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

tag_button

FMODB ID: 17G7Z

Calculation Name: 2X8X-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X8X

Chain ID: X

ChEMBL ID:

UniProt ID: Q8DI03

Base Structure: X-ray

Registration Date: 2023-09-20

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2439253.118008
FMO2-HF: Nuclear repulsion 2348957.867367
FMO2-HF: Total energy -90295.25064
FMO2-MP2: Total energy -90565.320311


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(X:67:ASP)


Summations of interaction energy for fragment #1(X:67:ASP)
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.
-43.607-41.725-0.015-0.768-1.10.004
Interaction energy analysis for fragmet #1(X:67:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.954 / q_NPA : -0.983
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].
3X69PRO0-0.023-0.0133.8270.4211.945-0.013-0.707-0.8040.004
4X70LYS10.8350.8863.742-40.006-39.817-0.001-0.039-0.1510.000
5X71VAL00.0040.0008.414-1.646-1.6460.0000.0000.0000.000
6X72LEU0-0.0060.00112.0000.5310.5310.0000.0000.0000.000
7X73ILE0-0.036-0.00814.097-0.597-0.5970.0000.0000.0000.000
8X74ALA00.0260.01516.839-0.311-0.3110.0000.0000.0000.000
9X75GLU-1-0.867-0.93420.61111.33611.3360.0000.0000.0000.000
10X76VAL00.006-0.00618.5740.6610.6610.0000.0000.0000.000
11X77VAL0-0.0140.00121.274-0.519-0.5190.0000.0000.0000.000
12X78VAL00.0040.00322.9300.6410.6410.0000.0000.0000.000
13X79GLU-1-0.886-0.94824.95110.83010.8300.0000.0000.0000.000
14X80GLY00.0270.00826.9930.2600.2600.0000.0000.0000.000
15X81ALA0-0.038-0.01628.024-0.119-0.1190.0000.0000.0000.000
16X82THR0-0.021-0.03030.089-0.101-0.1010.0000.0000.0000.000
17X83PRO00.0380.00331.8510.2670.2670.0000.0000.0000.000
18X84GLU-1-0.828-0.90731.9509.1569.1560.0000.0000.0000.000
19X85LEU0-0.033-0.01429.2020.2640.2640.0000.0000.0000.000
20X86GLU-1-0.861-0.91627.33611.15211.1520.0000.0000.0000.000
21X87GLN0-0.009-0.01326.6850.2380.2380.0000.0000.0000.000
22X88LEU0-0.0030.00525.6910.4230.4230.0000.0000.0000.000
23X89VAL00.0240.00822.1440.5540.5540.0000.0000.0000.000
24X90TYR0-0.037-0.03021.7740.9400.9400.0000.0000.0000.000
25X91GLN0-0.042-0.01221.7300.4180.4180.0000.0000.0000.000
26X92VAL0-0.051-0.02520.4480.3690.3690.0000.0000.0000.000
27X93ILE0-0.0620.00317.0860.8620.8620.0000.0000.0000.000
28X94SER0-0.074-0.05913.259-0.051-0.0510.0000.0000.0000.000
29X95THR0-0.038-0.04213.7590.3050.3050.0000.0000.0000.000
30X96ARG10.8250.91115.340-16.247-16.2470.0000.0000.0000.000
31X97PRO00.0170.01817.2730.7490.7490.0000.0000.0000.000
32X98GLY00.0090.00618.655-0.277-0.2770.0000.0000.0000.000
33X99SER0-0.067-0.03214.0560.7520.7520.0000.0000.0000.000
34X100THR00.013-0.0089.470-0.340-0.3400.0000.0000.0000.000
35X101THR00.0160.0069.2212.0402.0400.0000.0000.0000.000
36X102THR00.0610.0153.9660.4690.5200.000-0.019-0.0310.000
37X103ARG10.9340.9567.181-25.885-25.8850.0000.0000.0000.000
38X104THR00.0330.0054.619-5.869-5.751-0.001-0.003-0.1140.000
