Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MNR5Z

Calculation Name: 1RC2-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-o-octyl-beta-d-glucopyranose

ligand 3-letter code: BGL

PDB ID: 1RC2

Chain ID: A

ChEMBL ID:

UniProt ID: P60844

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2530749.220768
FMO2-HF: Nuclear repulsion 2449150.813301
FMO2-HF: Total energy -81598.407467
FMO2-MP2: Total energy -81841.278605


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-18.986-13.26814.712-6.705-13.722-0.037
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.012
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].
3A3ARG10.9990.9973.665-4.079-2.1420.005-0.819-1.1230.004
4A4LYS10.9410.9722.296-5.875-4.0435.151-2.122-4.8610.012
5A5LEU00.0440.0223.011-2.508-0.7720.342-0.447-1.630-0.001
6A6ALA00.0220.0155.659-0.325-0.3250.0000.0000.0000.000
7A7ALA0-0.023-0.0117.428-0.254-0.2540.0000.0000.0000.000
8A8GLU-1-0.699-0.8117.1130.7940.7940.0000.0000.0000.000
9A9CYS0-0.0460.0069.539-0.271-0.2710.0000.0000.0000.000
10A10PHE00.029-0.01211.334-0.109-0.1090.0000.0000.0000.000
11A11GLY00.0340.01012.616-0.094-0.0940.0000.0000.0000.000
12A12THR0-0.015-0.02812.710-0.099-0.0990.0000.0000.0000.000
13A13PHE0-0.0190.01915.391-0.069-0.0690.0000.0000.0000.000
14A14TRP0-0.0080.00217.182-0.052-0.0520.0000.0000.0000.000
15A15LEU0-0.007-0.00617.858-0.048-0.0480.0000.0000.0000.000
16A16VAL0-0.012-0.00319.106-0.038-0.0380.0000.0000.0000.000
17A17PHE00.011-0.00221.193-0.026-0.0260.0000.0000.0000.000
18A18GLY0-0.007-0.01022.650-0.019-0.0190.0000.0000.0000.000
19A19GLY0-0.005-0.02723.566-0.021-0.0210.0000.0000.0000.000
20A20CYS0-0.043-0.02424.739-0.016-0.0160.0000.0000.0000.000
21A21GLY00.0790.05126.124-0.016-0.0160.0000.0000.0000.000
22A22SER00.013-0.00127.998-0.017-0.0170.0000.0000.0000.000
23A23ALA0-0.021-0.01729.654-0.012-0.0120.0000.0000.0000.000
24A24VAL0-0.025-0.02329.816-0.010-0.0100.0000.0000.0000.000
25A25LEU0-0.050-0.01030.349-0.006-0.0060.0000.0000.0000.000
26A26ALA00.0290.00533.516-0.006-0.0060.0000.0000.0000.000
27A27ALA0-0.0410.00833.926-0.004-0.0040.0000.0000.0000.000
28A28GLY0-0.0050.00135.674-0.005-0.0050.0000.0000.0000.000
29A29PHE0-0.009-0.02739.0490.0020.0020.0000.0000.0000.000
30A30PRO0-0.039-0.01141.524-0.001-0.0010.0000.0000.0000.000
31A31GLU-1-0.865-0.93644.9730.0720.0720.0000.0000.0000.000
32A32LEU0-0.027-0.01641.9550.0010.0010.0000.0000.0000.000
33A33GLY0-0.0360.00439.0530.0060.0060.0000.0000.0000.000
34A34ILE0-0.024-0.01332.7860.0010.0010.0000.0000.0000.000
35A35GLY00.0230.01836.8210.0000.0000.0000.0000.0000.000
36A36PHE00.042-0.01234.2800.0070.0070.0000.0000.0000.000
37A37ALA00.0190.01233.2820.0080.0080.0000.0000.0000.000
