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: 94Y12

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2139437.160689
FMO2-HF: Nuclear repulsion 2051774.112466
FMO2-HF: Total energy -87663.048223
FMO2-MP2: Total energy -87921.290325


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.
-2.7990.032-0.034-1.523-1.2730.001
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 : -0.023 / q_NPA : -0.023
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].
3A28LEU00.0360.0183.814-1.9190.912-0.034-1.523-1.2730.001
4A29GLY00.0420.0296.387-0.045-0.0450.0000.0000.0000.000
5A30LYS10.8170.8905.658-1.219-1.2190.0000.0000.0000.000
6A31VAL00.0240.0017.868-0.187-0.1870.0000.0000.0000.000
7A32ASP-1-0.853-0.90010.2850.7330.7330.0000.0000.0000.000
8A33ARG10.8010.9039.665-0.688-0.6880.0000.0000.0000.000
9A34THR0-0.018-0.03313.459-0.038-0.0380.0000.0000.0000.000
10A35ALA00.034-0.00716.2670.0270.0270.0000.0000.0000.000
11A36ASP-1-0.853-0.94118.3920.1930.1930.0000.0000.0000.000
12A37GLU-1-0.814-0.86813.6900.3060.3060.0000.0000.0000.000
13A38ILE0-0.039-0.01813.6950.0350.0350.0000.0000.0000.000
14A39PHE00.005-0.00314.9510.0100.0100.0000.0000.0000.000
15A40ASP-1-0.883-0.94915.7360.2150.2150.0000.0000.0000.000
16A41ASP-1-0.853-0.90410.6830.5900.5900.0000.0000.0000.000
17A42HIS0-0.030-0.02413.6210.0530.0530.0000.0000.0000.000
18A43LEU00.0040.00116.335-0.009-0.0090.0000.0000.0000.000
19A44ASN0-0.038-0.01213.330-0.043-0.0430.0000.0000.0000.000
20A45ASN00.0010.00012.2520.0520.0520.0000.0000.0000.000
21A46PHE00.0500.04015.7220.0010.0010.0000.0000.0000.000
22A47ASN00.0110.00118.898-0.027-0.0270.0000.0000.0000.000
23A48ARG10.8840.93112.948-0.634-0.6340.0000.0000.0000.000
24A49GLN0-0.029-0.01418.0760.0100.0100.0000.0000.0000.000
25A50GLN00.0310.01119.750-0.015-0.0150.0000.0000.0000.000
26A51ALA0-0.038-0.02020.590-0.019-0.0190.0000.0000.0000.000
27A52SER0-0.062-0.04919.238-0.006-0.0060.0000.0000.0000.000
28A53ALA00.0150.01521.826-0.008-0.0080.0000.0000.0000.000
29A54ASN00.0360.01224.878-0.011-0.0110.0000.0000.0000.000
30A55ARG10.9470.97821.236-0.248-0.2480.0000.0000.0000.000
31A56LEU00.0130.01024.972-0.011-0.0110.0000.0000.0000.000
32A57GLN00.0380.00626.957-0.011-0.0110.0000.0000.0000.000
33A58LYS10.8980.96529.285-0.133-0.1330.0000.0000.0000.000
34A59GLU-1-0.898-0.97227.8420.1320.1320.0000.0000.0000.000
35A60PHE00.0210.02330.473-0.008-0.0080.0000.0000.0000.000
36A61ASN0-0.008-0.02132.041-0.014-0.0140.0000.0000.0000.000
37A62ASN0-0.027-0.00833.275-0.018-0.0180.0000.0000.0000.000
38A63TYR0-0.045-0.04833.090-0.010-0.0100.0000.0000.0000.000
39A64ILE00.0740.04135.169-0.008-0.0080.0000.0000.0000.000
