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: LZLK9

Calculation Name: 1URU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1URU

Chain ID: A

ChEMBL ID:

UniProt ID: Q7KLE5

Base Structure: X-ray

Registration Date: 2023-06-21

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136903.460668
FMO2-HF: Nuclear repulsion 2049242.510615
FMO2-HF: Total energy -87660.950054
FMO2-MP2: Total energy -87919.254999


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(A:26:GLN)


Summations of interaction energy for fragment #1(A:26:GLN)
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.
-3.137-0.383-0.033-1.453-1.2690.001
Interaction energy analysis for fragmet #1(A:26:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.024
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].
3A28LEU00.0370.0173.814-1.7970.957-0.033-1.453-1.2690.001
4A29GLY00.0440.0276.3940.0500.0500.0000.0000.0000.000
5A30LYS10.8820.9415.451-1.518-1.5180.0000.0000.0000.000
6A31VAL00.028-0.0017.899-0.143-0.1430.0000.0000.0000.000
7A32ASP-1-0.928-0.95610.5970.4330.4330.0000.0000.0000.000
8A33ARG10.8880.9679.730-0.435-0.4350.0000.0000.0000.000
9A34THR00.0070.01413.488-0.017-0.0170.0000.0000.0000.000
10A35ALA00.031-0.00616.2880.0190.0190.0000.0000.0000.000
11A36ASP-1-0.882-0.95518.4060.0930.0930.0000.0000.0000.000
12A37GLU-1-0.868-0.93513.7480.1340.1340.0000.0000.0000.000
13A38ILE0-0.039-0.01613.9020.0180.0180.0000.0000.0000.000
14A39PHE0-0.001-0.01214.9620.0110.0110.0000.0000.0000.000
15A40ASP-1-0.909-0.95815.5490.0650.0650.0000.0000.0000.000
16A41ASP-1-0.877-0.93210.6490.2500.2500.0000.0000.0000.000
17A42HIS0-0.026-0.02113.6160.0360.0360.0000.0000.0000.000
18A43LEU00.0050.00316.3270.0060.0060.0000.0000.0000.000
19A44ASN0-0.026-0.00812.767-0.009-0.0090.0000.0000.0000.000
20A45ASN0-0.029-0.02612.6380.0200.0200.0000.0000.0000.000
21A46PHE00.0500.04015.7850.0200.0200.0000.0000.0000.000
22A47ASN00.0150.00618.7900.0000.0000.0000.0000.0000.000
23A48ARG10.8890.94313.164-0.429-0.4290.0000.0000.0000.000
24A49GLN0-0.025-0.01918.1110.0140.0140.0000.0000.0000.000
25A50GLN00.0360.01419.871-0.009-0.0090.0000.0000.0000.000
26A51ALA0-0.051-0.02620.611-0.012-0.0120.0000.0000.0000.000
27A52SER0-0.055-0.03719.2220.0010.0010.0000.0000.0000.000
28A53ALA00.0220.01721.9230.0020.0020.0000.0000.0000.000
29A54ASN00.0470.02025.011-0.005-0.0050.0000.0000.0000.000
30A55ARG10.9360.97220.999-0.210-0.2100.0000.0000.0000.000
31A56LEU00.0170.01124.941-0.007-0.0070.0000.0000.0000.000
32A57GLN00.026-0.01326.912-0.011-0.0110.0000.0000.0000.000
33A58LYS10.8870.95229.670-0.098-0.0980.0000.0000.0000.000
34A59GLU-1-0.910-0.97427.4970.1170.1170.0000.0000.0000.000
35A60PHE00.0170.02330.412-0.005-0.0050.0000.0000.0000.000
