01634.6610.1890.1890.0000.0000.0000.000
222A233TYR0-0.001-0.00437.8400.2490.2490.0000.0000.0000.000
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224A235ARG10.9160.96835.3728.5458.5450.0000.0000.0000.000
225A236ILE0-0.0340.00440.7350.1310.1310.0000.0000.0000.000