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: ZVJ4N

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2813575.2303
FMO2-HF: Nuclear repulsion 2723854.285922
FMO2-HF: Total energy -89720.944378
FMO2-MP2: Total energy -89983.980024


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.
-11.728-3.6013.159-5.333-5.954-0.01
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 : -0.009 / q_NPA : -0.006
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].
3X2ASN00.0270.0063.7700.6422.648-0.022-0.989-0.9940.001
4X3VAL00.0800.0207.1240.2330.2330.0000.0000.0000.000
5X4GLY00.0090.00610.6380.1830.1830.0000.0000.0000.000
6X5GLU-1-0.886-0.9486.318-3.781-3.7810.0000.0000.0000.000
7X6ILE00.0570.0237.8060.2440.2440.0000.0000.0000.000
8X7LEU00.0090.0069.4760.2040.2040.0000.0000.0000.000
9X8ARG10.9190.97010.8841.5241.5240.0000.0000.0000.000
10X9HIS00.008-0.0018.6440.3060.3060.0000.0000.0000.000
11X10TYR0-0.045-0.03512.6490.0890.0890.0000.0000.0000.000
12X11ALA0-0.0180.00114.3420.0700.0700.0000.0000.0000.000
13X12ALA0-0.045-0.01815.7610.0360.0360.0000.0000.0000.000
14X13GLY00.0060.01017.1910.0320.0320.0000.0000.0000.000
15X14LYS10.8300.9279.274-0.092-0.0920.0000.0000.0000.000
16X15ARG10.9180.93514.262-0.041-0.0410.0000.0000.0000.000
17X16ASN00.0090.02111.8700.1580.1580.0000.0000.0000.000
18X17PHE0-0.007-0.0257.824-0.164-0.1640.0000.0000.0000.000
19X18GLN00.016-0.0028.1700.3560.3560.0000.0000.0000.000
20X19HIS0-0.020-0.0107.9660.2550.2550.0000.0000.0000.000
21X20ILE0-0.071-0.0132.7680.6661.1850.105-0.155-0.470-0.001
22X21ASN00.0470.0252.368-9.629-6.4642.617-2.471-3.3110.006
23X22LEU0-0.048-0.0432.929-5.029-2.5920.459-1.718-1.179-0.016
24X23GLN0-0.005-0.0165.131-1.105-1.1050.0000.0000.0000.000
25X24GLU-1-0.946-0.9686.927-0.649-0.6490.0000.0000.0000.000
26X25ILE0-0.089-0.0177.336-0.485-0.4850.0000.0000.0000.000
27X26GLU-1-0.783-0.8569.529-0.136-0.1360.0000.0000.0000.000
28X27LEU0-0.049-0.04310.755-0.126-0.1260.0000.0000.0000.000
29X28THR0-0.003-0.02714.7660.0800.0800.0000.0000.0000.000
30X29ASN0-0.092-0.04418.297-0.025-0.0250.0000.0000.0000.000
31X30ALA0-0.0110.02116.390-0.007-0.0070.0000.0000.0000.000
32X31SER0-0.009-0.01918.1880.0730.0730.0000.0000.0000.000
33X32LEU00.0160.01111.703-0.056-0.0560.0000.0000.0000.000
34X33THR0-0.028-0.00415.8640.0630.0630.0000.0000.0000.000
35X34GLY00.0490.03418.540-0.032-0.0320.0000.0000.0000.000
36X35ALA0-0.085-0.03413.0370.0140.0140.0000.0000.0000.000
37X36ASP-1-0.802-0.87814.0680.7990.7990.0000.0000.0000.000
38X37LEU0-0.024-0.0258.9630.0250.0250.0000.0000.0000.000
39X38SER00.024-0.01511.5630.1220.1220.0000.0000.0000.000
