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: 76Y9K

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2529670.962123
FMO2-HF: Nuclear repulsion 2448071.716818
FMO2-HF: Total energy -81599.245305
FMO2-MP2: Total energy -81842.008039


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.
-17.641-10.93311.05-4.828-12.928-0.011
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 : 0.009 / q_NPA : 0.000
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].
3A3ARG11.0050.9983.659-4.105-2.1980.004-0.797-1.1140.004
4A4LYS10.8790.9322.492-7.130-5.1694.199-1.690-4.4700.009
5A5LEU00.0390.0172.967-2.480-0.7800.678-0.519-1.859-0.001
6A6ALA00.0170.0145.638-0.513-0.419-0.001-0.009-0.0840.000
7A7ALA0-0.020-0.0117.399-0.290-0.2900.0000.0000.0000.000
8A8GLU-1-0.697-0.8086.9830.9700.9700.0000.0000.0000.000
9A9CYS0-0.069-0.0089.445-0.326-0.3260.0000.0000.0000.000
10A10PHE00.038-0.00811.266-0.131-0.1310.0000.0000.0000.000
11A11GLY00.0320.01712.595-0.111-0.1110.0000.0000.0000.000
12A12THR0-0.024-0.03412.588-0.118-0.1180.0000.0000.0000.000
13A13PHE0-0.0190.01515.236-0.081-0.0810.0000.0000.0000.000
14A14TRP0-0.016-0.00717.165-0.064-0.0640.0000.0000.0000.000
15A15LEU0-0.016-0.00817.748-0.054-0.0540.0000.0000.0000.000
16A16VAL0-0.002-0.00119.048-0.044-0.0440.0000.0000.0000.000
17A17PHE00.003-0.00421.030-0.031-0.0310.0000.0000.0000.000
18A18GLY0-0.004-0.00922.494-0.022-0.0220.0000.0000.0000.000
19A19GLY0-0.008-0.02023.413-0.024-0.0240.0000.0000.0000.000
20A20CYS0-0.040-0.02724.349-0.020-0.0200.0000.0000.0000.000
21A21GLY00.0700.04625.967-0.018-0.0180.0000.0000.0000.000
22A22SER0-0.004-0.00727.837-0.019-0.0190.0000.0000.0000.000
23A23ALA0-0.019-0.01529.501-0.014-0.0140.0000.0000.0000.000
24A24VAL0-0.017-0.02329.928-0.011-0.0110.0000.0000.0000.000
25A25LEU0-0.041-0.00130.519-0.007-0.0070.0000.0000.0000.000
26A26ALA00.014-0.00633.356-0.007-0.0070.0000.0000.0000.000
27A27ALA0-0.0290.01633.822-0.005-0.0050.0000.0000.0000.000
28A28GLY0-0.011-0.00135.524-0.006-0.0060.0000.0000.0000.000
29A29PHE0-0.005-0.02638.8920.0030.0030.0000.0000.0000.000
30A30PRO0-0.047-0.01641.367-0.001-0.0010.0000.0000.0000.000
31A31GLU-1-0.878-0.93944.7390.0830.0830.0000.0000.0000.000
32A32LEU0-0.008-0.00841.8080.0010.0010.0000.0000.0000.000
33A33GLY0-0.0400.00238.8970.0060.0060.0000.0000.0000.000
34A34ILE0-0.023-0.01632.3850.0000.0000.0000.0000.0000.000
35A35GLY00.0260.02136.6790.0000.0000.0000.0000.0000.000
36A36PHE00.026-0.02034.1680.0090.0090.0000.0000.0000.000
37A37ALA00.0240.01433.1520.0090.0090.0000.0000.0000.000
38A38GLY00.0560.02632.8470.0110.0110.0000.0000.0000.000
39A39VAL00.0220.02129.1930.0140.0140.0000.0000.0000.000
40A40ALA0-0.023-0.01728.7030.0180.0180.0000.0000.0000.000
41A41LEU00.0030.01928.2170.0160.0160.0000.0000.0000.000
42A42ALA00.0400.02227.3740.0220.0220.0000.0000.0000.000