39X105GLN00.0740.0586.5170.6920.6920.0000.0000.0000.000
40X106LEU00.0210.0319.027-2.496-2.4960.0000.0000.0000.000
41X107GLN0-0.004-0.00210.743-1.817-1.8170.0000.0000.0000.000
42X108GLN00.008-0.0027.579-1.988-1.9880.0000.0000.0000.000
43X109ASP-1-0.685-0.81812.45218.78218.7820.0000.0000.0000.000
44X110THR0-0.049-0.03415.096-1.367-1.3670.0000.0000.0000.000
45X111ASN0-0.006-0.01113.764-1.429-1.4290.0000.0000.0000.000
46X112ALA00.0100.01116.474-0.999-0.9990.0000.0000.0000.000
47X113ILE00.0470.02518.267-0.921-0.9210.0000.0000.0000.000
48X114PHE00.0020.01620.210-0.791-0.7910.0000.0000.0000.000
49X115ALA0-0.0160.00020.086-0.698-0.6980.0000.0000.0000.000
50X116THR0-0.021-0.02122.044-0.742-0.7420.0000.0000.0000.000
51X117GLY00.0000.00624.879-0.523-0.5230.0000.0000.0000.000
52X118PHE00.0380.01827.161-0.453-0.4530.0000.0000.0000.000
53X119PHE0-0.017-0.00925.059-0.322-0.3220.0000.0000.0000.000
54X120ALA0-0.0060.00126.5740.2120.2120.0000.0000.0000.000
55X121ASP-1-0.908-0.96124.12112.73012.7300.0000.0000.0000.000
56X122VAL00.002-0.00320.057-0.215-0.2150.0000.0000.0000.000
57X123ASN0-0.049-0.01019.3401.0041.0040.0000.0000.0000.000
58X124ALA00.0300.02415.825-0.362-0.3620.0000.0000.0000.000
59X125VAL0-0.034-0.02617.3520.4320.4320.0000.0000.0000.000
60X126PRO0-0.0010.01114.988-0.442-0.4420.0000.0000.0000.000
61X127ARG10.8760.92517.935-14.188-14.1880.0000.0000.0000.000
62X128ASP-1-0.861-0.92119.93114.72614.7260.0000.0000.0000.000
63X129THR0-0.076-0.07322.057-0.532-0.5320.0000.0000.0000.000
64X130PRO0-0.010-0.02224.8650.1350.1350.0000.0000.0000.000
65X131LEU0-0.021-0.00124.669-0.089-0.0890.0000.0000.0000.000
66X132GLY00.0360.03121.5160.2470.2470.0000.0000.0000.000
67X133VAL00.0230.02616.305-0.136-0.1360.0000.0000.0000.000
68X134ARG10.8740.95619.489-11.841-11.8410.0000.0000.0000.000
69X135ILE0-0.047-0.03115.1070.6070.6070.0000.0000.0000.000
70X136THR00.0350.02218.886-0.762-0.7620.0000.0000.0000.000
71X137PHE0-0.020-0.02015.9970.6330.6330.0000.0000.0000.000
72X138VAL00.0000.00121.323-0.580-0.5800.0000.0000.0000.000
73X139VAL00.0080.00923.4780.4520.4520.0000.0000.0000.000
74X140ARG10.9340.96925.678-11.239-11.2390.0000.0000.0000.000
75X141PRO00.0380.00428.6480.2550.2550.0000.0000.0000.000
76X142TYR0-0.063-0.01527.454-0.282-0.2820.0000.0000.0000.000
77X143PRO00.0470.02432.644-0.024-0.0240.0000.0000.0000.000
78X144VAL0-0.042-0.01636.3260.0710.0710.0000.0000.0000.000
79X145LEU0-0.0040.00738.342-0.116-0.1160.0000.0000.0000.000
80X146ARG10.9050.93939.876-7.639-7.6390.0000.0000.0000.000
81X147ALA00.0330.01542.987-0.197-0.1970.0000.0000.0000.000
82X148VAL0-0.0210.00441.1360.2010.2010.0000.0000.0000.000
83X149GLN0-0.0030.00543.704-0.313-0.3130.0000.0000.0000.000
84X150VAL0-0.026-0.01644.5210.2060.2060.0000.0000.0000.000
85X151ALA00.0150.01045.850-0.163-0.1630.0000.0000.0000.000
86X152GLY0-0.001-0.01246.8990.1260.1260.0000.0000.0000.000
87X153ASN0-0.065-0.04448.7700.0240.0240.0000.0000.0000.000
88X154GLN0-0.073-0.06450.413-0.146-0.1460.0000.0000.0000.000
