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: 9YJ32

Calculation Name: 1LT4-A-Xray307

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: 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 229
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2904907.611712
FMO2-HF: Nuclear repulsion 2812604.633025
FMO2-HF: Total energy -92302.978687
FMO2-MP2: Total energy -92574.85902


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:3:ACE )


Summations of interaction energy for fragment #1(A:3:ACE )
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.
0.8151.7540.018-0.394-0.5630
Interaction energy analysis for fragmet #1(A:3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.021
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].
3A5LEU 00.0470.0493.8930.9321.615-0.005-0.316-0.3620.000
4A6TYR 0-0.022-0.0126.380-0.129-0.1290.0000.0000.0000.000
5A7ARG 10.8150.89010.3610.3040.3040.0000.0000.0000.000
6A8ALA 0-0.0340.00413.884-0.016-0.0160.0000.0000.0000.000
7A9ASP -1-0.770-0.90617.297-0.177-0.1770.0000.0000.0000.000
8A10SER 00.0420.01619.818-0.007-0.0070.0000.0000.0000.000
9A11ARG 10.8620.96120.4290.1700.1700.0000.0000.0000.000
10A12PRO 00.0350.04321.317-0.027-0.0270.0000.0000.0000.000
11A13PRO 00.024-0.00119.7940.0010.0010.0000.0000.0000.000
12A14ASP -1-0.872-0.94221.397-0.144-0.1440.0000.0000.0000.000
13A15GLU -1-0.898-0.94524.360-0.123-0.1230.0000.0000.0000.000
14A16ILE 0-0.020-0.01318.235-0.001-0.0010.0000.0000.0000.000
15A17LYS 10.8910.94921.5880.1730.1730.0000.0000.0000.000
16A18ARG 10.8850.94422.6580.1240.1240.0000.0000.0000.000
17A19SER 00.0250.03123.0400.0110.0110.0000.0000.0000.000
18A20GLY 00.0010.00922.0550.0040.0040.0000.0000.0000.000
19A21GLY 00.003-0.02418.435-0.023-0.0230.0000.0000.0000.000
20A22LEU 0-0.069-0.02114.7430.0200.0200.0000.0000.0000.000
21A23MET 0-0.0090.02318.349-0.005-0.0050.0000.0000.0000.000
22A24PRO 00.0530.00620.058-0.004-0.0040.0000.0000.0000.000
23A25ARG 10.9050.95022.0100.0730.0730.0000.0000.0000.000
24A26GLY 0-0.014-0.00325.3880.0060.0060.0000.0000.0000.000
25A27HIS 0-0.0080.01623.2800.0080.0080.0000.0000.0000.000
26A28ASN 0-0.015-0.01925.352-0.011-0.0110.0000.0000.0000.000
27A29GLU -1-0.893-0.94825.483-0.110-0.1100.0000.0000.0000.000
28A30TYR 00.027-0.00117.9030.0030.0030.0000.0000.0000.000
29A31PHE 0-0.081-0.07621.8080.0050.0050.0000.0000.0000.000
30A32ASP -1-0.842-0.91225.539-0.071-0.0710.0000.0000.0000.000
31A33ARG 10.8250.88425.0190.0870.0870.0000.0000.0000.000
32A34GLY 00.0090.01829.9320.0050.0050.0000.0000.0000.000
33A35THR 00.0030.01930.5060.0070.0070.0000.0000.0000.000
34A36GLN 0-0.018-0.01526.252-0.008-0.0080.0000.0000.0000.000
35A37MET 00.0050.01122.5090.0000.0000.0000.0000.0000.000
36A38ASN 00.0040.01327.7970.0050.0050.0000.0000.0000.000
37A39ILE 0-0.085-0.05822.067-0.009-0.0090.0000.0000.0000.000
38A40ASN 00.0790.03223.8040.0090.0090.0000.0000.0000.000