43A43PHE00.0380.00422.9550.0300.0300.0000.0000.0000.000
44A44GLY0-0.0090.01722.9860.0320.0320.0000.0000.0000.000
45A45LEU00.0270.00523.3650.0320.0320.0000.0000.0000.000
46A46THR0-0.076-0.00620.5740.0430.0430.0000.0000.0000.000
47A47VAL00.017-0.00517.8870.0590.0590.0000.0000.0000.000
48A48LEU00.0210.02818.6300.0540.0540.0000.0000.0000.000
49A49THR0-0.002-0.02620.0030.0410.0410.0000.0000.0000.000
50A50MET00.0070.02214.5410.0890.0890.0000.0000.0000.000
51A51ALA0-0.011-0.00715.1540.1280.1280.0000.0000.0000.000
52A52PHE0-0.008-0.01715.7230.0510.0510.0000.0000.0000.000
53A53ALA0-0.0270.00216.0010.0390.0390.0000.0000.0000.000
54A54VAL0-0.015-0.02910.6880.1100.1100.0000.0000.0000.000
55A55GLY00.0500.03410.6240.2720.2720.0000.0000.0000.000
56A56HIS0-0.067-0.03211.5270.1320.1320.0000.0000.0000.000
57A57ILE0-0.040-0.0046.5000.2200.2200.0000.0000.0000.000
58A58SER0-0.075-0.0736.2400.4790.4790.0000.0000.0000.000
59A59GLY00.0210.0187.212-0.217-0.2170.0000.0000.0000.000
60A60GLY0-0.043-0.02710.151-0.213-0.2130.0000.0000.0000.000
61A61HIS10.8180.9117.639-0.859-0.8590.0000.0000.0000.000
62A62PHE0-0.0010.00711.584-0.100-0.1000.0000.0000.0000.000
63A63ASN00.0580.00112.740-0.116-0.1160.0000.0000.0000.000
64A64PRO00.0320.03012.3630.0010.0010.0000.0000.0000.000
65A65ALA00.0390.01113.357-0.048-0.0480.0000.0000.0000.000
66A66VAL0-0.0060.00712.721-0.035-0.0350.0000.0000.0000.000
67A67THR0-0.024-0.0077.8810.0520.0520.0000.0000.0000.000
68A68ILE00.0200.00910.698-0.099-0.0990.0000.0000.0000.000
69A69GLY00.0630.03112.745-0.054-0.0540.0000.0000.0000.000
70A70LEU00.009-0.00611.136-0.022-0.0220.0000.0000.0000.000
71A71TRP0-0.065-0.01310.370-0.029-0.0290.0000.0000.0000.000
72A72ALA00.0250.01612.001-0.034-0.0340.0000.0000.0000.000
73A73GLY00.0590.04215.216-0.009-0.0090.0000.0000.0000.000
74A74GLY0-0.093-0.04914.1840.0070.0070.0000.0000.0000.000
75A75ARG10.7900.88612.434-0.135-0.1350.0000.0000.0000.000
76A76PHE0-0.017-0.0104.136-0.152-0.037-0.001-0.010-0.1040.000
77A77PRO00.0560.0125.6410.0350.0350.0000.0000.0000.000
78A78ALA00.0780.0266.719-0.066-0.0660.0000.0000.0000.000
79A79LYS10.8650.9304.6842.8012.904-0.001-0.009-0.0930.000
80A80GLU-1-0.821-0.9002.293-5.685-6.0545.711-1.527-3.814-0.022
81A81VAL00.0030.0043.9661.0121.1800.0000.013-0.1800.000
82A82VAL00.0490.0247.1310.2930.2930.0000.0000.0000.000
83A83GLY00.0460.0275.217-0.099-0.033-0.001-0.012-0.0530.000
84A84TYR0-0.027-0.0452.861-0.5180.4450.462-0.268-1.157-0.001
85A85VAL00.0130.0086.985-0.132-0.1320.0000.0000.0000.000
86A86ILE00.0300.0189.422-0.022-0.0220.0000.0000.0000.000
87A87ALA0-0.0060.0027.331-0.053-0.0530.0000.0000.0000.000
88A88GLN0-0.024-0.0369.473-0.150-0.1500.0000.0000.0000.000
89A89VAL00.0230.01112.022-0.055-0.0550.0000.0000.0000.000
90A90VAL0-0.015-0.00412.301-0.026-0.0260.0000.0000.0000.000
91A91GLY00.0210.00313.474-0.020-0.0200.0000.0000.0000.000
