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: 2N4YR

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 OptAll
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 -2537062.413051
FMO2-HF: Nuclear repulsion 2455462.623642
FMO2-HF: Total energy -81599.789409
FMO2-MP2: Total energy -81842.434447


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.
-14.638-8.51312.192-4.786-13.527-0.015
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 : 0.027 / 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].
3A3ARG10.9910.9883.889-2.871-1.181-0.005-0.706-0.9780.002
4A4LYS10.8820.9352.448-5.614-4.3484.557-1.615-4.2080.005
5A5LEU00.0110.0012.542-2.366-1.0962.513-0.749-3.033-0.001
6A6ALA00.0350.0175.376-0.486-0.378-0.001-0.018-0.0900.000
7A7ALA00.0000.0017.686-0.217-0.2170.0000.0000.0000.000
8A8GLU-1-0.718-0.8186.9230.9690.9690.0000.0000.0000.000
9A9CYS0-0.0710.0029.360-0.304-0.3040.0000.0000.0000.000
10A10PHE00.0560.00411.140-0.123-0.1230.0000.0000.0000.000
11A11GLY00.0400.01812.799-0.091-0.0910.0000.0000.0000.000
12A12THR0-0.040-0.03912.471-0.099-0.0990.0000.0000.0000.000
13A13PHE0-0.0270.00015.063-0.071-0.0710.0000.0000.0000.000
14A14TRP0-0.027-0.01617.063-0.055-0.0550.0000.0000.0000.000
15A15LEU0-0.024-0.00917.531-0.045-0.0450.0000.0000.0000.000
16A16VAL0-0.009-0.01019.064-0.039-0.0390.0000.0000.0000.000
17A17PHE00.003-0.00620.954-0.026-0.0260.0000.0000.0000.000
18A18GLY00.0210.01922.589-0.019-0.0190.0000.0000.0000.000
19A19GLY00.0060.00723.506-0.022-0.0220.0000.0000.0000.000
20A20CYS0-0.020-0.02123.818-0.016-0.0160.0000.0000.0000.000
21A21GLY00.0600.03025.636-0.016-0.0160.0000.0000.0000.000
22A22SER0-0.013-0.02427.491-0.018-0.0180.0000.0000.0000.000
23A23ALA0-0.032-0.03129.048-0.013-0.0130.0000.0000.0000.000
24A24VAL0-0.020-0.00929.672-0.011-0.0110.0000.0000.0000.000
25A25LEU0-0.051-0.01330.376-0.006-0.0060.0000.0000.0000.000
26A26ALA00.002-0.00133.176-0.004-0.0040.0000.0000.0000.000
27A27ALA0-0.0280.00033.359-0.003-0.0030.0000.0000.0000.000
28A28GLY0-0.014-0.00535.190-0.005-0.0050.0000.0000.0000.000
29A29PHE0-0.021-0.01938.6170.0020.0020.0000.0000.0000.000
30A30PRO0-0.039-0.01541.184-0.002-0.0020.0000.0000.0000.000
31A31GLU-1-0.850-0.93344.5950.0740.0740.0000.0000.0000.000
32A32LEU0-0.016-0.00241.4450.0020.0020.0000.0000.0000.000
33A33GLY0-0.040-0.00238.8140.0060.0060.0000.0000.0000.000
34A34ILE0-0.009-0.01032.2450.0000.0000.0000.0000.0000.000
35A35GLY00.0420.02536.2490.0020.0020.0000.0000.0000.000
36A36PHE00.015-0.02233.5630.0090.0090.0000.0000.0000.000
37A37ALA00.0260.02032.5890.0080.0080.0000.0000.0000.000
38A38GLY00.0450.02232.4180.0100.0100.0000.0000.0000.000
39A39VAL00.0220.02028.8940.0140.0140.0000.0000.0000.000