39A41LEU 00.0180.01717.706-0.006-0.0060.0000.0000.0000.000
40A42TYR 00.0250.00921.551-0.001-0.0010.0000.0000.0000.000
41A43ASP -1-0.921-0.95623.917-0.026-0.0260.0000.0000.0000.000
42A44HIS 0-0.037-0.01018.569-0.006-0.0060.0000.0000.0000.000
43A45ALA 0-0.007-0.02020.085-0.004-0.0040.0000.0000.0000.000
44A46ARG 10.8650.93621.3890.0220.0220.0000.0000.0000.000
45A47GLY 00.0270.02024.8360.0020.0020.0000.0000.0000.000
46A48THR 0-0.029-0.01424.059-0.006-0.0060.0000.0000.0000.000
47A49GLN 00.026-0.00324.013-0.006-0.0060.0000.0000.0000.000
48A50THR 00.0180.02025.9900.0020.0020.0000.0000.0000.000
49A51GLY 00.003-0.00226.817-0.001-0.0010.0000.0000.0000.000
50A52PHE 0-0.014-0.01522.563-0.010-0.0100.0000.0000.0000.000
51A53VAL 00.0250.02316.9960.0110.0110.0000.0000.0000.000
52A54ARG 10.8700.94519.2200.0400.0400.0000.0000.0000.000
53A55TYR 0-0.048-0.03618.915-0.020-0.0200.0000.0000.0000.000
54A56ASP -1-0.788-0.87520.893-0.073-0.0730.0000.0000.0000.000
55A57ASP -1-0.817-0.90722.662-0.054-0.0540.0000.0000.0000.000
56A58GLY 00.0570.01422.6350.0010.0010.0000.0000.0000.000
57A59TYR 00.0130.00616.756-0.013-0.0130.0000.0000.0000.000
58A60VAL 0-0.045-0.01115.5150.0040.0040.0000.0000.0000.000
59A61SER 0-0.014-0.00114.900-0.033-0.0330.0000.0000.0000.000
60A62THR 0-0.057-0.02810.253-0.078-0.0780.0000.0000.0000.000
61A63LYS 10.9280.95911.1710.1190.1190.0000.0000.0000.000
62A64LEU 00.1100.0436.664-0.158-0.1580.0000.0000.0000.000
63A65SER 0-0.011-0.0067.1470.0570.0570.0000.0000.0000.000
64A66LEU 00.0530.0329.180-0.027-0.0270.0000.0000.0000.000
65A67ARG 10.9630.97911.4310.0930.0930.0000.0000.0000.000
66A68SER 00.0450.02512.7910.0170.0170.0000.0000.0000.000
67A69ALA 00.0010.01012.6440.0020.0020.0000.0000.0000.000
68A70HIS 0-0.025-0.03214.4550.0170.0170.0000.0000.0000.000
69A71LEU 0-0.006-0.00617.0790.0080.0080.0000.0000.0000.000
70A72ALA 00.0050.00517.6880.0080.0080.0000.0000.0000.000
71A73GLY 00.0320.00618.7980.0020.0020.0000.0000.0000.000
72A74GLN 00.0280.02820.436-0.001-0.0010.0000.0000.0000.000
73A75SER 0-0.029-0.00522.7280.0070.0070.0000.0000.0000.000
74A76ILE 0-0.026-0.01421.3350.0030.0030.0000.0000.0000.000
75A77LEU 0-0.061-0.03921.3550.0000.0000.0000.0000.0000.000
76A78SER 00.0050.00225.136-0.002-0.0020.0000.0000.0000.000
77A79GLY 0-0.0040.01427.1870.0020.0020.0000.0000.0000.000
78A80TYR 0-0.0180.00226.1850.0000.0000.0000.0000.0000.000
79A81SER 00.001-0.00727.356-0.001-0.0010.0000.0000.0000.000
80A82THR 0-0.036-0.01924.2910.0000.0000.0000.0000.0000.000
81A83TYR 0-0.007-0.00719.496-0.004-0.0040.0000.0000.0000.000
82A84TYR 00.0060.00318.2260.0010.0010.0000.0000.0000.000
83A85ILE 00.0280.02013.0140.0070.0070.0000.0000.0000.000
84A86TYR 0-0.058-0.06713.549-0.039-0.0390.0000.0000.0000.000
85A87VAL 0-0.009-0.0027.883-0.037-0.0370.0000.0000.0000.000
86A88ILE 0-0.016-0.0248.5450.0270.0270.0000.0000.0000.000
87A89ALA 00.0000.0075.750-0.723-0.7230.0000.0000.0000.000
