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: R8Z78

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2815535.383292
FMO2-HF: Nuclear repulsion 2725814.309546
FMO2-HF: Total energy -89721.073746
FMO2-MP2: Total energy -89984.100234


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.
-19.182-13.39112.018-7.856-9.956-0.01
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 : 0.018 / q_NPA : 0.017
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].
3X2ASN00.0390.0163.8260.6572.682-0.028-0.982-1.0160.003
4X3VAL00.0780.0177.0880.2140.2140.0000.0000.0000.000
5X4GLY00.0130.00810.4670.2240.2240.0000.0000.0000.000
6X5GLU-1-0.833-0.9096.652-3.253-3.2530.0000.0000.0000.000
7X6ILE00.0360.0227.4340.2620.2620.0000.0000.0000.000
8X7LEU00.0310.0209.3770.2390.2390.0000.0000.0000.000
9X8ARG10.8380.91710.2561.8561.8560.0000.0000.0000.000
10X9HIS00.000-0.0128.5690.3390.3390.0000.0000.0000.000
11X10TYR0-0.041-0.03112.6990.0990.0990.0000.0000.0000.000
12X11ALA0-0.009-0.00114.4150.0830.0830.0000.0000.0000.000
13X12ALA0-0.047-0.01515.6560.0460.0460.0000.0000.0000.000
14X13GLY00.0090.01217.4190.0370.0370.0000.0000.0000.000
15X14LYS10.8410.9298.9030.2460.2460.0000.0000.0000.000
16X15ARG10.8880.92714.0890.0510.0510.0000.0000.0000.000
17X16ASN00.0110.02211.5790.1450.1450.0000.0000.0000.000
18X17PHE0-0.023-0.0337.474-0.278-0.2780.0000.0000.0000.000
19X18GLN00.0340.0077.6460.3480.3480.0000.0000.0000.000
20X19HIS0-0.034-0.0167.7140.1800.1800.0000.0000.0000.000
21X20ILE0-0.073-0.0192.3170.5831.0131.071-0.466-1.0350.000
22X21ASN00.0220.0102.275-15.021-13.7797.983-3.879-5.3470.024
23X22LEU0-0.034-0.0362.380-8.402-6.3082.992-2.529-2.558-0.037
24X23GLN00.028-0.0065.123-0.724-0.7240.0000.0000.0000.000
25X24GLU-1-0.948-0.9676.996-0.847-0.8470.0000.0000.0000.000
26X25ILE0-0.087-0.0257.064-0.450-0.4500.0000.0000.0000.000
27X26GLU-1-0.797-0.8569.560-0.139-0.1390.0000.0000.0000.000
28X27LEU0-0.024-0.03710.591-0.137-0.1370.0000.0000.0000.000
29X28THR00.006-0.01714.6480.0900.0900.0000.0000.0000.000
30X29ASN0-0.101-0.05518.131-0.027-0.0270.0000.0000.0000.000
31X30ALA0-0.0130.01516.022-0.008-0.0080.0000.0000.0000.000
32X31SER0-0.026-0.03217.3430.0780.0780.0000.0000.0000.000
33X32LEU00.0210.01011.306-0.069-0.0690.0000.0000.0000.000
34X33THR0-0.028-0.00915.4830.0590.0590.0000.0000.0000.000
35X34GLY00.0390.03018.211-0.041-0.0410.0000.0000.0000.000
36X35ALA0-0.059-0.01912.908-0.006-0.0060.0000.0000.0000.000
37X36ASP-1-0.798-0.87613.5920.7710.7710.0000.0000.0000.000
38X37LEU0-0.006-0.0148.504-0.027-0.0270.0000.0000.0000.000
39X38SER00.020-0.01910.9990.1670.1670.0000.0000.0000.000
40X39TYR0-0.069-0.05810.9960.1100.1100.0000.0000.0000.000
41X40ALA0-0.0370.0087.1120.4860.4860.0000.0000.0000.000
