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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: JMJ19

Calculation Name: 1LTT-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2083166.523868
FMO2-HF: Nuclear repulsion 2008749.331869
FMO2-HF: Total energy -74417.191999
FMO2-MP2: Total energy -74636.653169


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.
-13.349-0.3750000000000415.032-9.766-18.24-0.063
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 : 0.953
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].
3A6TYR 0-0.013-0.0133.142-7.360-2.9950.263-2.037-2.5910.001
4A7ARG 10.8200.8805.75921.90421.9040.0000.0000.0000.000
5A8ALA 0-0.0170.0189.295-0.478-0.4780.0000.0000.0000.000
6A9ASP -1-0.768-0.89112.238-17.419-17.4190.0000.0000.0000.000
7A10SER 00.0670.03214.674-0.213-0.2130.0000.0000.0000.000
8A11ARG 10.8290.92715.87616.93116.9310.0000.0000.0000.000
9A12PRO 00.0090.02715.968-1.417-1.4170.0000.0000.0000.000
10A13PRO 00.015-0.00614.0630.1390.1390.0000.0000.0000.000
11A14ASP -1-0.831-0.91915.750-14.925-14.9250.0000.0000.0000.000
12A15GLU -1-0.880-0.96019.021-14.041-14.0410.0000.0000.0000.000
13A16ILE 0-0.0010.01512.988-0.038-0.0380.0000.0000.0000.000
14A17LYS 10.8420.92716.20118.12918.1290.0000.0000.0000.000
15A18ARG 10.8850.94517.23413.74313.7430.0000.0000.0000.000
16A19SER 00.0280.02818.1600.5650.5650.0000.0000.0000.000
17A20GLY 00.0140.01616.9930.1370.1370.0000.0000.0000.000
18A21GLY 0-0.007-0.02713.469-1.137-1.1370.0000.0000.0000.000
19A22LEU 0-0.073-0.01710.4341.0751.0750.0000.0000.0000.000
20A23MET 00.0120.04214.332-0.271-0.2710.0000.0000.0000.000
21A24PRO 00.027-0.00317.139-0.083-0.0830.0000.0000.0000.000
22A25ARG 10.9310.96718.83711.83311.8330.0000.0000.0000.000
23A26GLY 00.0030.01722.1030.2830.2830.0000.0000.0000.000
24A27HIS 10.8310.92420.24914.29014.2900.0000.0000.0000.000
25A28ASN 00.005-0.00922.019-0.403-0.4030.0000.0000.0000.000
26A29GLU -1-0.905-0.95121.229-13.079-13.0790.0000.0000.0000.000
27A30TYR 0-0.037-0.03415.5670.0040.0040.0000.0000.0000.000
28A31PHE 0-0.037-0.04917.1480.0050.0050.0000.0000.0000.000
29A32ASP -1-0.869-0.92021.766-11.124-11.1240.0000.0000.0000.000
30A33ARG 10.9620.96521.81212.80512.8050.0000.0000.0000.000
31A34GLY 00.0060.01626.9890.2910.2910.0000.0000.0000.000
32A35THR 0-0.0070.00327.5440.4630.4630.0000.0000.0000.000
33A36GLN 0-0.062-0.02827.035-0.716-0.7160.0000.0000.0000.000
34A37MET 0-0.0040.00720.160-0.124-0.1240.0000.0000.0000.000
35A38ASN 0-0.033-0.01425.3350.1420.1420.0000.0000.0000.000
36A39ILE 0-0.051-0.03220.292-0.567-0.5670.0000.0000.0000.000
37A40ASN 00.0590.03122.2910.0680.0680.0000.0000.0000.000
38A41LEU 00.0100.01616.763-0.334-0.3340.0000.0000.0000.000
39A42TYR 00.0490.01420.561-0.260-0.2600.0000.0000.0000.000
40A43ASP -1-0.889-0.95522.932-10.859-10.8590.0000.0000.0000.000
41A44HIS 10.7600.89415.67415.87315.8730.0000.0000.0000.000