88A90THR 00.0100.0123.4570.0020.2580.023-0.078-0.2010.000
89A91ALA 00.000-0.0155.9120.0990.0990.0000.0000.0000.000
90A92PRO 00.0520.0289.2950.0170.0170.0000.0000.0000.000
91A93ASN 00.0550.04112.0470.0010.0010.0000.0000.0000.000
92A94MET 0-0.074-0.0228.7940.0160.0160.0000.0000.0000.000
93A95PHE 00.0980.04711.5360.0430.0430.0000.0000.0000.000
94A96ASN 00.0240.00210.603-0.064-0.0640.0000.0000.0000.000
95A97VAL 00.0350.00612.5170.0100.0100.0000.0000.0000.000
96A98ASN 0-0.007-0.01015.102-0.019-0.0190.0000.0000.0000.000
97A99ASP -1-0.917-0.94913.2520.1980.1980.0000.0000.0000.000
98A100VAL 0-0.035-0.01216.078-0.005-0.0050.0000.0000.0000.000
99A101LEU 00.0110.01418.505-0.005-0.0050.0000.0000.0000.000
100A102GLY 00.0790.05019.806-0.001-0.0010.0000.0000.0000.000
101A103VAL 0-0.028-0.03121.258-0.003-0.0030.0000.0000.0000.000
102A104TYR 0-0.032-0.00523.752-0.007-0.0070.0000.0000.0000.000
103A105SER 0-0.037-0.02118.849-0.015-0.0150.0000.0000.0000.000
104A106PRO 00.0370.00921.9020.0030.0030.0000.0000.0000.000
105A107HIS 10.8180.92620.5900.0140.0140.0000.0000.0000.000
106A108PRO 00.0630.03419.152-0.002-0.0020.0000.0000.0000.000
107A109TYR 00.0380.00417.8560.0160.0160.0000.0000.0000.000
108A110GLU -1-0.954-0.98617.274-0.018-0.0180.0000.0000.0000.000
109A111GLN 0-0.067-0.02912.8040.0240.0240.0000.0000.0000.000
110A112GLU -1-0.872-0.93112.316-0.068-0.0680.0000.0000.0000.000
111A113VAL 00.0050.0048.4680.0360.0360.0000.0000.0000.000
112A114SER 0-0.019-0.01811.493-0.071-0.0710.0000.0000.0000.000
113A115ALA 0-0.002-0.00513.0130.0060.0060.0000.0000.0000.000
114A116LEU 00.0000.01314.2620.0100.0100.0000.0000.0000.000
115A117GLY 0-0.002-0.02217.555-0.010-0.0100.0000.0000.0000.000
116A118GLY 0-0.0100.00017.7670.0020.0020.0000.0000.0000.000
117A119ILE 0-0.080-0.03612.469-0.024-0.0240.0000.0000.0000.000
118A120PRO 00.0450.03314.5080.0130.0130.0000.0000.0000.000
119A121TYR 00.039-0.00715.364-0.062-0.0620.0000.0000.0000.000
120A122SER 0-0.014-0.00515.766-0.044-0.0440.0000.0000.0000.000
121A123GLN 0-0.002-0.0059.3500.0700.0700.0000.0000.0000.000
122A124ILE 0-0.024-0.00510.469-0.208-0.2080.0000.0000.0000.000
123A125TYR 00.002-0.0028.9530.0860.0860.0000.0000.0000.000
124A126GLY 00.0350.00411.0720.1210.1210.0000.0000.0000.000
125A127TRP 00.0110.01013.123-0.056-0.0560.0000.0000.0000.000
126A128TYR 00.0370.03411.619-0.016-0.0160.0000.0000.0000.000
127A129ARG 10.9470.97116.8390.1360.1360.0000.0000.0000.000
128A130VAL 0-0.0110.00719.1610.0020.0020.0000.0000.0000.000
129A131ASN 00.005-0.01321.6770.0040.0040.0000.0000.0000.000
130A132PHE 00.0430.00525.3760.0050.0050.0000.0000.0000.000
131A133GLY 00.0210.01723.8960.0060.0060.0000.0000.0000.000
132A134VAL 0-0.0060.00322.861-0.001-0.0010.0000.0000.0000.000
133A135ILE 0-0.053-0.03416.118-0.009-0.0090.0000.0000.0000.000
134A136ASP -1-0.851-0.90920.032-0.125-0.1250.0000.0000.0000.000
135A137GLU -1-0.952-0.98617.307-0.127-0.1270.0000.0000.0000.000
