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: V5151

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2437206.1209
FMO2-HF: Nuclear repulsion 2346912.969476
FMO2-HF: Total energy -90293.151424
FMO2-MP2: Total energy -90563.44921


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.
-32.396-30.667-0.013-0.813-0.9020.005
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 : -0.971 / q_NPA : -1.010
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].
3X69PRO0-0.047-0.0223.823-0.1951.384-0.011-0.797-0.7710.005
4X70LYS10.9620.9635.556-31.904-31.9040.0000.0000.0000.000
5X71VAL00.0100.0078.284-1.500-1.5000.0000.0000.0000.000
6X72LEU0-0.021-0.00811.9600.4920.4920.0000.0000.0000.000
7X73ILE0-0.038-0.00414.239-0.587-0.5870.0000.0000.0000.000
8X74ALA00.0250.00916.904-0.264-0.2640.0000.0000.0000.000
9X75GLU-1-0.906-0.97120.72610.96810.9680.0000.0000.0000.000
10X76VAL00.001-0.00318.8820.6130.6130.0000.0000.0000.000
11X77VAL00.0000.00021.556-0.516-0.5160.0000.0000.0000.000
12X78VAL00.0200.00823.2250.5960.5960.0000.0000.0000.000
13X79GLU-1-0.917-0.96225.19310.41810.4180.0000.0000.0000.000
14X80GLY00.0140.00127.0490.2420.2420.0000.0000.0000.000
15X81ALA0-0.044-0.02128.089-0.115-0.1150.0000.0000.0000.000
16X82THR0-0.001-0.00430.147-0.108-0.1080.0000.0000.0000.000
17X83PRO00.0320.00331.9760.2560.2560.0000.0000.0000.000
18X84GLU-1-0.860-0.93632.1468.8778.8770.0000.0000.0000.000
19X85LEU0-0.023-0.01229.1190.2500.2500.0000.0000.0000.000
20X86GLU-1-0.914-0.94927.82210.74910.7490.0000.0000.0000.000
21X87GLN00.015-0.00826.9210.4140.4140.0000.0000.0000.000
22X88LEU00.0010.01025.5740.4230.4230.0000.0000.0000.000
23X89VAL00.0220.00922.2570.5390.5390.0000.0000.0000.000
24X90TYR0-0.024-0.01121.9620.6880.6880.0000.0000.0000.000
25X91GLN0-0.041-0.00722.0670.4080.4080.0000.0000.0000.000
26X92VAL0-0.049-0.02620.3230.3720.3720.0000.0000.0000.000
27X93ILE0-0.0490.01317.2870.8270.8270.0000.0000.0000.000
28X94SER0-0.083-0.06413.6390.0500.0500.0000.0000.0000.000
29X95THR0-0.045-0.05914.0080.3920.3920.0000.0000.0000.000
30X96ARG10.8240.90315.623-15.783-15.7830.0000.0000.0000.000
31X97PRO00.0110.00017.3880.7060.7060.0000.0000.0000.000
32X98GLY00.0100.00418.595-0.248-0.2480.0000.0000.0000.000
33X99SER0-0.058-0.01214.3390.8530.8530.0000.0000.0000.000
34X100THR00.013-0.0109.187-0.296-0.2960.0000.0000.0000.000
35X101THR00.0130.0039.3661.9201.9200.0000.0000.0000.000
36X102THR00.0680.0064.3420.6230.689-0.001-0.012-0.0520.000
37X103ARG10.9370.9607.077-24.517-24.5170.0000.0000.0000.000
38X104THR00.0450.0134.515-4.648-4.564-0.001-0.004-0.0790.000
39X105GLN00.0760.0636.7321.3001.3000.0000.0000.0000.000
