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: G6K61

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2445463.944673
FMO2-HF: Nuclear repulsion 2355167.900301
FMO2-HF: Total energy -90296.044372
FMO2-MP2: Total energy -90566.00191


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.
-47.223-44.761-0.017-1.092-1.3510.005
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 : -0.940 / q_NPA : -0.975
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].
3X69PRO0-0.022-0.0123.875-0.7551.096-0.019-0.932-0.9000.004
4X70LYS10.8350.8903.467-42.280-41.8820.004-0.119-0.2820.001
5X71VAL0-0.012-0.0108.116-1.909-1.9090.0000.0000.0000.000
6X72LEU00.0010.01011.6660.4890.4890.0000.0000.0000.000
7X73ILE0-0.030-0.01313.967-0.443-0.4430.0000.0000.0000.000
8X74ALA00.0080.02116.618-0.374-0.3740.0000.0000.0000.000
9X75GLU-1-0.848-0.92220.31411.63511.6350.0000.0000.0000.000
10X76VAL0-0.012-0.01718.3690.7530.7530.0000.0000.0000.000
11X77VAL0-0.0020.01621.123-0.502-0.5020.0000.0000.0000.000
12X78VAL0-0.0020.00022.7240.6960.6960.0000.0000.0000.000
13X79GLU-1-0.849-0.92125.00411.15311.1530.0000.0000.0000.000
14X80GLY00.0380.01126.9610.2660.2660.0000.0000.0000.000
15X81ALA0-0.034-0.01227.796-0.167-0.1670.0000.0000.0000.000
16X82THR0-0.025-0.03129.800-0.129-0.1290.0000.0000.0000.000
17X83PRO00.0430.00931.5960.2960.2960.0000.0000.0000.000
18X84GLU-1-0.819-0.90631.7249.4049.4040.0000.0000.0000.000
19X85LEU0-0.029-0.01028.7980.2770.2770.0000.0000.0000.000
20X86GLU-1-0.866-0.91027.29711.36911.3690.0000.0000.0000.000
21X87GLN0-0.020-0.01326.4100.2480.2480.0000.0000.0000.000
22X88LEU00.0090.01425.3810.4070.4070.0000.0000.0000.000
23X89VAL00.001-0.00521.9180.6350.6350.0000.0000.0000.000
24X90TYR0-0.046-0.06021.7410.9490.9490.0000.0000.0000.000
25X91GLN0-0.068-0.02321.5840.3190.3190.0000.0000.0000.000
26X92VAL0-0.053-0.02520.0630.4110.4110.0000.0000.0000.000
27X93ILE0-0.0570.00117.0361.0501.0500.0000.0000.0000.000
28X94SER0-0.051-0.05213.001-0.176-0.1760.0000.0000.0000.000
29X95THR0-0.032-0.03913.5950.1060.1060.0000.0000.0000.000
30X96ARG10.8240.90215.152-16.936-16.9360.0000.0000.0000.000
31X97PRO00.0470.02817.3060.7100.7100.0000.0000.0000.000
32X98GLY0-0.0040.01118.613-0.142-0.1420.0000.0000.0000.000
33X99SER0-0.052-0.02314.0400.8980.8980.0000.0000.0000.000
34X100THR00.018-0.0049.399-0.412-0.4120.0000.0000.0000.000
35X101THR0-0.005-0.0059.2332.1022.1020.0000.0000.0000.000
36X102THR00.0740.0084.2941.2491.257-0.001-0.0090.0030.000
37X103ARG10.9140.9517.275-26.539-26.5390.0000.0000.0000.000
38X104THR00.0360.0134.244-6.643-6.438-0.001-0.032-0.1720.000
39X105GLN00.0550.0556.826-0.128-0.1280.0000.0000.0000.000
40X106LEU00.0190.0089.252-2.700-2.7000.0000.0000.0000.000
41X107GLN00.0020.01710.419-1.905-1.9050.0000.0000.0000.000
42X108GLN00.010-0.0057.652-0.807-0.8070.0000.0000.0000.000
43X109ASP-1-0.703-0.80012.01219.61119.6110.0000.0000.0000.000