40A65ARG10.8800.93937.827-0.093-0.0930.0000.0000.0000.000
41A66CYS0-0.096-0.05137.536-0.007-0.0070.0000.0000.0000.000
42A67VAL00.0330.02937.711-0.005-0.0050.0000.0000.0000.000
43A68ARG10.9010.94940.377-0.100-0.1000.0000.0000.0000.000
44A69ALA0-0.011-0.00843.160-0.004-0.0040.0000.0000.0000.000
45A70ALA00.0000.00542.161-0.004-0.0040.0000.0000.0000.000
46A71GLN00.0380.02244.191-0.001-0.0010.0000.0000.0000.000
47A72ALA0-0.045-0.02846.131-0.003-0.0030.0000.0000.0000.000
48A73ALA00.0100.00847.083-0.003-0.0030.0000.0000.0000.000
49A74SER00.008-0.00446.966-0.002-0.0020.0000.0000.0000.000
50A75LYS10.7750.88049.009-0.054-0.0540.0000.0000.0000.000
51A76THR00.0430.00951.937-0.002-0.0020.0000.0000.0000.000
52A77LEU0-0.054-0.00750.032-0.003-0.0030.0000.0000.0000.000
53A78MET00.0440.00851.642-0.002-0.0020.0000.0000.0000.000
54A79ASP-1-0.829-0.89454.3360.0470.0470.0000.0000.0000.000
55A80SER0-0.049-0.02856.617-0.002-0.0020.0000.0000.0000.000
56A81VAL0-0.041-0.01354.565-0.002-0.0020.0000.0000.0000.000
57A82CYS0-0.070-0.05057.270-0.001-0.0010.0000.0000.0000.000
58A83GLU-1-1.016-0.99759.9310.0320.0320.0000.0000.0000.000
59A84ILE00.0040.00460.078-0.001-0.0010.0000.0000.0000.000
60A85TYR0-0.078-0.05059.741-0.001-0.0010.0000.0000.0000.000
61A86GLU-1-0.831-0.91063.0310.0280.0280.0000.0000.0000.000
62A87PRO0-0.004-0.03166.4170.0000.0000.0000.0000.0000.000
63A88GLN0-0.082-0.05768.0590.0010.0010.0000.0000.0000.000
64A89TRP0-0.060-0.00463.0240.0000.0000.0000.0000.0000.000
65A90SER00.025-0.01365.4790.0010.0010.0000.0000.0000.000
66A91GLY00.0120.00162.0370.0010.0010.0000.0000.0000.000
67A92TYR00.0350.04961.5040.0020.0020.0000.0000.0000.000
68A93ASP-1-0.886-0.96062.2730.0390.0390.0000.0000.0000.000
69A94ALA0-0.053-0.03959.5930.0020.0020.0000.0000.0000.000
70A95LEU00.0250.03557.0400.0030.0030.0000.0000.0000.000
71A96GLN00.0440.02157.3760.0020.0020.0000.0000.0000.000
72A97ALA0-0.037-0.01457.8390.0020.0020.0000.0000.0000.000
73A98GLN0-0.011-0.01152.7830.0050.0050.0000.0000.0000.000
74A99THR00.0320.00752.8750.0030.0030.0000.0000.0000.000
75A100GLY00.0150.01053.0850.0020.0020.0000.0000.0000.000
76A101ALA0-0.021-0.02051.8430.0030.0030.0000.0000.0000.000
77A102SER00.0380.01048.8250.0050.0050.0000.0000.0000.000
78A103GLU-1-0.872-0.92848.4940.0600.0600.0000.0000.0000.000
79A104SER0-0.047-0.01949.2960.0020.0020.0000.0000.0000.000
80A105LEU00.0120.01945.1530.0040.0040.0000.0000.0000.000
81A106TRP00.022-0.00541.8830.0080.0080.0000.0000.0000.000
82A107ALA0-0.028-0.01944.4920.0030.0030.0000.0000.0000.000
83A108ASP-1-0.834-0.90043.6240.0960.0960.0000.0000.0000.000
84A109PHE0-0.039-0.00336.9870.0050.0050.0000.0000.0000.000