40A40ALA0-0.014-0.01128.2030.0170.0170.0000.0000.0000.000
41A41LEU00.0080.02027.6780.0160.0160.0000.0000.0000.000
42A42ALA00.0230.02026.8520.0210.0210.0000.0000.0000.000
43A43PHE00.016-0.00622.7450.0290.0290.0000.0000.0000.000
44A44GLY0-0.0070.02322.6360.0230.0230.0000.0000.0000.000
45A45LEU00.014-0.01422.9160.0330.0330.0000.0000.0000.000
46A46THR0-0.0180.01120.4090.0350.0350.0000.0000.0000.000
47A47VAL00.0070.00117.6390.0550.0550.0000.0000.0000.000
48A48LEU0-0.0020.01318.6040.0540.0540.0000.0000.0000.000
49A49THR00.006-0.02620.1580.0400.0400.0000.0000.0000.000
50A50MET00.0070.02314.6090.0780.0780.0000.0000.0000.000
51A51ALA00.003-0.01115.1920.1220.1220.0000.0000.0000.000
52A52PHE00.007-0.00115.8460.0490.0490.0000.0000.0000.000
53A53ALA0-0.0120.00016.4300.0510.0510.0000.0000.0000.000
54A54VAL0-0.027-0.03211.0480.0890.0890.0000.0000.0000.000
55A55GLY00.0400.02810.8910.2540.2540.0000.0000.0000.000
56A56HIS0-0.053-0.02411.5030.1870.1870.0000.0000.0000.000
57A57ILE0-0.0360.0016.3750.1610.1610.0000.0000.0000.000
58A58SER0-0.086-0.0776.5750.6740.6740.0000.0000.0000.000
59A59GLY00.0240.0207.528-0.210-0.2100.0000.0000.0000.000
60A60GLY0-0.020-0.01410.329-0.189-0.1890.0000.0000.0000.000
61A61HIS10.8130.9027.380-0.808-0.8080.0000.0000.0000.000
62A62PHE00.0010.00711.625-0.107-0.1070.0000.0000.0000.000
63A63ASN00.0730.01612.574-0.120-0.1200.0000.0000.0000.000
64A64PRO00.0380.02712.1990.0140.0140.0000.0000.0000.000
65A65ALA00.0470.02413.035-0.046-0.0460.0000.0000.0000.000
66A66VAL00.0010.01512.686-0.035-0.0350.0000.0000.0000.000
67A67THR0-0.036-0.0127.7410.0600.0600.0000.0000.0000.000
68A68ILE00.0040.00010.493-0.105-0.1050.0000.0000.0000.000
69A69GLY00.0600.02512.542-0.052-0.0520.0000.0000.0000.000
70A70LEU00.0170.00311.094-0.018-0.0180.0000.0000.0000.000
71A71TRP0-0.043-0.00910.246-0.035-0.0350.0000.0000.0000.000
72A72ALA00.0160.01111.940-0.017-0.0170.0000.0000.0000.000
73A73GLY00.0600.03615.445-0.009-0.0090.0000.0000.0000.000
74A74GLY0-0.085-0.03514.4210.0100.0100.0000.0000.0000.000
75A75ARG10.7840.86212.712-0.125-0.1250.0000.0000.0000.000
76A76PHE0-0.014-0.0064.172-0.0910.022-0.001-0.009-0.1030.000
77A77PRO00.0380.0095.7190.0240.0240.0000.0000.0000.000
78A78ALA00.0810.0326.527-0.163-0.1630.0000.0000.0000.000
79A79LYS10.8610.9174.6882.6652.762-0.001-0.007-0.0880.000
80A80GLU-1-0.809-0.8822.248-6.174-5.8084.518-1.394-3.489-0.020
81A81VAL0-0.0110.0033.8911.0181.1460.0000.038-0.1650.000
82A82VAL00.0560.0247.0810.3000.3000.0000.0000.0000.000
83A83GLY00.0390.0254.9280.0070.0070.0000.0000.0000.000
84A84TYR0-0.016-0.0472.658-0.3430.7440.612-0.326-1.373-0.001
85A85VAL0-0.0030.0086.625-0.127-0.1270.0000.0000.0000.000
