Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6YM1Z

Calculation Name: 3DU1-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DU1

Chain ID: X

ChEMBL ID:

UniProt ID: Q8YQS9

Base Structure: X-ray

Registration Date: 2023-09-24

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2811594.970839
FMO2-HF: Nuclear repulsion 2721874.792799
FMO2-HF: Total energy -89720.178039
FMO2-MP2: Total energy -89983.224565


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:0:HIS)


Summations of interaction energy for fragment #1(X:0:HIS)
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.
-3.0512.7251.593-3.295-4.075-0.002
Interaction energy analysis for fragmet #1(X:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.036
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].
3X2ASN00.0580.0213.8530.0591.706-0.022-0.760-0.866-0.001
4X3VAL00.0750.0187.1240.1810.1810.0000.0000.0000.000
5X4GLY0-0.004-0.00410.6480.0570.0570.0000.0000.0000.000
6X5GLU-1-0.923-0.9646.237-1.875-1.8750.0000.0000.0000.000
7X6ILE00.0610.0328.5760.0350.0350.0000.0000.0000.000
8X7LEU00.0070.0039.960-0.054-0.0540.0000.0000.0000.000
9X8ARG10.9140.96710.9630.4720.4720.0000.0000.0000.000
10X9HIS00.009-0.0018.5720.0630.0630.0000.0000.0000.000
11X10TYR0-0.045-0.04412.746-0.030-0.0300.0000.0000.0000.000
12X11ALA0-0.021-0.00514.791-0.036-0.0360.0000.0000.0000.000
13X12ALA0-0.048-0.02015.763-0.030-0.0300.0000.0000.0000.000
14X13GLY0-0.0020.00517.463-0.021-0.0210.0000.0000.0000.000
15X14LYS10.8550.9509.671-0.911-0.9110.0000.0000.0000.000
16X15ARG10.9350.95314.868-0.492-0.4920.0000.0000.0000.000
17X16ASN0-0.0070.00912.3660.2300.2300.0000.0000.0000.000
18X17PHE0-0.016-0.0338.341-0.124-0.1240.0000.0000.0000.000
19X18GLN00.0130.0029.0270.5330.5330.0000.0000.0000.000
20X19HIS0-0.017-0.0087.8110.2280.2280.0000.0000.0000.000
21X20ILE0-0.062-0.0183.8020.3290.7760.018-0.160-0.3050.001
22X21ASN00.0200.0132.526-5.917-3.7921.212-1.323-2.0140.007
23X22LEU0-0.035-0.0362.9530.5662.1230.385-1.052-0.890-0.009
24X23GLN0-0.013-0.0305.120-1.555-1.5550.0000.0000.0000.000
25X24GLU-1-0.946-0.9706.9240.6050.6050.0000.0000.0000.000
26X25ILE0-0.081-0.0147.714-0.575-0.5750.0000.0000.0000.000
27X26GLU-1-0.896-0.9589.5280.1880.1880.0000.0000.0000.000
28X27LEU0-0.042-0.04011.373-0.086-0.0860.0000.0000.0000.000
29X28THR00.010-0.00314.7740.0210.0210.0000.0000.0000.000
30X29ASN0-0.101-0.04518.304-0.041-0.0410.0000.0000.0000.000
31X30ALA0-0.0100.02216.775-0.036-0.0360.0000.0000.0000.000
32X31SER0-0.012-0.02218.9290.0500.0500.0000.0000.0000.000
33X32LEU00.0100.01112.5750.0110.0110.0000.0000.0000.000
34X33THR0-0.0150.00216.8600.0500.0500.0000.0000.0000.000
35X34GLY00.0430.03819.466-0.022-0.0220.0000.0000.0000.000
36X35ALA0-0.084-0.03313.9700.0010.0010.0000.0000.0000.000