40X106LEU00.0250.0389.115-2.107-2.1070.0000.0000.0000.000
41X107GLN0-0.022-0.01610.464-1.853-1.8530.0000.0000.0000.000
42X108GLN00.010-0.0057.478-2.215-2.2150.0000.0000.0000.000
43X109ASP-1-0.695-0.81012.37918.36318.3630.0000.0000.0000.000
44X110THR0-0.056-0.03115.069-1.322-1.3220.0000.0000.0000.000
45X111ASN00.0220.00313.738-1.624-1.6240.0000.0000.0000.000
46X112ALA0-0.015-0.00216.468-0.882-0.8820.0000.0000.0000.000
47X113ILE00.0430.02118.316-0.839-0.8390.0000.0000.0000.000
48X114PHE00.0080.02120.143-0.724-0.7240.0000.0000.0000.000
49X115ALA0-0.0120.00120.465-0.630-0.6300.0000.0000.0000.000
50X116THR0-0.041-0.03222.273-0.681-0.6810.0000.0000.0000.000
51X117GLY0-0.0050.00624.999-0.485-0.4850.0000.0000.0000.000
52X118PHE00.0400.01927.181-0.424-0.4240.0000.0000.0000.000
53X119PHE0-0.023-0.01324.993-0.309-0.3090.0000.0000.0000.000
54X120ALA0-0.0090.00226.5240.1670.1670.0000.0000.0000.000
55X121ASP-1-0.938-0.98123.77412.51412.5140.0000.0000.0000.000
56X122VAL0-0.016-0.00619.924-0.184-0.1840.0000.0000.0000.000
57X123ASN0-0.041-0.00319.3570.8060.8060.0000.0000.0000.000
58X124ALA00.0210.01515.853-0.315-0.3150.0000.0000.0000.000
59X125VAL0-0.034-0.02717.3320.4030.4030.0000.0000.0000.000
60X126PRO00.0100.01314.894-0.394-0.3940.0000.0000.0000.000
61X127ARG10.8630.92217.892-13.793-13.7930.0000.0000.0000.000
62X128ASP-1-0.828-0.90519.75814.46614.4660.0000.0000.0000.000
63X129THR0-0.086-0.06321.994-0.490-0.4900.0000.0000.0000.000
64X130PRO0-0.007-0.02024.8040.1610.1610.0000.0000.0000.000
65X131LEU0-0.0120.00024.489-0.050-0.0500.0000.0000.0000.000
66X132GLY00.0340.03221.5040.2740.2740.0000.0000.0000.000
67X133VAL00.0230.02816.374-0.162-0.1620.0000.0000.0000.000
68X134ARG10.9090.98419.504-11.553-11.5530.0000.0000.0000.000
69X135ILE0-0.031-0.01815.3290.5540.5540.0000.0000.0000.000
70X136THR00.0260.01019.018-0.725-0.7250.0000.0000.0000.000
71X137PHE0-0.013-0.01516.1100.5970.5970.0000.0000.0000.000
72X138VAL00.0130.00721.436-0.508-0.5080.0000.0000.0000.000
73X139VAL00.0040.00723.3800.3990.3990.0000.0000.0000.000
74X140ARG10.9860.99925.592-10.609-10.6090.0000.0000.0000.000
75X141PRO00.0460.00728.4670.2270.2270.0000.0000.0000.000
76X142TYR0-0.071-0.01827.944-0.229-0.2290.0000.0000.0000.000
77X143PRO00.0590.03132.505-0.014-0.0140.0000.0000.0000.000
78X144VAL0-0.047-0.01836.1660.0740.0740.0000.0000.0000.000
79X145LEU0-0.0190.00238.299-0.116-0.1160.0000.0000.0000.000
80X146ARG10.9210.94239.849-7.427-7.4270.0000.0000.0000.000
81X147ALA00.0270.01943.027-0.186-0.1860.0000.0000.0000.000
82X148VAL0-0.0060.00341.3990.1970.1970.0000.0000.0000.000