44X110THR0-0.010-0.01914.872-1.258-1.2580.0000.0000.0000.000
45X111ASN0-0.009-0.01013.983-1.385-1.3850.0000.0000.0000.000
46X112ALA00.0130.01116.116-1.020-1.0200.0000.0000.0000.000
47X113ILE00.0380.02217.823-0.961-0.9610.0000.0000.0000.000
48X114PHE0-0.0090.01419.901-0.764-0.7640.0000.0000.0000.000
49X115ALA00.0080.01119.561-0.713-0.7130.0000.0000.0000.000
50X116THR0-0.007-0.01821.555-0.782-0.7820.0000.0000.0000.000
51X117GLY00.0000.00924.527-0.533-0.5330.0000.0000.0000.000
52X118PHE00.0240.00826.691-0.418-0.4180.0000.0000.0000.000
53X119PHE0-0.025-0.01524.590-0.296-0.2960.0000.0000.0000.000
54X120ALA0-0.0020.00126.3120.1980.1980.0000.0000.0000.000
55X121ASP-1-0.864-0.93324.19212.74212.7420.0000.0000.0000.000
56X122VAL0-0.030-0.01419.885-0.217-0.2170.0000.0000.0000.000
57X123ASN0-0.050-0.01519.0981.1251.1250.0000.0000.0000.000
58X124ALA00.0230.02015.542-0.415-0.4150.0000.0000.0000.000
59X125VAL0-0.043-0.02816.8950.6010.6010.0000.0000.0000.000
60X126PRO00.0030.00714.909-0.530-0.5300.0000.0000.0000.000
61X127ARG10.8790.92017.794-14.495-14.4950.0000.0000.0000.000
62X128ASP-1-0.872-0.92019.92114.81514.8150.0000.0000.0000.000
63X129THR0-0.041-0.04121.964-0.571-0.5710.0000.0000.0000.000
64X130PRO0-0.021-0.02624.8890.1550.1550.0000.0000.0000.000
65X131LEU0-0.032-0.00224.590-0.187-0.1870.0000.0000.0000.000
66X132GLY00.0200.00521.2340.2890.2890.0000.0000.0000.000
67X133VAL00.0050.00316.047-0.156-0.1560.0000.0000.0000.000
68X134ARG10.8670.93219.238-12.051-12.0510.0000.0000.0000.000
69X135ILE0-0.049-0.02815.0490.5910.5910.0000.0000.0000.000
70X136THR00.0240.01318.830-0.817-0.8170.0000.0000.0000.000
71X137PHE0-0.002-0.00615.9120.5610.5610.0000.0000.0000.000
72X138VAL00.0290.02121.334-0.655-0.6550.0000.0000.0000.000
73X139VAL0-0.025-0.01623.0810.5480.5480.0000.0000.0000.000
74X140ARG10.9190.94925.353-11.609-11.6090.0000.0000.0000.000
75X141PRO00.0080.00028.3040.1960.1960.0000.0000.0000.000
76X142TYR0-0.029-0.00427.285-0.228-0.2280.0000.0000.0000.000
77X143PRO00.0060.00532.303-0.055-0.0550.0000.0000.0000.000
78X144VAL0-0.025-0.01036.0420.0720.0720.0000.0000.0000.000
79X145LEU0-0.0240.00038.064-0.180-0.1800.0000.0000.0000.000
80X146ARG10.8920.94839.655-7.770-7.7700.0000.0000.0000.000
81X147ALA00.0270.00542.940-0.186-0.1860.0000.0000.0000.000
82X148VAL0-0.0070.00840.6450.1800.1800.0000.0000.0000.000
83X149GLN0-0.0080.00443.209-0.325-0.3250.0000.0000.0000.000
84X150VAL0-0.025-0.00843.8840.2130.2130.0000.0000.0000.000
85X151ALA00.0490.02745.644-0.163-0.1630.0000.0000.0000.000
86X152GLY00.009-0.00546.4600.1480.1480.0000.0000.0000.000
87X153ASN0-0.053-0.03048.5090.0170.0170.0000.0000.0000.000
88X154GLN0-0.047-0.05050.148-0.142-0.1420.0000.0000.0000.000
89X155VAL0-0.001-0.00951.396-0.089-0.0890.0000.0000.0000.000
90X156LEU0-0.039-0.00245.854-0.011-0.0110.0000.0000.0000.000
91X157THR0-0.001-0.02450.3220.0550.0550.0000.0000.0000.000
92X158GLN00.042-0.00546.9970.1550.1550.0000.0000.0000.000