85A110ALA00.0310.00440.2570.0060.0060.0000.0000.0000.000
86A111HIS0-0.055-0.01641.618-0.001-0.0010.0000.0000.0000.000
87A112LYS10.9010.91738.931-0.103-0.1030.0000.0000.0000.000
88A113LEU0-0.035-0.01135.2960.0090.0090.0000.0000.0000.000
89A114GLY0-0.018-0.03536.9030.0060.0060.0000.0000.0000.000
90A115ASP-1-0.845-0.89639.3250.1100.1100.0000.0000.0000.000
91A116GLN0-0.023-0.04037.2940.0040.0040.0000.0000.0000.000
92A117VAL0-0.0200.00132.1780.0090.0090.0000.0000.0000.000
93A118LEU0-0.0250.01133.2840.0110.0110.0000.0000.0000.000
94A119ILE00.0420.02834.3250.0060.0060.0000.0000.0000.000
95A120PRO00.0220.01632.3480.0040.0040.0000.0000.0000.000
96A121LEU00.0120.01628.2190.0100.0100.0000.0000.0000.000
97A122ASN00.0220.02030.5150.0110.0110.0000.0000.0000.000
98A123THR0-0.049-0.03132.936-0.005-0.0050.0000.0000.0000.000
99A124TYR0-0.0010.01822.6610.0110.0110.0000.0000.0000.000
100A125THR0-0.005-0.03827.9340.0120.0120.0000.0000.0000.000
101A126GLY0-0.0070.00629.012-0.002-0.0020.0000.0000.0000.000
102A127GLN00.004-0.00327.610-0.001-0.0010.0000.0000.0000.000
103A128PHE0-0.0040.00422.6550.0000.0000.0000.0000.0000.000
104A129PRO0-0.017-0.01927.508-0.002-0.0020.0000.0000.0000.000
105A130GLU-1-0.942-0.96730.0970.1250.1250.0000.0000.0000.000
106A131MET00.0310.03425.112-0.005-0.0050.0000.0000.0000.000
107A132LYS10.9480.97626.190-0.145-0.1450.0000.0000.0000.000
108A133LYS10.9530.98327.404-0.113-0.1130.0000.0000.0000.000
109A134LYS10.7610.85428.560-0.168-0.1680.0000.0000.0000.000
110A135VAL00.0600.03023.674-0.005-0.0050.0000.0000.0000.000
111A136GLU-1-0.925-0.97626.6220.1160.1160.0000.0000.0000.000
112A137LYS10.8640.93528.814-0.120-0.1200.0000.0000.0000.000
113A138ARG10.8730.94322.587-0.182-0.1820.0000.0000.0000.000
114A139ASN00.0430.00023.798-0.002-0.0020.0000.0000.0000.000
115A140ARG10.9210.97727.585-0.103-0.1030.0000.0000.0000.000
116A141LYS10.8560.90331.332-0.088-0.0880.0000.0000.0000.000
117A142LEU00.0440.04625.376-0.004-0.0040.0000.0000.0000.000
118A143ILE00.0200.00029.015-0.006-0.0060.0000.0000.0000.000
119A144ASP-1-0.893-0.91831.2160.0630.0630.0000.0000.0000.000
120A145TYR00.0160.00429.907-0.008-0.0080.0000.0000.0000.000
121A146ASP-1-0.849-0.93828.7980.0830.0830.0000.0000.0000.000
122A147GLY0-0.036-0.01832.361-0.007-0.0070.0000.0000.0000.000
123A148GLN0-0.055-0.04835.296-0.007-0.0070.0000.0000.0000.000
124A149ARG10.9260.97832.840-0.067-0.0670.0000.0000.0000.000
125A150HIS00.0390.01434.992-0.004-0.0040.0000.0000.0000.000
126A151SER0-0.017-0.00236.607-0.003-0.0030.0000.0000.0000.000
127A152PHE0-0.0070.00239.404-0.003-0.0030.0000.0000.0000.000
128A153GLN00.0360.01034.9060.0020.0020.0000.0000.0000.000