89X155VAL0-0.003-0.01051.650-0.066-0.0660.0000.0000.0000.000
90X156LEU0-0.0390.01446.331-0.010-0.0100.0000.0000.0000.000
91X157THR00.021-0.01150.8120.0270.0270.0000.0000.0000.000
92X158GLN00.042-0.00647.5600.1520.1520.0000.0000.0000.000
93X159GLU-1-0.850-0.92550.0486.0676.0670.0000.0000.0000.000
94X160LYS10.8240.91048.631-6.428-6.4280.0000.0000.0000.000
95X161VAL00.0230.00644.7920.1550.1550.0000.0000.0000.000
96X162ASN0-0.004-0.00245.8050.2530.2530.0000.0000.0000.000
97X163GLU-1-0.842-0.90347.0076.5816.5810.0000.0000.0000.000
98X164ILE0-0.050-0.02942.4700.1200.1200.0000.0000.0000.000
99X165PHE00.005-0.00738.7090.2030.2030.0000.0000.0000.000
100X166ALA00.0330.02742.7070.1200.1200.0000.0000.0000.000
101X167PRO0-0.037-0.01941.3500.0400.0400.0000.0000.0000.000
102X168GLN0-0.056-0.04237.5280.1690.1690.0000.0000.0000.000
103X169ILE0-0.0230.01239.8870.1360.1360.0000.0000.0000.000
104X170GLY0-0.026-0.01542.028-0.076-0.0760.0000.0000.0000.000
105X171ARG10.8410.91335.932-8.495-8.4950.0000.0000.0000.000
106X172THR0-0.022-0.00932.606-0.156-0.1560.0000.0000.0000.000
107X173LEU00.0150.01933.9600.0330.0330.0000.0000.0000.000
108X174ASN00.031-0.00529.0340.3650.3650.0000.0000.0000.000
109X175LEU00.0260.00228.998-0.266-0.2660.0000.0000.0000.000
110X176ARG10.8590.92723.793-12.490-12.4900.0000.0000.0000.000
111X177GLU-1-0.848-0.92630.5818.8718.8710.0000.0000.0000.000
112X178LEU00.0190.01834.054-0.288-0.2880.0000.0000.0000.000
113X179GLN0-0.005-0.01131.881-0.140-0.1400.0000.0000.0000.000
114X180ALA00.0420.02034.274-0.195-0.1950.0000.0000.0000.000
115X181GLY0-0.059-0.03835.931-0.271-0.2710.0000.0000.0000.000
116X182ILE00.0390.02235.759-0.248-0.2480.0000.0000.0000.000
117X183GLU-1-0.822-0.90535.5878.5958.5950.0000.0000.0000.000
118X184LYS10.8570.93638.642-8.279-8.2790.0000.0000.0000.000
119X185ILE00.0240.02741.679-0.228-0.2280.0000.0000.0000.000
120X186ASN00.001-0.01938.667-0.361-0.3610.0000.0000.0000.000
121X187THR0-0.041-0.02141.387-0.091-0.0910.0000.0000.0000.000
122X188PHE0-0.0210.00743.889-0.151-0.1510.0000.0000.0000.000
123X189TYR0-0.027-0.04245.010-0.120-0.1200.0000.0000.0000.000
124X190ARG10.8350.91841.543-7.602-7.6020.0000.0000.0000.000
125X191ASP-1-0.835-0.91946.2826.9416.9410.0000.0000.0000.000
126X192ASN0-0.078-0.03748.891-0.263-0.2630.0000.0000.0000.000
127X193GLY0-0.0010.01450.705-0.151-0.1510.0000.0000.0000.000
128X194TYR00.0090.01949.995-0.089-0.0890.0000.0000.0000.000
129X195ILE0-0.029-0.04448.1400.1350.1350.0000.0000.0000.000
130X196LEU0-0.020-0.00446.6200.1160.1160.0000.0000.0000.000
131X197GLY0-0.0030.02645.8180.0920.0920.0000.0000.0000.000
132X198GLN0-0.034-0.01739.4580.0510.0510.0000.0000.0000.000
133X199VAL00.006-0.00839.100-0.130-0.1300.0000.0000.0000.000
134X200VAL0-0.056-0.02439.4530.1220.1220.0000.0000.0000.000
135X201GLY0-0.011-0.00837.545-0.088-0.0880.0000.0000.0000.000
136X202THR0-0.009-0.01232.7550.1160.1160.0000.0000.0000.000
137X203PRO0-0.016-0.01034.213-0.199-0.1990.0000.0000.0000.000