40X39TYR0-0.054-0.03311.2810.1360.1360.0000.0000.0000.000
41X40ALA0-0.0400.0077.8750.4420.4420.0000.0000.0000.000
42X41ASP-1-0.776-0.8556.6483.2783.2780.0000.0000.0000.000
43X42LEU0-0.023-0.0237.3200.1970.1970.0000.0000.0000.000
44X43ARG10.8260.8919.702-2.837-2.8370.0000.0000.0000.000
45X44GLN0-0.017-0.02210.335-0.002-0.0020.0000.0000.0000.000
46X45THR0-0.032-0.0029.663-0.225-0.2250.0000.0000.0000.000
47X46ARG10.8320.89112.1630.1120.1120.0000.0000.0000.000
48X47LEU00.0240.00612.463-0.094-0.0940.0000.0000.0000.000
49X48GLY00.0650.05916.3940.0120.0120.0000.0000.0000.000
50X49LYS10.8250.89020.076-0.075-0.0750.0000.0000.0000.000
51X50SER0-0.005-0.00217.614-0.008-0.0080.0000.0000.0000.000
52X51ASN0-0.011-0.00319.3260.0600.0600.0000.0000.0000.000
53X52PHE00.0550.00912.855-0.012-0.0120.0000.0000.0000.000
54X53SER00.0100.00118.4450.0460.0460.0000.0000.0000.000
55X54HIS0-0.029-0.02920.5650.0000.0000.0000.0000.0000.000
56X55THR0-0.057-0.01515.9980.0210.0210.0000.0000.0000.000
57X56CYS0-0.067-0.02216.309-0.011-0.0110.0000.0000.0000.000
58X57LEU00.008-0.00913.1010.0670.0670.0000.0000.0000.000
59X58ARG10.8860.92815.580-0.555-0.5550.0000.0000.0000.000
60X59GLU-1-0.864-0.93915.3430.9730.9730.0000.0000.0000.000
61X60ALA0-0.0130.02012.3500.1760.1760.0000.0000.0000.000
62X61ASP-1-0.794-0.87811.9771.2201.2200.0000.0000.0000.000
63X62LEU00.003-0.01112.0080.1570.1570.0000.0000.0000.000
64X63SER0-0.044-0.05414.366-0.205-0.2050.0000.0000.0000.000
65X64GLU-1-0.823-0.89114.7010.6660.6660.0000.0000.0000.000
66X65ALA0-0.0040.02514.347-0.071-0.0710.0000.0000.0000.000
67X66ILE0-0.005-0.00315.797-0.068-0.0680.0000.0000.0000.000
68X67LEU0-0.011-0.01215.988-0.019-0.0190.0000.0000.0000.000
69X68TRP00.0490.03619.497-0.013-0.0130.0000.0000.0000.000
70X69GLY0-0.017-0.02022.641-0.029-0.0290.0000.0000.0000.000
71X70ILE0-0.0150.01117.464-0.025-0.0250.0000.0000.0000.000
72X71ASP-1-0.802-0.87021.7150.1400.1400.0000.0000.0000.000
73X72LEU00.0510.00917.9660.0140.0140.0000.0000.0000.000
74X73SER0-0.029-0.03021.8950.0200.0200.0000.0000.0000.000
75X74GLU-1-0.858-0.93323.8700.1680.1680.0000.0000.0000.000
76X75ALA0-0.0300.01119.4650.0100.0100.0000.0000.0000.000
77X76ASP-1-0.845-0.92320.1000.4870.4870.0000.0000.0000.000
78X77LEU00.010-0.00517.1560.0600.0600.0000.0000.0000.000
79X78TYR0-0.0010.00119.7850.0210.0210.0000.0000.0000.000
80X79ARG10.8640.90919.695-0.572-0.5720.0000.0000.0000.000
81X80ALA00.0100.03517.2300.0830.0830.0000.0000.0000.000
82X81ILE0-0.026-0.02016.100-0.116-0.1160.0000.0000.0000.000
83X82LEU0-0.004-0.01016.7960.0650.0650.0000.0000.0000.000
84X83ARG10.8570.90617.306-0.757-0.7570.0000.0000.0000.000