129A154ASN0-0.051-0.02439.884-0.001-0.0010.0000.0000.0000.000
130A155LEU00.0210.02542.262-0.002-0.0020.0000.0000.0000.000
131A156GLN0-0.055-0.04640.7280.0000.0000.0000.0000.0000.000
132A157ALA0-0.029-0.00242.889-0.002-0.0020.0000.0000.0000.000
133A158ASN0-0.041-0.03244.823-0.003-0.0030.0000.0000.0000.000
134A159ALA00.0140.01647.586-0.002-0.0020.0000.0000.0000.000
135A160ASN0-0.034-0.00947.5350.0000.0000.0000.0000.0000.000
136A161LYS10.8890.94849.627-0.020-0.0200.0000.0000.0000.000
137A162ARG10.9540.94049.802-0.017-0.0170.0000.0000.0000.000
138A163LYS10.9140.96151.418-0.016-0.0160.0000.0000.0000.000
139A164ASP-1-0.817-0.88353.9510.0200.0200.0000.0000.0000.000
140A165ASP-1-0.765-0.84448.9820.0340.0340.0000.0000.0000.000
141A166VAL00.0770.03652.1770.0000.0000.0000.0000.0000.000
142A167LYS10.9440.95651.486-0.030-0.0300.0000.0000.0000.000
143A168LEU00.0510.03049.4210.0010.0010.0000.0000.0000.000
144A169THR00.007-0.01046.2990.0020.0020.0000.0000.0000.000
145A170LYS10.7870.88146.495-0.032-0.0320.0000.0000.0000.000
146A171GLY00.1080.06545.4870.0010.0010.0000.0000.0000.000
147A172ARG10.8570.91842.480-0.040-0.0400.0000.0000.0000.000
148A173GLU-1-0.917-0.97242.0740.0480.0480.0000.0000.0000.000
149A174GLN00.0090.01241.8600.0010.0010.0000.0000.0000.000
150A175LEU0-0.0040.00336.2400.0030.0030.0000.0000.0000.000
151A176GLU-1-0.851-0.90737.5140.0750.0750.0000.0000.0000.000
152A177GLU-1-0.911-0.93838.3300.0730.0730.0000.0000.0000.000
153A178ALA0-0.050-0.03135.6530.0060.0060.0000.0000.0000.000
154A179ARG10.8460.89832.639-0.075-0.0750.0000.0000.0000.000
155A180ARG10.9300.97333.186-0.089-0.0890.0000.0000.0000.000
156A181THR0-0.041-0.03134.1630.0080.0080.0000.0000.0000.000
157A182TYR00.009-0.00125.3780.0080.0080.0000.0000.0000.000
158A183GLU-1-0.855-0.92829.4660.1130.1130.0000.0000.0000.000
159A184ILE0-0.0260.00829.2420.0100.0100.0000.0000.0000.000
160A185LEU00.0080.00429.3110.0060.0060.0000.0000.0000.000
161A186ASN00.0360.00823.8100.0170.0170.0000.0000.0000.000
162A187THR0-0.027-0.03024.6850.0170.0170.0000.0000.0000.000
163A188GLU-1-0.834-0.90525.5650.1520.1520.0000.0000.0000.000
164A189LEU0-0.028-0.01923.5640.0090.0090.0000.0000.0000.000
165A190HIS0-0.039-0.02218.4770.0320.0320.0000.0000.0000.000
166A191ASP-1-0.893-0.92220.8920.2440.2440.0000.0000.0000.000
167A192GLU-1-0.872-0.94623.0220.1910.1910.0000.0000.0000.000
168A193LEU0-0.041-0.01820.1890.0090.0090.0000.0000.0000.000
169A194PRO00.0010.00017.5540.0230.0230.0000.0000.0000.000
170A195ALA00.0450.03719.2370.0210.0210.0000.0000.0000.000
171A196LEU0-0.0110.00322.4110.0050.0050.0000.0000.0000.000
172A197TYR00.0350.03812.9870.0170.0170.0000.0000.0000.000
173A198ASP-1-0.853-0.91717.3590.5260.5260.0000.0000.0000.000
