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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: ZY7QN

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 OptHSide
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 -2083198.070957
FMO2-HF: Nuclear repulsion 2008779.147737
FMO2-HF: Total energy -74418.923221
FMO2-MP2: Total energy -74638.496002


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.
-10.3451.125000000000117.235-9.734-18.97-0.069
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 : 0.892 / q_NPA : 0.946
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].
3A6TYR0-0.020-0.0232.705-5.276-1.1510.292-1.858-2.5580.002
4A7ARG10.8190.8895.99421.32421.3240.0000.0000.0000.000
5A8ALA0-0.0140.0159.526-0.461-0.4610.0000.0000.0000.000
6A9ASP-1-0.748-0.87312.445-17.084-17.0840.0000.0000.0000.000
7A10SER00.0480.02614.873-0.207-0.2070.0000.0000.0000.000
8A11ARG10.8220.91816.10016.78316.7830.0000.0000.0000.000
9A12PRO00.0200.03416.122-1.341-1.3410.0000.0000.0000.000
10A13PRO00.018-0.00814.3360.1320.1320.0000.0000.0000.000
11A14ASP-1-0.808-0.89015.988-14.813-14.8130.0000.0000.0000.000
12A15GLU-1-0.871-0.95219.239-14.146-14.1460.0000.0000.0000.000
13A16ILE00.0010.01813.173-0.074-0.0740.0000.0000.0000.000
14A17LYS10.7830.88016.06718.25918.2590.0000.0000.0000.000
15A18ARG10.8430.90917.38013.79413.7940.0000.0000.0000.000
16A19SER00.0160.01218.1580.5600.5600.0000.0000.0000.000
17A20GLY00.0200.01916.9350.1490.1490.0000.0000.0000.000
18A21GLY0-0.015-0.03413.570-1.174-1.1740.0000.0000.0000.000
19A22LEU0-0.063-0.01410.6621.0481.0480.0000.0000.0000.000
20A23MET00.0140.04314.455-0.453-0.4530.0000.0000.0000.000
21A24PRO00.021-0.00817.251-0.079-0.0790.0000.0000.0000.000
22A25ARG10.8730.92218.84711.81711.8170.0000.0000.0000.000
23A26GLY00.0210.02322.1140.2550.2550.0000.0000.0000.000
24A27HIS10.8400.92520.47914.17714.1770.0000.0000.0000.000
25A28ASN00.010-0.00622.038-0.473-0.4730.0000.0000.0000.000
26A29GLU-1-0.898-0.94521.297-13.058-13.0580.0000.0000.0000.000
27A30TYR0-0.035-0.03515.429-0.071-0.0710.0000.0000.0000.000
28A31PHE0-0.026-0.04216.7670.0200.0200.0000.0000.0000.000
29A32ASP-1-0.785-0.86421.579-11.115-11.1150.0000.0000.0000.000
30A33ARG10.9000.94121.93512.97312.9730.0000.0000.0000.000
31A34GLY00.0060.01526.9040.2910.2910.0000.0000.0000.000
32A35THR0-0.044-0.03427.3050.4640.4640.0000.0000.0000.000
33A36GLN0-0.062-0.03127.041-0.737-0.7370.0000.0000.0000.000
34A37MET00.0010.01320.049-0.117-0.1170.0000.0000.0000.000
35A38ASN0-0.040-0.02625.3370.1000.1000.0000.0000.0000.000
36A39ILE0-0.037-0.02720.239-0.543-0.5430.0000.0000.0000.000
37A40ASN00.0410.02522.2870.0360.0360.0000.0000.0000.000
38A41LEU00.0150.01816.795-0.292-0.2920.0000.0000.0000.000
39A42TYR00.0450.01320.566-0.245-0.2450.0000.0000.0000.000
40A43ASP-1-0.832-0.92122.946-10.833-10.8330.0000.0000.0000.000
41A44HIS10.7500.88415.67415.89715.8970.0000.0000.0000.000