37X36ASP-1-0.803-0.89214.7941.0571.0570.0000.0000.0000.000
38X37LEU0-0.016-0.0239.9750.1670.1670.0000.0000.0000.000
39X38SER00.017-0.01212.4660.0770.0770.0000.0000.0000.000
40X39TYR0-0.043-0.02611.4530.1550.1550.0000.0000.0000.000
41X40ALA0-0.0350.0098.5640.2710.2710.0000.0000.0000.000
42X41ASP-1-0.776-0.8616.6302.8352.8350.0000.0000.0000.000
43X42LEU0-0.023-0.0267.3430.7200.7200.0000.0000.0000.000
44X43ARG10.8800.9399.639-2.537-2.5370.0000.0000.0000.000
45X44GLN0-0.013-0.00910.3390.2250.2250.0000.0000.0000.000
46X45THR0-0.0230.0009.688-0.179-0.1790.0000.0000.0000.000
47X46ARG10.9360.97112.169-0.577-0.5770.0000.0000.0000.000
48X47LEU00.0250.00912.519-0.021-0.0210.0000.0000.0000.000
49X48GLY00.0470.05216.405-0.042-0.0420.0000.0000.0000.000
50X49LYS10.9060.93120.085-0.304-0.3040.0000.0000.0000.000
51X50SER0-0.009-0.01018.060-0.011-0.0110.0000.0000.0000.000
52X51ASN00.0020.00719.9640.0140.0140.0000.0000.0000.000
53X52PHE00.0410.00513.7170.0480.0480.0000.0000.0000.000
54X53SER00.0290.00719.4050.0200.0200.0000.0000.0000.000
55X54HIS0-0.013-0.02021.5700.0290.0290.0000.0000.0000.000
56X55THR0-0.063-0.01616.9410.0300.0300.0000.0000.0000.000
57X56CYS0-0.066-0.01817.185-0.078-0.0780.0000.0000.0000.000
58X57LEU00.011-0.00914.0070.1480.1480.0000.0000.0000.000
59X58ARG10.9010.92816.432-0.660-0.6600.0000.0000.0000.000
60X59GLU-1-0.917-0.97215.8250.9390.9390.0000.0000.0000.000
61X60ALA0-0.0150.01913.0430.1240.1240.0000.0000.0000.000
62X61ASP-1-0.836-0.91611.9021.1721.1720.0000.0000.0000.000
63X62LEU00.001-0.01212.0290.2650.2650.0000.0000.0000.000
64X63SER0-0.056-0.05414.385-0.207-0.2070.0000.0000.0000.000
65X64GLU-1-0.820-0.90414.7090.8130.8130.0000.0000.0000.000
66X65ALA0-0.0020.02614.409-0.030-0.0300.0000.0000.0000.000
67X66ILE0-0.018-0.00915.806-0.130-0.1300.0000.0000.0000.000
68X67LEU0-0.011-0.01316.0370.0450.0450.0000.0000.0000.000
69X68TRP00.0310.02619.510-0.033-0.0330.0000.0000.0000.000
70X69GLY0-0.033-0.02722.652-0.001-0.0010.0000.0000.0000.000
71X70ILE0-0.049-0.00317.831-0.024-0.0240.0000.0000.0000.000
72X71ASP-1-0.850-0.92322.1070.3780.3780.0000.0000.0000.000
73X72LEU00.033-0.00218.6010.0500.0500.0000.0000.0000.000
74X73SER0-0.016-0.00522.652-0.006-0.0060.0000.0000.0000.000
75X74GLU-1-0.922-0.97924.8510.3860.3860.0000.0000.0000.000
76X75ALA0-0.0300.00820.3820.0100.0100.0000.0000.0000.000
77X76ASP-1-0.861-0.92920.9410.5890.5890.0000.0000.0000.000
78X77LEU00.012-0.00317.8500.0830.0830.0000.0000.0000.000
79X78TYR00.0040.00220.587-0.009-0.0090.0000.0000.0000.000
80X79ARG10.8960.94120.163-0.512-0.5120.0000.0000.0000.000
81X80ALA00.0170.03717.6800.0590.0590.0000.0000.0000.000
82X81ILE0-0.034-0.02315.940-0.140-0.1400.0000.0000.0000.000
83X82LEU0-0.004-0.01016.8170.1090.1090.0000.0000.0000.000