36A61ASN00.0340.00531.960-0.009-0.0090.0000.0000.0000.000
37A62ASN0-0.073-0.03633.372-0.017-0.0170.0000.0000.0000.000
38A63TYR0-0.053-0.06833.033-0.011-0.0110.0000.0000.0000.000
39A64ILE00.0560.04035.088-0.007-0.0070.0000.0000.0000.000
40A65ARG10.9180.96037.805-0.081-0.0810.0000.0000.0000.000
41A66CYS0-0.074-0.03737.470-0.008-0.0080.0000.0000.0000.000
42A67VAL00.0400.03837.390-0.004-0.0040.0000.0000.0000.000
43A68ARG10.9390.96540.253-0.098-0.0980.0000.0000.0000.000
44A69ALA0-0.014-0.01043.073-0.004-0.0040.0000.0000.0000.000
45A70ALA0-0.0030.00642.024-0.004-0.0040.0000.0000.0000.000
46A71GLN00.0400.02444.074-0.001-0.0010.0000.0000.0000.000
47A72ALA0-0.045-0.02745.978-0.003-0.0030.0000.0000.0000.000
48A73ALA0-0.007-0.01047.030-0.003-0.0030.0000.0000.0000.000
49A74SER00.0300.00946.812-0.002-0.0020.0000.0000.0000.000
50A75LYS10.8880.97148.853-0.057-0.0570.0000.0000.0000.000
51A76THR0-0.027-0.02351.775-0.003-0.0030.0000.0000.0000.000
52A77LEU0-0.0050.01649.990-0.002-0.0020.0000.0000.0000.000
53A78MET00.026-0.00151.405-0.001-0.0010.0000.0000.0000.000
54A79ASP-1-0.852-0.93554.1480.0520.0520.0000.0000.0000.000
55A80SER0-0.019-0.01456.331-0.003-0.0030.0000.0000.0000.000
56A81VAL0-0.058-0.01654.391-0.002-0.0020.0000.0000.0000.000
57A82CYS0-0.072-0.05257.083-0.001-0.0010.0000.0000.0000.000
58A83GLU-1-1.010-0.99359.7290.0360.0360.0000.0000.0000.000
59A84ILE00.0060.01059.791-0.001-0.0010.0000.0000.0000.000
60A85TYR0-0.091-0.04659.6670.0000.0000.0000.0000.0000.000
61A86GLU-1-0.853-0.92762.8230.0340.0340.0000.0000.0000.000
62A87PRO00.002-0.02666.1800.0010.0010.0000.0000.0000.000
63A88GLN0-0.072-0.05067.8200.0010.0010.0000.0000.0000.000
64A89TRP0-0.0310.00963.3400.0000.0000.0000.0000.0000.000
65A90SER00.0370.01764.7100.0020.0020.0000.0000.0000.000
66A91GLY00.019-0.00161.7390.0010.0010.0000.0000.0000.000
67A92TYR00.0300.04661.2230.0020.0020.0000.0000.0000.000
68A93ASP-1-0.880-0.95362.0080.0460.0460.0000.0000.0000.000
69A94ALA0-0.061-0.04359.2240.0020.0020.0000.0000.0000.000
70A95LEU00.0230.03056.6700.0030.0030.0000.0000.0000.000
71A96GLN00.0500.01157.1140.0010.0010.0000.0000.0000.000
72A97ALA0-0.043-0.01757.5790.0020.0020.0000.0000.0000.000
73A98GLN0-0.016-0.01752.6060.0060.0060.0000.0000.0000.000
74A99THR00.0410.02052.5980.0040.0040.0000.0000.0000.000
75A100GLY00.0190.01352.8400.0020.0020.0000.0000.0000.000
76A101ALA0-0.027-0.01951.3930.0030.0030.0000.0000.0000.000
77A102SER00.0270.00548.6830.0060.0060.0000.0000.0000.000
78A103GLU-1-0.943-0.97748.2490.0670.0670.0000.0000.0000.000
79A104SER0-0.048-0.02249.0690.0010.0010.0000.0000.0000.000
80A105LEU00.0310.03544.8370.0040.0040.0000.0000.0000.000
81A106TRP00.007-0.01042.0300.0080.0080.0000.0000.0000.000
82A107ALA0-0.029-0.01444.2790.0030.0030.0000.0000.0000.000