42A45ALA0-0.026-0.03119.145-0.109-0.1090.0000.0000.0000.000
43A46ARG10.8640.93520.14210.72810.7280.0000.0000.0000.000
44A47GLY00.0270.03623.2530.2750.2750.0000.0000.0000.000
45A48THR00.001-0.01022.171-0.449-0.4490.0000.0000.0000.000
46A49GLN00.0290.00520.999-0.315-0.3150.0000.0000.0000.000
47A50THR00.0420.02822.691-0.128-0.1280.0000.0000.0000.000
48A51GLY00.0070.00322.0690.0520.0520.0000.0000.0000.000
49A52PHE0-0.029-0.02818.325-0.434-0.4340.0000.0000.0000.000
50A53VAL00.0670.04413.7220.3220.3220.0000.0000.0000.000
51A54ARG10.8620.92416.89414.26014.2600.0000.0000.0000.000
52A55TYR0-0.108-0.05716.280-1.033-1.0330.0000.0000.0000.000
53A56ASP-1-0.751-0.86318.026-11.997-11.9970.0000.0000.0000.000
54A57ASP-1-0.826-0.89420.316-12.258-12.2580.0000.0000.0000.000
55A58GLY00.0550.01520.151-0.236-0.2360.0000.0000.0000.000
56A59TYR00.0310.01514.961-0.565-0.5650.0000.0000.0000.000
57A60VAL0-0.040-0.01212.5610.5650.5650.0000.0000.0000.000
58A61SER0-0.044-0.04912.328-1.202-1.2020.0000.0000.0000.000
59A62THR0-0.071-0.0447.482-1.595-1.5950.0000.0000.0000.000
60A63SER00.0360.0228.5221.5771.5770.0000.0000.0000.000
61A64LEU00.1100.0446.081-4.132-4.1320.0000.0000.0000.000
62A65SER0-0.014-0.0075.614-1.441-1.4410.0000.0000.0000.000
63A66LEU00.0420.0356.6431.1531.1530.0000.0000.0000.000
64A67ARG10.9740.9987.96119.39919.3990.0000.0000.0000.000
65A68SER00.009-0.02710.4121.7061.7060.0000.0000.0000.000
66A69ALA00.0420.0279.0230.9790.9790.0000.0000.0000.000
67A70HIS0-0.035-0.02611.0300.7670.7670.0000.0000.0000.000
68A71LEU0-0.025-0.01313.4621.0111.0110.0000.0000.0000.000
69A72ALA00.0330.01814.0940.8920.8920.0000.0000.0000.000
70A73GLY00.0320.00714.8750.6540.6540.0000.0000.0000.000
71A74GLN00.0250.02516.2540.4850.4850.0000.0000.0000.000
72A75SER00.0170.01419.1430.7690.7690.0000.0000.0000.000
73A76ILE0-0.045-0.02318.6070.5700.5700.0000.0000.0000.000
74A77LEU0-0.052-0.02616.9010.2040.2040.0000.0000.0000.000
75A78SER0-0.006-0.00620.7580.1220.1220.0000.0000.0000.000
76A79GLY0-0.0240.00822.290-0.074-0.0740.0000.0000.0000.000
77A80TYR00.0310.02121.2110.2260.2260.0000.0000.0000.000
78A81SER0-0.013-0.01722.261-0.237-0.2370.0000.0000.0000.000
79A82THR0-0.075-0.05418.559-0.239-0.2390.0000.0000.0000.000
80A83TYR0-0.009-0.00314.474-0.149-0.1490.0000.0000.0000.000
81A84TYR00.008-0.00412.791-0.311-0.3110.0000.0000.0000.000
82A85ILE00.0110.0157.9580.1110.1110.0000.0000.0000.000
83A86TYR0-0.051-0.0528.091-1.753-1.7530.0000.0000.0000.000
84A87VAL00.0130.0112.452-1.889-1.1661.044-0.375-1.392-0.001
85A88ILE0-0.034-0.0343.390-2.094-1.2690.019-0.255-0.590-0.001
86A89ALA0-0.0150.0022.216-13.945-11.5536.230-3.821-4.801-0.024
87A90THR00.0150.0152.3996.8846.9870.4800.530-1.112-0.002
88A91ALA0-0.009-0.0175.106-1.412-1.337-0.001-0.004-0.0690.000
89A92PRO00.0500.0258.3090.5360.5360.0000.0000.0000.000
90A93ASN00.0330.01810.3400.0010.0010.0000.0000.0000.000