42A45ALA 0-0.023-0.03519.174-0.140-0.1400.0000.0000.0000.000
43A46ARG 10.9080.97420.12110.84710.8470.0000.0000.0000.000
44A47GLY 00.0210.03623.2630.2650.2650.0000.0000.0000.000
45A48THR 00.0050.00321.923-0.459-0.4590.0000.0000.0000.000
46A49GLN 00.0240.00820.892-0.301-0.3010.0000.0000.0000.000
47A50THR 00.0310.02122.449-0.308-0.3080.0000.0000.0000.000
48A51GLY 00.0240.01621.8460.0310.0310.0000.0000.0000.000
49A52PHE 0-0.055-0.03817.843-0.593-0.5930.0000.0000.0000.000
50A53VAL 00.0490.03713.4200.2920.2920.0000.0000.0000.000
51A54ARG 10.8750.91816.65114.15914.1590.0000.0000.0000.000
52A55TYR 0-0.073-0.04316.270-1.009-1.0090.0000.0000.0000.000
53A56ASP -1-0.800-0.90518.016-11.967-11.9670.0000.0000.0000.000
54A57ASP -1-0.815-0.90320.310-12.324-12.3240.0000.0000.0000.000
55A58GLY 00.0530.01420.147-0.266-0.2660.0000.0000.0000.000
56A59TYR 00.0310.01015.180-0.625-0.6250.0000.0000.0000.000
57A60VAL 0-0.040-0.01412.3020.5080.5080.0000.0000.0000.000
58A61SER 0-0.022-0.01412.322-1.206-1.2060.0000.0000.0000.000
59A62THR 0-0.084-0.0507.426-1.568-1.5680.0000.0000.0000.000
60A63SER 00.0360.0208.2692.1792.1790.0000.0000.0000.000
61A64LEU 00.0960.0406.037-4.448-4.4480.0000.0000.0000.000
62A65SER 00.0090.0185.641-2.006-2.0060.0000.0000.0000.000
63A66LEU 00.0540.0366.4781.2221.2220.0000.0000.0000.000
64A67ARG 10.9920.9997.78919.88019.8800.0000.0000.0000.000
65A68SER 0-0.002-0.03410.2271.8091.8090.0000.0000.0000.000
66A69ALA 00.0270.0238.8161.0131.0130.0000.0000.0000.000
67A70HIS 0-0.039-0.02710.8220.8360.8360.0000.0000.0000.000
68A71LEU 0-0.042-0.02013.2871.1321.1320.0000.0000.0000.000
69A72ALA 00.0440.02713.8820.9500.9500.0000.0000.0000.000
70A73GLY 00.0240.00214.6630.7010.7010.0000.0000.0000.000
71A74GLN 00.0300.02616.0460.6730.6730.0000.0000.0000.000
72A75SER 0-0.0120.00218.9340.9430.9430.0000.0000.0000.000
73A76ILE 0-0.017-0.01117.9890.5540.5540.0000.0000.0000.000
74A77LEU 0-0.061-0.03716.6710.2250.2250.0000.0000.0000.000
75A78SER 00.0140.00520.5560.0890.0890.0000.0000.0000.000
76A79GLY 0-0.0250.00922.106-0.063-0.0630.0000.0000.0000.000
77A80TYR 00.0240.02121.0540.2490.2490.0000.0000.0000.000
78A81SER 0-0.027-0.02422.110-0.271-0.2710.0000.0000.0000.000
79A82THR 0-0.067-0.04518.300-0.194-0.1940.0000.0000.0000.000
80A83TYR 0-0.0050.00214.427-0.180-0.1800.0000.0000.0000.000
81A84TYR 00.013-0.00312.670-0.338-0.3380.0000.0000.0000.000
82A85ILE 00.0210.0217.7140.0560.0560.0000.0000.0000.000
83A86TYR 0-0.045-0.0507.946-1.847-1.8470.0000.0000.0000.000
84A87VAL 00.0040.0082.402-2.263-1.5011.694-0.509-1.946-0.001
85A88ILE 0-0.024-0.0293.232-2.329-1.3040.041-0.339-0.727-0.002
86A89ALA 0-0.0130.0002.206-14.679-11.5475.048-3.735-4.446-0.025
87A90THR 00.0100.0092.4756.8317.3400.3850.109-1.003-0.002
88A91ALA 0-0.001-0.0135.121-0.897-0.8440.000-0.005-0.0480.000
89A92PRO 00.0550.0258.6330.4820.4820.0000.0000.0000.000
90A93ASN 00.0360.02910.351-0.087-0.0870.0000.0000.0000.000