42X41ASP-1-0.810-0.8756.5213.5493.5490.0000.0000.0000.000
43X42LEU00.014-0.0066.8960.1580.1580.0000.0000.0000.000
44X43ARG10.8310.8949.692-3.119-3.1190.0000.0000.0000.000
45X44GLN0-0.029-0.03410.436-0.036-0.0360.0000.0000.0000.000
46X45THR0-0.069-0.0179.527-0.262-0.2620.0000.0000.0000.000
47X46ARG10.8500.90012.0900.1250.1250.0000.0000.0000.000
48X47LEU00.0480.02912.047-0.115-0.1150.0000.0000.0000.000
49X48GLY00.0760.06616.1830.0130.0130.0000.0000.0000.000
50X49LYS10.8080.88019.924-0.070-0.0700.0000.0000.0000.000
51X50SER0-0.027-0.01117.498-0.004-0.0040.0000.0000.0000.000
52X51ASN0-0.0050.00718.9570.0680.0680.0000.0000.0000.000
53X52PHE00.0850.02612.262-0.020-0.0200.0000.0000.0000.000
54X53SER0-0.0030.00717.8660.0510.0510.0000.0000.0000.000
55X54HIS0-0.034-0.03820.255-0.012-0.0120.0000.0000.0000.000
56X55THR0-0.083-0.02815.6540.0230.0230.0000.0000.0000.000
57X56CYS0-0.061-0.02216.1890.0000.0000.0000.0000.0000.000
58X57LEU00.017-0.00312.7090.0490.0490.0000.0000.0000.000
59X58ARG10.9100.95415.070-0.543-0.5430.0000.0000.0000.000
60X59GLU-1-0.838-0.90614.9400.9970.9970.0000.0000.0000.000
61X60ALA00.0120.03211.6320.1850.1850.0000.0000.0000.000
62X61ASP-1-0.801-0.87611.5631.2541.2540.0000.0000.0000.000
63X62LEU00.008-0.00411.5470.2030.2030.0000.0000.0000.000
64X63SER0-0.040-0.05513.984-0.222-0.2220.0000.0000.0000.000
65X64GLU-1-0.832-0.89314.7440.8240.8240.0000.0000.0000.000
66X65ALA0-0.0130.02414.134-0.085-0.0850.0000.0000.0000.000
67X66ILE0-0.015-0.01315.721-0.064-0.0640.0000.0000.0000.000
68X67LEU00.002-0.01115.669-0.032-0.0320.0000.0000.0000.000
69X68TRP00.0530.03419.353-0.014-0.0140.0000.0000.0000.000
70X69GLY0-0.009-0.01522.768-0.032-0.0320.0000.0000.0000.000
71X70ILE0-0.0370.00417.172-0.028-0.0280.0000.0000.0000.000
72X71ASP-1-0.785-0.86221.4360.1270.1270.0000.0000.0000.000
73X72LEU00.0680.01617.4250.0080.0080.0000.0000.0000.000
74X73SER00.0070.00621.3800.0230.0230.0000.0000.0000.000
75X74GLU-1-0.857-0.92423.4380.1580.1580.0000.0000.0000.000
76X75ALA0-0.0230.01919.0880.0120.0120.0000.0000.0000.000
77X76ASP-1-0.811-0.91219.7700.4870.4870.0000.0000.0000.000
78X77LEU00.0190.00616.4440.0700.0700.0000.0000.0000.000
79X78TYR0-0.010-0.00519.1130.0260.0260.0000.0000.0000.000
80X79ARG10.8080.87419.381-0.613-0.6130.0000.0000.0000.000
81X80ALA00.0020.03116.4300.0820.0820.0000.0000.0000.000
82X81ILE0-0.045-0.02615.994-0.128-0.1280.0000.0000.0000.000
83X82LEU00.0260.00216.2600.0710.0710.0000.0000.0000.000
84X83ARG10.8530.91216.946-0.865-0.8650.0000.0000.0000.000
85X84GLU-1-0.856-0.93419.2210.4180.4180.0000.0000.0000.000
86X85ALA0-0.0030.02218.238-0.022-0.0220.0000.0000.0000.000
87X86ASP-1-0.825-0.90119.7400.1290.1290.0000.0000.0000.000