38A38GLY00.0560.02632.9790.0100.0100.0000.0000.0000.000
39A39VAL00.0180.02129.3190.0130.0130.0000.0000.0000.000
40A40ALA0-0.027-0.02128.8400.0160.0160.0000.0000.0000.000
41A41LEU00.0030.00828.3440.0140.0140.0000.0000.0000.000
42A42ALA00.0410.02127.4180.0190.0190.0000.0000.0000.000
43A43PHE00.0220.00223.1070.0260.0260.0000.0000.0000.000
44A44GLY0-0.0040.01423.1200.0270.0270.0000.0000.0000.000
45A45LEU00.0140.00223.3850.0280.0280.0000.0000.0000.000
46A46THR0-0.079-0.01020.5790.0400.0400.0000.0000.0000.000
47A47VAL00.0280.00117.9380.0520.0520.0000.0000.0000.000
48A48LEU00.0360.02918.6530.0470.0470.0000.0000.0000.000
49A49THR0-0.016-0.02320.0350.0370.0370.0000.0000.0000.000
50A50MET00.0200.03014.6880.0760.0760.0000.0000.0000.000
51A51ALA0-0.024-0.01415.1890.1150.1150.0000.0000.0000.000
52A52PHE0-0.010-0.01515.7580.0450.0450.0000.0000.0000.000
53A53ALA0-0.030-0.00116.0120.0370.0370.0000.0000.0000.000
54A54VAL0-0.022-0.02910.7210.1110.1110.0000.0000.0000.000
55A55GLY00.0480.03010.6640.2410.2410.0000.0000.0000.000
56A56HIS0-0.053-0.02111.5600.1160.1160.0000.0000.0000.000
57A57ILE0-0.035-0.0036.5390.2260.2260.0000.0000.0000.000
58A58SER0-0.090-0.0916.2820.4050.4050.0000.0000.0000.000
59A59GLY00.0210.0177.151-0.271-0.2710.0000.0000.0000.000
60A60GLY0-0.037-0.0289.880-0.177-0.1770.0000.0000.0000.000
61A61HIS10.8010.9028.459-0.719-0.7190.0000.0000.0000.000
62A62PHE0-0.0060.00711.703-0.080-0.0800.0000.0000.0000.000
63A63ASN00.033-0.00713.041-0.100-0.1000.0000.0000.0000.000
64A64PRO00.0370.03112.8970.0040.0040.0000.0000.0000.000
65A65ALA00.0410.00913.970-0.035-0.0350.0000.0000.0000.000
66A66VAL0-0.0040.00813.188-0.031-0.0310.0000.0000.0000.000
67A67THR0-0.0110.0028.5890.0500.0500.0000.0000.0000.000
68A68ILE00.0040.00811.200-0.077-0.0770.0000.0000.0000.000
69A69GLY00.0600.02613.379-0.049-0.0490.0000.0000.0000.000
70A70LEU00.014-0.00511.491-0.024-0.0240.0000.0000.0000.000
71A71TRP0-0.067-0.01111.115-0.027-0.0270.0000.0000.0000.000
72A72ALA00.0230.01512.459-0.033-0.0330.0000.0000.0000.000
73A73GLY00.0500.03515.599-0.010-0.0100.0000.0000.0000.000
74A74GLY0-0.093-0.05114.4320.0030.0030.0000.0000.0000.000
75A75ARG10.8330.91712.455-0.108-0.1080.0000.0000.0000.000
76A76PHE0-0.007-0.0084.482-0.155-0.063-0.001-0.005-0.0850.000
77A77PRO00.0590.0155.8890.0700.0700.0000.0000.0000.000
78A78ALA00.0800.0237.2950.0130.0130.0000.0000.0000.000
79A79LYS10.9210.9724.4772.2952.381-0.001-0.006-0.0790.000
80A80GLU-1-0.887-0.9602.065-7.530-8.6178.773-3.025-4.661-0.050
81A81VAL00.0090.0094.6400.8331.009-0.001-0.009-0.1650.000
82A82VAL00.0480.0227.9710.2140.2140.0000.0000.0000.000
83A83GLY00.0410.0235.254-0.165-0.106-0.001-0.010-0.0480.000