174A199SER0-0.083-0.05719.8440.0000.0000.0000.0000.0000.000
175A200ARG10.8550.91914.819-0.619-0.6190.0000.0000.0000.000
176A201ILE0-0.015-0.00217.1420.0000.0000.0000.0000.0000.000
177A202LEU00.0550.02021.143-0.016-0.0160.0000.0000.0000.000
178A203PHE00.0380.02424.547-0.022-0.0220.0000.0000.0000.000
179A204LEU00.0060.00420.993-0.018-0.0180.0000.0000.0000.000
180A205VAL0-0.0150.00222.822-0.012-0.0120.0000.0000.0000.000
181A206THR0-0.029-0.02825.276-0.024-0.0240.0000.0000.0000.000
182A207ASN0-0.064-0.03027.734-0.012-0.0120.0000.0000.0000.000
183A208LEU00.0470.00623.621-0.014-0.0140.0000.0000.0000.000
184A209GLN0-0.0200.01827.990-0.017-0.0170.0000.0000.0000.000
185A210THR0-0.002-0.01230.045-0.016-0.0160.0000.0000.0000.000
186A211LEU00.0030.01029.120-0.011-0.0110.0000.0000.0000.000
187A212PHE0-0.006-0.03125.640-0.007-0.0070.0000.0000.0000.000
188A213ALA00.0390.03331.590-0.009-0.0090.0000.0000.0000.000
189A214THR0-0.052-0.02734.642-0.014-0.0140.0000.0000.0000.000
190A215GLU-1-0.797-0.88232.8440.1300.1300.0000.0000.0000.000
191A216GLN0-0.046-0.01634.696-0.013-0.0130.0000.0000.0000.000
192A217VAL00.0080.00236.369-0.007-0.0070.0000.0000.0000.000
193A218PHE00.0180.01239.178-0.006-0.0060.0000.0000.0000.000
194A219HIS00.000-0.00236.206-0.012-0.0120.0000.0000.0000.000
195A220ASN0-0.051-0.01639.687-0.006-0.0060.0000.0000.0000.000
196A221GLU-1-0.821-0.89841.3600.0850.0850.0000.0000.0000.000
197A222THR00.035-0.00743.274-0.006-0.0060.0000.0000.0000.000
198A223ALA0-0.034-0.01142.545-0.004-0.0040.0000.0000.0000.000
199A224LYS10.7920.87544.594-0.091-0.0910.0000.0000.0000.000
200A225ILE0-0.0130.01047.441-0.004-0.0040.0000.0000.0000.000
201A226TYR00.016-0.00346.208-0.005-0.0050.0000.0000.0000.000
202A227SER00.0370.03248.412-0.002-0.0020.0000.0000.0000.000
203A228GLU-1-0.934-0.97350.0930.0480.0480.0000.0000.0000.000
204A229LEU0-0.032-0.02651.265-0.003-0.0030.0000.0000.0000.000
205A230GLU-1-0.947-0.97549.8870.0520.0520.0000.0000.0000.000
206A231ALA0-0.0090.00453.348-0.003-0.0030.0000.0000.0000.000
207A232ILE0-0.078-0.05555.829-0.003-0.0030.0000.0000.0000.000
208A233VAL00.0420.02556.326-0.002-0.0020.0000.0000.0000.000
209A234ASP-1-0.925-0.94856.8520.0360.0360.0000.0000.0000.000
210A235LYS10.8540.93558.052-0.046-0.0460.0000.0000.0000.000
211A236LEU00.0320.03361.545-0.002-0.0020.0000.0000.0000.000
212A237ALA00.0120.01460.477-0.002-0.0020.0000.0000.0000.000
213A238THR0-0.023-0.02461.889-0.002-0.0020.0000.0000.0000.000
214A239GLU-1-0.955-0.94864.3460.0290.0290.0000.0000.0000.000
215A240SER00.003-0.01166.362-0.001-0.0010.0000.0000.0000.000
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