83X149GLN0-0.0090.00543.899-0.290-0.2900.0000.0000.0000.000
84X150VAL0-0.028-0.02344.8060.1980.1980.0000.0000.0000.000
85X151ALA00.0100.01746.232-0.156-0.1560.0000.0000.0000.000
86X152GLY0-0.011-0.02047.3450.1230.1230.0000.0000.0000.000
87X153ASN0-0.048-0.02749.3540.0290.0290.0000.0000.0000.000
88X154GLN0-0.070-0.05550.910-0.146-0.1460.0000.0000.0000.000
89X155VAL0-0.013-0.01152.219-0.064-0.0640.0000.0000.0000.000
90X156LEU0-0.0510.00746.734-0.006-0.0060.0000.0000.0000.000
91X157THR00.0680.02051.3440.0340.0340.0000.0000.0000.000
92X158GLN00.040-0.00747.7410.1330.1330.0000.0000.0000.000
93X159GLU-1-0.908-0.96950.3665.9165.9160.0000.0000.0000.000
94X160LYS10.9320.99048.545-6.348-6.3480.0000.0000.0000.000
95X161VAL00.0140.00245.2050.1500.1500.0000.0000.0000.000
96X162ASN00.0190.00446.1330.2780.2780.0000.0000.0000.000
97X163GLU-1-0.919-0.96247.2636.3636.3630.0000.0000.0000.000
98X164ILE0-0.084-0.03942.7610.1170.1170.0000.0000.0000.000
99X165PHE0-0.004-0.02039.1960.2030.2030.0000.0000.0000.000
100X166ALA00.0400.03142.9120.1170.1170.0000.0000.0000.000
101X167PRO0-0.034-0.02441.6560.0500.0500.0000.0000.0000.000
102X168GLN0-0.035-0.01737.6090.2590.2590.0000.0000.0000.000
103X169ILE0-0.0130.02139.9370.1290.1290.0000.0000.0000.000
104X170GLY0-0.030-0.01941.989-0.071-0.0710.0000.0000.0000.000
105X171ARG10.8720.91236.596-8.224-8.2240.0000.0000.0000.000
106X172THR0-0.026-0.00232.177-0.156-0.1560.0000.0000.0000.000
107X173LEU00.0140.01533.9140.0310.0310.0000.0000.0000.000
108X174ASN00.0490.00829.1700.3100.3100.0000.0000.0000.000
109X175LEU00.019-0.00729.399-0.233-0.2330.0000.0000.0000.000
110X176ARG10.8690.93324.200-12.013-12.0130.0000.0000.0000.000
111X177GLU-1-0.886-0.94630.9558.8028.8020.0000.0000.0000.000
112X178LEU00.0160.01034.353-0.276-0.2760.0000.0000.0000.000
113X179GLN0-0.003-0.00432.280-0.143-0.1430.0000.0000.0000.000
114X180ALA00.0200.00634.757-0.182-0.1820.0000.0000.0000.000
115X181GLY0-0.069-0.05336.447-0.261-0.2610.0000.0000.0000.000
116X182ILE00.0380.02136.144-0.248-0.2480.0000.0000.0000.000
117X183GLU-1-0.859-0.93836.2908.4258.4250.0000.0000.0000.000
118X184LYS10.8940.97039.281-8.058-8.0580.0000.0000.0000.000
119X185ILE00.0090.02042.241-0.218-0.2180.0000.0000.0000.000
120X186ASN00.0330.01039.470-0.343-0.3430.0000.0000.0000.000
121X187THR0-0.036-0.01942.166-0.063-0.0630.0000.0000.0000.000
122X188PHE0-0.0160.00244.622-0.145-0.1450.0000.0000.0000.000
123X189TYR0-0.034-0.05245.643-0.113-0.1130.0000.0000.0000.000
124X190ARG10.9260.96241.802-7.576-7.5760.0000.0000.0000.000
125X191ASP-1-0.900-0.94947.4996.7486.7480.0000.0000.0000.000
126X192ASN0-0.083-0.03449.700-0.247-0.2470.0000.0000.0000.000
