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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: R5QJ8

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2088822.529264
FMO2-HF: Nuclear repulsion 2014403.098168
FMO2-HF: Total energy -74419.431096
FMO2-MP2: Total energy -74639.018496


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.
-20.285-9.57225.572-13.045-23.239-0.105
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 : 0.872 / q_NPA : 0.935
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].
3A6TYR00.002-0.0072.834-5.671-1.5450.294-1.952-2.467-0.002
4A7ARG10.8020.8685.90821.24521.2450.0000.0000.0000.000
5A8ALA00.0040.0239.412-0.317-0.3170.0000.0000.0000.000
6A9ASP-1-0.776-0.87112.489-17.031-17.0310.0000.0000.0000.000
7A10SER00.0390.01614.917-0.200-0.2000.0000.0000.0000.000
8A11ARG10.8180.91316.17316.67116.6710.0000.0000.0000.000
9A12PRO00.0160.03016.333-1.208-1.2080.0000.0000.0000.000
10A13PRO00.0310.00214.3200.0450.0450.0000.0000.0000.000
11A14ASP-1-0.797-0.88515.874-15.049-15.0490.0000.0000.0000.000
12A15GLU-1-0.872-0.94518.957-14.025-14.0250.0000.0000.0000.000
13A16ILE0-0.0170.01012.883-0.105-0.1050.0000.0000.0000.000
14A17LYS10.8110.88916.05018.23218.2320.0000.0000.0000.000
15A18ARG10.8300.89217.06113.86913.8690.0000.0000.0000.000
16A19SER00.0180.01317.8270.5570.5570.0000.0000.0000.000
17A20GLY00.0250.01616.9620.0000.0000.0000.0000.0000.000
18A21GLY0-0.002-0.02113.426-1.347-1.3470.0000.0000.0000.000
19A22LEU0-0.049-0.01410.4041.0291.0290.0000.0000.0000.000
20A23MET0-0.0090.03314.200-0.372-0.3720.0000.0000.0000.000
21A24PRO00.0530.01017.159-0.039-0.0390.0000.0000.0000.000
22A25ARG10.8550.91218.99111.67511.6750.0000.0000.0000.000
23A26GLY00.0000.00222.2910.2140.2140.0000.0000.0000.000
24A27HIS10.8340.92620.44214.28714.2870.0000.0000.0000.000
25A28ASN00.007-0.00221.850-0.572-0.5720.0000.0000.0000.000
26A29GLU-1-0.897-0.94320.871-13.237-13.2370.0000.0000.0000.000
27A30TYR0-0.038-0.04015.447-0.084-0.0840.0000.0000.0000.000
28A31PHE0-0.004-0.02317.0740.0110.0110.0000.0000.0000.000
29A32ASP-1-0.746-0.83321.659-11.194-11.1940.0000.0000.0000.000
30A33ARG10.8910.93422.20813.07813.0780.0000.0000.0000.000
31A34GLY00.0130.02827.0890.3540.3540.0000.0000.0000.000
32A35THR0-0.053-0.05626.8250.4770.4770.0000.0000.0000.000
33A36GLN0-0.064-0.04326.766-0.795-0.7950.0000.0000.0000.000
34A37MET0-0.0220.00520.408-0.120-0.1200.0000.0000.0000.000
35A38ASN0-0.027-0.02025.6390.0560.0560.0000.0000.0000.000
36A39ILE0-0.041-0.03420.386-0.590-0.5900.0000.0000.0000.000
37A40ASN0-0.009-0.01022.346-0.078-0.0780.0000.0000.0000.000
38A41LEU00.0230.02016.673-0.271-0.2710.0000.0000.0000.000
39A42TYR00.0410.02220.424-0.209-0.2090.0000.0000.0000.000
40A43ASP-1-0.828-0.89423.262-10.777-10.7770.0000.0000.0000.000
41A44HIS10.7790.88815.99015.85815.8580.0000.0000.0000.000
42A45ALA0-0.007-0.01319.398-0.200-0.2000.0000.0000.0000.000
