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: MVMQZ

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2143463.753788
FMO2-HF: Nuclear repulsion 2055799.845061
FMO2-HF: Total energy -87663.908727
FMO2-MP2: Total energy -87922.214418


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.
-1.5840.388-0.02-1.014-0.9380.003
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 : -0.012 / q_NPA : -0.016
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].
3A28LEU00.0300.0063.871-0.6741.298-0.020-1.014-0.9380.003
4A29GLY00.0380.0306.1200.0520.0520.0000.0000.0000.000
5A30LYS10.7750.8765.784-1.526-1.5260.0000.0000.0000.000
6A31VAL00.0290.0107.993-0.139-0.1390.0000.0000.0000.000
7A32ASP-1-0.817-0.88310.6110.8590.8590.0000.0000.0000.000
8A33ARG10.8210.9019.418-0.857-0.8570.0000.0000.0000.000
9A34THR0-0.034-0.05513.657-0.051-0.0510.0000.0000.0000.000
10A35ALA00.0310.00016.3280.0370.0370.0000.0000.0000.000
11A36ASP-1-0.848-0.91918.6260.2920.2920.0000.0000.0000.000
12A37GLU-1-0.807-0.86913.5420.5140.5140.0000.0000.0000.000
13A38ILE0-0.018-0.00613.5970.0580.0580.0000.0000.0000.000
14A39PHE00.0140.00714.9290.0100.0100.0000.0000.0000.000
15A40ASP-1-0.851-0.93815.8620.4050.4050.0000.0000.0000.000
16A41ASP-1-0.860-0.90410.8540.9560.9560.0000.0000.0000.000
17A42HIS0-0.0160.00213.4560.0790.0790.0000.0000.0000.000
18A43LEU0-0.012-0.00716.342-0.007-0.0070.0000.0000.0000.000
19A44ASN0-0.034-0.02213.576-0.035-0.0350.0000.0000.0000.000
20A45ASN0-0.063-0.02711.6790.1210.1210.0000.0000.0000.000
21A46PHE00.0460.02415.317-0.016-0.0160.0000.0000.0000.000
22A47ASN00.006-0.00518.756-0.050-0.0500.0000.0000.0000.000
23A48ARG10.8720.93012.887-0.971-0.9710.0000.0000.0000.000
24A49GLN0-0.010-0.00418.0390.0000.0000.0000.0000.0000.000
25A50GLN00.0520.02819.749-0.025-0.0250.0000.0000.0000.000
26A51ALA0-0.035-0.01520.584-0.027-0.0270.0000.0000.0000.000
27A52SER0-0.063-0.04719.287-0.009-0.0090.0000.0000.0000.000
28A53ALA00.0050.01421.835-0.023-0.0230.0000.0000.0000.000
29A54ASN00.0410.00424.885-0.016-0.0160.0000.0000.0000.000
30A55ARG10.9360.97521.404-0.372-0.3720.0000.0000.0000.000
31A56LEU00.0210.01325.068-0.018-0.0180.0000.0000.0000.000
32A57GLN00.0290.00226.980-0.015-0.0150.0000.0000.0000.000
33A58LYS10.8500.91929.460-0.220-0.2200.0000.0000.0000.000
34A59GLU-1-0.828-0.92028.0420.1920.1920.0000.0000.0000.000
35A60PHE00.0220.02430.363-0.011-0.0110.0000.0000.0000.000
36A61ASN0-0.004-0.01631.951-0.022-0.0220.0000.0000.0000.000
37A62ASN0-0.046-0.01932.618-0.025-0.0250.0000.0000.0000.000
38A63TYR0-0.037-0.03933.012-0.011-0.0110.0000.0000.0000.000
39A64ILE00.0500.02735.052-0.012-0.0120.0000.0000.0000.000