138X204GLN0-0.050-0.02835.7560.2290.2290.0000.0000.0000.000
139X205VAL0-0.011-0.01434.430-0.163-0.1630.0000.0000.0000.000
140X206ASP-1-0.844-0.88637.0208.0348.0340.0000.0000.0000.000
141X207PRO0-0.014-0.03737.5150.0630.0630.0000.0000.0000.000
142X208ASP-1-0.893-0.94338.7187.4647.4640.0000.0000.0000.000
143X209GLY0-0.017-0.01439.481-0.109-0.1090.0000.0000.0000.000
144X210VAL00.0110.03140.552-0.056-0.0560.0000.0000.0000.000
145X211VAL00.001-0.00938.1430.1640.1640.0000.0000.0000.000
146X212THR00.0040.01040.609-0.303-0.3030.0000.0000.0000.000
147X213LEU00.0160.01138.6370.2580.2580.0000.0000.0000.000
148X214GLN00.0570.03941.490-0.353-0.3530.0000.0000.0000.000
149X215VAL00.0100.01542.5120.2010.2010.0000.0000.0000.000
150X216ALA0-0.046-0.01944.964-0.130-0.1300.0000.0000.0000.000
151X217GLU-1-0.667-0.80846.3856.4346.4340.0000.0000.0000.000
152X218GLY00.0720.03648.940-0.018-0.0180.0000.0000.0000.000
153X219VAL0-0.061-0.03450.469-0.109-0.1090.0000.0000.0000.000
154X220VAL00.0320.03253.6980.0860.0860.0000.0000.0000.000
155X221GLU-1-0.851-0.91354.8855.8585.8580.0000.0000.0000.000
156X222GLN0-0.039-0.03557.466-0.078-0.0780.0000.0000.0000.000
157X223VAL00.0370.02058.9100.0980.0980.0000.0000.0000.000
158X224THR0-0.047-0.01660.106-0.120-0.1200.0000.0000.0000.000
159X225TYR00.007-0.00761.9210.0270.0270.0000.0000.0000.000
160X226ARG10.8520.89456.874-5.660-5.6600.0000.0000.0000.000
161X227PHE00.0310.01164.2350.0190.0190.0000.0000.0000.000
162X228LEU0-0.017-0.01061.7030.0140.0140.0000.0000.0000.000
163X229ASN0-0.004-0.01266.3500.0060.0060.0000.0000.0000.000
164X230LYS10.9940.97365.856-4.817-4.8170.0000.0000.0000.000
165X231GLU-1-0.879-0.93565.0874.8924.8920.0000.0000.0000.000
166X232GLY0-0.047-0.02062.4060.1010.1010.0000.0000.0000.000
167X233GLU-1-0.897-0.93862.5955.3005.3000.0000.0000.0000.000
168X234PRO0-0.0020.00264.002-0.066-0.0660.0000.0000.0000.000
169X235THR0-0.042-0.01166.595-0.088-0.0880.0000.0000.0000.000
170X236LYS10.8990.94770.112-4.238-4.2380.0000.0000.0000.000
171X237GLN0-0.031-0.01270.7000.0260.0260.0000.0000.0000.000
172X238ARG10.8150.88472.562-4.410-4.4100.0000.0000.0000.000
173X239THR0-0.022-0.00371.990-0.083-0.0830.0000.0000.0000.000
174X240ARG10.9420.96373.658-4.159-4.1590.0000.0000.0000.000
175X241ASP-1-0.776-0.89170.4384.6034.6030.0000.0000.0000.000
176X242PHE0-0.021-0.02171.1580.0330.0330.0000.0000.0000.000
177X243VAL0-0.046-0.01572.7990.0070.0070.0000.0000.0000.000
178X244ILE00.0590.03067.0980.0090.0090.0000.0000.0000.000
179X245SER00.0340.01367.8280.0310.0310.0000.0000.0000.000
180X246ARG10.7970.89168.636-4.333-4.3330.0000.0000.0000.000
181X247GLU-1-0.828-0.90568.7244.4874.4870.0000.0000.0000.000
182X248MET0-0.114-0.03462.4280.0510.0510.0000.0000.0000.000
183X249ASP-1-0.805-0.89663.3574.9464.9460.0000.0000.0000.000
184X250THR0-0.121-0.08258.5040.1010.1010.0000.0000.0000.000
185X251GLN0-0.046-0.02961.320-0.036-0.0360.0000.0000.0000.000
186X252PRO00.003-0.01660.3170.0950.0950.0000.0000.0000.000