92A92GLY00.0190.00614.974-0.020-0.0200.0000.0000.0000.000
93A93ILE00.0270.00317.764-0.022-0.0220.0000.0000.0000.000
94A94VAL00.0240.01416.886-0.018-0.0180.0000.0000.0000.000
95A95ALA00.0040.01219.367-0.015-0.0150.0000.0000.0000.000
96A96ALA0-0.004-0.00921.202-0.017-0.0170.0000.0000.0000.000
97A97ALA00.0050.00922.691-0.018-0.0180.0000.0000.0000.000
98A98LEU0-0.021-0.02522.044-0.011-0.0110.0000.0000.0000.000
99A99LEU0-0.0270.00325.211-0.007-0.0070.0000.0000.0000.000
100A100TYR00.0120.00927.045-0.012-0.0120.0000.0000.0000.000
101A101LEU0-0.022-0.01028.381-0.010-0.0100.0000.0000.0000.000
102A102ILE0-0.008-0.01028.015-0.006-0.0060.0000.0000.0000.000
103A103ALA0-0.0050.00131.129-0.007-0.0070.0000.0000.0000.000
104A104SER0-0.036-0.02132.723-0.010-0.0100.0000.0000.0000.000
105A105GLY0-0.0280.00534.638-0.007-0.0070.0000.0000.0000.000
106A106LYS10.9240.96536.287-0.097-0.0970.0000.0000.0000.000
107A107THR0-0.019-0.02438.824-0.002-0.0020.0000.0000.0000.000
108A108GLY00.000-0.00541.5050.0000.0000.0000.0000.0000.000
109A109PHE0-0.038-0.00532.1360.0020.0020.0000.0000.0000.000
110A110ASP-1-0.850-0.93837.0620.0570.0570.0000.0000.0000.000
111A111ALA0-0.0260.00431.9020.0040.0040.0000.0000.0000.000
112A112ALA00.0330.01833.8700.0030.0030.0000.0000.0000.000
113A113ALA00.0340.02835.5770.0020.0020.0000.0000.0000.000
114A114SER0-0.048-0.03135.4080.0040.0040.0000.0000.0000.000
115A115GLY00.0160.00333.6150.0020.0020.0000.0000.0000.000
116A116PHE0-0.027-0.01526.8310.0060.0060.0000.0000.0000.000
117A117ALA00.0120.00128.7040.0100.0100.0000.0000.0000.000
118A118SER00.0260.01527.9290.0130.0130.0000.0000.0000.000
119A119ASN0-0.087-0.04725.8350.0100.0100.0000.0000.0000.000
120A120GLY00.0410.01528.877-0.006-0.0060.0000.0000.0000.000
121A121TYR00.007-0.00530.7430.0030.0030.0000.0000.0000.000
122A122GLY00.0660.01633.8070.0000.0000.0000.0000.0000.000
123A123GLU-1-0.913-0.93637.4010.0280.0280.0000.0000.0000.000
124A124HIS10.7550.88334.953-0.040-0.0400.0000.0000.0000.000
125A125SER00.0190.03134.4940.0040.0040.0000.0000.0000.000
126A126PRO0-0.025-0.02534.347-0.004-0.0040.0000.0000.0000.000
127A127GLY0-0.0150.00037.319-0.003-0.0030.0000.0000.0000.000
128A128GLY00.0290.01638.500-0.004-0.0040.0000.0000.0000.000
129A129TYR0-0.041-0.01736.590-0.003-0.0030.0000.0000.0000.000
130A130SER00.0660.02937.675-0.002-0.0020.0000.0000.0000.000
131A131MET00.034-0.00232.0520.0040.0040.0000.0000.0000.000
132A132LEU00.0290.02333.5980.0010.0010.0000.0000.0000.000
133A133SER00.0250.00534.3030.0010.0010.0000.0000.0000.000
134A134ALA00.0070.00331.2300.0050.0050.0000.0000.0000.000
135A135LEU0-0.018-0.00328.8210.0070.0070.0000.0000.0000.000
136A136VAL00.0230.01229.6550.0020.0020.0000.0000.0000.000
137A137VAL00.010-0.00230.1720.0040.0040.0000.0000.0000.000
138A138GLU-1-0.700-0.83025.2290.1240.1240.0000.0000.0000.000