40A65ARG10.8650.92037.181-0.140-0.1400.0000.0000.0000.000
41A66CYS0-0.075-0.03437.439-0.009-0.0090.0000.0000.0000.000
42A67VAL00.0280.02437.588-0.007-0.0070.0000.0000.0000.000
43A68ARG10.9020.93840.316-0.127-0.1270.0000.0000.0000.000
44A69ALA0-0.020-0.00242.967-0.006-0.0060.0000.0000.0000.000
45A70ALA0-0.017-0.00742.020-0.005-0.0050.0000.0000.0000.000
46A71GLN00.0480.02744.037-0.001-0.0010.0000.0000.0000.000
47A72ALA0-0.028-0.01446.035-0.005-0.0050.0000.0000.0000.000
48A73ALA00.0120.00746.866-0.004-0.0040.0000.0000.0000.000
49A74SER00.0200.00246.744-0.003-0.0030.0000.0000.0000.000
50A75LYS10.7810.88748.799-0.067-0.0670.0000.0000.0000.000
51A76THR0-0.001-0.00551.703-0.002-0.0020.0000.0000.0000.000
52A77LEU0-0.039-0.00849.762-0.003-0.0030.0000.0000.0000.000
53A78MET00.0400.01051.513-0.003-0.0030.0000.0000.0000.000
54A79ASP-1-0.823-0.89454.2230.0570.0570.0000.0000.0000.000
55A80SER0-0.037-0.02856.455-0.003-0.0030.0000.0000.0000.000
56A81VAL0-0.056-0.02554.668-0.002-0.0020.0000.0000.0000.000
57A82CYS0-0.062-0.04457.341-0.002-0.0020.0000.0000.0000.000
58A83GLU-1-1.031-0.99760.0690.0410.0410.0000.0000.0000.000
59A84ILE00.0070.00459.985-0.002-0.0020.0000.0000.0000.000
60A85TYR0-0.074-0.04959.961-0.001-0.0010.0000.0000.0000.000
61A86GLU-1-0.820-0.89962.8930.0330.0330.0000.0000.0000.000
62A87PRO0-0.004-0.02466.5800.0000.0000.0000.0000.0000.000
63A88GLN0-0.081-0.04767.8300.0010.0010.0000.0000.0000.000
64A89TRP0-0.066-0.02062.605-0.001-0.0010.0000.0000.0000.000
65A90SER00.005-0.03265.4830.0020.0020.0000.0000.0000.000
66A91GLY00.0070.00162.2380.0010.0010.0000.0000.0000.000
67A92TYR00.0340.04561.5150.0020.0020.0000.0000.0000.000
68A93ASP-1-0.880-0.95261.8110.0420.0420.0000.0000.0000.000
69A94ALA0-0.043-0.02159.3960.0020.0020.0000.0000.0000.000
70A95LEU00.0410.02657.1900.0030.0030.0000.0000.0000.000
71A96GLN00.0300.01857.2340.0030.0030.0000.0000.0000.000
72A97ALA0-0.037-0.01857.8270.0030.0030.0000.0000.0000.000
73A98GLN0-0.002-0.01052.6690.0050.0050.0000.0000.0000.000
74A99THR00.0300.00952.8770.0040.0040.0000.0000.0000.000
75A100GLY00.0230.01652.9790.0030.0030.0000.0000.0000.000
76A101ALA0-0.0100.00151.7730.0030.0030.0000.0000.0000.000
77A102SER00.0420.01648.9410.0060.0060.0000.0000.0000.000
78A103GLU-1-0.874-0.93748.3570.0720.0720.0000.0000.0000.000
79A104SER0-0.056-0.03549.1780.0040.0040.0000.0000.0000.000
80A105LEU0-0.0030.00645.1900.0050.0050.0000.0000.0000.000
81A106TRP00.0260.00141.8500.0100.0100.0000.0000.0000.000
82A107ALA0-0.043-0.02144.6390.0050.0050.0000.0000.0000.000
83A108ASP-1-0.827-0.89543.8440.1120.1120.0000.0000.0000.000
84A109PHE00.0100.00237.0880.0070.0070.0000.0000.0000.000