93X159GLU-1-0.849-0.91249.5096.1526.1520.0000.0000.0000.000
94X160LYS10.8160.89948.332-6.485-6.4850.0000.0000.0000.000
95X161VAL00.0170.00344.3200.1600.1600.0000.0000.0000.000
96X162ASN00.002-0.00745.4040.2480.2480.0000.0000.0000.000
97X163GLU-1-0.850-0.90246.5086.6856.6850.0000.0000.0000.000
98X164ILE0-0.040-0.01842.1750.1210.1210.0000.0000.0000.000
99X165PHE0-0.006-0.00938.3300.2370.2370.0000.0000.0000.000
100X166ALA00.0340.02942.2030.1200.1200.0000.0000.0000.000
101X167PRO0-0.041-0.02240.9780.0390.0390.0000.0000.0000.000
102X168GLN0-0.040-0.02137.3750.2390.2390.0000.0000.0000.000
103X169ILE0-0.0320.00039.3990.1350.1350.0000.0000.0000.000
104X170GLY0-0.022-0.00641.661-0.078-0.0780.0000.0000.0000.000
105X171ARG10.8210.88835.808-8.574-8.5740.0000.0000.0000.000
106X172THR0-0.004-0.00331.925-0.187-0.1870.0000.0000.0000.000
107X173LEU00.0110.01733.6780.0850.0850.0000.0000.0000.000
108X174ASN00.038-0.00228.5670.4050.4050.0000.0000.0000.000
109X175LEU00.0340.01428.410-0.277-0.2770.0000.0000.0000.000
110X176ARG10.8380.92023.585-12.652-12.6520.0000.0000.0000.000
111X177GLU-1-0.845-0.91330.4788.8998.8990.0000.0000.0000.000
112X178LEU00.0320.02833.784-0.276-0.2760.0000.0000.0000.000
113X179GLN0-0.006-0.01531.903-0.161-0.1610.0000.0000.0000.000
114X180ALA00.0290.01134.143-0.221-0.2210.0000.0000.0000.000
115X181GLY0-0.037-0.00335.730-0.280-0.2800.0000.0000.0000.000
116X182ILE00.0360.01335.601-0.261-0.2610.0000.0000.0000.000
117X183GLU-1-0.798-0.88735.5898.6438.6430.0000.0000.0000.000
118X184LYS10.8500.92538.612-8.286-8.2860.0000.0000.0000.000
119X185ILE00.0250.02541.650-0.227-0.2270.0000.0000.0000.000
120X186ASN00.004-0.02438.419-0.354-0.3540.0000.0000.0000.000
121X187THR0-0.052-0.03141.301-0.114-0.1140.0000.0000.0000.000
122X188PHE0-0.034-0.00343.748-0.155-0.1550.0000.0000.0000.000
123X189TYR0-0.030-0.03544.813-0.140-0.1400.0000.0000.0000.000
124X190ARG10.8480.89941.497-7.647-7.6470.0000.0000.0000.000
125X191ASP-1-0.819-0.88446.0456.9906.9900.0000.0000.0000.000
126X192ASN0-0.079-0.04448.627-0.261-0.2610.0000.0000.0000.000
127X193GLY0-0.0190.00550.376-0.156-0.1560.0000.0000.0000.000
128X194TYR00.0120.02049.705-0.093-0.0930.0000.0000.0000.000
129X195ILE0-0.038-0.04247.7110.1340.1340.0000.0000.0000.000
130X196LEU0-0.0100.00846.5840.1050.1050.0000.0000.0000.000
131X197GLY0-0.0220.01046.0890.0650.0650.0000.0000.0000.000
132X198GLN0-0.048-0.03339.0610.0570.0570.0000.0000.0000.000
133X199VAL00.0430.00538.607-0.136-0.1360.0000.0000.0000.000
134X200VAL0-0.074-0.02839.1810.1180.1180.0000.0000.0000.000
135X201GLY00.0120.00636.934-0.090-0.0900.0000.0000.0000.000
136X202THR0-0.019-0.01732.4440.0670.0670.0000.0000.0000.000
137X203PRO0-0.008-0.00433.968-0.214-0.2140.0000.0000.0000.000
138X204GLN0-0.053-0.02335.2380.2920.2920.0000.0000.0000.000
139X205VAL0-0.019-0.02334.154-0.133-0.1330.0000.0000.0000.000
140X206ASP-1-0.818-0.88536.6108.0828.0820.0000.0000.0000.000