88X87LEU0-0.002-0.00820.227-0.017-0.0170.0000.0000.0000.000
89X88THR0-0.023-0.04223.274-0.023-0.0230.0000.0000.0000.000
90X89GLY0-0.042-0.03025.964-0.017-0.0170.0000.0000.0000.000
91X90ALA0-0.057-0.00923.586-0.017-0.0170.0000.0000.0000.000
92X91LYS10.7450.84924.889-0.111-0.1110.0000.0000.0000.000
93X92LEU00.0480.00822.2560.0120.0120.0000.0000.0000.000
94X93VAL00.0120.00825.6970.0090.0090.0000.0000.0000.000
95X94LYS10.8650.91027.195-0.155-0.1550.0000.0000.0000.000
96X95THR0-0.031-0.01022.120-0.001-0.0010.0000.0000.0000.000
97X96ARG10.7630.87323.118-0.386-0.3860.0000.0000.0000.000
98X97LEU00.039-0.00321.0110.0390.0390.0000.0000.0000.000
99X98GLU-1-0.803-0.87623.6620.3700.3700.0000.0000.0000.000
100X99GLU-1-0.823-0.90723.9790.5320.5320.0000.0000.0000.000
101X100ALA0-0.0110.02221.2590.0460.0460.0000.0000.0000.000
102X101ASN0-0.026-0.01720.630-0.095-0.0950.0000.0000.0000.000
103X102LEU00.0530.01321.0640.0410.0410.0000.0000.0000.000
104X103ILE00.0050.00423.522-0.050-0.0500.0000.0000.0000.000
105X104LYS10.8070.88023.742-0.282-0.2820.0000.0000.0000.000
106X105ALA00.0030.03322.864-0.013-0.0130.0000.0000.0000.000
107X106SER00.0080.00624.076-0.027-0.0270.0000.0000.0000.000
108X107LEU0-0.005-0.01224.7510.0180.0180.0000.0000.0000.000
109X108CYS0-0.0100.00427.199-0.012-0.0120.0000.0000.0000.000
110X109GLY00.0610.02029.738-0.013-0.0130.0000.0000.0000.000
111X110ALA0-0.0440.00427.484-0.014-0.0140.0000.0000.0000.000
112X111ASN0-0.010-0.00528.7550.0010.0010.0000.0000.0000.000
113X112LEU00.0480.01126.7790.0100.0100.0000.0000.0000.000
114X113ASN0-0.041-0.04029.8520.0050.0050.0000.0000.0000.000
115X114SER0-0.027-0.02831.3510.0010.0010.0000.0000.0000.000
116X115ALA0-0.0250.01427.6000.0090.0090.0000.0000.0000.000
117X116ASN0-0.015-0.00927.793-0.006-0.0060.0000.0000.0000.000
118X117LEU00.0470.01626.3130.0300.0300.0000.0000.0000.000
119X118SER00.0430.00528.116-0.006-0.0060.0000.0000.0000.000
120X119ARG10.7990.87228.517-0.349-0.3490.0000.0000.0000.000
121X120CYS0-0.0430.01725.9750.0180.0180.0000.0000.0000.000
122X121LEU0-0.006-0.00825.271-0.027-0.0270.0000.0000.0000.000
123X122LEU00.0440.00425.9060.0260.0260.0000.0000.0000.000
124X123PHE00.0150.01328.339-0.028-0.0280.0000.0000.0000.000
125X124GLN0-0.035-0.03228.5600.0280.0280.0000.0000.0000.000
126X125ALA00.0460.04427.818-0.002-0.0020.0000.0000.0000.000
127X126ASP-1-0.807-0.88628.4380.1340.1340.0000.0000.0000.000
128X127LEU00.0330.00429.3220.0070.0070.0000.0000.0000.000
129X128ARG10.8500.93731.827-0.146-0.1460.0000.0000.0000.000
130X129PRO0-0.027-0.02433.0680.0040.0040.0000.0000.0000.000
131X130SER00.0230.03631.332-0.002-0.0020.0000.0000.0000.000
132X131SER0-0.032-0.03932.994-0.002-0.0020.0000.0000.0000.000