84X83ARG10.8500.90816.947-0.815-0.8150.0000.0000.0000.000
85X84GLU-1-0.954-0.98919.2330.5110.5110.0000.0000.0000.000
86X85ALA0-0.0110.01318.7490.0010.0010.0000.0000.0000.000
87X86ASP-1-0.830-0.90920.0050.3270.3270.0000.0000.0000.000
88X87LEU0-0.008-0.01920.9570.0260.0260.0000.0000.0000.000
89X88THR0-0.013-0.02323.487-0.041-0.0410.0000.0000.0000.000
90X89GLY0-0.060-0.03725.9410.0080.0080.0000.0000.0000.000
91X90ALA0-0.0250.00824.087-0.008-0.0080.0000.0000.0000.000
92X91LYS10.8760.94225.525-0.350-0.3500.0000.0000.0000.000
93X92LEU00.016-0.00223.5000.0360.0360.0000.0000.0000.000
94X93VAL00.0170.00926.935-0.012-0.0120.0000.0000.0000.000
95X94LYS10.9410.96128.619-0.268-0.2680.0000.0000.0000.000
96X95THR0-0.0160.00123.6520.0000.0000.0000.0000.0000.000
97X96ARG10.8790.94524.587-0.493-0.4930.0000.0000.0000.000
98X97LEU00.0380.00622.2960.0490.0490.0000.0000.0000.000
99X98GLU-1-0.922-0.95524.9930.4110.4110.0000.0000.0000.000
100X99GLU-1-0.879-0.94724.8130.4870.4870.0000.0000.0000.000
101X100ALA00.0030.02622.1770.0320.0320.0000.0000.0000.000
102X101ASN0-0.027-0.01521.059-0.086-0.0860.0000.0000.0000.000
103X102LEU00.0400.00721.6780.0530.0530.0000.0000.0000.000
104X103ILE0-0.001-0.00123.948-0.046-0.0460.0000.0000.0000.000
105X104LYS10.9070.94523.889-0.307-0.3070.0000.0000.0000.000
106X105ALA00.0370.04823.4000.0020.0020.0000.0000.0000.000
107X106SER0-0.015-0.00224.355-0.058-0.0580.0000.0000.0000.000
108X107LEU00.011-0.00425.3650.0290.0290.0000.0000.0000.000
109X108CYS00.0270.02127.719-0.012-0.0120.0000.0000.0000.000
110X109GLY00.0040.00329.7360.0070.0070.0000.0000.0000.000
111X110ALA0-0.0260.01227.834-0.004-0.0040.0000.0000.0000.000
112X111ASN00.0180.00429.540-0.021-0.0210.0000.0000.0000.000
113X112LEU00.0260.00028.0890.0240.0240.0000.0000.0000.000
114X113ASN0-0.042-0.02830.848-0.009-0.0090.0000.0000.0000.000
115X114SER0-0.041-0.03432.4010.0100.0100.0000.0000.0000.000
116X115ALA0-0.0120.02228.6560.0110.0110.0000.0000.0000.000
117X116ASN0-0.010-0.00828.964-0.027-0.0270.0000.0000.0000.000
118X117LEU00.0280.00727.4330.0350.0350.0000.0000.0000.000
119X118SER00.0510.01129.287-0.018-0.0180.0000.0000.0000.000
120X119ARG10.8350.90429.483-0.322-0.3220.0000.0000.0000.000
121X120CYS0-0.0170.03626.6190.0140.0140.0000.0000.0000.000
122X121LEU0-0.011-0.00925.565-0.036-0.0360.0000.0000.0000.000
123X122LEU00.036-0.00326.5840.0300.0300.0000.0000.0000.000
124X123PHE00.0100.01528.712-0.023-0.0230.0000.0000.0000.000
125X124GLN0-0.016-0.02928.7240.0320.0320.0000.0000.0000.000
126X125ALA00.0150.03028.1790.0010.0010.0000.0000.0000.000
127X126ASP-1-0.787-0.88728.7360.2250.2250.0000.0000.0000.000
128X127LEU00.005-0.00729.8040.0190.0190.0000.0000.0000.000
129X128ARG10.8240.91832.245-0.232-0.2320.0000.0000.0000.000