85X84GLU-1-0.845-0.92719.2230.3730.3730.0000.0000.0000.000
86X85ALA0-0.0130.01318.749-0.022-0.0220.0000.0000.0000.000
87X86ASP-1-0.824-0.89819.9940.1170.1170.0000.0000.0000.000
88X87LEU0-0.007-0.01920.874-0.007-0.0070.0000.0000.0000.000
89X88THR0-0.012-0.02823.473-0.020-0.0200.0000.0000.0000.000
90X89GLY0-0.053-0.03425.929-0.014-0.0140.0000.0000.0000.000
91X90ALA0-0.038-0.00224.030-0.016-0.0160.0000.0000.0000.000
92X91LYS10.8060.89425.198-0.125-0.1250.0000.0000.0000.000
93X92LEU00.017-0.00322.9560.0170.0170.0000.0000.0000.000
94X93VAL00.0190.01226.3690.0060.0060.0000.0000.0000.000
95X94LYS10.8790.92027.672-0.157-0.1570.0000.0000.0000.000
96X95THR0-0.028-0.00522.7760.0020.0020.0000.0000.0000.000
97X96ARG10.8150.89823.798-0.371-0.3710.0000.0000.0000.000
98X97LEU00.0420.00621.6900.0380.0380.0000.0000.0000.000
99X98GLU-1-0.815-0.88924.2960.3670.3670.0000.0000.0000.000
100X99GLU-1-0.831-0.90324.3490.5070.5070.0000.0000.0000.000
101X100ALA00.0010.02721.8790.0440.0440.0000.0000.0000.000
102X101ASN0-0.024-0.01721.039-0.092-0.0920.0000.0000.0000.000
103X102LEU00.0380.00721.6580.0330.0330.0000.0000.0000.000
104X103ILE0-0.006-0.00323.934-0.048-0.0480.0000.0000.0000.000
105X104LYS10.8130.88523.877-0.254-0.2540.0000.0000.0000.000
106X105ALA00.0210.04323.357-0.010-0.0100.0000.0000.0000.000
107X106SER00.0070.00424.346-0.026-0.0260.0000.0000.0000.000
108X107LEU00.003-0.00925.3510.0110.0110.0000.0000.0000.000
109X108CYS00.0180.01827.704-0.010-0.0100.0000.0000.0000.000
110X109GLY00.0260.01429.723-0.008-0.0080.0000.0000.0000.000
111X110ALA0-0.044-0.00127.906-0.011-0.0110.0000.0000.0000.000
112X111ASN00.0120.00829.3160.0020.0020.0000.0000.0000.000
113X112LEU00.0300.00027.5310.0130.0130.0000.0000.0000.000
114X113ASN0-0.041-0.03630.4050.0060.0060.0000.0000.0000.000
115X114SER0-0.035-0.03131.6310.0030.0030.0000.0000.0000.000
116X115ALA0-0.0180.02028.0110.0110.0110.0000.0000.0000.000
117X116ASN0-0.033-0.01928.266-0.007-0.0070.0000.0000.0000.000
118X117LEU00.0320.01026.9070.0280.0280.0000.0000.0000.000
119X118SER00.0480.00828.747-0.008-0.0080.0000.0000.0000.000
120X119ARG10.7950.87429.017-0.335-0.3350.0000.0000.0000.000
121X120CYS0-0.0300.02726.5290.0190.0190.0000.0000.0000.000
122X121LEU0-0.012-0.01325.652-0.028-0.0280.0000.0000.0000.000
123X122LEU00.0400.00226.5640.0190.0190.0000.0000.0000.000
124X123PHE00.0130.01228.707-0.026-0.0260.0000.0000.0000.000
125X124GLN0-0.036-0.02928.7120.0210.0210.0000.0000.0000.000
126X125ALA00.0300.03728.162-0.006-0.0060.0000.0000.0000.000
127X126ASP-1-0.793-0.87528.7240.1210.1210.0000.0000.0000.000
128X127LEU00.007-0.01029.7910.0070.0070.0000.0000.0000.000