85A110ALA00.003-0.00240.4590.0080.0080.0000.0000.0000.000
86A111HIS0-0.079-0.03141.8840.0010.0010.0000.0000.0000.000
87A112LYS10.8540.90838.931-0.109-0.1090.0000.0000.0000.000
88A113LEU0-0.009-0.00435.1130.0110.0110.0000.0000.0000.000
89A114GLY0-0.025-0.03236.6250.0100.0100.0000.0000.0000.000
90A115ASP-1-0.831-0.89139.0060.1300.1300.0000.0000.0000.000
91A116GLN0-0.014-0.02937.1330.0080.0080.0000.0000.0000.000
92A117VAL0-0.0110.01731.8820.0100.0100.0000.0000.0000.000
93A118LEU00.0060.01233.1090.0150.0150.0000.0000.0000.000
94A119ILE00.0180.02034.3200.0090.0090.0000.0000.0000.000
95A120PRO00.0180.01732.0550.0070.0070.0000.0000.0000.000
96A121LEU00.0090.01728.2530.0130.0130.0000.0000.0000.000
97A122ASN00.0210.01130.2720.0200.0200.0000.0000.0000.000
98A123THR0-0.052-0.03132.484-0.001-0.0010.0000.0000.0000.000
99A124TYR00.0160.01622.3300.0140.0140.0000.0000.0000.000
100A125THR0-0.018-0.03627.6740.0170.0170.0000.0000.0000.000
101A126GLY00.0000.00728.7720.0020.0020.0000.0000.0000.000
102A127GLN00.001-0.00227.420-0.004-0.0040.0000.0000.0000.000
103A128PHE0-0.0020.00822.4200.0020.0020.0000.0000.0000.000
104A129PRO0-0.007-0.00727.2920.0020.0020.0000.0000.0000.000
105A130GLU-1-0.830-0.89829.8570.1710.1710.0000.0000.0000.000
106A131MET00.0330.02624.861-0.004-0.0040.0000.0000.0000.000
107A132LYS10.9730.99125.942-0.250-0.2500.0000.0000.0000.000
108A133LYS10.8450.91326.980-0.172-0.1720.0000.0000.0000.000
109A134LYS10.7470.86328.265-0.224-0.2240.0000.0000.0000.000
110A135VAL00.0570.02623.389-0.007-0.0070.0000.0000.0000.000
111A136GLU-1-0.906-0.95926.1880.2010.2010.0000.0000.0000.000
112A137LYS10.8740.94828.448-0.170-0.1700.0000.0000.0000.000
113A138ARG10.8680.92322.519-0.286-0.2860.0000.0000.0000.000
114A139ASN00.0330.00723.468-0.006-0.0060.0000.0000.0000.000
115A140ARG10.8780.93027.369-0.181-0.1810.0000.0000.0000.000
116A141LYS10.8350.90430.754-0.145-0.1450.0000.0000.0000.000
117A142LEU00.0380.03925.143-0.009-0.0090.0000.0000.0000.000
118A143ILE00.017-0.00128.860-0.009-0.0090.0000.0000.0000.000
119A144ASP-1-0.853-0.88130.9950.1090.1090.0000.0000.0000.000
120A145TYR00.0200.01129.762-0.013-0.0130.0000.0000.0000.000
121A146ASP-1-0.838-0.93928.8950.1480.1480.0000.0000.0000.000
122A147GLY0-0.018-0.00232.354-0.008-0.0080.0000.0000.0000.000
123A148GLN0-0.032-0.04035.185-0.014-0.0140.0000.0000.0000.000
124A149ARG10.9020.95732.710-0.114-0.1140.0000.0000.0000.000
125A150HIS00.0050.00134.949-0.007-0.0070.0000.0000.0000.000
126A151SER0-0.023-0.01436.610-0.007-0.0070.0000.0000.0000.000
127A152PHE0-0.0070.01539.326-0.006-0.0060.0000.0000.0000.000
128A153GLN00.0210.00734.8050.0000.0000.0000.0000.0000.000