130X129PRO0-0.024-0.01733.3530.0120.0120.0000.0000.0000.000
131X130SER00.0280.03831.336-0.006-0.0060.0000.0000.0000.000
132X131SER0-0.030-0.02532.979-0.006-0.0060.0000.0000.0000.000
133X132ASN0-0.030-0.01931.942-0.025-0.0250.0000.0000.0000.000
134X133GLN0-0.022-0.02831.816-0.021-0.0210.0000.0000.0000.000
135X134ARG10.8980.94634.990-0.167-0.1670.0000.0000.0000.000
136X135THR00.005-0.01831.6940.0060.0060.0000.0000.0000.000
137X136ASP-1-0.871-0.92233.6150.2160.2160.0000.0000.0000.000
138X137LEU00.005-0.00432.3800.0200.0200.0000.0000.0000.000
139X138GLY00.0500.03234.996-0.003-0.0030.0000.0000.0000.000
140X139TYR0-0.044-0.04836.2370.0090.0090.0000.0000.0000.000
141X140VAL0-0.0320.01332.0130.0100.0100.0000.0000.0000.000
142X141LEU0-0.018-0.01033.057-0.017-0.0170.0000.0000.0000.000
143X142LEU00.012-0.00731.5170.0240.0240.0000.0000.0000.000
144X143THR00.0260.00934.039-0.002-0.0020.0000.0000.0000.000
145X144GLY0-0.017-0.01134.0850.0200.0200.0000.0000.0000.000
146X145ALA0-0.047-0.00431.5770.0120.0120.0000.0000.0000.000
147X146ASP-1-0.866-0.91831.4900.2630.2630.0000.0000.0000.000
148X147LEU0-0.001-0.00831.4320.0220.0220.0000.0000.0000.000
149X148SER00.001-0.01533.440-0.021-0.0210.0000.0000.0000.000
150X149TYR0-0.070-0.05533.4470.0140.0140.0000.0000.0000.000
151X150ALA0-0.0020.02432.6380.0000.0000.0000.0000.0000.000
152X151ASP-1-0.784-0.88733.3160.1820.1820.0000.0000.0000.000
153X152LEU00.0220.00634.4190.0120.0120.0000.0000.0000.000
154X153ARG10.8120.88936.571-0.185-0.1850.0000.0000.0000.000
155X154ALA0-0.017-0.00638.1170.0070.0070.0000.0000.0000.000
156X155ALA00.0010.02136.4210.0000.0000.0000.0000.0000.000
157X156SER0-0.027-0.02037.690-0.016-0.0160.0000.0000.0000.000
158X157LEU00.014-0.00336.4520.0140.0140.0000.0000.0000.000
159X158HIS0-0.043-0.03639.395-0.001-0.0010.0000.0000.0000.000
160X159HIS0-0.017-0.00640.4530.0100.0100.0000.0000.0000.000
161X160ALA00.0080.03237.7630.0080.0080.0000.0000.0000.000
162X161ASN00.0140.01737.680-0.011-0.0110.0000.0000.0000.000
163X162LEU00.017-0.01537.1030.0150.0150.0000.0000.0000.000
164X163ASP-1-0.765-0.85138.6840.2000.2000.0000.0000.0000.000
165X164GLY0-0.012-0.02338.7750.0150.0150.0000.0000.0000.000
166X165ALA0-0.055-0.00836.4470.0080.0080.0000.0000.0000.000
167X166LYS10.9450.97434.728-0.289-0.2890.0000.0000.0000.000
168X167LEU00.008-0.00636.2730.0140.0140.0000.0000.0000.000
169X168CYS00.0380.03538.503-0.008-0.0080.0000.0000.0000.000
170X169ARG10.8930.94238.220-0.149-0.1490.0000.0000.0000.000
171X170ALA00.0310.04237.3510.0020.0020.0000.0000.0000.000
172X171ASN0-0.020-0.01437.937-0.020-0.0200.0000.0000.0000.000
173X172PHE00.0530.01238.6310.0090.0090.0000.0000.0000.000
174X173GLY00.0630.03341.394-0.007-0.0070.0000.0000.0000.000