83A108ASP-1-0.891-0.94643.7350.1030.1030.0000.0000.0000.000
84A109PHE0-0.048-0.00936.6960.0050.0050.0000.0000.0000.000
85A110ALA00.0290.00040.0320.0060.0060.0000.0000.0000.000
86A111HIS0-0.026-0.00341.437-0.001-0.0010.0000.0000.0000.000
87A112LYS10.9770.96938.676-0.124-0.1240.0000.0000.0000.000
88A113LEU0-0.043-0.01135.0680.0090.0090.0000.0000.0000.000
89A114GLY0-0.005-0.03336.7230.0050.0050.0000.0000.0000.000
90A115ASP-1-0.890-0.94139.1660.1140.1140.0000.0000.0000.000
91A116GLN0-0.012-0.02136.9960.0040.0040.0000.0000.0000.000
92A117VAL0-0.0300.00031.9950.0100.0100.0000.0000.0000.000
93A118LEU0-0.0060.01133.0920.0100.0100.0000.0000.0000.000
94A119ILE00.0170.02834.2900.0030.0030.0000.0000.0000.000
95A120PRO00.015-0.00332.2810.0010.0010.0000.0000.0000.000
96A121LEU00.0190.02228.2650.0080.0080.0000.0000.0000.000
97A122ASN00.0230.03230.6980.0050.0050.0000.0000.0000.000
98A123THR0-0.040-0.01132.906-0.007-0.0070.0000.0000.0000.000
99A124TYR00.0010.01122.9000.0080.0080.0000.0000.0000.000
100A125THR0-0.012-0.03728.0830.0060.0060.0000.0000.0000.000
101A126GLY0-0.0040.00629.163-0.007-0.0070.0000.0000.0000.000
102A127GLN00.0120.00127.6550.0060.0060.0000.0000.0000.000
103A128PHE0-0.0070.00422.938-0.005-0.0050.0000.0000.0000.000
104A129PRO0-0.029-0.02427.610-0.008-0.0080.0000.0000.0000.000
105A130GLU-1-0.935-0.96630.1520.0990.0990.0000.0000.0000.000
106A131MET00.0280.03725.052-0.008-0.0080.0000.0000.0000.000
107A132LYS10.9480.97325.857-0.080-0.0800.0000.0000.0000.000
108A133LYS10.9740.99027.388-0.076-0.0760.0000.0000.0000.000
109A134LYS10.7990.89628.456-0.127-0.1270.0000.0000.0000.000
110A135VAL00.0610.03023.723-0.006-0.0060.0000.0000.0000.000
111A136GLU-1-0.938-0.97426.6140.0520.0520.0000.0000.0000.000
112A137LYS10.8580.93528.806-0.081-0.0810.0000.0000.0000.000
113A138ARG10.9530.98322.456-0.094-0.0940.0000.0000.0000.000
114A139ASN00.033-0.00924.0990.0010.0010.0000.0000.0000.000
115A140ARG10.9250.97927.584-0.052-0.0520.0000.0000.0000.000
116A141LYS10.9320.95031.230-0.051-0.0510.0000.0000.0000.000
117A142LEU00.0520.04825.333-0.001-0.0010.0000.0000.0000.000
118A143ILE00.0120.00129.044-0.004-0.0040.0000.0000.0000.000
119A144ASP-1-0.974-0.97831.2230.0210.0210.0000.0000.0000.000
120A145TYR0-0.003-0.00630.050-0.002-0.0020.0000.0000.0000.000
121A146ASP-1-0.870-0.94328.6740.0220.0220.0000.0000.0000.000
122A147GLY0-0.039-0.02032.375-0.005-0.0050.0000.0000.0000.000
123A148GLN0-0.033-0.03135.308-0.003-0.0030.0000.0000.0000.000
124A149ARG10.9570.98132.770-0.022-0.0220.0000.0000.0000.000
125A150HIS00.0250.01935.043-0.001-0.0010.0000.0000.0000.000
126A151SER0-0.029-0.00436.625-0.002-0.0020.0000.0000.0000.000
127A152PHE00.0230.01039.436-0.001-0.0010.0000.0000.0000.000