129A154ASN00.0200.00239.881-0.004-0.0040.0000.0000.0000.000
130A155LEU00.0300.03341.955-0.005-0.0050.0000.0000.0000.000
131A156GLN0-0.061-0.05140.917-0.001-0.0010.0000.0000.0000.000
132A157ALA0-0.026-0.01042.810-0.003-0.0030.0000.0000.0000.000
133A158ASN0-0.048-0.03244.569-0.006-0.0060.0000.0000.0000.000
134A159ALA00.0130.01547.513-0.003-0.0030.0000.0000.0000.000
135A160ASN0-0.0200.01347.737-0.002-0.0020.0000.0000.0000.000
136A161LYS10.8630.93349.606-0.037-0.0370.0000.0000.0000.000
137A162ARG10.9610.94649.904-0.035-0.0350.0000.0000.0000.000
138A163LYS10.9180.97351.804-0.031-0.0310.0000.0000.0000.000
139A164ASP-1-0.819-0.89953.9680.0360.0360.0000.0000.0000.000
140A165ASP-1-0.745-0.85848.7820.0580.0580.0000.0000.0000.000
141A166VAL00.0660.04351.8020.0000.0000.0000.0000.0000.000
142A167LYS10.9870.97451.059-0.049-0.0490.0000.0000.0000.000
143A168LEU00.0490.03549.0970.0020.0020.0000.0000.0000.000
144A169THR0-0.016-0.01445.8580.0030.0030.0000.0000.0000.000
145A170LYS10.7950.86746.677-0.055-0.0550.0000.0000.0000.000
146A171GLY00.0580.04445.5130.0020.0020.0000.0000.0000.000
147A172ARG10.8220.91342.356-0.062-0.0620.0000.0000.0000.000
148A173GLU-1-0.897-0.95541.7810.0730.0730.0000.0000.0000.000
149A174GLN0-0.024-0.01441.6090.0010.0010.0000.0000.0000.000
150A175LEU00.0000.00736.1490.0050.0050.0000.0000.0000.000
151A176GLU-1-0.841-0.90137.3880.1100.1100.0000.0000.0000.000
152A177GLU-1-0.915-0.94837.7370.1060.1060.0000.0000.0000.000
153A178ALA0-0.048-0.02335.9590.0070.0070.0000.0000.0000.000
154A179ARG10.8300.88432.807-0.107-0.1070.0000.0000.0000.000
155A180ARG10.8940.94633.049-0.115-0.1150.0000.0000.0000.000
156A181THR0-0.031-0.03034.2220.0080.0080.0000.0000.0000.000
157A182TYR00.0180.00425.3000.0110.0110.0000.0000.0000.000
158A183GLU-1-0.848-0.93129.4790.1500.1500.0000.0000.0000.000
159A184ILE0-0.0120.02129.0770.0120.0120.0000.0000.0000.000
160A185LEU00.0030.00229.0970.0090.0090.0000.0000.0000.000
161A186ASN00.0260.01123.8470.0300.0300.0000.0000.0000.000
162A187THR0-0.028-0.02224.4700.0190.0190.0000.0000.0000.000
163A188GLU-1-0.856-0.92925.2330.1990.1990.0000.0000.0000.000
164A189LEU0-0.017-0.01823.4820.0120.0120.0000.0000.0000.000
165A190HIS0-0.029-0.01618.1400.0390.0390.0000.0000.0000.000
166A191ASP-1-0.896-0.92520.7590.2810.2810.0000.0000.0000.000
167A192GLU-1-0.856-0.94922.7580.2490.2490.0000.0000.0000.000
168A193LEU0-0.021-0.00219.8330.0120.0120.0000.0000.0000.000
169A194PRO00.0100.01317.3910.0350.0350.0000.0000.0000.000
170A195ALA00.0240.02219.0050.0160.0160.0000.0000.0000.000
171A196LEU0-0.019-0.00622.277-0.002-0.0020.0000.0000.0000.000
172A197TYR00.0330.04012.7760.0260.0260.0000.0000.0000.000