133X132ASN0-0.046-0.00532.638-0.012-0.0120.0000.0000.0000.000
134X133GLN0-0.005-0.02431.421-0.016-0.0160.0000.0000.0000.000
135X134ARG10.8090.90035.010-0.089-0.0890.0000.0000.0000.000
136X135THR00.004-0.02131.204-0.006-0.0060.0000.0000.0000.000
137X136ASP-1-0.843-0.89533.0470.1160.1160.0000.0000.0000.000
138X137LEU00.0140.00431.7470.0120.0120.0000.0000.0000.000
139X138GLY00.0510.04034.0670.0040.0040.0000.0000.0000.000
140X139TYR0-0.044-0.04035.2750.0030.0030.0000.0000.0000.000
141X140VAL0-0.0380.00630.9770.0080.0080.0000.0000.0000.000
142X141LEU0-0.014-0.00131.846-0.007-0.0070.0000.0000.0000.000
143X142LEU00.027-0.00430.6830.0200.0200.0000.0000.0000.000
144X143THR00.012-0.00432.8590.0070.0070.0000.0000.0000.000
145X144GLY0-0.013-0.00733.2310.0210.0210.0000.0000.0000.000
146X145ALA0-0.046-0.00430.7550.0180.0180.0000.0000.0000.000
147X146ASP-1-0.832-0.88830.8240.2730.2730.0000.0000.0000.000
148X147LEU00.0240.01230.7460.0200.0200.0000.0000.0000.000
149X148SER0-0.004-0.02132.859-0.024-0.0240.0000.0000.0000.000
150X149TYR0-0.059-0.05233.3530.0090.0090.0000.0000.0000.000
151X150ALA0-0.0040.03132.170-0.004-0.0040.0000.0000.0000.000
152X151ASP-1-0.812-0.89433.1500.1210.1210.0000.0000.0000.000
153X152LEU00.0340.01233.9050.0060.0060.0000.0000.0000.000
154X153ARG10.8240.89736.207-0.126-0.1260.0000.0000.0000.000
155X154ALA0-0.024-0.01738.1050.0000.0000.0000.0000.0000.000
156X155ALA0-0.0100.02035.826-0.006-0.0060.0000.0000.0000.000
157X156SER0-0.084-0.05937.136-0.006-0.0060.0000.0000.0000.000
158X157LEU00.040-0.00335.4960.0110.0110.0000.0000.0000.000
159X158HIS0-0.012-0.01138.3690.0020.0020.0000.0000.0000.000
160X159HIS0-0.036-0.02439.4630.0070.0070.0000.0000.0000.000
161X160ALA00.0060.03036.7320.0060.0060.0000.0000.0000.000
162X161ASN0-0.026-0.01836.7240.0040.0040.0000.0000.0000.000
163X162LEU00.023-0.00435.9710.0150.0150.0000.0000.0000.000
164X163ASP-1-0.721-0.80437.5420.1730.1730.0000.0000.0000.000
165X164GLY00.011-0.00537.8600.0150.0150.0000.0000.0000.000
166X165ALA0-0.069-0.01635.3760.0140.0140.0000.0000.0000.000
167X166LYS10.8380.90633.786-0.304-0.3040.0000.0000.0000.000
168X167LEU00.022-0.00135.4790.0120.0120.0000.0000.0000.000
169X168CYS00.0320.02237.760-0.009-0.0090.0000.0000.0000.000
170X169ARG10.8760.92337.981-0.138-0.1380.0000.0000.0000.000
171X170ALA0-0.0080.02736.899-0.003-0.0030.0000.0000.0000.000
172X171ASN0-0.026-0.03037.603-0.020-0.0200.0000.0000.0000.000
173X172PHE00.0650.01637.7860.0020.0020.0000.0000.0000.000
174X173GLY00.0550.03740.990-0.007-0.0070.0000.0000.0000.000
175X174ARG10.8800.92142.583-0.070-0.0700.0000.0000.0000.000
176X175THR0-0.008-0.00739.3120.0010.0010.0000.0000.0000.000
177X176ILE00.011-0.00542.557-0.003-0.0030.0000.0000.0000.000