91A94MET0-0.082-0.0256.6461.1261.1260.0000.0000.0000.000
92A95PHE00.0940.04610.5940.0080.0080.0000.0000.0000.000
93A96ASN00.001-0.01110.627-0.385-0.3850.0000.0000.0000.000
94A97VAL00.0260.00011.8991.0001.0000.0000.0000.0000.000
95A98ASN0-0.007-0.00314.5291.3151.3150.0000.0000.0000.000
96A99ASP-1-0.858-0.91013.378-16.926-16.9260.0000.0000.0000.000
97A100VAL0-0.033-0.01315.8860.5660.5660.0000.0000.0000.000
98A101LEU0-0.0110.00018.3020.7060.7060.0000.0000.0000.000
99A102GLY00.0550.03319.5080.6500.6500.0000.0000.0000.000
100A103VAL0-0.006-0.00821.064-0.177-0.1770.0000.0000.0000.000
101A104TYR0-0.087-0.06223.7580.3600.3600.0000.0000.0000.000
102A105SER0-0.064-0.04818.204-0.089-0.0890.0000.0000.0000.000
103A106PRO00.0250.00520.6930.2290.2290.0000.0000.0000.000
104A107HIS0-0.056-0.01719.1670.6650.6650.0000.0000.0000.000
105A108PRO00.0390.02518.305-0.795-0.7950.0000.0000.0000.000
106A109TYR00.009-0.01017.104-0.739-0.7390.0000.0000.0000.000
107A110GLU-1-0.885-0.94115.712-15.194-15.1940.0000.0000.0000.000
108A111GLN0-0.148-0.07412.095-1.624-1.6240.0000.0000.0000.000
109A112GLU-1-0.770-0.83111.225-18.306-18.3060.0000.0000.0000.000
110A113VAL0-0.014-0.0117.4650.3280.3280.0000.0000.0000.000
111A114SER0-0.0150.00010.221-0.476-0.4760.0000.0000.0000.000
112A115ALA00.007-0.00310.402-0.430-0.4300.0000.0000.0000.000
113A116LEU0-0.004-0.00312.1500.9850.9850.0000.0000.0000.000
114A117GLY00.0400.00615.447-0.492-0.4920.0000.0000.0000.000
115A118GLY0-0.024-0.00914.5790.4790.4790.0000.0000.0000.000
116A119ILE0-0.063-0.0228.655-1.190-1.1900.0000.0000.0000.000
117A120PRO00.0460.02911.0230.4580.4580.0000.0000.0000.000
118A121TYR00.0500.00010.870-2.369-2.3690.0000.0000.0000.000
119A122SER0-0.056-0.0339.903-2.015-2.0150.0000.0000.0000.000
120A123GLN00.0140.0156.4910.0000.0000.0000.0000.0000.000
121A124ILE0-0.0190.0045.883-6.332-6.3320.0000.0000.0000.000
122A125TYR00.0360.0062.747-5.399-3.5793.768-1.355-4.233-0.011
123A126GLY00.015-0.0065.5123.3413.3410.0000.0000.0000.000
124A127TRP00.0100.0097.781-1.295-1.2950.0000.0000.0000.000
125A128TYR00.0170.0276.902-1.304-1.3040.0000.0000.0000.000
126A129ARG10.8950.94511.45415.76115.7610.0000.0000.0000.000
127A130VAL00.0040.01614.100-0.181-0.1810.0000.0000.0000.000
128A131ASN00.0260.01516.5870.6490.6490.0000.0000.0000.000
129A132PHE00.0470.00720.3550.1090.1090.0000.0000.0000.000
130A133GLY00.0450.02819.2110.2700.2700.0000.0000.0000.000
131A134VAL0-0.0080.00918.693-0.465-0.4650.0000.0000.0000.000
132A135ILE0-0.042-0.03212.063-0.169-0.1690.0000.0000.0000.000
133A136ASP-1-0.811-0.86715.548-16.688-16.6880.0000.0000.0000.000
134A137GLU-1-0.894-0.96313.281-18.188-18.1880.0000.0000.0000.000
135A138ARG10.8240.88612.49516.46316.4630.0000.0000.0000.000
136A139LEU0-0.062-0.0246.024-0.838-0.8380.0000.0000.0000.000
137A140HIS0-0.023-0.00610.3732.1412.1410.0000.0000.0000.000
138A141ARG10.9100.9535.28835.45835.4580.0000.0000.0000.000