175X174ARG10.9010.93042.584-0.113-0.1130.0000.0000.0000.000
176X175THR0-0.016-0.00839.503-0.002-0.0020.0000.0000.0000.000
177X176ILE00.0180.00442.500-0.001-0.0010.0000.0000.0000.000
178X177GLN0-0.025-0.01539.415-0.005-0.0050.0000.0000.0000.000
179X178TRP00.0090.01738.5130.0000.0000.0000.0000.0000.000
180X179GLY00.0460.01441.9070.0020.0020.0000.0000.0000.000
181X180ASN0-0.007-0.00745.0050.0000.0000.0000.0000.0000.000
182X181LEU0-0.0260.00642.421-0.002-0.0020.0000.0000.0000.000
183X182ALA00.0530.02443.3940.0040.0040.0000.0000.0000.000
184X183ALA0-0.0320.00440.8070.0030.0030.0000.0000.0000.000
185X184ASP-1-0.815-0.88341.7670.1490.1490.0000.0000.0000.000
186X185LEU00.008-0.00340.5030.0090.0090.0000.0000.0000.000
187X186SER0-0.035-0.04543.605-0.006-0.0060.0000.0000.0000.000
188X187GLY0-0.052-0.03044.9340.0060.0060.0000.0000.0000.000
189X188ALA0-0.0120.02041.8750.0050.0050.0000.0000.0000.000
190X189SER0-0.068-0.07242.311-0.015-0.0150.0000.0000.0000.000
191X190LEU0-0.011-0.01241.6040.0110.0110.0000.0000.0000.000
192X191GLN0-0.0020.00043.289-0.010-0.0100.0000.0000.0000.000
193X192GLY0-0.005-0.00343.3830.0100.0100.0000.0000.0000.000
194X193ALA0-0.046-0.00941.2360.0060.0060.0000.0000.0000.000
195X194ASP-1-0.800-0.89040.7320.1760.1760.0000.0000.0000.000
196X195LEU0-0.018-0.01841.1790.0090.0090.0000.0000.0000.000
197X196SER00.0110.00343.386-0.007-0.0070.0000.0000.0000.000
198X197TYR0-0.080-0.07042.9840.0040.0040.0000.0000.0000.000
199X198ALA00.0070.02642.1760.0020.0020.0000.0000.0000.000
200X199ASN0-0.063-0.04642.533-0.015-0.0150.0000.0000.0000.000
201X200LEU00.0370.00443.6120.0070.0070.0000.0000.0000.000
202X201GLU-1-0.903-0.94646.0280.1100.1100.0000.0000.0000.000
203X202SER0-0.102-0.06447.3120.0020.0020.0000.0000.0000.000
204X203ALA0-0.0090.01545.2890.0010.0010.0000.0000.0000.000
205X204ILE0-0.021-0.00746.134-0.006-0.0060.0000.0000.0000.000
206X205LEU00.0570.01945.6730.0070.0070.0000.0000.0000.000
207X206ARG10.8810.93548.335-0.119-0.1190.0000.0000.0000.000
208X207LYS10.8990.94149.233-0.119-0.1190.0000.0000.0000.000
209X208ALA00.0430.05746.3860.0030.0030.0000.0000.0000.000
210X209ASN00.012-0.00546.792-0.010-0.0100.0000.0000.0000.000
211X210LEU00.024-0.00746.5010.0080.0080.0000.0000.0000.000
212X211GLN00.0390.03448.2620.0000.0000.0000.0000.0000.000
213X212GLY0-0.023-0.03448.0360.0070.0070.0000.0000.0000.000
214X213ALA0-0.042-0.00645.8900.0040.0040.0000.0000.0000.000
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224X223ALA00.0020.02549.9320.0010.0010.0000.0000.0000.000
225X224GLU-1-0.916-0.95550.6310.1140.1140.0000.0000.0000.000
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232X231PRO00.0410.02450.2090.0000.0000.0000.0000.0000.000
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