128A153GLN00.0160.00334.814-0.001-0.0010.0000.0000.0000.000
129A154ASN0-0.068-0.03239.9070.0000.0000.0000.0000.0000.000
130A155LEU00.0210.02442.284-0.001-0.0010.0000.0000.0000.000
131A156GLN0-0.055-0.05640.782-0.001-0.0010.0000.0000.0000.000
132A157ALA0-0.0250.00242.934-0.001-0.0010.0000.0000.0000.000
133A158ASN0-0.007-0.01344.941-0.001-0.0010.0000.0000.0000.000
134A159ALA00.0010.00947.609-0.001-0.0010.0000.0000.0000.000
135A160ASN00.0170.02946.3490.0010.0010.0000.0000.0000.000
136A161LYS10.9230.98449.652-0.001-0.0010.0000.0000.0000.000
137A162ARG10.9760.94950.1380.0030.0030.0000.0000.0000.000
138A163LYS10.8980.94851.4470.0010.0010.0000.0000.0000.000
139A164ASP-1-0.869-0.92653.8940.0040.0040.0000.0000.0000.000
140A165ASP-1-0.858-0.91449.1260.0090.0090.0000.0000.0000.000
141A166VAL00.013-0.01052.1910.0010.0010.0000.0000.0000.000
142A167LYS10.9110.93751.507-0.013-0.0130.0000.0000.0000.000
143A168LEU00.0590.03049.4670.0010.0010.0000.0000.0000.000
144A169THR0-0.0110.00446.5920.0010.0010.0000.0000.0000.000
145A170LYS10.8620.92946.516-0.012-0.0120.0000.0000.0000.000
146A171GLY00.1270.07645.5020.0010.0010.0000.0000.0000.000
147A172ARG10.9190.95542.063-0.017-0.0170.0000.0000.0000.000
148A173GLU-1-0.918-0.97242.0920.0250.0250.0000.0000.0000.000
149A174GLN00.0390.02142.4770.0010.0010.0000.0000.0000.000
150A175LEU0-0.0100.00336.3780.0020.0020.0000.0000.0000.000
151A176GLU-1-0.867-0.91837.5300.0390.0390.0000.0000.0000.000
152A177GLU-1-0.916-0.94038.3440.0440.0440.0000.0000.0000.000
153A178ALA0-0.037-0.02835.6190.0050.0050.0000.0000.0000.000
154A179ARG10.8500.90332.903-0.039-0.0390.0000.0000.0000.000
155A180ARG11.0041.01233.200-0.058-0.0580.0000.0000.0000.000
156A181THR0-0.072-0.04434.1740.0070.0070.0000.0000.0000.000
157A182TYR00.006-0.00425.3080.0060.0060.0000.0000.0000.000
158A183GLU-1-0.927-0.96429.4570.0730.0730.0000.0000.0000.000
159A184ILE0-0.036-0.00829.2520.0070.0070.0000.0000.0000.000
160A185LEU00.0010.00729.2160.0060.0060.0000.0000.0000.000
161A186ASN00.020-0.00423.8210.0120.0120.0000.0000.0000.000
162A187THR0-0.012-0.00224.6910.0130.0130.0000.0000.0000.000
163A188GLU-1-0.840-0.92325.5710.1160.1160.0000.0000.0000.000
164A189LEU0-0.042-0.02923.5950.0090.0090.0000.0000.0000.000
165A190HIS0-0.041-0.02118.7820.0270.0270.0000.0000.0000.000
166A191ASP-1-0.894-0.92020.8950.1970.1970.0000.0000.0000.000
167A192GLU-1-0.888-0.97523.0180.1560.1560.0000.0000.0000.000
168A193LEU0-0.046-0.01820.1380.0110.0110.0000.0000.0000.000
169A194PRO00.001-0.00117.6460.0240.0240.0000.0000.0000.000
170A195ALA00.0570.04819.2270.0290.0290.0000.0000.0000.000
171A196LEU00.0190.01622.4010.0130.0130.0000.0000.0000.000
172A197TYR00.0190.05613.3420.0220.0220.0000.0000.0000.000