178X177GLN0-0.015-0.01239.760-0.008-0.0080.0000.0000.0000.000
179X178TRP00.0120.01938.421-0.002-0.0020.0000.0000.0000.000
180X179GLY00.0500.02141.6750.0040.0040.0000.0000.0000.000
181X180ASN0-0.041-0.02044.9250.0030.0030.0000.0000.0000.000
182X181LEU00.0150.02542.6420.0020.0020.0000.0000.0000.000
183X182ALA00.0310.01643.4430.0030.0030.0000.0000.0000.000
184X183ALA0-0.026-0.00139.970-0.001-0.0010.0000.0000.0000.000
185X184ASP-1-0.821-0.89840.9120.0910.0910.0000.0000.0000.000
186X185LEU00.0420.02539.5600.0040.0040.0000.0000.0000.000
187X186SER0-0.028-0.02742.624-0.002-0.0020.0000.0000.0000.000
188X187GLY0-0.024-0.01543.9060.0030.0030.0000.0000.0000.000
189X188ALA0-0.0280.00640.8870.0040.0040.0000.0000.0000.000
190X189SER0-0.079-0.06941.291-0.009-0.0090.0000.0000.0000.000
191X190LEU00.004-0.00940.6230.0100.0100.0000.0000.0000.000
192X191GLN00.001-0.01442.186-0.008-0.0080.0000.0000.0000.000
193X192GLY0-0.008-0.00742.4920.0100.0100.0000.0000.0000.000
194X193ALA0-0.041-0.00340.3140.0090.0090.0000.0000.0000.000
195X194ASP-1-0.808-0.87040.0050.1800.1800.0000.0000.0000.000
196X195LEU00.023-0.00640.3870.0070.0070.0000.0000.0000.000
197X196SER0-0.015-0.02142.600-0.009-0.0090.0000.0000.0000.000
198X197TYR0-0.047-0.05042.7660.0030.0030.0000.0000.0000.000
199X198ALA00.0010.02641.753-0.001-0.0010.0000.0000.0000.000
200X199ASN0-0.043-0.02942.204-0.013-0.0130.0000.0000.0000.000
201X200LEU00.0380.00543.0370.0050.0050.0000.0000.0000.000
202X201GLU-1-0.834-0.89545.5740.0770.0770.0000.0000.0000.000
203X202SER0-0.073-0.05647.011-0.003-0.0030.0000.0000.0000.000
204X203ALA0-0.0120.00944.551-0.002-0.0020.0000.0000.0000.000
205X204ILE0-0.032-0.01445.463-0.003-0.0030.0000.0000.0000.000
206X205LEU00.0490.01544.8820.0060.0060.0000.0000.0000.000
207X206ARG10.8430.90747.519-0.074-0.0740.0000.0000.0000.000
208X207LYS10.8880.93448.333-0.080-0.0800.0000.0000.0000.000
209X208ALA00.0380.04945.6430.0020.0020.0000.0000.0000.000
210X209ASN0-0.023-0.02145.745-0.007-0.0070.0000.0000.0000.000
211X210LEU00.0290.00145.3150.0080.0080.0000.0000.0000.000
212X211GLN0-0.0020.01647.1810.0030.0030.0000.0000.0000.000
213X212GLY0-0.003-0.02547.1750.0070.0070.0000.0000.0000.000
214X213ALA0-0.049-0.00644.9210.0060.0060.0000.0000.0000.000
215X214ASP-1-0.831-0.88345.0910.1410.1410.0000.0000.0000.000
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224X223ALA00.0240.03449.342-0.001-0.0010.0000.0000.0000.000
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232X231PRO00.0230.00349.3760.0000.0000.0000.0000.0000.000
233X232ASP-1-0.789-0.87151.1060.1030.1030.0000.0000.0000.000
234X233GLY00.0270.00353.3940.0010.0010.0000.0000.0000.000
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