86A86ILE00.0200.0148.884-0.007-0.0070.0000.0000.0000.000
87A87ALA00.0030.0026.919-0.047-0.0470.0000.0000.0000.000
88A88GLN0-0.032-0.0389.070-0.200-0.2000.0000.0000.0000.000
89A89VAL00.0180.00211.698-0.058-0.0580.0000.0000.0000.000
90A90VAL0-0.0010.00311.823-0.026-0.0260.0000.0000.0000.000
91A91GLY00.027-0.00312.930-0.019-0.0190.0000.0000.0000.000
92A92GLY00.013-0.00314.365-0.024-0.0240.0000.0000.0000.000
93A93ILE00.0240.00617.139-0.023-0.0230.0000.0000.0000.000
94A94VAL0-0.0030.00116.080-0.018-0.0180.0000.0000.0000.000
95A95ALA0-0.0090.00418.613-0.010-0.0100.0000.0000.0000.000
96A96ALA0-0.005-0.00420.499-0.015-0.0150.0000.0000.0000.000
97A97ALA00.0230.01622.051-0.015-0.0150.0000.0000.0000.000
98A98LEU0-0.021-0.01521.455-0.009-0.0090.0000.0000.0000.000
99A99LEU0-0.0190.01024.518-0.007-0.0070.0000.0000.0000.000
100A100TYR00.0080.00226.397-0.010-0.0100.0000.0000.0000.000
101A101LEU0-0.018-0.00327.610-0.008-0.0080.0000.0000.0000.000
102A102ILE0-0.011-0.01627.216-0.004-0.0040.0000.0000.0000.000
103A103ALA0-0.012-0.00430.448-0.005-0.0050.0000.0000.0000.000
104A104SER0-0.023-0.01832.096-0.008-0.0080.0000.0000.0000.000
105A105GLY0-0.0080.01333.808-0.006-0.0060.0000.0000.0000.000
106A106LYS10.9000.95935.605-0.082-0.0820.0000.0000.0000.000
107A107THR00.003-0.01738.012-0.003-0.0030.0000.0000.0000.000
108A108GLY0-0.001-0.00840.9910.0010.0010.0000.0000.0000.000
109A109PHE0-0.048-0.00831.5520.0010.0010.0000.0000.0000.000
110A110ASP-1-0.800-0.90336.2840.0410.0410.0000.0000.0000.000
111A111ALA0-0.0330.01831.3010.0060.0060.0000.0000.0000.000
112A112ALA00.0240.01233.3250.0020.0020.0000.0000.0000.000
113A113ALA00.0070.00435.5100.0030.0030.0000.0000.0000.000
114A114SER0-0.045-0.04734.7860.0030.0030.0000.0000.0000.000
115A115GLY00.0120.00833.2340.0030.0030.0000.0000.0000.000
116A116PHE0-0.014-0.01026.1750.0050.0050.0000.0000.0000.000
117A117ALA00.0380.01728.2200.0100.0100.0000.0000.0000.000
118A118SER00.008-0.00827.3590.0100.0100.0000.0000.0000.000
119A119ASN0-0.095-0.05925.5330.0090.0090.0000.0000.0000.000
120A120GLY00.0350.01828.623-0.007-0.0070.0000.0000.0000.000
121A121TYR00.011-0.00730.7210.0040.0040.0000.0000.0000.000
122A122GLY00.001-0.01033.6740.0000.0000.0000.0000.0000.000
123A123GLU-1-0.895-0.94237.5220.0140.0140.0000.0000.0000.000
124A124HIS10.7680.88234.392-0.026-0.0260.0000.0000.0000.000
125A125SER0-0.0150.01534.3340.0050.0050.0000.0000.0000.000
126A126PRO0-0.013-0.01533.842-0.003-0.0030.0000.0000.0000.000
127A127GLY00.0140.01536.807-0.001-0.0010.0000.0000.0000.000
128A128GLY0-0.011-0.00138.726-0.003-0.0030.0000.0000.0000.000
129A129TYR0-0.032-0.00836.413-0.004-0.0040.0000.0000.0000.000