141X207PRO0-0.009-0.03337.5890.0440.0440.0000.0000.0000.000
142X208ASP-1-0.881-0.93438.6437.5657.5650.0000.0000.0000.000
143X209GLY0-0.003-0.01039.139-0.059-0.0590.0000.0000.0000.000
144X210VAL0-0.0060.00840.180-0.061-0.0610.0000.0000.0000.000
145X211VAL0-0.010-0.00737.8370.2280.2280.0000.0000.0000.000
146X212THR00.0150.01640.112-0.286-0.2860.0000.0000.0000.000
147X213LEU0-0.002-0.00338.5810.2200.2200.0000.0000.0000.000
148X214GLN00.0410.02141.185-0.337-0.3370.0000.0000.0000.000
149X215VAL00.0090.01342.0810.1850.1850.0000.0000.0000.000
150X216ALA0-0.015-0.00444.494-0.092-0.0920.0000.0000.0000.000
151X217GLU-1-0.674-0.81146.1796.4656.4650.0000.0000.0000.000
152X218GLY00.0640.03448.771-0.041-0.0410.0000.0000.0000.000
153X219VAL0-0.072-0.03950.127-0.096-0.0960.0000.0000.0000.000
154X220VAL00.0290.01753.5470.0750.0750.0000.0000.0000.000
155X221GLU-1-0.832-0.90954.5335.8935.8930.0000.0000.0000.000
156X222GLN0-0.041-0.02857.001-0.100-0.1000.0000.0000.0000.000
157X223VAL00.0430.02158.6800.0960.0960.0000.0000.0000.000
158X224THR0-0.031-0.02260.073-0.106-0.1060.0000.0000.0000.000
159X225TYR0-0.008-0.02061.6730.0270.0270.0000.0000.0000.000
160X226ARG10.8280.87956.848-5.672-5.6720.0000.0000.0000.000
161X227PHE00.0420.02564.1020.0200.0200.0000.0000.0000.000
162X228LEU0-0.014-0.00361.5910.0030.0030.0000.0000.0000.000
163X229ASN00.008-0.01066.283-0.001-0.0010.0000.0000.0000.000
164X230LYS10.9720.97566.498-4.774-4.7740.0000.0000.0000.000
165X231GLU-1-0.874-0.93465.0104.9074.9070.0000.0000.0000.000
166X232GLY0-0.035-0.02462.5200.1050.1050.0000.0000.0000.000
167X233GLU-1-0.875-0.92362.8375.2915.2910.0000.0000.0000.000
168X234PRO0-0.008-0.00963.937-0.060-0.0600.0000.0000.0000.000
169X235THR0-0.039-0.01466.545-0.090-0.0900.0000.0000.0000.000
170X236LYS10.8950.94770.098-4.245-4.2450.0000.0000.0000.000
171X237GLN0-0.038-0.01470.8750.0130.0130.0000.0000.0000.000
172X238ARG10.7800.86472.576-4.417-4.4170.0000.0000.0000.000
173X239THR0-0.0160.00271.957-0.088-0.0880.0000.0000.0000.000
174X240ARG10.9380.96774.146-4.220-4.2200.0000.0000.0000.000
175X241ASP-1-0.795-0.89970.6394.5654.5650.0000.0000.0000.000
176X242PHE00.007-0.01170.9470.0500.0500.0000.0000.0000.000
177X243VAL0-0.047-0.02572.8590.0000.0000.0000.0000.0000.000
178X244ILE00.0400.02667.0270.0110.0110.0000.0000.0000.000
179X245SER00.0320.00767.5950.0260.0260.0000.0000.0000.000
180X246ARG10.8020.88268.438-4.352-4.3520.0000.0000.0000.000
181X247GLU-1-0.791-0.87368.6114.5184.5180.0000.0000.0000.000
182X248MET0-0.084-0.01962.3540.0580.0580.0000.0000.0000.000
183X249ASP-1-0.783-0.87063.3254.9544.9540.0000.0000.0000.000
184X250THR0-0.123-0.08958.2650.0950.0950.0000.0000.0000.000
185X251GLN0-0.041-0.02661.1600.0230.0230.0000.0000.0000.000
186X252PRO0-0.017-0.02560.2930.1030.1030.0000.0000.0000.000
187X253GLY0-0.0150.00158.977-0.080-0.0800.0000.0000.0000.000