173A198ASP-1-0.841-0.92116.6410.6100.6100.0000.0000.0000.000
174A199SER0-0.066-0.04519.154-0.013-0.0130.0000.0000.0000.000
175A200ARG10.8420.91014.780-0.726-0.7260.0000.0000.0000.000
176A201ILE0-0.018-0.00516.935-0.003-0.0030.0000.0000.0000.000
177A202LEU00.0450.02320.896-0.021-0.0210.0000.0000.0000.000
178A203PHE00.0460.03224.433-0.024-0.0240.0000.0000.0000.000
179A204LEU0-0.0070.00120.396-0.017-0.0170.0000.0000.0000.000
180A205VAL0-0.006-0.00522.844-0.020-0.0200.0000.0000.0000.000
181A206THR0-0.020-0.02425.326-0.026-0.0260.0000.0000.0000.000
182A207ASN0-0.046-0.01627.835-0.012-0.0120.0000.0000.0000.000
183A208LEU00.0290.00423.647-0.013-0.0130.0000.0000.0000.000
184A209GLN0-0.0130.00827.938-0.023-0.0230.0000.0000.0000.000
185A210THR0-0.013-0.01529.933-0.018-0.0180.0000.0000.0000.000
186A211LEU0-0.0040.01229.182-0.013-0.0130.0000.0000.0000.000
187A212PHE00.004-0.01725.838-0.008-0.0080.0000.0000.0000.000
188A213ALA00.0140.01631.765-0.012-0.0120.0000.0000.0000.000
189A214THR0-0.031-0.02434.854-0.014-0.0140.0000.0000.0000.000
190A215GLU-1-0.796-0.88532.7940.1510.1510.0000.0000.0000.000
191A216GLN0-0.054-0.01934.880-0.016-0.0160.0000.0000.0000.000
192A217VAL00.008-0.00336.591-0.008-0.0080.0000.0000.0000.000
193A218PHE00.0270.02439.371-0.007-0.0070.0000.0000.0000.000
194A219HIS00.003-0.00636.084-0.014-0.0140.0000.0000.0000.000
195A220ASN0-0.041-0.01539.874-0.009-0.0090.0000.0000.0000.000
196A221GLU-1-0.798-0.88741.4980.0820.0820.0000.0000.0000.000
197A222THR00.022-0.00943.254-0.006-0.0060.0000.0000.0000.000
198A223ALA0-0.023-0.00842.673-0.005-0.0050.0000.0000.0000.000
199A224LYS10.7680.87744.584-0.088-0.0880.0000.0000.0000.000
200A225ILE00.0150.02047.677-0.004-0.0040.0000.0000.0000.000
201A226TYR00.009-0.00946.308-0.004-0.0040.0000.0000.0000.000
202A227SER0-0.028-0.00648.320-0.003-0.0030.0000.0000.0000.000
203A228GLU-1-0.814-0.92250.1260.0450.0450.0000.0000.0000.000
204A229LEU0-0.021-0.01651.506-0.003-0.0030.0000.0000.0000.000
205A230GLU-1-0.959-0.97450.1060.0510.0510.0000.0000.0000.000
206A231ALA00.0190.00153.497-0.003-0.0030.0000.0000.0000.000
207A232ILE0-0.091-0.04555.879-0.003-0.0030.0000.0000.0000.000
208A233VAL00.0360.02256.308-0.002-0.0020.0000.0000.0000.000
209A234ASP-1-0.938-0.96056.7640.0340.0340.0000.0000.0000.000
210A235LYS10.7990.90157.499-0.047-0.0470.0000.0000.0000.000
211A236LEU00.0400.03661.597-0.002-0.0020.0000.0000.0000.000
212A237ALA0-0.009-0.00260.458-0.002-0.0020.0000.0000.0000.000
213A238THR0-0.042-0.02561.737-0.002-0.0020.0000.0000.0000.000
214A239GLU-1-0.902-0.91864.3300.0300.0300.0000.0000.0000.000
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