130A130SER00.0630.02037.015-0.001-0.0010.0000.0000.0000.000
131A131MET00.0400.01631.7180.0040.0040.0000.0000.0000.000
132A132LEU00.0480.03133.3440.0010.0010.0000.0000.0000.000
133A133SER00.0120.00134.2010.0010.0010.0000.0000.0000.000
134A134ALA00.0350.01531.2180.0050.0050.0000.0000.0000.000
135A135LEU0-0.030-0.00728.6230.0060.0060.0000.0000.0000.000
136A136VAL00.002-0.00229.4350.0030.0030.0000.0000.0000.000
137A137VAL00.0190.00530.2320.0040.0040.0000.0000.0000.000
138A138GLU-1-0.687-0.83125.1910.1060.1060.0000.0000.0000.000
139A139LEU0-0.0140.01724.9150.0090.0090.0000.0000.0000.000
140A140VAL00.0230.00625.3340.0050.0050.0000.0000.0000.000
141A141LEU00.0040.00426.2260.0070.0070.0000.0000.0000.000
142A142SER0-0.007-0.02221.2580.0210.0210.0000.0000.0000.000
143A143ALA0-0.027-0.00821.3400.0100.0100.0000.0000.0000.000
144A144GLY00.0240.00422.7790.0040.0040.0000.0000.0000.000
145A145PHE0-0.009-0.00618.1870.0150.0150.0000.0000.0000.000
146A146LEU0-0.0250.00315.3840.0220.0220.0000.0000.0000.000
147A147LEU00.0040.03019.1850.0050.0050.0000.0000.0000.000
148A148VAL00.010-0.00121.8590.0060.0060.0000.0000.0000.000
149A149ILE0-0.003-0.00415.5580.0170.0170.0000.0000.0000.000
150A150HIS0-0.057-0.01516.1130.0010.0010.0000.0000.0000.000
151A151GLY00.0490.03318.7300.0050.0050.0000.0000.0000.000
152A152ALA0-0.041-0.02120.4260.0010.0010.0000.0000.0000.000
153A153THR0-0.043-0.04916.1550.0240.0240.0000.0000.0000.000
154A154ASP-1-0.769-0.84517.6770.0970.0970.0000.0000.0000.000
155A155LYS10.8780.94120.068-0.031-0.0310.0000.0000.0000.000
156A156PHE00.0210.00621.3690.0000.0000.0000.0000.0000.000
157A157ALA0-0.0110.02122.002-0.005-0.0050.0000.0000.0000.000
158A158PRO00.009-0.01423.9740.0110.0110.0000.0000.0000.000
159A159ALA00.0480.02821.8190.0230.0230.0000.0000.0000.000
160A160GLY0-0.011-0.00520.546-0.005-0.0050.0000.0000.0000.000
161A161PHE00.023-0.00121.5770.0200.0200.0000.0000.0000.000
162A162ALA00.0120.01418.848-0.004-0.0040.0000.0000.0000.000
163A163PRO0-0.002-0.00318.310-0.015-0.0150.0000.0000.0000.000
164A164ILE00.0180.00820.406-0.013-0.0130.0000.0000.0000.000
165A165ALA00.0090.01422.944-0.017-0.0170.0000.0000.0000.000
166A166ILE00.0090.00017.247-0.019-0.0190.0000.0000.0000.000
167A167GLY00.0110.00621.253-0.010-0.0100.0000.0000.0000.000
168A168LEU00.0250.00622.678-0.019-0.0190.0000.0000.0000.000
169A169ALA00.0130.01723.352-0.020-0.0200.0000.0000.0000.000
170A170LEU0-0.0020.00220.326-0.018-0.0180.0000.0000.0000.000
171A171THR0-0.010-0.00923.956-0.008-0.0080.0000.0000.0000.000
172A172LEU00.0150.00127.351-0.014-0.0140.0000.0000.0000.000
173A173ILE00.004-0.01123.681-0.012-0.0120.0000.0000.0000.000
174A174HIS10.8450.92423.671-0.187-0.1870.0000.0000.0000.000