173A198ASP-1-0.912-0.95117.5130.4890.4890.0000.0000.0000.000
174A199SER0-0.107-0.10119.6800.0130.0130.0000.0000.0000.000
175A200ARG10.9060.95114.083-0.639-0.6390.0000.0000.0000.000
176A201ILE0-0.0070.00416.7340.0060.0060.0000.0000.0000.000
177A202LEU00.0520.01720.730-0.012-0.0120.0000.0000.0000.000
178A203PHE00.0410.02124.230-0.020-0.0200.0000.0000.0000.000
179A204LEU00.0140.00521.110-0.017-0.0170.0000.0000.0000.000
180A205VAL0-0.040-0.00522.509-0.010-0.0100.0000.0000.0000.000
181A206THR0-0.037-0.02724.927-0.027-0.0270.0000.0000.0000.000
182A207ASN0-0.042-0.02727.600-0.013-0.0130.0000.0000.0000.000
183A208LEU00.0390.00123.444-0.015-0.0150.0000.0000.0000.000
184A209GLN0-0.0080.02427.698-0.011-0.0110.0000.0000.0000.000
185A210THR00.006-0.00529.691-0.016-0.0160.0000.0000.0000.000
186A211LEU0-0.0010.02628.818-0.012-0.0120.0000.0000.0000.000
187A212PHE00.003-0.02725.405-0.007-0.0070.0000.0000.0000.000
188A213ALA00.0300.03331.272-0.009-0.0090.0000.0000.0000.000
189A214THR0-0.080-0.06134.290-0.016-0.0160.0000.0000.0000.000
190A215GLU-1-0.811-0.88332.5900.1520.1520.0000.0000.0000.000
191A216GLN0-0.045-0.02134.471-0.017-0.0170.0000.0000.0000.000
192A217VAL00.001-0.00236.028-0.008-0.0080.0000.0000.0000.000
193A218PHE00.0130.01238.807-0.007-0.0070.0000.0000.0000.000
194A219HIS00.0180.00536.104-0.011-0.0110.0000.0000.0000.000
195A220ASN0-0.024-0.00239.369-0.007-0.0070.0000.0000.0000.000
196A221GLU-1-0.893-0.94841.0130.1060.1060.0000.0000.0000.000
197A222THR00.021-0.00542.959-0.008-0.0080.0000.0000.0000.000
198A223ALA0-0.024-0.01242.253-0.005-0.0050.0000.0000.0000.000
199A224LYS10.8590.92544.324-0.113-0.1130.0000.0000.0000.000
200A225ILE00.0020.02147.094-0.004-0.0040.0000.0000.0000.000
201A226TYR00.001-0.01345.808-0.004-0.0040.0000.0000.0000.000
202A227SER00.0470.03348.099-0.002-0.0020.0000.0000.0000.000
203A228GLU-1-0.958-0.97149.7710.0680.0680.0000.0000.0000.000
204A229LEU0-0.081-0.04750.870-0.004-0.0040.0000.0000.0000.000
205A230GLU-1-0.922-0.97249.3040.0700.0700.0000.0000.0000.000
206A231ALA0-0.0150.00953.056-0.003-0.0030.0000.0000.0000.000
207A232ILE0-0.090-0.05155.508-0.003-0.0030.0000.0000.0000.000
208A233VAL00.0470.02056.090-0.003-0.0030.0000.0000.0000.000
209A234ASP-1-0.903-0.94155.7560.0520.0520.0000.0000.0000.000
210A235LYS10.8930.94158.497-0.057-0.0570.0000.0000.0000.000
211A236LEU00.0190.03161.254-0.002-0.0020.0000.0000.0000.000
212A237ALA00.0070.00760.223-0.002-0.0020.0000.0000.0000.000
213A238THR0-0.039-0.03461.502-0.002-0.0020.0000.0000.0000.000
214A239GLU-1-0.970-0.98864.0520.0370.0370.0000.0000.0000.000
215A240SER0-0.048-0.02365.304-0.002-0.0020.0000.0000.0000.000
216A241GLN0-0.0100.00163.662-0.003-0.0030.0000.0000.0000.000
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