127X193GLY0-0.0080.00751.534-0.145-0.1450.0000.0000.0000.000
128X194TYR00.0040.01350.677-0.085-0.0850.0000.0000.0000.000
129X195ILE0-0.018-0.03449.0340.1270.1270.0000.0000.0000.000
130X196LEU0-0.028-0.01547.5010.1160.1160.0000.0000.0000.000
131X197GLY0-0.0010.03046.6110.0880.0880.0000.0000.0000.000
132X198GLN0-0.039-0.02740.8760.0580.0580.0000.0000.0000.000
133X199VAL0-0.001-0.00939.594-0.123-0.1230.0000.0000.0000.000
134X200VAL0-0.042-0.01140.0970.1180.1180.0000.0000.0000.000
135X201GLY0-0.025-0.02038.071-0.084-0.0840.0000.0000.0000.000
136X202THR0-0.017-0.01333.1930.1190.1190.0000.0000.0000.000
137X203PRO0-0.006-0.00334.479-0.206-0.2060.0000.0000.0000.000
138X204GLN0-0.0150.00036.0060.0520.0520.0000.0000.0000.000
139X205VAL0-0.013-0.01334.248-0.155-0.1550.0000.0000.0000.000
140X206ASP-1-0.853-0.91037.0087.8117.8110.0000.0000.0000.000
141X207PRO0-0.044-0.04837.6520.0790.0790.0000.0000.0000.000
142X208ASP-1-0.901-0.94938.6617.2617.2610.0000.0000.0000.000
143X209GLY0-0.019-0.01339.399-0.101-0.1010.0000.0000.0000.000
144X210VAL00.0200.03640.463-0.049-0.0490.0000.0000.0000.000
145X211VAL0-0.006-0.01138.1100.1570.1570.0000.0000.0000.000
146X212THR00.0200.02240.788-0.287-0.2870.0000.0000.0000.000
147X213LEU0-0.002-0.00439.1540.2500.2500.0000.0000.0000.000
148X214GLN00.0610.04141.526-0.375-0.3750.0000.0000.0000.000
149X215VAL0-0.0060.00243.0220.1950.1950.0000.0000.0000.000
150X216ALA0-0.030-0.00745.526-0.124-0.1240.0000.0000.0000.000
151X217GLU-1-0.678-0.82247.0786.3086.3080.0000.0000.0000.000
152X218GLY00.0660.03349.617-0.017-0.0170.0000.0000.0000.000
153X219VAL0-0.070-0.03251.222-0.102-0.1020.0000.0000.0000.000
154X220VAL00.0430.03354.4420.0820.0820.0000.0000.0000.000
155X221GLU-1-0.855-0.92255.4975.7425.7420.0000.0000.0000.000
156X222GLN0-0.034-0.03258.197-0.045-0.0450.0000.0000.0000.000
157X223VAL00.0310.01559.7430.0940.0940.0000.0000.0000.000
158X224THR0-0.054-0.02460.736-0.112-0.1120.0000.0000.0000.000
159X225TYR00.016-0.00462.8700.0300.0300.0000.0000.0000.000
160X226ARG10.8790.94357.985-5.544-5.5440.0000.0000.0000.000
161X227PHE00.0280.00765.1250.0220.0220.0000.0000.0000.000
162X228LEU0-0.010-0.00562.4730.0140.0140.0000.0000.0000.000
163X229ASN00.0230.00867.1120.0030.0030.0000.0000.0000.000
164X230LYS10.9670.96665.439-4.853-4.8530.0000.0000.0000.000
165X231GLU-1-0.946-0.98365.8174.8794.8790.0000.0000.0000.000
166X232GLY0-0.037-0.01263.0670.0950.0950.0000.0000.0000.000
167X233GLU-1-0.904-0.93663.3025.2495.2490.0000.0000.0000.000
168X234PRO0-0.012-0.00664.669-0.066-0.0660.0000.0000.0000.000
169X235THR0-0.037-0.01267.366-0.085-0.0850.0000.0000.0000.000