129X128ARG10.8250.91632.230-0.132-0.1320.0000.0000.0000.000
130X129PRO0-0.019-0.01533.3400.0040.0040.0000.0000.0000.000
131X130SER00.0250.03531.289-0.004-0.0040.0000.0000.0000.000
132X131SER0-0.022-0.02732.972-0.002-0.0020.0000.0000.0000.000
133X132ASN0-0.050-0.02332.352-0.013-0.0130.0000.0000.0000.000
134X133GLN0-0.006-0.01631.746-0.014-0.0140.0000.0000.0000.000
135X134ARG10.8830.93434.977-0.086-0.0860.0000.0000.0000.000
136X135THR00.000-0.02331.620-0.003-0.0030.0000.0000.0000.000
137X136ASP-1-0.847-0.91133.5010.1150.1150.0000.0000.0000.000
138X137LEU00.003-0.00432.3820.0130.0130.0000.0000.0000.000
139X138GLY00.0550.04234.6770.0040.0040.0000.0000.0000.000
140X139TYR0-0.040-0.04535.6210.0040.0040.0000.0000.0000.000
141X140VAL0-0.0320.01231.4760.0100.0100.0000.0000.0000.000
142X141LEU0-0.012-0.00732.381-0.008-0.0080.0000.0000.0000.000
143X142LEU00.013-0.00831.3430.0190.0190.0000.0000.0000.000
144X143THR00.0320.00633.6080.0030.0030.0000.0000.0000.000
145X144GLY0-0.014-0.01033.6410.0210.0210.0000.0000.0000.000
146X145ALA0-0.044-0.00331.4590.0170.0170.0000.0000.0000.000
147X146ASP-1-0.820-0.87931.4440.2510.2510.0000.0000.0000.000
148X147LEU00.002-0.00531.4130.0170.0170.0000.0000.0000.000
149X148SER00.002-0.01333.422-0.022-0.0220.0000.0000.0000.000
150X149TYR0-0.062-0.05133.4330.0080.0080.0000.0000.0000.000
151X150ALA0-0.0020.02932.603-0.005-0.0050.0000.0000.0000.000
152X151ASP-1-0.782-0.88833.3030.1110.1110.0000.0000.0000.000
153X152LEU00.0180.00634.4060.0040.0040.0000.0000.0000.000
154X153ARG10.8200.88936.556-0.116-0.1160.0000.0000.0000.000
155X154ALA0-0.015-0.00738.1040.0000.0000.0000.0000.0000.000
156X155ALA0-0.0050.02336.441-0.005-0.0050.0000.0000.0000.000
157X156SER0-0.053-0.02837.668-0.007-0.0070.0000.0000.0000.000
158X157LEU00.017-0.00836.2780.0090.0090.0000.0000.0000.000
159X158HIS0-0.031-0.02339.1510.0020.0020.0000.0000.0000.000
160X159HIS0-0.013-0.00639.9360.0070.0070.0000.0000.0000.000
161X160ALA00.0110.03537.4150.0070.0070.0000.0000.0000.000
162X161ASN0-0.016-0.00837.1170.0020.0020.0000.0000.0000.000
163X162LEU00.011-0.01536.7150.0130.0130.0000.0000.0000.000
164X163ASP-1-0.724-0.82238.3300.1670.1670.0000.0000.0000.000
165X164GLY00.003-0.01338.3380.0150.0150.0000.0000.0000.000
166X165ALA0-0.053-0.00536.2960.0120.0120.0000.0000.0000.000
167X166LYS10.8640.91434.570-0.283-0.2830.0000.0000.0000.000
168X167LEU00.001-0.01236.2540.0090.0090.0000.0000.0000.000
169X168CYS00.0280.02838.485-0.008-0.0080.0000.0000.0000.000
170X169ARG10.8940.94438.205-0.128-0.1280.0000.0000.0000.000
171X170ALA00.0240.03937.353-0.001-0.0010.0000.0000.0000.000