188X254VAL0-0.0190.00557.6530.0700.0700.0000.0000.0000.000
189X255VAL0-0.008-0.00552.0490.0760.0760.0000.0000.0000.000
190X256LEU00.0190.01852.060-0.088-0.0880.0000.0000.0000.000
191X257ASN0-0.004-0.03052.7340.1080.1080.0000.0000.0000.000
192X258GLN00.0420.02350.979-0.149-0.1490.0000.0000.0000.000
193X259LYS10.9180.94252.489-6.218-6.2180.0000.0000.0000.000
194X260THR00.0420.03057.296-0.077-0.0770.0000.0000.0000.000
195X261VAL00.0510.03156.047-0.088-0.0880.0000.0000.0000.000
196X262GLN0-0.023-0.01156.320-0.167-0.1670.0000.0000.0000.000
197X263ALA0-0.015-0.00259.644-0.079-0.0790.0000.0000.0000.000
198X264ASP-1-0.717-0.82761.9695.1265.1260.0000.0000.0000.000
199X265LEU0-0.021-0.01358.893-0.074-0.0740.0000.0000.0000.000
200X266ARG10.8980.95960.772-5.293-5.2930.0000.0000.0000.000
201X267ARG10.8370.89264.906-5.007-5.0070.0000.0000.0000.000
202X268LEU0-0.008-0.00764.729-0.083-0.0830.0000.0000.0000.000
203X269PHE0-0.042-0.01966.363-0.060-0.0600.0000.0000.0000.000
204X270GLU-1-0.931-0.97668.3774.6804.6800.0000.0000.0000.000
205X271LEU0-0.070-0.01771.215-0.092-0.0920.0000.0000.0000.000
206X272GLY0-0.0010.00772.157-0.067-0.0670.0000.0000.0000.000
207X273LEU0-0.043-0.02372.225-0.051-0.0510.0000.0000.0000.000
208X274PHE0-0.036-0.02968.139-0.021-0.0210.0000.0000.0000.000
209X275GLU-1-0.928-0.96868.7994.5984.5980.0000.0000.0000.000
210X276ASP-1-0.873-0.93362.4115.3635.3630.0000.0000.0000.000
211X277VAL0-0.013-0.01062.381-0.065-0.0650.0000.0000.0000.000
212X278GLN0-0.037-0.01157.8280.1690.1690.0000.0000.0000.000
213X279VAL00.0090.00155.590-0.021-0.0210.0000.0000.0000.000
214X280ALA0-0.025-0.00753.9940.0970.0970.0000.0000.0000.000
215X281LEU0-0.015-0.01550.646-0.070-0.0700.0000.0000.0000.000
216X282GLU-1-0.791-0.85351.3905.9985.9980.0000.0000.0000.000
217X283PRO0-0.002-0.01248.133-0.045-0.0450.0000.0000.0000.000
218X284GLY00.0070.01750.628-0.120-0.1200.0000.0000.0000.000
219X285GLN0-0.049-0.04851.7890.0750.0750.0000.0000.0000.000
220X286ASN0-0.033-0.00949.5820.2170.2170.0000.0000.0000.000
221X287PRO00.0310.00646.542-0.015-0.0150.0000.0000.0000.000
222X288ARG10.8060.89244.023-7.151-7.1510.0000.0000.0000.000
223X289ARG10.8500.93747.557-6.107-6.1070.0000.0000.0000.000
224X290VAL00.0170.01250.2300.0800.0800.0000.0000.0000.000
225X291ASN00.0320.03252.745-0.179-0.1790.0000.0000.0000.000
226X292LEU00.008-0.00255.2250.0960.0960.0000.0000.0000.000
227X293ILE0-0.030-0.00855.928-0.135-0.1350.0000.0000.0000.000
228X294LEU00.003-0.00158.4120.0400.0400.0000.0000.0000.000
229X295ASN0-0.023-0.02357.585-0.103-0.1030.0000.0000.0000.000
230X296ILE0-0.009-0.00161.7050.0030.0030.0000.0000.0000.000
231X297LYS10.8840.95362.985-5.203-5.2030.0000.0000.0000.000
232X298GLU-1-0.745-0.88167.5134.4874.4870.0000.0000.0000.000
233X299ARG10.9070.96771.033-4.350-4.3500.0000.0000.0000.000
234X300ASN00.0300.03273.471-0.053-0.0530.0000.0000.0000.000
235X301THR0-0.046-0.02475.794-0.023-0.0230.0000.0000.0000.000