84A84TYR0-0.034-0.0373.130-0.8560.0310.445-0.262-1.070-0.002
85A85VAL00.0080.0047.079-0.151-0.1510.0000.0000.0000.000
86A86ILE00.0290.0219.273-0.033-0.0330.0000.0000.0000.000
87A87ALA0-0.008-0.0037.363-0.053-0.0530.0000.0000.0000.000
88A88GLN0-0.023-0.0319.415-0.117-0.1170.0000.0000.0000.000
89A89VAL00.0180.00912.160-0.042-0.0420.0000.0000.0000.000
90A90VAL0-0.018-0.00211.688-0.020-0.0200.0000.0000.0000.000
91A91GLY00.014-0.00213.425-0.013-0.0130.0000.0000.0000.000
92A92GLY00.0290.00814.925-0.012-0.0120.0000.0000.0000.000
93A93ILE00.0320.00917.736-0.015-0.0150.0000.0000.0000.000
94A94VAL00.0150.01016.500-0.014-0.0140.0000.0000.0000.000
95A95ALA00.0030.00619.322-0.010-0.0100.0000.0000.0000.000
96A96ALA0-0.011-0.00921.157-0.013-0.0130.0000.0000.0000.000
97A97ALA00.0060.00722.644-0.015-0.0150.0000.0000.0000.000
98A98LEU0-0.027-0.02821.804-0.008-0.0080.0000.0000.0000.000
99A99LEU0-0.0230.00425.159-0.005-0.0050.0000.0000.0000.000
100A100TYR00.0120.00826.998-0.009-0.0090.0000.0000.0000.000
101A101LEU0-0.015-0.00928.160-0.008-0.0080.0000.0000.0000.000
102A102ILE0-0.016-0.01227.814-0.005-0.0050.0000.0000.0000.000
103A103ALA0-0.0070.00131.084-0.006-0.0060.0000.0000.0000.000
104A104SER0-0.040-0.02732.677-0.008-0.0080.0000.0000.0000.000
105A105GLY0-0.0280.00734.591-0.006-0.0060.0000.0000.0000.000
106A106LYS10.9280.96636.246-0.082-0.0820.0000.0000.0000.000
107A107THR0-0.025-0.04538.780-0.003-0.0030.0000.0000.0000.000
108A108GLY0-0.0020.01241.4570.0000.0000.0000.0000.0000.000
109A109PHE0-0.037-0.00232.1230.0020.0020.0000.0000.0000.000
110A110ASP-1-0.850-0.93537.0560.0460.0460.0000.0000.0000.000
111A111ALA0-0.0300.00031.9100.0040.0040.0000.0000.0000.000
112A112ALA00.0690.02133.8150.0030.0030.0000.0000.0000.000
113A113ALA00.0010.02535.6120.0020.0020.0000.0000.0000.000
114A114SER0-0.050-0.03535.4800.0040.0040.0000.0000.0000.000
115A115GLY00.0280.01233.7480.0020.0020.0000.0000.0000.000
116A116PHE0-0.0180.01826.9780.0050.0050.0000.0000.0000.000
117A117ALA00.0100.00328.6790.0090.0090.0000.0000.0000.000
118A118SER00.001-0.02528.0580.0110.0110.0000.0000.0000.000
119A119ASN0-0.065-0.02625.7650.0090.0090.0000.0000.0000.000
120A120GLY00.0350.00628.987-0.006-0.0060.0000.0000.0000.000
121A121TYR00.0200.01130.9880.0030.0030.0000.0000.0000.000
122A122GLY00.0500.00434.1430.0000.0000.0000.0000.0000.000
123A123GLU-1-0.915-0.93037.6260.0250.0250.0000.0000.0000.000
124A124HIS10.8090.90934.807-0.038-0.0380.0000.0000.0000.000
125A125SER00.0010.01134.5990.0040.0040.0000.0000.0000.000
126A126PRO0-0.024-0.01434.404-0.004-0.0040.0000.0000.0000.000
127A127GLY0-0.012-0.00137.433-0.003-0.0030.0000.0000.0000.000
128A128GLY00.0230.01538.785-0.003-0.0030.0000.0000.0000.000