136A138ARG 10.8830.95017.1220.1360.1360.0000.0000.0000.000
137A139LEU 0-0.075-0.03411.485-0.015-0.0150.0000.0000.0000.000
138A140HIS 0-0.055-0.02715.6310.0410.0410.0000.0000.0000.000
139A141ARG 10.9780.97213.3130.2710.2710.0000.0000.0000.000
140A142ASN 0-0.0190.00114.7950.1020.1020.0000.0000.0000.000
141A143ARG 10.9420.95715.9970.1550.1550.0000.0000.0000.000
142A144GLU -1-0.889-0.95618.161-0.186-0.1860.0000.0000.0000.000
143A145TYR 0-0.0190.0248.369-0.124-0.1240.0000.0000.0000.000
144A146ARG 10.8230.90113.6710.2590.2590.0000.0000.0000.000
145A147ASP -1-0.810-0.92110.564-0.459-0.4590.0000.0000.0000.000
146A148ARG 10.9500.96011.2050.1200.1200.0000.0000.0000.000
147A149TYR 0-0.021-0.00312.6980.0360.0360.0000.0000.0000.000
148A150TYR 00.047-0.0028.6160.0340.0340.0000.0000.0000.000
149A151ARG 10.8250.9397.6520.1070.1070.0000.0000.0000.000
150A152ASN 00.003-0.0057.0460.0020.0020.0000.0000.0000.000
151A153LEU 0-0.062-0.0068.0270.1170.1170.0000.0000.0000.000
152A154ASN 00.039-0.0085.5040.0330.0330.0000.0000.0000.000
153A155ILE 0-0.023-0.0026.069-0.137-0.1370.0000.0000.0000.000
154A156ALA 0-0.0010.0118.5580.0580.0580.0000.0000.0000.000
155A157PRO 00.0030.00712.3020.0270.0270.0000.0000.0000.000
156A158ALA 00.0530.00113.675-0.031-0.0310.0000.0000.0000.000
157A159GLU -1-0.914-0.95616.1120.0810.0810.0000.0000.0000.000
158A160ASP -1-0.951-0.96016.9140.0260.0260.0000.0000.0000.000
159A161GLY 0-0.055-0.04718.056-0.018-0.0180.0000.0000.0000.000
160A162TYR 00.0130.02218.890-0.007-0.0070.0000.0000.0000.000
161A163ARG 11.0071.00221.185-0.001-0.0010.0000.0000.0000.000
162A164LEU 0-0.097-0.04919.727-0.007-0.0070.0000.0000.0000.000
163A165ALA 0-0.0150.00021.896-0.007-0.0070.0000.0000.0000.000
164A166GLY 00.027-0.00122.886-0.004-0.0040.0000.0000.0000.000
165A167PHE 0-0.0120.00424.396-0.002-0.0020.0000.0000.0000.000
166A168PRO 00.0720.04327.992-0.002-0.0020.0000.0000.0000.000
167A169PRO 00.0870.02031.6700.0040.0040.0000.0000.0000.000
168A170ASP -1-0.968-0.96734.1840.0040.0040.0000.0000.0000.000
169A171HIS 00.0200.01228.809-0.001-0.0010.0000.0000.0000.000
170A172GLN 00.0520.03131.427-0.001-0.0010.0000.0000.0000.000
171A173ALA 00.0670.03827.3850.0020.0020.0000.0000.0000.000
172A174TRP 0-0.054-0.02426.2990.0040.0040.0000.0000.0000.000
173A175ARG 10.7700.87030.862-0.014-0.0140.0000.0000.0000.000
174A176GLU -1-0.899-0.95329.0400.0380.0380.0000.0000.0000.000
175A177GLU -1-0.928-0.92727.5950.0530.0530.0000.0000.0000.000
176A178PRO 00.013-0.01222.8180.0010.0010.0000.0000.0000.000
177A179TRP 0-0.035-0.03922.601-0.002-0.0020.0000.0000.0000.000
178A180ILE 0-0.005-0.00326.514-0.005-0.0050.0000.0000.0000.000
179A181HIS 0-0.045-0.01927.468-0.007-0.0070.0000.0000.0000.000
180A182HIS 0-0.080-0.04524.1650.0000.0000.0000.0000.0000.000
181A183ALA 0-0.0020.00327.225-0.005-0.0050.0000.0000.0000.000
182A184PRO 00.0010.00727.954-0.001-0.0010.0000.0000.0000.000