175A175LEU0-0.012-0.01028.668-0.009-0.0090.0000.0000.0000.000
176A176ILE0-0.0320.01230.414-0.009-0.0090.0000.0000.0000.000
177A177SER00.0190.01728.372-0.003-0.0030.0000.0000.0000.000
178A178ILE00.0060.02929.694-0.004-0.0040.0000.0000.0000.000
179A179PRO00.036-0.00131.951-0.005-0.0050.0000.0000.0000.000
180A180VAL0-0.053-0.01832.812-0.006-0.0060.0000.0000.0000.000
181A181THR0-0.009-0.04228.781-0.005-0.0050.0000.0000.0000.000
182A182ASN0-0.027-0.00729.7090.0060.0060.0000.0000.0000.000
183A183THR0-0.016-0.02325.3420.0130.0130.0000.0000.0000.000
184A184SER00.0040.00622.5680.0160.0160.0000.0000.0000.000
185A185VAL0-0.029-0.02721.1300.0230.0230.0000.0000.0000.000
186A186ASN0-0.016-0.01516.8420.0120.0120.0000.0000.0000.000
187A187PRO00.0530.03217.0630.0020.0020.0000.0000.0000.000
188A188ALA0-0.013-0.00115.145-0.016-0.0160.0000.0000.0000.000
189A189ARG10.7840.89217.296-0.154-0.1540.0000.0000.0000.000
190A190SER0-0.0070.00320.300-0.008-0.0080.0000.0000.0000.000
191A191THR0-0.011-0.01818.465-0.017-0.0170.0000.0000.0000.000
192A192ALA0-0.037-0.01119.482-0.012-0.0120.0000.0000.0000.000
193A193VAL00.0000.00521.184-0.007-0.0070.0000.0000.0000.000
194A194ALA00.0210.00624.683-0.012-0.0120.0000.0000.0000.000
195A195ILE0-0.013-0.01521.438-0.011-0.0110.0000.0000.0000.000
196A196PHE0-0.001-0.00422.603-0.008-0.0080.0000.0000.0000.000
197A197GLN0-0.038-0.00327.439-0.004-0.0040.0000.0000.0000.000
198A198GLY0-0.0020.02429.399-0.005-0.0050.0000.0000.0000.000
199A199GLY00.042-0.00131.138-0.004-0.0040.0000.0000.0000.000
200A200TRP00.020-0.00331.659-0.001-0.0010.0000.0000.0000.000
201A201ALA00.0360.03128.493-0.002-0.0020.0000.0000.0000.000
202A202LEU0-0.024-0.02326.3250.0010.0010.0000.0000.0000.000
203A203GLU-1-0.838-0.90328.7180.0080.0080.0000.0000.0000.000
204A204GLN0-0.0010.00029.5390.0030.0030.0000.0000.0000.000
205A205LEU0-0.0310.00322.1080.0050.0050.0000.0000.0000.000
206A206TRP00.039-0.00824.0290.0040.0040.0000.0000.0000.000
207A207PHE00.0240.02724.243-0.003-0.0030.0000.0000.0000.000
208A208PHE0-0.016-0.01124.2890.0050.0050.0000.0000.0000.000
209A209TRP00.0260.00315.6000.0160.0160.0000.0000.0000.000
210A210VAL00.004-0.00520.3380.0020.0020.0000.0000.0000.000
211A211VAL00.0300.02422.180-0.003-0.0030.0000.0000.0000.000
212A212PRO0-0.010-0.00220.0170.0000.0000.0000.0000.0000.000
213A213ILE0-0.013-0.00416.5270.0080.0080.0000.0000.0000.000
214A214VAL00.0030.00418.836-0.008-0.0080.0000.0000.0000.000
215A215GLY00.0420.02521.583-0.004-0.0040.0000.0000.0000.000
216A216GLY00.0290.00218.2980.0040.0040.0000.0000.0000.000
217A217ILE0-0.044-0.03217.088-0.004-0.0040.0000.0000.0000.000
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