139A139LEU0-0.0090.02625.1980.0080.0080.0000.0000.0000.000
140A140VAL00.0290.00225.6580.0040.0040.0000.0000.0000.000
141A141LEU00.0050.00426.2460.0080.0080.0000.0000.0000.000
142A142SER00.008-0.01221.4260.0230.0230.0000.0000.0000.000
143A143ALA0-0.0100.00321.3950.0110.0110.0000.0000.0000.000
144A144GLY00.012-0.00322.7750.0040.0040.0000.0000.0000.000
145A145PHE0-0.016-0.01518.1400.0170.0170.0000.0000.0000.000
146A146LEU0-0.036-0.01015.5870.0250.0250.0000.0000.0000.000
147A147LEU00.0140.02719.3340.0020.0020.0000.0000.0000.000
148A148VAL0-0.0010.00321.8560.0030.0030.0000.0000.0000.000
149A149ILE00.0050.00215.3860.0140.0140.0000.0000.0000.000
150A150HIS0-0.056-0.00816.166-0.004-0.0040.0000.0000.0000.000
151A151GLY00.0610.03718.588-0.002-0.0020.0000.0000.0000.000
152A152ALA0-0.025-0.01320.4660.0000.0000.0000.0000.0000.000
153A153THR0-0.058-0.05515.7770.0160.0160.0000.0000.0000.000
154A154ASP-1-0.803-0.88617.7460.0860.0860.0000.0000.0000.000
155A155LYS10.9030.96119.755-0.023-0.0230.0000.0000.0000.000
156A156PHE00.009-0.00320.917-0.001-0.0010.0000.0000.0000.000
157A157ALA0-0.0160.02322.299-0.006-0.0060.0000.0000.0000.000
158A158PRO00.002-0.01123.8800.0090.0090.0000.0000.0000.000
159A159ALA00.0370.01621.9050.0220.0220.0000.0000.0000.000
160A160GLY00.005-0.00320.675-0.002-0.0020.0000.0000.0000.000
161A161PHE00.0210.00121.7010.0200.0200.0000.0000.0000.000
162A162ALA00.0150.01418.727-0.004-0.0040.0000.0000.0000.000
163A163PRO00.0140.01118.137-0.013-0.0130.0000.0000.0000.000
164A164ILE00.0230.00920.346-0.011-0.0110.0000.0000.0000.000
165A165ALA00.0130.01122.701-0.018-0.0180.0000.0000.0000.000
166A166ILE0-0.002-0.01317.085-0.018-0.0180.0000.0000.0000.000
167A167GLY00.0130.00421.153-0.008-0.0080.0000.0000.0000.000
168A168LEU00.0180.00122.468-0.019-0.0190.0000.0000.0000.000
169A169ALA00.0080.01223.168-0.022-0.0220.0000.0000.0000.000
170A170LEU0-0.008-0.00220.798-0.018-0.0180.0000.0000.0000.000
171A171THR00.0060.00024.221-0.009-0.0090.0000.0000.0000.000
172A172LEU00.0170.00427.575-0.014-0.0140.0000.0000.0000.000
173A173ILE00.008-0.00123.944-0.013-0.0130.0000.0000.0000.000
174A174HIS10.8390.91524.150-0.209-0.2090.0000.0000.0000.000
175A175LEU0-0.030-0.00729.146-0.008-0.0080.0000.0000.0000.000
176A176ILE0-0.037-0.00430.724-0.010-0.0100.0000.0000.0000.000
177A177SER00.0440.02628.486-0.005-0.0050.0000.0000.0000.000
178A178ILE0-0.0200.02030.267-0.004-0.0040.0000.0000.0000.000
179A179PRO00.0370.00932.241-0.004-0.0040.0000.0000.0000.000
180A180VAL0-0.035-0.01032.952-0.006-0.0060.0000.0000.0000.000
181A181THR00.013-0.01428.947-0.003-0.0030.0000.0000.0000.000
182A182ASN0-0.033-0.02130.0110.0070.0070.0000.0000.0000.000
183A183THR0-0.010-0.02025.8050.0140.0140.0000.0000.0000.000
184A184SER0-0.011-0.02123.3730.0140.0140.0000.0000.0000.000