43A46ARG10.8710.92120.48710.60510.6050.0000.0000.0000.000
44A47GLY00.0110.02723.3180.3330.3330.0000.0000.0000.000
45A48THR0-0.010-0.01322.296-0.387-0.3870.0000.0000.0000.000
46A49GLN00.0470.01320.951-0.343-0.3430.0000.0000.0000.000
47A50THR00.0330.02522.418-0.172-0.1720.0000.0000.0000.000
48A51GLY00.0420.01622.1530.0780.0780.0000.0000.0000.000
49A52PHE0-0.025-0.01818.369-0.424-0.4240.0000.0000.0000.000
50A53VAL00.0610.04013.6000.3640.3640.0000.0000.0000.000
51A54ARG10.8360.90116.66314.15414.1540.0000.0000.0000.000
52A55TYR0-0.116-0.06916.288-1.001-1.0010.0000.0000.0000.000
53A56ASP-1-0.723-0.84518.268-12.015-12.0150.0000.0000.0000.000
54A57ASP-1-0.852-0.90120.278-12.366-12.3660.0000.0000.0000.000
55A58GLY00.0600.01920.382-0.224-0.2240.0000.0000.0000.000
56A59TYR00.0190.00915.083-0.515-0.5150.0000.0000.0000.000
57A60VAL0-0.051-0.02012.6780.4730.4730.0000.0000.0000.000
58A61SER0-0.025-0.03112.390-1.347-1.3470.0000.0000.0000.000
59A62THR0-0.086-0.0417.726-1.420-1.4200.0000.0000.0000.000
60A63SER00.0660.0248.5161.5061.5060.0000.0000.0000.000
61A64LEU00.0710.0236.574-3.676-3.6760.0000.0000.0000.000
62A65SER00.0010.0036.340-0.643-0.6430.0000.0000.0000.000
63A66LEU00.0100.0246.5331.6381.6380.0000.0000.0000.000
64A67ARG10.9720.9788.01319.16019.1600.0000.0000.0000.000
65A68SER0-0.001-0.01110.6771.8901.8900.0000.0000.0000.000
66A69ALA00.0520.0279.2140.9550.9550.0000.0000.0000.000
67A70HIS0-0.028-0.01911.2210.6250.6250.0000.0000.0000.000
68A71LEU0-0.019-0.00513.6220.9500.9500.0000.0000.0000.000
69A72ALA00.0290.01514.0520.8340.8340.0000.0000.0000.000
70A73GLY00.0370.00814.9280.5170.5170.0000.0000.0000.000
71A74GLN00.0430.02316.2640.4840.4840.0000.0000.0000.000
72A75SER0-0.0110.00119.0880.7520.7520.0000.0000.0000.000
73A76ILE0-0.045-0.01418.5350.5150.5150.0000.0000.0000.000
74A77LEU0-0.044-0.02216.7240.2480.2480.0000.0000.0000.000
75A78SER0-0.019-0.01220.6810.1290.1290.0000.0000.0000.000
76A79GLY0-0.028-0.00122.1740.1380.1380.0000.0000.0000.000
77A80TYR0-0.0080.00621.1960.2850.2850.0000.0000.0000.000
78A81SER00.022-0.00522.308-0.301-0.3010.0000.0000.0000.000
79A82THR0-0.081-0.05118.942-0.239-0.2390.0000.0000.0000.000
80A83TYR0-0.023-0.01014.861-0.115-0.1150.0000.0000.0000.000
81A84TYR00.0200.00913.096-0.355-0.3550.0000.0000.0000.000
82A85ILE00.0050.0038.4150.1720.1720.0000.0000.0000.000
83A86TYR0-0.016-0.0268.308-2.003-2.0030.0000.0000.0000.000
84A87VAL00.0030.0002.669-1.862-1.1110.743-0.299-1.195-0.001
85A88ILE0-0.025-0.0203.213-1.300-0.5040.024-0.235-0.585-0.001
86A89ALA0-0.016-0.0072.418-14.394-11.0765.313-3.788-4.844-0.027
87A90THR0-0.013-0.0012.4695.4215.6990.5770.502-1.357-0.003
88A91ALA0-0.004-0.0104.735-1.231-1.135-0.001-0.008-0.0880.000
89A92PRO00.0620.0318.2810.7430.7430.0000.0000.0000.000
90A93ASN00.0160.00910.159-0.022-0.0220.0000.0000.0000.000