91A94MET 0-0.106-0.0406.5341.2741.2740.0000.0000.0000.000
92A95PHE 00.1140.06210.6100.0620.0620.0000.0000.0000.000
93A96ASN 00.0350.00410.2910.2470.2470.0000.0000.0000.000
94A97VAL 00.0410.00411.8821.0121.0120.0000.0000.0000.000
95A98ASN 00.0150.00714.4931.2481.2480.0000.0000.0000.000
96A99ASP -1-0.904-0.93713.408-16.611-16.6110.0000.0000.0000.000
97A100VAL 0-0.056-0.02415.7280.6040.6040.0000.0000.0000.000
98A101LEU 0-0.013-0.00518.2890.7040.7040.0000.0000.0000.000
99A102GLY 00.0560.03719.4850.6560.6560.0000.0000.0000.000
100A103VAL 0-0.009-0.00821.037-0.178-0.1780.0000.0000.0000.000
101A104TYR 0-0.041-0.01423.7090.3500.3500.0000.0000.0000.000
102A105SER 0-0.076-0.04818.149-0.154-0.1540.0000.0000.0000.000
103A106PRO 00.025-0.00120.8280.1990.1990.0000.0000.0000.000
104A107HIS 0-0.042-0.00119.1540.6850.6850.0000.0000.0000.000
105A108PRO 00.0190.01318.263-0.801-0.8010.0000.0000.0000.000
106A109TYR 0-0.012-0.02217.057-0.733-0.7330.0000.0000.0000.000
107A110GLU -1-0.920-0.95515.818-15.160-15.1600.0000.0000.0000.000
108A111GLN 0-0.125-0.05911.958-1.616-1.6160.0000.0000.0000.000
109A112GLU -1-0.781-0.88411.181-18.459-18.4590.0000.0000.0000.000
110A113VAL 0-0.017-0.0107.4020.3750.3750.0000.0000.0000.000
111A114SER 0-0.0240.00410.202-0.480-0.4800.0000.0000.0000.000
112A115ALA 00.0220.00410.480-0.414-0.4140.0000.0000.0000.000
113A116LEU 0-0.0070.00512.1490.9740.9740.0000.0000.0000.000
114A117GLY 00.0390.00515.447-0.439-0.4390.0000.0000.0000.000
115A118GLY 0-0.028-0.01114.5730.4460.4460.0000.0000.0000.000
116A119ILE 0-0.050-0.0208.788-1.152-1.1520.0000.0000.0000.000
117A120PRO 00.0410.02211.2950.4240.4240.0000.0000.0000.000
118A121TYR 00.0490.00310.857-2.474-2.4740.0000.0000.0000.000
119A122SER 0-0.024-0.01710.061-2.044-2.0440.0000.0000.0000.000
120A123GLN 00.0030.0086.513-0.197-0.1970.0000.0000.0000.000
121A124ILE 0-0.0190.0035.801-6.540-6.5400.0000.0000.0000.000
122A125TYR 00.006-0.0062.960-4.355-2.1283.323-1.243-4.308-0.007
123A126GLY 00.0310.0015.3673.5543.6260.000-0.002-0.0690.000
124A127TRP 00.0250.0177.500-1.457-1.4570.0000.0000.0000.000
125A128TYR 00.0310.0296.811-1.471-1.4710.0000.0000.0000.000
126A129ARG 10.9320.96211.40316.01716.0170.0000.0000.0000.000
127A130VAL 0-0.0040.01314.019-0.200-0.2000.0000.0000.0000.000
128A131ASN 00.018-0.00116.4810.8020.8020.0000.0000.0000.000
129A132PHE 00.0380.00920.2570.1260.1260.0000.0000.0000.000
130A133GLY 00.0370.02219.0690.2590.2590.0000.0000.0000.000
131A134VAL 0-0.016-0.00118.617-0.512-0.5120.0000.0000.0000.000
132A135ILE 0-0.040-0.03011.938-0.195-0.1950.0000.0000.0000.000
133A136ASP -1-0.908-0.94515.483-17.077-17.0770.0000.0000.0000.000
134A137GLU -1-0.926-0.97812.894-18.507-18.5070.0000.0000.0000.000
135A138ARG 10.9250.96812.17116.66616.6660.0000.0000.0000.000
136A139LEU 0-0.068-0.0275.596-1.045-1.0450.0000.0000.0000.000
137A140HIS 0-0.023-0.00310.0582.2152.2150.0000.0000.0000.000
138A141ARG 10.9130.9475.23936.15836.1580.0000.0000.0000.000