185A185VAL0-0.073-0.03821.1790.0250.0250.0000.0000.0000.000
186A186ASN00.0120.00516.9630.0150.0150.0000.0000.0000.000
187A187PRO00.0520.03217.3310.0010.0010.0000.0000.0000.000
188A188ALA0-0.013-0.01715.363-0.016-0.0160.0000.0000.0000.000
189A189ARG10.8340.93117.517-0.170-0.1700.0000.0000.0000.000
190A190SER0-0.008-0.01520.364-0.013-0.0130.0000.0000.0000.000
191A191THR0-0.004-0.00918.802-0.019-0.0190.0000.0000.0000.000
192A192ALA0-0.042-0.01219.838-0.013-0.0130.0000.0000.0000.000
193A193VAL0-0.0010.00321.653-0.006-0.0060.0000.0000.0000.000
194A194ALA00.0370.00924.995-0.013-0.0130.0000.0000.0000.000
195A195ILE0-0.026-0.01721.704-0.012-0.0120.0000.0000.0000.000
196A196PHE0-0.010-0.00823.143-0.010-0.0100.0000.0000.0000.000
197A197GLN0-0.0160.01528.080-0.005-0.0050.0000.0000.0000.000
198A198GLY00.0070.00829.782-0.006-0.0060.0000.0000.0000.000
199A199GLY00.027-0.00531.517-0.002-0.0020.0000.0000.0000.000
200A200TRP00.0280.00132.059-0.002-0.0020.0000.0000.0000.000
201A201ALA00.0290.02728.780-0.001-0.0010.0000.0000.0000.000
202A202LEU0-0.017-0.02326.3910.0030.0030.0000.0000.0000.000
203A203GLU-1-0.894-0.93528.7140.0220.0220.0000.0000.0000.000
204A204GLN00.0150.01130.0240.0020.0020.0000.0000.0000.000
205A205LEU0-0.0430.00722.4270.0040.0040.0000.0000.0000.000
206A206TRP00.0400.00724.5560.0060.0060.0000.0000.0000.000
207A207PHE00.0350.00824.799-0.002-0.0020.0000.0000.0000.000
208A208PHE0-0.040-0.02724.0550.0020.0020.0000.0000.0000.000
209A209TRP00.004-0.01515.6950.0200.0200.0000.0000.0000.000
210A210VAL0-0.015-0.00420.184-0.002-0.0020.0000.0000.0000.000
211A211VAL00.0280.02422.454-0.003-0.0030.0000.0000.0000.000
212A212PRO00.0070.00720.2730.0000.0000.0000.0000.0000.000
213A213ILE0-0.010-0.00816.4200.0100.0100.0000.0000.0000.000
214A214VAL00.0060.01019.126-0.009-0.0090.0000.0000.0000.000
215A215GLY00.0490.02421.823-0.006-0.0060.0000.0000.0000.000
216A216GLY00.0330.00818.4630.0030.0030.0000.0000.0000.000
217A217ILE0-0.038-0.02617.099-0.004-0.0040.0000.0000.0000.000
218A218ILE00.0060.01119.052-0.010-0.0100.0000.0000.0000.000
219A219GLY00.0310.01921.326-0.003-0.0030.0000.0000.0000.000
220A220GLY0-0.010-0.01117.9300.0040.0040.0000.0000.0000.000
221A221LEU0-0.032-0.03118.861-0.011-0.0110.0000.0000.0000.000
222A222ILE00.0160.02221.329-0.005-0.0050.0000.0000.0000.000
223A223TYR0-0.016-0.02620.2020.0010.0010.0000.0000.0000.000
224A224ARG10.8410.90716.7940.1190.1190.0000.0000.0000.000
225A225THR0-0.080-0.06421.250-0.015-0.0150.0000.0000.0000.000
226A226LEU0-0.060-0.01324.630-0.003-0.0030.0000.0000.0000.000
227A227LEU0-0.0150.02321.3720.0090.0090.0000.0000.0000.000
228A228GLU-1-0.966-0.98524.9560.0540.0540.0000.0000.0000.000
229A229LYS10.8180.88124.801-0.006-0.0060.0000.0000.0000.000
230A230ARG10.9050.94816.5040.0480.0480.0000.0000.0000.000
231A231ASP-1-0.816-0.87023.388-0.024-0.0240.0000.0000.0000.000