187X253GLY0-0.029-0.01558.883-0.071-0.0710.0000.0000.0000.000
188X254VAL0-0.0110.01857.9770.0450.0450.0000.0000.0000.000
189X255VAL0-0.026-0.01652.2280.0700.0700.0000.0000.0000.000
190X256LEU00.0400.01352.100-0.069-0.0690.0000.0000.0000.000
191X257ASN00.004-0.02553.0280.1040.1040.0000.0000.0000.000
192X258GLN00.0350.02651.002-0.175-0.1750.0000.0000.0000.000
193X259LYS10.9270.94152.864-6.130-6.1300.0000.0000.0000.000
194X260THR00.0410.02557.193-0.066-0.0660.0000.0000.0000.000
195X261VAL00.0490.02856.172-0.079-0.0790.0000.0000.0000.000
196X262GLN0-0.049-0.02355.840-0.167-0.1670.0000.0000.0000.000
197X263ALA0-0.008-0.00759.675-0.078-0.0780.0000.0000.0000.000
198X264ASP-1-0.700-0.81462.0945.0995.0990.0000.0000.0000.000
199X265LEU0-0.009-0.00559.077-0.079-0.0790.0000.0000.0000.000
200X266ARG10.9140.96060.749-5.269-5.2690.0000.0000.0000.000
201X267ARG10.8450.90665.069-4.992-4.9920.0000.0000.0000.000
202X268LEU0-0.010-0.00764.696-0.076-0.0760.0000.0000.0000.000
203X269PHE0-0.066-0.03766.447-0.070-0.0700.0000.0000.0000.000
204X270GLU-1-0.961-0.98368.5354.6424.6420.0000.0000.0000.000
205X271LEU0-0.054-0.00971.344-0.090-0.0900.0000.0000.0000.000
206X272GLY00.0110.01872.275-0.069-0.0690.0000.0000.0000.000
207X273LEU0-0.047-0.02472.413-0.052-0.0520.0000.0000.0000.000
208X274PHE0-0.023-0.03168.116-0.024-0.0240.0000.0000.0000.000
209X275GLU-1-0.942-0.96968.5914.6174.6170.0000.0000.0000.000
210X276ASP-1-0.891-0.93862.3205.3495.3490.0000.0000.0000.000
211X277VAL0-0.009-0.01062.139-0.059-0.0590.0000.0000.0000.000
212X278GLN0-0.046-0.02557.7870.1670.1670.0000.0000.0000.000
213X279VAL00.002-0.00355.638-0.037-0.0370.0000.0000.0000.000
214X280ALA0-0.014-0.00353.9760.1050.1050.0000.0000.0000.000
215X281LEU0-0.023-0.01250.471-0.085-0.0850.0000.0000.0000.000
216X282GLU-1-0.790-0.86251.3995.9805.9800.0000.0000.0000.000
217X283PRO00.002-0.00548.100-0.053-0.0530.0000.0000.0000.000
218X284GLY0-0.005-0.00950.515-0.104-0.1040.0000.0000.0000.000
219X285GLN0-0.029-0.02951.8720.1070.1070.0000.0000.0000.000
220X286ASN0-0.0070.00249.8580.2270.2270.0000.0000.0000.000
221X287PRO00.0250.01346.696-0.020-0.0200.0000.0000.0000.000
222X288ARG10.8440.91343.868-7.137-7.1370.0000.0000.0000.000
223X289ARG10.8680.95147.790-6.066-6.0660.0000.0000.0000.000
224X290VAL00.0050.01250.5570.0740.0740.0000.0000.0000.000
225X291ASN00.0560.03352.940-0.187-0.1870.0000.0000.0000.000
226X292LEU00.0060.00055.2750.0950.0950.0000.0000.0000.000
227X293ILE0-0.032-0.01656.208-0.139-0.1390.0000.0000.0000.000
228X294LEU00.0090.00858.4450.0510.0510.0000.0000.0000.000
229X295ASN0-0.038-0.02057.787-0.091-0.0910.0000.0000.0000.000
230X296ILE00.0050.00261.8020.0080.0080.0000.0000.0000.000
231X297LYS10.9140.97462.933-5.189-5.1890.0000.0000.0000.000
232X298GLU-1-0.760-0.89067.4214.4914.4910.0000.0000.0000.000
233X299ARG10.9130.96871.033-4.327-4.3270.0000.0000.0000.000
234X300ASN00.0020.01173.508-0.046-0.0460.0000.0000.0000.000
235X301THR0-0.023-0.00675.889-0.022-0.0220.0000.0000.0000.000