139A142ASN 0-0.003-0.0028.2985.1805.1800.0000.0000.0000.000
140A143ARG 10.9690.9649.21515.73815.7380.0000.0000.0000.000
141A144GLU -1-0.931-0.96911.420-19.423-19.4230.0000.0000.0000.000
142A145TYR 0-0.0120.0332.048-12.875-12.3374.278-1.986-2.831-0.027
143A146ARG 10.9310.9467.66223.56423.5640.0000.0000.0000.000
144A147ASP -1-0.821-0.9134.632-45.721-45.6390.000-0.005-0.0760.000
145A148ARG 10.9400.9556.39319.89719.8970.0000.0000.0000.000
146A149TYR 0-0.047-0.0178.7550.8310.8310.0000.0000.0000.000
147A150TYR 00.0890.0194.2591.0051.1020.000-0.010-0.0880.000
148A151ARG 10.7960.9144.62628.16328.2750.000-0.004-0.1070.000
149A152ASN 00.0370.0135.549-2.172-2.1720.0000.0000.0000.000
150A153LEU 0-0.0320.0176.8813.2103.2100.0000.0000.0000.000
151A154ASN 00.024-0.0026.366-4.051-4.0510.0000.0000.0000.000
152A155ILE 0-0.005-0.0145.7100.4560.4560.0000.0000.0000.000
153A156ALA 00.0010.0138.5980.9290.9290.0000.0000.0000.000
154A157PRO 0-0.017-0.00612.454-0.232-0.2320.0000.0000.0000.000
155A158ALA 00.0430.00514.2910.4880.4880.0000.0000.0000.000
156A159GLU -1-0.926-0.97216.342-12.915-12.9150.0000.0000.0000.000
157A160ASP -1-0.916-0.94216.907-14.853-14.8530.0000.0000.0000.000
158A161GLY 0-0.050-0.04217.8910.0220.0220.0000.0000.0000.000
159A162TYR 00.0160.01918.7690.3960.3960.0000.0000.0000.000
160A163ARG 11.0001.00420.73813.27413.2740.0000.0000.0000.000
161A164LEU 0-0.129-0.06718.8980.1840.1840.0000.0000.0000.000
162A165ALA 00.0010.01021.325-0.204-0.2040.0000.0000.0000.000
163A166GLY 00.012-0.00322.339-0.099-0.0990.0000.0000.0000.000
164A167PHE 00.0070.00724.0630.1200.1200.0000.0000.0000.000
165A168PRO 00.0520.02327.2460.1100.1100.0000.0000.0000.000
166A169PRO 00.0610.01530.8430.0020.0020.0000.0000.0000.000
167A170ASP -1-0.945-0.95033.380-8.267-8.2670.0000.0000.0000.000
168A171HIS 0-0.0030.00528.2140.2100.2100.0000.0000.0000.000
169A172GLN 00.0310.00731.527-0.057-0.0570.0000.0000.0000.000
170A173ALA 00.0650.03427.1270.0230.0230.0000.0000.0000.000
171A174TRP 0-0.064-0.02925.810-0.221-0.2210.0000.0000.0000.000
172A175ARG 10.8150.90230.4478.6648.6640.0000.0000.0000.000
173A176GLU -1-0.885-0.95428.957-9.239-9.2390.0000.0000.0000.000
174A177GLU -1-0.921-0.94328.152-9.648-9.6480.0000.0000.0000.000
175A178PRO 0-0.028-0.03722.823-0.042-0.0420.0000.0000.0000.000
176A179TRP 0-0.038-0.03722.3320.1290.1290.0000.0000.0000.000
177A180ILE 00.0230.02526.4470.0180.0180.0000.0000.0000.000
178A181HIS 0-0.051-0.01527.6850.1960.1960.0000.0000.0000.000
179A182HIS 0-0.075-0.03923.875-0.206-0.2060.0000.0000.0000.000
180A183ALA 00.0440.02127.136-0.282-0.2820.0000.0000.0000.000
181A184PRO 0-0.041-0.02327.4380.1690.1690.0000.0000.0000.000
182A185GLN 0-0.016-0.00930.1410.1690.1690.0000.0000.0000.000
183A186GLY 0-0.022-0.01533.9550.0500.0500.0000.0000.0000.000
184A187CYS 0-0.107-0.03829.8300.0500.0500.0000.0000.0000.000
185A188GLY -1-0.886-0.93533.007-8.265-8.2650.0000.0000.0000.000