91A94MET0-0.069-0.0126.6531.4041.4040.0000.0000.0000.000
92A95PHE00.0940.03810.4650.1480.1480.0000.0000.0000.000
93A96ASN0-0.037-0.03511.178-0.165-0.1650.0000.0000.0000.000
94A97VAL00.0220.00412.5080.8790.8790.0000.0000.0000.000
95A98ASN00.0070.00315.1461.3291.3290.0000.0000.0000.000
96A99ASP-1-0.844-0.90813.403-17.214-17.2140.0000.0000.0000.000
97A100VAL0-0.0240.00016.1110.5870.5870.0000.0000.0000.000
98A101LEU00.0040.01018.5740.6650.6650.0000.0000.0000.000
99A102GLY00.0450.02920.0240.6300.6300.0000.0000.0000.000
100A103VAL0-0.035-0.03221.639-0.188-0.1880.0000.0000.0000.000
101A104TYR0-0.081-0.05924.0050.4250.4250.0000.0000.0000.000
102A105SER0-0.023-0.02718.740-0.109-0.1090.0000.0000.0000.000
103A106PRO0-0.018-0.01721.2520.2350.2350.0000.0000.0000.000
104A107HIS0-0.0250.00419.5980.6240.6240.0000.0000.0000.000
105A108PRO00.0210.01518.921-0.738-0.7380.0000.0000.0000.000
106A109TYR0-0.014-0.02617.583-0.654-0.6540.0000.0000.0000.000
107A110GLU-1-0.845-0.90616.250-14.839-14.8390.0000.0000.0000.000
108A111GLN0-0.141-0.07212.489-1.764-1.7640.0000.0000.0000.000
109A112GLU-1-0.779-0.82811.688-18.044-18.0440.0000.0000.0000.000
110A113VAL00.0020.0017.9630.2110.2110.0000.0000.0000.000
111A114SER0-0.009-0.00410.417-0.646-0.6460.0000.0000.0000.000
112A115ALA00.000-0.01310.510-0.114-0.1140.0000.0000.0000.000
113A116LEU00.0300.01212.2061.0441.0440.0000.0000.0000.000
114A117GLY00.000-0.00715.420-0.605-0.6050.0000.0000.0000.000
115A118GLY00.001-0.00814.8200.6570.6570.0000.0000.0000.000
116A119ILE0-0.053-0.0138.623-1.174-1.1740.0000.0000.0000.000
117A120PRO00.0440.03411.4000.3450.3450.0000.0000.0000.000
118A121TYR00.058-0.00410.503-2.599-2.5990.0000.0000.0000.000
119A122SER0-0.037-0.02510.194-1.281-1.2810.0000.0000.0000.000
120A123GLN0-0.022-0.0096.4660.3180.3180.0000.0000.0000.000
121A124ILE0-0.0210.0025.543-6.913-6.9130.0000.0000.0000.000
122A125TYR00.0250.0062.239-10.609-10.50010.113-3.197-7.025-0.029
123A126GLY00.008-0.0095.0762.4212.491-0.001-0.002-0.0660.000
124A127TRP00.0190.0137.767-1.209-1.2090.0000.0000.0000.000
125A128TYR00.0190.0266.867-0.958-0.9580.0000.0000.0000.000
126A129ARG10.8400.90511.35315.76115.7610.0000.0000.0000.000
127A130VAL0-0.0080.01114.474-0.260-0.2600.0000.0000.0000.000
128A131ASN00.0290.01416.9330.5300.5300.0000.0000.0000.000
129A132PHE00.0360.01220.7370.1210.1210.0000.0000.0000.000
130A133GLY00.0500.03219.6490.3110.3110.0000.0000.0000.000
131A134VAL0-0.0060.00118.851-0.563-0.5630.0000.0000.0000.000
132A135ILE0-0.027-0.02112.527-0.178-0.1780.0000.0000.0000.000
133A136ASP-1-0.787-0.85315.754-16.342-16.3420.0000.0000.0000.000
134A137GLU-1-0.889-0.96013.346-18.153-18.1530.0000.0000.0000.000
135A138ARG10.8400.89012.13315.98715.9870.0000.0000.0000.000
136A139LEU0-0.045-0.0165.519-0.685-0.6850.0000.0000.0000.000
137A140HIS0-0.014-0.0039.8951.3801.3800.0000.0000.0000.000
138A141ARG10.8950.9434.98037.13037.1300.0000.0000.0000.000