183A185GLN 0-0.004-0.00730.4360.0030.0030.0000.0000.0000.000
184A186GLY 00.0200.00934.140-0.002-0.0020.0000.0000.0000.000
185A199CYS 0-0.0830.00631.629-0.003-0.0030.0000.0000.0000.000
186A188GLY 00.025-0.01333.5990.0020.0020.0000.0000.0000.000
187A189NME 0-0.045-0.00434.7000.0020.0020.0000.0000.0000.000
188A195ACE 00.0230.00039.8710.0000.0000.0000.0000.0000.000
189A196GLY 00.003-0.01438.9020.0000.0000.0000.0000.0000.000
190A197ASP -1-0.900-0.95236.634-0.019-0.0190.0000.0000.0000.000
191A198THR 00.0470.02035.432-0.001-0.0010.0000.0000.0000.000
192A200ASN 00.007-0.01731.330-0.003-0.0030.0000.0000.0000.000
193A201GLU -1-0.964-0.99030.988-0.024-0.0240.0000.0000.0000.000
194A202GLU -1-0.853-0.93531.151-0.015-0.0150.0000.0000.0000.000
195A203THR 0-0.031-0.00225.808-0.001-0.0010.0000.0000.0000.000
196A204GLN 00.0310.02926.672-0.005-0.0050.0000.0000.0000.000
197A205ASN 0-0.020-0.00527.619-0.010-0.0100.0000.0000.0000.000
198A206LEU 00.0260.00525.603-0.004-0.0040.0000.0000.0000.000
199A207SER 0-0.006-0.01322.986-0.005-0.0050.0000.0000.0000.000
200A208THR 0-0.062-0.03923.063-0.014-0.0140.0000.0000.0000.000
201A209ILE 00.0070.00824.912-0.008-0.0080.0000.0000.0000.000
202A210TYR 00.0150.00515.4340.0010.0010.0000.0000.0000.000
203A211LEU 0-0.026-0.00419.913-0.013-0.0130.0000.0000.0000.000
204A212ARG 10.8810.94421.2490.0570.0570.0000.0000.0000.000
205A213GLU -1-0.918-0.94921.820-0.047-0.0470.0000.0000.0000.000
206A214TYR 0-0.0010.00013.705-0.012-0.0120.0000.0000.0000.000
207A215GLN 00.0440.01519.060-0.003-0.0030.0000.0000.0000.000
208A216SER 00.0030.00921.085-0.005-0.0050.0000.0000.0000.000
209A217LYS 10.9100.95617.9710.0800.0800.0000.0000.0000.000
210A218VAL 00.0280.01816.872-0.008-0.0080.0000.0000.0000.000
211A219LYS 10.9510.98719.2130.0970.0970.0000.0000.0000.000
212A220ARG 10.9620.97921.5760.0770.0770.0000.0000.0000.000
213A221GLN 0-0.0630.00316.984-0.007-0.0070.0000.0000.0000.000
214A222ILE 0-0.008-0.02719.6130.0030.0030.0000.0000.0000.000
215A223PHE 00.009-0.00221.9510.0060.0060.0000.0000.0000.000
216A224SER 0-0.012-0.02523.7490.0130.0130.0000.0000.0000.000
217A225ASP -1-0.841-0.90222.761-0.145-0.1450.0000.0000.0000.000
218A226TYR 0-0.073-0.03725.6060.0020.0020.0000.0000.0000.000
219A227GLN 0-0.065-0.00628.6430.0040.0040.0000.0000.0000.000
220A228SER 0-0.022-0.01030.5920.0000.0000.0000.0000.0000.000
221A229GLU -1-0.895-0.95931.793-0.051-0.0510.0000.0000.0000.000
222A230VAL 0-0.031-0.01935.1940.0010.0010.0000.0000.0000.000
223A231ASP -1-0.875-0.92938.956-0.029-0.0290.0000.0000.0000.000
224A232ILE 0-0.015-0.03539.8420.0010.0010.0000.0000.0000.000
225A233TYR 00.0260.00043.2920.0010.0010.0000.0000.0000.000
226A234ASN 0-0.0140.00745.3610.0020.0020.0000.0000.0000.000
227A235ARG 10.9070.97140.9080.0360.0360.0000.0000.0000.000
228A236ILE 0-0.0320.00345.9620.0010.0010.0000.0000.0000.000
229A237NME 0-0.016-0.01448.6950.0000.0000.0000.0000.0000.000