172X171ASN0-0.026-0.02537.923-0.017-0.0170.0000.0000.0000.000
173X172PHE00.0540.01238.5550.0030.0030.0000.0000.0000.000
174X173GLY00.0660.03741.379-0.007-0.0070.0000.0000.0000.000
175X174ARG10.8810.92342.570-0.065-0.0650.0000.0000.0000.000
176X175THR0-0.010-0.00739.3740.0000.0000.0000.0000.0000.000
177X176ILE00.007-0.00142.490-0.003-0.0030.0000.0000.0000.000
178X177GLN0-0.020-0.01439.508-0.008-0.0080.0000.0000.0000.000
179X178TRP00.0150.01938.593-0.003-0.0030.0000.0000.0000.000
180X179GLY00.0430.01541.8970.0040.0040.0000.0000.0000.000
181X180ASN0-0.028-0.01845.0070.0030.0030.0000.0000.0000.000
182X181LEU0-0.0050.01342.8040.0020.0020.0000.0000.0000.000
183X182ALA00.0580.02543.3800.0030.0030.0000.0000.0000.000
184X183ALA0-0.034-0.00340.777-0.001-0.0010.0000.0000.0000.000
185X184ASP-1-0.836-0.90541.7440.0880.0880.0000.0000.0000.000
186X185LEU00.0150.00240.2320.0050.0050.0000.0000.0000.000
187X186SER0-0.028-0.03243.426-0.001-0.0010.0000.0000.0000.000
188X187GLY0-0.045-0.02544.5210.0030.0030.0000.0000.0000.000
189X188ALA0-0.0180.01541.5590.0040.0040.0000.0000.0000.000
190X189SER0-0.071-0.07141.836-0.009-0.0090.0000.0000.0000.000
191X190LEU0-0.020-0.01541.3430.0090.0090.0000.0000.0000.000
192X191GLN00.000-0.00542.974-0.007-0.0070.0000.0000.0000.000
193X192GLY0-0.004-0.00342.9860.0100.0100.0000.0000.0000.000
194X193ALA0-0.048-0.01041.1430.0080.0080.0000.0000.0000.000
195X194ASP-1-0.785-0.86940.6810.1680.1680.0000.0000.0000.000
196X195LEU0-0.007-0.01741.1600.0060.0060.0000.0000.0000.000
197X196SER0-0.004-0.01043.261-0.008-0.0080.0000.0000.0000.000
198X197TYR0-0.075-0.07242.9690.0030.0030.0000.0000.0000.000
199X198ALA00.0110.03042.1940.0000.0000.0000.0000.0000.000
200X199ASN0-0.052-0.03742.519-0.011-0.0110.0000.0000.0000.000
201X200LEU00.0400.00643.5980.0030.0030.0000.0000.0000.000
202X201GLU-1-0.850-0.90546.0120.0710.0710.0000.0000.0000.000
203X202SER0-0.088-0.05947.298-0.002-0.0020.0000.0000.0000.000
204X203ALA0-0.0110.02045.259-0.002-0.0020.0000.0000.0000.000
205X204ILE0-0.027-0.01346.115-0.003-0.0030.0000.0000.0000.000
206X205LEU00.0520.01745.4730.0060.0060.0000.0000.0000.000
207X206ARG10.8290.89348.218-0.071-0.0710.0000.0000.0000.000
208X207LYS10.9020.94248.894-0.079-0.0790.0000.0000.0000.000
209X208ALA00.0390.05446.1250.0030.0030.0000.0000.0000.000
210X209ASN00.007-0.00646.339-0.007-0.0070.0000.0000.0000.000
211X210LEU00.019-0.00846.1440.0070.0070.0000.0000.0000.000
212X211GLN00.0290.03048.0050.0020.0020.0000.0000.0000.000
213X212GLY0-0.014-0.02947.6830.0070.0070.0000.0000.0000.000
214X213ALA0-0.043-0.00645.7930.0050.0050.0000.0000.0000.000
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