139A142ASN00.0220.0197.7415.4445.4440.0000.0000.0000.000
140A143ARG10.9630.9728.29615.68415.6840.0000.0000.0000.000
141A144GLU-1-0.859-0.92210.456-20.515-20.5150.0000.0000.0000.000
142A145TYR0-0.032-0.0181.955-16.840-17.3878.502-3.319-4.636-0.037
143A146ARG10.9440.9777.27523.71523.7150.0000.0000.0000.000
144A147ASP-1-0.777-0.8673.530-55.380-54.5660.003-0.447-0.370-0.003
145A148ARG10.9220.9515.45620.00220.0020.0000.0000.0000.000
146A149TYR0-0.0030.0168.0171.6781.6780.0000.0000.0000.000
147A150TYR00.0700.0023.7070.9221.1280.001-0.035-0.1710.000
148A151ARG10.8160.9073.42327.03627.6740.005-0.262-0.381-0.002
149A152ASN0-0.012-0.0054.3291.0041.062-0.001-0.003-0.0540.000
150A153LEU0-0.0200.0145.7154.5544.5540.0000.0000.0000.000
151A154ASN00.0430.0095.953-5.669-5.6690.0000.0000.0000.000
152A155ILE0-0.021-0.0165.8310.3210.3210.0000.0000.0000.000
153A156ALA00.0150.0288.9690.8290.8290.0000.0000.0000.000
154A157PRO00.0170.01512.785-0.160-0.1600.0000.0000.0000.000
155A158ALA00.0410.00214.7790.4020.4020.0000.0000.0000.000
156A159GLU-1-0.934-0.96916.864-13.306-13.3060.0000.0000.0000.000
157A160ASP-1-0.849-0.91117.403-14.644-14.6440.0000.0000.0000.000
158A161GLY0-0.018-0.01518.0350.1340.1340.0000.0000.0000.000
159A162TYR0-0.021-0.01418.8670.4500.4500.0000.0000.0000.000
160A163ARG10.8690.92621.09213.72313.7230.0000.0000.0000.000
161A164LEU0-0.083-0.04118.9000.2320.2320.0000.0000.0000.000
162A165ALA0-0.0110.00221.588-0.182-0.1820.0000.0000.0000.000
163A166GLY00.0200.00522.565-0.018-0.0180.0000.0000.0000.000
164A167PHE00.0150.00924.0650.1490.1490.0000.0000.0000.000
165A168PRO00.0330.03227.8190.0420.0420.0000.0000.0000.000
166A169PRO00.0600.00631.342-0.030-0.0300.0000.0000.0000.000
167A170ASP-1-0.899-0.93933.842-8.438-8.4380.0000.0000.0000.000
168A171HIS00.0070.00428.2840.2270.2270.0000.0000.0000.000
169A172GLN0-0.0020.00631.1040.0190.0190.0000.0000.0000.000
170A173ALA00.0900.04227.5820.0610.0610.0000.0000.0000.000
171A174TRP0-0.065-0.03626.039-0.140-0.1400.0000.0000.0000.000
172A175ARG10.7600.85430.9548.7668.7660.0000.0000.0000.000
173A176GLU-1-0.823-0.87629.358-9.299-9.2990.0000.0000.0000.000
174A177GLU-1-0.878-0.90628.276-9.763-9.7630.0000.0000.0000.000
175A178PRO00.002-0.00923.023-0.006-0.0060.0000.0000.0000.000
176A179TRP0-0.039-0.05022.6420.1530.1530.0000.0000.0000.000
177A180ILE0-0.0130.00626.8590.0360.0360.0000.0000.0000.000
178A181HIS0-0.089-0.05827.5880.2240.2240.0000.0000.0000.000
179A182HIS0-0.061-0.03623.635-0.219-0.2190.0000.0000.0000.000
180A183ALA00.0180.01527.435-0.226-0.2260.0000.0000.0000.000
181A184PRO0-0.0080.00128.0480.1990.1990.0000.0000.0000.000
182A185GLN00.006-0.00230.6990.1330.1330.0000.0000.0000.000
183A186GLY0-0.002-0.00134.4630.0560.0560.0000.0000.0000.000
184A187CYS0-0.063-0.00131.7160.0540.0540.0000.0000.0000.000
185A188GLY0-0.020-0.00633.4790.3820.3820.0000.0000.0000.000