170X236LYS10.9020.95070.888-4.198-4.1980.0000.0000.0000.000
171X237GLN0-0.0110.00271.7210.0270.0270.0000.0000.0000.000
172X238ARG10.8250.89673.433-4.382-4.3820.0000.0000.0000.000
173X239THR0-0.0180.00672.711-0.083-0.0830.0000.0000.0000.000
174X240ARG10.9490.95974.597-4.098-4.0980.0000.0000.0000.000
175X241ASP-1-0.765-0.88371.4394.6004.6000.0000.0000.0000.000
176X242PHE0-0.042-0.03272.0650.0270.0270.0000.0000.0000.000
177X243VAL0-0.067-0.02673.6930.0040.0040.0000.0000.0000.000
178X244ILE00.0690.03868.0240.0040.0040.0000.0000.0000.000
179X245SER00.0120.00368.7320.0240.0240.0000.0000.0000.000
180X246ARG10.9360.95769.500-4.238-4.2380.0000.0000.0000.000
181X247GLU-1-0.881-0.93769.7644.4794.4790.0000.0000.0000.000
182X248MET0-0.116-0.01863.0850.0520.0520.0000.0000.0000.000
183X249ASP-1-0.849-0.91964.0874.8924.8920.0000.0000.0000.000
184X250THR0-0.128-0.08159.5490.0980.0980.0000.0000.0000.000
185X251GLN0-0.051-0.04362.157-0.041-0.0410.0000.0000.0000.000
186X252PRO0-0.015-0.02561.0530.0870.0870.0000.0000.0000.000
187X253GLY0-0.026-0.01059.545-0.069-0.0690.0000.0000.0000.000
188X254VAL0-0.0160.02458.7170.0410.0410.0000.0000.0000.000
189X255VAL0-0.028-0.01853.0080.0660.0660.0000.0000.0000.000
190X256LEU00.0380.01052.798-0.065-0.0650.0000.0000.0000.000
191X257ASN00.024-0.00453.8440.0960.0960.0000.0000.0000.000
192X258GLN0-0.003-0.00252.422-0.201-0.2010.0000.0000.0000.000
193X259LYS10.9550.96154.759-5.926-5.9260.0000.0000.0000.000
194X260THR00.0520.02858.107-0.056-0.0560.0000.0000.0000.000
195X261VAL00.0480.03157.069-0.080-0.0800.0000.0000.0000.000
196X262GLN0-0.058-0.02157.316-0.114-0.1140.0000.0000.0000.000
197X263ALA0-0.027-0.02360.604-0.077-0.0770.0000.0000.0000.000
198X264ASP-1-0.693-0.82762.9955.0335.0330.0000.0000.0000.000
199X265LEU0-0.010-0.01060.009-0.081-0.0810.0000.0000.0000.000
200X266ARG10.9120.95861.238-5.228-5.2280.0000.0000.0000.000
201X267ARG10.8930.93965.669-4.924-4.9240.0000.0000.0000.000
202X268LEU0-0.012-0.01065.602-0.072-0.0720.0000.0000.0000.000
203X269PHE0-0.071-0.03766.777-0.064-0.0640.0000.0000.0000.000
204X270GLU-1-0.962-0.98669.3724.5744.5740.0000.0000.0000.000
205X271LEU0-0.054-0.00772.029-0.087-0.0870.0000.0000.0000.000
206X272GLY00.0010.01373.124-0.068-0.0680.0000.0000.0000.000
207X273LEU0-0.042-0.02473.199-0.052-0.0520.0000.0000.0000.000
208X274PHE0-0.024-0.03268.892-0.025-0.0250.0000.0000.0000.000
209X275GLU-1-0.941-0.96869.3324.5614.5610.0000.0000.0000.000
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211X277VAL0-0.006-0.00862.929-0.059-0.0590.0000.0000.0000.000
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