139A142ASN00.0130.0068.2215.2455.2450.0000.0000.0000.000
140A143ARG10.9760.9689.01715.62515.6250.0000.0000.0000.000
141A144GLU-1-0.864-0.91911.106-19.691-19.6910.0000.0000.0000.000
142A145TYR00.0050.0362.001-18.355-17.4705.407-2.522-3.771-0.032
143A146ARG10.9150.9477.46624.31324.3130.0000.0000.0000.000
144A147ASP-1-0.798-0.8954.130-49.755-49.584-0.001-0.039-0.1320.000
145A148ARG10.9490.9645.89719.99919.9990.0000.0000.0000.000
146A149TYR0-0.030-0.0118.4280.6370.6370.0000.0000.0000.000
147A150TYR00.0810.0103.9700.8821.031-0.001-0.022-0.1260.000
148A151ARG10.7920.9004.30329.55429.720-0.001-0.013-0.1510.000
149A152ASN00.0170.0065.193-0.935-0.899-0.0010.000-0.0350.000
150A153LEU0-0.0360.0136.4693.6043.6040.0000.0000.0000.000
151A154ASN00.021-0.0026.570-4.274-4.2740.0000.0000.0000.000
152A155ILE00.009-0.0105.4150.3610.3610.0000.0000.0000.000
153A156ALA0-0.0110.0148.5770.9600.9600.0000.0000.0000.000
154A157PRO00.0040.00112.445-0.162-0.1620.0000.0000.0000.000
155A158ALA00.0480.00814.2820.4740.4740.0000.0000.0000.000
156A159GLU-1-0.932-0.97616.343-13.194-13.1940.0000.0000.0000.000
157A160ASP-1-0.848-0.90817.272-14.495-14.4950.0000.0000.0000.000
158A161GLY0-0.030-0.02017.886-0.006-0.0060.0000.0000.0000.000
159A162TYR0-0.0010.01318.7620.3920.3920.0000.0000.0000.000
160A163ARG10.9130.94820.72113.60213.6020.0000.0000.0000.000
161A164LEU0-0.106-0.05618.8100.2160.2160.0000.0000.0000.000
162A165ALA0-0.0110.00321.328-0.188-0.1880.0000.0000.0000.000
163A166GLY00.0140.00622.343-0.095-0.0950.0000.0000.0000.000
164A167PHE00.0160.01123.7520.1420.1420.0000.0000.0000.000
165A168PRO00.0540.03627.2560.0820.0820.0000.0000.0000.000
166A169PRO00.0650.01130.8520.0010.0010.0000.0000.0000.000
167A170ASP-1-0.935-0.95333.386-8.362-8.3620.0000.0000.0000.000
168A171HIS00.0040.01628.1480.2170.2170.0000.0000.0000.000
169A172GLN0-0.007-0.00630.9520.0350.0350.0000.0000.0000.000
170A173ALA00.0930.05627.1080.0370.0370.0000.0000.0000.000
171A174TRP0-0.059-0.04125.744-0.175-0.1750.0000.0000.0000.000
172A175ARG10.7640.85830.4568.6828.6820.0000.0000.0000.000
173A176GLU-1-0.827-0.89528.969-9.297-9.2970.0000.0000.0000.000
174A177GLU-1-0.862-0.89728.109-9.749-9.7490.0000.0000.0000.000
175A178PRO0-0.010-0.02222.809-0.004-0.0040.0000.0000.0000.000
176A179TRP0-0.059-0.05922.2340.1220.1220.0000.0000.0000.000
177A180ILE0-0.0030.01326.4540.0210.0210.0000.0000.0000.000
178A181HIS0-0.088-0.05227.6450.2320.2320.0000.0000.0000.000
179A182HIS0-0.062-0.03223.418-0.185-0.1850.0000.0000.0000.000
180A183ALA00.0070.00527.130-0.256-0.2560.0000.0000.0000.000
181A184PRO00.0010.00427.4580.1830.1830.0000.0000.0000.000
182A185GLN0-0.011-0.01030.1320.1480.1480.0000.0000.0000.000
183A186GLY0-0.002-0.00333.9450.0470.0470.0000.0000.0000.000
184A187CYS0-0.0580.00231.2890.0220.0220.0000.0000.0000.000
185A188GLY0-0.019-0.01032.9540.2590.2590.0000.0000.0000.000