129A129TYR0-0.035-0.01237.106-0.003-0.0030.0000.0000.0000.000
130A130SER00.0790.03138.1310.0000.0000.0000.0000.0000.000
131A131MET00.040-0.00333.1420.0040.0040.0000.0000.0000.000
132A132LEU00.0220.01634.2720.0010.0010.0000.0000.0000.000
133A133SER00.0200.00434.9290.0020.0020.0000.0000.0000.000
134A134ALA00.006-0.00831.7410.0050.0050.0000.0000.0000.000
135A135LEU00.0100.00329.5770.0060.0060.0000.0000.0000.000
136A136VAL00.0200.01730.2590.0020.0020.0000.0000.0000.000
137A137VAL0-0.0080.00330.7020.0040.0040.0000.0000.0000.000
138A138GLU-1-0.743-0.88825.7990.1090.1090.0000.0000.0000.000
139A139LEU0-0.0170.01825.9130.0070.0070.0000.0000.0000.000
140A140VAL00.020-0.00226.1600.0040.0040.0000.0000.0000.000
141A141LEU00.0090.00826.5670.0070.0070.0000.0000.0000.000
142A142SER00.001-0.01821.9890.0200.0200.0000.0000.0000.000
143A143ALA0-0.0080.00621.8070.0100.0100.0000.0000.0000.000
144A144GLY00.011-0.00523.1080.0030.0030.0000.0000.0000.000
145A145PHE0-0.017-0.01618.5600.0130.0130.0000.0000.0000.000
146A146LEU0-0.027-0.00416.0750.0200.0200.0000.0000.0000.000
147A147LEU00.0140.04019.5350.0010.0010.0000.0000.0000.000
148A148VAL0-0.0070.00021.9630.0010.0010.0000.0000.0000.000
149A149ILE00.0120.00715.4910.0110.0110.0000.0000.0000.000
150A150HIS0-0.080-0.02116.602-0.005-0.0050.0000.0000.0000.000
151A151GLY00.0700.02818.629-0.003-0.0030.0000.0000.0000.000
152A152ALA0-0.028-0.01320.3600.0000.0000.0000.0000.0000.000
153A153THR0-0.065-0.07515.7080.0130.0130.0000.0000.0000.000
154A154ASP-1-0.824-0.87917.4850.0760.0760.0000.0000.0000.000
155A155LYS10.9010.95419.424-0.016-0.0160.0000.0000.0000.000
156A156PHE0-0.007-0.01720.5600.0000.0000.0000.0000.0000.000
157A157ALA0-0.0230.01722.051-0.004-0.0040.0000.0000.0000.000
158A158PRO0-0.008-0.01623.4950.0080.0080.0000.0000.0000.000
159A159ALA00.0410.01721.4460.0180.0180.0000.0000.0000.000
160A160GLY00.003-0.00220.6240.0000.0000.0000.0000.0000.000
161A161PHE00.0290.00221.5760.0190.0190.0000.0000.0000.000
162A162ALA00.0180.01518.398-0.004-0.0040.0000.0000.0000.000
163A163PRO00.0020.00418.128-0.012-0.0120.0000.0000.0000.000
164A164ILE00.0300.01620.129-0.010-0.0100.0000.0000.0000.000
165A165ALA00.0100.00722.582-0.016-0.0160.0000.0000.0000.000
166A166ILE0-0.002-0.01317.115-0.016-0.0160.0000.0000.0000.000
167A167GLY00.0160.00321.144-0.007-0.0070.0000.0000.0000.000
168A168LEU00.0270.00622.458-0.017-0.0170.0000.0000.0000.000
169A169ALA0-0.0010.00723.226-0.019-0.0190.0000.0000.0000.000
170A170LEU0-0.018-0.00621.200-0.016-0.0160.0000.0000.0000.000
171A171THR00.0060.00324.405-0.008-0.0080.0000.0000.0000.000
172A172LEU00.0260.00927.722-0.012-0.0120.0000.0000.0000.000
173A173ILE00.0160.00324.154-0.011-0.0110.0000.0000.0000.000
174A174HIS10.8440.92724.569-0.181-0.1810.0000.0000.0000.000
175A175LEU0-0.013-0.00329.447-0.007-0.0070.0000.0000.0000.000
176A176ILE0-0.034-0.00130.985-0.008-0.0080.0000.0000.0000.000
177A177SER00.0320.02329.373-0.005-0.0050.0000.0000.0000.000
178A178ILE0-0.0250.01730.744-0.004-0.0040.0000.0000.0000.000
179A179PRO00.0310.00232.501-0.004-0.0040.0000.0000.0000.000
180A180VAL00.0030.01133.365-0.005-0.0050.0000.0000.0000.000
181A181THR00.0120.01029.217-0.002-0.0020.0000.0000.0000.000
182A182ASN0-0.011-0.00330.0800.0010.0010.0000.0000.0000.000
183A183THR0-0.037-0.03826.2900.0110.0110.0000.0000.0000.000
184A184SER0-0.015-0.01423.6490.0120.0120.0000.0000.0000.000
185A185VAL0-0.062-0.02521.6790.0210.0210.0000.0000.0000.000
186A186ASN00.0230.00017.1900.0190.0190.0000.0000.0000.000
187A187PRO00.0410.03017.6420.0010.0010.0000.0000.0000.000
188A188ALA00.005-0.01215.476-0.015-0.0150.0000.0000.0000.000
189A189ARG10.8350.90817.630-0.156-0.1560.0000.0000.0000.000
190A190SER0-0.006-0.01020.491-0.010-0.0100.0000.0000.0000.000
191A191THR0-0.016-0.00518.857-0.016-0.0160.0000.0000.0000.000
192A192ALA0-0.033-0.00420.025-0.013-0.0130.0000.0000.0000.000
193A193VAL00.0130.01021.787-0.006-0.0060.0000.0000.0000.000
194A194ALA00.0280.00125.122-0.011-0.0110.0000.0000.0000.000
195A195ILE0-0.022-0.01721.502-0.010-0.0100.0000.0000.0000.000
196A196PHE0-0.013-0.01023.080-0.008-0.0080.0000.0000.0000.000
197A197GLN0-0.0020.02128.025-0.003-0.0030.0000.0000.0000.000
198A198GLY00.0060.01129.723-0.005-0.0050.0000.0000.0000.000
199A199GLY00.023-0.00531.459-0.002-0.0020.0000.0000.0000.000
200A200TRP00.033-0.00332.308-0.002-0.0020.0000.0000.0000.000
201A201ALA00.0370.02828.8160.0000.0000.0000.0000.0000.000
202A202LEU0-0.031-0.03326.4570.0030.0030.0000.0000.0000.000
203A203GLU-1-0.964-0.94628.7970.0180.0180.0000.0000.0000.000
204A204GLN00.0330.00130.1300.0010.0010.0000.0000.0000.000
205A205LEU0-0.0410.00822.6700.0040.0040.0000.0000.0000.000
206A206TRP00.0430.01124.7140.0060.0060.0000.0000.0000.000
207A207PHE00.0310.01025.2450.0000.0000.0000.0000.0000.000
208A208PHE0-0.030-0.02124.3030.0020.0020.0000.0000.0000.000
209A209TRP00.009-0.01215.8990.0210.0210.0000.0000.0000.000
210A210VAL0-0.0110.00120.8610.0010.0010.0000.0000.0000.000
211A211VAL00.0310.02023.183-0.002-0.0020.0000.0000.0000.000
212A212PRO0-0.006-0.00321.0200.0000.0000.0000.0000.0000.000
213A213ILE0-0.007-0.00117.4610.0100.0100.0000.0000.0000.000
214A214VAL00.0040.00919.800-0.007-0.0070.0000.0000.0000.000
215A215GLY00.0530.02122.490-0.006-0.0060.0000.0000.0000.000
216A216GLY00.0310.00918.9870.0020.0020.0000.0000.0000.000
217A217ILE0-0.033-0.02417.735-0.003-0.0030.0000.0000.0000.000
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